# Patent

## Title
Polynucleotides encoding polypeptides and methods using same

## Abstract

Novel polypeptides and polynucleotides encoding same are provided. Also provided methods and pharmaceutical compositions which can be used to treat various disorders such as cancer, immunological-related, blood-related and skin-related disorders using the polypeptides and polynucleotides of the present invention. Also provided are methods and kits for diagnosing, determining predisposition and/or prognosis of various disorders using as diagnostic markers the novel polypeptides and polynucleotides of the present invention.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
The present application claims priority from U.S. Provisional Patent Application Nos. 60/607,246, filed Sep. 7, 2004, U.S. Provisional Patent Application No. 60/587,851, filed Jul. 15, 2004, and from U.S. Provisional Patent Application No. 60/539,127, filed Jan. 27, 2004, the contents of which are hereby incorporated by reference.


FIELD AND BACKGROUND OF THE INVENTION
The present invention relates to novel secreted and non-secreted polypeptides and polynucleotides encoding same and more particularly, to therapeutic and diagnostic methods and kits utilizing same.
Extracellular proteins including receptors and their corresponding ligands play active roles in the formation, differentiation and maintenance of multicellular organisms. Any fate of an individual cell including proliferation, migration, differentiation, or interaction with other cells is typically governed by information received from distant cells and/or the immediate environment. This information is often transmitted by secreted polypeptides such as, mitogenic factors, survival factors, cytotoxic factors, differentiation factors, neuropeptides, and hormones, which are, in turn, received and interpreted by diverse cell receptors or membrane-bound proteins. These secreted polypeptides or signaling molecules are normally transferred through the cellular secretory pathway to reach their site of action at the extracellular environment.
Secreted proteins have various industrial applications, including as pharmaceuticals, diagnostics, biosensors and bioreactors. Most protein drugs available to date, including thrombolytic polypeptide sequences, interferons, interleukins, erythropoietins, colony stimulating factors, and various other cytokines, are secretory proteins. Their receptors, which are membrane proteins, also have potential as therapeutic or diagnostic polynucleotide or polypeptide sequences. For example, receptor immunoadhesins can be employed as therapeutic polynucleotide or polypeptide sequences to block receptor-ligand interactions. The membrane-bound proteins can also be employed for screening of potential peptide or small molecule inhibitors of the relevant receptor/ligand interaction.
Non-secreted proteins may also find application as therapeutics or diagnostics. For example, over expression of an intracellular protein (or transcript thereof) which correlates with a disease may be used to diagnose the presence of a disease or for estimating the risk of developing a disease, by the development of probes which specifically identify the over-expressed transcript or protein. In instances where the individual is at risk of suffering from a disease or other undesirable phenotype as a result of over expression of such transcript, the expression of the protein may be reduced using, for example, antisense or triple helix based strategies.
For these reasons, efforts are being made by both industry and academia to identify new, native, membrane-bound, secreted or non-secreted proteins. Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for such proteins. Examples of such screening methods and techniques are described in, for example, Klein et al., Proc. Natl. Acad. Sci. 93:7108-7113 (1996); U.S. Pat. No. 5,536,637
The present inventors have previously designed algorithms which allow for the mass prediction of new genes and gene products and for annotating these genes and gene products [see U.S. Pat. No. 6,625,545; U.S. patent application Ser. No. 10/426,002; U.S. Patent Application No. 60/539,129 entitled Methods and systems for annotating biomolecular sequences and U.S. Patent Application No. 60/539,128 entitled METHODS OF IDENTIFYING PUTATIVE GENE PRODUCTS BY INTERSPECIES SEQUENCE COMPARISON filed concurrently herewith, assigned to the same assignee hereof and contain subject matter related, in certain respects, to the subject matter of the instant application, the teachings of all of which are incorporated herein by reference; and Example 1 of the Examples section which follows].
While applying the above-mentioned algorithms the present inventors uncovered novel naturally occurring variants of extracellular gene products, which as described above, play pivotal roles in disease onset and progression. As such these variants can be used in the diagnosis and therapy of a wide range of diseases.
SUMMARY OF THE INVENTION
According to one aspect of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 1, as determined using the LALIGN software of EMBnet Switzerland using default parameters, a nucleic acid construct comprising said isolated polynucleotide, and a host cell comprising the nucleic acid construct.
According to further features in preferred embodiments of the invention described below the nucleic acid construct further comprises a promoter for regulating transcription of the isolated polynucleotide in sense or antisense orientation.
According to yet further features in preferred embodiments of the invention described below the nucleic acid construct further comprises positive and negative selection markers for selecting for homologous recombination events.
According to another aspect of the present invention there is provided an isolated polypeptide comprising an amino acid sequence at least 70% identical to SEQ ID NO: 1, as determined using the LALIGN software of EMBnet Switzerland using default parameters or an active portion thereof.
According to yet another aspect of the present invention there is provided an antibody or an antibody fragment being capable of specifically binding a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 1, as determined using the LALIGN software of EMBnet Switzerland using default parameters.
According to still another aspect of the present invention there is provided an oligonucleotide specifically hybridizable with a nucleic acid sequence encoding a polypeptide having an amino acid at least 70% identical to SEQ ID NO: 1, as determined using the LALIGN software of EMBnet Switzerland using default parameters.
According to another aspect of the present invention there is provided a pharmaceutical composition comprising a therapeutically effective amount of a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 1, as determined using the LALIGN software of EMBnet Switzerland using default parameters and a pharmaceutically acceptable carrier or diluent.
According to further features in preferred embodiments of the invention described below the nucleic acid sequence of the isolated polynucleotide is as set forth in SEQ ID NO: 3 or 4.
According to yet further features in preferred embodiments of the invention described below, the polypeptide encoded by said isolated polynucleotide is as set forth in SEQ ID NO: 1 or 2.
According to still another aspect of the present invention there is provided an isolated polynucleotide as set forth in SEQ ID NO: 3 or 4.
According to yet another aspect of the present invention there is provided an isolated polypeptide as set forth in SEQ ID NO: 1 or 2.
According to another aspect of the present invention there is provided a method of treating GCSF-related disease in a subject, the method comprising upregulating in the subject an expression level of a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 1 as determined using the LALIGN software of EMBnet Switzerland using default parameters, thereby treating the GCSF-related disease in a subject.
According to further features in preferred embodiments of the invention described below, upregulating the expression level of the polypeptide is effected by (i) administering the polypeptide to the subject; and/or (ii) administering an expressible polynucleotide encoding the polypeptide to the subject.
According to yet further features in preferred embodiments of the invention described below the expressible polynucleotide includes a nucleic acid sequence at least 90% to SEQ ID NO:3, or is as set forth in SEQ ID NO:3.
According to another aspect of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 5, as determined using the LALIGN software of EMBnet Switzerland using default parameters, a nucleic acid construct comprising said isolated polynucleotide, and a host cell comprising the nucleic acid construct.
According to further features in preferred embodiments of the invention described below the nucleic acid construct further comprises a promoter for regulating transcription of the isolated polynucleotide in sense or antisense orientation.
According to yet further features in preferred embodiments of the invention described below the nucleic acid construct further comprises positive and negative selection markers for selecting for homologous recombination events.
According to another aspect of the present invention there is provided an isolated polypeptide comprising an amino acid sequence at least 70% identical to SEQ ID NO: 5, as determined using the LALIGN software of EMBnet Switzerland using default parameters or an active portion thereof.
According to yet another aspect of the present invention there is provided an antibody or an antibody fragment being capable of specifically binding a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 5, as determined using the LALIGN software of EMBnet Switzerland using default parameters.
According to still another aspect of the present invention there is provided an oligonucleotide specifically hybridizable with a nucleic acid sequence encoding a polypeptide having an amino acid at least 70% identical to SEQ ID NO: 5, as determined using the LALIGN software of EMBnet Switzerland using default parameters.
According to another aspect of the present invention there is provided a pharmaceutical composition comprising a therapeutically effective amount of a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 5, as determined using the LALIGN software of EMBnet Switzerland using default parameters and a pharmaceutically acceptable carrier or diluent.
According to further features in preferred embodiments of the invention described below the nucleic acid sequence of the isolated polynucleotide is as set forth in SEQ ID NO: 7 or 8.
According to yet further features in preferred embodiments of the invention described below, the polypeptide encoded by said isolated polynucleotide is as set forth in SEQ ID NO: 5 or 6.
According to still another aspect of the present invention there is provided an isolated polynucleotide as set forth in SEQ ID NO: 7 or 8.
According to yet another aspect of the present invention there is provided an isolated polypeptide as set forth in SEQ ID NO: 5 or 6.
According to another aspect of the present invention there is provided a method of treating TNR-3-related disease in a subject, the method comprising upregulating in the subject an expression level of a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 5 as determined using the LALIGN software of EMBnet Switzerland using default parameters, thereby treating the TNR-3-related disease in a subject.
According to further features in preferred embodiments of the invention described below, upregulating the expression level of the polypeptide is effected by (i) administering the polypeptide to the subject; and/or (ii) administering an expressible polynucleotide encoding the polypeptide to the subject.
According to yet further features in preferred embodiments of the invention described below the expressible polynucleotide includes a nucleic acid sequence at least 90% identical to SEQ ID NO:7, or is as set forth in SEQ ID NO:7.
According to another aspect of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 9, as determined using the LALIGN software of EMBnet Switzerland using default parameters, a nucleic acid construct comprising said isolated polynucleotide, and a host cell comprising the nucleic acid construct.
According to further features in preferred embodiments of the invention described below the nucleic acid construct further comprises a promoter for regulating transcription of the isolated polynucleotide in sense or antisense orientation.
According to yet further features in preferred embodiments of the invention described below the nucleic acid construct further comprises positive and negative selection markers for selecting for homologous recombination events.
According to another aspect of the present invention there is provided an isolated polypeptide comprising an amino acid sequence at least 70% identical to SEQ ID NO: 9, as determined using the LALIGN software of EMBnet Switzerland using default parameters or an active portion thereof.
According to yet another aspect of the present invention there is provided an antibody or an antibody fragment being capable of specifically binding a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 9, as determined using the LALIGN software of EMBnet Switzerland using default parameters.
According to still another aspect of the present invention there is provided an oligonucleotide specifically hybridizable with a nucleic acid sequence encoding a polypeptide having an amino acid at least 70% identical to SEQ ID NO: 9, as determined using the LALIGN software of EMBnet Switzerland using default parameters.
According to another aspect of the present invention there is provided a pharmaceutical composition comprising a therapeutically effective amount of an IL-4 polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 9, as determined using the LALIGN software of EMBnet Switzerland using default parameters and a pharmaceutically acceptable carrier or diluent.
According to further features in preferred embodiments of the invention described below the nucleic acid sequence of the isolated polynucleotide is as set forth in SEQ ID NO: 11 or 12.
According to yet further features in preferred embodiments of the invention described below, the polypeptide encoded by said isolated polynucleotide is as set forth in SEQ ID NO: 9 or 10.
According to still another aspect of the present invention there is provided an isolated polynucleotide as set forth in SEQ ID NO: 11 or 12.
According to yet another aspect of the present invention there is provided an isolated polypeptide as set forth in SEQ ID NO: 9 or 10.
According to another aspect of the present invention there is provided a method of treating IL-4-related disease in a subject, the method comprising upregulating in the subject an expression level of a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 9 as determined using the LALIGN software of EMBnet Switzerland using default parameters, thereby treating the IL-4-related disease in a subject.
According to further features in preferred embodiments of the invention described below, upregulating the expression level of the polypeptide is effected by (i) administering the polypeptide to the subject; and/or (ii) administering an expressible polynucleotide encoding the polypeptide to the subject.
According to yet further features in preferred embodiments of the invention described below the expressible polynucleotide includes a nucleic acid sequence at least 90% identical to SEQ ID NO:11, or is as set forth in SEQ ID NO:11.
According to another aspect of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 13, as determined using the LALIGN software of EMBnet Switzerland using default parameters, a nucleic acid construct comprising said isolated polynucleotide, and a host cell comprising the nucleic acid construct.
According to further features in preferred embodiments of the invention described below the nucleic acid construct further comprises a promoter for regulating transcription of the isolated polynucleotide in sense or antisense orientation.
According to yet further features in preferred embodiments of the invention described below the nucleic acid construct further comprises positive and negative selection markers for selecting for homologous recombination events.
According to another aspect of the present invention there is provided an isolated polypeptide comprising an amino acid sequence at least 70% identical to SEQ ID NO: 13, as determined using the LALIGN software of EMBnet Switzerland using default parameters or an active portion thereof.
According to yet another aspect of the present invention there is provided an antibody or an antibody fragment being capable of specifically binding a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 13, as determined using the LALIGN software of EMBnet Switzerland using default parameters.
According to still another aspect of the present invention there is provided an oligonucleotide specifically hybridizable with a nucleic acid sequence encoding a polypeptide having an amino acid at least 70% identical to SEQ ID NO: 13, as determined using the LALIGN software of EMBnet Switzerland using default parameters.
According to another aspect of the present invention there is provided a pharmaceutical composition comprising a therapeutically effective amount of a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 13, as determined using the LALIGN software of EMBnet Switzerland using default parameters and a pharmaceutically acceptable carrier or diluent.
According to further features in preferred embodiments of the invention described below the nucleic acid sequence of the isolated polynucleotide is as set forth in SEQ ID NO: 15 or 16.
According to yet further features in preferred embodiments of the invention described below, the polypeptide encoded by said isolated polynucleotide is as set forth in SEQ ID NO: 13 or 14.
According to still another aspect of the present invention there is provided an isolated polynucleotide as set forth in SEQ ID NO: 15 or 16.
According to yet another aspect of the present invention there is provided an isolated polypeptide as set forth in SEQ ID NO: 13 or 14.
According to another aspect of the present invention there is provided a method of treating ITAV-related disease in a subject, the method comprising upregulating in the subject an expression level of a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 5 as determined using the LALIGN software of EMBnet Switzerland using default parameters, thereby treating the ITAV-related disease in a subject.
According to further features in preferred embodiments of the invention described below, upregulating the expression level of the polypeptide is effected by (i) administering the polypeptide to the subject; and/or (ii) administering an expressible polynucleotide encoding the polypeptide to the subject.
According to yet further features in preferred embodiments of the invention described below the expressible polynucleotide includes a nucleic acid sequence at least 90% identical to SEQ ID NO:15, or is as set forth in SEQ ID NO:15.
According to another aspect of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 17, as determined using the LALIGN software of EMBnet Switzerland using default parameters, a nucleic acid construct comprising said isolated polynucleotide, and a host cell comprising the nucleic acid construct.
According to further features in preferred embodiments of the invention described below the nucleic acid construct further comprises a promoter for regulating transcription of the isolated polynucleotide in sense or antisense orientation.
According to yet further features in preferred embodiments of the invention described below the nucleic acid construct further comprises positive and negative selection markers for selecting for homologous recombination events.
According to another aspect of the present invention there is provided an isolated polypeptide comprising an amino acid sequence at least 70% identical to SEQ ID NO: 17, as determined using the LALIGN software of EMBnet Switzerland using default parameters or an active portion thereof.
According to yet another aspect of the present invention there is provided an antibody or an antibody fragment being capable of specifically binding a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 17, as determined using the LALIGN software of EMBnet Switzerland using default parameters.
According to still another aspect of the present invention there is provided an oligonucleotide specifically hybridizable with a nucleic acid sequence encoding a polypeptide having an amino acid at least 70% identical to SEQ ID NO: 17, as determined using the LALIGN software of EMBnet Switzerland using default parameters.
According to another aspect of the present invention there is provided a pharmaceutical composition comprising a therapeutically effective amount of a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 17, as determined using the LALIGN software of EMBnet Switzerland using default parameters and a pharmaceutically acceptable carrier or diluent.
According to further features in preferred embodiments of the invention described below the nucleic acid sequence of the isolated polynucleotide is as set forth in SEQ ID NO: 19 or 20.
According to yet further features in preferred embodiments of the invention described below, the polypeptide encoded by said isolated polynucleotide is as set forth in SEQ ID NO: 17 or 18.
According to still another aspect of the present invention there is provided an isolated polynucleotide as set forth in SEQ ID NO: 19 or 20.
According to yet another aspect of the present invention there is provided an isolated polypeptide as set forth in SEQ ID NO: 17 or 18.
According to another aspect of the present invention there is provided a method of treating INR-related disease in a subject, the method comprising upregulating in the subject an expression level of a polypeptide having an amino acid sequence at least 70% identical to SEQ ID NO: 17 as determined using the LALIGN software of EMBnet Switzerland using default parameters, thereby treating the INR-related disease in a subject.
According to further features in preferred embodiments of the invention described below, upregulating the expression level of the polypeptide is effected by (i) administering the polypeptide to the subject; and/or (ii) administering an expressible polynucleotide encoding the polypeptide to the subject.
According to yet further features in preferred embodiments of the invention described below the expressible polynucleotide includes a nucleic acid sequence at least 90% identical to SEQ ID NO:19, or is as set forth in SEQ ID NO:19.
According to an additional aspect of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide having an amino acid sequence at least 70% homologous to SEQ ID NO: 54, as determined using the BlastP software of the National Center of Biotechnology Information (NCBI) using default parameters, a nucleic acid construct comprising said isolated polynucleotide, and a host cell comprising the nucleic acid construct.
According to further features in preferred embodiments of the invention described below the nucleic acid construct further comprises a promoter for regulating transcription of the isolated polynucleotide in sense or antisense orientation.
According to yet further features in preferred embodiments of the invention described below the nucleic acid construct further comprises positive and negative selection markers for selecting for homologous recombination events. The isolated polynucleotide, wherein said nucleic acid sequence is as set forth in one of SEQ ID NO: 45-53.
According to a further aspect of the present invention said polypeptide is as set forth in one of SEQ ID NO: 54-61.
According to yet an additional aspect of the present invention there is provided an isolated polynucleotide as set forth in one of SEQ ID NO: 45-53.
According to an additional aspect of the present invention there is provided an isolated polypeptide as set forth in one of SEQ ID NO: 54-61.
According to yet an additional aspect of the present invention there is provided an isolated polypeptide comprising an amino acid sequence at least 70% homologous to SEQ ID NO: 54, as determined using the BlastP software of the National Center of Biotechnology information (NCBI) using default parameters or an active portion thereof.
According to still an additional aspect of the present invention there is provided an antibody or an antibody fragment being capable of specifically binding a polypeptide having an amino acid sequence at least 70% homologous to SEQ ID NO: 54, as determined using the BlastP software of the National Center of Biotechnology Information (NCBI) using default parameters.
According to yet an additional aspect of the present invention there is provided an oligonucleotide specifically hybridizable with a nucleic acid sequence encoding a polypeptide having an amino acid at least 70% homologous to SEQ ID NO: 54, as determined using the BlastP software of the National Center of Biotechnology Information (NCBI) using default parameters.
According to still an additional aspect of the present invention there is provided a method of diagnosing predisposition to, or presence of cancer in a subject, the method comprising determining an expression level of a polypeptide having an amino acid at least 70% homologous to SEQ ID NO: 54, as determined using the BlastP software of the National Center of Biotechnology Information (NCBI) using default parameters, or of a polynucleotide encoding said polypeptide in a biological sample obtained from the subject, wherein said level of said polynucleotide or said level of said polypeptide is correlatable with predisposition to, or presence or absence of cancer, thereby diagnosing predisposition to, or presence of cancer in the subject.
According to further features in preferred embodiments of the invention described below the cancer is selected from the group consisting of ovarian cancer, colon cancer and lung cancer.
According to yet further features in preferred embodiments of the invention described below said determining said expression level of said polypeptide is effected via an assay selected from the group consisting of immunohistochemistry, ELISA, RIA, Western blot analysis, FACS analysis, an immunofluorescence assay, and a light emission immunoassay.
According to further features in preferred embodiments of the invention described below said determining level of said polynucleotide is effected via an assay selected from the group consisting of PCR, RT-PCR, quantitative RT-PCR, chip hybridization, RNase protection, in-situ hybridization, primer extension, Southern blot, Northern blot and dot blot analysis.
According to yet an additional aspect of the present invention there is provided a kit for diagnosing cancer or a predisposition thereto in a subject, the kit comprising the antibody or antibody fragment being capable of specifically binding a polypeptide having an amino acid sequence at least 70% homologous to SEQ ID NO: 54, as determined using the BlastP software of the National Center of Biotechnology Information (NCBI) using default parameters and reagents for detecting hybridization of the antibody or antibody fragment.
According to further features in preferred embodiments of the invention described below the cancer is selected from the group consisting of ovarian cancer, colon cancer and lung cancer.
According to yet further features in preferred embodiments of the invention described below detecting hybridization of the antibody or antibody fragment is effected by an assay selected from the group consisting of immunohistochemistry, ELISA, RIA, Western blot analysis, FACS analysis, an immunofluorescence assay, and a light emission immunoassay.
According to still further features in preferred embodiments of the invention described below said antibody or antibody fragment is coupled to an enzyme.
According to further features in preferred embodiments of the invention described below said antibody or antibody fragment is coupled to a detectable moiety selected from the group consisting of a chromogenic moiety, a fluorogenic moiety, a radioactive moiety and a light-emitting moiety.
According to yet a further aspect of the present invention there is provided a kit for diagnosing cancer or a predisposition thereto in a subject, the kit comprising oligonucleotide specifically hybridizable with a nucleic acid sequence encoding a polypeptide having an amino acid at least 70% homologous to SEQ ID NO: 54, as determined using the BlastP software of the National Center of Biotechnology Information (NCBI) using default parameters.
According to further features in preferred embodiments of the invention described below the kit further comprising reagents for detecting hybridization of the oligonucleotide.
According to yet further features in preferred embodiments of the invention described below the cancer is selected from the group consisting of ovarian cancer and lung cancer.
According to yet a further aspect of the present invention there is provided an isolated E-Selectin T1 polypeptide comprising a first amino acid sequence being at least 90% homologous to amino acids 1-176 of wild type E-SElectin corresponding to LEM2_HUMAN, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence SKSGSCLFLHLRW (SEQ ID NO:67), wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for a tail of E-Selectin T1, comprising a polypeptide having the sequence SKSGSCLFLHLRW (SEQ ID NO: 67).
According to yet a further aspect of the present invention there is provided an isolated L-Selectin T2 polypeptide comprising an amino acid sequence being at least 90% homologous to amino acids 1-254 of wild type L-Selectin corresponding to LEM1_HUMAN, contiguous to and in sequential order bridged by GE.
According to yet a further aspect of the present invention there is provided an isolated L-Selectin T3 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-317 of wild type L-Selectin corresponding to LEM1_HUMAN, bridged by S and a second amino acid sequence being at least 90% homologous to amino acids 361-372 of wild type L-Selectin corresponding to LEM1_HUMAN, wherein said first amino acid is contiguous to said bridging amino acid and said second amino acid sequence is contiguous to said bridging amino acid, and wherein said first amino acid, said bridging amino acid and said second amino acid sequence are in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for an edge portion of L-Selectin T3, comprising a first amino acid sequence being at least 90% homologous to amino acids 307-317 of wild type L-Selectin corresponding to LEM1_HUMAN, bridged by S and a second amino acid sequence being at least 90% homologous to amino acids 361-371 of wild type L-Selectin corresponding to LEM1_HUMAN, wherein said first amino acid is contiguous to said bridging amino acid and said second amino acid sequence is contiguous to said bridging amino acid, and wherein said first amino acid, said bridging amino acid and said second amino acid sequence are in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated L-Selectin T6 polypeptide consisting essentially of an amino acid sequence being at least 90% homologous to amino acids 1-316 of wild type L-Selectin corresponding to LEM1_HUMAN, contiguous to and in sequential order bridged by SE.
According to yet a further aspect of the present invention there is provided an isolated Integrin alpha M variant T8 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-288 of wild type Integrin alpha M, corresponding to ITAM_HUMAN, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence NAALRLMLLWRVSMWIHPPFNLQILLKSK (SEQ ID NO:79), wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for a tail of Integrin alpha M variant T8, comprising a polypeptide having the sequence NAALRLMLLWRVSMWIHPPFNLQILLKSK (SEQ ID NO:79).
According to yet a further aspect of the present invention there is provided an isolated Integrin alpha L variant T11 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-745 of wild type Integrin alpha L, corresponding to ITAL_HUMAN, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VRRDG (SEQ ID NO:82), wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for a tail of Integrin alpha L variant T11, comprising a polypeptide having the sequence VRRDG (SEQ ID NO:82).
According to yet a further aspect of the present invention there is provided an isolated Integrin alpha IIb variant T9 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-866 of wild type Integrin alpha IIb, corresponding to ITAB_HUMAN, and a second amino acid sequence being at least 90% homologous to amino acids 1020-1039 of wild type Integrin alpha IIb, corresponding to ITAB_HUMAN, wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for an edge portion of Integrin alpha IIb variant T9, comprising a first amino acid sequence being at least 90% homologous to amino acids 856-866 of wild type Integrin alpha IIb, corresponding to ITAB_HUMAN, and a second amino acid sequence being at least 90% homologous to amino acids 1020-1030 of wild type Integrin alpha IIb, corresponding to ITAB_HUMAN, wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated Integrin alpha IIb variant T8 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-981 of wild type Integrin alpha IIb, corresponding to ITAB_HUMAN, and a second amino acid sequence being at least 90% homologous to amino acids 1021-1039 of wild type Integrin alpha IIb, corresponding to ITAB_HUMAN, wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for an edge portion of Integrin alpha IIb variant T8, comprising a first amino acid sequence being at least 90% homologous to amino acids 971-981 of wild type Integrin alpha IIb, corresponding to ITAB_HUMAN, and a second amino acid sequence being at least 90% homologous to amino acids 1021-1031 of wild type Integrin alpha IIb, corresponding to ITAB_HUMAN, wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated Integrin beta-7 variant T6 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-191 of wild type Integrin beta-7, corresponding to ITB7_HUMAN, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence EPSAASRPVSPCLFNHCPSLCQHPGLTRAPTCPPSC (SEQ ID NO:91), wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for a tail of Integrin beta-7 variant T6, comprising a polypeptide having the sequence EPSAASRPVSPCLFNHCPSLCQHPGLTRAPTCPPSC (SEQ ID NO:91).
According to yet a further aspect of the present invention there is provided an isolated Interleukin 13 Receptor 1 variant T1 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-225 of wild type Interleukin 13 Receptor 1, corresponding to I131_HUMAN, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GPTSPYCHIGDEVST (SEQ ID NO:94), wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for a tail of Interleukin 13 Receptor 1variant T1, comprising a polypeptide having the sequence GPTSPYCHIGDEVST (SEQ ID NO:94).
According to yet a further aspect of the present invention there is provided an isolated Complement Component C1s variant T7 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-423 of wild type Complement Component C1s, corresponding to C1S_HUMAN, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GLNSDLPESSSVRWQYHCAVGCQGRGEPPQPH (SEQ ID NO:97), wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for a tail of Complement Component C1s variant T7, comprising a polypeptide having the sequence GLNSDLPESSSVRWQYHCAVGCQGRGEPPQPH (SEQ ID NO:97).
According to yet a further aspect of the present invention there is provided an isolated Complement Component C1s variant T8 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-65 of wild type Complement Component C1s, corresponding to C1S_HUMAN, bridged by Y and a second amino acid sequence being at least 90% homologous to amino acids 132-688 of wild type Complement Component C1s, corresponding to C1S_HUMAN, wherein said first amino acid is contiguous to said bridging amino acid and said second amino acid sequence is contiguous to said bridging amino acid, and wherein said first amino acid, said bridging amino acid and said second amino acid sequence are in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for an edge portion of Complement Component C1s variant T8, comprising a first amino acid sequence being at least 90% homologous to amino acids 55-65 of wild type Complement Component C1s, corresponding to C1S_HUMAN, bridged by Y and a second amino acid sequence being at least 90% homologous to amino acids 132-142 of wild type Complement Component C1s, corresponding to C1S_HUMAN, wherein said first amino acid is contiguous to said bridging amino acid and said second amino acid sequence is contiguous to said bridging amino acid, and wherein said first amino acid, said bridging amino acid and said second amino acid sequence are in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated Complement Component C5 variant T7 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-854 of wild type Complement Component C5 corresponding to CO5_HUMAN, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence SLALSPRLECNGKISGQLQVRLPGSSDSPASASQVAGITGTHHHAQPT (SEQ ID NO:103), wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for a tail of Complement Component C5 variant T7, comprising a polypeptide having the sequence SLALSPRLECNGKISGQLQVRLPGSSDSPASASQVAGITGTHHHAQPT (SEQ ID NO:103).
According to yet a further aspect of the present invention there is provided an isolated Complement Component C5 variant T11 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-292 of wild type Complement Component C5 corresponding to CO5_HUMAN, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence RAEVR, wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for a tail of Complement Component C5 variant T11, comprising a polypeptide having the sequence RAEVR.
According to yet a further aspect of the present invention there is provided an isolated Complement Receptor CR1 variant T5 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-162 of wild type Complement Component C5 corresponding to CR1_HUMAN, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence SELKYPFLFLLPTHSNFSLE (SEQ ID NO:109), wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for a tail of Complement Receptor CR1 variant T5, comprising a polypeptide having the sequence SELKYPFLFLLPTHSNFSLE (SEQ ID NO:109).
According to yet a further aspect of the present invention there is provided an isolated Integrin alpha 4 variant T2 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-697 of wild type Integrin alpha 4 corresponding to ITA4_HUMAN, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence LFHFSH (SEQ ID NO:112), wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for a tail for Integrin alpha 4 variant T2, comprising a polypeptide having the sequence LFHFSH (SEQ ID NO:112).
According to yet a further aspect of the present invention there is provided an isolated Tissue plasminogen activator (t-PA) variant T6 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-53 of wild type Tissue plasminogen activator, corresponding to TPA_HUMAN, bridged by H, and a second amino acid sequence being at least 90% homologous to amino acids 135-562 of TPA_HUMAN, wherein said first amino acid is contiguous to said bridging amino acid and said second amino acid sequence is contiguous to said bridging amino acid, and wherein said first amino acid, said bridging amino acid and said second amino acid sequence are in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for an edge portion of Tissue plasminogen activator (t-PA) variant T6, comprising a first amino acid sequence being at least 90% homologous to amino acids 43-53 of wild type Tissue plasminogen activator, corresponding to TPA_HUMAN, bridged by H and a second amino acid sequence being at least 90% homologous to amino acids 135-145 of TPA_HUMAN, wherein said first amino acid is contiguous to said bridging amino acid and said second amino acid sequence is contiguous to said bridging amino acid, and wherein said first amino acid, said bridging amino acid and said second amino acid sequence are in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated Tissue plasminogen activator (t-PA) variant T9 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-180 of wild type Tissue plasminogen activator, corresponding to TPA_HUMAN, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence TPVPRHWAWANIITAGILMGMPSPGATC (SEQ ID NO:117), wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for a tail of Tissue plasminogen activator (t-PA) variant T9, comprising a polypeptide having the sequence TPVPRHWAWANIITAGILMGMPSPGATC (SEQ ID NO: 117).
According to yet a further aspect of the present invention there is provided an isolated Thrombopoirtin variant T8 polypeptide, comprising a first amino acid sequence being at least 90% homologous to amino acids 1-132 of wild type Thrombopoietin corresponding to TPO_HUMAN, and a second amino acid sequence being at least 90% homologous to amino acids 160-353 of TPO_HUMAN, wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet a further aspect of the present invention there is provided an isolated polypeptide for an edge portion of Thrombopoirtin variant T8, comprising a first amino acid sequence being at least 90% homologous to amino acids 122-132 of TPO_HUMAN, and a second amino acid sequence being at least 90% homologous to amino acids 160-170 of TPO_HUMAN, wherein said first and said second amino acid sequences are contiguous and in a sequential order.
According to yet further aspect of the present invention there is provided an isolated chimeric polypeptide HSFLT_PEA—1_P10, comprising a first amino acid sequence being at least 90% homologous to MVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQ CRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGF YSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRV TSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHL YKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSY PDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKS VNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKD GLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNV KPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARC DFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYIC IASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVT WILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNV YTGEEILQKKEITIRDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWF KNNHKIQQEP corresponding to amino acids 1-705 of VGR1_HUMAN, which also corresponds to amino acids 1-705 of HSFLT_PEA—1_P10, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence ELYTSTSPSSSSSSPLSSSSSSSSSSSS corresponding to amino acids 706-733 of HSFLT_PEA—1_P10, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
According to yet further aspect of the present invention there is provided and antibody or binding fragment thereof which specifically binds to the tail portion of the Vascular endothelial growth factor (VEGF) receptor HSFLT PEA-1 P10 of SEQ ID NO:533, wherein the tail portion consisting of the amino acid sequence ELYTSTSPSSSSSSPLSSSSSSSSSSSS corresponding to amino acids 706-733 of SEQ ID NO:533.
According to additional aspect of the present invention there is provided a kit comprising an antibody or binding fragment thereof which specifically binds to the tail portion of the Vascular endothelial growth factor (VEGF) receptor HSFLT PEA-1 P10 of SEQ ID NO:533, wherein the tail portion consisting of the amino acid sequence ELYTSTSPSSSSSSPLSSSSSSSSSSSS corresponding to amino acids 706-733 of SEQ ID NO:533, and at least one reagent for performing immunoassay.
According to yet further aspect of the present invention there is provided a method of detecting the binding of an antibody or binding fragment thereof which specifically binds to the tail portion of the Vascular endothelial growth factor (VEGF) receptor HSFLT PEA-1 P10 of SEQ ID NO:533, wherein the tail portion consisting of the amino acid sequence ELYTSTSPSSSSSSPLSSSSSSSSSSSS corresponding to amino acids 706-733 of SEQ ID NO:533 to a polypeptide comprising the amino acids 706-733 SEQ ID NO:533 in a sample obtained from a patient.
According to certain embodiments, the patient is suspected of having a disease selected from the group consisting of cancer, diabetes, ulcers, peripheral vascular disease and ischemia.



BRIEF DESCRIPTION OF THE DRAWINGS
The invention is herein described, by way of example only, with reference to the accompanying drawings. With specific reference now to the drawings in detail, it is stressed that the particulars shown are by way of example and for purposes of illustrative discussion of the preferred embodiments of the present invention only, and are presented in the cause of providing what is believed to be the most useful and readily understood description of the principles and conceptual aspects of the invention. In this regard, no attempt is made to show structural details of the invention in more detail than is necessary for a fundamental understanding of the invention, the description taken with the drawings making apparent to those skilled in the art how the several forms of the invention may be embodied in practice.
In the drawings:
FIGS. 1a-b present the nucleic acid sequence (FIG. 1a) and amino acid sequence (FIG. 1b) of the GCSF variant of the present invention (SEQ ID NO:3 and 1, respectively), described in Example 2 of the Examples section which follows. The unique sequence is marked in bold and italics. The ATG and the stop codon are marked in bold and underlined.
FIG. 2 is a schematic illustration depicting the graphical viewer scheme presenting the new variant of GCSF (transcript—3) as compared to the wild type mRNA. The ESTs supporting the new variant are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as follows: =genomic DNA; =refseq mRNA; =known GenBank mRNAs; =ESTs aligned in the same orientation as their annotation; =ESTs aligned in the opposite orientation to their annotation; =ESTs without direction annotation; =predicted transcripts; =predicted polypeptide.
FIG. 3 is an amino acid sequence alignment between wild-type GCSF protein (SwissProt locus: CSF3_HUMAN; SEQ ID NO:128) and the protein variant of the present invention, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 4 is a schematic illustration showing the protein domain structure of wild-type GCSF protein (SwissProt locus: CSF3_HUMAN) and the variant of the present invention (SEQ ID NO:1). Unique region is indicated by U and arrow (SEQ ID NO:2).
FIGS. 5a-b present the nucleic acid sequence (FIG. 5a) and amino acid sequence (FIG. 5b) of the TNR3 variant of the present invention (SEQ ID NOs:7 and 5, respectively), described in Example 3 of the Examples section which follows. The unique sequence is marked in bold and italics. The ATG and the stop codon are marked in bold and underlined.
FIG. 6 is a schematic illustration depicting the graphical viewer scheme presenting the new variant of TNR3 (transcript—19) as compared to the wild type mRNA. The ESTs supporting the new variant are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 7 is an amino acid sequence alignment between wild-type TNR3 protein (GenBank Accession No. P36941; TRN3_HUMAN; SEQ ID NO:129) and the protein variant of the present invention, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 8 is a schematic illustration showing the protein domain structure of wild-type TNR3 protein (SwissProt locus: TRN3_HUMAN) and the variant of the present invention (SEQ ID NO:5). Unique region is indicated by U and arrow (SEQ ID NO:6).
FIGS. 9a-b presents the nucleic acid sequence (FIG. 9a) and amino acid sequence (FIG. 9b) of the IL4R variant of the present invention (Variant T5) (SEQ ID NO:11 and 9, respectively), described in Example 4 of the Examples section which follows. The unique sequence is marked in bold and italics. The ATG and the stop codon are marked in bold and underlined.
FIG. 10 is an amino acid sequence alignment between wild-type IL4R protein (SwissProt accession: IL4R_Human) and the protein variant of the present invention, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40 -dfmt=fastap.
FIG. 11 is a schematic illustration showing the protein domain structure of wild-type IL4R protein (SwissProt accession: IL4R_Human; GenBank Accession No. P24394; SEQ ID NO:130) and the variant of the present invention (SEQ ID NO:9). Unique regions are indicated by U and arrow (SEQ ID NO:10). FIGS. 12a-b present the nucleic acid sequence (HUMVTNR_T5 (SEQ ID NO:15; FIG. 12a) and amino acid sequence (HUMVTNR_P5; SEQ ID NO:13, FIG. 12b) of the ITAV variant of the present invention (SEQ ID NOs:15 and 13, respectively), described in Example 5 of the Examples section which follows. The unique sequence is marked in bold and italics. The ATG and the stop codon are marked in bold and underlined.
FIG. 13 is a schematic illustration depicting the graphical viewer scheme presenting the new variant of integrin α5 ITAV (Transcript—5) as compared to the wild type mRNA. The ESTs supporting the new variant are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 14 is an amino acid sequence alignment between wild-type ITAV protein (SwissProt locus: ITAV_HUMAN; P06756; SEQ ID NO:131) and the protein variant of the present invention, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 15 is a schematic illustration showing the protein domain structure of wild-type ITAV protein (ITAV_HUMAN; SEQ ID NO:131) and the variant of the present invention (SEQ ID NO:13). Unique region is indicated by U (SEQ ID NO:14).
FIGS. 16a-b present the nucleic acid sequence (FIG. 16a; SEQ ID NO:19) and amino acid sequence (FIG. 16b; SEQ ID NO:17) of the INR1 variant of the present invention (SEQ ID NOs:19 and 17, respectively), described in Example 6 of the Examples section which follows. The unique sequence is marked in bold and italics (SEQ ID NO:18). The ATG and the stop codon are marked in bold and underlined.
FIG. 17 is a schematic illustration depicting the viewer scheme presenting the new variant of INR1 (Transcript—12) as compared to the wild type mRNA. The ESTs supporting the new variant are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 18 is an amino acid sequence alignment between wild-type INR1 protein (SwissProt locus: INR1_HUMAN; GenBank Accession No. P17181; SEQ ID NO:132) and the protein variant of the present invention, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 19 is a schematic illustration showing the protein domain structure of wild-type INR1 protein (SwissProt locus: INR1_HUMAN; SEQ ID NO:132) and the INR1 variant T12 of the present invention (SEQ ID NO:17). Unique region is indicated by U and arrow (SEQ ID NO:18).
FIG. 20 is a schematic illustration showing the protein domain structure of wild-type HGF protein (SwissProt locus: HGF_HUMAN; GenBank Accession No. P14210; SEQ ID NO:133) and the HGF variants of the present invention, as described in Example 45a-d below. The novel splice variants are as follows: Variant a: skipping exon 3; Variant b: skipping exon 4; Variant c: skipping exon 7; and Variant d: skipping exon 9.
FIG. 21 RT-PCR for identification of exon 7 skipping in Hepatocyte Growth Factor. The protocol used is described in Example 45c-2 of the Examples section which follows. Primers were taken from exon 6 (f) and 8 (r). Predicted product of full length product was 302 bp, which was found in all tissue samples. Skipping exon 7 (163 bp) was found exclusively in Colon (lane 6-arrowhead). A larger product (probably a novel exon) was found in Breast (lane 5). Tissue type cDNA pools: 1—Cervix+HeLa; 2—Uterus; 3—Ovary; 4—Placenta; 5—Breast; 6—Colon; 7—Pancreas; 8—Liver+Spleen; 9—Brain; 10—Prostate; 11—Testis; 12—Kidney; 13—Thyroid; 14—Assorted Cell-lines (5). M=1 kb ladder marker; H=H2O negative control.
FIG. 22 is a schematic illustration showing the protein domain structure of wild-type CART protein (SwissProt locus: CART_HUMAN; GenBank Accession No. Q16568; SEQ ID NO:134) and the CART variants of the present invention, as described in Example 46 below. Unique regions are indicated.
FIG. 23a-b are schematic illustrations showing the protein domain structure of wild-type DPP4 protein (SwissProt locus: DPP4_HUMAN; GenBank Accession No. P27487; SEQ ID NO:135) and the DPP4 variants of the present invention, as described in Examples 47a-h below. Unique regions are indicated. The novel splice variants of DPP4 are as follows: Variant a: skipping exon 7; Variant b: skipping exon 9; Variant c: skipping exon 19; Variant d: skipping exon 21; Variant e: skipping exon 22; Variant f: skipping exon 24; and Variant g: skipping exon 25.
FIG. 24 is an illustration depicting schematic alignment of the nucleic acid sequences of wild type Troponin transcript (GenBank Accession No. NM—003283) and variants 1, 4, 6, 9, 10, 14 and 16 (SEQ ID NOs: 46, 47, 48, 49, 50, 51, 52, and 53, respectively), as described in Example 7 below. Coding regions are shaded. Sequence region 4a codes for the unique amino acid sequence. Other regions marked in dotes code for additional novel amino acids sequences. Red arrows indicate the location of the primers and SEQ ID NOs. thereof, which were used for real-time PCR validation.
FIG. 25 is a histogram depicting the expression of troponin transcripts of the present invention in normal, benign and tumor derived ovarian samples as determined by real time PCR using a troponin-S69208_unique_region derived fragment (amplicon—SEQ ID NO:23; forward primer—SEQ ID NO:21; reverse primer—SEQ ID NO:22), as described in Example 7 of the Examples section which follows. Expression was normalized to the averaged expression of four housekeeping genes PBGD, HPRT, GAPDH and SDHA.
FIG. 26 is a histogram depicting the expression of troponin transcripts of the present invention in normal and tumor derived lung samples as determined by real time PCR using a troponin-S69208_unique_region derived fragment (amplicon—SEQ ID NO:23; forward primer—SEQ ID NO:21; reverse primer—SEQ ID NO:22), as described in Example 7 of the Examples section which follows. Expression was normalized to the averaged expression of four housekeeping genes PBGD, HPRT, Ubiquitin and SDHA.
FIG. 27 is a histogram depicting the expression of troponin transcripts for the present invention in non-cancerous, and tumor derived colon samples as determined by real time PCR using a troponin-S69208_unique_region derived fragment (SEQ ID NOs:23-amplicon), as described in Example 7c below. Expression was normalized to the averaged expression of four housekeeping genes PBGD, HPRT, RPS27A and G6PD.
FIGS. 28a-b presents the nucleic acid sequence (FIG. 28a) and amino acid sequence (FIG. 28b) of the CD154 splice variant skipping exon 3 of the present invention. The novel splice variant of CD154 is described in Example 48 below. The unique sequence is marked in bold and italics. The ATG and the stop codon are marked in bold and underlined.
FIGS. 28c-d presents the amino acid sequence (FIG. 28c) and nucleic acid sequence alignment (FIG. 28d) of the CD154 splice variant skipping exon 3 of the present invention and the mRNA derived from Hyper IgM syndrome (Ramesh N, et al., Int Immunol. 1993 July; 5(7): 769-73; gi AAD13982), as described in Example 48 below. Unique amino acids shared by both polypeptides are marked in bold and italics Amino acids unique for the mutated form of CD154 derived from Hyper IgM syndrome patients are marked as italics.
FIG. 28e-f presents the nucleic acid sequence (FIG. 28e) and amino acid sequence (FIG. 280 of the CD154 splice variant skipping exon 4 of the present invention. The novel splice variant of CD154 is described in Example 48 below. The ATG and the stop codon are marked in bold and underlined.
FIG. 29 is an amino acid sequence alignment between wild-type CD154 protein (TNF5_HUMAN; GenBank Accession No. P29965; SEQ ID NO:136) and the skipping exon 3 CD154 variant of the present invention, as determined using the BlastP algorithm and default parameters. The novel splice variant of CD154 is described in Example 48 below.
FIG. 30 is an amino acid sequence alignment between wild-type CD154 protein (TNF5_HUMAN; SEQ ID NO:136) and the skipping exon 4 protein variant of the present invention, as determined using the BlastP algorithm and default parameters. The amino acids crucial for CD40 binding and for integrin α2,βIII R binding are marked. The novel splice variant of CD154 is described in Example 48 below.
FIG. 31a presents the amino acid sequence of Macaca nemestrina CD154 protein (gi|21363028|sp|Q9BDM7|TNF5_MACNE; SEQ ID NO:137).
FIG. 31b is an amino acid sequence alignment between wild-type CD154 protein (TNF5_HUMAN; SEQ ID NO:136) and the Macaca nemestrina CD154 protein (gi|21363028|sp|Q9BDM7|TNF5_MACNE; SEQ ID NO:137), as determined using the BlastP algorithm and default parameters. The amino acids crucial for CD40 binding and for integrin α2, βIII R binding are marked in bold.
FIG. 31c is an amino acid sequence alignment between the CD154 skipping exon 4 splice variant of the present invention and the Macaca nemestrina CD154 protein (gi|21363028|sp|Q9BDM7|TNF5_MACNE; SEQ ID NO:137), as determined using the BlastP algorithm and default parameters. The novel splice variant of CD154 is described in Example 48 below.
FIG. 32 is a structural prediction of the partial wild type CD154 protein, demonstrating the predicted modular structure of the regions involved in CD40 binding and these involved in integrin α2,βIII binding. The prediction was performed using Cn3Dv4.1 structural viewer of NCBI.
FIG. 33 summarizes the domain structures of the variants described in Example 10.
FIG. 34 presents the domain structure of the variants described in Example 42.
FIG. 35 depicts the structure domain of the variants described in Example 49 in comparison to the known or wild-type (WT) protein.
FIG. 36 depicts the structure domain of the variants described in Example 50 in comparison to the known or wild-type (WT) protein
FIGS. 37a-b present the nucleic acid sequence (FIG. 37a) and amino acid sequence (FIG. 37b) of the E-Selectin variant of the present invention (SEQ ID NO: 66 and 65, respectively), described in Example 17 below. The unique sequence is marked in bold and italics.
FIG. 38 is a schematic illustration depicting the graphical viewer scheme presenting the new variant of E-Selectin (transcript—1) as compared to the wild type mRNA. The ESTs supporting the new variant are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 39 is an amino acid sequence alignment between wild-type E-Selectin (SwissProt locus: LEM2_HUMAN; GenBank Accession No. P16581; SEQ ID NO:139) and the protein variant of the present invention, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 40 is a schematic illustration showing the protein domain structure of wild-type E-Selectin (SwissProt locus: LEM2_HUMAN; SEQ ID NO:139) and the variant of the present invention (SEQ ID NO:65). Unique region is indicated (SEQ ID NO:67).
FIGS. 41a-b present the nucleic acid sequence (FIG. 41a) and amino acid sequence (FIG. 41b) of the L-Selectin variant T2 of the present invention (SEQ ID NO: 69 and 68, respectively), described in Example 33 below. The unique sequence is marked in bold and italics. The ATG and the stop codon are marked in bold and underlined.
FIGS. 41c-d present the nucleic acid sequence (FIG. 41c) and amino acid sequence (FIG. 41d) of the L-Selectin variant T3 of the present invention (SEQ ID NOs:72 and 71, respectively), described in Example 33 below. The unique edge, giving rise to a unique sequence combination, is marked by H.
FIGS. 41e-f present the nucleic acid sequence (FIG. 41e) and amino acid sequence (FIG. 410 of the L-Selectin variant T6 of the present invention (SEQ ID NOs:75 and 74, respectively), described in Example 33 below. The unique sequence is marked in bold and italics.
FIGS. 42a-b is a schematic illustration depicting the graphical viewer scheme presenting the new variants of L-Selectin (transcripts_T2, T3 and T6) as compared to the wild type mRNA. The EST supporting the new variant T2 and T6 are indicated (FIGS. 42a and 42b, respectively). Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 43a-c is an amino acid sequence alignment between wild-type L-Selectin (SwissProt locus: LEM1_HUMAN; GenBank Accession No. P14151; SEQ ID NO:140) and the protein variants of the present invention, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. FIG. 43a is an alignment of L-selectin variant T2; FIG. 43b is an alignment of L-selectin variant T3; FIG. 43c is an alignment of L-selectin variant T6;
FIG. 44 is a schematic illustration showing the protein domain structure of wild-type L-Selectin (SwissProt locus: LEM1_HUMAN; SEQ ID NO:140) and the variants of the present invention (SEQ ID NOs: 68, 71 and 74). Unique region is indicated by U and arrow (SEQ ID NOs: 70, 73, and 76).
FIGS. 45a-b present the nucleic acid sequence (FIG. 45a; SEQ ID NO:78) and amino acid sequence (FIG. 45b; SEQ ID NO:77) of the Integrin alpha-M variant of the present invention (integrin α-M variant Transcript_T8), described in Example 8 of the Examples section which follows. The unique sequence is marked in bold and italics. Note that there is prediction of an SNP G→C at position 2 of the transcript of the new variant (SEQ ID NO:78).
FIG. 46 is a schematic illustration depicting the graphical viewer scheme presenting the new variant of Integrin alpha-M (transcript_T8) as compared to the wild type mRNA. The ESTs supporting the new variant are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 47 is an amino acid sequence alignment between wild-type Integrin alpha-M (SwissProt locus: ITAM_HUMAN; GenBank Accession No. P11215; SEQ ID NO:141) and the protein variant of the present invention, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 48 is a schematic illustration showing the protein domain structure of wild-type Integrin alpha-M (SwissProt locus: ITAM_HUMAN; SEQ ID NO:141) and the variant of the present invention (SEQ ID NO:77). Unique region is indicated by U and arrow (SEQ ID NO:79).
FIGS. 49a-b present the nucleic acid sequence (FIG. 49a) and amino acid sequence (FIG. 49b) of the Integrin alpha-L variant of the present invention (SEQ ID NO: 81 and 80, respectively), described in Example 18 below. The unique sequence is marked in bold and italics. The ATG and the stop codon are marked in green.
FIG. 50 is a schematic illustration depicting the graphical viewer scheme presenting the new variant of Integrin alpha-L (transcript_T11) as compared to the wild type mRNA. The ESTs supporting the new variant are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 51 is an amino acid sequence alignment between wild-type Integrin alpha-L (SwissProt locus: ITAL_HUMAN; GenBank Accession No. P20701; SEQ ID NO:142) and the protein variant of the present invention, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 52 is a schematic illustration showing the protein domain structure of wild-type Integrin alpha-L (SwissProt locus: ITAL_HUMAN; SEQ ID NO:142) and the variant of the present invention (SEQ ID NO:80). Unique region is indicated (SEQ ID NO: 82).
FIGS. 53a-b present the nucleic acid sequence (FIG. 53a) and amino acid sequence (FIG. 53b) of the Integrin alpha-IIb variant of the present invention, transcript T9 (SEQ ID NOs:84 and 83, respectively), described in Example 28 below. The new edge, giving rise to a unique sequence combination, is marked with “][”.
FIGS. 54a-b present the nucleic acid sequence (FIG. 54a) and amino acid sequence (FIG. 54b) of the Integrin alpha-IIb variant of the present invention, transcript T8 (SEQ ID NOs:87 and 86, respectively), described in Example 28 below. The new edge, giving rise to a unique sequence combination, is marked with “][”.
FIG. 55a is an amino acid sequence alignment between wild-type Integrin alpha-IIb (SwissProt locus: ITAB_HUMAN; GenBank Accession No. P08514; SEQ ID NO:143) and the protein variant T9 of the present invention, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 55b is an amino acid sequence alignment between wild-type Integrin alpha-IIb (SwissProt locus: ITAB_HUMAN; SEQ ID NO:143) and the protein variant T8 of the present invention, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 56 is a schematic illustration showing the protein domain structure of wild-type Integrin alpha-IIb (SwissProt locus: ITAB_HUMAN; SEQ ID NO:143) and the variants of the present invention (SEQ ID NOs:83 and 86).
FIGS. 57a-b present the nucleic acid sequence (FIG. 57a) and amino acid sequence (FIG. 57b) of the Integrin beta-7 variant of the present invention (SEQ ID NOs:90 and 89, respectively), described in Example 20 below. The unique sequence is marked in bold and italics.
FIG. 58 is a schematic illustration depicting the graphical viewer scheme presenting the new variant of Integrin beta-7 (transcript_T6) as compared to the wild type mRNA. The ESTs supporting the new variant are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 59 is an amino acid sequence alignment between wild-type Integrin beta-7 (SwissProt locus: ITB7_HUMAN; GenBank Accession No. P26010; SEQ ID NO:144) and the protein variant of the present invention, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 60 is a schematic illustration showing the protein domain structure of wild-type Integrin beta-7 (SwissProt locus: ITB7_HUMAN; SEQ ID NO:144) and the variant of the present invention (SEQ ID NO:89). Unique region is indicated (SEQ ID NO:91).
FIGS. 61a-b present the nucleic acid sequence (FIG. 61a) and amino acid sequence (FIG. 61b) of the Interleukin 13 receptor alpha-1 (IL-13-RA1) variant of the present invention (SEQ ID NOs:93 and 92, respectively), described in Example 31 below. The unique sequence is marked in bold and italics.
FIG. 62 is a schematic illustration depicting the graphical viewer scheme presenting the new variant of Interleukin 13 receptor alpha-1 (transcript_TD as compared to the wild type mRNA. The ESTs supporting the new variant are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 63 is an amino acid sequence alignment between wild-type Interleukin 13 receptor alpha-1 (SwissProt locus: I131_HUMAN; GenBank Accession No. P78552; SEQ ID NO:145) and the protein variant of the present invention, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 64 is a schematic illustration showing the protein domain structure of wild-type Interleukin 13 receptor alpha-1 (SwissProt locus: I131_HUMAN; SEQ ID NO:145) and the variant of the present invention (SEQ ID NO:92). Unique region is indicated (SEQ ID NO:94).
FIGS. 65a-b present the nucleic acid sequence (FIG. 65a) and amino acid sequence (FIG. 65b) of the Complement component C1s variant transcript T7 of the present invention (SEQ ID NOs:99 and 98, described in Example 26 below. The unique sequence is marked in bold and italics.
FIGS. 65c-d present the nucleic acid sequence (FIG. 65c) and amino acid sequence (FIG. 65d) of the Complement component C1s variant transcript T8 of the present invention (SEQ ID NOs:96 and 95, respectively), described in Example 26 below. The new edge, giving rise to a unique sequence combination, is marked with “][”.
FIG. 66 is a schematic illustration depicting the graphical viewer scheme presenting the new variants of Complement component C1s (transcripts_T7 and T8) as compared to the wild type mRNA. The ESTs supporting the new variants are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 67a is an amino acid sequence alignment between wild-type Complement component C1s (SwissProt locus: C1S_HUMAN; GenBank Accession No. P09871; SEQ ID NO:146) and the protein variant of the present invention, T7, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 67b is an amino acid sequence alignment between wild-type Complement component C1s (SwissProt locus: C1S_HUMAN; SEQ ID NO:146) and the protein variant of the present invention, T8, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 68 is a schematic illustration showing the protein domain structure of wild-type Complement component C1s (SwissProt locus: C1S_HUMAN; SEQ ID NO:146) and the variants of the present invention (SEQ ID NO: 95 and 98). Unique regions are indicated (SEQ ID NO: 97 and 100).
FIGS. 69a-b present the nucleic acid sequence (FIG. 69a) and amino acid sequence (FIG. 69b) of the Complement component C5 variant transcript T7 of the present invention (SEQ ID NOs:102 and 101, respectively), described in Example 21 below. The unique sequence is marked in bold and italics.
FIGS. 69c-d present the nucleic acid sequence (FIG. 69c) and amino acid sequence (FIG. 69d) of the Complement component C5 variant transcript T11 of the present invention (SEQ ID NOs:105 and 104, respectively), described in Example 21 below. The unique sequence is marked in bold and italics.
FIGS. 70a-b is a schematic illustration depicting the graphical viewer scheme presenting the new variants of Complement component C5 (FIG. 70a is for transcript_T7 and FIG. 70b is for transcript T11) as compared to the wild type mRNA. The ESTs supporting the new variants are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 71a is an amino acid sequence alignment between wild-type Complement component C5 (SwissProt locus: CO5_HUMAN; GenBank Accession No. P01031; SEQ ID NO:147) and the protein variant of the present invention, T7, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 71b is an amino acid sequence alignment between wild-type Complement component C5 (SwissProt locus: CO5_HUMAN; SEQ ID NO:147) and the protein variant of the present invention, T11, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 72 is a schematic illustration showing the protein domain structure of wild-type Complement component C5 (SwissProt locus: CO5_HUMAN; SEQ ID NO:147) and the variants of the present invention (SEQ ID NO: 101 and 104). Unique regions are indicated (SEQ ID NO: 103 and 106).
FIGS. 73a-b present the nucleic acid sequence (FIG. 65a) and amino acid sequence (FIG. 65b) of the Complement Receptor CR1 variant transcript T5 of the present invention (SEQ ID NOs:108 and 107, respectively), described in Example 25 below. The unique sequence is marked in bold and italics.
FIG. 74 is a schematic illustration depicting the graphical viewer scheme presenting the new variant of Complement Receptor CR1 (transcript_T5) as compared to the wild type mRNA. The ESTs supporting the new variants are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 75 is an amino acid sequence alignment between wild-type Complement Receptor CR1 (SwissProt locus: CR1_HUMAN; GenBank Accession No. P17927; SEQ ID NO:148) and the protein variant of the present invention, T5, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 76 is a schematic illustration showing the protein domain structure of wild-type Complement Receptor CR1 (SwissProt locus: CR1_HUMAN; SEQ ID NO:148) and the variants of the present invention (SEQ ID NO: 107). Unique regions are indicated (SEQ ID NO:109).
FIG. 77 represents the nucleic acid sequence of the Integrin alpha 4 variant of the present invention (SEQ ID NO: 111), described in Example 29 below. The unique sequence is marked in bold and italics.
FIG. 78 represents the amino acid sequence of the Integrin alpha 4 variant of the present invention (SEQ ID NO:110), described in Example 29 below. The unique sequence is marked in bold and italics.
FIG. 79 is a schematic illustration depicting the graphical viewer scheme presenting the new variant of Integrin alpha 4 (transcript—2) as compared to the wild type mRNA. The ESTs supporting the new variant are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 80 is an amino acid sequence alignment between wild-type Integrin alpha 4 (SwissProt locus: ITA4_HUMAN; GenBank Accession No. P13612; SEQ ID NO:149) and the protein variant of the present invention, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 81 is a schematic illustration showing the protein domain structure of wild-type Integrin alpha 4 (SwissProt locus: ITA4_HUMAN; SEQ ID NO:149) and the variant of the present invention (SEQ ID NO:110). Unique region is indicated (SEQ ID NO:112).
FIGS. 82a-b present the nucleic acid sequence (FIG. 82a) and amino acid sequence (FIG. 82b) of the Tissue plasminogen activator (tPA) variant, transcript T6, of the present invention (SEQ ID NOs:114 and 113, respectively), described in Example 32 below. The new edge giving rise to a unique sequence junction is marked with “][”.
FIGS. 82c-d present the nucleic acid sequence (FIG. 82c) and amino acid sequence (FIG. 82d) of the Tissue plasminogen activator (tPA) variant, transcript T9, of the present invention (SEQ ID NOs:116 and 115, respectively), described in Example 32 below. The unique sequence is marked in bold and italics. The new edge giving rise to a unique sequence junction is marked with “][”.
FIG. 83a is a schematic illustration depicting the graphical viewer scheme presenting the new variant of Tissue plasminogen activator (tPA) transcript_T6 as compared to the wild type mRNA. The ESTs supporting the new variant are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 83b is a schematic illustration depicting the graphical viewer scheme presenting the new variant of Tissue plasminogen activator (tPA) transcript_T9 as compared to the wild type mRNA. The ESTs supporting the new variant are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 84a is an amino acid sequence alignment between wild-type Tissue plasminogen activator (tPA) (SwissProt locus: TPA_HUMAN; GenBank Accession No. P00750; SEQ ID NO:150) and the protein variant of the present invention, Tissue plasminogen activator (tPA) transcript_T6 (HUMUPAA_P4), as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 84b is an amino acid sequence alignment between wild-type Tissue plasminogen activator (tPA) (SwissProt locus: TPA_HUMAN; SEQ ID NO:150) and the protein variant of the present invention, Tissue plasminogen activator (tPA) transcript_T9, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 85 is a schematic illustration showing the protein domain structure of wild-type Tissue plasminogen activator (tPA) (SwissProt locus: TPA_HUMAN; SEQ ID NO:150) and the variants of the present invention (SEQ ID NOs:113 and 115). Unique region is indicated (SEQ ID NO:117).
FIGS. 86a-b present the nucleic acid sequence (FIG. 86a) and amino acid sequence (FIG. 86b) of the Thrombopoietin variant, transcript T8, of the present invention (SEQ ID NOs:119 and 118, respectively), described in Example 40 below. The new edge giving rise to a unique sequence junction is marked with “][”.
FIG. 87 is a schematic illustration depicting the graphical viewer scheme presenting the new variant of Thrombopoietin transcript_T8 as compared to the wild type mRNA. The ESTs supporting the new variant are indicated. Transcript indicated as “0” represents known mRNA. The pattern code is as in FIG. 2.
FIG. 88 is an amino acid sequence alignment between wild-type
Thrombopoietin (SwissProt locus: TPO_HUMAN; GenBank Accession No. P40225; SEQ ID NO:151) and the protein variant of the present invention, Thrombopoietin transcript_T8, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 89 is a schematic illustration showing the protein domain structure of wild-type Thrombopoietin (SwissProt locus: TPO_HUMAN; SEQ ID NO:151) and the variant of the present invention (SEQ ID NO:118).
FIG. 90 is an amino acid sequence alignment between wild-type Bone morphogenetic protein receptor type II (SwissProt locus: BMR2_HUMAN; GenBank Accession No. Q13873; SEQ ID NO:152) and the protein variant of the present invention, Bone morphogenetic protein receptor type II variant (HSU20165_P5 (SEQ ID NO:120), described in Example 22, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 91 is a schematic illustration showing the protein domain structure of wild-type Bone morphogenetic protein receptor type II (SwissProt locus: BMR2_HUMAN; SEQ ID NO:152) and the variant of the present invention (SEQ ID NO:120).
FIG. 92 is an amino acid sequence alignment between wild-type Atrial natriuretic peptide receptor B (SwissProt locus: ANPB_HUMAN; GenBank Accession No. P20594; SEQ ID NO:153) and the protein variant of the present invention, Atrial natriuretic peptide receptor B variant, described in Example 35, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40 -dfmt=fastap.
FIG. 93 is a schematic illustration showing the protein domain structure of wild-type Atrial natriuretic peptide receptor B (SwissProt locus: ANPB_HUMAN; SEQ ID NO:153) and the variant of the present invention (SEQ ID NO:122).
FIG. 94a-b is an amino acid sequence alignment between wild-type Intracellular adhesion molecule 2 (SwissProt locus: ICA2_HUMAN; GenBank Accession No. P13598; SEQ ID NO:154) and the protein variants of the present invention, Intracellular adhesion molecule 2 variant T12 (FIGS. 94a) and T8 FIG. 94b), described in Example 41, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 95 is a schematic illustration showing the protein domain structure of wild-type Intracellular adhesion molecule 2 (SwissProt locus: ICA2_HUMAN; SEQ ID NO:154) and the variants of the present invention (SEQ ID NOs:124 and 126).
FIGS. 96a-b present the nucleic acid sequence (FIG. 96a; HSIFNABR_T14) and amino acid sequence (FIG. 96b; HSIFNABR_P8) of the INR2 receptor variant, transcript T14, of the present invention (SEQ ID NOs:156 and 155, respectively), described in Example 9 of the Examples section which follows.
FIG. 97 is an amino acid sequence alignment between wild-type INR2 protein (GenBank Accession No. P48551; INR2_HUMAN; SEQ ID NO:157) and the protein variant of the present invention, HSIFNABR_P8 (SEQ ID NO:155) as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:158) in the variant of the present invention.
FIGS. 98a-b present the nucleic acid sequence (FIG. 98a; Z42185_T13) and amino acid sequence (FIG. 98b; Z42185_P5) of the TR14 variant, transcript T13, of the present invention (SEQ ID NOs:159 and 160, respectively), described in Example 11 of the Examples section which follows.
FIG. 99 is an amino acid sequence alignment between wild-type TR14 protein (GenBank Accession No. Q92956; TR14_HUMAN; SEQ ID NO:161) and the protein variant of the present invention, Z42185_P5 (SEQ ID NO:160) as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:162) in the variant of the present invention.
FIGS. 100a-b present the nucleic acid sequence (FIG. 100a; HUMLAP_T18) and amino acid sequence (FIG. 100b; HUMLAP_P15) of the ITB2 (integrin β2) variant, transcript T18, of the present invention (SEQ ID NOs:163 and 164, respectively), described in Example 12 of the Examples section which follows.
FIG. 101 is an amino acid sequence alignment between wild-type ITB2 protein (GenBank Accession No. P05107; ITB2_HUMAN; SEQ ID NO:165) and the protein variant of the present invention, HUMLAP_P15 (SEQ ID NO:164) as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40 -dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:166) in the variant of the present invention.
FIG. 102 is an amino acid sequence alignment between wild-type protein (ITB2_HUMAN; SEQ ID NO: 165) and the protein variant of the present invention, HUMLAP_P12 (SEQ ID NO: 168), described in Example 13 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:169) in the variant of the present invention.
FIG. 103 is an amino acid sequence alignment between wild-type protein (FC3A_HUMAN; SEQ ID NO: 173) and the protein variant of the present invention, HUMGCRFC_P3 (SEQ ID NO:171), described in Example 14 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:172) in the variant of the present invention.
FIG. 104 is an amino acid sequence alignment between wild-type protein [FC3A_HUMAN (SEQ ID NO:173)] and the protein variant of the present invention, HUMGCRFC_P4 (SEQ ID NO:175), described in Example 14 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:176) in the variant of the present invention.
FIG. 105 is an amino acid sequence alignment between wild-type protein [TNR3_HUMAN (SEQ ID NO:129)] and the protein variant of the present invention, HUMTNFRRP_P2 (SEQ ID NO:178), described in Example 15 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:179) in the variant of the present invention.
FIG. 106 is an amino acid sequence alignment between wild-type protein GCSR_HUMAN (SEQ ID NO:183) and the protein variant of the present invention, HSGCSFR2_P11 (SEQ ID NO:182), described in Example 16 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:184) in the variant of the present invention.
FIG. 107 is an amino acid sequence alignment between wild-type protein GCSR_HUMAN (SEQ ID NO:183) and the protein variant of the present invention, HSGCSFR2_P7 (SEQ ID NO:186), described in Example 16 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the absence of amino acid sequence (marked in yellow; SEQ ID NO:187) in the variant of the present invention.
FIG. 108 is an amino acid sequence alignment between wild-type protein GCSR_HUMAN (SEQ ID NO:183) and the protein variant of the present invention, HSGCSFR2_P8 (SEQ ID NO:189), described in Example 16 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in bold and italics; SEQ ID NO:190) in the variant of the present invention.
FIG. 109 is an amino acid sequence alignment between wild-type protein MI2B_HUMAN (SEQ ID NO:193) and the protein variant of the present invention, T11329_P2 (SEQ ID NO:192), described in Example 19 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:88) in the variant of the present invention.
FIG. 110 is an amino acid sequence alignment between wild-type protein VEGA_HUMAN (SEQ ID NO:196) and the protein variant of the present invention, HUMEGFAA_P6 (SEQ ID NO:195), described in Example 23 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the absence of a amino acid sequence (marked in yellow; SEQ ID NO:197) in the variant of the present invention.
FIG. 111 is an amino acid sequence alignment between wild-type protein VEGA_HUMAN (SEQ ID NO:196) and the protein variant of the present invention, HUMEGFAA_P8 (SEQ ID NO:199), described in Example 23 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the absence of amino acid sequence (marked in yellow; SEQ ID NO:200) in the variant of the present invention.
FIG. 112 is an amino acid sequence alignment between wild-type protein IL1R_HUMAN (SEQ ID NO:203) and the protein variant of the present invention, HUMIL1RA_P3 (SEQ ID NO:202), described in Example 24 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:204) in the variant of the present invention.
FIG. 113 is an amino acid sequence alignment between wild-type protein CR1_HUMAN_V4 (SEQ ID NO:260) and the protein variant of the present invention, HSCR1RS_PEA—1_P13 (SEQ ID NO:261), described in Example 25 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 114 is an amino acid sequence alignment between wild-type protein CR1_HUMAN (SEQ ID NO:148) and the protein variant of the present invention, HSCR1RS_PEA—1_P14 (SEQ ID NO:262), described in Example 25 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 115 is an amino acid sequence alignment between wild-type protein CR1_HUMAN (SEQ ID NO:148) and the protein variant of the present invention, HSCR1RS_PEA—1_P15 (SEQ ID NO:263), described in Example 25 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 116 is an amino acid sequence alignment between wild-type protein CR1_HUMAN_V1 (SEQ ID NO:259) and the protein variant of the present invention, HSCR1RS_PEA—1_P17 (SEQ ID NO:264), described in Example 25 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 117 is an amino acid sequence alignment between wild-type protein IL1B_HUMAN (SEQ ID NO:265) and the protein variant of the present invention, HSPROI1B_X1 (SEQ ID NO:270), described in Example 27 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO: 266) in the variant of the present invention.
FIG. 118 is an amino acid sequence alignment between wild-type protein PGDR_HUMAN (SEQ ID NO:267) and the protein variant of the present invention, HUMPDGFR_P6 (SEQ ID NO:272), described in Example 30 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:268) in the variant of the present invention.
FIG. 119 is an amino acid sequence alignment between wild-type protein EL3B_HUMAN (SEQ ID NO:328) and the protein variant of the present invention, HUMPRE_P4 (SEQ ID NO:274), described in Example 34 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:329) in the variant of the present invention.
FIG. 120 is an amino acid sequence alignment between wild-type protein SOMA_HUMAN (SEQ ID NO:640) and the protein variant of the present invention, HSGROW1_P11 (SEQ ID NO:276), described in Example 36 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 121 is an amino acid sequence alignment between wild-type protein (CSH_HUMAN; SEQ ID NO:330) and the protein variant of the present invention, HUMCS2_P3 (SEQ ID NO:278), described in Example 37 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:331) in the variant of the present invention.
FIG. 122 is an amino acid sequence alignment between wild-type protein (CSH_HUMAN—SEQ ID NO:330) and the protein variant of the present invention, HUMCS2_P9 (SEQ ID NO:280), described in Example 37 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:641) in the variant of the present invention.
FIG. 123 is an amino acid sequence alignment between wild-type FINC_HUMAN (SEQ ID NO:644) and the protein variant of the present invention, HUMFNC_P54 (SEQ ID NO:282), described in Example 38 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:645) in the variant of the present invention.
FIG. 124 is an amino acid sequence alignment between wild-type ITA8_HUMAN 9SEQ ID NO:327) and the protein variant of the present invention, M85929_P3 (SEQ ID NO:284), described in Example 39 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of R (marked in yellow) in the variant of the present invention.
FIG. 125 is an amino acid sequence alignment between wild-type IBP3_HUMAN (SEQ ID NO:647) and the protein variant of the present invention, S56205_P7 (SEQ ID NO:285), described in Example 43 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:659) in the variant of the present invention.
FIG. 126 is an amino acid sequence alignment between wild-type IBP3_HUMAN (SEQ ID NO:647) and the protein variant of the present invention, S56205_P15 (SEQ ID NO:287), described in Example 43 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:660) in the variant of the present invention.
FIG. 127 is an amino acid sequence alignment between wild-type RNBP_HUMAN (SEQ ID NO:648) and the protein variant of the present invention, HUMREBP_P2 (SEQ ID NO:289), described in Example 44 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:661) in the variant of the present invention.
FIG. 128 is an amino acid sequence alignment between wild-type RNBP_HUMAN (SEQ ID NO:648) and the protein variant of the present invention, HUMREBP_Skippingexon—10_P (SEQ ID NO:291), described in Example 44 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:662) in the variant of the present invention.
FIG. 129 is an amino acid sequence alignment between wild-type RNBP_HUMAN (SEQ ID NO:648) and the protein variant of the present invention, HUMREBP_P3 (SEQ ID NO:293), described in Example 44 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:663) in the variant of the present invention.
FIG. 130 is an amino acid sequence alignment between wild-type RNBP_HUMAN (SEQ ID NO:648) and the protein variant of the present invention, HUMREBP_P4 (SEQ ID NO:295), described in Example 44 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the absence of amino acid sequence (marked in yellow) in the variant of the present invention.
FIG. 131 is an amino acid sequence alignment between wild-type RNBP_HUMAN (SEQ ID NO:648) and the protein variant of the present invention, HUMREBP_P1 (SEQ ID NO:297), described in Example 44 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:664) in the variant of the present invention.
FIG. 132 is an amino acid sequence alignment between wild-type HGF_HUMAN (SEQ ID NO:649) and the protein variant of the present invention, HSHGFR_Skipping_exon—3_P (SEQ ID NO:299), described in Example 45 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence LH (marked in yellow;) in the variant of the present invention.
FIG. 133 is an amino acid sequence alignment between wild-type HGF_HUMAN (SEQ ID NO:649) and the protein variant of the present invention, HSHGFR_Skipping_exon—4_P (SEQ ID NO:301), described in Example 45 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:665) in the variant of the present invention.
FIG. 134 is an amino acid sequence alignment between wild-type HGF_HUMAN (SEQ ID NO:649) and the protein variant of the present invention, HSHGFR_Skipping_exon—7_P (SEQ ID NO:303), described in Example 45 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid S (marked in yellow) in the variant of the present invention.
FIG. 135 is an amino acid sequence alignment between wild-type HGF_HUMAN (SEQ ID NO:649) and the protein variant of the present invention, HSHGFR_Skipping_exon—9_P (SEQ ID NO:305), described in Example 45 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:666) in the variant of the present invention.
FIG. 136 is an amino acid sequence alignment between wild-type CART_HUMAN (SEQ ID NO:650) and the protein variant of the present invention, HSU16826_Skippingexon—2_P (SEQ ID NO:307) described in Example 46 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap. Note the absence of amino acid sequence (marked in yellow) in the variant of the present invention.
FIG. 137 is an amino acid sequence alignment between wild-type DPP4_HUMAN (SEQ ID NO:651) and the protein variant of the present invention, HSPCHDP7_Skippingexon—7_P (SEQ ID NO:309), described in Example 47 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:667) in the variant of the present invention.
FIG. 138 is an amino acid sequence alignment between wild-type DPP4_HUMAN (SEQ ID NO:651) and the protein variant of the present invention, HSPCHDP7_Skippingexon—9_P (SEQ ID NO:311), described in Example 47 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:668) in the variant of the present invention.
FIG. 139 is an amino acid sequence alignment between wild-type DPP4_HUMAN (SEQ ID NO:651) and the protein variant of the present invention, HSPCHDP7_Skippingexon—19_P (SEQ ID NO:313), described in Example 47 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:669) in the variant of the present invention.
FIG. 140 is an amino acid sequence alignment between wild-type DPP4_HUMAN (SEQ ID NO:651) and the protein variant of the present invention, HSPCHDP7_Skippingexon—21_P (SEQ ID NO:315), described in Example 47 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap. Note the presence of a unique amino acid sequence (marked in yellow; SEQ ID NO:670) in the variant of the present invention.
FIG. 141 is an amino acid sequence alignment between wild-type DPP4_HUMAN SEQ ID NO:651 and the protein variant of the present invention, HSPCHDP_Skippingexon—22_P (SEQ ID NO:317), described in Example 47 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap. Note the unique amino acid sequence (marked in yellow; SEQ ID NO:671) in the variant of the present invention.
FIG. 142 is an amino acid sequence alignment between wild-type DPP4_HUMAN (SEQ ID NO:651) and the protein variant of the present invention, HSPCHDP7_Skippingexon—24_P (SEQ ID NO:319), described in Example 47 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap. Note the unique amino acid sequence (marked in yellow; SEQ ID NO:672) in the variant of the present invention.
FIG. 143 is an amino acid sequence alignment between wild-type DPP4_HUMAN (SEQ ID NO:651) and the protein variant of the present invention, HSPCHDP7_Skippingexon—25_P (SEQ ID NO:321), described in Example 47 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap. Note the unique amino acid sequence (marked in yellow; SEQ ID NO:673) in the variant of the present invention.
FIG. 144 is an amino acid sequence alignment between wild-type DPP4_HUMAN (SEQ ID NO:651) and the protein variant of the present invention, HSPCHDP7_skippingexon—24—25_P (SEQ ID NO:323), described in Example 47 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap. Note the missing amino acid sequence (marked in yellow) in the variant of the present invention.
FIG. 145 is an amino acid sequence alignment between wild-type TFPI_HUMAN (SEQ ID NO:366) and the protein variant of the present invention, D12020_P5 (SEQ ID NO:367), described in Example 10 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 146 is an amino acid sequence alignment between wild-type TFPI_HUMAN (SEQ ID NO:366) and the protein variant of the present invention, D12020_P10 (SEQ ID NO:368), described in Example 10 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 147 is an amino acid sequence alignment between wild-type TFPI_HUMAN (SEQ ID NO:366) and the protein variant of the present invention, D12020_P11 (SEQ ID NO:369), described in Example 10 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 148 is an amino acid sequence alignment between wild-type EGFR_HUMAN(SEQ ID NO:427) and the protein variant of the present invention, HSEGF01_PEA—1_P11 (SEQ ID NO:423), described in Example 42 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 149 is an amino acid sequence alignment between wild-type EGFR_HUMAN (SEQ ID NO:427) and the protein variant of the present invention, HSEGF01_PEA—1_P14 (SEQ ID NO:424), described in Example 42 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 150 is an amino acid sequence alignment between wild-type EGFR_HUMAN (SEQ ID NO:427) and the protein variant of the present invention, HSEGF01_PEA—1_P18 (SEQ ID NO:425), described in Example 42 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 151 is an amino acid sequence alignment between wild-type EGFR_HUMAN (SEQ ID NO:427) and the protein variant of the present invention, HSEGF01_PEA—1_P24 (SEQ ID NO:426), described in Example 42 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 152 is an amino acid sequence alignment between wild-type VEGA_HUMAN (SEQ ID NO:196) and the protein variant of the present invention, HUMEGFAA_PEA—2_P3 (SEQ ID NO:495), described in Example 49 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 153 is an amino acid sequence alignment between wild-type VEGA_HUMAN (SEQ ID NO:196) and the protein variant of the present invention, HUMEGFAA_PEA—2_P14 (SEQ ID NO:496), described in Example 49 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 154 is an amino acid sequence alignment between wild-type VGR1_HUMAN (SEQ ID NO:530) and the protein variant of the present invention, HSFLT_PEA—1_P3 (SEQ ID NO:531), described in Example 50 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 155 is an amino acid sequence alignment between wild-type VGR1_HUMAN (SEQ ID NO:530) and the protein variant of the present invention, HSFLT_PEA—1_P4 (SEQ ID NO:532), described in Example 50 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 156 is an amino acid sequence alignment between wild-type VGR1_HUMAN (SEQ ID NO:530) and the protein variant of the present invention, HSFLT_PEA—1_P10 (SEQ ID NO:533), described in Example 50 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 157 is an amino acid sequence alignment between wild-type VGR1_HUMAN (SEQ ID NO:530) and the protein variant of the present invention, HSFLT_PEA—1_P12 (SEQ ID NO:534), described in Example 50 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 158 is an amino acid sequence alignment between wild-type VGR1_HUMAN (SEQ ID NO:530) and the protein variant of the present invention, HSFLT_PEA—1_P13 (SEQ ID NO:535), described in Example 50 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 159 is an amino acid sequence alignment between wild-type VGR1_HUMAN (SEQ ID NO:530) and the protein variant of the present invention, HSFLT_PEA—1_P14 (SEQ ID NO:536), described in Example 50 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 160 is an amino acid sequence alignment between wild-type VGR1_HUMAN (SEQ ID NO:530) and the protein variant of the present invention, HSFLT_PEA—1_P19 (SEQ ID NO:537), described in Example 50 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 161 is an amino acid sequence alignment between wild-type VGR2_HUMAN (SEQ ID NO:555) and the protein variant of the present invention, HUMKDRZ_P8 (SEQ ID NO:556), described in Example 51 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 162 is an amino acid sequence alignment between wild-type VGR2_HUMAN (SEQ ID NO:555) and the protein variant of the present invention, HUMKDRZ_P9 (SEQ ID NO:557), described in Example 51 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 163 is an amino acid sequence alignment between wild-type CTL4_HUMAN (SEQ ID NO:564) and the protein variant of the present invention, HUMCTLA4B_PEA—1_P3 (SEQ ID NO:565), described in Example 52 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 164 is an amino acid sequence alignment between wild-type TR1A_HUMAN (SEQ ID NO:631) and the protein variant of the present invention, HSTNFR1A_PEA—1_P11 (SEQ ID NO:632), described in Example 53 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 165 is an amino acid sequence alignment between wild-type TR1A_HUMAN (SEQ ID NO:631) and the protein variant of the present invention, HSTNFR1A_PEA—1_P15 (SEQ ID NO:633), described in Example 53 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 166 is an amino acid sequence alignment between wild-type TR1A_HUMAN (SEQ ID NO:631) and the protein variant of the present invention, HSTNFR1A_PEA—1_P19 (SEQ ID NO:634), described in Example 53 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 167 is an amino acid sequence alignment between wild-type TR1A_HUMAN (SEQ ID NO:631) and the protein variant of the present invention, HSTNFR1A_PEA—1_P20 (SEQ ID NO:635), described in Example 53 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 168 is an amino acid sequence alignment between wild-type TR1A_HUMAN (SEQ ID NO:631) and the protein variant of the present invention, HSTNFR1A_PEA—1_P22 (SEQ ID NO:636), described in Example 53 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 169 is an amino acid sequence alignment between wild-type TR1A_HUMAN (SEQ ID NO:631) and the protein variant of the present invention, HSTNFR1A_PEA—1_P23 (SEQ ID NO:637), described in Example 53 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 170 is an amino acid sequence alignment between wild-type TR1A_HUMAN (SEQ ID NO:631) and the protein variant of the present invention, HSTNFR1A_PEA—1_P24 (SEQ ID NO:638), described in Example 53 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 171 is an amino acid sequence alignment between wild-type TR1A_HUMAN (SEQ ID NO:631) and the protein variant of the present invention, HSTNFR1A_PEA—1_P28 (SEQ ID NO:639), described in Example 53 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 172 is an amino acid sequence alignment between wild-type CO5_HUMAN_V1 (SEQ ID NO:730) and the protein variant of the present invention, HUMC5_PEA—3_P12 (SEQ ID NO:727, described in Example 54 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 173 is an amino acid sequence alignment between wild-type CO5_HUMAN (SEQ ID NO:730) and the protein variant of the present invention, HUMC5_PEA—3_P13 (SEQ ID NO:728), described in Example 54 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 174 is an amino acid sequence alignment between wild-type CO5_HUMAN (SEQ ID NO:730) and the protein variant of the present invention, HUMC5_PEA—3_P15 (SEQ ID NO:729), described in Example 54 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 175 is an amino acid sequence alignment between wild-type FA8_HUMAN (SEQ ID NO:769) and the protein variant of the present invention, HUMFVIII_PEA—1_P9 (SEQ ID NO:765), described in Example 55 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 176 is an amino acid sequence alignment between wild-type FA8_HUMAN (SEQ ID NO:769) and the protein variant of the present invention, HUMFVIII_PEA—1_P10 (SEQ ID NO:766), described in Example 55 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 177 is an amino acid sequence alignment between wild-type FA8_HUMAN (SEQ ID NO:768) and the protein variant of the present invention, HUMFVIII_PEA—1_P11 (SEQ ID NO:767), described in Example 55 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 178 is an amino acid sequence alignment between wild-type FA8_HUMAN (SEQ ID NO:769) and the protein variant of the present invention, HUMFVIII_PEA—1_P13 (SEQ ID NO:768), described in Example 55 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 179 is an amino acid sequence alignment between wild-type C1S_HUMAN (SEQ ID NO:821) and the protein variant of the present invention, HUMC1RS_PEA—1_P8 (SEQ ID NO:816), described in Example 56 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 180 is an amino acid sequence alignment between wild-type C1S_HUMAN (SEQ ID NO:821) and the protein variant of the present invention, HUMC1RS_PEA—1_P21 (SEQ ID NO:817), described in Example 56 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 181 is an amino acid sequence alignment between wild-type C1S_HUMAN (SEQ ID NO:821) and the protein variant of the present invention, HUMC1RS_PEA—1_P22 (SEQ ID NO:818), described in Example 56 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 182 is an amino acid sequence alignment between wild-type C1S_HUMAN (SEQ ID NO:821) and the protein variant of the present invention, HUMC1RS_PEA—1_P23 (SEQ ID NO:819), described in Example 56 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 183 is an amino acid sequence alignment between wild-type C1S_HUMAN (SEQ ID NO:821) and the protein variant of the present invention, HUMC1RS_PEA—1_P24 (SEQ ID NO:820), described in Example 56 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 184 is an amino acid sequence alignment between wild-type SOMA_HUMAN (SEQ ID NO:850) and the protein variant of the present invention, HSGROW1_PEA—1_P7 (SEQ ID NO:851), described in Example 57 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 185 is an amino acid sequence alignment between wild-type SOMA_HUMAN (SEQ ID NO:850) and the protein variant of the present invention, HSGROW1_PEA—1_P11 (SEQ ID NO:852), described in Example 57 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 186 is an amino acid sequence alignment between wild-type SOMA_HUMAN (SEQ ID NO:850) and the protein variant of the present invention, HSGROW1_PEA—1_P12 (SEQ ID NO:853), described in Example 57 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 187 is an amino acid sequence alignment between wild-type SOMA_HUMAN (SEQ ID NO:850) and the protein variant of the present invention, HSGROW1_PEA—1_P18 (SEQ ID NO:854), described in Example 57 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 188 is an amino acid sequence alignment between wild-type SOMA_HUMAN (SEQ ID NO:850) and the protein variant of the present invention, HSGROW1_PEA—1_P21 (SEQ ID NO:855), described in Example 57 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 189 depicts the variants domain structure in comparison to the known or wild-type (WT) protein. T11 contains the convertase binding site on the β-chain (and maybe other, not yet know, binding sites), and thus, might interfere with the binding of the convertase with the WT C5, and might serve as an antagonist. T16, T14 might compete with C5 on its interaction with C5 convertase, and may thus serve as an antagonist of complement activation.
FIG. 190 depicts factor VIII launched products.
FIG. 191 depicts factor VIII related development.
FIG. 192 depicts factor VIII clinical and preclinical developments.
FIG. 193 depicts the domain structure of the variants described in Example 55 in comparison to the known or wild-type (WT) protein (Factor VIII).
FIG. 194 depicts the Complement Pathway, described in Example 56 of the Examples section which follows.
FIG. 195 depicts C5 clinical developments, described in Example 56 of the Examples section which follows.
FIG. 196 depicts C5 preclinical developments, described in Example 56 of the Examples section which follows.
FIG. 197 depicts CR1 clinical developments, described in Example 56 of the Examples section which follows.
FIGS. 198a-b depict the C1s clinical development (FIG. 198a) and related drugs (FIG. 198b), described in Example 56 of the Examples section which follows.
FIG. 199 depict the domain structure of the variants described in Example 56 compared to WT. P455 is predicted to be bound and cleaved by C1r, and to bind but not cleave, C4. P292, P330 and P405 are predicted to interact with C1r and to act as dominant negative. P621 will not be bound and cleaved by C1r, thus will not get activated however, it is predicted to retain its ability to bind C4 and thus, might serve as an antagonist.
FIG. 200 depicts GH antagonists-launched products, described in Example 57 of the Examples section which follows.
FIG. 201 depicts GH antagonists-clinical development, described in Example 57 of the Examples section which follows.
FIG. 202 depicts the domain structure of the variants described in Example 57 of the Examples section which follows, in comparison to WT.
FIG. 203 depicts the domain structure of the variants described in Example 51 of the Examples section which follows, in comparison to WT.
FIG. 204 depicts the domain structure of the variants described in Example 53 of the Examples section which follows, in comparison to WT.
FIG. 205 is an amino acid sequence alignment between wild-type PSPD_HUMAN (SEQ ID NO:858) and the protein variant of the present invention, D45608_P3 (SEQ ID NO:857), described in Example 58 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap. Note the amino acid sequence which is missing in the D45608_P3 variant (marked in yellow).
FIG. 206 is an amino acid sequence alignment between wild-type TR1B_HUMAN (SEQ ID NO:862) and the protein variant of the present invention, HUMTNFRII_PEA—1_P7 (SEQ ID NO:696), described in Example 59 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 207 is an amino acid sequence alignment between wild-type TR1B_HUMAN (SEQ ID NO:862) and the protein variant of the present invention, HUMTNFRII_PEA—1_P15 (SEQ ID NO:697), described in Example 59 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 208 is an amino acid sequence alignment between wild-type TR1B_HUMAN (SEQ ID NO:862) and the protein variant of the present invention, HUMTNFRII_PEA—1_P17 (SEQ ID NO:699), described in Example 59 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 209 is an amino acid sequence alignment between wild-type TR1B_HUMAN (SEQ ID NO:862) and the protein variant of the present invention, HUMTNFRII_PEA—1_P18 (SEQ ID NO:860), described in Example 59 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 210 is an amino acid sequence alignment between wild-type TR1B_HUMAN (SEQ ID NO:862) and the protein variant of the present invention, HUMTNFRII_PEA—1_P19 (SEQ ID NO:861), described in Example 59 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 211 depicts the domain structure of TNFRII variants in comparison to the known or wild-type (WT) protein, described in Example 59.
FIG. 212 depicts the clinical trials involve TNR3 lymphotoxin beta.
FIG. 213 is an amino acid sequence alignment between wild-type TNR3_HUMAN (SEQ ID NO:129) and the protein variant of the present invention, HUMTNFRRP_P2 (SEQ ID NO:898), described in Example 60 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 214 is an amino acid sequence alignment between wild-type TNR3_HUMAN (SEQ ID NO:129) and the protein variant of the present invention, HUMTNFRRP_P4 (SEQ ID NO:899), described in Example 60 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 215 is an amino acid sequence alignment between wild-type TNR3_HUMAN (SEQ ID NO:129) and the protein variant of the present invention, HUMTNFRRP_P9 (SEQ ID NO:900), described in Example 60 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 216 depicts the domain structure of the variants described in Example 60 of the Examples section which follows in comparison to WT TNR3_HUMAN (SEQ ID NO:129)
FIG. 217 depicts the IL-12 clinical developments.
FIG. 218 is an amino acid sequence alignment between wild-type I12A_HUMAN (SEQ ID NO:933) and the protein variant of the present invention, HUMCLMF35_PEA—1_PEA—2_P14 (SEQ ID NO:927), described in Example 61 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 219 is an amino acid sequence alignment between wild-type I12A_HUMAN (SEQ ID NO:933) and the protein variant of the present invention, HUMCLMF35_PEA—1_PEA—2_P15 (SEQ ID NO:928), described in Example 61 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 220 is an amino acid sequence alignment between wild-type I12A_HUMAN (SEQ ID NO:933) and the protein variant of the present invention, HUMCLMF35_PEA—1_PEA—2_P16 (SEQ ID NO:929), described in Example 61 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 221 is an amino acid sequence alignment between wild-type I12A_HUMAN (SEQ ID NO:933) and the protein variant of the present invention, HUMCLMF35_PEA—1_PEA—2_P17 (SEQ ID NO:930), described in Example 61 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 222 is an amino acid sequence alignment between wild-type I12A_HUMAN (SEQ ID NO:933) and the protein variant of the present invention, HUMCLMF35_PEA—1_PEA—2_P20 (SEQ ID NO:931), described in Example 61 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 223 is an amino acid sequence alignment between wild-type I12A_HUMAN (SEQ ID NO:933) and the protein variant of the present invention, HUMCLMF35_PEA—1_PEA—2_P22 (SEQ ID NO:932), described in Example 61 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 224 depicts the domain structure of the variants described in Example 61 of the Example section which follows in comparison with the WT IL12.
FIG. 225 depicts the IL6 clinical developments.
FIG. 226 depicts the domain structure of the variants described in Example 62 of the Examples section which follows in comparison to WT IL6.
FIG. 227 is an amino acid sequence alignment between wild-type IL6_HUMAN (SEQ ID NO:959) and the protein variant of the present invention, S56892_PEA—1_PEA—1_P8 (SEQ ID NO:956), described in Example 62 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 228 is an amino acid sequence alignment between wild-type IL6_HUMAN (SEQ ID NO:959) and the protein variant of the present invention, S56892_PEA—1_PEA—1_P9 (SEQ ID NO:957), described in Example 62 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 229 is an amino acid sequence alignment between wild-type IL6_HUMAN (SEQ ID NO:959) and the protein variant of the present invention, S56892_PEA—1_PEA—1_P11 (SEQ ID NO:958), described in Example 62 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 230 is an amino acid sequence alignment between wild-type TGR2_HUMAN (SEQ ID NO:974) and the protein variant of the present invention, HUMTGFBIIR_PEA—1_P9 (SEQ ID NO:972), described in Example 63 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 231 is an amino acid sequence alignment between wild-type TGR2_HUMAN (SEQ ID NO:974) and the protein variant of the present invention, HUMTGFBIIR_PEA—1_P14 (SEQ ID NO:973), described in Example 63 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 232 depicts the domain structure of the variants described in Example 63 of the Examples section which follows in comparison to TGR2_HUMAN variant.
FIG. 233 depicts GCSF launched products, described in Example 64 of the Examples section which follows.
FIG. 234 depicts GCSF clinical developments described in Example 64 of the Examples section which follows.
FIG. 235 depicts GCSF Preclinical developments described in Example 64 of the Examples section which follows.
FIG. 236 depicts GCSF domain structure of the variants described in Example 64 of the Examples section which follows, in comparison to WT GCSF.
FIG. 237 is an amino acid sequence alignment between wild-type CSF3_HUMAN (SEQ ID NO:128) and the protein variant of the present invention, HUMGCSF_PEA—1_P5 (SEQ ID NO:1000), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 238 is an amino acid sequence alignment between wild-type CSF3_HUMAN (SEQ ID NO:128) and the protein variant of the present invention, HUMGCSF_PEA—1_P6 (SEQ ID NO:1001), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 239 is an amino acid sequence alignment between wild-type CSF3_HUMAN (SEQ ID NO:128) and the protein variant of the present invention, HUMGCSF_PEA—1_P7 (SEQ ID NO:1002), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 240 is an amino acid sequence alignment between wild-type CSF3_HUMAN (SEQ ID NO:128) and the protein variant of the present invention, HUMGCSF_PEA—1_P8 (SEQ ID NO:1003), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 241 is an amino acid sequence alignment between wild-type Q8N4W3 (SEQ ID NO:1012) and the protein variant of the present invention, HUMGCSF_PEA—1_P8 (SEQ ID NO:1003), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 242 is an amino acid sequence alignment between wild-type CSF3_HUMAN (SEQ ID NO:128) and the protein variant of the present invention, HUMGCSF_PEA—1_P9 (SEQ ID NO:1004), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 243 is an amino acid sequence alignment between wild-type CSF3_HUMAN (SEQ ID NO:128) and the protein variant of the present invention, HUMGCSF_PEA—1_P13 (SEQ ID NO:1005), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 244 is an amino acid sequence alignment between wild-type CSF3_HUMAN (SEQ ID NO:128) and the protein variant of the present invention, HUMGCSF_PEA—1_P14 (SEQ ID NO:1006), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 245 is an amino acid sequence alignment between Q8N4W3 (SEQ ID NO:1012) and the protein variant of the present invention, HUMGCSF_PEA—1_P14 (SEQ ID NO:1006), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40 -dfmt=fastap.
FIG. 246 is an amino acid sequence alignment between wild-type CSF3_HUMAN (SEQ ID NO:128) and the protein variant of the present invention, HUMGCSF_PEA—1_P16 (SEQ ID NO:1007), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 247 is an amino acid sequence alignment between wild-type CSF3_HUMAN (SEQ ID NO:128) and the protein variant of the present invention, HUMGCSF_PEA—1_P18 (SEQ ID NO:1008), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 248 is an amino acid sequence alignment between wild-type CSF3_HUMAN (SEQ ID NO:128) and the protein variant of the present invention, HUMGCSF_PEA—1_P19 (SEQ ID NO:1009), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 249 is an amino acid sequence alignment between wild-type CSF3_HUMAN (SEQ ID NO:128) and the protein variant of the present invention, HUMGCSF_PEA—1_P20 (SEQ ID NO:1010), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 250 is an amino acid sequence alignment between Q8N4W3 (SEQ ID NO:1012) and the protein variant of the present invention, HUMGCSF_PEA—1_P20 (SEQ ID NO:1010), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40 -dfmt=fastap.
FIG. 251 is an amino acid sequence alignment between wild-type CSF3_HUMAN (SEQ ID NO:128) and the protein variant of the present invention, HUMGCSF_PEA—1_P21 (SEQ ID NO:1011), described in Example 64 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 252 depicts the TGF beta clinical studies described in Example 65 of the Examples section which follows.
FIG. 253 depicts TGF beta preclinical studies described in Example 65 of the Examples section which follows.
FIG. 254 depicts domain structure of the variants described in Example 65 of the Examples section which follows in comparison to WT TGF-beta.
FIG. 255 is an amino acid sequence alignment between wild-type TGF1_HUMAN (SEQ ID NO:1048) and the protein variant of the present invention, HSTGFB1_PEA—1_P2 (SEQ ID NO:1043), described in Example 65 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 256 is an amino acid sequence alignment between wild-type TGF1_HUMAN (SEQ ID NO:1048) and the protein variant of the present invention, HSTGFB1_PEA—1_P3 (SEQ ID NO:1044), described in Example 65 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 257 is an amino acid sequence alignment between wild-type TGF1_HUMAN (SEQ ID NO:1048) and the protein variant of the present invention, HSTGFB1_PEA—1_P5 (SEQ ID NO:1045), described in Example 65 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 258 is an amino acid sequence alignment between wild-type TGF1_HUMAN (SEQ ID NO:1048) and the protein variant of the present invention, HSTGFB1_PEA—1_P7 (SEQ ID NO:1046), described in Example 65 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 259 is an amino acid sequence alignment between wild-type TGF1_HUMAN (SEQ ID NO:1048) and the protein variant of the present invention, HSTGFB1_PEA—1_P10 (SEQ ID NO:1047), described in Example 65 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 260 is an amino acid sequence alignment between wild-type TPA_HUMAN (SEQ ID NO:150) and the protein variant of the present invention, HUMUPAA_P14 (SEQ ID NO:1102), described in Example 66 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 261 is an amino acid sequence alignment between wild-type TPA_HUMAN (SEQ ID NO:150) and the protein variant of the present invention, HUMUPAA_P17 (SEQ ID NO:1103), described in Example 66 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 262 is an amino acid sequence alignment between wild-type TPA_HUMAN (SEQ ID NO:150) and the protein variant of the present invention, HUMUPAA_P20 (SEQ ID NO:1104), described in Example 66 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 263 depicts the domain structure of the variants described in Example 66 of the Examples section which follows in comparison to the WT TPA_HUMAN.
FIG. 264 is an amino acid sequence alignment between wild-type DRN1_HUMAN (SEQ ID NO:1131) and the protein variant of the present invention, HUMDNASEI_PEA—1_P3 (SEQ ID NO:1127), described in Example 67 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 265 is an amino acid sequence alignment between wild-type DRN1_HUMAN (SEQ ID NO:1131) and the protein variant of the present invention, HUMDNASEI_PEA—1_P4 (SEQ ID NO:1128), described in Example 67 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 266 is an amino acid sequence alignment between wild-type DRN1_HUMAN (SEQ ID NO:1131) and the protein variant of the present invention, HUMDNASEI_PEA—1_P6 (SEQ ID NO:1129), described in Example 67 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 267 is an amino acid sequence alignment between wild-type DRN1_HUMAN (SEQ ID NO:1131) and the protein variant of the present invention, HUMDNASEI_PEA—1_P10 (SEQ ID NO:1130), described in Example 67 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 268 is an amino acid sequence alignment between wild-type TNFA_HUMAN (SEQ ID NO:1155) and the protein variant of the present invention, HUMTNFAA_PEA—1_P6 (SEQ ID NO:1144), described in Example 68 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 269 is an amino acid sequence alignment between wild-type TNFA_HUMAN (SEQ ID NO:1155) and the protein variant of the present invention, HUMTNFAA_PEA—1_P7 (SEQ ID NO:1145), described in Example 68 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 270 is an amino acid sequence alignment between wild-type TNFA_HUMAN_V1 (SEQ ID NO:1147) and the protein variant of the present invention, HUMTNFAA_PEA—1_P8 (SEQ ID NO:1146), described in Example 68 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0 -matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 271 is an amino acid sequence alignment between wild-type MEC2_HUMAN (SEQ ID NO:1154) and the protein variant of the present invention, M62144_P3 SEQ ID NO:1148), described in Example 69 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 272 is an amino acid sequence alignment between wild-type MEC2_HUMAN (SEQ ID NO:1154) and the protein variant of the present invention, M62144_P2 (SEQ ID NO:1150), described in Example 69 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.
FIG. 273 is an amino acid sequence alignment between wild-type MEC2_HUMAN (SEQ ID NO:1154) and the protein variant of the present invention, M62144_P4 (SEQ ID NO:1152), described in Example 69 of the Examples section which follows, as determined using the Smith&Waterman model query db, with the following parameters: -mode=qglobal -onestrand -gapext=0-matrix=identity -out=g -gapop=40-dfmt=fastap.



DESCRIPTION OF THE PREFERRED EMBODIMENTS
The present invention is of novel secreted and non-secreted polypeptides and polynucleotides encoding same, which can be used for the diagnosis and treatment of a wide range of diseases, such as cancer and inflammatory diseases.
According to still other preferred embodiments, the present invention optionally and preferably encompasses any amino acid sequence or fragment thereof encoded by a nucleic acid sequence corresponding to a splice variant protein as described herein, including any oligopeptide or peptide relating to such an amino acid sequence or fragment, including but not limited to the unique amino acid sequences of these proteins that are depicted as tails, heads, insertions, edges or bridges. The present invention also optionally encompasses antibodies capable of recognizing, and/or being elicited by, such oligopeptides or peptides.
The present invention also optionally and preferably encompasses any nucleic acid sequence or fragment thereof, or amino acid sequence or fragment thereof, corresponding to a splice variant of the present invention as described above, optionally for any application.
In another embodiment, the present invention relates to bridges, tails, heads and/or insertions, and/or analogs, homologs and derivatives of such peptides. Such bridges, tails, heads and/or insertions are described in greater detail below with regard to the Examples.
As used herein a “tail” refers to a peptide sequence at the end of an amino acid sequence that is unique to a splice variant according to the present invention. Therefore, a splice variant having such a tail may optionally be considered as a chimera, in that at least a first portion of the splice variant is typically highly homologous (often 100% identical) to a portion of the corresponding known protein, while at least a second portion of the variant comprises the tail.
As used herein a “head” refers to a peptide sequence at the beginning of an amino acid sequence that is unique to a splice variant according to the present invention. Therefore, a splice variant having such a head may optionally be considered as a chimera, in that at least a first portion of the splice variant comprises the head, while at least a second portion is typically highly homologous (often 100% identical) to a portion of the corresponding known protein.
As used herein “an edge portion” refers to a connection between two portions of a splice variant according to the present invention that were not joined in the wild type or known protein. An edge may optionally arise due to a join between the above “known protein” portion of a variant and the tail, for example, and/or may occur if an internal portion of the wild type sequence is no longer present, such that two portions of the sequence are now contiguous in the splice variant that were not contiguous in the known protein. A “bridge” may optionally be an edge portion as described above, but may also include a join between a head and a “known protein” portion of a variant, or a join between a tail and a “known protein” portion of a variant, or a join between an insertion and a “known protein” portion of a variant.
In another embodiment, this invention provides antibodies specifically recognizing the splice variants and polypeptide fragments thereof of this invention. Preferably such antibodies differentially recognize splice variants of the present invention but do not recognize a corresponding known protein (such known proteins are discussed with regard to their splice variants in the Examples below).
In another embodiment, this invention provides an isolated nucleic acid molecule encoding for a splice variant according to the present invention, having a nucleotide sequence as set forth in any one of the sequences listed herein, or a sequence complementary thereto. In another embodiment, this invention provides an isolated nucleic acid molecule, having a nucleotide sequence as set forth in any one of the sequences listed herein, or a sequence complementary thereto. In another embodiment, this invention provides an oligonucleotide of at least about 12 nucleotides, specifically hybridizable with the nucleic acid molecules of this invention. In another embodiment, this invention provides vectors, cells, liposomes and compositions comprising the isolated nucleic acids of this invention.
Nucleic Acid Sequences and Oligonucleotides
Various embodiments of the present invention encompass nucleic acid sequences described hereinabove; fragments thereof, sequences hybridizable therewith, sequences homologous thereto, sequences encoding similar polypeptides with different codon usage, altered sequences characterized by mutations, such as deletion, insertion or substitution of one or more nucleotides, either naturally occurring or artificially induced, either randomly or in a targeted fashion.
The present invention encompasses nucleic acid sequences described herein; fragments thereof, sequences hybridizable therewith, sequences homologous thereto [e.g., at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 95% or more say 100% identical to the nucleic acid sequences set forth below], sequences encoding similar polypeptides with different codon usage, altered sequences characterized by mutations, such as deletion, insertion or substitution of one or more nucleotides, either naturally occurring or man induced, either randomly or in a targeted fashion. The present invention also encompasses homologous nucleic acid sequences (i.e., which form a part of a polynucleotide sequence of the present invention) which include sequence regions unique to the polynucleotides of the present invention.
In cases where the polynucleotide sequences of the present invention encode previously unidentified polypeptides, the present invention also encompasses novel polypeptides or portions thereof, which are encoded by the isolated polynucleotide and respective nucleic acid fragments thereof described hereinabove.
Thus, the present invention provides isolated polynucleotides each encoding a polypeptide which is at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, %, at least 85%, %, at least 90%, at least 95% or more, say 100% identical to a polypeptide sequence listed in the Examples section or sequence listing, as determined using the LALIGN software of EMBnet Switzerland using default parameters.
A “nucleic acid fragment” or an “oligonucleotide” or a “polynucleotide” are used herein interchangeably to refer to a polymer of nucleic acids. A polynucleotide sequence of the present invention refers to a single or double stranded nucleic acid sequences which is isolated and provided in the form of an RNA sequence, a complementary polynucleotide sequence (cDNA), a genomic polynucleotide sequence and/or a composite polynucleotide sequences (e.g., a combination of the above).
As used herein the phrase “complementary polynucleotide sequence” refers to a sequence, which results from reverse transcription of messenger RNA using a reverse transcriptase or any other RNA dependent DNA polymerase. Such a sequence can be subsequently amplified in vivo or in vitro using a DNA dependent DNA polymerase.
As used herein the phrase “genomic polynucleotide sequence” refers to a sequence derived (isolated) from a chromosome and thus it represents a contiguous portion of a chromosome.
As used herein the phrase “composite polynucleotide sequence” refers to a sequence, which is composed of genomic and cDNA sequences. A composite sequence can include some exonal sequences required to encode the polypeptide of the present invention, as well as some intronic sequences interposing therebetween. The intronic sequences can be of any source, including of other genes, and typically will include conserved splicing signal sequences. Such intronic sequences may further include cis acting expression regulatory elements.
Preferred embodiments of the present invention encompass oligonucleotide probes.
An example of an oligonucleotide probe which can be utilized by the present invention is a single stranded polynucleotide which includes a sequence complementary to the unique sequence region of any variant according to the present invention, including but not limited to a nucleotide sequence coding for an amino sequence of a bridge, tail, head and/or insertion according to the present invention, and/or the equivalent portions of any nucleotide sequence given herein (including but not limited to a nucleotide sequence of a node, segment or amplicon described herein).
Alternatively, an oligonucleotide probe of the present invention can be designed to hybridize with a nucleic acid sequence encompassed by any of the above nucleic acid sequences, particularly the portions specified above, including but not limited to a nucleotide sequence coding for an amino sequence of a bridge, tail, head and/or insertion according to the present invention, and/or the equivalent portions of any nucleotide sequence given herein (including but not limited to a nucleotide sequence of a node, segment or amplicon described herein).
Oligonucleotides designed according to the teachings of the present invention can be generated according to any oligonucleotide synthesis method known in the art such as enzymatic synthesis or solid phase synthesis. Equipment and reagents for executing solid-phase synthesis are commercially available from, for example, Applied Biosystems. Any other means for such synthesis may also be employed; the actual synthesis of the oligonucleotides is well within the capabilities of one skilled in the art and can be accomplished via established methodologies as detailed in, for example, “Molecular Cloning: A laboratory Manual” Sambrook et al., (1989); “Current Protocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., “Current Protocols in Molecular Biology”, John Wiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide to Molecular Cloning”, John Wiley & Sons, New York (1988) and “Oligonucleotide Synthesis” Gait, M. J., ed. (1984) utilizing solid phase chemistry, e.g. cyanoethyl phosphoramidite followed by deprotection, desalting and purification by for example, an automated trityl-on method or HPLC.
Oligonucleotides used according to this aspect of the present invention are those having a length selected from a range of about 10 to about 200 bases preferably about 15 to about 150 bases, more preferably about 20 to about 100 bases, most preferably about 20 to about 50 bases. Preferably, the oligonucleotide of the present invention features at least 17, at least 18, at least 19, at least 20, at least 22, at least 25, at least 30 or at least 40, bases specifically hybridizable with the biomarkers of the present invention.
The oligonucleotides of the present invention may comprise heterocylic nucleosides consisting of purines and the pyrimidines bases, bonded in a 3′ to 5′ phosphodiester linkage.
Preferably used oligonucleotides are those modified at one or more of the backbone, internucleoside linkages or bases, as is broadly described hereinunder.
Specific examples of preferred oligonucleotides useful according to this aspect of the present invention include oligonucleotides containing modified backbones or non-natural internucleoside linkages. Oligonucleotides having modified backbones include those that retain a phosphorus atom in the backbone, as disclosed in U.S. Pat. Nos. 4,469,863; 4,476,301; 5,023,243; 5,177,196; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466, 677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799; 5,587,361; and 5,625,050.
Preferred modified oligonucleotide backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkyl phosphotriesters, methyl and other alkyl phosphonates including 3′-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3′-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3′-5′ linkages, 2′-5′ linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′. Various salts, mixed salts and free acid forms can also be used.
Alternatively, modified oligonucleotide backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH2 component parts, as disclosed in U.S. Pat. Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and 5,677,439.
Other oligonucleotides which can be used according to the present invention, are those modified in both sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups. The base units are maintained for complementation with the appropriate polynucleotide target. An example for such an oligonucleotide mimetic, includes peptide nucleic acid (PNA). United States patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Pat. Nos. 5,539,082; 5,714,331; and 5,719,262, each of which is herein incorporated by reference. Other backbone modifications, which can be used in the present invention are disclosed in U.S. Pat. No. 6,303,374.
Oligonucleotides of the present invention may also include base modifications or substitutions. As used herein, “unmodified” or “natural” bases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified bases include but are not limited to other synthetic and natural bases such as 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine. Further bases particularly useful for increasing the binding affinity of the oligomeric compounds of the invention include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2° C. and are presently preferred base substitutions, even more particularly when combined with 2′-O-methoxyethyl sugar modifications.
Another modification of the oligonucleotides of the invention involves chemically linking to the oligonucleotide one or more moieties or conjugates, which enhance the activity, cellular distribution or cellular uptake of the oligonucleotide. Such moieties include but are not limited to lipid moieties such as a cholesterol moiety, cholic acid, a thioether, e.g., hexyl-5-tritylthiol, a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undecyl residues, a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, a polyamine or a polyethylene glycol chain, or adamantane acetic acid, a palmityl moiety, or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety, as disclosed in U.S. Pat. No. 6,303,374.
It is not necessary for all positions in a given oligonucleotide molecule to be uniformly modified, and in fact more than one of the aforementioned modifications may be incorporated in a single compound or even at a single nucleoside within an oligonucleotide.
It will be appreciated that oligonucleotides of the present invention may include further modifications for more efficient use as diagnostic agents and/or to increase bioavailability, therapeutic efficacy and reduce cytotoxicity.
Expression of the Polynucleotide Sequence of the Present Invention
To enable cellular expression of the polynucleotides of the present invention, a nucleic acid construct (or an “expression vector”) according to the present invention may be used, which includes at least a coding region of one of the above nucleic acid sequences, and further includes at least one cis acting regulatory element. As used herein, the phrase “cis acting regulatory element” refers to a polynucleotide sequence, preferably a promoter, which binds a trans acting regulator and regulates the transcription of a coding sequence located downstream thereto.
Eukaryotic promoters typically contain two types of recognition sequences, the TATA box and upstream promoter elements. The TATA box, located 25-30 base pairs upstream of the transcription initiation site, is thought to be involved in directing RNA polymerase to begin RNA synthesis. The other upstream promoter elements determine the rate at which transcription is initiated.
Preferably, the promoter utilized by the nucleic acid construct of the present invention is active in the specific cell population transformed. Examples of cell type-specific and/or tissue-specific promoters include promoters such as albumin that is liver specific [Pinkert et al., (1987) Genes Dev. 1:268-277], lymphoid specific promoters [Calame et al., (1988) Adv. Immunol. 43:235-275]; in particular promoters of T-cell receptors [Winoto et al., (1989) EMBO J. 8:729-733] and immunoglobulins; [Banerji et al. (1983) Cell 33729-740], neuron-specific promoters such as the neurofilament promoter [Byrne et al. (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477], pancreas-specific promoters [Edlunch et al. (1985) Science 230:912-916] or mammary gland-specific promoters such as the milk whey promoter (U.S. Pat. No. 4,873,316 and European Application Publication No. 264,166). The nucleic acid construct of the present invention can further include an enhancer, which can be adjacent or distant to the promoter sequence and can function in up regulating the transcription therefrom.
Enhancer elements can stimulate transcription up to 1,000 fold from linked homologous or heterologous promoters. Enhancers are active when placed downstream or upstream from the transcription initiation site. Many enhancer elements derived from viruses have a broad host range and are active in a variety of tissues. For example, the SV40 early gene enhancer is suitable for many cell types. Other enhancer/promoter combinations that are suitable for the present invention include those derived from polyoma virus, human or murine cytomegalovirus (CMV), the long term repeat from various retroviruses such as murine leukemia virus, murine or Rous sarcoma virus and HIV. See, Enhancers and Eukaryotic Expression, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. 1983, which is incorporated herein by reference.
In the construction of the expression vector, the promoter is preferably positioned approximately the same distance from the heterologous transcription start site as it is from the transcription start site in its natural setting. As is known in the art, however, some variation in this distance can be accommodated without loss of promoter function.
Polyadenylation sequences can also be added to the expression vector in order to increase the efficiency of mRNA translation. Two distinct sequence elements are required for accurate and efficient polyadenylation: GU or U rich sequences located downstream from the polyadenylation site and a highly conserved sequence of six nucleotides, AAUAAA, located 11-30 nucleotides upstream. Termination and polyadenylation signals that are suitable for the present invention include those derived from SV40.
In addition to the elements already described, the expression vector of the present invention may typically contain other specialized elements intended to increase the level of expression of cloned nucleic acids or to facilitate the identification of cells that carry the recombinant DNA. For example, a number of animal viruses contain DNA sequences that promote the extra chromosomal replication of the viral genome in permissive cell types. Plasmids bearing these viral replicons are replicated episomally as long as the appropriate factors are provided by genes either carried on the plasmid or with the genome of the host cell.
The vector may or may not include a eukaryotic replicon. If a eukaryotic replicon is present, then the vector is amplifiable in eukaryotic cells using the appropriate selectable marker. If the vector does not comprise a eukaryotic replicon, no episomal amplification is possible. Instead, the recombinant DNA integrates into the genome of the engineered cell, where the promoter directs expression of the desired nucleic acid.
The expression vector of the present invention can further include additional polynucleotide sequences that allow, for example, the translation of several proteins from a single mRNA such as an internal ribosome entry site (IRES) and sequences for genomic integration of the promoter-chimeric polypeptide.
The nucleic acid construct of the present invention preferably further includes an appropriate selectable marker and/or an origin of replication. Preferably, the nucleic acid construct utilized is a shuttle vector, which can propagate both in E. coli (wherein the construct comprises an appropriate selectable marker and origin of replication) and be compatible for propagation in cells, or integration in a gene and a tissue of choice. The construct according to the present invention can be, for example, a plasmid, a bacmid, a phagemid, a cosmid, a phage, a virus or an artificial chromosome.
Examples of suitable constructs include, but are not limited to, pcDNA3, pcDNA3.1 (+/−), pGL3, PzeoSV2 (+/−), pDisplay, pEF/myc/cyto, pCMV/myc/cyto each of which is commercially available from Invitrogen Co. Examples of retroviral vector and packaging systems are those sold by Clontech, San Diego, Calif., includingRetro-X vectors pLNCX and pLXSN, which permit cloning into multiple cloning sites and the transgene is transcribed from CMV promoter. Vectors derived from Mo-MuLV are also included such as pBabe, where the transgene will be transcribed from the 5′LTR promoter.
Viruses are very specialized infectious agents that have evolved, in many cases, to elude host defense mechanisms. Typically, viruses infect and propagate in specific cell types. The targeting specificity of viral vectors utilizes its natural specificity to specifically target predetermined cell types and thereby introduce a recombinant gene into the infected cell. Thus, the type of vector used by the present invention will depend on the cell type transformed. The ability to select suitable vectors according to the cell type transformed is well within the capabilities of the ordinary skilled artisan and as such no general description of selection consideration is provided herein. For example, bone marrow cells can be targeted using the human T cell leukemia virus type I (HTLV-I) and kidney cells may be targeted using the heterologous promoter present in the baculovirus Autographa californica nucleopolyhedrovirus (AcMNPV) as described in Liang C Y et al., 2004 (Arch Virol. 149: 51-60).
Recombinant viral vectors are useful for in vivo expression of the polynucleotide sequence of the present invention (e.g., SEQ ID NO: 3, 7, 11, 15, 19, or 45) since they offer advantages such as lateral infection and targeting specificity. Lateral infection is inherent in the life cycle of, for example, retrovirus and is the process by which a single infected cell produces many progeny virions that bud off and infect neighboring cells. The result is that a large area becomes rapidly infected, most of which was not initially infected by the original viral particles. This is in contrast to vertical-type of infection in which the infectious agent spreads only through daughter progeny. Viral vectors can also be produced that are unable to spread laterally. This characteristic can be useful if the desired purpose is to introduce a specified gene into only a localized number of targeted cells.
Various methods can be used to introduce the expression vector of the present invention into stem cells. Such methods are generally described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Laboratory, New York (1989, 1992), in Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1989), Chang et al., Somatic Gene Therapy, CRC Press, Ann Arbor, Mich. (1995), Vega et al., Gene Targeting, CRC Press, Ann Arbor Mich. (1995), Vectors: A Survey of Molecular Cloning Vectors and Their Uses, Butterworths, Boston Mass. (1988) and Gilboa et al. [Biotechniques 4 (6): 504-512, 1986] and include, for example, stable or transient transfection, lipofection, electroporation and infection with recombinant viral vectors. In addition, see U.S. Pat. Nos. 5,464,764 and 5,487,992 for positive-negative selection methods.
Introduction of nucleic acids by viral infection offers several advantages over other methods such as lipofection and electroporation, since higher transfection efficiency can be obtained due to the infectious nature of viruses.
Currently preferred in vivo nucleic acid transfer techniques include transfection with viral or non-viral constructs, such as adenovirus, lentivirus, Herpes simplex I virus, or adeno-associated virus (AAV) and lipid-based systems. Useful lipids for lipid-mediated transfer of the gene are, for example, DOTMA, DOPE, and DC-Chol [Tonkinson et al., Cancer Investigation, 14(1): 54-65 (1996)]. The most preferred constructs for use in gene therapy are viruses, most preferably adenoviruses, AAV, lentiviruses, or retroviruses. A viral construct such as a retroviral construct includes at least one transcriptional promoter/enhancer or locus-defining element(s), or other elements that control gene expression by other means such as alternate splicing, nuclear RNA export, or post-translational modification of messenger. Such vector constructs also include a packaging signal, long terminal repeats (LTRs) or portions thereof, and positive and negative strand primer binding sites appropriate to the virus used, unless it is already present in the viral construct. In addition, such a construct typically includes a signal sequence for secretion of the peptide from a host cell in which it is placed. Preferably the signal sequence for this purpose is a mammalian signal sequence or the signal sequence of the polypeptide variants of the present invention. Optionally, the construct may also include a signal that directs polyadenylation, as well as one or more restriction sites and a translation termination sequence. By way of example, such constructs will typically include a 5′ LTR, a tRNA binding site, a packaging signal, an origin of second-strand DNA synthesis, and a 3′ LTR or a portion thereof. Other vectors can be used that are non-viral, such as cationic lipids, polylysine, and dendrimers.
Other than containing the necessary elements for the transcription and translation of the inserted coding sequence, the expression construct of the present invention can also include sequences engineered to enhance stability, production, purification, yield or toxicity of the expressed peptide. For example, the expression of a fusion protein or a cleavable fusion protein comprising Met variant of the present invention and a heterologous protein can be engineered. Such a fusion protein can be designed so that the fusion protein can be readily isolated by affinity chromatography; e.g., by immobilization on a column specific for the heterologous protein. Where a cleavage site is engineered between the Met moiety and the heterologous protein, the Met moiety can be released from the chromatographic column by treatment with an appropriate enzyme or agent that disrupts the cleavage site [e.g., see Booth et al. (1988) Immunol. Lett. 19:65-70; and Gardella et al., (1990) J. Biol. Chem. 265:15854-158591.
As mentioned hereinabove, a variety of prokaryotic or eukaryotic cells can be used as host-expression systems to express the polypeptides of the present invention. These include, but are not limited to, microorganisms, such as bacteria transformed with a recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vector containing the coding sequence; yeast transformed with recombinant yeast expression vectors containing the coding sequence; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors, such as Ti plasmid, containing the coding sequence. Mammalian expression systems can also be used to express the polypeptides of the present invention.
Examples of bacterial constructs include the pET series of E. coli expression vectors [Studier et al. (1990) Methods in Enzymol. 185:60-89).
In yeast, a number of vectors containing constitutive or inducible promoters can be used, as disclosed in U.S. Pat. No. 5,932,447. Alternatively, vectors can be used which promote integration of foreign DNA sequences into the yeast chromosome.
In cases where plant expression vectors are used, the expression of the coding sequence can be driven by a number of promoters. For example, viral promoters such as the 35S RNA and 19S RNA promoters of CaMV [Brisson et al. (1984) Nature 310:511-514], or the coat protein promoter to TMV [Takamatsu et al. (1987) EMBO J. 6:307-311] can be used. Alternatively, plant promoters such as the small subunit of RUBISCO [Coruzzi et al. (1984) EMBO J. 3:1671-1680 and Brogli et al., (1984) Science 224:838-843] or heat shock promoters, e.g., soybean hsp17.5-E or hsp17.3-B [Gurley et al. (1986) Mol. Cell. Biol. 6:559-565] can be used. These constructs can be introduced into plant cells using Ti plasmid, Ri plasmid, plant viral vectors, direct DNA transformation, microinjection, electroporation and other techniques well known to the skilled artisan. See, for example, Weissbach & Weissbach, 1988, Methods for Plant Molecular Biology, Academic Press, NY, Section VIII, pp 421-463.
Other expression systems such as insects and mammalian host cell systems which are well known in the art and are further described hereinbelow can also be used by the present invention.
Recovery of the recombinant polypeptide is effected following an appropriate time in culture. The phrase “recovering the recombinant polypeptide” refers to collecting the whole fermentation medium containing the polypeptide and need not imply additional steps of separation or purification. Not withstanding the above, polypeptides of the present invention can be purified using a variety of standard protein purification techniques, such as, but not limited to, affinity chromatography, ion exchange chromatography, filtration, electrophoresis, hydrophobic interaction chromatography, gel filtration chromatography, reverse phase chromatography, concanavalin A chromatography, chromatofocusing and differential solubilization.
Hybridization Assays
Detection of a nucleic acid of interest in a biological sample may optionally be effected by hybridization-based assays using an oligonucleotide probe (non-limiting examples of probes according to the present invention were previously described). Traditional hybridization assays include PCR, RT-PCR, Real-time PCR, RNase protection, in-situ hybridization, primer extension, Southern blots (DNA detection), dot or slot blots (DNA, RNA), and Northern blots (RNA detection) (NAT type assays are described in greater detail below). More recently, PNAs have been described (Nielsen et al. 1999, Current Opin. Biotechnol. 10:71-75). Other detection methods include kits containing probes on a dipstick setup and the like.
Hybridization based assays which allow the detection of a variant of interest (i.e., DNA or RNA) in a biological sample rely on the use of oligonucleotides which can be 10, 15, 20, or 30 to 100 nucleotides long preferably from 10 to 50, more preferably from 40 to 50 nucleotides long.
Thus, the isolated polynucleotides (oligonucleotides) of the present invention are preferably hybridizable with any of the herein described nucleic acid sequences under moderate to stringent hybridization conditions.
Moderate to stringent hybridization conditions are characterized by a hybridization solution such as containing 10% dextrane sulfate, 1 M NaCl, 1% SDS and 5×106 cpm 32P labeled probe, at 65° C., with a final wash solution of 0.2×SSC and 0.1% SDS and final wash at 65° C. and whereas moderate hybridization is effected using a hybridization solution containing 10% dextrane sulfate, 1 M NaCl, 1% SDS and 5×106 cpm 32P labeled probe, at 65° C., with a final wash solution of 1×SSC and 0.1% SDS and final wash at 50° C.
More generally, hybridization of short nucleic acids (below 200 bp in length, e.g. 17-40 bp in length) can be effected using the following exemplary hybridization protocols which can be modified according to the desired stringency; (i) hybridization solution of 6×SSC and 1% SDS or 3 M TMACI, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5% SDS, 100 mg/ml denatured salmon sperm DNA and 0.1% nonfat dried milk, hybridization temperature of 1-1.5° C. below the Tm, final wash solution of 3 M TMACI, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5% SDS at 1-1.5° C. below the Tm; (ii) hybridization solution of 6×SSC and 0.1% SDS or 3 M TMACI, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5% SDS, 100 mg/ml denatured salmon sperm DNA and 0.1% nonfat dried milk, hybridization temperature of 2-2.5° C. below the Tm, final wash solution of 3 M TMACI, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5% SDS at 1-1.5° C. below the Tm, final wash solution of 6×SSC, and final wash at 22° C.; (iii) hybridization solution of 6×SSC and 1% SDS or 3 M TMACI, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5% SDS, 100 mg/ml denatured salmon sperm DNA and 0.1% nonfat dried milk, hybridization temperature.
The detection of hybrid duplexes can be carried out by a number of methods. Typically, hybridization duplexes are separated from unhybridized nucleic acids and the labels bound to the duplexes are then detected. Such labels refer to radioactive, fluorescent, biological or enzymatic tags or labels of standard use in the art. A label can be conjugated to either the oligonucleotide probes or the nucleic acids derived from the biological sample.
Probes can be labeled according to numerous well known methods. Non-limiting examples of radioactive labels include 3H, 14C, 32P, and 35S, Non-limiting examples of detectable markers include ligands, fluorophores, chemiluminescent agents, enzymes, and antibodies. Other detectable markers for use with probes, which can enable an increase in sensitivity of the method of the invention, include biotin and radio-nucleotides. It will become evident to the person of ordinary skill that the choice of a particular label dictates the manner in which it is bound to the probe.
For example, oligonucleotides of the present invention can be labeled subsequent to synthesis, by incorporating biotinylated dNTPs or rNTP, or some similar means (e.g., photo-cross-linking a psoralen derivative of biotin to RNAs), followed by addition of labeled streptavidin (e.g., phycoerythrin-conjugated streptavidin) or the equivalent. Alternatively, when fluorescently-labeled oligonucleotide probes are used, fluorescein, lissamine, phycoerythrin, rhodamine (Perkin Elmer Cetus), Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Cy7, FluorX (Amersham) and others [e.g., Kricka et al. (1992), Academic Press San Diego, Calif] can be attached to the oligonucleotides.
Those skilled in the art will appreciate that wash steps may be employed to wash away excess target DNA or probe as well as unbound conjugate. Further, standard heterogeneous assay formats are suitable for detecting the hybrids using the labels present on the oligonucleotide primers and probes.
It will be appreciated that a variety of controls may be usefully employed to improve accuracy of hybridization assays. For instance, samples may be hybridized to an irrelevant probe and treated with RNAse A prior to hybridization, to assess false hybridization.
Although the present invention is not specifically dependent on the use of a label for the detection of a particular nucleic acid sequence, such a label might be beneficial, by increasing the sensitivity of the detection. Furthermore, it enables automation. Probes can be labeled according to numerous well known methods. As commonly known, radioactive nucleotides can be incorporated into probes of the invention by several methods. Non-limiting examples of radioactive labels include 3H, 14C, 32P, and 35S.
Those skilled in the art will appreciate that wash steps may be employed to wash away excess target DNA or probe as well as unbound conjugate. Further, standard heterogeneous assay formats are suitable for detecting the hybrids using the labels present on the oligonucleotide primers and probes.
It will be appreciated that a variety of controls may be usefully employed to improve accuracy of hybridization assays.
Probes of the invention can be utilized with naturally occurring sugar-phosphate backbones as well as modified backbones including phosphorothioates, dithionates, alkyl phosphonates and a-nucleotides and the like. Probes of the invention can be constructed of either ribonucleic acid (RNA) or deoxyribonucleic acid (DNA), and preferably of DNA.
Amino Acid Sequences and Peptides
The terms “polypeptide,” “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an analog or mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers. Polypeptides can be modified, e.g., by the addition of carbohydrate residues to form glycoproteins. The terms “polypeptide,” “peptide” and “protein” include glycoproteins, as well as non-glycoproteins.
Polypeptide products can be biochemically synthesized such as by employing standard solid phase techniques. Such methods include but are not limited to exclusive solid phase synthesis, partial solid phase synthesis methods, fragment condensation, classical solution synthesis. These methods are preferably used when the peptide is relatively short (i.e., 10 kDa) and/or when it cannot be produced by recombinant techniques (i.e., not encoded by a nucleic acid sequence) and therefore involves different chemistry.
Solid phase polypeptide synthesis procedures are well known in the art and further described by John Morrow Stewart and Janis Dillaha Young, Solid Phase Peptide Syntheses (2nd Ed., Pierce Chemical Company, 1984).
Synthetic polypeptides can optionally be purified by preparative high performance liquid chromatography [Creighton T. (1983) Proteins, structures and molecular principles. WH Freeman and Co. N.Y.], after which their composition can be confirmed via amino acid sequencing.
In cases where large amounts of a polypeptide are desired, it can be generated using recombinant techniques such as described by Bitter et al., (1987) Methods in Enzymol. 153:516-544, Studier et al. (1990) Methods in Enzymol. 185:60-89, Brisson et al. (1984) Nature 310:511-514, Takamatsu et al. (1987) EMBO J. 6:307-311, Coruzzi et al. (1984) EMBO J. 3:1671-1680 and Brogli et al., (1984) Science 224:838-843, Gurley et al. (1986) Mol. Cell. Biol. 6:559-565 and Weissbach & Weissbach, 1988, Methods for Plant Molecular Biology, Academic Press, NY, Section VIII, pp 421-463.
The present invention also encompasses polypeptides encoded by the polynucleotide sequences of the present invention, as well as polypeptides according to the amino acid sequences described herein. The present invention also encompasses homologues of these polypeptides, such homologues can be at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 95% or more say 100% homologous to the amino acid sequences set forth below, as can be determined using BlastP software of the National Center of Biotechnology Information (NCBI) using default parameters, optionally and preferably including the following: filtering on (this option filters repetitive or low-complexity sequences from the query using the Seg (protein) program), scoring matrix is BLOSUM62 for proteins, word size is 3, E value is 10, gap costs are 11, 1 (initialization and extension), and number of alignments shown is 50. Finally, the present invention also encompasses fragments of the above described polypeptides and polypeptides having mutations, such as deletions, insertions or substitutions of one or more amino acids, either naturally occurring or artificially induced, either randomly or in a targeted fashion.
It will be appreciated that peptides identified according the present invention may be degradation products, synthetic peptides or recombinant peptides as well as peptidomimetics, typically, synthetic peptides and peptoids and semipeptoids which are peptide analogs, which may have, for example, modifications rendering the peptides more stable while in a body or more capable of penetrating into cells. Such modifications include, but are not limited to N terminus modification, C terminus modification, peptide bond modification, including, but not limited to, CH2-NH, CH2-S, CH2-S═O, O═C—NH, CH2-O, CH2-CH2, S═C—NH, CH═CH or CF═CH, backbone modifications, and residue modification. Methods for preparing peptidomimetic compounds are well known in the art and are specified. Further details in this respect are provided hereinunder.
Peptide bonds (—CO—NH—) within the peptide may be substituted, for example, by N-methylated bonds (—N(CH3)-CO—), ester bonds (—C(R)H—C—O—O—C(R)—N—), ketomethylen bonds (—CO—CH2-), *-aza bonds (—NH—N(R)—CO—), wherein R is any alkyl, e.g., methyl, carba bonds (—CH2-NH—), hydroxyethylene bonds (—CH(OH)—CH2-), thioamide bonds (—CS—NH—), olefinic double bonds (—CH═CH—), retro amide bonds (—NH—CO—), peptide derivatives (—N(R)—CH2-CO—), wherein R is the “normal” side chain, naturally presented on the carbon atom. These modifications can occur at any of the bonds along the peptide chain and even at several (2-3) at the same time.
Natural aromatic amino acids, Trp, Tyr and Phe, may be substituted for synthetic non-natural acid such as Phenylglycine, TIC, naphthylelanine (Nol), ring-methylated derivatives of Phe, halogenated derivatives of Phe or o-methyl-Tyr.
In addition to the above, the peptides of the present invention may also include one or more modified amino acids or one or more non-amino acid monomers (e.g. fatty acids, complex carbohydrates etc).
As used herein in the specification and in the claims section below the term “amino acid” or “amino acids” is understood to include the 20 naturally occurring amino acids; those amino acids often modified post-translationally in vivo, including, for example, hydroxyproline, phosphoserine and phosphothreonine; and other unusual amino acids including, but not limited to, 2-aminoadipic acid, hydroxylysine, isodesmosine, nor-valine, nor-leucine and ornithine. Furthermore, the term “amino acid” includes both D- and L-amino acids.
Table 1 non-conventional or modified amino acids which can be used with the present invention.










TABLE 1





Non-conventional amino acid
Code
Non-conventional amino acid
Code







α-aminobutyric acid
Abu
L-N-methylalanine
Nmala


α-amino-α-methylbutyrate
Mgabu
L-N-methylarginine
Nmarg


aminocyclopropane-
Cpro
L-N-methylasparagine
Nmasn


Carboxylate

L-N-methylaspartic acid
Nmasp


aminoisobutyric acid
Aib
L-N-methylcysteine
Nmcys


aminonorbornyl-
Norb
L-N-methylglutamine
Nmgin


Carboxylate

L-N-methylglutamic acid
Nmglu


Cyclohexylalanine
Chexa
L-N-methylhistidine
Nmhis


Cyclopentylalanine
Cpen
L-N-methylisolleucine
Nmile


D-alanine
Dal
L-N-methylleucine
Nmleu


D-arginine
Darg
L-N-methyllysine
Nmlys


D-aspartic acid
Dasp
L-N-methylmethionine
Nmmet


D-cysteine
Dcys
L-N-methylnorleucine
Nmnle


D-glutamine
Dgln
L-N-methylnorvaline
Nmnva


D-glutamic acid
Dglu
L-N-methylornithine
Nmorn


D-histidine
Dhis
L-N-methylphenylalanine
Nmphe


D-isoleucine
Dile
L-N-methylproline
Nmpro


D-leucine
Dleu
L-N-methylserine
Nmser


D-lysine
Dlys
L-N-methylthreonine
Nmthr


D-methionine
Dmet
L-N-methyltryptophan
Nmtrp


D-ornithine
Dorn
L-N-methyltyrosine
Nmtyr


D-phenylalanine
Dphe
L-N-methylvaline
Nmval


D-proline
Dpro
L-N-methylethylglycine
Nmetg


D-serine
Dser
L-N-methyl-t-butylglycine
Nmtbug


D-threonine
Dthr
L-norleucine
Nle


D-tryptophan
Dtrp
L-norvaline
Nva


D-tyrosine
Dtyr
α-methyl-aminoisobutyrate
Maib


D-valine
Dval
α-methyl-γ-aminobutyrate
Mgabu


D-α-methylalanine
Dmala
α-methylcyclohexylalanine
Mchexa


D-α-methylarginine
Dmarg
α-methylcyclopentylalanine
Mcpen


D-α-methylasparagine
Dmasn
α-methyl-α-napthylalanine
Manap


D-α-methylaspartate
Dmasp
α-methylpenicillamine
Mpen


D-α-methylcysteine
Dmcys
N-(4-aminobutyl)glycine
Nglu


D-α-methylglutamine
Dmgln
N-(2-aminoethyl)glycine
Naeg


D-α-methylhistidine
Dmhis
N-(3-aminopropyl)glycine
Norn


D-α-methylisoleucine
Dmile
N-amino-α-methylbutyrate
Nmaabu


D-α-methylleucine
Dmleu
α-napthylalanine
Anap


D-α-methyllysine
Dmlys
N-benzylglycine
Nphe


D-α-methylmethionine
Dmmet
N-(2-carbamylethyl)glycine
Ngln


D-α-methylornithine
Dmorn
N-(carbamylmethyl)glycine
Nasn


D-α-methylphenylalanine
Dmphe
N-(2-carboxyethyl)glycine
Nglu


D-α-methylproline
Dmpro
N-(carboxymethyl)glycine
Nasp


D-α-methylserine
Dmser
N-cyclobutylglycine
Ncbut


D-α-methylthreonine
Dmthr
N-cycloheptylglycine
Nchep


D-α-methyltryptophan
Dmtrp
N-cyclohexylglycine
Nchex


D-α-methyltyrosine
Dmty
N-cyclodecylglycine
Ncdec


D-α-methylvaline
Dmval
N-cyclododeclglycine
Ncdod


D-α-methylalnine
Dnmala
N-cyclooctylglycine
Ncoct


D-α-methylarginine
Dnmarg
N-cyclopropylglycine
Ncpro


D-α-methylasparagine
Dnmasn
N-cycloundecylglycine
Ncund


D-α-methylasparatate
Dnmasp
N-(2,2-diphenylethyl)glycine
Nbhm


D-α-methylcysteine
Dnmcys
N-(3,3-diphenylpropyl)glycine
Nbhe


D-N-methylleucine
Dnmleu
N-(3-indolylyethyl) glycine
Nhtrp


D-N-methyllysine
Dnmlys
N-methyl-γ-aminobutyrate
Nmgabu


N-methylcyclohexylalanine
Nmchexa
D-N-methylmethionine
Dnmmet


D-N-methylornithine
Dnmorn
N-methylcyclopentylalanine
Nmcpen


N-methylglycine
Nala
D-N-methylphenylalanine
Dnmphe


N-methylaminoisobutyrate
Nmaib
D-N-methylproline
Dnmpro


N-(1-methylpropyl)glycine
Nile
D-N-methylserine
Dnmser


N-(2-methylpropyl)glycine
Nile
D-N-methylserine
Dnmser


N-(2-methylpropyl)glycine
Nleu
D-N-methylthreonine
Dnmthr


D-N-methyltryptophan
Dnmtrp
N-(1-methylethyl)glycine
Nva


D-N-methyltyrosine
Dnmtyr
N-methyla-napthylalanine
Nmanap


D-N-methylvaline
Dnmval
N-methylpenicillamine
Nmpen


γ-aminobutyric acid
Gabu
N-(p-hydroxyphenyl)glycine
Nhtyr


L-t-butylglycine
Tbug
N-(thiomethyl)glycine
Ncys


L-ethylglycine
Etg
penicillamine
Pen


L-homophenylalanine
Hphe
L-α-methylalanine
Mala


L-α-methylarginine
Marg
L-α-methylasparagine
Masn


L-α-methylaspartate
Masp
L-α-methyl-t-butylglycine
Mtbug


L-α-methylcysteine
Mcys
L-methylethylglycine
Metg


L-α-methylglutamine
Mgln
L-α-methylglutamate
Mglu


L-α-methylhistidine
Mhis
L-α-methylhomophenylalanine
Mhphe


L-α-methylisoleucine
Mile
N-(2-methylthioethyl)glycine
Nmet


D-N-methylglutamine
Dnmgln
N-(3-guanidinopropyl)glycine
Narg


D-N-methylglutamate
Dnmglu
N-(1-hydroxyethyl)glycine
Nthr


D-N-methylhistidine
Dnmhis
N-(hydroxyethyl)glycine
Nser


D-N-methylisoleucine
Dnmile
N-(imidazolylethyl)glycine
Nhis


D-N-methylleucine
Dnmleu
N-(3-indolylyethyl)glycine
Nhtrp


D-N-methyllysine
Dnmlys
N-methyl-γ-aminobutyrate
Nmgabu


N-methylcyclohexylalanine
Nmchexa
D-N-methylmethionine
Dnmmet


D-N-methylornithine
Dnmorn
N-methylcyclopentylalanine
Nmcpen


N-methylglycine
Nala
D-N-methylphenylalanine
Dnmphe


N-methylaminoisobutyrate
Nmaib
D-N-methylproline
Dnmpro


N-(1-methylpropyl)glycine
Nile
D-N-methylserine
Dnmser


N-(2-methylpropyl)glycine
Nleu
D-N-methylthreonine
Dnmthr


D-N-methyltryptophan
Dnmtrp
N-(1-methylethyl)glycine
Nval


D-N-methyltyrosine
Dnmtyr
N-methyla-napthylalanine
Nmanap


D-N-methylvaline
Dnmval
N-methylpenicillamine
Nmpen


γ-aminobutyric acid
Gabu
N-(p-hydroxyphenyl)glycine
Nhtyr


L-t-butylglycine
Tbug
N-(thiomethyl)glycine
Ncys


L-ethylglycine
Etg
penicillamine
Pen


L-homophenylalanine
Hphe
L-α-methylalanine
Mala


L-α-methylarginine
Marg
L-α-methylasparagine
Masn


L-α-methylaspartate
Masp
L-α-methyl-t-butylglycine
Mtbug


L-α-methylcysteine
Mcys
L-methylethylglycine
Metg


L-α-methylglutamine
Mgln
L-α-methylglutamate
Mglu


L-α-methylhistidine
Mhis
L-α-methylhomophenylalanine
Mhphe


L-α-methylisoleucine
Mile
N-(2-methylthioethyl)glycine
Nmet


L-α-methylleucine
Mleu
L-α-methyllysine
Mlys


L-α-methylmethionine
Mmet
L-α-methylnorleucine
Mnle


L-α-methylnorvaline
Mnva
L-α-methylornithine
Morn


L-α-methylphenylalanine
Mphe
L-α-methylproline
Mpro


L-α-methylserine
mser
L-α-methylthreonine
Mthr


L-α-methylvaline
Mtrp
L-α-methyltyrosine
Mtyr


L-α-methylleucine
Mval
L-N-methylhomophenylalanine
Nmhphe



Nnbhm
N-(N-(3,3-diphenylpropyl)
Nnbhe


N-(N-(2,2-diphenylethyl)
Nnbhm
carbamylmethyl(1)glycine


carbamylmethyl-glycine


1-carboxy-1-(2,2-diphenyl
Nmbc


ethylamino)cyclopropane









Since the peptides of the present invention are preferably utilized in therapeutics which require the peptides to be in soluble form, the peptides of the present invention preferably include one or more non-natural or natural polar amino acids, including but not limited to serine and threonine which are capable of increasing peptide solubility due to their hydroxyl-containing side chain.
The peptides of the present invention are preferably utilized in a linear form, although it will be appreciated that in cases where cyclicization does not severely interfere with peptide characteristics, cyclic forms of the peptide can also be utilized.
The peptides of present invention can be biochemically synthesized such as by using standard solid phase techniques. These methods include exclusive solid phase synthesis well known in the art, partial solid phase synthesis methods, fragment condensation, classical solution synthesis. These methods are preferably used when the peptide is relatively short (i.e., 10 kDa) and/or when it cannot be produced by recombinant techniques (i.e., not encoded by a nucleic acid sequence) and therefore involves different chemistry.
Synthetic peptides can be purified by preparative high performance liquid chromatography and the composition of which can be confirmed via amino acid sequencing.
In cases where large amounts of the peptides of the present invention are desired, the peptides of the present invention can be generated using recombinant techniques such as described by Bitter et al., (1987) Methods in Enzymol. 153:516-544, Studier et al. (1990) Methods in Enzymol. 185:60-89, Brisson et al. (1984) Nature 310:511-514, Takamatsu et al. (1987) EMBO J. 6:307-311, Coruzzi et al. (1984) EMBO J. 3:1671-1680 and Brogli et al., (1984) Science 224:838-843, Gurley et al. (1986) Mol. Cell. Biol. 6:559-565 and Weissbach & Weissbach, 1988, Methods for Plant Molecular Biology, Academic Press, NY, Section VIII, pp 421-463 and also as described above.
Peptide sequences which exhibit high therapeutic activity, such as by competing with wild type signaling proteins of the same signaling pathway, can be also uncovered using computational biology. Software programs useful for displaying three-dimensional structural models, such as RIBBONS (Carson, M., 1997. Methods in Enzymology 277, 25), O (Jones, T A. et al., 1991. Acta Crystallogr. A47, 110), DINO (DINO: Visualizing Structural Biology (2001); and QUANTA, INSIGHT, SYBYL, MACROMODE, ICM, MOLMOL, RASMOL and GRASP (reviewed in Kraulis, J., 1991. Appl Crystallogr. 24, 946) can be utilized to model interactions between the polypeptides of the present invention and prospective peptide sequences to thereby identify peptides which display the highest probability of binding for example to a respective ligand (e.g., IL-10). Computational modeling of protein-peptide interactions has been successfully used in rational drug design, for further details, see Lam et al., 1994. Science 263, 380; Wlodawer et al., 1993. Ann Rev Biochem. 62, 543; Appelt, 1993. Perspectives in Drug Discovery and Design 1, 23; Erickson, 1993. Perspectives in Drug Discovery and Design 1, 109, and Mauro M J. et al., 2002. J Clin Oncol. 20, 325-34.
Antibodies
“Antibody” refers to a polypeptide ligand that is preferably substantially encoded by an immunoglobulin gene or immunoglobulin genes, or fragments thereof, which specifically binds and recognizes an epitope (e.g., an antigen). The recognized immunoglobulin genes include the kappa and lambda light chain constant region genes, the alpha, gamma, delta, epsilon and mu heavy chain constant region genes, and the myriad-immunoglobulin variable region genes. Antibodies exist, e.g., as intact immunoglobulins or as a number of well characterized fragments produced by digestion with various peptidases. This includes, e.g., Fab′ and F(ab)′2 fragments. The term “antibody,” as used herein, also includes antibody fragments either produced by the modification of whole antibodies or those synthesized de novo using recombinant DNA methodologies. It also includes polyclonal antibodies, monoclonal antibodies, chimeric antibodies, humanized antibodies, or single chain antibodies. “Fc” portion of an antibody refers to that portion of an immunoglobulin heavy chain that comprises one or more heavy chain constant region domains, CH1, CH2 and CH3, but does not include the heavy chain variable region.
The functional fragments of antibodies, such as Fab, F(ab′)2, and Fv that are capable of binding to macrophages, are described as follows: (1) Fab, the fragment which contains a monovalent antigen-binding fragment of an antibody molecule, can be produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain; (2) Fab′, the fragment of an antibody molecule that can be obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain; two Fab′ fragments are obtained per antibody molecule; (3) (Fab′)2, the fragment of the antibody that can be obtained by treating whole antibody with the enzyme pepsin without subsequent reduction; F(ab′)2 is a dimer of two Fab′ fragments held together by two disulfide bonds; (4) Fv, defined as a genetically engineered fragment containing the variable region of the light chain and the variable region of the heavy chain expressed as two chains; and (5) Single chain antibody (“SCA”), a genetically engineered molecule containing the variable region of the light chain and the variable region of the heavy chain, linked by a suitable polypeptide linker as a genetically fused single chain molecule.
Methods of producing polyclonal and monoclonal antibodies as well as fragments thereof are well known in the art (See for example, Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York, 1988, incorporated herein by reference).
Antibody fragments according to the present invention can be prepared by proteolytic hydrolysis of the antibody or by expression in E. coli or mammalian cells (e.g. Chinese hamster ovary cell culture or other protein expression systems) of DNA encoding the fragment. Antibody fragments can be obtained by pepsin or papain digestion of whole antibodies by conventional methods. For example, antibody fragments can be produced by enzymatic cleavage of antibodies with pepsin to provide a 5S fragment denoted F(ab′)2. This fragment can be further cleaved using a thiol reducing agent, and optionally a blocking group for the sulfhydryl groups resulting from cleavage of disulfide linkages, to produce 3.5S Fab′ monovalent fragments. Alternatively, an enzymatic cleavage using pepsin produces two monovalent Fab′ fragments and an Fc fragment directly. These methods are described, for example, by Goldenberg, U.S. Pat. Nos. 4,036,945 and 4,331,647, and references contained therein, which patents are hereby incorporated by reference in their entirety. See also Porter, R. R. [Biochem. J. 73: 119-126 (1959)]. Other methods of cleaving antibodies, such as separation of heavy chains to form monovalent light-heavy chain fragments, further cleavage of fragments, or other enzymatic, chemical, or genetic techniques may also be used, so long as the fragments bind to the antigen that is recognized by the intact antibody.
Fv fragments comprise an association of VH and VL chains. This association may be noncovalent, as described in Inbar et al. [Proc. Nat'l Acad. Sci. USA 69:2659-62 (19720]. Alternatively, the variable chains can be linked by an intermolecular disulfide bond or cross-linked by chemicals such as glutaraldehyde. Preferably, the Fv fragments comprise VH and VL chains connected by a peptide linker. These single-chain antigen binding proteins (sFv) are prepared by constructing a structural gene comprising DNA sequences encoding the VH and VL domains connected by an oligonucleotide. The structural gene is inserted into an expression vector, which is subsequently introduced into a host cell such as E. coli. The recombinant host cells synthesize a single polypeptide chain with a linker peptide bridging the two V domains. Methods for producing sFvs are described, for example, by [Whitlow and Filpula, Methods 2: 97-105 (1991); Bird et al., Science 242:423-426 (1988); Pack et al., Bio/Technology 11:1271-77 (1993); and U.S. Pat. No. 4,946,778, which is hereby incorporated by reference in its entirety.
Another form of an antibody fragment is a peptide coding for a single complementarity-determining region (CDR). CDR peptides (“minimal recognition units”) can be obtained by constructing genes encoding the CDR of an antibody of interest. Such genes are prepared, for example, by using the polymerase chain reaction to synthesize the variable region from RNA of antibody-producing cells. See, for example, Larrick and Fry [Methods, 2: 106-10 (1991)].
Humanized forms of non-human (e.g., murine) antibodies are chimeric molecules of immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab′, F(ab′) or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin. Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a complementary determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity. In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies may also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin [Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol., 2:593-596 (1992)].
Methods for humanizing non-human antibodies are well known in the art. Generally, a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human. These non-human amino acid residues are often referred to as import residues, which are typically taken from an import variable domain. Humanization can be essentially performed following the method of Winter and co-workers [Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature 332:323-327 (1988); Verhoeyen et al., Science, 239:1534-1536 (1988)1, by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. Accordingly, such humanized antibodies are chimeric antibodies (U.S. Pat. No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species. In practice, humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.
Human antibodies can also be produced using various techniques known in the art, including phage display libraries [Hoogenboom and Winter, J. Mol. Biol., 227:381 (1991); Marks et al., J. Mol. Biol., 222:581 (1991)]. The techniques of Cole et al. and Boerner et al. are also available for the preparation of human monoclonal antibodies (Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 77 (1985) and Boerner et al., J. Immunol., 147(1):86-95 (1991)]. Similarly, human antibodies can be made by introduction of human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin genes have been partially or completely inactivated. Upon challenge, human antibody production is observed, which closely resembles that seen in humans in all respects, including gene rearrangement, assembly, and antibody repertoire. This approach is described, for example, in U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016, and in the following scientific publications: Marks et al., Bio/Technology 10,: 779-783 (1992); Lonberg et al., Nature 368: 856-859 (1994); Morrison, Nature 368 812-13 (1994); Fishwild et al., Nature Biotechnology 14, 845-51 (1996); Neuberger, Nature Biotechnology 14: 826 (1996); and Lonberg and Huszar, Intern. Rev. Immunol. 13, 65-93 (1995).
Preferably, the antibody of this aspect of the present invention specifically binds at least one epitope of the polypeptide variants of the present invention. As used herein, the term “epitope” refers to any antigenic determinant on an antigen to which the paratope of an antibody binds.
Epitopic determinants usually consist of chemically active surface groupings of molecules such as amino acids or carbohydrate side chains and usually have specific three dimensional structural characteristics, as well as specific charge characteristics.
Optionally, a unique epitope may be created in a variant due to a change in one or more post-translational modifications, including but not limited to glycosylation and/or phosphorylation, as described below. Such a change may also cause a new epitope to be created, for example through removal of glycosylation at a particular site.
An epitope according to the present invention may also optionally comprise part or all of a unique sequence portion of a variant according to the present invention in combination with at least one other portion of the variant which is not contiguous to the unique sequence portion in the linear polypeptide itself, yet which are able to form an epitope in combination. One or more unique sequence portions may optionally combine with one or more other non-contiguous portions of the variant (including a portion which may have high homology to a portion of the known protein) to form an epitope.
Display Libraries
According to still another aspect of the present invention there is provided a display library comprising a plurality of display vehicles (such as phages, viruses or bacteria) each displaying at least 6, at least 7, at least 8, at least 9, at least 10, 10-15, 12-17, 15-20, 15-30 or 20-50 consecutive amino acids derived from the polypeptide sequences of the present invention.
Since in therapeutic applications it is highly desirable to employ the minimal and most efficacious polypeptide regions, which still exert therapeutic function, identification of such peptide regions can be effected using various approaches, including, for example, display techniques as described herein.
Methods of constructing such display libraries are well known in the art. Such methods are described in, for example, Young A C, et al., “The three-dimensional structures of a polysaccharide binding antibody to Cryptococcus neoformans and its complex with a peptide from a phage display library: implications for the identification of peptide mimotopes” J Mol Biol 1997 Dec. 12; 274(4):622-34; Giebel L B et al. “Screening of cyclic peptide phage libraries identifies ligands that bind streptavidin with high affinities” Biochemistry 1995 Nov. 28; 34(47):15430-5; Davies E L et al., “Selection of specific phage-display antibodies using libraries derived from chicken immunoglobulin genes” J Immunol Methods 1995 Oct. 12; 186(1):125-35; Jones C RT al. “Current trends in molecular recognition and bioseparation” J Chromatogr A 1995 Jul. 14; 707(1):3-22; Deng S J et al. “Basis for selection of improved carbohydrate-binding single-chain antibodies from synthetic gene libraries” Proc Natl Acad Sci USA 1995 May 23; 92(11):4992-6; and Deng S J et al. “Selection of antibody single-chain variable fragments with improved carbohydrate binding by phage display” J Biol Chem 1994 Apr. 1; 269(13):9533-8, which are incorporated herein by reference.
The principles and operation of the present invention may be better understood with reference to the drawings and accompanying descriptions.
Before explaining at least one embodiment of the invention in detail, it is to be understood that the invention is not limited in its application to the details set forth in the following description or exemplified by the Examples. The invention is capable of other embodiments or of being practiced or carried out in various ways. Also, it is to be understood that the phraseology and terminology employed herein is for the purpose of description and should not be regarded as limiting.
A “variant-treatable” disease refers to any disease that is treatable by using a splice variant of any of the therapeutic proteins according to the present invention. “Treatment” also encompasses prevention, amelioration, elimination and control of the disease and/or pathological condition. The diseases for which such variants may be useful therapeutic agents are described in greater detail below for each of the variants. The variants themselves are described by “cluster” or by gene, as these variants are splice variants of known proteins. Therefore, a “cluster-related disease” or a “protein-related disease” refers to a disease that may be treated by a particular protein, with regard to the description of such diseases below a therapeutic protein variant according to the present invention.
The term “biologically active”, as used herein, refers to a protein having structural, regulatory, or biochemical functions of a naturally occurring molecule. Likewise, “immunologically active” refers to the capability of the natural, recombinant, or synthetic ligand, or any oligopeptide thereof, to induce a specific immune response in appropriate animals or cells and to bind with specific antibodies.
The term “modulate”, as used herein, refers to a change in the activity of at least one receptor mediated activity. For example, modulation may cause an increase or a decrease in protein activity, binding characteristics, or any other biological, functional or immunological properties of a ligand.
Methods of Treatment
As mentioned hereinabove the novel therapeutic protein variants of the present invention and compositions derived therefrom (i.e., peptides, oligonucleotides) can be used to treat cluster or protein-related diseases, disorders or conditions.
Thus, according to an additional aspect of the present invention there is provided a method of treating cluster or protein-related disease, disorder or condition in a subject.
The subject according to the present invention is a mammal, preferably a human which is diagnosed with one of the disease, disorder or conditions described hereinabove, or alternatively is predisposed to at least one type of the cluster or protein-related disease, disorder or conditions described hereinabove.
As used herein the term “treating” refers to preventing, curing, reversing, attenuating, alleviating, minimizing, suppressing or halting the deleterious effects of the above-described diseases, disorders or conditions.
Treating, according to the present invention, can be effected by specifically upregulating or alternatively downregulating the expression of at least one of the polypeptides of the present invention in the subject.
Optionally, upregulation may be effected by administering to the subject at least one of the polypeptides of the present invention (e.g., recombinant or synthetic) or an active portion thereof, as described herein (e.g., SEQ ID NO:1, 5, 9, 13, 17 or 54). However, since the bioavailability of large polypeptides may potentially be relatively small due to high degradation rate and low penetration rate, administration of polypeptides is preferably confined to small peptide fragments (e.g., about 100 amino acids). The polypeptide or peptide may optionally be administered in as part of a pharmaceutical composition, described in more detail below.
It will be appreciated that treatment of the above-described diseases according to the present invention may be combined with other treatment methods known in the art (i.e., combination therapy). Thus, treatment of malignancies using the agents of the present invention may be combined with, for example, radiation therapy, antibody therapy and/or chemotherapy.
Alternatively or additionally, an upregulating method may optionally be effected by specifically upregulating the amount (optionally expression) in the subject of at least one of the polypeptides of the present invention (e.g., SEQ ID NO: 1, 5, 9, 13, 17 or 54) or active portions thereof.
As is mentioned hereinabove and in the Examples section which follows, the biomolecular sequences of this aspect of the present invention may be used as valuable therapeutic tools in the treatment of diseases, disorders or conditions in which altered activity or expression of the wild-type gene product is known to contribute to disease, disorder or condition onset or progression. For example, in case a disease is caused by overexpression of a membrane bound-receptor, a soluble variant thereof may be used as an antagonist which competes with the receptor for binding the ligand, to thereby terminate signaling from the receptor. Examples of such diseases are listed in the Examples section which follows.
It will be appreciated that the polypeptides of the present invention may also have agonistic properties. These include increasing the stability of the ligand (e.g., IL-4), protection from proteolysis and modification of the pharmacokinetic properties of the ligand (i.e., increasing the half-life of the ligand, while decreasing the clearance thereof). As such, the biomolecular sequences of this aspect of the present invention may be used to treat conditions or diseases in which the wild-type gene product plays a favorable role, for example, increasing angiogenesis in cases of diabetes or ischemia.
Upregulating expression of the therapeutic protein or polypeptide variants of the present invention may be effected via the administration of at least one of the exogenous polynucleotide sequences of the present invention (e.g., SEQ ID NO:3, 11, 15, 19, 45), ligated into a nucleic acid expression construct (as described in greater detail hereinabove) designed for expression of coding sequences in eukaryotic cells (e.g., mammalian cells), as described above. Accordingly, the exogenous polynucleotide sequence may be a DNA or RNA sequence encoding the variants of the present invention or active portions thereof.
It will be appreciated that the nucleic acid construct can be administered to the individual employing any suitable mode of administration including in vivo gene therapy (e.g., using viral transformation as described hereinabove). Alternatively, the nucleic acid construct is introduced into a suitable cell via an appropriate gene delivery vehicle/method (transfection, transduction, homologous recombination, etc.) and an expression system as needed and then the modified cells are expanded in culture and returned to the individual (i.e., ex-vivo gene therapy).
Such cells (i.e., which are transfected with the nucleic acid construct of the present invention) can be any suitable cells, such as kidney, bone marrow, keratinocyte, lymphocyte, adult stem cells, cord blood cells, embryonic stem cells which are derived from the individual and are transfected ex vivo with an expression vector containing the polynucleotide designed to express the polypeptide of the present invention as described hereinabove.
Administration of the ex vivo transfected cells of the present invention can be effected using any suitable route such as intravenous, intra peritoneal, intra kidney, intra gastrointestinal track, subcutaneous, transcutaneous, intramuscular, intracutaneous, intrathecal, epidural and rectal. According to presently preferred embodiments, the ex vivo transfected cells of the present invention are introduced to the individual using intravenous, intra kidney, intra gastrointestinal track and/or intra peritoneal administrations.
The ex vivo transfected cells of the present invention can be derived from either autologous sources such as self bone marrow cells or from allogeneic sources such as bone marrow or other cells derived from non-autologous sources. Since non-autologous cells are likely to induce an immune reaction when administered to the body several approaches have been developed to reduce the likelihood of rejection of non-autologous cells. These include either suppressing the recipient immune system or encapsulating the non-autologous cells or tissues in immunoisolating, semipermeable membranes before transplantation.
Encapsulation techniques are generally classified as microencapsulation, involving small spherical vehicles and macroencapsulation, involving larger flat-sheet and hollow-fiber membranes (Uludag, H. et al. Technology of mammalian cell encapsulation. Adv Drug Deliv Rev. 2000; 42: 29-64).
Methods of preparing microcapsules are known in the arts and include for example those disclosed by Lu M Z, et al., Cell encapsulation with alginate and alpha-phenoxycinnamylidene-acetylated poly(allylamine). Biotechnol Bioeng. 2000, 70: 479-83, Chang T M and Prakash S. Procedures for microencapsulation of enzymes, cells and genetically engineered microorganisms. Mol Biotechnol. 2001, 17: 249-60, and Lu M Z, et al., A novel cell encapsulation method using photosensitive poly(allylamine alpha-cyanocinnamylideneacetate). J Microencapsul. 2000, 17: 245-51.
For example, microcapsules are prepared by complexing modified collagen with a ter-polymer shell of 2-hydroxyethyl methylacrylate (HEMA), methacrylic acid (MAA) and methyl methacrylate (MMA), resulting in a capsule thickness of 2-5 μm. Such microcapsules can be further encapsulated with additional 2-5 μm ter-polymer shells in order to impart a negatively charged smooth surface and to minimize plasma protein absorption (Chia, S. M. et al. Multi-layered microcapsules for cell encapsulation Biomaterials. 2002 23: 849-56).
Other microcapsules are based on alginate, a marine polysaccharide (Sambanis, A. Encapsulated islets in diabetes treatment. Diabetes Thechnol. Ther. 2003, 5: 665-8) or its derivatives. For example, microcapsules can be prepared by the polyelectrolyte complexation between the polyanions sodium alginate and sodium cellulose sulphate with the polycation poly(methylene-co-guanidine) hydrochloride in the presence of calcium chloride.
It will be appreciated that cell encapsulation is improved when smaller capsules are used. Thus, the quality control, mechanical stability, diffusion properties, and in vitro activities of encapsulated cells improved when the capsule size was reduced from 1 mm to 400 μm (Canaple L. et al., Improving cell encapsulation through size control. J Biomater Sci Polym Ed. 2002; 13: 783-96). Moreover, nanoporous biocapsules with well-controlled pore size as small as 7 nm, tailored surface chemistries and precise microarchitectures were found to successfully immunoisolate microenvironments for cells (Williams D. Small is beautiful: microparticle and nanoparticle technology in medical devices. Med Device Technol. 1999, 10: 6-9; Desai, T. A. Microfabrication technology for pancreatic cell encapsulation. Expert Opin Biol Ther. 2002, 2: 633-46).
It will be appreciated that the present methodology may also be effected by specifically upregulating the expression of the variants of the present invention endogenously in the subject. Agents for upregulating endogenous expression of specific splice variants of a given gene include antisense oligonucleotides, which are directed at splice sites of interest, thereby altering the splicing pattern of the gene. This approach has been successfully used for shifting the balance of expression of the two isoforms of Bcl-x [Taylor (1999) Nat. Biotechnol. 17:1097-1100; and Mercatante (2001) J. Biol. Chem. 276:16411-164171; IL-5R [Karras (2000) Mol. Pharmacol. 58:380-3871; and c-myc [Giles (1999) Antisense Acid Drug Dev. 9:213-2201.
For example, interleukin 5 and its receptor play a critical role as regulators of hematopoiesis and as mediators in some inflammatory diseases such as allergy and asthma. Two alternatively spliced isoforms are generated from the IL-5R gene, which include (i.e., long form) or exclude (i.e., short form) exon 9. The long form encodes for the intact membrane-bound receptor, while the shorter form encodes for a secreted soluble non-functional receptor. Using 2′-O-MOE-oligonucleotides specific to regions of exon 9, Karras and co-workers (supra) were able to significantly decrease the expression of the wild type receptor and increase the expression of the shorter isoforms. Design and synthesis of oligonucleotides which can be used according to the present invention are described hereinbelow and by Sazani and Kole (2003) Progress in Moleclular and Subcellular Biology 31:217-239.
Treatment can preferably effected by agents which are capable of specifically downregulating expression (or activity) of at least one of the polypeptide variants of the present invention.
Down regulating the expression of the therapeutic protein variants of the present invention may be achieved using oligonucleotide agents such as those described in greater detail below.
SiRNA molecules—Small interfering RNA (siRNA) molecules can be used to down-regulate expression of the therapeutic protein variants of the present invention.
RNA interference is a two-step process. The first step, which is termed as the initiation step, input dsRNA is digested into 21-23 nucleotide (nt) small interfering RNAs (siRNA), probably by the action of Dicer, a member of the RNase III family of dsRNA-specific ribonucleases, which processes (cleaves) dsRNA (introduced directly or via a transgene or a virus) in an ATP-dependent manner. Successive cleavage events degrade the RNA to 19-21 bp duplexes (siRNA), each with 2-nucleotide 3′ overhangs [Hutvagner and Zamore Curr. Opin. Genetics and Development 12:225-232 (2002); and Bernstein Nature 409:363-366 (2001)].
In the effector step, the siRNA duplexes bind to a nuclease complex to from the RNA-induced silencing complex (RISC). An ATP-dependent unwinding of the siRNA duplex is required for activation of the RISC. The active RISC then targets the homologous transcript by base pairing interactions and cleaves the mRNA into 12 nucleotide fragments from the 3′ terminus of the siRNA [Hutvagner and Zamore Curr. Opin. Genetics and Development 12:225-232 (2002); Hammond et al. (2001) Nat. Rev. Gen. 2:110-119 (2001); and Sharp Genes. Dev. 15:485-90 (2001)]. Although the mechanism of cleavage is still to be elucidated, research indicates that each RISC contains a single siRNA and an RNase [Hutvagner and Zamore Curr. Opin. Genetics and Development 12:225-232 (2002)].
Because of the remarkable potency of RNAi, an amplification step within the RNAi pathway has been suggested. Amplification could occur by copying of the input dsRNAs which would generate more siRNAs, or by replication of the siRNAs formed. Alternatively or additionally, amplification could be effected by multiple turnover events of the RISC [Hammond et al. Nat. Rev. Gen. 2:110-119 (2001), Sharp Genes. Dev. 15:485-90 (2001); Hutvagner and Zamore Curr. Opin. Genetics and Development 12:225-232 (2002)]. For more information on RNAi see the following reviews Tuschl ChemBiochem. 2:239-245 (2001); Cullen Nat. Immunol. 3:597-599 (2002); and Brantl Biochem. Biophys. Act. 1575:15-25 (2002).
Synthesis of RNAi molecules suitable for use with the present invention can be effected as follows. First, the mRNA sequence is scanned downstream of the AUG start codon for AA dinucleotide sequences. Occurrence of each AA and the 3′ adjacent 19 nucleotides is recorded as potential siRNA target sites. Preferably, siRNA target sites are selected from the open reading frame, as untranslated regions (UTRs) are richer in regulatory protein binding sites. UTR-binding proteins and/or translation initiation complexes may interfere with binding of the siRNA endonuclease complex [Tuschl ChemBiochem. 2:239-245]. It will be appreciated though, that siRNAs directed at untranslated regions may also be effective, as demonstrated for GAPDH wherein siRNA directed at the 5′ UTR mediated about 90% decrease in cellular GAPDH mRNA and completely abolished protein level.
Second, potential target sites are compared to an appropriate genomic database (e.g., human, mouse, rat etc.) using any sequence alignment software, such as the BLAST software available from the NCBI server. Putative target sites which exhibit significant homology to other coding sequences are filtered out. Qualifying target sequences are selected as template for siRNA synthesis.
Preferred sequences are those including low G/C content as these have proven to be more effective in mediating gene silencing as compared to those with G/C content higher than 55%. Several target sites are preferably selected along the length of the target gene for evaluation. Target sites are selected from the unique nucleotide sequences of each of the polynucleotides of the present invention, such that each polynucleotide is specifically down regulated. For better evaluation of the selected siRNAs, a negative control is preferably used in conjunction. Negative control siRNA preferably include the same nucleotide composition as the siRNAs but lack significant homology to the genome. Thus, a scrambled nucleotide sequence of the siRNA is preferably used, provided it does not display any significant homology to any other gene.
DNAzyme molecules—Another agent capable of downregulating expression of the polypeptides of the present invention is a DNAzyme molecule capable of specifically cleaving an mRNA transcript or DNA sequence of the polynucleotides of the present invention. DNAzymes are single-stranded polynucleotides which are capable of cleaving both single and double stranded target sequences (Breaker, R. R. and Joyce, G. Chemistry and Biology 1995; 2:655; Santoro, S. W. & Joyce, G. F. Proc. Natl, Acad. Sci. USA 1997; 943:4262) A general model (the “10-23” model) for the DNAzyme has been proposed. “10-23” DNAzymes have a catalytic domain of 15 deoxyribonucleotides, flanked by two substrate-recognition domains of seven to nine deoxyribonucleotides each. This type of DNAzyme can effectively cleave its substrate RNA at purine:pyrimidine junctions (Santoro, S. W. & Joyce, G. F. Proc. Natl, Acad. Sci. USA 199; for rev of DNAzymes see Khachigian, L M [Curr Opin Mol Ther 4:119-21 (2002)].
Target sites for DNAzymes are selected from the unique nucleotide sequences of each of the polynucleotides of the present invention, such that each polynucleotide is specifically down regulated.
Examples of construction and amplification of synthetic, engineered DNAzymes recognizing single and double-stranded target cleavage sites have been disclosed in U.S. Pat. No. 6,326,174 to Joyce et al. DNAzymes of similar design directed against the human Urokinase receptor were recently observed to inhibit Urokinase receptor expression, and successfully inhibit colon cancer cell metastasis in vivo (Itoh et al, 20002, Abstract 409, Ann Meeting Am Soc Gen Ther). In another application, DNAzymes complementary to bcr-abl oncogenes were successful in inhibiting the oncogenes expression in leukemia cells, and lessening relapse rates in autologous bone marrow transplant in cases of CML and ALL.
Antisense molecules—Downregulation of the polynucleotides of the present invention can also be effected by using an antisense polynucleotide capable of specifically hybridizing with an mRNA transcript encoding the polypeptide variants of the present invention.
The term “antisense”, as used herein, refers to any composition containing nucleotide sequences, which are complementary to a specific DNA or RNA sequence.
The term “antisense strand” is used in reference to a nucleic acid strand that is complementary to the “sense” strand. Antisense molecules also include peptide nucleic acids and may be produced by any method including synthesis or transcription. Once introduced into a cell, the complementary nucleotides combine with natural sequences produced by the cell to form duplexes and block either transcription or translation. The designation “negative” is sometimes used in reference to the antisense strand, and “positive” is sometimes used in reference to the sense strand. Antisense oligonucleotides are also used for modulation of alternative splicing in vivo and for diagnostics in vivo and in vitro (Khelifi C. et al., 2002, Current Pharmaceutical Design 8:451-1466; Sazani, P., and Kole. R. Progress in Molecular and Cellular Biology, 2003, 31:217-239).
Design of antisense molecules which can be used to efficiently down-regulate expression of the polypeptides of the present invention must be effected while considering two aspects important to the antisense approach. The first aspect is delivery of the oligonucleotide into the cytoplasm of the appropriate cells, while the second aspect is design of an oligonucleotide which specifically binds the designated mRNA within cells in a way which inhibits translation thereof.
The prior art teaches of a number of delivery strategies which can be used to efficiently deliver oligonucleotides into a wide variety of cell types [see, for example, Luft J Mol Med 76: 75-6 (1998); Kronenwett et al. Blood 91: 852-62 (1998); Rajur et al. Bioconjug Chem 8: 935-40 (1997); Lavigne et al. Biochem Biophys Res Commun 237: 566-71 (1997) and Aoki et al. (1997) Biochem Biophys Res Commun 231: 540-5 (1997)].
In addition, algorithms for identifying those sequences with the highest predicted binding affinity for their target mRNA based on a thermodynamic cycle that accounts for the energetics of structural alterations in both the target mRNA and the oligonucleotide are also available [see, for example, Walton et al. Biotechnol Bioeng 65: 1-9 (1999)].
Such algorithms have been successfully used to implement an antisense approach in cells. For example, the algorithm developed by Walton et al. enabled scientists to successfully design antisense oligonucleotides for rabbit beta-globin (RBG) and mouse tumor necrosis factor-alpha (TNF alpha) transcripts. The same research group has more recently reported that the antisense activity of rationally selected oligonucleotides against three model target mRNAs (human lactate dehydrogenase A and B and rat gp130) in cell culture as evaluated by a kinetic PCR technique proved effective in almost all cases, including tests against three different targets in two cell types with phosphodiester and phosphorothioate oligonucleotide chemistries.
In addition, several approaches for designing and predicting efficiency of specific oligonucleotides using an in vitro system were also published (Matveeva et al., Nature Biotechnology 16: 1374-1375 (1998)].
Several clinical trials have demonstrated safety, feasibility and activity of antisense oligonucleotides. For example, antisense oligonucleotides suitable for the treatment of cancer have been successfully used [Holmund et al., Curr Opin Mol Ther 1:372-85 (1999)], while treatment of hematological malignancies via antisense oligonucleotides targeting c-myb gene, p53 and Bcl-2 had entered clinical trials and had been shown to be tolerated by patients [Gerwitz Curr Opin Mol Ther 1:297-306 (1999)].
More recently, antisense-mediated suppression of human heparanase gene expression has been reported to inhibit pleural dissemination of human cancer cells in a mouse model [Uno et al., Cancer Res 61:7855-60 (2001)].
Thus, the current consensus is that recent developments in the field of antisense technology which, as described above, have led to the generation of highly accurate antisense design algorithms and a wide variety of oligonucleotide delivery systems, enable an ordinarily skilled artisan to design and implement antisense approaches suitable for downregulating expression of known sequences without having to resort to undue trial and error experimentation.
Target sites for antisense molecules are selected from the unique nucleotide sequences of each of the polynucleotides of the present invention, such that each polynucleotide is specifically down regulated.
Ribozymes—Another agent capable of downregulating expression of the polypeptides of the present invention is a ribozyme molecule capable of specifically cleaving an mRNA transcript encoding the polypeptide variants of the present invention. Ribozymes are being increasingly used for the sequence-specific inhibition of gene expression by the cleavage of mRNAs encoding proteins of interest [Welch et al., Curr Opin Biotechnol. 9:486-96 (1998)]. The possibility of designing ribozymes to cleave any specific target RNA has rendered them valuable tools in both basic research and therapeutic applications. In therapeutics area, ribozymes have been exploited to target viral RNAs in infectious diseases, dominant oncogenes in cancers and specific somatic mutations in genetic disorders [Welch et al., Clin Diagn Virol. 10:163-71 (1998)]. Most notably, several ribozyme gene therapy protocols for HIV patients are already in Phase 1 trials. More recently, ribozymes have been used for transgenic animal research, gene target validation and pathway elucidation. Several ribozymes are in various stages of clinical trials. ANGIOZYME was the first chemically synthesized ribozyme to be studied in human clinical trials. ANGIOZYME specifically inhibits formation of the VEGF-r (Vascular Endothelial Growth Factor receptor), a key component in the angiogenesis pathway. Ribozyme Pharmaceuticals, Inc., as well as other firms have demonstrated the importance of anti-angiogenesis therapeutics in animal models. HEPTAZYME, a ribozyme designed to selectively destroy Hepatitis C Virus (HCV) RNA, was found effective in decreasing Hepatitis C viral RNA in cell culture assays (Ribozyme Pharmaceuticals, Incorporated—WEB home page).
An additional method of regulating the expression of a specific gene in cells is via triplex forming oligonucleotides (TFOs). Recent studies have shown that TFOs can be designed which can recognize and bind to polypurine/polypirimidine regions in double-stranded helical DNA in a sequence-specific manner. These recognition rules are outlined by Maher III, L. J., et al., Science, 1989; 245:725-730; Moser, H. E., et al., Science, 1987; 238:645-630; Beal, P. A., et al, Science, 1992; 251:1360-1363; Cooney, M., et al., Science, 1988; 241:456-459; and Hogan, M. E., et al., EP Publication 375408. Modification of the oligonucleotides, such as the introduction of intercalators and backbone substitutions, and optimization of binding conditions (pH and cation concentration) have aided in overcoming inherent obstacles to TFO activity such as charge repulsion and instability, and it was recently shown that synthetic oligonucleotides can be targeted to specific sequences (for a recent review see Seidman and Glazer, J Clin Invest 2003; 112:487-94).
In general, the triplex-forming oligonucleotide has the sequence correspondence:



















oligo
3′--A
G
G
T



duplex
5′--A
G
C
T



duplex
3′--T
C
G
A










However, it has been shown that the A-AT and G-GC triplets have the greatest triple helical stability (Reither and Jeltsch, BMC Biochem, 2002, Sep. 12, Epub). The same authors have demonstrated that TFOs designed according to the A-AT and G-GC rule do not form non-specific triplexes, indicating that the triplex formation is indeed sequence specific.
Thus for any given sequence in the gene regulatory region a triplex forming sequence may be devised. Triplex-forming oligonucleotides preferably are at least 15, more preferably 25, still more preferably 30 or more nucleotides in length, up to 50 or 100 bp.
Transfection of cells (for example, via cationic liposomes) with TFOs, and formation of the triple helical structure with the target DNA induces steric and functional changes, blocking transcription initiation and elongation, allowing the introduction of desired sequence changes in the endogenous DNA and resulting in the specific downregulation of gene expression. Examples of such suppression of gene expression in cells treated with TFOs include knockout of episomal supFG1 and endogenous HPRT genes in mammalian cells (Vasquez et al., Nucl Acids Res. 1999; 27:1176-81, and Puri, et al, J Biol Chem, 2001; 276:28991-98), and the sequence- and target specific downregulation of expression of the Ets2 transcription factor, important in prostate cancer etiology (Carbone, et al, Nucl Acid Res. 2003; 31:833-43), and the pro-inflammatory ICAM-1 gene (Besch et al, J Biol Chem, 2002; 277:32473-79). In addition, Vuyisich and Beal have recently shown that sequence specific TFOs can bind to dsRNA, inhibiting activity of dsRNA-dependent enzymes such as RNA-dependent kinases (Vuyisich and Beal, Nuc. Acids Res 2000; 28:2369-74).
Additionally, TFOs designed according to the abovementioned principles can induce directed mutagenesis capable of effecting DNA repair, thus providing both downregulation and upregulation of expression of endogenous genes (Seidman and Glazer, J Clin Invest 2003; 112:487-94). Detailed description of the design, synthesis and administration of effective TFOs can be found in U.S. Patent Application Nos. 2003 017068 and 2003 0096980 to Froehler et al, and 2002 0128218 and 2002 0123476 to Emanuele et al, and U.S. Pat. No. 5,721,138 to Lawn.
Alternatively, down regulation of the polypeptide variants of the present invention may be achieved at the polypeptide level using downregulating agents such as antibodies or antibody fragments capable of specifically binding the polypeptides of the present invention and inhibiting the activity thereof (i.e., neutralizing antibodies). Such antibodies can be directed for example, to the heterodimerizing domain on the variant, or to a putative ligand binding domain. Further description of antibodies and methods of generating same is provided below.
Alternatively, down regulation of the polypeptide variants of the present invention may be achieved using small, unique peptide sequences (e.g., of about 50-100 amino acids) which are capable of specifically binding to their target molecules (e.g., a receptor subunit) and thus prevent endogenous subunit assembly or association and therefore antagonize the receptor activity. Such peptides can be natural or synthetic peptides which are derived from the polypeptide of the present invention (e.g., SEQ ID NO:9, 77 or 164).
Pharmaceutical Compositions and Delivery Thereof
The present invention features a pharmaceutical composition comprising a therapeutically effective amount of a therapeutic agent according to the present invention, which is preferably a therapeutic protein variant as described herein. Optionally and alternatively, the therapeutic agent could be an antibody or an oligonucleotide that specifically recognizes and binds to the therapeutic protein variant, but not to the corresponding full length known protein.
Alternatively, the pharmaceutical composition of the present invention includes a therapeutically effective amount of at least an active portion of a therapeutic protein variant polypeptide.
The pharmaceutical composition according to the present invention is preferably used for the treatment of cluster or protein-related disease, disorder or condition.
“Treatment” refers to both therapeutic treatment and prophylactic or preventative measures. Those in need of treatment include those already with the disorder as well as those in which the disorder is to be prevented. Hence, the mammal to be treated herein may have been diagnosed as having the disorder or may be predisposed or susceptible to the disorder. “Mammal” for purposes of treatment refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, horses, cats, cows, etc. Preferably, the mammal is human.
A “disorder” is any condition that would benefit from treatment with the agent according to the present invention. This includes chronic and acute disorders or diseases including those pathological conditions which predispose the mammal to the disorder in question. Non-limiting examples of disorders to be treated herein are described with regard to specific examples given herein.
The term “therapeutically effective amount” refers to an amount of agent according to the present invention that is effective to treat a disease or disorder in a mammal. In the case of cancer, the therapeutically effective amount of the agent may reduce the number of cancer cells; reduce the tumor size; inhibit (i.e., slow to some extent and preferably stop) cancer cell infiltration into peripheral organs; inhibit (i.e., slow to some extent and preferably stop) tumor metastasis; inhibit, to some extent, tumor growth; and/or relieve to some extent one or more of the symptoms associated with the cancer. To the extent the agent may prevent growth and/or kill existing cancer cells, it may be cytostatic and/or cytotoxic. For cancer therapy, efficacy can, for example, be measured by assessing the time to disease progression (TTP) and/or determining the response rate (RR).
The therapeutic agents of the present invention can be provided to the subject per se, or as part of a pharmaceutical composition where they are mixed with a pharmaceutically acceptable carrier.
As used herein a “pharmaceutical composition” refers to a preparation of one or more of the active ingredients described herein with other chemical components such as physiologically suitable carriers and excipients. The purpose of a pharmaceutical composition is to facilitate administration of a compound to an organism.
Herein the term “active ingredient” refers to the preparation accountable for the biological effect.
Hereinafter, the phrases “physiologically acceptable carrier” and “pharmaceutically acceptable carrier” which may be interchangeably used refer to a carrier or a diluent that does not cause significant irritation to an organism and does not abrogate the biological activity and properties of the administered compound. An adjuvant is included under these phrases. One of the ingredients included in the pharmaceutically acceptable carrier can be for example polyethylene glycol (PEG), a biocompatible polymer with a wide range of solubility in both organic and aqueous media (Mutter et al. (1979).
Herein the term “excipient” refers to an inert substance added to a pharmaceutical composition to further facilitate administration of an active ingredient. Examples, without limitation, of excipients include calcium carbonate, calcium phosphate, various sugars and types of starch, cellulose derivatives, gelatin, vegetable oils and polyethylene glycols.
Techniques for formulation and administration of drugs may be found in “Remington's Pharmaceutical Sciences,” Mack Publishing Co., Easton, Pa., latest edition, which is incorporated herein by reference.
Suitable routes of administration may, for example, include oral, rectal, transmucosal, especially transnasal, intestinal or parenteral delivery, including intramuscular, subcutaneous and intramedullary injections as well as intrathecal, direct intraventricular, intravenous, intraperitoneal, intranasal, or intraocular injections. Alternately, one may administer a preparation in a local rather than systemic manner, for example, via injection of the preparation directly into a specific region of a patient's body.
Pharmaceutical compositions of the present invention may be manufactured by processes well known in the art, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes.
Pharmaceutical compositions for use in accordance with the present invention may be formulated in conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries, which facilitate processing of the active ingredients into preparations which, can be used pharmaceutically. Proper formulation is dependent upon the route of administration chosen.
For injection, the active ingredients of the invention may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hank's solution, Ringer's solution, or physiological salt buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.
For oral administration, the compounds can be formulated readily by combining the active compounds with pharmaceutically acceptable carriers well known in the art. Such carriers enable the compounds of the invention to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for oral ingestion by a patient. Pharmacological preparations for oral use can be made using a solid excipient, optionally grinding the resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carbomethylcellulose; and/or physiologically acceptable polymers such as polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.
Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, titanium dioxide, lacquer solutions and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.
Pharmaceutical compositions, which can be used orally, include push-fit capsules made of gelatin as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. The push-fit capsules may contain the active ingredients in admixture with filler such as lactose, binders such as starches, lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active ingredients may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added. All formulations for oral administration should be in dosages suitable for the chosen route of administration.
For buccal administration, the compositions may take the form of tablets or lozenges formulated in conventional manner.
For administration by nasal inhalation, the active ingredients for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from a pressurized pack or a nebulizer with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichloro-tetrafluoroethane or carbon dioxide. In the case of a pressurized aerosol, the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, e.g., gelatin for use in a dispenser may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.
The preparations described herein may be formulated for parenteral administration, e.g., by bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multidose containers with optionally, an added preservative. The compositions may be suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
Pharmaceutical compositions for parenteral administration include aqueous solutions of the active preparation in water-soluble form. Additionally, suspensions of the active ingredients may be prepared as appropriate oily or water based injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acids esters such as ethyl oleate, triglycerides or liposomes. Aqueous injection suspensions may contain substances, which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol or dextran. Optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the active ingredients to allow for the preparation of highly concentrated solutions.
Alternatively, the active ingredient may be in powder form for constitution with a suitable vehicle, e.g., sterile, pyrogen-free water based solution, before use.
The preparation of the present invention may also be formulated in rectal compositions such as suppositories or retention enemas, using, e.g., conventional suppository bases such as cocoa butter or other glycerides.
Pharmaceutical compositions suitable for use in context of the present invention include compositions wherein the active ingredients are contained in an amount effective to achieve the intended purpose. More specifically, a therapeutically effective amount means an amount of active ingredients effective to prevent, alleviate or ameliorate symptoms of disease or prolong the survival of the subject being treated. Determination of a therapeutically effective amount is well within the capability of those skilled in the art.
For any preparation used in the methods of the invention, the therapeutically effective amount or dose can be estimated initially from in vitro assays. For example, a dose can be formulated in animal models and such information can be used to more accurately determine useful doses in humans.
Toxicity and therapeutic efficacy of the active ingredients described herein can be determined by standard pharmaceutical procedures in vitro, in cell cultures or experimental animals. The data obtained from these in vitro and cell culture assays and animal studies can be used in formulating a range of dosage for use in human.
The dosage may vary depending upon the dosage form employed and the route of administration utilized. The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. (See e.g., Fingl, et al., 1975, in “The Pharmacological Basis of Therapeutics”, Ch. 1 p. 1).
Depending on the severity and responsiveness of the condition to be treated, dosing can be of a single or a plurality of administrations, with course of treatment lasting from several days to several weeks or until cure is effected or diminution of the disease state is achieved.
The amount of a composition to be administered will, of course, be dependent on the subject being treated, the severity of the affliction, the manner of administration, the judgment of the prescribing physician, etc. Compositions including the preparation of the present invention formulated in a compatible pharmaceutical carrier may also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.
Pharmaceutical compositions of the present invention may, if desired, be presented in a pack or dispenser device, such as an FDA approved kit, which may contain one or more unit dosage forms containing the active ingredient. The pack may, for example, comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration. The pack or dispenser may also be accommodated by a notice associated with the container in a form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the compositions or human or veterinary administration. Such notice, for example, may be of labeling approved by the U.S. Food and Drug Administration for prescription drugs or of an approved product insert.
Immunogenic Compositions
A therapeutic agent according to the present invention may optionally be a molecule, which promotes a specific immunogenic response against at least one of the polypeptides of the present invention in the subject. The molecule can be polypeptide variants of the present invention, a fragment derived therefrom or a nucleic acid sequence encoding thereof. Although such a molecule can be provided to the subject per se, the agent is preferably administered with an immunostimulant in an immunogenic composition. An immunostimulant may be any substance that enhances or potentiates an immune response (antibody and/or cell-mediated) to an exogenous antigen. Examples of immunostimulants include adjuvants, biodegradable microspheres (e.g., polylactic galactide) and liposomes into which the compound is incorporated (see e.g., U.S. Pat. No. 4,235,877). Vaccine preparation is generally described in, for example, M. F. Powell and M. J. Newman, eds., “Vaccine Design (the subunit and adjuvant approach),” Plenum Press (NY, 1995).
Illustrative immunogenic compositions may contain DNA encoding one or more of the polypeptides as described above, such that the polypeptide is generated in situ. The DNA may be present within any of a variety of delivery systems known to those of ordinary skill in the art, including nucleic acid expression systems (see below), bacteria and viral expression systems. Numerous gene delivery techniques are well known in the art, such as those described by Rolland, Crit. Rev. Therap. Drug Carrier Systems 15:143-198, 1998, and references cited therein. Appropriate nucleic acid expression systems contain the necessary DNA sequences for expression in the subject (such as a suitable promoter and terminating signal). Bacterial delivery systems involve the administration of a bacterium (such as Bacillus-Calmette-Guerrin) that expresses an immunogenic portion of the polypeptide on its cell surface or secretes such an epitope. In a preferred embodiment, the DNA may be introduced using a viral expression system (e.g., vaccinia or other pox virus, retrovirus, or adenovirus), which may involve the use of a non-pathogenic (defective), replication competent virus. Suitable systems are disclosed, for example, in Fisher-Hoch et al., Proc. Natl. Acad. Sci. USA 86:317-321, 1989; Flexner et al., Ann N.Y. Acad. Sci. 569:86-103, 1989; Flexner et al., Vaccine 8:17-21, 1990; U.S. Pat. Nos. 4,603,112, 4,769,330, and 5,017,487; WO 89/01973; U.S. Pat. No. 4,777,127; GB 2,200,651; EP 0,345,242; WO 91/02805; Berkner, Biotechniques 6:616-627, 1988; Rosenfeld et al., Science 252:431-434, 1991; Kolls et al., Proc. Natl. Acad. Sci. USA 91:215-219, 1994; Kass-Eisler et al., Proc. Natl. Acad. Sci. USA 90:11498-11502, 1993; Guzman et al., Circulation 88:2838-2848, 1993; and Guzman et al., Cir. Res. 73:1202-1207, 1993. Techniques for incorporating DNA into such expression systems are well known to those of ordinary skill in the art. The DNA may also be “naked,” as described, for example, in Ulmer et al., Science 259:1745-1749, 1993 and reviewed by Cohen, Science 259:1691-1692, 1993. The uptake of naked DNA may be increased by coating the DNA onto biodegradable beads, which are efficiently transported into the cells.
It will be appreciated that an immunogenic composition may comprise both a polynucleotide and a polypeptide component. Such immunogenic compositions may provide for an enhanced immune response.
Any of a variety of immunostimulants may be employed in the immunogenic compositions of this invention. For example, an adjuvant may be included. Most adjuvants contain a substance designed to protect the antigen from rapid catabolism, such as aluminum hydroxide or mineral oil, and a stimulator of immune responses, such as lipid A, Bortadella pertussis or Mycobacterium tuberculosis derived proteins. Suitable adjuvants are commercially available as, for example, Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, Mich.); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.); AS-2 (SmithKline Beecham, Philadelphia, Pa.); aluminum salts such as aluminum hydroxide gel (alum) or aluminum phosphate; salts of calcium, iron or zinc; an insoluble suspension of acylated tyrosine; acylated sugars; cationically or anionically derivatized polysaccharides; polyphosphazenes; biodegradable microspheres; monophosphoryl lipid A and quil A. Cytokines, such as GM-CSF or interleukin-2, -7, or -12, may also be used as adjuvants.
The adjuvant composition may be designed to induce an immune response predominantly of the Th1 type. High levels of Th1-type cytokines (e.g., IFN-.gamma, TNF.alpha., IL-2 and IL-12) tend to favor the induction of cell mediated immune responses to an administered antigen. In contrast, high levels of Th2-type cytokines (e.g., IL-4, IL-5, IL-6 and IL-10) tend to favor the induction of humoral immune responses. Following application of an immunogenic composition as provided herein, the subject will support an immune response that includes Th1- and Th2-type responses. The levels of these cytokines may be readily assessed using standard assays. For a review of the families of cytokines, see Mosmann and Coffinan, Ann Rev. Immunol. 7:145-173, 1989.
Preferred adjuvants for use in eliciting a predominantly Th1-type response include, for example, a combination of monophosphoryl lipid A, preferably 3-de-O-acylated monophosphoryl lipid A (3D-MPL), together with an aluminum salt. MPL adjuvants are available from Corixa Corporation (Seattle, Wash.; see U.S. Pat. Nos. 4,436,727; 4,877,611; 4,866,034 and 4,912,094). CpG-containing oligonucleotides (in which the CpG dinucleotide is unmethylated) also induce a predominantly Th1 response. Such oligonucleotides are well known and are described, for example, in WO 96/02555, WO 99/33488 and U.S. Pat. Nos. 6,008,200 and 5,856,462. Immunostimulatory DNA sequences are also described, for example, by Sato et al., Science 273:352, 1996. Another preferred adjuvant is a saponin, preferably QS21 (Aquila Biopharmaceuticals Inc., Framingham, Mass.), which may be used alone or in combination with other adjuvants. For example, an enhanced system involves the combination of a monophosphoryl lipid A and saponin derivative, such as the combination of QS21 and 3D-MPL as described in WO 94/00153, or a less reactogenic composition where the QS21 is quenched with cholesterol, as described in WO 96/33739. Other preferred formulations comprise an oil-in-water emulsion and tocopherol. A particularly potent adjuvant formulation involving QS21, 3D-MPL and tocopherol in an oil-in-water emulsion is described in WO 95/17210.
Other preferred adjuvants include Montanide ISA 720 (Seppic, France), SAF (Chiron, Calif., United States), ISCOMS (CSL), MF-59 (Chiron), the SBAS series of adjuvants (e.g., SBAS-2 or SBAS-4, available from SmithKline Beecham, Rixensart, Belgium), Detox (Corixa, Hamilton, Mont.), RC-529 (Corixa, Hamilton, Mont.) and other aminoalkyl glucosaminide 4-phosphates (AGPs), such as those described in pending U.S. patent application Ser. Nos. 08/853,826 and 09/074,720.
A delivery vehicle may be employed within the immunogenic composition of the present invention to facilitate production of an antigen-specific immune response that targets tumor cells. Delivery vehicles include antigen presenting cells (APCs), such as dendritic cells, macrophages, B cells, monocytes and other cells that may be engineered to be efficient APCs. Such cells may be genetically modified to increase the capacity for presenting the antigen, to improve activation and/or maintenance of the T cell response, to have anti-tumor effects per se and/or to be immunologically compatible with the receiver (i.e., matched HLA haplotype). APCs may generally be isolated from any of a variety of biological fluids and organs, including tumor and peritumoral tissues, and may be autologous, allogeneic, syngeneic or xenogeneic cells.
Dendritic cells are highly potent APCs (Banchereau and Steinman, Nature 392:245-251, 1998) and have been shown to be effective as a physiological adjuvant for eliciting prophylactic or therapeutic antitumor immunity (see Timmernan and Levy, Ann Rev. Med. 50:507-529, 1999). In general, dendritic cells may be identified based on their typical shape (stellate in situ, with marked cytoplasmic processes (dendrites) visible in vitro), their ability to take up, process and present antigens with high efficiency and their ability to activate naive T cell responses. Dendritic cells may, of course, be engineered to express specific cell-surface receptors or ligands that are not commonly found on dendritic cells in vivo or ex vivo, and such modified dendritic cells are contemplated by the present invention. As an alternative to dendritic cells, secreted vesicles antigen-loaded dendritic cells (called exosomes) may be used within an immunogenic composition (see Zitvogel et al., Nature Med. 4:594-600, 1998).
Dendritic cells and progenitors may be obtained from peripheral blood, bone marrow, tumor-infiltrating cells, peritumoral tissues-infiltrating cells, lymph nodes, spleen, skin, umbilical cord blood or any other suitable tissue or fluid. For example, dendritic cells may be differentiated ex vivo by adding a combination of cytokines such as GM-CSF, IL-4, IL-13 and/or TNF.alpha. to cultures of monocytes harvested from peripheral blood. Alternatively, CD34 positive cells harvested from peripheral blood, umbilical cord blood or bone marrow may be differentiated into dendritic cells by adding to the culture medium combinations of GM-CSF, IL-3, TNF.alpha., CD40 ligand, LPS, flt3 ligand and/or other compound(s) that induce differentiation, maturation and proliferation of dendritic cells.
Dendritic cells are categorized as “immature” and “mature” cells, which allows a simple way to discriminate between two well characterized phenotypes. Immature dendritic cells are characterized as APC with a high capacity for antigen uptake and processing, which correlates with the high expression of Fcy receptor and mannose receptor. The mature phenotype is typically characterized by a lower expression of these markers, but a high expression of cell surface molecules responsible for T cell activation such as class I and class II MHC, adhesion molecules (e.g., CD54 and CD11) and costimulatory molecules (e.g., CD40, CD80, CD86 and 4-1BB).
APCs may generally be transfected with at least one polynucleotide encoding a polypeptide of the present invention, such that variant II, or an immunogenic portion thereof, is expressed on the cell surface. Such transfection may take place ex vivo, and a composition comprising such transfected cells may then be used for therapeutic purposes, as described herein. Alternatively, a gene delivery vehicle that targets a dendritic or other antigen presenting cell may be administered to the subject, resulting in transfection that occurs in vivo. In vivo and ex vivo transfection of dendritic cells, for example, may generally be performed using any methods known in the art, such as those described in WO 97/24447, or the gene gun approach described by Mahvi et al., Immunology and cell Biology 75:456-460, 1997. Antigen loading of dendritic cells may be achieved by incubating dendritic cells or progenitor cells with a polypeptide of the present invention, DNA (naked or within a plasmid vector) or RNA; or with antigen-expressing recombinant bacterium or viruses (e.g., vaccinia, fowlpox, adenovirus or lentivirus vectors). Prior to loading, the polypeptide may be covalently conjugated to an immunological partner that provides T cell help (e.g., a carrier molecule) such as described above. Alternatively, a dendritic cell may be pulsed with a non-conjugated immunological partner, separately or in the presence of the polypeptide.
Preferred embodiments of the present invention encompass novel naturally occurring secreted (i.e., extracellular) and non-secreted (i.e., intracellular or membranal) variants of genes and gene products, which, as is described in the Examples section which follows, play pivotal roles in disease onset and progression. As such these variants can be used for a wide range of diagnostic and/or therapeutic uses.
Diagnostic Methods
The term “marker” in the context of the present invention refers to a nucleic acid fragment, a peptide, or a polypeptide, which is differentially present in a sample taken from patients having or predisposed to a cluster or protein-related disease, disorder or condition as compared to a comparable sample taken from subjects who do not have a such a disease, disorder or condition.
The methods for detecting these markers have many applications. For example, one marker or combination of markers can be measured to differentiate between various types of cluster or protein-related disease, disorder or condition, and thus are useful as an aid in the accurate diagnosis of cluster or protein-related disease, disorder or condition in a patient. For example, one marker or combination of markers can be measured to differentiate between various types of lung cancers, such as small cell or non-small cell lung cancer, and further between non-small cell lung cancer types, such as adenocarcinomas, squamous cell and large cell carcinomas, and thus are useful as an aid in the accurate diagnosis of lung cancer in a patient. In another example, the present methods for detecting these markers can be applied to in vitro cluster or protein-related cancers cells or in vivo animal models for cluster or protein-related cancers to assay for and identify compounds that modulate expression of these markers.
The phrase “differentially present” refers to differences in the quantity of a marker present in a sample taken from patients having cluster or protein-related disease, disorder or condition as compared to a comparable sample taken from patients who do not have such disease, disorder or condition. For example, a nucleic acid fragment may optionally be differentially present between the two samples if the amount of the nucleic acid fragment in one sample is significantly different from the amount of the nucleic acid fragment in the other sample, for example as measured by hybridization and/or NAT-based assays. A polypeptide is differentially present between the two samples if the amount of the polypeptide in one sample is significantly different from the amount of the polypeptide in the other sample. It should be noted that if the marker is detectable in one sample and not detectable in the other, then such a marker can be considered to be differentially present. One of ordinary skill in the art could easily determine such relative levels of the markers; further guidance is provided below.
As used herein the phrase “diagnostic” means identifying the presence or nature of a pathologic condition. Diagnostic methods differ in their sensitivity and specificity. The “sensitivity” of a diagnostic assay is the percentage of diseased individuals who test positive (percent of “true positives”). Diseased individuals not detected by the assay are “false negatives.” Subjects who are not diseased and who test negative in the assay are termed “true negatives.” The “specificity” of a diagnostic assay is 1 minus the false positive rate, where the “false positive” rate is defined as the proportion of those without the disease who test positive. While a particular diagnostic method may not provide a definitive diagnosis of a condition, it suffices if the method provides a positive indication that aids in diagnosis.
The phrase “predisposition” used herein refers to the susceptibility to develop a disorder. A subject with a predisposition to develop a disorder is more likely to develop the disorder than a non-predisposed subject.
As used herein the phrase “diagnosing” refers to classifying a disease or a symptom, determining a severity of the disease, monitoring disease progression, forecasting an outcome of a disease and/or prospects of recovery. The term “detecting” may also optionally encompass any of the above.
Diagnosis of a disease according to the present invention can be effected by determining a level of a polynucleotide or a polypeptide of the present invention in a biological sample obtained from the subject, wherein the level determined can be correlated with predisposition to, or presence or absence of the disease.
As used herein “a biological sample” refers to a sample of tissue or fluid isolated from a subject, including but not limited to, for example, plasma, serum, spinal fluid, lymph fluid, the external sections of the skin, respiratory, intestinal, and genitourinary tracts, tears, saliva, sputum, milk, blood cells, tumors, neuronal tissue, organs, and also samples of in vivo cell culture constituents. It should be noted that a “biological sample obtained from the subject” may also optionally comprise a sample that has not been physically removed from the subject, as described in greater detail below.
As used herein, the term “level” refers to expression levels of RNA and/or protein or to DNA copy number of a marker of the present invention.
Typically the level of the marker in a biological sample obtained from the subject is different (i.e., increased or decreased) from the level of the same variant in a similar sample obtained from a healthy individual.
Numerous well known tissue or fluid collection methods can be utilized to collect the biological sample from the subject in order to determine the level of DNA, RNA and/or polypeptide of the variant of interest in the subject.
Examples include, but are not limited to, fine needle biopsy, needle biopsy, core needle biopsy and surgical biopsy (e.g., brain biopsy), and lavage. Regardless of the procedure employed, once a biopsy/sample is obtained the level of the variant can be determined and a diagnosis can thus be made.
Determining the level of the same variant in normal tissues of the same origin is preferably effected along-side to detect an elevated expression and/or amplification and/or a decreased expression, of the variant as opposed to the normal tissues.
A “test amount” of a marker refers to an amount of a marker in a subject's sample that is consistent with a diagnosis of a cluster or protein-related disease, disorder or condition related cancer or other UbCH10 related disease. A test amount can be either in absolute amount (e.g., microgram/ml) or a relative amount (e.g., relative intensity of signals).
A “control amount” of a marker can be any amount or a range of amounts to be compared against a test amount of a marker. For example, a control amount of a marker can be the amount of a marker in a patient which does not have the cluster or protein-related disease, disorder or condition. A control amount can be either in absolute amount (e.g., microgram/ml) or a relative amount (e.g., relative intensity of signals).
“Detect” refers to identifying the presence, absence or amount of the object to be detected.
A “label” includes any moiety or item detectable by spectroscopic, photo chemical, biochemical, immunochemical, or chemical means. For example, useful labels include 32P, 35S, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin-streptavidin, digoxigenin, haptens and proteins for which antisera or monoclonal antibodies are available, or nucleic acid molecules with a sequence complementary to a target. The label often generates a measurable signal, such as a radioactive, chromogenic, or fluorescent signal, that can be used to quantify the amount of bound label in a sample. The label can be incorporated in or attached to a primer or probe either covalently, or through ionic, van der Waals or hydrogen bonds, e.g., incorporation of radioactive nucleotides, or biotinylated nucleotides that are recognized by streptavidin. The label may be directly or indirectly detectable. Indirect detection can involve the binding of a second label to the first label, directly or indirectly. For example, the label can be the ligand of a binding partner, such as biotin, which is a binding partner for streptavidin, or a nucleotide sequence, which is the binding partner for a complementary sequence, to which it can specifically hybridize. The binding partner may itself be directly detectable, for example, an antibody may be itself labeled with a fluorescent molecule. The binding partner also may be indirectly detectable, for example, a nucleic acid having a complementary nucleotide sequence can be a part of a branched DNA molecule that is in turn detectable through hybridization with other labeled nucleic acid molecules (see, e.g., P. D. Fahrlander and A. Klausner, Bio/Technology 6:1165 (1988)). Quantitation of the signal is achieved by, e.g., scintillation counting, densitometry, or flow cytometry.
Exemplary detectable labels, optionally and preferably for use with immunoassays, include but are not limited to magnetic beads, fluorescent dyes, radiolabels, enzymes (e.g., horse radish peroxide, alkaline phosphatase and others commonly used in an ELISA), and calorimetric labels such as colloidal gold or colored glass or plastic beads. Alternatively, the marker in the sample can be detected using an indirect assay, wherein, for example, a second, labeled antibody is used to detect bound marker-specific antibody, and/or in a competition or inhibition assay wherein, for example, a monoclonal antibody which binds to a distinct epitope of the marker are incubated simultaneously with the mixture.
“Immunoassay” is an assay that uses an antibody to specifically bind an antigen. The immunoassay is characterized by the use of specific binding properties of a particular antibody to isolate, target, and/or quantify the antigen.
The phrase “specifically (or selectively) binds” to an antibody or “specifically (or selectively) immunoreactive with” when referring to a protein or peptide (or other epitope), refers to a binding reaction that is determinative of the presence of the protein in a heterogeneous population of proteins and other biologics. Thus, under designated immunoassay conditions, the specified antibodies bind to a particular protein at least two times greater than the background (non-specific signal) and do not substantially bind in a significant amount to other proteins present in the sample. Specific binding to an antibody under such conditions may require an antibody that is selected for its specificity for a particular protein. For example, polyclonal antibodies raised to seminal basic protein from specific species such as rat, mouse, or human can be selected to obtain only those polyclonal antibodies that are specifically immunoreactive with seminal basic protein and not with other proteins, except for polymorphic variants and alleles of seminal basic protein. This selection may be achieved by subtracting out antibodies that cross-react with seminal basic protein molecules from other species. A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein. For example, solid-phase ELISA immunoassays are routinely used to select antibodies specifically immunoreactive with a protein (see, e.g., Harlow & Lane, Antibodies, A Laboratory Manual (1988), for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity). Typically a specific or selective reaction will be at least twice background signal or noise and more typically more than 10 to 100 times background.
In another embodiment, this invention provides antibodies specifically recognizing the splice variants and polypeptide fragments thereof of this invention. Preferably such antibodies differentially recognize splice variants of the present invention but do not recognize a corresponding known protein (such known proteins are discussed with regard to their splice variants in the Examples below).
In another embodiment, this invention provides a method for detecting a splice variant according to the present invention in a biological sample, comprising: contacting a biological sample with an antibody specifically recognizing a splice variant according to the present invention under conditions whereby the antibody specifically interacts with the splice variant in the biological sample but do not recognize known corresponding proteins (wherein the known protein is discussed with regard to its splice variant(s) in the Examples below), and detecting the interaction; wherein the presence of an interaction correlates with the presence of a splice variant in the biological sample.
In another embodiment, this invention provides a method for detecting a splice variant nucleic acid sequences in a biological sample, comprising: hybridizing the isolated nucleic acid molecules or oligonucleotide fragments of at least about a minimum length to a nucleic acid material of a biological sample and detecting a hybridization complex; wherein the presence of a hybridization complex correlates with the presence of a splice variant nucleic acid sequence in the biological sample.
According to another embodiment of the present invention the detection of the splice variant nucleic acid sequences in the biological sample is effected by detecting at least one nucleic acid change within a nucleic acid material derived from the biological sample; wherein the presence of the at least one nucleic acid change correlates with the presence of a splice variant nucleic acid sequence in the biological sample.
According to the present invention, the splice variants described herein are non-limiting examples of markers for diagnosing the cluster or protein-related disease, disorder or condition. Each splice variant marker of the present invention can be used alone or in combination, for various uses, including but not limited to, prognosis, prediction, screening, early diagnosis, determination of progression, therapy selection and treatment monitoring of such a cancer, disease or pathology.
According to optional but preferred embodiments of the present invention, any marker according to the present invention may optionally be used alone or combination. Such a combination may optionally comprise a plurality of markers described herein, optionally including any subcombination of markers, and/or a combination featuring at least one other marker, for example a known marker. Furthermore, such a combination may optionally and preferably be used as described above with regard to determining a ratio between a quantitative or semi-quantitative measurement of any marker described herein to any other marker described herein, and/or any other known marker, and/or any other marker. With regard to such a ratio between any marker described herein (or a combination thereof) and a known marker, more preferably the known marker comprises the “known protein” as described in greater detail below with regard to each cluster or gene.
According to other preferred embodiments of the present invention, a splice variant protein or a fragment thereof, or a splice variant nucleic acid sequence or a fragment thereof, may be featured as a biomarker for detecting the cluster or protein-related disease, disorder or condition, such that a biomarker may optionally comprise any of the above.
Non-limiting examples of methods or assays are described below.
The present invention also relates to kits based upon such diagnostic methods or assays.
NAT Assays
Detection of a nucleic acid of interest in a biological sample may also optionally be effected by NAT-based assays, which involve nucleic acid amplification technology, such as PCR, or variations thereof (e.g., real-time PCR, RT-PCR and in situ RT-PCR).
As used herein, a “primer” defines an oligonucleotide which is capable of annealing to (hybridizing with) a target sequence, thereby creating a double stranded region which can serve as an initiation point for DNA synthesis under suitable conditions.
Amplification of a selected, or target, nucleic acid sequence may be carried out by a number of suitable methods. See generally Kwoh et al., 1990, Am. Biotechnol. Lab. 8:14. Numerous amplification techniques have been described and can be readily adapted to suit particular needs of a person of ordinary skill. Non-limiting examples of amplification techniques include polymerase chain reaction (PCR), ligase chain reaction (LCR), strand displacement amplification (SDA), transcription-based amplification, the q3 replicase system and NASBA (Kwoh et al., 1989, Proc. Natl. Acad. Sci. USA 86, 1173-1177; Lizardi et al., 1988, BioTechnology 6:1197-1202; Malek et al., 1994, Methods Mol. Biol., 28:253-260; and Sambrook et al., 1989, supra).
The terminology “amplification pair” (or “primer pair”) refers herein to a pair of oligonucleotides (oligos) of the present invention, which are selected to be used together in amplifying a selected nucleic acid sequence by one of a number of types of amplification processes, preferably a polymerase chain reaction. Other types of amplification processes include ligase chain reaction, strand displacement amplification, or nucleic acid sequence-based amplification, as explained in greater detail below. As commonly known in the art, the oligos are designed to bind to a complementary sequence under selected conditions.
In one particular embodiment, amplification of a nucleic acid sample from a patient is amplified under conditions which favor the amplification of the most abundant differentially expressed nucleic acid. In one preferred embodiment, RT-PCR is carried out on an mRNA sample from a patient under conditions which favor the amplification of the most abundant mRNA. In another preferred embodiment, the amplification of the differentially expressed nucleic acids is carried out simultaneously. It will be realized by a person skilled in the art that such methods could be adapted for the detection of differentially expressed proteins instead of differentially expressed nucleic acid sequences.
The nucleic acid (i.e. DNA or RNA) for practicing the present invention may be obtained according to well known methods.
Oligonucleotide primers of the present invention may be of any suitable length, depending on the particular assay format and the particular needs and targeted genomes employed. Optionally, the oligonucleotide primers are at least 12 nucleotides in length, preferably between 15 and 24 molecules, and they may be adapted to be especially suited to a chosen nucleic acid amplification system. As commonly known in the art, the oligonucleotide primers can be designed by taking into consideration the melting point of hybridization thereof with its targeted sequence (Sambrook et al., 1989, Molecular Cloning—A Laboratory Manual, 2nd Edition, CSH Laboratories; Ausubel et al., 1989, in Current Protocols in Molecular Biology, John Wiley & Sons Inc., N.Y.).
It will be appreciated that antisense oligonucleotides may be employed to quantify expression of a splice isoform of interest. Such detection is effected at the pre-mRNA level. Essentially the ability to quantitate transcription from a splice site of interest can be effected based on splice site accessibility. Oligonucleotides may compete with splicing factors for the splice site sequences. Thus, low activity of the antisense oligonucleotide is indicative of splicing activity.
The polymerase chain reaction and other nucleic acid amplification reactions are well known in the art (various non-limiting examples of these reactions are described in greater detail below). The pair of oligonucleotides according to this aspect of the present invention are preferably selected to have compatible melting temperatures (Tm), e.g., melting temperatures which differ by less than that 7° C., preferably less than 5° C., more preferably less than 4° C., most preferably less than 3° C., ideally between 3° C. and 0° C.
Polymerase Chain Reaction (PCR): The polymerase chain reaction (PCR), as described in U.S. Pat. Nos. 4,683,195 and 4,683,202 to Mullis and Mullis et al., is a method of increasing the concentration of a segment of target sequence in a mixture of genomic DNA without cloning or purification. This technology provides one approach to the problems of low target sequence concentration. PCR can be used to directly increase the concentration of the target to an easily detectable level. This process for amplifying the target sequence involves the introduction of a molar excess of two oligonucleotide primers which are complementary to their respective strands of the double-stranded target sequence to the DNA mixture containing the desired target sequence. The mixture is denatured and then allowed to hybridize. Following hybridization, the primers are extended with polymerase so as to form complementary strands. The steps of denaturation, hybridization (annealing), and polymerase extension (elongation) can be repeated as often as needed, in order to obtain relatively high concentrations of a segment of the desired target sequence.
The length of the segment of the desired target sequence is determined by the relative positions of the primers with respect to each other, and, therefore, this length is a controllable parameter. Because the desired segments of the target sequence become the dominant sequences (in terms of concentration) in the mixture, they are the to be “PCR-amplified.”
Ligase Chain Reaction (LCR or LAR): The ligase chain reaction [LCR; sometimes referred to as “Ligase Amplification Reaction” (LAR)] has developed into a well-recognized alternative method of amplifying nucleic acids. In LCR, four oligonucleotides, two adjacent oligonucleotides which uniquely hybridize to one strand of target DNA, and a complementary set of adjacent oligonucleotides, which hybridize to the opposite strand are mixed and DNA ligase is added to the mixture. Provided that there is complete complementarity at the junction, ligase will covalently link each set of hybridized molecules. Importantly, in LCR, two probes are ligated together only when they base-pair with sequences in the target sample, without gaps or mismatches. Repeated cycles of denaturation, and ligation amplify a short segment of DNA. LCR has also been used in combination with PCR to achieve enhanced detection of single-base changes: see for example Segev, PCT Publication No. WO9001069 A1 (1990). However, because the four oligonucleotides used in this assay can pair to form two short ligatable fragments, there is the potential for the generation of target-independent background signal. The use of LCR for mutant screening is limited to the examination of specific nucleic acid positions.
Self-Sustained Synthetic Reaction (3SR/NASBA): The self-sustained sequence replication reaction (3SR) is a transcription-based in vitro amplification system that can exponentially amplify RNA sequences at a uniform temperature. The amplified RNA can then be utilized for mutation detection. In this method, an oligonucleotide primer is used to add a phage RNA polymerase promoter to the 5′ end of the sequence of interest. In a cocktail of enzymes and substrates that includes a second primer, reverse transcriptase, RNase H, RNA polymerase and ribo- and deoxyribonucleoside triphosphates, the target sequence undergoes repeated rounds of transcription, cDNA synthesis and second-strand synthesis to amplify the area of interest. The use of 3SR to detect mutations is kinetically limited to screening small segments of DNA (e.g., 200-300 base pairs).
Q-Beta (Qβ) Replicase: In this method, a probe which recognizes the sequence of interest is attached to the replicatable RNA template for Qβ replicase. A previously identified major problem with false positives resulting from the replication of unhybridized probes has been addressed through use of a sequence-specific ligation step. However, available thermostable DNA ligases are not effective on this RNA substrate, so the ligation must be performed by T4 DNA ligase at low temperatures (37 degrees C.). This prevents the use of high temperature as a means of achieving specificity as in the LCR, the ligation event can be used to detect a mutation at the junction site, but not elsewhere.
A successful diagnostic method must be very specific. A straight-forward method of controlling the specificity of nucleic acid hybridization is by controlling the temperature of the reaction. While the 3SR/NASBA, and Qβ systems are all able to generate a large quantity of signal, one or more of the enzymes involved in each cannot be used at high temperature (i.e., >55 degrees C.). Therefore the reaction temperatures cannot be raised to prevent non-specific hybridization of the probes. If probes are shortened in order to make them melt more easily at low temperatures, the likelihood of having more than one perfect match in a complex genome increases. For these reasons, PCR and LCR currently dominate the research field in detection technologies.
The basis of the amplification procedure in the PCR and LCR is the fact that the products of one cycle become usable templates in all subsequent cycles, consequently doubling the population with each cycle. The final yield of any such doubling system can be expressed as: (1+X)n=y, where “X” is the mean efficiency (percent copied in each cycle), “n” is the number of cycles, and “y” is the overall efficiency, or yield of the reaction. If every copy of a target DNA is utilized as a template in every cycle of a polymerase chain reaction, then the mean efficiency is 100%. If 20 cycles of PCR are performed, then the yield will be 220, or 1,048,576 copies of the starting material. If the reaction conditions reduce the mean efficiency to 85%, then the yield in those 20 cycles will be only 1.8520, or 220,513 copies of the starting material. In other words, a PCR running at 85% efficiency will yield only 21% as much final product, compared to a reaction running at 100% efficiency. A reaction that is reduced to 50% mean efficiency will yield less than 1% of the possible product.
In practice, routine polymerase chain reactions rarely achieve the theoretical maximum yield, and PCRs are usually run for more than 20 cycles to compensate for the lower yield. At 50% mean efficiency, it would take 34 cycles to achieve the million-fold amplification theoretically possible in 20, and at lower efficiencies, the number of cycles required becomes prohibitive. In addition, any background products that amplify with a better mean efficiency than the intended target will become the dominant products.
Also, many variables can influence the mean efficiency of PCR, including target DNA length and secondary structure, primer length and design, primer and dNTP concentrations, and buffer composition, to name but a few. Contamination of the reaction with exogenous DNA (e.g., DNA spilled onto lab surfaces) or cross-contamination is also a major consideration. Reaction conditions must be carefully optimized for each different primer pair and target sequence, and the process can take days, even for an experienced investigator. The laboriousness of this process, including numerous technical considerations and other factors, presents a significant drawback to using PCR in the clinical setting. Indeed, PCR has yet to penetrate the clinical market in a significant way. The same concerns arise with LCR, as LCR must also be optimized to use different oligonucleotide sequences for each target sequence. In addition, both methods require expensive equipment, capable of precise temperature cycling.
Many applications of nucleic acid detection technologies, such as in studies of allelic variation, involve not only detection of a specific sequence in a complex background, but also the discrimination between sequences with few, or single, nucleotide differences. One method of the detection of allele-specific variants by PCR is based upon the fact that it is difficult for Taq polymerase to synthesize a DNA strand when there is a mismatch between the template strand and the 3′ end of the primer. An allele-specific variant may be detected by the use of a primer that is perfectly matched with only one of the possible alleles; the mismatch to the other allele acts to prevent the extension of the primer, thereby preventing the amplification of that sequence. This method has a substantial limitation in that the base composition of the mismatch influences the ability to prevent extension across the mismatch, and certain mismatches do not prevent extension or have only a minimal effect.
A similar 3′-mismatch strategy is used with greater effect to prevent ligation in the LCR. Any mismatch effectively blocks the action of the thermostable ligase, but LCR still has the drawback of target-independent background ligation products initiating the amplification. Moreover, the combination of PCR with subsequent LCR to identify the nucleotides at individual positions is also a clearly cumbersome proposition for the clinical laboratory.
The direct detection method according to various preferred embodiments of the present invention may be, for example a cycling probe reaction (CPR) or a branched DNA analysis.
When a sufficient amount of a nucleic acid to be detected is available, there are advantages to detecting that sequence directly, instead of making more copies of that target, (e.g., as in PCR and LCR). Most notably, a method that does not amplify the signal exponentially is more amenable to quantitative analysis. Even if the signal is enhanced by attaching multiple dyes to a single oligonucleotide, the correlation between the final signal intensity and amount of target is direct. Such a system has an additional advantage that the products of the reaction will not themselves promote further reaction, so contamination of lab surfaces by the products is not as much of a concern. Recently devised techniques have sought to eliminate the use of radioactivity and/or improve the sensitivity in automatable formats. Two examples are the “Cycling Probe Reaction” (CPR), and “Branched DNA” (bDNA).
Cycling probe reaction (CPR): The cycling probe reaction (CPR), uses a long chimeric oligonucleotide in which a central portion is made of RNA while the two termini are made of DNA. Hybridization of the probe to a target DNA and exposure to a thermostable RNase H causes the RNA portion to be digested. This destabilizes the remaining DNA portions of the duplex, releasing the remainder of the probe from the target DNA and allowing another probe molecule to repeat the process. The signal, in the form of cleaved probe molecules, accumulates at a linear rate. While the repeating process increases the signal, the RNA portion of the oligonucleotide is vulnerable to RNases that may carried through sample preparation.
Branched DNA: Branched DNA (bDNA), involves oligonucleotides with branched structures that allow each individual oligonucleotide to carry 35 to 40 labels (e.g., alkaline phosphatase enzymes). While this enhances the signal from a hybridization event, signal from non-specific binding is similarly increased.
The NAT assays of the present invention also include methods of detecting at least one nucleic acid change [e.g., a single nucleotide polymorphism (SNP] in the biological sample of the present invention.
The demand for tests which allow the detection of specific nucleic acid sequences and sequence changes is growing rapidly in clinical diagnostics. As nucleic acid sequence data for genes from humans and pathogenic organisms accumulates, the demand for fast, cost-effective, and easy-to-use tests for as yet mutations within specific sequences is rapidly increasing.
A handful of methods have been devised to scan nucleic acid segments for mutations or nucleic acid changes. One option is to determine the entire gene sequence of each test sample (e.g., a bacterial isolate). For sequences under approximately 600 nucleotides, this may be accomplished using amplified material (e.g., PCR reaction products). This avoids the time and expense associated with cloning the segment of interest. However, specialized equipment and highly trained personnel are required, and the method is too labor-intense and expensive to be practical and effective in the clinical setting.
In view of the difficulties associated with sequencing, a given segment of nucleic acid may be characterized on several other levels. At the lowest resolution, the size of the molecule can be determined by electrophoresis by comparison to a known standard run on the same gel. A more detailed picture of the molecule may be achieved by cleavage with combinations of restriction enzymes prior to electrophoresis, to allow construction of an ordered map. The presence of specific sequences within the fragment can be detected by hybridization of a labeled probe, or the precise nucleotide sequence can be determined by partial chemical degradation or by primer extension in the presence of chain-terminating nucleotide analogs.
Restriction fragment length polymorphism (RFLP): For detection of single-base differences between like sequences, the requirements of the analysis are often at the highest level of resolution. For cases in which the position of the nucleotide in question is known in advance, several methods have been developed for examining single base changes without direct sequencing. For example, if a mutation of interest happens to fall within a restriction recognition sequence, a change in the pattern of digestion can be used as a diagnostic tool (e.g., restriction fragment length polymorphism [RFLP] analysis).
Single point mutations have been also detected by the creation or destruction of RFLPs. Mutations are detected and localized by the presence and size of the RNA fragments generated by cleavage at the mismatches. Single nucleotide mismatches in DNA heteroduplexes are also recognized and cleaved by some chemicals, providing an alternative strategy to detect single base substitutions, generically named the “Mismatch Chemical Cleavage” (MCC). However, this method requires the use of osmium tetroxide and piperidine, two highly noxious chemicals which are not suited for use in a clinical laboratory.
RFLP analysis suffers from low sensitivity and requires a large amount of sample. When RFLP analysis is used for the detection of point mutations, it is, by its nature, limited to the detection of only those single base changes which fall within a restriction sequence of a known restriction endonuclease. Moreover, the majority of the available enzymes have 4 to 6 base-pair recognition sequences, and cleave too frequently for many large-scale DNA manipulations. Thus, it is applicable only in a small fraction of cases, as most mutations do not fall within such sites.
A handful of rare-cutting restriction enzymes with 8 base-pair specificities have been isolated and these are widely used in genetic mapping, but these enzymes are few in number, are limited to the recognition of G+C-rich sequences, and cleave at sites that tend to be highly clustered. Recently, endonucleases encoded by group I introns have been discovered that might have greater than 12 base-pair specificity, but again, these are few in number.
Allele specific oligonucleotide (ASO): If the change is not in a recognition sequence, then allele-specific oligonucleotides (ASOs), can be designed to hybridize in proximity to the mutated nucleotide, such that a primer extension or ligation event can bused as the indicator of a match or a mis-match. Hybridization with radioactively labeled allelic specific oligonucleotides (ASO) also has been applied to the detection of specific point mutations. The method is based on the differences in the melting temperature of short DNA fragments differing by a single nucleotide. Stringent hybridization and washing conditions can differentiate between mutant and wild-type alleles. The ASO approach applied to PCR products also has been extensively utilized by various researchers to detect and characterize point mutations in ras genes and gsp/gip oncogenes. Because of the presence of various nucleotide changes in multiple positions, the ASO method requires the use of many oligonucleotides to cover all possible oncogenic mutations.
With either of the techniques described above (i.e., RFLP and ASO), the precise location of the suspected mutation must be known in advance of the test. That is to say, they are inapplicable when one needs to detect the presence of a mutation within a gene or sequence of interest.
Denaturing/Temperature Gradient Gel Electrophoresis (DGGE/TGGE): Two other methods rely on detecting changes in electrophoretic mobility in response to minor sequence changes. One of these methods, termed “Denaturing Gradient Gel Electrophoresis” (DGGE) is based on the observation that slightly different sequences will display different patterns of local melting when electrophoretically resolved on a gradient gel. In this manner, variants can be distinguished, as differences in melting properties of homoduplexes versus heteroduplexes differing in a single nucleotide can detect the presence of mutations in the target sequences because of the corresponding changes in their electrophoretic mobilities. The fragments to be analyzed, usually PCR products, are “clamped” at one end by a long stretch of G-C base pairs (30-80) to allow complete denaturation of the sequence of interest without complete dissociation of the strands. The attachment of a GC “clamp” to the DNA fragments increases the fraction of mutations that can be recognized by DGGE. Attaching a GC clamp to one primer is critical to ensure that the amplified sequence has a low dissociation temperature. Modifications of the technique have been developed, using temperature gradients, and the method can be also applied to RNA:RNA duplexes.
Limitations on the utility of DGGE include the requirement that the denaturing conditions must be optimized for each type of DNA to be tested. Furthermore, the method requires specialized equipment to prepare the gels and maintain the needed high temperatures during electrophoresis. The expense associated with the synthesis of the clamping tail on one oligonucleotide for each sequence to be tested is also a major consideration. In addition, long running times are required for DGGE. The long running time of DGGE was shortened in a modification of DGGE called constant denaturant gel electrophoresis (CDGE). CDGE requires that gels be performed under different denaturant conditions in order to reach high efficiency for the detection of mutations.
A technique analogous to DGGE, termed temperature gradient gel electrophoresis (TGGE), uses a thermal gradient rather than a chemical denaturant gradient. TGGE requires the use of specialized equipment which can generate a temperature gradient perpendicularly oriented relative to the electrical field. TGGE can detect mutations in relatively small fragments of DNA therefore scanning of large gene segments requires the use of multiple PCR products prior to running the gel.
Single-Strand Conformation Polymorphism (SSCP): Another common method, called “Single-Strand Conformation Polymorphism” (SSCP) was developed by Hayashi, Sekya and colleagues and is based on the observation that single strands of nucleic acid can take on characteristic conformations in non-denaturing conditions, and these conformations influence electrophoretic mobility. The complementary strands assume sufficiently different structures that one strand may be resolved from the other. Changes in sequences within the fragment will also change the conformation, consequently altering the mobility and allowing this to be used as an assay for sequence variations.
The SSCP process involves denaturing a DNA segment (e.g., a PCR product) that is labeled on both strands, followed by slow electrophoretic separation on a non-denaturing polyacrylamide gel, so that intra-molecular interactions can form and not be disturbed during the run. This technique is extremely sensitive to variations in gel composition and temperature. A serious limitation of this method is the relative difficulty encountered in comparing data generated in different laboratories, under apparently similar conditions.
Dideoxy fingerprinting (ddF): The dideoxy fingerprinting (ddF) is another technique developed to scan genes for the presence of mutations. The ddF technique combines components of Sanger dideoxy sequencing with SSCP. A dideoxy sequencing reaction is performed using one dideoxy terminator and then the reaction products are electrophoresed on nondenaturing polyacrylamide gels to detect alterations in mobility of the termination segments as in SSCP analysis. While ddF is an improvement over SSCP in terms of increased sensitivity, ddF requires the use of expensive dideoxynucleotides and this technique is still limited to the analysis of fragments of the size suitable for SSCP (i.e., fragments of 200-300 bases for optimal detection of mutations).
In addition to the above limitations, all of these methods are limited as to the size of the nucleic acid fragment that can be analyzed. For the direct sequencing approach, sequences of greater than 600 base pairs require cloning, with the consequent delays and expense of either deletion sub-cloning or primer walking, in order to cover the entire fragment. SSCP and DGGE have even more severe size limitations. Because of reduced sensitivity to sequence changes, these methods are not considered suitable for larger fragments. Although SSCP is reportedly able to detect 90% of single-base substitutions within a 200 base-pair fragment, the detection drops to less than 50% for 400 base pair fragments. Similarly, the sensitivity of DGGE decreases as the length of the fragment reaches 500 base-pairs. The ddF technique, as a combination of direct sequencing and SSCP, is also limited by the relatively small size of the DNA that can be screened.
Reverse dot blot: This technique uses labeled sequence specific oligonucleotide probes and unlabeled nucleic acid samples. Activated primary amine-conjugated oligonucleotides are covalently attached to carboxylated nylon membranes. After hybridization and washing, the labeled probe, or a labeled fragment of the probe, can be released using oligomer restriction, i.e., the digestion of the duplex hybrid with a restriction enzyme. Circular spots or lines are visualized colorimetrically after hybridization through the use of streptavidin horseradish peroxidase incubation followed by development using tetramethylbenzidine and hydrogen peroxide, or via chemiluminescence after incubation with avidin alkaline phosphatase conjugate and a luminous substrate susceptible to enzyme activation, such as CSPD, followed by exposure to x-ray film.
It will be appreciated that advances in the field of SNP detection have provided additional accurate, easy, and inexpensive large-scale SNP genotyping techniques, such as PyrosequencingTM, AcycloprimeTM, dynamic allele-specific hybridization (DASH, Howell, W. M. et al., 1999. Dynamic allele-specific hybridization (DASH). Nat. Biotechnol. 17: 87-8), microplate array diagonal gel electrophoresis [MADGE, Day, I. N. et al., 1995. High-throughput genotyping using horizontal polyacrylamide gels with wells arranged for microplate array diagonal gel electrophoresis (MADGE). Biotechniques. 19: 830-5], the TaqMan system (Holland, P. M. et al., 1991. Detection of specific polymerase chain reaction product by utilizing the 5′→3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci USA. 88: 7276-80), as well as various DNA “chip” technologies such as the GeneChip microarrays (e.g., Affymetrix SNP chips) which are disclosed in U.S. Pat. No. 6,300,063 to Lipshutz, et al. 2001, which is fully incorporated herein by reference, Genetic Bit Analysis (GBATM) which is described by Goelet, P. et al. (PCT Appl. No. 92/15712), peptide nucleic acid (PNA, Ren B, et al., 2004. Nucleic Acids Res. 32: e42) and locked nucleic acids (LNA, Latorra D, et al., 2003. Hum. Mutat. 22: 79-85) probes, Molecular Beacons (Abravaya K, et al., 2003. Clin Chem Lab Med. 41: 468-74), intercalating dye [Germer, S. and Higuchi, R. Single-tube genotyping without oligonucleotide probes. Genome Res. 9:72-78 (1999)], FRET primers (Solinas A et al., 2001. Nucleic Acids Res. 29: E96), AlphaScreen (Beaudet L, et al., Genome Res. 2001, 11(4): 600-8), SNPstream (Bell P A, et al., 2002. Biotechniques. Suppl.: 70-2, 74, 76-7), Multiplex minisequencing (Curcio M, et al., 2002. Electrophoresis. 23: 1467-72), SnaPshot (Turner D, et al., 2002. Hum Immunol. 63: 508-13), MassEXTEND (Cashman J R, et al., 2001. Drug Metab Dispos. 29: 1629-37), GOOD assay (Sauer S, and Gut I G. 2003. Rapid Commun. Mass. Spectrom. 17: 1265-72), Microarray minisequencing (Liljedahl U, et al., 2003. Pharmacogenetics. 13: 7-17), arrayed primer extension (APEX) (Tonisson N, et al., 2000. Clin. Chem. Lab. Med. 38: 165-70), Microarray primer extension (O'Meara D, et al., 2002. Nucleic Acids Res. 30: e75), Tag arrays (Fan J B, et al., 2000. Genome Res. 10: 853-60), Template-directed incorporation (TDI) (Akula N, et al., 2002. Biotechniques. 32: 1072-8), fluorescence polarization (Hsu T M, et al., 2001. Biotechniques. 31: 560, 562, 564-8), Colorimetric oligonucleotide ligation assay (OLA, Nickerson D A, et al., 1990. Proc. Natl. Acad. Sci. USA. 87: 8923-7), Sequence-coded OLA (Gasparini P, et al., 1999. J. Med. Screen. 6: 67-9), Microarray ligation, Ligase chain reaction, Padlock probes, Rolling circle amplification, Invader assay (reviewed in Shi M M. 2001. Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies. Clin Chem. 47: 164-72), coded microspheres (Rao K V et al., 2003. Nucleic Acids Res. 31: e66) and MassArray (Leushner J, Chiu N H, 2000. Mol Diagn. 5: 341-80).
According to a presently preferred embodiment of the present invention the step of searching for any of the nucleic acid sequences described here, in tumor cells or in cells derived from a cancer patient is effected by any suitable technique, including, but not limited to, nucleic acid sequencing, polymerase chain reaction, ligase chain reaction, self-sustained synthetic reaction, QP-Replicase, cycling probe reaction, branched DNA, restriction fragment length polymorphism analysis, mismatch chemical cleavage, heteroduplex analysis, allele-specific oligonucleotides, denaturing gradient gel electrophoresis, constant denaturant gel electrophoresis, temperature gradient gel electrophoresis, dideoxy fingerprinting, PyrosequencingTM, AcycloprimeTM, and reverse dot blot.
Detection may also optionally be performed with a chip or other such device. The nucleic acid sample which includes the candidate region to be analyzed is preferably isolated, amplified and labeled with a reporter group. This reporter group can be a fluorescent group such as phycoerythrin. The labeled nucleic acid is then incubated with the probes immobilized on the chip using a fluidics station. For example, Manz et al. (1993) Adv in Chromatogr 1993; 33:1-66 describe the fabrication of fluidics devices and particularly microcapillary devices, in silicon and glass substrates.
Once the reaction is completed, the chip is inserted into a scanner and patterns of hybridization are detected. The hybridization data is collected, as a signal emitted from the reporter groups already incorporated into the nucleic acid, which is now bound to the probes attached to the chip. Since the sequence and position of each probe immobilized on the chip is known, the identity of the nucleic acid hybridized to a given probe can be determined.
Preferably, the detection of at least one nucleic acid change and/or the splice variant sequence of the present invention is effected in a biological sample containing RNA molecules using, for example, RT-PCR or in situ RT-PCR.
RT-PCR analysis: This method uses PCR amplification of relatively rare RNAs molecules. First, RNA molecules are purified from the cells and converted into complementary DNA (cDNA) using a reverse transcriptase enzyme (such as an MMLV-RT) and primers such as, oligo dT, random hexamers or gene specific primers. Then by applying gene specific primers and Taq DNA polymerase, a PCR amplification reaction is carried out in a PCR machine. Those of skills in the art are capable of selecting the length and sequence of the gene specific primers and the PCR conditions (i.e., annealing temperatures, number of cycles and the like) which are suitable for detecting specific RNA molecules. It will be appreciated that a semi-quantitative RT-PCR reaction can be employed by adjusting the number of PCR cycles and comparing the amplification product to known controls.
In situ RT-PCR stain: This method is described in Nuovo G J, et al. [Intracellular localization of polymerase chain reaction (PCR)-amplified hepatitis C cDNA. Am J Surg Pathol. 1993, 17: 683-90] and Komminoth P, et al. [Evaluation of methods for hepatitis C virus detection in archival liver biopsies. Comparison of histology, immunohistochemistry, in situ hybridization, reverse transcriptase polymerase chain reaction (RT-PCR) and in situ RT-PCR. Pathol Res Pract. 1994, 190: 1017-251. Briefly, the RT-PCR reaction is performed on fixed cells by incorporating labeled nucleotides to the PCR reaction. The reaction is carried on using a specific in situ RT-PCR apparatus such as the laser-capture microdissection PixCell I LCM system available from Arcturus Engineering (Mountainview, Calif.).
It will be appreciated that when utilized along with automated equipment, the above described detection methods can be used to screen multiple samples for a disease and/or pathological condition both rapidly and easily.
Additional objects, advantages, and novel features of the present invention will become apparent to one ordinarily skilled in the art upon examination of the following examples, which are not intended to be limiting. Additionally, each of the various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below finds experimental support in the following examples.
EXAMPLES
Reference is now made to the following examples, which together with the above descriptions, illustrate the invention in a non limiting fashion.
Generally, the nomenclature used herein and the laboratory procedures utilized in the present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the literature. See, for example, “Molecular Cloning: A laboratory Manual” Sambrook et al., (1989); “Current Protocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., “Current Protocols in Molecular Biology”, John Wiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide to Molecular Cloning”, John Wiley & Sons, New York (1988); Watson et al., “Recombinant DNA”, Scientific American Books, New York; Birren et al. (eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, Cold Spring Harbor Laboratory Press, New York (1998); methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis, J. E., ed. (1994); “Current Protocols in Immunology” Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds), “Basic and Clinical Immunology” (8th Edition), Appleton & Lange, Norwalk, Conn. (1994); Mishell and Shiigi (eds), “Selected Methods in Cellular Immunology”, W. H. Freeman and Co., New York (1980); available immunoassays are extensively described in the patent and scientific literature, see, for example, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521; “Oligonucleotide Synthesis” Gait, M. J., ed. (1984); “Nucleic Acid Hybridization” Hames, B. D., and Higgins S. J., eds. (1985); “Transcription and Translation” Hames, B. D., and Higgins S. J., Eds. (1984); “Animal Cell Culture” Freshney, R. I., ed. (1986); “Immobilized Cells and Enzymes” IRL Press, (1986); “A Practical Guide to Molecular Cloning” Perbal, B., (1984) and “Methods in Enzymology” Vol. 1-317, Academic Press; “PCR Protocols: A Guide To Methods And Applications”, Academic Press, San Diego, Calif. (1990); Marshak et al., “Strategies for Protein Purification and Characterization—A Laboratory Course Manual” CSHL Press (1996); all of which are incorporated by reference as if fully set forth herein. Other general references are provided throughout this document. The procedures therein are believed to be well known in the art and are provided for the convenience of the reader. All the information contained therein is incorporated herein by reference.
Example 1
Description of the methodology undertaken to uncover the biomolecular sequences of the present invention and uses therefore.
Human ESTs and cDNAs were obtained from GenBank versions 136 (Jun. 15, 2003 ftp://ftp.ncbi.nih.gov/genbank/release.notes/gb136.release.notes) and NCBI genome assembly of April 2003. Novel splice variants were predicted using the LEADS clustering and assembly system as described in U.S. Pat. No. 6,625,545, U.S. patent application Ser. No. 10/426,002, both of which are hereby incorporated by reference as if fully set forth herein. Briefly, the software cleans the expressed sequences from repeats, vectors and immunoglobulins. It then aligns the expressed sequences to the genome taking alternatively splicing into account and clusters overlapping expressed sequences into “clusters” that represent genes or partial genes.
These were annotated using the GeneCarta (Compugen, Tel-Aviv, Israel) platform. The GeneCarta platform includes a rich pool of annotations, sequence information (particularly of spliced sequences), chromosomal information, alignments, and additional information such as SNPs, gene ontology terms, expression profiles, functional analyses, detailed domain structures, known and predicted proteins and detailed homology reports.
Brief description of the methodology used to obtain annotative sequence information is summarized infra (for detailed description see U.S. patent application Ser. No. 10/426,002, published as US20040101876 on May 27, 2004).
The ontological annotation approach—An ontology refers to the body of knowledge in a specific knowledge domain or discipline such as molecular biology, microbiology, immunology, virology, plant sciences, pharmaceutical chemistry, medicine, neurology, endocrinology, genetics, ecology, genomics, proteomics, cheminformatics, pharmacogenomics, bioinformatics, computer sciences, statistics, mathematics, chemistry, physics and artificial intelligence.
An ontology includes domain-specific concepts—referred to, herein, as sub-ontologies. A sub-ontology may be classified into smaller and narrower categories. The ontological annotation approach is effected as follows.
First, biomolecular (i.e., polynucleotide or polypeptide) sequences are computationally clustered according to a progressive homology range, thereby generating a plurality of clusters each being of a predetermined homology of the homology range.
Progressive homology is used to identify meaningful homologies among biomolecular sequences and to thereby assign new ontological annotations to sequences, which share requisite levels of homologies. Essentially, a biomolecular sequence is assigned to a specific cluster if displays a predetermined homology to at least one member of the cluster (i.e., single linkage). A “progressive homology range” refers to a range of homology thresholds, which progress via predetermined increments from a low homology level (e.g. 35%) to a high homology level (e.g. 99%).
Following generation of clusters, one or more ontologies are assigned to each cluster. Ontologies are derived from an annotation preassociated with at least one biomolecular sequence of each cluster; and/or generated by analyzing (e.g., text-mining) at least one biomolecular sequence of each cluster thereby annotating biomolecular sequences.
The hierarchical annotation approach—“Hierarchical annotation” refers to any ontology and subontology, which can be hierarchically ordered, such as, a tissue expression hierarchy, a developmental expression hierarchy, a pathological expression hierarchy, a cellular expression hierarchy, an intracellular expression hierarchy, a taxonomical hierarchy, a functional hierarchy and so forth.
The hierarchical annotation approach is effected as follows. First, a dendrogram representing the hierarchy of interest is computationally constructed. A “dendrogram” refers to a branching diagram containing multiple nodes and representing a hierarchy of categories based on degree of similarity or number of shared characteristics.
Each of the multiple nodes of the dendrogram is annotated by at least one keyword describing the node, and enabling literature and database text mining, such as by using publicly available text mining software. A list of keywords can be obtained from the GO Consortium. However, measures are taken to include as many keywords, and to include keywords which might be out of date. For example, for tissue annotation, a hierarchy is built using all available tissue/libraries sources available in the GenBank, while considering the following parameters: ignoring GenBank synonyms, building anatomical hierarchies, enabling flexible distinction between tissue types (normal versus pathology) and tissue classification levels (organs, systems, cell types, etc.).
In a second step, each of the biomolecular sequences is assigned to at least one specific node of the dendrogram.
The biomolecular sequences can be annotated biomolecular sequences, unannotated biomolecular sequences or partially annotated biomolecular sequences.
Annotated biomolecular sequences can be retrieved from pre-existing annotated databases as described hereinabove.
For example, in GenBank, relevant annotational information is provided in the definition and keyword fields. In this case, classification of the annotated biomolecular sequences to the dendrogram nodes is directly effected. A search for suitable annotated biomolecular sequences is performed using a set of keywords which are designed to classify the biomolecular sequences to the hierarchy (i.e., same keywords that populate the dendrogram).
In cases where the biomolecular sequences are unannotated or partially annotated, extraction of additional annotational information is effected prior to classification to dendrogram nodes. This can be effected by sequence alignment, as described hereinabove. Alternatively, annotational information can be predicted from structural studies. Where needed, nucleic acid sequences can be transformed to amino acid sequences to thereby enable more accurate annotational prediction.
Finally, each of the assigned biomolecular sequences is recursively classified to nodes hierarchically higher than the specific nodes, such that the root node of the dendrogram encompasses the full biomolecular sequence set, which can be classified according to a certain hierarchy, while the offspring of any node represent a partitioning of the parent set.
For example, a biomolecular sequence found to be specifically expressed in “rhabdomyosarcoma”, will be classified also to a higher hierarchy level, which is “sarcoma”, and then to “Mesenchymal cell tumors” and finally to a highest hierarchy level “Tumor”. In another example, a sequence found to be differentially expressed in endometrium cells, will be classified also to a higher hierarchy level, which is “uterus”, and then to “women genital system” and to “genital system” and finally to a highest hierarchy level “genitourinary system”. The retrieval can be performed according to each one of the requested levels.
Annotating gene expression according to relative abundance—Spatial and temporal gene annotations are also assigned by comparing relative abundance in libraries of different origins. This approach can be used to find genes, which are differentially expressed in tissues, pathologies and different developmental stages. In principal, the presentation of a contigue in at least two tissues of interest is determined and significant over or under representation of the contigue in one of the at least two tissues is assessed to identify differential expression. Significant over or under representation is analyzed by statistical pairing.
Annotating spatial and temporal expression can also be effected on splice variants. This is effected as follows. First, a contigue which includes exonal sequence presentation of the at least two splice variants of the gene of interest is obtained. This contigue is assembled from a plurality of expressed sequences; Then, at least one contigue sequence region, unique to a portion (i.e., at least one and not all) of the at least two splice variants of the gene of interest, is identified. Identification of such unique sequence region is effected using computer alignment software. Finally, the number of the plurality of expressed sequences in the tissue having the at least one contigue sequence region is compared with the number of the plurality of expressed sequences not-having the at least one contigue sequence region, to thereby compare the expression level of the at least two splice variants of the gene of interest in the tissue.
Data concerning therapies, indications and possible pharmacological activities of the polypeptides of the present invention was obtained from PharmaProject (PJB Publications Ltd 2003) and public databases, including LocusLink and Swissprot). Functional structural analysis of the polypeptides of the present invention was effected using Interpro domain analysis software (Interpro default parameters, the analyses that were run are HMMPfam, HMMSmart, ProfileScan, FprintScan, and BlastProdom). Subecllular localization was analysed using ProLoc software (Einat Hazkani-Covo, Erez Y. Levanon, Galit Rotman, Dan Graur, Amit Novik. Evolution of multicellularity in metazoa: comparative analysis of the subcellular localization of proteins in Saccharomyces, Drosophila and Caenorhabditis. Cell Biology International (2004; 28(3): 171-8).
Identifying gene products by interspecies sequence comparison—The present inventors have designed and configured a method of predicting gene expression products based on interspecies sequence comparison. Specifically, the method is based on the identification of conserved alternatively spliced exons for which there might be no supportive expression data.
Alternatively spliced exons have unique characteristics differentiating them from constitutively spliced ones. Using machine-learning techniques a combination of such characteristics was elucidated that defines alternatively spliced exons with very high probability. Any human exon having this combination of characteristics is therefore predicted to be alternatively spliced. Using this method, the present inventors were able to detect putative splice variants that are not supported by human ESTs.
The method is effected as follows. First, alternatively spliced exons of a gene of interest are identified by scoring exon sequences of the gene of interest according to at least one sequence parameter as follows: (i) exon length—conserved alternatively spliced exons are relatively shorter than constitutively spliced ones; (ii) division by 3—alternatively spliced exons are cassette exons that are sometimes inserted and sometimes skipped; Since alternatively spliced exons frequently contain sequences that regulate their splicing important parameters for scoring alternatively spliced exons include (iii) conservation level to a non-human ortholohgous sequence; (iv) length of conserved intron sequences upstream of each of the exon sequences; (v) length of conserved intron sequences downstream of each of the exon sequences; (vi) conservation level of the intron sequences upstream of each of the exon sequences; and (vii) conservation level of the intron sequences downstream of each of the exon sequences.
Exon sequences scoring above a predetermined threshold represent alternatively spliced exons of the gene of interest.
Once alternatively spliced exons are identified, the chromosomal location of each of the alternatively spliced exons is analyzed with respect to coding sequence of the gene of interest to thereby predict expression products of the gene of interest. When performed along with computerized means, mass prediction of gene products can be effected.
In addition, for identifying new gene products by interspecies sequence comparison, the expressed sequences derived from non-human species can be used for new human splice variants prediction.
More details are provided in U.S. patent application Ser. No. 10/000,000 filed concurrently herewith and assigned to the same assignee hereof. This application contains subject matter related in certain respects, to the subject matter of the present application, the teachings of which applications are incorporated herein by reference.
Example 2
Granulocyte Colony Stimulating Factor (GCSF)
Background
The first line of defense against infectious agents is comprised primarily of polymorphonuclear granulocytes, macrophages, natural killer cells and cytotoxic lymphocytes. GCSF, a central mediator of the endogenous response to infection and inflammation, plays a critical role in the process of hematopoiesis, regulating the proliferation, differentiation and survival of neutrophils and neutrophilic progenitor cells. It is produced mainly by hematopoietic cells, such as monocytes/macrophages and lymphocytes. Other cells, such as fibroblast, endothelial cells, astrocytes and bone marrow stromal cells, can also produce GCSF following activation by LPS, IL-1 or TNF-α. Indeed, GCSF production is sharply increased in response to bacterial infection and cell-mediated immune responses, supporting its role in vivo as a host defense against microorganisms. In vitro, GCSF exhibits stimulation of neutrophil production from precursor cells and enhancement of mature neutrophil function as augmentation of their antibody-dependant cellular cytotoxicity (ADCC). The dual action of GCSF in vitro, suggested that it would be useful clinically to stimulate hematopoietic recovery in situations of reduced bone marrow capacity or to enhance the ability to resolve infections in immunocompromised hosts. In its native form, the GCSF protein is O-glycosylated with a molecular mass of approximately 20 kD. It is a member of a family of cytokines that have a four-α-helical bundle structure which contribute importantly to its three-dimensional structure. GCSF mediates its biological actions by binding to a specific cell surface receptor, the GCSF-R, which is expressed on neutrophils, their precursors and some leukemic cell lines. Binding of GCSF causes receptor dimerization and activation of signaling cascades such as the Jak-STAT and mitogen-activated kinase pathways. The receptor has no intrinsic tyrosine kinases activity but rather it activates a number of cytoplasmic tyrosine kinases that initiate the cascade of signaling events. There are four tyrosine residues in the cytoplasmic region of the GCSF-R that are rapidly phosphorylated following ligand binding and have been shown to have specific roles in mediating the various activities of GCSF (Basu et al. 2002. International Journal of molecular Medicine. 10:3-10; Layton J. E. 1992. Growth Factors Vol. 6, Pp. 17-186; Young et al. 1997. Protein Science. 6:1228-1236; Layton et al. 1999. The Journal of Biological Chemistry. Vol. 274, No. 25, Pp. 17445-17451; Bishop et al. 2001. The Journal of Biological Chemistry. Vol. 276, No. 36, Pp. 33465-33470; Hubei et al. 2003. Ann Hematol. 82:207-213; Kuga et al. 1989. Biochemical and biophysical research communications. Vol. 159, No. 1. Pp 103-111; Clark-Lewis et al. 1988. The Journal of Immunology. Vol. 141, No. 3, Pp 881-889).
Clinical Application
Neutropenia (low neutrophils in the blood) is still the leading factor limiting the use of chemotherapy for the treatment of neoplastic diseases and a major cause of morbidity and mortality following hematopoietic stem cell transplantation. GCSF is widely employed clinically to treat cancer patients undergoing chemotherapy in order to alleviate the depression of white blood cells levels produced by cytotoxic therapeutic agents. It has been also used to accelerate hematopoietic recovery after transplantation and therefore reduce the risks of serious infection. Use of this cytokine reduces the duration of neutropenia, enhances hematopoietic reconstitution and increases the yield of the progenitor cells. Since GCSF treatment leads to rapid expansion of bone marrow cellularity and the appearance of progenitors in peripheral blood, it has been used to mobilize CD34+ hematopoietic stem cells from the marrow to the blood (peripheral blood stem cells) for use in hematopoietic transplantation. Approved pharmaceutical forms of GCSF for human use include a recombinant nonglycosylated protein expressed in Escherichia coli (filgrastim, produced by Amgen, Thousand Oaks, Calif., USA) and a glycosylated form expressed in Chinese hamster ovary cells (lenograstim, produced by Chugai Pharmaceuticals, Tokyo, Japan). Both forms have similar biological activities and bioavailability following subcutaneous or intravenous administration.
GCSF Splice Variants Structure
A brief description is now provided of GCSF splice variants according to the present invention. GCSF splice variant T3 [HUMGCSF_P4 (SEQ ID NO:1); HUMGCSF_T3 (SEQ ID NO:3), FIGS. 1a and b, respectively, shown according to the name of the cluster, HUMGCSF) results from alternative splicing of the GCSF gene, thus causing a retention of intron 2 (according to refsec GenBank Accession No. NM—172220), leading to an insertion of a stop codon and the generation of a truncated protein (FIGS. 2-4; FIG. 2 shows the EST support for the variant T3; FIG. 3 shows the alignment of the variant T3 (with the name HUMGCSF_P4) and the known protein; FIG. 4 shows the known protein [e.g., wild type (WT); CSF3_HUMAN—SEQ ID NO:1281 structure as compared to variant T3 according to the present invention). GCSF splice variant T3 encodes a 104 amino acids long protein, which contains amino acids 14-101 of WT GCSF and a unique sequences of six amino acids at the C-terminus of the protein (VSVRKG—SEQ ID NO:2). This splice variant has a novel signal P (signal peptide) and contains part of the IL6/GCSF/MGF family domain (residues 47-97, out of 51-202 of the WT or known protein sequence).
Comparison Report Between HUMGCSF_P4 and CSF3_HUMAN
1. An isolated chimeric polypeptide HUMGCSF_P4 (SEQ ID NO:1), comprising a first amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence MSPEPALSP corresponding to amino acids 1-9 of HUMGCSF_P4 (SEQ ID NO:1), a second amino acid sequence being at least 90% homologous to ALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQVRKIQGDGAALQEKL corresponding to amino acids 14-65 of CSF3_HUMAN (SEQ ID NO:128), which also corresponds to amino acids 10-61 of HUMGCSF_P4 (SEQ ID NO:1), a third amino acid sequence being at least 90% homologous to CATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQL corresponding to amino acids 69-104 of CSF3_HUMAN (SEQ ID NO:128), which also corresponds to amino acids 62-97 of HUMGCSF_P4 (SEQ ID NO:1), and a fourth amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSVRKG (SEQ ID NO:2) corresponding to amino acids 98-103 of HUMGCSF_P4 (SEQ ID NO:1), wherein said first amino acid sequence, second amino acid sequence, third amino acid sequence and fourth amino acid sequence are contiguous and in a sequential order.
2. An isolated head of HUMGCSF_P4 (SEQ ID NO:1), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence MSPEPALSP of HUMGCSF_P4 (SEQ ID NO:1).
3. An isolated chimeric polypeptide for an edge portion of HUMGCSF_P4 (SEQ ID NO:1), comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise LC, having a structure as follows: a sequence starting from any of amino acid numbers 61-x to 61; and ending at any of amino acid numbers 62+((n−2)−x), in which x varies from 0 to n−2.
4. An isolated polypeptide for a tail of HUMGCSF_P4 (SEQ ID NO:1), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSVRKG (SEQ ID NO:2) in HUMGCSF_P4 (SEQ ID NO:1).
Therapeutic Potential of GCSF Splice Variant
GCSF is widely employed clinically to treat cancer patients undergoing chemotherapy in order to alleviate the depression of white blood cells levels and to accelerate hematopoietic recovery after transplantation. Furthermore, much interest has focused on the use of GCSF to mobilize CD34+ hematopoietic stem cells from the marrow to the blood for use in hematopoietic transplantation. In addition, human recombinant GCSF (HR-GCSF) can be used to stimulate a sustained elevation of circulating neutrophils in lactating dairy cows which suffer from mastitis (Cullor J S, et al., 1990; Vet. Clin. Pathol. 19: 9-12).
GCSF is currently administered as frequent injections of significant quantities of the cytokine throughout the course of the treatment. In addition, GCSF requires stringent formulation and storage conditions. Much effort was placed in developing alternative or improved molecules that demonstrate cytokine function but have superior pharmacological properties. GCSF splice variants according to the present invention may fulfill these requirements, exhibiting an increased stability while retaining part or all of the biological activity of GCSF.
Thus, the present inventors uncovered a therapeutic agent which can be used to: (i) increase white blood cell counts (e.g., neutrophils, neutrophil progenitor cells) in a subject in need thereof [e.g., a subject undergoing chemotherapy, hematopoietic stem cell transplantation, a subject suffering from mastitis (such as a lactating cow)], and (ii) mobilize CD24+ hematopietic stem cells from the bone marrow to the peripheral blood. Such an agent is a polypeptide homologous to the GCSF variant of the present invention (SEQ ID NO:1), and/or a polynucleotide homologous to SEQ ID NO:3.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 3
Tumor Necrosis Factor Receptor-3 (TNR3)/Lymphotoxin-β Receptor (LT-βR)
Background
Lymphotoxin-β receptor (LT-βR) is a member of the tumor necrosis factor receptor (TNFR) superfamily and is expressed on the surface of most of cell types, including cells of epithelial and myeloid lineages but not on T and B lymphocytes. LT-βR can specifically bind two ligands: the membrane form of lymphotoxin, LT-α1/β2, which is uniquely expressed on activated lymphoid cells and LIGHT, a member of the TNF superfamily, which is induced on the cell surface during T cell activation. LT-βR has been speculated to play an essential role in the development of lymphoid organs. Thus, LT-β knock-out mice exhibit impaired lymph node development and loss of splenic architecture. In addition, LT-βR deficient mice were found to lack Peyer's patches, colon-associated lymphoid tissues and all lymph nodes. Moreover, stimulation of LT-βR on certain cell lines by LT-α1/β2 or anti-LTβR antibodies was found to induce cell death, chemokine secretion, and activation of nuclear factor κB (NFκB), suggesting an important biological function for LT-βR in mature individuals.
Like other members of the TNF receptor family, the cytoplasmic domain (CD) of LT-βR does not include consensus sequences characteristic of enzymatic activity. Thus, signaling is thought to be mediated by the proteins interacting with LT-βR such as the two serine/threonine protein kinases, p50 and p80 and the two members of the TNF receptor-associated factor (TRAF) family, TRAF3 and TRAF5, which specifically associate with the LT-βR(CD). Further study has indicated that TRAF3 plays an important role in mediating LT-βR-induced apoptosis, whereas TRAF5 involves in the activation of NFκB. On the other hand, several members of the TNFR superfamily (such as TNFRI, Fas, DR3, DR4, and DR5) contain a common motif, the death domain, in their cytoplasmic region that initiate the activation of caspase cascades to execute apoptosis. LT-βR(CD) does not contain a death domain, but signaling through LT-βR can also induce apoptosis. It was shown that the cytoplasmic domain of TNFRI can self-associate through its death domain, therefore overexpression of TNFRI or of the cytoplasmic domain thereof can induce receptor clustering, a crucial step for subsequent intracellular signaling. Despite the absence of the death domain, the LT-βR(CD) is capable of self-association. Thus, overexpression of LT-βR is sufficient to trigger apoptosis without the need for ligand conjugation (Tamada et al. 2002. The Journal of Clinical Investigation. Vol. 109, No. 4, Pp. 549-557; Shao et al. 2003. Eur. J. Immunol. 33:1736-1743; Ettinger et al. 1996. Proc. Natl. Acad. Sci. USA. Vol. 93, Pp. 13102-13107; Wu et al. 1999. The Journal of Biological Chemistry. Vol. 274, No. 17, Pp. 11868-11873; Hehlgans et al. 2002. Cancer Research 62:4034-4040).
Clinical Application
It has been shown that signaling through LT-βR induced cell death in some human adenocarcinoma tumor lines (HT-29 and WiDr) in the presence of IFN-γ. Combined in vivo treatment of human adenocarcinoma cells (WiDr), which form solid tumors in immunocompromised mice, with an agonistic anti-LT-βR antibody and human IFN-γ resulted in tumor growth arrest. Contrary to these findings, it has been shown that activation of LT-βR on fibrosarcoma tumor cells is necessary for angiogenesis and solid tumor growth. Prevention of LT-α1/β2-LT-βR signaling, by the release of LTβR-Fc from the tumor cells, inhibited tumor angiogenesis and neovascularization, and resulted in tumor growth arrest in mice. In addition, LT-βR activation on the tumor cells induced enhanced release of MIP-2, an angiogenic CXC chemokine. Thus, the interaction of activated LT-α1/β2-carrying lymphocytes with LT-βR-expressing tumor cells can initiate a novel pro-angiogenic pathway, leading to organized tumor tissue development. In addition to its modulation of tumor growth, LT-βR was shown to be involved in immune regulation. In vivo blockade of LIGHT and LTα1/β2 by administration of soluble lymphotoxin β receptor-Ig (LTβR-Ig) inhibited the cytotoxic T lymphocyte (CTL) response to host antigenic disparities and ameliorated lethal graft-versus-host disease (GVHD) in a B6 to BDF1 mouse model. In addition, it has been shown that treatment of rodents with the fusion protein, LT-βR-Ig, prevents the development of autoimmune diseases as insulitis and uveitis.
TNR3-LT-βR Splice Variant Structure
A brief description is now provided of TNR3-LT-βR splice variants according to the present invention. TNR3 splice variant transcript—19 (SEQ ID NOs:5 and 7, FIGS. 5a-b; FIG. 5a shows the nucleic acid sequence with the name of the cluster, HUMTNFRRP, with start and stop codons marked in bold and underlined; FIG. 5b shows the corresponding amino acid sequence encoded by this nucleic acid sequence, with the protein name HUMTNFRRP_P14 and with the unique region highlighted) results from alternative splicing of the TNR3 gene, thus causing the extension of exon 4, leading to an insertion of a stop codon and the generation of a truncated protein [FIGS. 6-8; FIG. 6 shows EST support for the variant; FIG. 7 shows the alignment of the variant protein HUMTNFRRP_P14 with a portion of the known protein, TNR3_HUMAN; FIG. 8 compares the structure of the WT or known TNFR3 protein to the variant protein (shown with the name T19)]. This TNR3 splice variant encodes a 166 amino acids long protein which contains the N-terminal signal sequence (residues 1-30), three TNFR CYS repeats (out of four of the WT or known protein) and a unique sequence of 9 amino acids at the C-terminus of the protein (SEQ ID NO:6). It is predicated to be a secreted protein due to the fact that it lacks the transmembrane domain of the WT or known protein.
Comparison Report Between HUMTNFRRP_P14 (SEQ ID NO:5) and TNR3_HUMAN (SEQ ID NO:129)
1. An isolated chimeric polypeptide HUMTNFRRP_P14 (SEQ ID NO:5), comprising a first amino acid sequence being at least 90% homologous to MLLPWATSAPGLAWGPLVLGLFGLLAASQPQAVPPYASENQTCRDQEKEYY EPQHRICCSRCPPGTYVSAKCSRIRDTVCATCAENSYNEHWNYLTICQLCRPC DPVMGLEEIAPCTSKRKTQCRCQPGMFCAAWALECTHCELLSDCPPGTEAEL K corresponding to amino acids 1-157 of TNR3_HUMAN (SEQ ID NO:129), which also corresponds to amino acids 1-157 of HUMTNFRRP_P14 (SEQ ID NO:5), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GQRSLRGWM (SEQ ID NO:6) corresponding to amino acids 158-166 of HUMTNFRRP_P14 (SEQ ID NO:5), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMTNFRRP_P14 (SEQ ID NO:5), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GQRSLRGWM (SEQ ID NO:6) in HUMTNFRRP_P14 (SEQ ID NO:5).
The Therapeutic Potential of TNR3-LT-βR Splice Variant
TNR3 splice variant T19 encodes a soluble receptor which contains three TNFR CYS repeats (out of four of the WT or known protein). It can inhibit TNR3 signaling by competing on the ligand with the membrane-bound receptor, thus preventing LT-α1/β2 from binding to the cell surface receptor and activating it. A soluble form of TNR3 was shown already to bind LT-α1/β2 in vitro. Blocking LTαβ/TNR3 interactions was shown in vivo by administration of TNR3-Fc fusion protein or by the creation of mice which constitutively express a soluble murine TNR3-human IgG1 (Fc) transgene. Blocking TNR3 signaling could have important therapeutic potential for the treatment of cancer, graft-vs-host disease and autoimmune diseases, such as rheumatoid arthritis, Crohn's disease, insulitis and uveitis.
Thus, the present inventors uncovered a therapeutic agent which can be used to: (i) inhibit or prevent the binding of LT-α1/β2 to its TNR3 receptor in vivo or ex vivo, (ii) prevent tumor growth (e.g., solid tumor, such as fibrisarcoma) by preventing the activation of LT-βR, (iii) prevent and/or treat graft-versus-host disease (GVHD) by inhibition of the cytotoxic T lymphocyte (CTL) response, (iv) prevent and/or treat autoimmune diseases (e.g., insulitis, uveitis). Such an agent is a polypeptide homologous to the TNR3 splice variant T19 of the present invention (SEQ ID NO:5) and/or a polynucleotide homologous to SEQ ID NO:7.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 4
Interleukin-4 Receptor (IL-4R)
Background
IL-4 is a pleiotropic and multifunctional cytokine produced by activated T cells, mast cells and basophils. IL-4 plays a critical role in regulating the outcome of an immune response by facilitating Th2 cell differentiation and suppressing the differentiation of IFN-γ-producing CD4+ T cells, thereby favoring humoral immune responses. The other important function of IL-4 is the regulation of immunoglobulin class-switching. It induces class-switching to IgE and IgG4 in human B cells, suggesting a preeminent role of IL-4 in the regulation of allergic conditions. IL-4 also exerts a wide variety of other effects on hematopoietic and nonhematopoietic cells. It enhances the expression of CD23 and class II MHC molecules in B cells and upregulates surface expression of the receptor complex for IL-4. On vascular endothelial cells, IL-4 together with TNF induces the expression of VCAM-1 (vascular cell adhesion molecule 1) and downregulates the expression of E-selectin, thereby changing the adhesive characteristics of endothelial cells and facilitating tissue infiltration by allergic inflammatory cells, such as eosinophils.
IL-4 receptors (IL-4R) are expressed on hematopoietic cells and a range of nonhematopoietic cells including epithelial, endothelial, muscle, fibroblast and liver cells. On hematopoietic cells, the receptor complex for IL-4 is composed of a 140 kDa high-affinity ligand-binding chain, the IL-4-receptor a chain (IL-4Rα) and the so-called common γ chain (γC) that is shared between IL-2, IL-7, IL-9 and IL-15. In contrast, in non-hematopoietic cells, the predominant accessory chain of the IL-4 receptor complex is IL-13Rα1. Furthermore, the receptor complex for IL-13 consists of various combinations of the IL-4Rα, IL-13Rα1 and IL-13Rα2. This may explain the redundancy in biological responses mediated by IL-4 and IL-13. Both IL-4 and IL-13 have been implicated in allergic diseases, probably through redundant and independent pathways. Although homodimerized IL-4Rα can generate biological signals within the cell, physiologic signaling requires heterodimerization of IL-4Rα and the accessory chain (γC). Neither IL-4Rα nor γC contains intrinsic kinase activities; rather the IL-4R requires receptor-associated kinases for the initiation of signal transduction.
Three members of the Janus kinase (Jak) family-Jak-1, Jak-2 and Jak-3 have been shown to be activated in response to IL-4R engagement and to associate with the components of the receptor complex for IL-4. Jak-1 has been proposed to bind IL-4Rα whereas Jak-3 associates with the γC chain. IL-4-IL-4R engagement results in tyrosine phosphorylation of Jak-1 and Jak-3, leading to tyrosine phosphorylation of IL-4Rα itself, a process occurring immediately after IL-4R engagement. Five conserved tyrosine residues (Tyr497, Tyr575, Tyr603, Tyr631 and Tyr713) that can be potentially phosphorylated are present in the cytoplasmic domain of IL-4Rα. Following tyrosine phosphorylation, these conserved tyrosine residues become potential docking sites for downstream signaling molecules containing Src-homology-domain 2 (SH2) or phosphotyrosine-binding domains (Mueller et al. 2002. Biochimica et Biophysica Acta. 1592:237-250; Nelms et al. 1999. Annu. Rev. Immunol. 17:701-738; Pan et al. 1999. Current Opinion in Immunology. 11:615-620; Gessner et al. 1999/2000. Immunobiology. 201, 285-307).
IL-4R Splice Variants-Structure
The present inventors uncovered a novel IL-4R isoform by applying the LEADS clustering and assembly algorithm and the annotation process, as described above.
IL-4R splice variant T5 (amino acid sequence—SEQ ID NO:9, nucleic acid sequence—SEQ ID NO:11, FIGS. 9a-b) results from an alternative splicing of the IL-4R gene, thus introducing a new exon, named 4a′, between exons 4 and 5, leading to an insertion of a stop codon and the generation of a truncated protein (FIGS. 10-11). IL-4R splice variant T5 encodes a 126 amino acids long protein which contains the N-terminal signal sequence (residues 1-25), the complete CRIA domain and a unique sequence of 5 amino acids at the C-terminus of the protein (SEQ ID NO:10). Since the new IL-4R variant lacks the transmembrane domain, it is predicated to be a secreted protein.
Therapeutic Applications for the IL-4R Splice Variants of the Present Invention
Since IL-4Rα is an independent high affinity IL-4 binding subunit, the new secreted form of IL-4Rα (splice variant T5; SEQ ID NO:9), can serve as a powerful antagonist of the IL-4/IL-4R interaction since it contains the complete CRIA domain of IL-4Rα it can compete with the membrane-bound receptor on the ligand and prevent the activation of the membrane-bound IL-4R receptor. Indeed, in a murine model of allo-transplantation, the recombinant extracellular domain of IL-4R was found to block IL-4 functions both in vitro and in vivo.
IL-4-IL4R signaling pathways play a major role in the pathogenesis of allergic diseases. Moreover, naturally occurring mutations of the IL-4Rα chain have been identified and implicated in a genetic predisposition for atopic asthma. Blocking of IL-4 signaling could therefore have an important therapeutic potential for the treatment of asthma and other allergic disorders. In addition to its role in allergic disorders, IL-4R signaling was shown to be involved in autoimmune diseases and in organ transplantation. Recently, it has been shown that IL-4 may serve multiples roles in the development of lupus. Evidence for a novel role for IL-4 in the development of lupus nephritis comes from recent studies, which suggest that IL-4 may directly promote extracellular matrix deposition in the glomeruli. Blockage of IL-4 signaling may ameliorates glomerulosclerosis and prevents the development of end-stage renal disease and in general might have a therapeutic potential in the treatment of lupus, organ transplant rejection and graft-vs-host diseases.
Thus, the present inventors uncovered a therapeutic agent which can be used to: (i) prevent the association between IL4 and IL4R, (ii) treat a disorder associated with IL-4-IL-4R signaling such as asthma (e.g., atopic asthma), allergic disorder, autoimmune diseases (e.g., lupus nephritis), organ transplantation rejection, graft-vs-host disease by preventing the association between IL-4 and IL-4R. Such an agent is a polypeptide homologous to the IL-4Rα splice variant of the present invention (SEQ ID NO:9), and/or a polynucleotide homologous to SEQ ID NO:11.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 5
Integrin Alpha-V
Background
The integrin family is composed of 15 α and 8 β subunits that form over twenty different αβ heterodimeric combinations on cell surfaces. Integrins recognize extracellular matrix (ECM) proteins and cell surface immunoglobulin family molecules through short peptide sequences. Several integrins (e.g., αvβ3, α5β1, αIIbβ3) strongly interact with the tripeptide Arg-Gly-Asp (RGD) sequence within the context of specific ECM or cell surface proteins. While some integrins recognize only a single ECM protein ligand (e.g. α5β1 recognizes only fibronectin), others can bind to several ligands (e.g., αvβ3 binds vitronectin, fibronectin, osteopontin, fibrinogen, denatured or proteolysed collagen and other matrix proteins). The integrin-mediated adhesion of cells to the ECM leads to bi-directional intracellular signaling events that can regulate cell survival, proliferation and migration. In contrast, inhibition of integrin-ligands interactions suppresses cellular growth or induces apoptotic cell death.
Integrin αvβ3, the most promiscuous member of the integrin family, exhibits no expression on normal tissues such as epithelial cells and very low levels on resting vascular, uterine smooth muscle, endothelium, certain activated leukocytes, macrophages and osteoclasts. On the other hand, it is expressed on tumor cells including late-stage glioblastomas, ovarian carcinoma and melanomas. Thus, integrin αvβ3 was found to contribute to the progression of melanoma by regulating melanoma cell proliferation, survival and metastases. On endothelium cells, integrin αvβ3 involves in the angiogenic process in several ways. It regulates cell adhesion to the matrix, transmit signals to the cell nucleus and is exhibits a pro-angiogenic effect by co-operating with VEGFR-2 receptor through the activation of cell signaling and the regulation of cell cycle gene expression.
Several integrin β subunits are involved in angiogenesis processes. For example, the β3 and β5 chains which associate with the αv chain. These subunits share 53% homology, however their ligand specificities are different. While αvβ3 prefers the binding to osteopontin, the αvβ5 prefers the binding to vitronectin. In fact, two different cytokine-dependent pathways participate in the activation of these integrins. While the αvβ3 pathway involves basic FGF (FGF-2) or TNF-α, αvβ5 uses VEGF, TGF-α, or PMA. Since the integrin αv subunit is widely expressed on most cell types and associates with several different β subunits, the expression of αvβ3 is likely to be regulated by the transcription of the β subunit. Other angiogenesis related αv integrin complexes include the αvβ1 which is associated with brain blood vessels and cell migration in squamous cell carcinoma; αvβ8, identified on tumor cells; and αvβ6 which induces secretion of MMP-2 in colon cancer and is important in colon cancer progression (Kerr et al. 2000. Exp. Opin. Invest. Drugs 9(6): 1271-1279; Tucker G. C. 2003. Current Opinion in Investigational Drugs. 4(6): 722-731; Mould et al. 2000. The Journal of Biological Chemistry. Vol. 275, No. 27, Pp. 20324-20336).
Clinical Applications
Integrins were found to be involved in pathological processes of both acute and chronic diseases such as ocular disease, cancer (primary tumors and metastasis), cardiovascular (stroke and heart failure) and inflammatory conditions (rheumatoid arthritis). Evidence clearly demonstrates that the αv integrin is associated with multiple tumor cells, including human breast, renal, cervical, colon, prostate, bladder, lung and melanoma. Antibodies to αv prevent human melanoma tumor formation in nude mice and antagonists of αvβ3 potentially inhibit angiogenesis in a number of animal models. Thus, blocking the αv integrin serves as an important therapeutic strategy in cancer therapy. Inhibitors of integrin function such as monoclonal antibody and peptide antagonist, which mimics the RGD ligand recognition domain common to αv integrin ligands, are now in phase II clinical trials.
ITAV-Splice Variant T5 Structure
The present inventors uncovered a novel isoform of integrin αV (ITAV; HUMVTNR_P5—SEQ ID NO:13, HUMVTNR_T5 (SEQ ID NO:15)—SEQ ID NO:15, FIGS. 12a-b) by applying LEADS clustering and assembly algorithm and the annotation process, as described above.
The ITAV splice variant T5 results from alternative splicing of the ITAV gene thereby introducing a novel exon, named exon 7a, between exons 7 and 8, leading to the insertion of a stop codon and the generation of a truncated ITAV protein (FIGS. 12-15). ITAV splice variant T5 encodes a 298 amino acids long protein which contains the N-terminal signal sequence (residues 1-30), part of the extracellular domain of WT ITAV (SEQ ID NO:131) and a unique sequence of 45 amino acids at the C-terminus of the protein (ENTEALRRKITCPKSLACNLLFRDSNGDSLTPEVFFMMLNKSFGL SEQ ID NO:14). Since the ITAV splice variant of the present invention (SEQ ID NO:13) does not include the transmembrane domain present in the WT protein (amino acids 993-1016 of the WT protein, SEQ ID NO:131), it is predicated to be a secreted protein.
Comparison Report Between HUMVTNR_P5 (SEQ ID NO:13) and ITAV_HUMAN (SEQ ID NO:131)
1. An isolated chimeric polypeptide HUMVTNR_P5 (SEQ ID NO:13), comprising a first amino acid sequence being at least 90% homologous to MAFPPRRRLRLGPRGLPLLLSGLLLPLCRAFNLDVDSPAEYSGPEGSYFGFAV DPPVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCDWSSTRRCQPIEFDATG NRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQEREPVGT CFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYW QGQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLG corresponding to amino acids 1-253 of ITAV_HUMAN (SEQ ID NO:131), which also corresponds to amino acids 1-253 of HUMVTNR_P5 (SEQ ID NO:13), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence ENTEALRRKITCPKSLACNLLFRDSNGDSLTPEVFFMMLNKSFGL (SEQ ID NO:14) corresponding to amino acids 254-298 of HUMVTNR_P5 (SEQ ID NO:13), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMVTNR_P5, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence ENTEALRRKITCPKSLACNLLFRDSNGDSLTPEVFFMMLNKSFGL (SEQ ID NO:14) in HUMVTNR_P5 (SEQ ID NO:13).
Therapeutic Applications for the ITAV Splice Variant of the Present Invention
ITAV splice variant T3 could serve as a powerful antagonist of a variety of integrin interactions. It contains most of the extracellular region of ITAV and therefore is likely to bind the integrin αv ligands. This splice variant can inhibit the integrin signaling by competing with the membrane-bound receptor for the different ligands, thus preventing their binding to the cell surface receptor and as a consequence blocking integrin activation and signaling pathway. Alternatively, it can compete with the WT membrane ITAV for binding of the β subunit, thus preventing the heterodimerization of αv with the β subunit and the subsequent signaling.
Because of the overwhelming evidence favoring the role of αv integrin in the pathogenesis of a wide array of diseases as cancer, cardiovascular and inflammation, inhibitors of this molecule, such as ITAV splice variant T5 (SEQ ID NO:13), may have an important therapeutic potential. ITAV splice variant can play a crucial role in the treatment of the following pathological conditions: cancer (in general, but in particular colon and melanoma); cardiovascular diseases, such as atherosclerosis, restenosis, ischemia and reperfusion injury; immunological related diseases such as immunodeficiency, allergies, asthma, psoriasis, RA and inflammatory bowl diseases/chrone's disease; metabolism related diseases, such as diabetes and diabetes related retinopathy; osteoporosis, sepsis and wound healing.
Thus, the present inventors uncovered a therapeutic agent which can be used to: (i) prevent the binding of endogenous integrin αv with an integrin αv ligand (e.g., ECM proteins or cell surface proteins via e.g., the RGD sequence), (ii) prevent the binding of endogenous integrin αv with a β subunit (e.g., β1, β3, β5, β6, and β8) and thus prevent integrin αv-mediated cell signaling, (iii) treat a disorder associated with integrin αv-mediated cell signaling such as cancer (e.g., colon cancer and melanoma), cardiovascular diseases (e.g., atherosclerosis, restenosis, ischemia and reperfusion injury), immunological related diseases (e.g., immunodeficiency, allergies, asthma, psoriasis, rheumatoid arthritis (RA), inflammatory bowl disease, Crohn's disease, metabolism related diseases (e.g., diabetes and diabetes related retinopathy), osteoporosis, sepsis and wound healing by preventing the binding of the endogenous αv integrin with at least one αv ligand (e.g., ECM proteins or cell surface proteins via e.g., the RGD sequence) and/or β subunit (e.g., β1, β3, β5, β6, and β8). Such an agent is a polypeptide homologous to the integrin αv (ITAV) variant of the present invention (SEQ ID NO:13), and/or a polynucleotide homologous to SEQ ID NO: 15, and/or the unique peptide derived from the ITAV variant of the present invention (SEQ ID NO:14).
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 6
Interferon-α/β-Receptor-1-INR1
Background
Type I interferons (IFNs), initially identified for their ability to protect cells from viral infections, are truly pleiotropic cytokines. IFNs are implicated in both normal and neoplastic cell growth regulation and in modulating both innate and adaptive immune responses to microbial challenge. All type I IFNs, IFN-αs, IFN-β, IFN-ω, IFN-κ, and IFN-τ, are functionally active as monomers and activate a specific receptor complex composed of two major subunits, IFNAR-1/INR1 and IFNAR-2/INR2. The high affinity interaction between IFN-α/β and its specific cell surface receptor leads to receptor aggregation and the activation of receptor-associated cytoplasmic tyrosine kinases of the Jak family-Jak1 and Tyk2. These in turn phosphorylate intracellular tyrosine residues of the IFNAR-1 and IFNAR-2 chains, that serve as recruitment sites for the signal transducers and activators of transcription (STAT) proteins, Stat 1-5. Once associated with the activated receptor, the STAT become phosphorylated and form both homodimers and heterodimers, which translocate to the nucleus and bind specific DNA sequences within the promoter regions of IFN-sensitive genes (ISG). The Jak-Stat pathway is an essential signaling pathway for the transcription of many ISGs, whose protein products mediate specific IFN-dependent biologic responses. IFNs mediate a critical role in innate cellular defense against viral infection. Mice deficient in IFN-β or in IFNAR-1 are highly susceptible to viral infections. The antiviral activity of INFs include inhibition of viral replication and protein synthesis and the induction of viral mRNA degradation. In addition to their antiviral activity, IFNs exhibit growth inhibitory activity, either by mediating cell death (through caspases) or by modulating the expression of proteins regulating cell cycle entry and exit, hence mediating growth arrest. IFNs are also involved in the regulation of immune response towards viral or tumor challenge; A well-characterized function of IFNs is their ability to upregulate MHC class I expression and consequently promote CD8+ T cell responses. Moreover, IFNs can regulate the expression of key cytokines that influence T cell responses, namely, IL-12, IL-15 and IFN-γ and of CC-chemokines. IFNs-α/β regulate the functions of immune cells from different lineages including NK cells, dentritic cells and B/T lymphocytes (Deonarain et al. 2002. Current Pharmaceutical Design. Vol. 8, No. 24, Pp. 2131-2137; Brierley et al. 2002. Journal of Interferon and Cytokine Research. 22:835-845).
Clinical Application
Due to their growth inhibitory activity and the modulation of immune responses, type I interferons have been used as therapeutic polynucleotide or polypeptide sequences against a variety of solid tumors and hematological malignancies. IFN-α has been approved for the treatment of chronic myelogenous leukemia (CML), multiple myeloma, hairy cell leukemia and several lymphomas. Thus, IFN-α is the treatment of choice for CML patients which are not eligible for allogeneic bone marrow transplantation. In addition, the therapeutic efficacy of IFNs polynucleotide or polypeptide sequences in the treatment of viral infections and autoimmune diseases has been proved. Thus, IFN-α is the treatment of choice for hepatitis B and C infections and accumulating evidence supports the use of IFN-β for the treatment of multiple sclerosis.
However, although the activity and specificity of function make the IFNs potentially powerful therapeutic agents, they are not the ideal drugs, mainly due to their low stability in vivo.
Thus, there is an intense interest and effort to develop alternative or improved molecules demonstrating IFNs function with superior pharmacological properties. For example, PEGylation of type I IFNs extends the serum half-life and duration of therapeutic activity. PEGylation of IFN-α and IFN-β increased their serum half-life by 6 and 5 fold, respectively, however the PEGylated form of IFN-β exhibited less efficient systemic distribution with some evidence of induction of neutralizing antibodies. In addition, as opposed to their well-characterized function as competitive inhibitors (antagonists), soluble receptors have been shown to exhibit agonistic properties. These include increasing the molecular internal stability of the ligand, protection from proteolysis and modification of the pharmacokinetic properties of the ligand, namely, increasing the in vivo half-life of the ligand while decreasing its clearance. Thus, a soluble form of an IFN receptor should increase the in vivo stability of the ligand (i.e., IFN) and its agonistic properties.
INR1-Splice Variant Structure
The present inventors uncovered a novel isoform of interferon α/β receptor 1 (INR1) named INR1 splice variant T12 [T07758_P6—SEQ ID NO:17 (FIG. 16B); T07758_T12—SEQ ID NO:19 (FIG. 16a)]. INR1 splice variant T12 results from alternative splicing of the INR1 gene, thus introducing a novel exon, named exon 6a, between exons 6 and 7, leading to an insertion of a stop codon and the generation of a truncated protein. INR1 splice variant T12 (SEQ ID NO:19) encodes a 269 amino acids long protein (SEQ ID NO:17) containing the N-terminal signal sequence (residues 1-27), part of the extracellular portion of the WT INR1 (INR1_HUMAN SEQ ID NO:132), including the first two fibronectin type III-like domains and part of the third domain and a unique sequence of 7 amino acids (LYFRRPR—SEQ ID NO:18) at the C-terminus of the protein. Since the INR1 variant T12 (SEQ ID NO:17) does not include the transmembrane domain (which corresponds to residues 437-457 of WT INR1 SEQ ID NO:132), it is predicated to be a secreted protein.
Comparison Report Between T07758_P6 (SEQ ID NO:17) and INR1_HUMAN_V1 (SEQ ID NO:658)
1. An isolated chimeric polypeptide T07758_P6 (SEQ ID NO:17), comprising a first amino acid sequence being at least 90% homologous to MVVLLGATTLVLVAVAPWVLSAAAGGKNLKSPQKVEVDIIDDNFILRWNRS DESVGNVTFSFDYQKTGMDNWIKLSGCQNITSTKCNFSSLKLNVYEEIKLRIR AEKENTSSWYEVDSFTPFRKAQIGPPEVHLEAEDKAIVIHISPGTKDSVMWAL DGLSFTYSLVIWKNSSGVEERIENIYSRHKIYKLSPETTYCLKVKAALLTSWKI GVYSPVHClKTTVENELPPPENIEVSVQNQNYVLKWDYTYANMTFQVQWLH corresponding to amino acids 2-263 of INR1_HUMAN_V1, which also corresponds to amino acids 1-262 of T07758_P6 (SEQ ID NO:17), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence LYFRRPR (SEQ ID NO:18) corresponding to amino acids 263-269 of T07758_P6 (SEQ ID NO:17), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of T07758_P6 (SEQ ID NO:17), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence LYFRRPR (SEQ ID NO:18) in T07758_P6 (SEQ ID NO:17).
Comparison Report Between T07758_P6 (SEQ ID NO:17) and INR1_HUMAN (SEQ ID NO:132)
1. An isolated chimeric polypeptide T07758_P6 (SEQ ID NO:17), comprising a first amino acid sequence being at least 90% homologous to MVVLLGATTLVLVAV corresponding to amino acids 2-16 of INR1_HUMAN (SEQ ID NO:132), which also corresponds to amino acids 1-15 of T07758_P6 (SEQ ID NO:17), a bridging amino acid A corresponding to amino acid 16 of T07758_P6 (SEQ ID NO:17), a second amino acid sequence being at least 90% homologous to PWVLSAAAGGKNLKSPQKVEVDIIDDNFILRWNRSDESVONVTFSFDYQKTG MDNWIKLSGCQNITSTKCNFSSLKLNVYEEIKLRIRAEKENTSSWYEVDSFTPF RKAQIGPPEVHLEAEDKAIVIHISPGTKDSVMWALDGLSFTYSL corresponding to amino acids 18-167 of INR1_HUMAN (SEQ ID NO:132), which also corresponds to amino acids 17-166 of T07758_P6 (SEQ ID NO:17), a bridging amino acid V corresponding to amino acid 167 of T07758_P6 (SEQ ID NO:17), a third amino acid sequence being at least 90% homologous to IWKNSSGVEERIENIYSRHKIYKLSPETTYCLKVKAALLTSWKIGVYSPVHCIK TTVENELPPPENIEVSVQNQNYVLKWDYTYANMTFQVQWLH corresponding to amino acids 169-263 of INR1_HUMAN (SEQ ID NO:132), which also corresponds to amino acids 168-262 of T07758_P6 (SEQ ID NO:17), and a fourth amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence LYFRRPR (SEQ ID NO:18) corresponding to amino acids 263-269 of T07758_P6 (SEQ ID NO:17), wherein said first amino acid sequence, bridging amino acid, second amino acid sequence, bridging amino acid, third amino acid sequence and fourth amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of T07758_P6 (SEQ ID NO:17), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence LYFRRPR (SEQ ID NO:18) in T07758_P6 (SEQ ID NO:17).
Therapeutic Applications for the INR1 Splice Variant T12 of the Present Invention
The INR1 splice variant T12 of the present invention encodes a soluble receptor and can serve as an agonist of the INR1 by increasing the half-life of IFNs in vivo and enhancing their biological effect. Thus, the INR1 splice variant T12 (SEQ ID NO:17) may have an important therapeutic potential for the treatment of the following pathological conditions: cancer, such as solid tumors (e.g., glioblastoma, renal cell carcinoma, melanoma) and hematological malignancies (e.g., chronic myelogenous leukemia (CML), multiple myeloma, non-Hodgkin's lymphoma and hairy cell leukemia), viral infections (e.g., hepatitis B/C, herpes and human papilloma virus) and autoimmune diseases such as multiple sclerosis.
Thus, the present inventors uncovered a therapeutic agent which can be used to: (i) increase the in vivo stability of INF (e.g., IFN-α, IFN-β, IFN-ω, IFN-κ, and IFN-τ), (ii) increase INR1-mediated signaling by stabilizing the interaction between INF (e.g., IFN-α, IFN-β, IFN-ω, IFN-κ, and IFN-τ) and INR1, (iii) treat a disorder associated with INR1 signaling such as cancer [e.g., solid tumors (glioblastoma, renal cell carcinoma, melanoma) or hematological malignancies (chronic myelogenous leukemia (CML), multiple myeloma, non-Hodgkin's lymphoma and hairy cell leukemia)], viral infections (e.g., hepatitis B, hepatitis C, herpes and human papilloma virus) and autoimmune diseases such as multiple sclerosis, by stabilizing the INF (e.g., IFN-α, IFN-β, IFN-ω, IFN-κ, and IFN-τ) or the INF-INR1 interaction. Such an agent is a polypeptide homologous to the interferon a/13 receptor 1 (INR1) variant T12 of the present invention (SEQ ID NO:17), and/or a polynucleotide homologous to SEQ ID NO:19.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 7
Overexpression of a Troponin Variant in Cancer
Background
The regulatory protein troponin (Tn) located on actin filament consists of three subunits: TnT, which binds troponin to tropomyosin, TnC, which binds divalent calcium ions, and TnI, which affects myosin-actin interactions. Tn subunits display several molecular and calcium binding variations. During ontogenetic development of cardiac and skeletal muscles the synthesis of multiple isoforms of Tn subunits was detected. Expression of Tn isoforms and the extent of phosphorylation of both TnT and TnI via protein kinase C or protein kinase A under different pathological situations (e.g. ischemia, congenital heart disease, heart failure) can affect the Ca2+-stimulated contraction function and the myofibrillar ATPase activity of the heart [Adamcova (1999) Physiol. Res. 48:235-2471. Troponin is commonly used as a marker for predicting cancer-therapy-induced cardiotoxicity. To date no reliable association has been made between cancer onset or progression and troponin expression.
By applying the teachings of the present invention, the present inventors uncovered elevated levels of novel troponin isoforms (see FIG. 24 and SEQ ID NOs:46-61) in lung, ovarian and colon cancers, suggesting the use of troponin alone or in combination with wild type troponin for diagnosis and treatment of cancer (see Examples 7a-c).
Materials and Experimental Procedures
RNA preparation—RNA was purchased from various sources including Clontech (Franklin Lakes, N.J. USA 07417), BioChain Inst. Inc., ABS or Ambion. Alternatively, RNA was purified from tissue samples using TRI-Reagent (Molecular Research Center), according to Manufacturer's instructions. Tissue samples were obtained from cancer patients or from postmortem. Total RNA samples were treated with DNaseI (Ambion) then purified using RNeasy columns (Qiagen).
RT PCR—1 μg of DNaseI-treated RNA was mixed with 150 ng of Random Hexamer primers (Invitrogen) and 500 μM dNTP in a total volume of 15.6 μl. The mixture was incubated for 5 min at 65° C. and then quickly chilled on ice. Thereafter, 5 μl of 5× SuperscriptII first strand buffer (Invitrogen), 2.4 μl of 0.1M DTT and 40 units RNasin (Promega) were added, and the mixture was incubated for 10 minutes at 25° C., followed by a 2-minutes at 42° C. Reverse transcription was effected by the addition of 1 μl (200 units) of SuperscriptII (Invitrogen) to the reaction mixture (final volume of 25 μl) and incubation at 42° C. for 50 minutes, following which the enzyme was inactivated at 70° C. for 15 minutes. The resulting cDNA was diluted 1:20 in TE (10 mM Tris pH=8, 1 mM EDTA pH=8).
Real-Time RT-PCR analysis—5 μl of diluted cDNA generated as described above were used as a template in Real-Time PCR reactions using the SYBR Green I assay (PE Applied Biosystem) with specific primers (for example, SEQ ID NOs:42 and 43). UNG Enzyme (Eurogentech Cat. No. 2L, or ABI Cat. No. D12107 or Roche Cat. No. 10232921) was also included in the reactions. The gene-specific amplification was effected as follows: 50° C. for 2 minutes, 95° C. for 10 minutes, and then 40 cycles of 95° C. for 15 seconds, followed by 60° C. for 1 minute. Detection was effected using the SDS 7000 apparatus (PE Applied Biosystem). The cycle in which the reactions achieved a threshold level (Ct) of fluorescence was registered and served to calculate the relative transcript quantity in the RT reactions. The relative quantity was calculated using the following equation: Q=efficiency^-Ct. The efficiency of the PCR reaction was calculated from a standard curve created using serial dilutions of reverse transcription (RT) reactions prepared from RNA purified from 5 cell-lines (HCT116, H1299, DU145, MCF7, ES-2). To minimize inherent differences in the RT reaction, the resulting relative quantities were normalized to the geometric mean of the relative quantities of several housekeeping genes.
Detection of the expression level of troponin isoforms in normal, benign and cancerous ovary tissues—Expression of the troponin isoforms of the present invention (S69208_unique_region; SEQ ID NO:45) was measured by real time PCR using a fragment derived therefrom (amplicon—SEQ ID NO:23, primers are set forth in SEQ ID NOs:21 and 22). In addition the expression of four housekeeping genes—PBGD (GenBank Accession No. BC019323; amplicon—SEQ ID NO:32; Forward primer—SEQ ID NO:30; Reverse primer—SEQ ID NO:31), HPRT (GenBank Accession No. NM—000194; amplicon—SEQ ID NO:29; Forward primer—SEQ ID NO:27; Reverse primer—SEQ ID NO:28), GAPDH (GenBank Accession No. BC026907; amplicon—SEQ ID NO:35; Forward primer—SEQ ID NO:33; Reverse primer—SEQ ID NO:34) and SDHA (GenBank Accession No. NM—004168; amplicon—SEQ ID NO:26; Forward primer—SEQ ID NO:24; Reverse primer—SEQ ID NO:25) was measured by real time PCR. In each RT sample, the expression level of troponin-S69208_unique_region amplicon (SEQ ID NO:23) was normalized to the geometric mean of the quantities of the housekeeping genes. The normalized quantity of each RT sample was then divided by the averaged quantity of the normal post-mortem samples (no. 45-48, 71, Table 3, hereinbelow) to obtain a value of fold up-regulation of each sample relative to averaged normal samples.
Detection of the expression level of troponin isoforms in normal and cancerous lung tissues—was performed as described hereinabove for ovary tissues except that the expression level of Ubiquitin (GenBank Accession No. BC000449; amplicon—SEQ ID NO:38; forward primer—SEQ ID NO:36; reverse primer—SEQ ID NO:37) was determined instead of that of GAPDH and was used to normalize the expression level of the troponin-S69208_unique_region amplicon (SEQ ID NO:23). The normalized quantity of each RT sample was then divided by the averaged quantity of the normal post-mortem samples (no. 47-50, 90-93, 96-99, Table 4, hereinbelow) to obtain a value of fold up-regulation of each sample relative to averaged normal samples.
Detection of the expression level of troponin isoforms in normal and cancerous colon tissues—was performed as described hereinabove for ovary tissues except that the expression level of RPS27A (GenBank Accession No. NM—002954; amplicon—SEQ ID NO:44; forward primer—SEQ ID NO:42; reverse primer—SEQ ID NO:43) and G6PD (GenBank Accession No. NM—000402; amplicon—SEQ ID NO:41; forward primer—SEQ ID NO:39; reverse primer—SEQ ID NO:40) was determined instead of that of GAPDH and SDHA and was used to normalize the expression level of the troponin-S69208_unique_region amplicon (SEQ ID NO:23). The normalized quantity of each RT sample was then divided by the averaged quantity of the normal post-mortem samples (no. 41,52,62-67, 69-71 Table 5, hereinbelow) to obtain a value of fold up-regulation of each sample relative to averaged normal samples.
Experimental Results
Expression of troponin isoforms in normal, benign and cancerous ovary tissues—As shown in FIG. 25, the expression of troponin-S69208_unique_region (SEQ ID NO:23) in normal samples (samples no. 45-52, 67-69, 71-75, Table 3, hereinbelow) and benign samples (samples 56-64, Table 2, hereinbelow) was significantly lower than in cancerous samples. Notably, troponin-S69208_unique_region up-regulation of at least 10 fold was found in 8 out of 15 adenocacinoma, 2 out of 7 Mucinus adenocarcinoma, 4 out of 9 Serous adenocarcinoma, 3 out of 5 mix serous-endometroid adenocarcinoma, 1 out of 3 endometroid adenocarcinoma, and in 2 of 2 clear-cell adenocarcinoma samples. A 10-15 fold up-regulation was observed also in 2 of the 11 matched normal samples. However, since matched samples are histologically non-cancerous tissue that surrounds the tumor, such samples could have been contaminated with cancer or pre-cancer cells.











TABLE 2





Sample name
Lot number
Source
Tissue
Pathology







2-A-Pap Adeno
ILS-1408
ABS
ovary
Papillary


G2



adenocarcinoma


3-A-Pap Adeno
ILS-1431
ABS
ovary
Papillary


G2



adenocarcinoma


4-A-Pap
ILS-7286
ABS
ovary
Papillary


CystAdeno G2



cystadenocarcinoma


1-A-Pap Adeno
ILS-1406
ABS
ovary
Papillary


G3



adenocarcinoma


14-B-Adeno G2
A501111
BioChain
ovary
Adenocarcinoma


5-G-Adeno G3
99-12-G432
GOG
ovary
Adenocarcinoma






(Stage3C)


6-A-Adeno G3
A0106
ABS
ovary
adenocarcinoma


7-A-Adeno G3
IND-00375
ABS
ovary
adenocarcinoma


8-B-Adeno G3
A501113
BioChain
ovary
adenocarcinoma


9-G-Adeno G3
99-06-G901
GOG
ovary
Adenocarcinoma






(maybe serous)


10-B-Adeno G3
A407069
Biochain
ovary
Adenocarcinoma


11-B-Adeno G3
A407068
Biochain
ovary
Adenocarcinoma


12-B-Adeno G3
A406023
Biochain
ovary
Adenocarcinoma


13-G-Adeno G3
94-05-7603
GOG
right ovary
Metastasis






adenocarcinoma


15-B-Adeno G3
A407065
BioChain
ovary
Carcinoma


16-Ct-Adeno
1090387
Clontech
ovary
Carcinoma NOS


22-A-Muc
A0139
ABS
ovary
Mucinous


CystAde G2



cystadenocarcinoma






(Stage1C)


21-G-Muc
95-10-G020
GOG
ovary
Mucinous


CystAde G2-3



cystadenocarcinoma






(Stage2)


23-A-Muc
VNM-00187
ABS
ovary
Mucinous


CystAde G3



cystadenocarcinoma






with low malignant


17-B-Muc
A504084
BioChain
ovary
Mucinous


Adeno G3



adenocarcinoma


18-B-Muc
A504083
BioChain
ovary
Mucinous


Adeno G3



adenocarcinoma


19-B-Muc
A504085
BioChain
ovary
Mucinous


Adeno G3



adenocarcinoma


20-A-Pap Muc
USA-00273
ABS
ovary
Papillary mucinous


CystAde



cystadenocarcinoma


33-B-Pap Sero
A503175
BioChain
ovary
Serous papillary


CystAde G1



cystadenocarcinoma


25-A-Pap Sero
N0021
ABS
ovary
Papillary serous


Adeno G3



adenocarcinoma






(StageT3CN1MX)


24-G-Pap Sero
2001-07-G801
GOG
ovary
Papillary serous


Adeno G3



adenocarcinoma


30-G-Pap Sero
2001-08-G011
GOG
ovary
Papillary serous


Adeno G3



carcinoma (Stage1C)


70-G-Pap Sero
95-08-G069
GOG
ovary
Papillary serous


Adeno G3



adenocarcinoma


31-B-Pap Sero
A503176
BioChain
ovary
Serous papillary


CystAde G3



cystadenocarcinoma


32-G-Pap Sero
93-09-4901
GOG
ovary
Serous papillary


CystAde G3



cystadenocarcinoma


66-G-Pap Sero
2000-01-G413
GOG
ovary
Papillary serous


Adeno G3 SIV



carcinoma (metastais






of primary peritoneum)






(Stage4)


29-G-Sero
2001-12-G035
GOG
right ovary
Serous


Adeno G3



adenocarcinoma






(Stage3A)


41-G-Mix
98-03-G803
GOG
ovary
Mixed epithelial


Sero/Muc/Endo G2



cystadenocarcinoma






with mucinous,






endometrioid,






squamous and papillary






serous (Stage2)


40-G-Mix
95-11-G006
GOG
ovary,
Papillary serous and


Sero/Endo G2


endometrium
endometrioid






cystadenocarcinoma






(Stage3C)


37-G-Mix
2002-05-G513
GOG
ovary
Mixed serous and


Sero/Endo G3



endometrioid






adenocarcinoma


38-G-Mix
2002-05-G509
GOG
ovary
Mixed serous and


Sero/Endo G3



endometrioid






adenocarcinoma of






mullerian (Stage3C)


39--G-Mix
2001-12-G037
GOG
ovary
Mixed serous and


Sero/Endo G3



endometrioid






adenocarcinoma


36-G-Endo
2000-09-G621
GOG
ovary
Endometrial


Adeno G1-2



adenocarcinoma


35-G-Endo
94-08-7604
GOG
right ovary
Endometrioid


Adeno G2



adenocarcinoma


34-G-Pap Endo
95-04-2002
GOG
ovary
Papillary endometrioid


Adeno G3



adenocarcinoma






(Stage3C)


43-G-Clear cell
2001-10-G002
GOG
ovary
Clear cell


Adeno G3



adenocarcinoma


44-G-Clear cell
2001-07-G084
GOG
ovary
Clear cell


Adeno



adenocarcinoma






(Stage3A)


42-G-Adeno
98-08-G001
GOG
ovary
Epithelial


borderline



adenocarcinoma of






borderline malignancy


59-G-Sero
98-12-G401
GOG
ovary
Serous


CysAdenoFibroma



CysAdenoFibroma


63-G-Sero
2000-10-G620
GOG
ovary
Serous


CysAdenoFibroma



CysAdenoFibroma of






borderline malignancy


64-G-Ben Sero
99-06-G039
GOG
ovary
Bengin Serous


CysAdenoma



CysAdenoma


56-G-Ben Muc
99-01-G407
GOG
left ovary
Bengin mucinus


CysAdeno



cysadenoma


62-G-Ben Muc
99-10-G442
GOG
ovary
Bengin mucinus


CysAdenoma



cysadenoma


60-G-Muc
99-01-G043
GOG
ovary
Mucinous Cysadenoma


CysAdenoma


61-G-Muc
99-07-G011
GOG
ovary
Mucinous Cysadenoma


CysAdenoma


57-B-Thecoma
A407066
BioChain
ovary
Thecoma


58-CG-Stru
CG-177
Ichilov
ovary
Struma


teratoma



ovary/monodermal






teratoma


50-B-N M8
A501114
BioChain
ovary
Normal (matched






tumor A501113)


49-B-N M14
A501112
BioChain
ovary
Normal (matched






tumor A501111)


69-G-N M24
2001-07-G801N
GOG
ovary
Normal (matched






tumor 2001-07-G801)


67-G-N M38
2002-05-509N
GOG
ovary
Normal (matched






tumor 2002-05-G509)


51-G-N M41
98-03-G803N
GOG
ovary
Normal (matched






tumor 98-03-G803)


52-G-N M42
98-08-G001N
GOG
ovary
Normal (matched






tumor 98-08-G001)


68-G-N M56
99-01-G407N
GOG
ovary
Normal (matched






bengin 99-01-G407)


72-G-N M66
2000-01-G413N
GOG
ovary
Normal (matched






tumor 2000-01-G413)


73-G-N M59
98-12-G401N
GOG
ovary
Normal (matched






tumor 98-12-G401)


74-G-N M65
97-11-G320N
GOG
ovary
Normal (matched






tumor 97-11G320)


75-G-N M60
99-01-G043N
GOG
ovary
Normal (matched






tumor 99-01-G043)


45-B-N
A503274
BioChain
ovary
Normal PM


46-B-N
A504086
BioChain
ovary
Normal PM


48-B-N
A504087
BioChain
ovary
Normal PM


47-Am-N
061P43A
Ambion
ovary
Normal PM


71-CG-N
CG-188-7
Ichilov
ovary
Normal PM









Expression level of troponin isoforms in normal and cancerous lung tissues—As shown in FIG. 26, the expression of troponin-S69208_unique_region (SEQ ID NO:23) was upregulated in several cancer samples relative to the normal samples. Specifically, troponin-S69208_unique_region up-regulation of at least 10 fold was found in 2 of 15 adenocarcinoma, 2 out of 16 squamous, 3 out of 4 large cell, and 2 out of 8 small cell samples. Notably, up-regulation of troponin-S69208_unique_region seems to be more specific to large cell tumors.












TABLE 3





Sample rename
Lot No.
Source
Pathology
Grade
Gender/age







1-B-Adeno G1
A504117
Biochain
Adenocarcinoma
1
F/29


2-B-Adeno G1
A504118
Biochain
Adenocarcinoma
1
M/64


95-B-Adeno G1
A610063
Biochain
Adenocarcinoma
1
F/54


12-B-Adeno G2
A504119
Biochain
Adenocarcinoma
2
F/74


75-B-Adeno G2
A609217
Biochain
Adenocarcinoma
2
M/65


77-B-Adeno G2
A608301
Biochain
Adenocarcinoma
2
M/44


13-B-Adeno G2-3
A504116
Biochain
Adenocarcinoma
2-3
M/64


89-B-Adeno G2-3
A609077
Biochain
Adenocarcinoma
2-3
M/62


76-B-Adeno G3
A609218
Biochain
Adenocarcinoma
3
M/57


94-B-Adeno G3
A610118
Biochain
Adenocarcinoma
3
M/68


3-CG-Adeno
CG-200
Ichilov
Adenocarcinoma

NA


14-CG-Adeno
CG-111
Ichilov
Adenocarcinoma

M/68


15-CG-Bronch adeno
CG-244
Ichilov
Bronchioloalveolar

M/74





adenocarcinoma


45-B-Alvelous Adeno
A501221
Biochain
Alveolus

F/50





carcinoma


44-B-Alvelous Adeno G2
A501123
Biochain
Alveolus
2
F/61





carcinoma


19-B-Squamous G1
A408175
Biochain
Squamous
1
M/78





carcinoma


16-B-Squamous G2
A409091
Biochain
Squamous
2
F/68





carcinoma


17-B-Squamous G2
A503183
Biochain
Squamous
2
M/57





carcinoma


21-B-Squamous G2
A503187
Biochain
Squamous
2
M/52





carcinoma


78-B-Squamous G2
A607125
Biochain
Squamous Cell
2
M/62





Carcinoma


80-B-Squamous G2
A609163
Biochain
Squamous Cell
2
M/74





Carcinoma


18-B-Squamous G2-3
A503387
Biochain
Squamous Cell
2-3
M/63





Carcinoma


81-B-Squamous G3
A609076
Biochain
Squamous
3
m/53





Carcinoma


79-B-Squamous G3
A609018
Biochain
Squamous Cell
3
M/67





Carcinoma


20-B-Squamous
A501121
Biochain
Squamous

M/64





Carcinoma


22-B-Squamous
A503386
Biochain
Squamous

M/48





Carcinoma


88-B-Squamous
A609219
Biochain
Squamous Cell

M/64





Carcinoma


100-B-Squamous
A409017
Biochain
Squamous

M/64





Carcinoma


23-CG-Squamous
CG-109 (1)
Ichilov
Squamous

M/65





Carcinoma


24-CG-Squamous
CG-123
Ichilov
Squamous

M/76





Carcinoma


25-CG-Squamous
CG-204
Ichilov
Squamous

M/72





Carcinoma


87-B-Large cell G3
A609165
Biochain
Large Cell
3
F/47





Carcinoma


38-B-Large cell
A504113
Biochain
Large cell

M/58


39-B-Large cell
A504114
Biochain
Large cell

F/35


82-B-Large cell
A609170
Biochain
Large Cell

M/68





Neuroendocrine





Carcinoma


30-B-Small cell carci G3
A501389
Biochain
small cell
3
M/34


31-B-Small cell carci G3
A501390
Biochain
small cell
3
F/59


32-B-Small cell carci G3
A501391
Biochain
small cell
3
M/30


33-B-Small cell carci G3
A504115
Biochain
small cell
3
M


86-B-Small cell carci G3
A608032
Biochain
Small Cell
3
F/52





Carcinoma


83-B-Small cell carci
A609162
Biochain
Small Cell

F/47





Carcinoma


84-B-Small cell carci
A609167
Biochain
Small Cell

F/59





Carcinoma


85-B-Small cell carci
A609169
Biochain
Small Cell

M/66





Carcinoma


46-B-N M44
A501124
Biochain
Normal M44

F/61


47-B-N
A503205
Biochain
Normal PM

M/26


48-B-N
A503206
Biochain
Normal PM

M/44


49-B-N
A503384
Biochain
Normal PM

M/27


50-B-N
A503385
Biochain
Normal PM

M/28


90-B-N
A608152
Biochain
Normal (Pool 2)

pool 2





PM


91-B-N
A607257
Biochain
Normal (Pool 2)

pool 2





PM


92-B-N
A503204
Biochain
Normal PM

m/28


93-Am-N
111P0103A
Ambion
Normal ICH

F/61


96-Am-N
36853
Ambion
Normal PM

F/43


97-Am-N
36854
Ambion
Normal PM

M/46


98-Am-N
36855
Ambion
Normal PM

F/72


99-Am-N
36856
Ambion
Normal PM

M/31









Expression of troponin isoforms in normal and cancerous colon tissues—As shown in FIG. 27, the expression of troponin-S69208_unique_region was upregulated at least 10 fold (4 samples showed at least 5 fold) in two cancer samples relative to the normal samples. One of the 3 autoimmune disease samples also showed up-regulation in the expression of troponin S69208_unique_region.











TABLE 4





Sample rename
Lot No.
Tissue
Source
Pathology







68-B-Adeno G1
A610024
Sigmoid
biochain
Adenocarcinoma




colon


58-B-Adeno G1
A609152
Colon
biochain
Adenocarcinoma


59-B-Adeno G1
A609059
Colon
biochain
Adenocarcinoma, Ulcer


14-CG-Polypoid
CG-222 (2)
Rectum
Ichilov
Well polypoid adeocarcinoma


Adeno G1 D-C



Duke's C


17-CG-Adeno
CG-163
Rectum
Ichilov
Adenocarcinoma


G1-2


10-CG-Adeno
CG-311
Sigmod
Ichilov
Adenocarcinoma Astler-Coller


G1-2 D-B2

colon

B2.


11-CG-Adeno
CG-337
Colon
Ichilov
Adenocarcinoma Astler-Coller


G1-2 D-C2



C2.


6-CG-Adeno
CG-303 (3)
Colon
Ichilov
Adenocarcinoma Astler-Coller


G1-2 D-C2



C2.


5-CG-Adeno G2
CG-308
Colon Sigma
Ichilov
Adenocarcinoma.


16-CG-Adeno
CG-278C
colon
Ichilov
Adenocarcinoma


G2


56-B-Adeno G2
A609148
Colon
biochain
Adenocarcinoma


61-B-Adeno G2
A606258
Colon
biochain
Adenocarcinoma, Ulcer


60-B-Adeno G2
A609058
Colon
biochain
Adenocarcinoma, Ulcer


22-CG-Adeno G2
CG-229C
Colon
Ichilov
Adenocarcinoma Duke's B


D-B


1-CG-Adeno G2
CG-335
Cecum
Ichilov
Adenocarcinoma Dukes B2.


D-B2


12-CG-Adeno G2
CG-340
Colon Sigma
Ichilov
Adenocarcinoma Astler-Coller


D-B2



B2.


28-CG-Adeno G2
CG-284
sigma
Ichilov
Adenocarcinoma Duke's B2


D-B2


2-CG-Adeno G2
CG-307 X2
Cecum
Ichilov
Adenocarcinoma Astler-Coller


D-C2



C2.


9-CG-Adeno G2
CG-297 X2
Rectum
Ichilov
Adenocarcinoma Dukes D.


D-D


13-CG-Adeno G2
CG-290 X2
Rectosigmodal
Ichilov
Adenocarcinoma Dukes D.


D-D

colon


26-CG-Adeno G2
CG-283
sigma
Ichilov
Colonic adenocarcinoma


D-D



Duke's D


4-CG-Adeno G3
CG-276
Colon
Ichilov
Carcinoma.


53-B-Adeno G3
A609161
Colon
biochain
Adenocarcinoma


54-B-Adeno G3
A609142
Colon
biochain
Adenocarcinoma


55-B-Adeno G3
A609144
Colon
biochain
Adenocarcinoma


57-B-Adeno G3
A609150
Colon
biochain
Adenocarcinoma


72-CG-Adeno
CG-309
colon
Ichilov
Adenocarcinoma


G3


20-CG-Adeno G3
CG-249
Colon
Ichilov
Ulcerated adenocarcinoma


D-B2



Duke's B2


7-CG-Adeno
CG-235
Rectum
Ichilov
Adenocarcinoma intramucosal


D-A



Duke's A.


23-CG-Adeno
CG-282
sigma
Ichilov
Mucinus adenocarcinoma


D-C



Astler Coller C


3-CG-Muc adeno
CG-224
Colon
Ichilov
Mucinois adenocarcinoma


D-D



Duke's D


18-CG-Adeno
CG-22C
Colon
Ichilov
Adenocarcinoma


19-CG-Adeno
CG-19C (1)
Colon
Ichilov
Adenocarcinoma


21-CG-Adeno
CG-18C
Colon
Ichilov
Adenocarcinoma


24-CG-Adeno
CG-12 (2)
Colon
Ichilov
Adenocarcinoma


25-CG-Adeno
CG-2
Colon
Ichilov
Adenocarcinoma


27-CG-Adeno
CG-4
Colon
Ichilov
Adenocarcinoma


8-CG-
CG-291
Wall of
Ichilov
Diverticolosis and


diverticolosis,

sigma

diverticulitis


diverticulitis



of the Colon


46-CG-Crohn's
CG-338C
Cecum
Ichilov
Crohn's disease


disease


47-CG-Crohn's
CG-338AC
Colon
Ichilov
Crohn's disease.


disease


42-CG-N M20
CG-249N
Colon
Ichilov
Normal


43-CG-N M8
CG-291N
Wall of
Ichilov
Normal




sigma


44-CG-N M21
CG-18N
Colon
Ichilov
Normal


45-CG-N M11
CG-337N
Colon
Ichilov
Normal


49-CG-N M14
CG-222N
Rectum
Ichilov
Normal


50-CG-N M5
CG-308N
Sigma
Ichilov
Within normal limits


51-CG-N M26
CG-283N
Sigma
Ichilov
Normal


41-B-N
A501156
Colon
biochain
Normal PM


52-CG-N
CG-309TR
Colon
Ichilov
Within normal limits


62-B-N
A608273
Colon
biochain
Normal PM


63-B-N
A609260
Colon
biochain
Normal PM


64-B-N
A609261
Colon
biochain
Normal PM


65-B-N
A607115
Colon
biochain
Normal PM


66-B-N
A609262
Colon
biochain
Normal PM


67-B-N
A406029
Colon
biochain
Normal PM (Pool 10)


69-B-N
A411078
Colon
biochain
Normal PM (Pool 10)


70-Cl-N
1110101
Colon
clontech
Normal PM (Pool of 3)


71-Am-N
071P10B
Colon
Ambion
Normal (IC BLEED)









Thus, these results demonstrate that troponin S69208_unique_region (SEQ ID NO:45) is upregulated in various cancers including lung, ovarian and colon cancers.
While reducing the present invention to practice, the present inventors have uncovered that the troponin variant of the present invention (SEQ ID NO:45), the PCR amplicon (SEQ ID NO:23) and/or the PCR primers (SEQ ID NO:21 and 22) used to detect such a variant, alone or in any combination thereof, can be used as diagnostic markers for diagnosing cancers (e.g., lung, ovarian and colon cancers). Detection of the expression level of the troponin variant of the present invention can be effected using methods immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence and the like, using an antibody directed against the troponin variant (SEQ ID NO:54), or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
While further reducing the present invention to practice, the present inventors have uncovered a method and pharmaceutical compositions for treating a troponin—related cancer (e.g., lung, ovarian and colon cancers). The method comprising downregulating the expression level and/or activity of at least one tropoinin variant, a polypeptide homologous to SEQ ID NO:54, to thereby treat the troponin—related cancer. Downregulating is effected using an agent selected from the group consisting of a troponin S69208_unique_region specific antisense oligonucleotide, a troponin S69208_unique_region specific siRNA, a troponin S69208_unique_region specific DNAzyme, a troponin S69208_unique_region specific Ribozyme, a troponin S69208_unique_region specific antibody, and a non-functional analogue of the troponin S69208_unique_region. Such an agent is provided at a therapeutic concentration along with a pharmaceutically acceptable carrier (e.g., PEG and liposomes).
Example 8
Splice Variant of Integrin Alpha-M Precursor
Background
Integrin αM associates in a non-covalent manner with β2 and generates the leukocyte membrane glycoprotein known as Mac-1, CR3, CD11b/CD18, or αMβ2-integrin. Mac-1 is one of four members of leukocyte-restricted β2-integrin family. It is expressed by granulocytes, monocytes, macrophages, dendritic cells, neutrophils eosenophils, natural killers (NKs) and some specific subsets of T and B lymphocytes. The expression and functional activity of Mac-1 is regulated during leukocyte differentiation and activation. Mac-1 is stored in intracellular vesicular compartments and is rapidly mobilized to the surface upon chemoattractants or other cellular stimuli. Mac-1 has two distinct functions; it mediates the migration of myeloid leukocytes and NKs out of blood vessels and into inflammatory sites by generating a high affinity binding site for intercellular adhesion molecule-1 (ICAM-1) expressed by activated endothelium. Additionally, as complement receptor type 3 (CR3), it mediates phagocytosis and cytotoxic degranulation in response to microorganisms or immune complexes opsonized with iC3b. It also forms complexes with other membrane glycoproteins, functioning as signal transducing partners for them. For this purpose, Mac-1 goes through series of “inside-out” and/or “outside-in” signaling steps that result in exposure of high affinity binding sites and/or an altered linkage to cytoskeletal elements (Ross, 2000, Critical Reviews in Immunology 20:197-222).
As is shown in FIG. 48, the extracellular portion of Mac-1 encompasses seven (I-VII) homologues tandem repeats (FG-GAPS). Between FG-GAP II-III there is a von Willebrand sequence that contains the I-domain, which includes the binding site for all known protein ligands of Mac-1. A conformational shift that occurs upon binding a metal cation to MIDAS (metal-ion-dependent adhesion site) is responsible for the ligand binding activity of the I-domain (Takagi and Springer, 2002, Immunological Reviews 186:141-163). Domains V-VII contain putative divalent cation binding sites (also designated EF-hands). The seven FG-GAPS fold into a β propeller structure. The extracellular C-terminal region was found to contain a lectin-like site, which was shown to mediate both adhesion and cytotoxicity. Additionally Mac-1 has a transmembrane domain and a cytoplasmic tail.
Mac-1 recognizes a wide variety of ligands including collagen, fibronectin, heparan sulfate, ICAM-1, the complement component iC3b, Neutrophil inhibitory factor (NIF), factor X, and lipopolysaccharide (LPS) [Ross, 2000 (Supra)].
Clinical Applications
Increased expression of Mac-1 on circulating leukocytes occurs in several inflammatory disorders associated with neutrophil and monocyte activation e.g., in patients with burns, sepsis, hemodialysis, systemic lupus erythromatosis, diabetes mellitus, and in coronary artery disease. Neutrophil accumulation has been also demonstrated in ischemia reperfusion injury. Mac-1 deficiencies eliminate or markedly attenuate acute cellular inflammatory responses in vivo, suggesting that blocking Mac-1 activity may attenuate the tissue damage induced by cells overexpressing Mac-1. Thus, a mAb directed against the integrin αM subunit was found to be efficient in a dog model of myocardial reperfusion injury but only if administered well before reperfusion (Mazzone and Ricevuti, 1995, Haematologica 80:161-175). In addition, a recombinant NIF was tested in a phase II clinical trial as a possible therapeutic agent for the treatment of ischemia [Ross, 2000, (Supra); Takagi and Springer, 2002 (Supra); Mazzone and Ricevuti, 1995, (Supra); Zhou et al., 1994, JBC 269:17075-17079; Ueda et al., 1994, PNAS, 91: 10680-10684].
Splice Variant Structure
The present inventors uncovered a novel splice variant of Integrin alpha M Transcript T8 (HUMLAPA_T8—SEQ ID NO:78, HUMLAPA_P8—SEQ ID NO:77; FIGS. 45a-b). The T8 splice variant results from alternative splicing of the integrin αM gene, thus introducing an extension of exon 8 leading to the insertion of a stop codon and the generation of a truncated protein (FIGS. 46-48). This splice variant (SEQ ID NO:78) encodes a 317 amino acids long protein (SEQ ID NO:77), containing 288 amino acids of the wild type sequence, and 29 unique amino acids (NAALRLMLLWRVSMWIHPPFNLQILLKSK—SEQ ID NO:79). It encompasses the FG-GAPS I and II and part of the von Willebrand domain, while lacking the FG-GAPs III-VII, the lectin domain (whose exact location is unknown), the TM and the cytoplasmic domain (see FIG. 48).
Comparison Report Between HUMLAPA_P8 and ITAM_HUMAN
1. An isolated chimeric polypeptide HUMLAPA_P8 (SEQ ID NO:77), comprising a first amino acid sequence being at least 90% homologous to MALRVLLLTALTLCHGFNLDTENAMTFQENARGFGQSVVQLQGSRVVVGAP QEIVAANQRGSLYQCDYSTGSCEPIRLQVPVEAVNMSLGLSLAATTSPPQLLA CGPTVHQTCSENTYVKGLCFLEGSNLRQQPQKFPEALRGCPQEDSDIAFLIDG SGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFIFKEFQNNPNP RSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKFGDP LGYEDVIPEADREGVIRYVIGVG corresponding to amino acids 1-288 of ITAM_HUMAN (SEQ ID NO:141), which also corresponds to amino acids 1-288 of HUMLAPA_P8 (SEQ ID NO:77), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence NAALRLMLLWRVSMWIHPPFNLQILLKSK (SEQ ID NO:79) corresponding to amino acids 289-317 of HUMLAPA_P8 (SEQ ID NO:77), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMLAPA_P8, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence NAALRLMLLWRVSMWIHPPFNLQILLKSK (SEQ ID NO:79) in HUMLAPA_P8 (SEQ ID NO:77).
Therapeutic Applications of the Variant
Three potential activities with therapeutic value could be attributed to a soluble αM molecule: (i) competing for dimerization with the β2 subunit and blocking the formation of an active αMβ2 Mac-1 integrin; (ii) competing with Mac-1 for ligand binding and blocking Mac-1-mediated adhesion; and (iii) competing with Mac-1 for binding the complement factor iC3b that mediates phagocytosis of opsonized tumor and bacterial cells.
Zhou et al. (1994, Supra) have demonstrated that recombinant soluble I-domain of αM binds fibrinogen and ICAM-1 (but not factor X) in vitro. The construct used in that work encompasses a larger region of the von Willebrand domain (Gly-127-Ala-334) that is included in the T8 variant of the present invention (SEQ ID NO:77). In addition, Ueda and colleagues (1994, Supra) have shown that immobilized recombinant (rCD11b) I-domain of CD11b is capable of binding complement component-coated erythrocytes (EAiC3b I-domain) in a dose-dependent manner and that such binding is inhibited by soluble rCD11b I-domain. Furthermore, they have shown that a short, linear, I domain peptide (residues 232-245) (i) binds the ligand in a dose dependent manner; (ii) inhibits ligand binding to immobilized rCD11b I-domain, (iii) inhibits binding of erythrocytes to rCD11b I-domain; and (iv) inhibits binding of erythrocytes to neutrophils.
Altogether, these data support a role for T8 (SEQ ID NO:77) as an antagonist of Mac-1 ligand binding and of Mac-1-dependent complement activation.
Thus, the present inventors uncovered a therapeutic agent which can be used to: (i) prevent the dimerization of endogenous αM integrin (SEQ ID NO:141) with β2 (SEQ ID NO:165) and thus block the formation of an active αMβ2 Mac-1 integrin, (ii) prevent the binding of a Mac-1 ligand [e.g., collagen, fibronectin, heparan sulfate, ICAM-1, the complement component iC3b, Neutrophil inhibitory factor (NIF), factor X, and lipopolysaccharide (LPS)] with an endogenous Mac-1 and thus block Mac-1-mediated adhesion (iii) prevent binding of endogenous Mac-1 with the complement factor iC3b and thus prevent Mac-1-mediated phagocytosis of opsonized tumor and bacterial cells, (iv) prevent and/or treat a disorder associated with increased expression of Mac-1 (e.g., increased expression on circulating leukocytes). Such an agent is a polypeptide homologous to the αM variant T8 of the present invention (SEQ ID NO:77), and/or a polynucleotide homologous to SEQ ID NO:78 and/or the peptide derived from the αM variant T8 (SEQ ID NO:79). Such an agent can prevent the binding of a Mac-1 ligand [e.g., collagen, fibronectin, heparan sulfate, ICAM-1, the complement component iC3b, Neutrophil inhibitory factor (NIF), factor X, and lipopolysaccharide (LPS)] or an endogenous β2 (SEQ ID NO:165) with the endogenous αM (SEQ ID NO:141). Non-limiting examples of disorders which can be treated according to this aspect of the present invention include burns, sepsis, hemodialysis, systemic lupus erythromatosis, diabetes mellitus, in coronary artery disease, and ischemia reperfusion injury.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 9
Splice Variant of Interferon-Alpha/Beta Receptor Beta Chain Precursor
Background
Type I interferons (IFNs; e.g., IFN-α, IFN-β, IFN-ω, IFN-κ, and IFN-τ) are implicated in both normal and neoplastic cell growth regulation and in modulating both innate and adaptive immune responses to microbial challenge. Thus ISNs exhibit antiviral, antiproliferative, immunomodulatory and developmental activities. All type I IFNs are functionally active as monomers and activate a specific receptor complex composed of two major subunits, IFNAR-1/INR1 and IFNAR-2/INR2. The high affinity interaction between IFN-α/β and its specific cell surface receptor leads to receptor aggregation and the activation of receptor-associated cytoplasmic tyrosine kinases of the Jak family-Jak1 and Tyk2. These in turn phosphorylate intracellular tyrosine residues of the IFNAR-1 and IFNAR-2 chains, that serve as recruitment sites for the signal transducers and activators of transcription (STAT) proteins, Stat 1-5. Once associated with the activated receptor, the STAT become phosphorylated and form both homodimers and heterodimers, which translocate to the nucleus and bind specific DNA sequences within the promoter regions of IFN-sensitive genes (ISG). The Jak-Stat pathway is an essential signaling pathway for the transcription of many ISGs, whose protein products mediate specific IFN-dependent biologic responses. IFNs mediate a critical role in innate cellular defense against viral infection. The antiviral activity of INFs include inhibition of viral replication and protein synthesis and the induction of viral mRNA degradation. In addition to their antiviral activity, IFNs exhibit growth inhibitory activity, either by mediating cell death (through caspases) or by modulating the expression of proteins regulating cell cycle entry and exit, hence mediating growth arrest. IFNs are also involved in the regulation of immune response towards viral or tumor challenge; A well-characterized function of IFNs is their ability to upregulate MHC class I expression and consequently promote CD8+ T cell responses. Moreover, IFNs can regulate the expression of key cytokines that influence T cell responses, namely, IL-12, IL-15 and IFN-γ and of CC-chemokines. IFNs-α/β regulate the functions of immune cells from different lineages including NK cells, dentritic cells and B/T lymphocytes (Deonarain et al. 2002. Current Pharmaceutical Design. Vol. 8, No. 24, Pp. 2131-2137; Brierley et al. 2002. Journal of Interferon and Cytokine Research. 22:835-845).
Prior attempts to inhibit the interferon mediated activities included the use of mono clonal antibodies directed against the IFNAR-2 receptor. These receptors neutralized type I IFN-mediated antiviral, antiproliferative, and major histocompatibility complex (MHC) class I upregulation functions (Novick D, et al., 2000; J. Interferon Cytokine Res. 20: 971-82).
Clinical Application
Due to their growth inhibitory activity and the modulation of immune responses, type I interferons have been used as therapeutic polynucleotide or polypeptide sequences against a variety of solid tumors and hematological malignancies. IFN-α has been approved for the treatment of chronic myelogenous leukemia (CML), multiple myeloma, hairy cell leukemia and several lymphomas. Thus, IFN-α is the treatment of choice for CML patients which are not eligible for allogeneic bone marrow transplantation. In addition, the therapeutic efficacy of IFNs polynucleotide or polypeptide sequences in the treatment of viral infections and autoimmune diseases has been proved. Thus, IFN-α is the treatment of choice for hepatitis B and C infections and accumulating evidence supports the use of IFN-β for the treatment of multiple sclerosis.
In addition, since INR2 is overexpressed in lymph nodes-tumors it can be used as a marker for lymph node tumors.
Splice Variant HSIFNABR_T14 (Transcript) Encodes a Secreted Form of INR2 (HSIFNABR_P8)
The present inventors have uncovered a new INR2 variant [HSIFNABR_P8-SEQ ID NO:155 (FIG. 96b); HSIFNABR_T14—SEQ ID NO:156 (FIG. 96a)]. The protein coordinates on the transcript start from nucleotide 361 and end at nucleotide 951 as set forth in SEQ ID NO:156 (HSIFNABR_T14 transcript).
Alignment of the new INR2 variant (HSIFNABR_P8—SEQ ID NO:155) with the WT protein (GenBank Accession No. P48551; SEQ ID NO:157) revealed that the new variant includes the first 180 amino acids as of the WT protein (GenBank Accession No. P48551) followed by a unique 17 amino acid sequence RGEDEKLDISQFCHRQAL (SEQ ID NO:158), FIG. 97]. The new variant uncovered by the present invention lacks the Cytokine receptor class 2 (IPR000282) and the transmembrane domain of the WT protein (amino acids 244-264 of GenBank Accession No. P48551) and therefore is expected to be a secreted or a soluble protein.
Comparison Report Between HSIFNABR_P8 and INR2_HUMAN
1. An isolated chimeric polypeptide HSIFNABR_P8, comprising a first amino acid sequence being at least 90% homologous to MLLSQNAFIPRSLNLVLMVYISLVFGISYDSPDYTDESCTFKISLRNFRSILSWE LKNHSIVPTHYTLLYTIMSKPEDLKVVKNCANTTRSFCDLTDEWRSTHEAYV TVLEGFSGNTTLFSCSHNFWLAIDMSFEPPEFEIVGFTNHINVMVKFPSIVEEEL QFDLSLVIEEQSEGIVKK corresponding to amino acids 1-180 of INR2_HUMAN (SEQ ID NO:157), which also corresponds to amino acids 1-180 of HSIFNABR_P8 (SEQ ID NO:155), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GEDEKLDISQFCHRQAL (SEQ ID NO:158) corresponding to amino acids 181-197 of HSIFNABR_P8 (SEQ ID NO:155), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSIFNABR_P8 (SEQ ID NO:155), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GEDEKLDISQFCHRQAL (SEQ ID NO:158) in HSIFNABR_P8 (SEQ ID NO:155).
Thus, the present inventors uncovered a therapeutic agent which can be used to: (i) increase the in vivo stability of INF (e.g., IFN-α, IFN-β, IFN-ω, IFN-κ, and IFN-τ), (ii) increase INR2-mediated signaling by stabilizing the interaction between INF (e.g., IFN-α, IFN-β, IFN-ω, IFN-κ, and IFN-τ) and INR2, (iii) treat a disorder associated with INR2 signaling such as cancer (e.g., leukaemia, chronic myelogenous, hairy cell cancer, lymphoma, non-Hodgkin's lymphoma, melanoma, myeloma, renal cancer, bone cancer, sarcoma, Kaposi's sarcoma, brain cancer, cervical cancer, head and neck cancer, skin cancer), infection [e.g., HIV/AIDS infection, coronavirus infection, prophylaxis infection, general infection, hepatitis virus infection (such as hepatitis-B, hepatitis-C), herpes simplex virus, herpes virus, human papilloma virus, varicella zoster virus], multiple sclerosis, Pemphigus, Behcet's disease, chronic fatigue syndrome, hepatic cirrhosis, fibromyalgia, pulmonary fibrosis, inflammation (brain), Keratoconjunctivitis, and macular degeneration. Such an agent is a polypeptide homologous to the INR2 variant of the present invention (HSIFNABR_P8) (SEQ ID NO: 155), and/or a polynucleotide homologous to SEQ ID NO:156, and/or a peptide homologous to GEDEKLDISQFCHRQAL (SEQ ID NO:158). It will be appreciated that such an agent can be administered per se or as part of a pharmaceutical composition along with a suitable pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Thus, the present invention provides therapeutic agents which can be used as anticancer, antifungal, antiviral, anti-HIV, anti-AIDS, immunostimulant, immunomodulator, hepatoprotective, antiinfective agents, as well as for the treatment of Multiple sclerosis, musculoskeletal, neurological, ophthalmological, respiratory and stomatological diseases.
While further reducing the present invention to practice, the present inventors have uncovered that the INR2 variant of the present invention i.e., HSIFNABR_P8 (SEQ ID NO:155), HSIFNABR_T14 (SEQ ID NO:156) or the peptide derived therefrom [GEDEKLDISQFCHRQAL (SEQ ID NO:158)] can be used as a diagnostic marker for various cancers such as lymph node tumors.
Example 10
Description for Cluster D12020
Cluster D12020 features 3 transcript(s) and 22 segment(s) of interest, the names for which are given in Tables 5 and 6, respectively, the sequences themselves are given in SEQ ID NOs: 341-343; 344-365 and 367-369, for transcripts; segments and proteins, respectively. The selected protein variants are given in Table 7.







TABLE 5







Transcripts of interest










Transcript Name
SEQ ID NO







D12020_T23
341



D12020_T31
342



D12020_T35
343

















TABLE 6







Segments of interest










Segment Name
SEQ ID NO







D12020_node_2
344



D12020_node_4
345



D12020_node_12
346



D12020_node_15
347



D12020_node_26
348



D12020_node_29
349



D12020_node_30
350



D12020_node_38
351



D12020_node_42
352



D12020_node_47
353



D12020_node_49
354



D12020_node_52
355



D12020_node_53
356



D12020_node_7
357



D12020_node_16
358



D12020_node_17
359



D12020_node_21
360



D12020_node_28
361



D12020_node_32
362



D12020_node_41
363



D12020_node_50
364



D12020_node_51
365

















TABLE 7







Proteins of interest













Corresponding


Protein Name
Protein Length
SEQ ID NO
Transcript(s)





D12020_P5
P279
367
D12020_T23


D12020_P10
P225
368
D12020_T31


D12020_P11
P130
369
D12020_T35









These sequences are variants of the known protein Tissue factor pathway inhibitor precursor (SwissProt accession identifier TFPI_HUMAN; known also according to the synonyms TFPI; Lipoprotein-associated coagulation inhibitor; LACI; Extrinsic pathway inhibitor; EPI) (SEQ ID NO:366), referred to herein as the previously known protein.
Protein Tissue factor pathway inhibitor precursor is known or believed to have the following function(s): Inhibits factor X (X(a)) directly and, in a Xa-dependent way, inhibits VIIa/tissue factor activity, presumably by forming a quaternary Xa/LACI/VIIa/TF complex. It possesses an antithrombotic action and also the ability to associate with lipoproteins in plasma. Tissue factor pathway inhibitor precursor is (“Tissue factor pathway inhibitor precursor amino acid sequence”) is set forth by SEQ ID NO:366. Known polymorphisms for this sequence are as shown in Table 8.







TABLE 8







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment











292
V → M (in dbSNP: 5940)./FTId = VAR_012004.


64
K → I: ABOLISHES INHIBITION OF VII(A)/TF.


135
R → L: ABOLISHES INHIBITION OF X(A).


227
R → L: ABOLISHES INHIBITION OF VII(A)/TF.









Protein Tissue factor pathway inhibitor precursor localization is believed to be secreted.
The previously known protein also has the following indication(s) and/or potential therapeutic use(s): haemorrhage; oedema; inflammation, pulmonary; sepsis; thrombosis; cancer. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein are as follows: angiogenesis inhibitor; elastase inhibitor; factor Xa inhibitor; kallikrein antagonist. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Anticancer; Anticoagulant; Antithrombotic; Septic shock treatment; Cardiovascular; Anti-inflammatory; Haemostatic.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: blood coagulation, which are annotation(s) related to Biological Process; proteinase inhibitor; serine protease inhibitor, which are annotation(s) related to Molecular Function; and extracellular, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
Tissue Factor Pathway Inhibitor (TFPI) is a serine protease inhibitor which inhibits factor X (X(a)) directly and, in a Xa-dependent way, inhibits VIIa/tissue factor activity, presumably by forming a quaternary Xa/LACI/VIIa/TF complex. It is anti-thrombotic and it also inhibits the extrinsic pathway complex: TF/F7/F10.
As noted above, cluster D12020 features 3 transcript(s), which were listed in Table 1 above. These transcript(s) encode for protein(s) which are variant(s) of protein Tissue factor pathway inhibitor precursor. A description of each variant protein according to the present invention is now provided.
Variant protein D12020_P5 (SEQ ID NO:367) according to the present invention is encoded by transcript(s) D12020_T23 (SEQ ID NO:341). An alignment is given to the known protein (Tissue factor pathway inhibitor precursor; SEQ ID NO:366) in FIG. 145. One or more alignments to one or more previously published protein sequences are given in FIGS. 146-147. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between D12020_P5 (SEQ ID NO:367) and TFPI_HUMAN(SEQ ID NO:366):
1. An isolated chimeric polypeptide D12020_P5 (SEQ ID NO:367), comprising a first amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence MHFGLLYACCLILPLPLLMLILRKMKNTQLSQ corresponding to amino acids 1-32 of D12020_P5 (SEQ ID NO:367), and a second amino acid sequence being at least 90% homologous to ADDGPCKAIMKRFFFNIFTRQCEEFIYGGCEGNQNRFESLEECKKMCTRDNAN RIIKTTLQQEKPDFCFLEEDPGICRGYITRYFYNNQTKQCERFKYGGCLGNMN NFETLEECKNICEDGPNGFQVDNYGTQLNAVNNSLTPQSTKVPSLFEFHGPSW CLTPADRGLCRANENRFYYNSVIGKCRPFKYSGCGGNENNFTSKQECLRACK KGFIQRISKGGLIKTKRKRKKQRVKIAYEEIFVKNM corresponding to amino acids 58-304 of TFPI_HUMAN (SEQ ID NO:366), which also corresponds to amino acids 33-279 of D12020_P5 (SEQ ID NO:367), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a head of D12020_P5 (SEQ ID NO:367), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence MHFGLLYACCLILPLPLLMLILRKMKNTQLSQ of D12020_P5.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein D12020_P5 (SEQ ID NO:367) also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 9, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein D12020_P5 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 9







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





116
Y →
No


122
T →
No


136
N →
No


144
E →
No


267
V → M
Yes









The glycosylation sites of variant protein D12020_P5 (SEQ ID NO:367), as compared to the known protein Tissue factor pathway inhibitor precursor, are described in Table 10 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 10







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





202
yes
177


203
yes
178


145
yes
120


195
yes
170









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 11:







TABLE 11







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR002223
Pancreatic trypsin
FPrintScan
125-135, 227-242,



inhibitor (Kunitz)

97-111


IPR008296
Tissue factor
HMMPIR
1-279



pathway



inhibitor


IPR002223
Pancreatic trypsin
HMMPfam
100-150, 192-242,



inhibitor (Kunitz)

30-79


IPR002223
Pancreatic trypsin
HMMSmart
190-243, 27-80,



inhibitor (Kunitz)

98-151


IPR002223
Pancreatic trypsin
ScanRegExp
128-146, 220-238,



inhibitor (Kunitz)

57-75


IPR002223
Pancreatic trypsin
BlastProDom
107-150, 199-242,



inhibitor (Kunitz)

36-82


IPR002223
Pancreatic trypsin
ProfileScan
100-150, 192-242,



inhibitor (Kunitz)

34-79









Variant protein D12020_P5 (SEQ ID NO:367) is encoded by the following transcript(s): D12020_T23 (SEQ ID NO:341). The coding portion of transcript D12020_T23 (SEQ ID NO:341) starts at position 274 and ends at position 1110. The transcript also has the following SNPs as listed in Table 12 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein D12020_P5 (SEQ ID NO:367) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 12







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












450
T → C
Yes


621
T →
No


639
A →
No


639
A → C
No


679
A →
No


704
A →
No


1072
G → A
Yes


1255
G → A
Yes


1592
T → A
Yes


2381
C → T
Yes


2465
T →
No


2482
G → A
Yes


2587
G → A
Yes


2639
A → T
Yes


2766
A → G
Yes


2870
G → A
Yes


3197
T → C
No


3430
G → A
Yes


3807
C → T
No









Variant protein D12020_P10 (SEQ ID NO:368) according to the present invention is encoded by transcript(s) D12020_T31 (SEQ ID NO:342). An alignment is given to the known protein (Tissue factor pathway inhibitor precursor), in FIG. 146. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between D12020_P10 (SEQ ID NO:368) and TFPI_HUMAN (SEQ ID NO:366):
1. An isolated chimeric polypeptide D12020_P10 (SEQ ID NO:368), comprising a first amino acid sequence being at least 90% homologous to MIYTMKKVHALWASVCLLLNLAPAPLNADSEEDEEHTIITDTELPPLKLMHSF CAFKADDGPCKAIMKREFFNIFTRQCEEFIYGGCEGNQNREESLEECKKMCTR DNANRIIKTTLQQEKPDFCFLEEDPGICRGYITRYFYNNQTKQCERFKYGGCL GNMNNFETLEECKNICEDGPNGFQVDNYGTQLNAVNNSLTPQSTKVPSLF corresponding to amino acids 1-209 of TFPI_HUMAN (SEQ ID NO:366), which also corresponds to amino acids 1-209 of D12020_P10 (SEQ ID NO:368), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GKNLVDFIASRKLLSC corresponding to amino acids 210-225 of D12020_P10 (SEQ ID NO:368), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of D12020_P10 (SEQ ID NO:368), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GKNLVDFIASRKLLSC in D12020_P10.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein D12020_P10 (SEQ ID NO:368) also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 13, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein D12020_P10 (SEQ ID NO:368) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 13







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












53
→
No


141
→
No


147
→
No


161
→
No


169
→
No









The glycosylation sites of variant protein D12020_P10 (SEQ ID NO:368), as compared to the known protein Tissue factor pathway inhibitor precursor, are described in Table 14 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 14







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





202
yes
202


203
yes
203


145
yes
145


195
yes
195









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 15:







TABLE 15







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR002223
Pancreatic trypsin
FPrintScan
51-65, 79-89,



inhibitor (Kunitz)

89-104


IPR002223
Pancreatic trypsin
HMMPfam
125-175, 54-104



inhibitor (Kunitz)


IPR002223
Pancreatic trypsin
HMMSmart
123-176, 52-105



inhibitor (Kunitz)


IPR002223
Pancreatic trypsin
ScanRegExp
153-171, 82-100



inhibitor (Kunitz)


IPR002223
Pancreatic trypsin
BlastProDom
132-175, 61-107



inhibitor (Kunitz)


IPR002223
Pancreatic trypsin
ProfileScan
125-175, 54-104



inhibitor (Kunitz)









Variant protein D12020_P10 (SEQ ID NO:368) is encoded by the following transcript(s): D12020_T31 (SEQ ID NO:342). The coding portion of transcript D12020_T31 starts at position 330 and ends at position 1004. The transcript also has the following SNPs as listed in Table 16 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein D12020_P10 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 16







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












284
T →
No


486
T →
No


581
T → C
Yes


752
T →
No


770
A →
No


770
A → C
No


810
A →
No


835
A →
No


965
T → C
Yes


1138
A → C
Yes


1196
T → C
Yes


1226
T → A
Yes









Variant protein D12020_P11 (SEQ ID NO:369) according to the present invention is encoded by transcript(s) D12020_T35 (SEQ ID NO:343). An alignment is given to the known protein (Tissue factor pathway inhibitor precursor) in 147. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between D12020_P11 (SEQ ID NO:369) and TFPI_HUMAN (SEQ ID NO:366):
1. An isolated chimeric polypeptide D12020_P11 (SEQ ID NO:369), comprising a first amino acid sequence being at least 90% homologous to MIYTMKKVHALWASVCLLLNLAPAPLNADSEEDEEHTIITDTELPPLKLMHSF CAFKADDGPCKAIMKRFFFNIFTRQCEEFIYGGCEGNQNREESLEECKKMCTR corresponding to amino acids 1-106 of TFPI_HUMAN (SEQ ID NO:366), which also corresponds to amino acids 1-106 of D12020_P11 (SEQ ID NO:369), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GRFLGTLITQDPLGLLSLIMDLII corresponding to amino acids 107-130 of D12020_P11 (SEQ ID NO:369), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of D12020_P11 (SEQ ID NO:369), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GRFLGTLITQDPLGLLSLIMDLII in D12020_P11 (SEQ ID NO:369).
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein D12020_P11 (SEQ ID NO:369) also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 17, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein D12020_P11 (SEQ ID NO:369) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 17







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












53
F →
No


110
L → P
Yes









The glycosylation sites of variant protein D12020_P11 (SEQ ID NO:369), as compared to the known protein Tissue factor pathway inhibitor precursor, are described in Table 18 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 18







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





202
no



203
no


145
no


195
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 19:







TABLE 19







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR002223
Pancreatic trypsin
FPrintScan
51-65, 79-89,



inhibitor (Kunitz)

89-104


IPR002223
Pancreatic trypsin
HMMPfam
54-104



inhibitor (Kunitz)


IPR002223
Pancreatic trypsin
HMMSmart
52-105



inhibitor (Kunitz)


IPR002223
Pancreatic trypsin
ScanRegExp
82-100



inhibitor (Kunitz)


IPR002223
Pancreatic trypsin
BlastProDom
61-106



inhibitor (Kunitz)


IPR002223
Pancreatic trypsin
ProfileScan
54-104



inhibitor (Kunitz)









Variant protein D12020_P11 (SEQ ID NO:369) is encoded by the following transcript(s): D12020_T35 (SEQ ID NO:343). The coding portion of transcript D12020_T35 (SEQ ID NO:343) starts at position 615 and ends at position 1004. The transcript also has the following SNPs as listed in Table 20 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein D12020_P11 (SEQ ID NO:369) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 20







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












284
T →
No


771
T →
No


866
T → C
Yes


943
T → C
Yes


1084
C → G
Yes









FIG. 33 summarizes the domain structures of the above variants.
Example 11
Splice Variant of Tumor Necrosis Factor Receptor Superfamily Member 14
Background
The tumor necrosis factor receptor superfamily member 14 (TR14_HUMAN; GenBank Accession No. Q92956; SEQ ID NO:161; Type I membrane protein; Herpesvirus entry mediator A; Tumor necrosis factor receptor-like 2; TR2; The HUGO gene symbol of this product: HVEA; HVEM; TNFRSF14) is a cellular receptor for TNF superfamily 14 (LIGHT) which involves in immune response, cell surface receptor linked signal transduction and apoptosis. TR14 is overexpressed in skin and can be used as a marker for proliferation of this tissue or as a marker for pathological de-differentiation of this tissue or tissue damage. In addition, since TR14 is overexpressed in skin and pancreas tumors it can be used as a marker for these pathologies.
Splice Variant Z42185_T13 (SEQ ID NO:159) Encodes a New Secreted form of the TR14 Receptor, Z42185_P5 (SEQ ID NO:160)
The present inventors have uncovered a new TR14 variant V42185_P5—SEQ
ID NO:160 (FIG. 98b); Z42185_T13—SEQ ID NO:159 (FIG. 98a)]. The protein coordinates on the transcript start from nucleotide 891 and end at nucleotide 1481 as set forth in SEQ ID NO:159 (Z42185_T13 transcript).
Alignment of the new TR14 variant (Z42185_P5—SEQ ID NO:160) with the WT protein (GenBank Accession No. Q92956; SEQ ID NO:161) revealed that the new variant includes the first 183 amino acids as of the WT protein (GenBank Accession No. Q92956) followed by a unique 14 amino acid sequence [(NWPNHMCEKKKAKG (SEQ ID NO:162), FIG. 99]. The new variant uncovered by the present invention lacks the transmembrane domain of the WT protein (amino acids 203-223 of GenBank Accession No. Q92956) and therefore is expected to be a secreted, soluble protein (i.e., extracellular).
Comparison Report Between Z42185_P5 (SEQ ID NO:160) and TR14_HUMAN (SEQ ID NO:161)
1. An isolated chimeric polypeptide Z42185_P5 (SEQ ID NO:160), comprising a first amino acid sequence being at least 90% homologous to MEPPGDWGPPPWRSTPKTDVLRLVLYLTFLGAPCYAPALPSCKEDEYPVGSE CCPKCSPGYRVKEACGELTGTVCEPCPPGTYIAHLNGLSKCLQCQMCDPAMG LRASRNCSRTENAVCGCSPGHFCIVQDGDHCAACRAYATSSPGQRVQKGGTE SQDTLCQNCPPGTFSPNGTLEECQHQT corresponding to amino acids 1-183 of TR14_HUMAN (SEQ ID NO:161), which also corresponds to amino acids 1-183 of Z42185_P5 (SEQ ID NO:160), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence NWPNHMCEKKKAKG (SEQ ID NO:162) corresponding to amino acids 184-197 of Z42185_P5 (SEQ ID NO:160), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of Z42185_P5 (SEQ ID NO:160), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence NWPNHMCEKKKAKG (SEQ ID NO:162) in Z42185_P5 (SEQ ID NO:160).
These results suggest the use of the new TR14 variant of the present invention (Z42185_P5—SEQ ID NO:160), the polynucleotide encoding same (Z42185_T13—SEQ ID NO:159) and/or the peptide derived from the Z42185_P5 TR14 variant (NWPNHMCEKKKAKG—SEQ ID NO:162) as a diagnostic marker for skin proliferation or de-differentiation, as well as skin and pancreas tumors. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the TR14 variant (Z42185_P5—SEQ ID NO:160)], nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 12
Splice Variant of Integrin Beta-2 Precursor
Background
The β2 integrin receptors (e.g., LFA-1, Mac-1, and p150,95) are expressed on leukocytes and play a major role in leukocyte cell-cell and cell-matrix adhesions during inflammation and other immune responses.
The integrin beta-2 precursor (Cell surface adhesion glycoproteins LFA-1/CR3/p150,95 beta-subunit; CD18; Complement receptor C3 beta-subunit; GenBank Accession No. P05107; ITB2_HUMAN; ITGB2) associates with an integrin α subunit (α-L, α-M, α-X, α-D) to form a Type I membrane protein receptor. Thus, integrin α-L/β-2 is a receptor for ICAM1, ICAM2, ICAM3 and ICAM4; integrins α-M/β-2 and α-X/β-2 are receptors for the iC3b fragment of the third complement component and for fibrinogen; integrin α-M/β-2 is also a receptor for factor X; integrin α-D/β-2 is a receptor for ICAM3 and VCAM1. The integrin receptors recognize specific ligands via recognition sequences such as the G-P—R in fibrinogen alpha-chain which is recognized by integrin α-X/β-2 and the P1 and P2 peptides of fibrinogen gamma chain which is recognized by integrin α-M/β-2.
Defects in ITGB2 are the cause of leukocyte adhesion deficiency type I (LAD1) [MIM:116920]. LAD1 patients have recurrent bacterial infections and their leukocytes are deficient in a wide range of adhesion-dependent functions. The integrin β-2 precursor protein contains one VWFA-like domain.
Clinical Applications
Since β2 integrin receptors are expressed on leukocytes and are involved in various cell-cell and cell-matrix adhesions during inflammation and other immune responses, inhibition of β2 integrins or the introducing of soluble forms of β2 integrins can be used as anti-inflammatory agents for the treatment of various diseases including cancers (e.g., breast cancer), coronary artery bypass grafting, haemorrhage, myocardial infarction, inflammation (e.g., pulmonary inflammation), cerebral ischaemia, osteoporosis, reperfusion injury, transplant rejection (e.g., bone marrow transplant rejection) and hepatic dysfunction.
For example, prior studies have shown that murine monoclonal antibodies directed against the CD11b/CD18 (CR3) heterodimer are capable of reducing the phagocyte-mediated ischemia-reperfusion injury in several organ systems, such as the myocardium, liver, and gastrointestinal tract, as well as inhibiting the development of insulin-dependent diabetes mellitus in nonobese diabetic (NOD) mice (Dana N, et al., 1991; Proc. Natl. Acad. Sci. USA, 88: 3106-10).
Splice Variant HUMLAP_T18 (SEQ ID NO:163) Encodes a New Secreted Form of Integrin β2, HUMLAP_P15 (SEQ ID NO:164)
The present inventors have uncovered a new integrin β2 variant [HUMLAP_P15—SEQ ID NO:164 (FIG. 100b); HUMLAP_T18SEQ ID NO:163 (FIG. 100a)]. The protein coordinates on the transcript start from nucleotide 414 and end at nucleotide 737 as set forth in SEQ ID NO:163 (HUMLAP_T18 transcript).
Alignment of the new integrin β2 variant (HUMLAP_P15—SEQ ID NO:164) with the WT protein (GenBank Accession No. P05107; SEQ ID NO:165) revealed that the new variant includes the first 49 amino acids as of the WT protein (GenBank Accession No. P05107) followed by a unique 59 amino acid sequence [G AALGPPAHATAASSPRRRSRVAPVCPRTEQGGQAPGGNYLGQAGFFPSPFWR FSAPLK (SEQ ID NO:166), FIG. 101]. The new variant uncovered by the present invention lacks the majority of the ITGB2 mature sequence (IPR002369 Integrin, beta chain IPR003659 Plexin/semaphorin/integrin) including potential sites of glycosylation and the transmembrane domain of the WT protein (amino acids 701-723 of GenBank Accession No. P05107) and therefore is expected to be a secreted, soluble and extracellular protein.
Comparison Report Between HUMLAP_P15 and ITB2_HUMAN
1. An isolated chimeric polypeptide HUMLAP_P15, comprising a first amino acid sequence being at least 90% homologous to MLGLRPPLLALVGLLSLGCVLSQECTKFKVSSCRECIESGPGCTWCQKL corresponding to amino acids 1-49 of ITB2_HUMAN (SEQ ID NO:165), which also corresponds to amino acids 1-49 of HUMLAP_P15 (SEQ ID NO:164), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GAALGPPAHATAASSPRRRSRVAPVCPRTEQGGQAPGGNYLGQAGFFPSPFW RFSAPLK (SEQ ID NO:166) corresponding to amino acids 50-108 of HUMLAP_P15 (SEQ ID NO:164), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMLAP_P15 (SEQ ID NO:164), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GAALGPPAHATAASSPRRRSRVAPVCPRTEQGGQAPGGNYLGQAGFFPSPFW RFSAPLK (SEQ ID NO:166) in HUMLAP_P15 (SEQ ID NO:164).
Clinical Applications of Using the Integrin β2 Variant of the Present Invention
Since the integrin variant of the present invention, HUMLAP_P15 (SEQ ID NO:164), is a soluble extracellular protein it can be used as an integrin β2 antagonist and/or an anti-inflammatory agent in the treatment of various diseases.
Thus, the present inventors uncovered a therapeutic agent which can be used to treat an integrin β2-related disease or condition [e.g., various cancers such as breast cancer, cardiovascular disease, coronary artery bypass grafting, haemorrhage, myocardial infraction, inflammation (e.g., pulmonary inflammation, asthma, GI inflammation, bowel disorder), cerebral ischaemia, osteoporosis, reperfusion injury, transplant rejection (e.g., bone marrow transplant rejection), psoriasis, osteoporosis treatment, respiratory disease, and hepatic dysfunction. Such an agent is a polypeptide homologous to the integrin β2 variant of the present invention (SEQ ID NO:164), and/or a polynucleotide homologous to SEQ ID NO:163, and/or a peptide homologous to SEQ ID NO:166. It will be appreciated that the polypeptide, polynucleotide and/or peptide used according to this aspect of the present can be administered or provided per se, or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
While further reducing the present invention to practice, the present inventors have uncovered that the integrin β2 variant of the present invention HUMLAP_P15 (SEQ ID NO:164), the peptide derived therefrom (SEQ ID NO:166) and/or the polynucleotide encoding same (SEQ ID NO:163), each and in any combination, can be used as diagnostic markers for various cancers including leukemia (blood malignancies) and muscle tumors. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the integrin β2 variant (SEQ ID NO:164), or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 13
Splice Variant of Integrin Beta-2 Precursor
Background
The β2 integrin receptors (e.g., LFA-1, Mac-1, and p150,95) are expressed on leukocytes and play a major role in leukocyte cell-cell and cell-matrix adhesions during inflammation and other immune responses.
The integrin beta-2 precursor (Cell surface adhesion glycoproteins LFA-1/CR3/p150,95 beta-subunit; CD18; Complement receptor C3 beta-subunit; GenBank Accession No. P05107; ITB2_HUMAN; ITGB2) associates with an integrin α subunit (α-L, α-M, α-X, α-D) to form a Type I membrane protein receptor. Thus, integrin α-L/β-2 is a receptor for ICAM1, ICAM2, ICAM3 and ICAM4; integrins α-M/β-2 and α-X/β-2 are receptors for the iC3b fragment of the third complement component and for fibrinogen; integrin α-M/β-2 is also a receptor for factor X; integrin α-D/β-2 is a receptor for ICAM3 and VCAM1. The integrin receptors recognize specific ligands via recognition sequences such as the G-P—R in fibrinogen alpha-chain which is recognized by integrin α-X/β-2 and the P1 and P2 peptides of fibrinogen gamma chain which is recognized by integrin α-M/β-2.
Defects in ITGB2 are the cause of leukocyte adhesion deficiency type I (LAD1) [MIM:116920]. LAD1 patients have recurrent bacterial infections and their leukocytes are deficient in a wide range of adhesion-dependent functions. The integrin β-2 precursor protein contains one VWFA-like domain.
Clinical Applications
Since β2 integrin receptors are expressed on leukocytes and are involved in various cell-cell and cell-matrix adhesions during inflammation and other immune responses, inhibition of β2 integrins or the introducing of soluble forms of β2 integrins can be used as anti-inflammatory agents for the treatment of various diseases including cancers (e.g., breast cancer), coronary artery bypass grafting, haemorrhage, myocardial infarction, inflammation (e.g., pulmonary inflammation), cerebral ischaemia, osteoporosis, reperfusion injury, transplant rejection (e.g., bone marrow transplant rejection) and hepatic dysfunction.
For example, prior studies have shown that murine monoclonal antibodies directed against the CD11b/CD18 (CR3) heterodimer are capable of reducing the phagocyte-mediated ischemia-reperfusion injury in several organ systems, such as the myocardium, liver, and gastrointestinal tract, as well as inhibiting the development of insulin-dependent diabetes mellitus in nonobese diabetic (NOD) mice (Dana N, et al., 1991; Proc. Natl. Acad. Sci. USA, 88: 3106-10).
Splice Variant HUMLAP_T14 (SEQ ID NO:167) Encodes a New Secreted Form of Integrin β2, HUMLAP_P12 (SEQ ID NO:168)
The present inventors have uncovered a new integrin β2 variant [HUMLAP_P12 (SEQ ID NO:168); HUMLAP_T14 (SEQ ID NO:167)]. The protein coordinates on the transcript start from nucleotide 414 and end at nucleotide 1229 as set forth in SEQ ID NO:167 (HUMLAP_T14 transcript).
Alignment of the new integrin β2 variant (HUMLAP_P12—SEQ ID NO:168) with the WT protein (GenBank Accession No. P05107; SEQ ID NO:165) revealed that the new variant includes the first 217 amino acids as of the WT protein (GenBank Accession No. P05107) followed by a unique 55 amino acid sequence [SALKMTAMAGRVLLGARRGDSSTLTGTVFAWRLEEGGLEVGEVRCVFPVQ VRTSV (SEQ ID NO:169), FIG. 102]. The new variant uncovered by the present invention lacks the majority of the ITGB2 mature sequence (IPR002369 Integrin, beta chain), exhibits a truncated VWFA-like domain (amino acids 124-363 of GenBank Accession No. P05107) and lacks the transmembrane domain of the WT protein (amino acids 701-723 of GenBank Accession No. P05107) and therefore is expected to be a secreted, soluble and extracellular protein.
Comparison Report Between HUMLAP_P12 and ITB2_HUMAN
1. An isolated chimeric polypeptide HUMLAP_P12, comprising a first amino acid sequence being at least 90% homologous to MLGLRPPLLALVGLLSLGCVLSQECTKFKVSSCRECIESGPGCTWCQKLNFTG PGDPDSIRCDTRPQLLMRGCAADDIMDPTSLAETQEDHNGGQKQLSPQKVTL YLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDDLRNVKKLGGDLLRA LNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPFAFRHVLKL TNNSNQF corresponding to amino acids 1-217 of ITB2_HUMAN (SEQ ID NO:165), which also corresponds to amino acids 1-217 of HUMLAP_P12 (SEQ ID NO:168), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 90% homologous to a polypeptide having the sequence SALKMTAMAGRVLLGARRGDSSTLTGTVFAWRLEEGGLEVGEVRCVFPVQV RTSV (SEQ ID NO:169) corresponding to amino acids 218-272 of HUMLAP_P12 (SEQ ID NO:168), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMLAP_P12 (SEQ ID NO:168), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence SALKMTAMAGRVLLGARRGDSSTLTGTVFAWRLEEGGLEVGEVRCVFPVQV RTSV (SEQ ID NO:169) in HUMLAP_P12 (SEQ ID NO:168).
Clinical Applications of Using the Integrin β2 Variant of the Present Invention
Since the integrin variant of the present invention, HUMLAP_P12 (SEQ ID NO:168), is a soluble extracellular protein it can be used as an integrin β2 antagonist and/or an anti-inflammatory agent in the treatment of various diseases.
Thus, the present inventors uncovered a therapeutic agent which can be used to treat an integrin β2-related disease or condition [e.g., various cancers such as breast cancer, cardiovascular disease, coronary artery bypass grafting, haemorrhage, myocardial infraction, inflammation (e.g., pulmonary inflammation, asthma, GI inflammation, bowel disorder), cerebral ischaemia, osteoporosis, reperfusion injury, transplant rejection (e.g., bone marrow transplant rejection), psoriasis, osteoporosis treatment, respiratory disease, and hepatic dysfunction. Such an agent is a polypeptide homologous to the integrin β2 variant of the present invention (SEQ ID NO:168), and/or a polynucleotide homologous to SEQ ID NO:167, and/or a peptide homologous to SEQ ID NO:169. It will be appreciated that the polypeptide, polynucleotide and/or peptide used according to this aspect of the present can be administered or provided per se, or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
While further reducing the present invention to practice, the present inventors have uncovered that the integrin β2 variant of the present invention HUMLAP_P12 (SEQ ID NO:168), the peptide derived therefrom (SEQ ID NO:169) and/or the polynucleotide encoding same (SEQ ID NO:167), each and in any combination, can be used as diagnostic markers for various cancers including leukemia (blood malignancies) and muscle tumors.
Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the integrin β2 variant (SEQ ID NO:168), or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 14
Splice Variant of Low Affinity Immunoglobulin Gamma Fc Region Receptor III-A Precursor
Background
An essential element in the regulation of immune effector responses is via the antibody Fc receptors (FcRs) which are expressed or displayed in immune effectors. Fc receptors belong to the immunoglobulin superfamily, and have been shown to mediate the removal of antibody-coated pathogens by phagocytosis of immune complexes and the lysis of erythrocytes and various other cellular targets (e.g. tumor cells) coated with the corresponding antibody, via antibody dependent cell mediated cytotoxicity (ADCC) [Van de Winkel and Anderson, J. Leuk. Biol. 49:511-24 (1991)]. One subclass of Fc receptors includes the Fc gamma receptors, which are specific for the IgG antibodies. These include the FcγRI (CD64), FcγRII (CD32) and FcγRIII (CD16). FcγRIII is a low-affinity receptor interacting with complexed or aggregated IgG.
The Fc region receptor III-A precursor Low affinity immunoglobulin gamma Fc region receptor III-A precursor (IgG FC receptor III-2; Fc-gamma RIII-alpha; FcRIIIA; CD16-A; FcR-10), is a type-I membrane protein, which, following proteolytic cleavage can exist as a soluble receptor [e.g., neutrophil-derived soluble FcRIII (S-FcRIII)]. It is expressed on natural killer cells, macrophages, mast cells, subpopulation of T cells, immature thymocytes and placental trophoblasts. The protein contains an extracellular domain (amino acids 17-208), Ig-like C2 type 1 and 2 domains (amino acids 24-105 and 107-189, respectively), five potential glycosylation sites (amino acids 56, 63, 92, 180 and 187), two potential disulfide bonds (amino acids 47, 89; and 128, 172), a transmembrane domain (amino acids 209-229) and a potential cytoplasmic domain (amino acids 230-254); all amino acids positions relate to GenBank Accession No. P08637; SEQ ID NO:173).
Clinical Applications
The FcγRII-A exhibits an important role in the immune response. It may be involved in various diseases or conditions such as allergy reactions, anaemia, rheumatoid arthritis, asthma, inflammation, lupus erythematosus, thrombocytopenia, and thrombocytopenic purpura. In addition, abnormal accumulation of CD16+ cells was associated with large granular lymphocyte proliferative disease (Blancho G, et al., 1992, Transplantation, 53(6):1242-7) and the kidney allograft failure.
Splice Variant HUMGCRFC_T4 (SEQ ID NO:170) Encodes a New Secreted Form of FCγRIII-A, HUMGCRFC_P3 (SEQ ID NO:171)
The present inventors have uncovered a new FCγRIII-A variant [HUMGCRFC_P3 (SEQ ID NO:171); HUMGCRFC_T4 (SEQ ID NO:170)]. The protein coordinates on the transcript start from nucleotide 106 and end at nucleotide 465 as set forth in SEQ ID NO:170 (HUMGCRFC_T4 transcript).
Alignment of the new FCγRIII-A variant (HUMGCRFC_P3—SEQ ID NO:171) with the WT protein (GenBank Accession No.; SEQ ID NO:173) revealed that the new variant includes the first 107 amino acids as of the WT protein (GenBank Accession No. P08637) followed by a unique 13 amino acid sequence [ELMKGKRKITNKG (SEQ ID NO:172), FIG. 103]. The new variant uncovered by the present invention lacks the Immunoglobulin/major histocompatibility complex (IPR003006) and the Immunoglobulin subtype (IPR003599) and therefore is expected to be a secreted, soluble and extracellular protein.
Comparison Report Between HUMGCRFC_P3 and FC3A_HUMAN
1. An isolated chimeric polypeptide HUMGCRFC_P3 (SEQ ID NO:171), comprising a first amino acid sequence being at least 90% homologous to MWQLLLPTALLLLVSAGMRTEDLPKAVVFLEPQWYRVLEKDSVTLKCQGAY SPEDNSTQWFHNESLISSQASSYFIDAATVDDSGEYRCQTNLSTLSDPVQLEV HIG corresponding to amino acids 1-107 of FC3A_HUMAN (SEQ ID NO:173), which also corresponds to amino acids 1-107 of HUMGCRFC_P3 (SEQ ID NO:171), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence ELMKGKRKITNKG (SEQ ID NO:172) corresponding to amino acids 108-120 of HUMGCRFC_P3 (SEQ ID NO:171), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMGCRFC_P3 (SEQ ID NO:171), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence ELMKGKRKITNKG (SEQ ID NO:172) in HUMGCRFC_P3 (SEQ ID NO:171).
Splice Variant HUMGCRFC_T5 (SEQ ID NO:174) Encodes a New Secreted Form of the FCγRIII-A, HUMGCRFC_P4 (SEQ ID NO:175)
The present inventors have uncovered a new FCγRIII-A variant [HUMGCRFC_T5—SEQ ID NO:174; HUMGCRFC_P4—SEQ ID NO:1751. The protein coordinates on the transcript start from nucleotide 106 and end at nucleotide 483 as set forth in SEQ ID NO:174 (HUMGCRFC_T5 transcript).
Alignment of the new FCγRIII-A variant (HUMGCRFC_P4—SEQ ID NO:175) with the WT protein (GenBank Accession No. P08637; FC3A_HUMAN; SEQ ID NO:173) revealed that the new variant includes the first 107 amino acids as of the WT protein (GenBank Accession No. P08637) followed by a unique 19 amino acid sequence [PFPTMTSCSLFVKSDYLVT (SEQ ID NO:176), FIG. 104]. The new variant uncovered by the present invention lacks the immunoglobulin/major histocompatibility complex (IPR003006) and immunoglobulin subtype (IPR003599) domain of the WT protein and therefore is expected to be a secreted, soluble protein (i.e., extracellular).
Comparison Report Between HUMGCRFC_P4 (SEQ ID NO:175) and FC3A_HUMAN (SEQ ID NO:173)
1. An isolated chimeric polypeptide HUMGCRFC_P4 (SEQ ID NO:175), comprising a first amino acid sequence being at least 90% homologous to MWQLLLPTALLLLVSAGMRTEDLPKAVVFLEPQWYRVLEKDSVTLKCQGAY SPEDNSTQWFHNESLISSQASSYFIDAATVDDSGEYRCQTNLSTLSDPVQLEV HIG corresponding to amino acids 1-107 of FC3A_HUMAN (SEQ ID NO:173), which also corresponds to amino acids 1-107 of HUMGCRFC_P4 (SEQ ID NO:175), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least % homologous to a polypeptide having the sequence PFPTMTSCSLFVKSDYLVT (SEQ ID NO:176) corresponding to amino acids 108-126 of HUMGCRFC_P4 (SEQ ID NO:175), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMGCRFC_P4 (SEQ ID NO:175), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence PFPTMTSCSLFVKSDYLVT (SEQ ID NO:176) in HUMGCRFC_P4 (SEQ ID NO:175).
Clinical Applications of the New FORM-A Variants
Since the variants uncovered by the present inventors, HUMGCRFC_P3 (SEQ ID NO:171) and HUMGCRFC_P4 (SEQ ID NO:175), include the first 107 amino acids of the WT FCγRIII-A, but yet, are missing the transmembrane domain and the immunoglobulin/major histocompatibility complex and immunoglobulin subtype domains, they can be used as antagonists for the endogenous FCγRIII-A. Thus, the FCγRIII-A variants of the present invention, SEQ ID NO:171 and/or SEQ ID NO:175 can be used as an anti-inflammatory, antiallergic, anti-asthma, antianaemic, antithrombotic, antiarthritic agent as well as an immunological, a cytokine, and an immunosuppressant agent.
Thus, the present inventors uncovered a therapeutic agent which can be used to treat inflammation, allergy, asthma, anaemic, thrombosis, and/or arthritis. Such an agent is a polypeptide homologous to SEQ ID NO:171 or 175, and/or a polynucleotide homologous to SEQ ID NO:174 or 170.
While further reducing the present invention to practice, the new variants of the present invention (HUMGCRFC_P3—SEQ ID NO:171 and/or HUMGCRFC_P4—SEQ ID NO: 175), the polynucleotide encoding same (HUMGCRFC_T4 (SEQ ID NO:170 and/or HUMGCRFC_T5—SEQ ID NO:174) and/or the peptide(s) derived from such variants (SEQ ID NO:172 and/or 176) can be used as diagnostic markers for allergy reactions, anaemia, rheumatoid arthritis, asthma, inflammation, lupus erythematosus, thrombocytopenia, thrombocytopenic purpura, large granular lymphocyte proliferative disease, and/or susceptibility to allograft failure (e.g., kidney allograft failure). Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the HUMGCRFC_P3 and/or HUMGCRFC_P4 (SEQ ID NO:171 and/or 175, respectively), or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 15
Splice Variant of Tumor Necrosis Factor Receptor Superfamily Member 3 Precursor
Background
Lymphotoxin-β receptor (LT-βR) is a member of the tumor necrosis factor receptor (TNFR) superfamily and is expressed on the surface of most of cell types, including cells of epithelial and myeloid lineages but not on T and B lymphocytes. LT-βR can specifically bind two ligands: the membrane form of lymphotoxin, LT-α1/β2, which is uniquely expressed on activated lymphoid cells and LIGHT, a member of the TNF superfamily, which is induced on the cell surface during T cell activation. LT-βR has been speculated to play an essential role in the development of lymphoid organs. Thus, LT-β knock-out mice exhibit impaired lymph node development and loss of splenic architecture. In addition, LT-βR deficient mice were found to lack Peyer's patches, colon-associated lymphoid tissues and all lymph nodes. Moreover, stimulation of LT-βR on certain cell lines by LT-α1/β2 or anti-LTβR antibodies was found to induce cell death, chemokine secretion, and activation of nuclear factor κB (NFκB), suggesting an important biological function for LT-βR in mature individuals.
Like other members of the TNF receptor family, the cytoplasmic domain (CD) of LT-βR does not include consensus sequences characteristic of enzymatic activity. Thus, signaling is thought to be mediated by the proteins interacting with LT-βR such as the two serine/threonine protein kinases, p50 and p80 and the two members of the TNF receptor-associated factor (TRAF) family, TRAF3 and TRAF5, which specifically associate with the LT-βR(CD). Further study has indicated that TRAF3 plays an important role in mediating LT-βR-induced apoptosis, whereas TRAF5 involves in the activation of NFκB. On the other hand, several members of the TNFR superfamily (such as TNFRI, Fas, DR3, DR4, and DR5) contain a common motif, the death domain, in their cytoplasmic region that initiate the activation of caspase cascades to execute apoptosis. LT-βR(CD) does not contain a death domain, but signaling through LT-βR can also induce apoptosis. It was shown that the cytoplasmic domain of TNFRI can self-associate through its death domain, therefore overexpression of TNFRI or of the cytoplasmic domain thereof can induce receptor clustering, a crucial step for subsequent intracellular signaling. Despite the absence of the death domain, the LT-βR(CD) is capable of self-association. Thus, overexpression of LT-βR is sufficient to trigger apoptosis without the need for ligand conjugation (Tamada et al. 2002. The Journal of Clinical Investigation. Vol. 109, No. 4, Pp. 549-557; Shao et al. 2003. Eur. J. Immunol. 33:1736-1743; Ettinger et al. 1996. Proc. Natl. Acad. Sci. USA. Vol. 93, Pp. 13102-13107; Wu et al. 1999. The Journal of Biological Chemistry. Vol. 274, No. 17, Pp. 11868-11873; Hehlgans et al. 2002. Cancer Research 62:4034-4040).
Clinical Application
It has been shown that signaling through LT-βR induced cell death in some human adenocarcinoma tumor lines (HT-29 and WiDr) in the presence of IFN-γ. Combined in vivo treatment of human adenocarcinoma cells (WiDr), which form solid tumors in immunocompromised mice, with an agonistic anti-LT-βR antibody and human IFN-γ resulted in tumor growth arrest. Contrary to these findings, it has been shown that activation of LT-βR on fibrosarcoma tumor cells is necessary for angiogenesis and solid tumor growth. Prevention of LT-α1/β2-LT-βR signaling, by the release of LTβR-Fc from the tumor cells, inhibited tumor angiogenesis and neovascularization, and resulted in tumor growth arrest in mice. In addition, LT-βR activation on the tumor cells induced enhanced release of MIP-2, an angiogenic CXC chemokine. Thus, the interaction of activated LT-α1/β2-carrying lymphocytes with LT-βR-expressing tumor cells can initiate a novel pro-angiogenic pathway, leading to organized tumor tissue development. In addition to its modulation of tumor growth, LT-βR was shown to be involved in immune regulation. In vivo blockade of LIGHT and LTα1/β2 by administration of soluble lymphotoxin β receptor-Ig (LTβR-Ig) inhibited the cytotoxic T lymphocyte (CTL) response to host antigenic disparities and ameliorated lethal graft-versus-host disease (GVHD) in a B6 to BDF1 mouse model. In addition, it has been shown that treatment of rodents with the fusion protein, LT-βR-Ig, prevents the development of autoimmune diseases as insulitis and uveitis.
TNR3-LT-βR Splice Variant T2 Structure
A brief description is now provided of TNR3-LT-βR splice variants according to the present invention. TNR3 splice variant transcript—2 (HUMTNFRRP_T2—SEQ ID NO:177; HUMTNFRRP_P2—SEQ ID NO:178). The protein coordinates on the transcript start from nucleotide 261 and end at nucleotide 1025 as set forth in SEQ ID NO:177.
TNR3 splice variant T2 results from alternative splicing of the TNR3 gene, introducing a novel exon, named exon 6a, between exons 6 and 7, leading to an insertion of a stop codon and the generation of a truncated protein. TNR3 splice variant T2 encodes a 255 amino acids long protein (HUMTNFRRP_P2—SEQ ID NO:178) which contains the N-terminal signal sequence (residues 1-30), the complete extracellular domain of TNR3, including all the TNFR CYS repeats, and a unique sequence of 33 amino acids [EPALSKGVENLQALLYQAATGSSEASFPTLSPL (SEQ ID NO:179), FIG. 105] at the C-terminus of the protein. However, as can see using the alignment with the WT sequence (TNR3_HUMAN; SEQ ID NO:129), the new variant uncovered by the present invention lacks the transmembrane domain (amino acids 228-248 of SEQ ID NO:129) and therefore is expected to be a secreted, soluble and extracellular protein.
Comparison Report Between HUMTNFRRP_P2 (SEQ ID NO:178) and TNR3_HUMAN (SEQ ID NO:129)
1. An isolated chimeric polypeptide HUMTNFRRP_P2 (SEQ ID NO:178), comprising a first amino acid sequence being at least 90% homologous to MLLPWATSAPGLAWGPLVLGLFGLLAASQPQAVPPYASENQTCRDQEKEYY EPQHRICCSRCPPGTYVSAKCSRIRDTVCATCAENSYNEHWNYLTICQLCRPC DPVMGLEEIAPCTSKRKTQCRCQPGMFCAAWALECTHCELLSDCPPGTEAEL KDEVGKGNNHCVPCKAGHFQNTSSPSARCQPHTRCENQGLVEAAPGTAQSD TTCKNPLEPLPPEMS corresponding to amino acids 1-222 of TNR3_HUMAN (SEQ ID NO:129), which also corresponds to amino acids 1-222 of HUMTNFRRP_P2 (SEQ ID NO:178), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence EPALSKGVENLQALLYQAATGSSEASFPTLSPL (SEQ ID NO:179) corresponding to amino acids 223-255 of HUMTNFRRP_P2 (SEQ ID NO:178), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMTNFRRP_P2 (SEQ ID NO:178), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence EPALSKGVENLQALLYQAATGSSEASFPTLSPL (SEQ ID NO:179) in HUMTNFRRP_P2 (SEQ ID NO:178).
TNR3-LT-βR Splice Variant T18 Structure
TNR3 splice variant transcript—18 (HUMTNFRRP_T18—SEQ ID NO:180; HUMTNFRRP_P2—SEQ ID NO:178). The protein coordinates on the transcript start from nucleotide 261 and end at nucleotide 1025 as set forth in SEQ ID NO:180. The protein encoded by this transcript (SEQ ID NO:180) is identical to the protein encoded by HUMTNFRRP_T2—SEQ ID NO:177, and is referred to herein as HUMTNFRRP_P2—SEQ ID NO:178.
The Therapeutic Potential of TNR3-LT-βR Splice Variants T2 and T18
TNR3 splice variants T2 and T18, each encode a soluble receptor which contains all four TNFR CYS repeats of the WT or known protein (TNR3_HUMAN; SEQ ID NO:129), but yet is a soluble, secreted protein. It can inhibit TNR3 signaling by competing on the ligand with the membrane-bound receptor, thus preventing LT-α1/β2 from binding to the cell surface receptor and activating it. A soluble form of TNR3 was shown already to bind LT-α1/β2 in vitro. Blocking LTαβ/TNR3 interactions was shown in vivo by administration of TNR3-Fc fusion protein or by the creation of mice which constitutively express a soluble murine TNR3-human IgG1 (Fc) transgene. Blocking TNR3 signaling could have important therapeutic potential for the treatment of cancer, graft-vs-host disease and autoimmune diseases, such as rheumatoid arthritis, Crohn's disease, insulitis and uveitis.
Thus, the TNR3 HUMTNFRRP_P2 (SEQ ID NO:178) of the present invention, the polynucleotide encoding same (TNR3 splice variants T2 and T18, SEQ ID NOs:177 and 180, respectively) and/or the unique peptide derived from the TNR3 HUMTNFRRP_P2 variant of the present invention (SEQ ID NO:179) can serve as a TNFR3 antagonist.
The present inventors uncovered a therapeutic agent which can be used to: (i) inhibit or prevent the binding of LT-α1/β2 to its TNR3 receptor in vivo or ex vivo, (ii) prevent tumor growth (e.g., solid tumor, such as fibrisarcoma) by preventing the activation of LT-βR, (iii) prevent and/or treat graft-versus-host disease (GVHD) by inhibition of the cytotoxic T lymphocyte (CTL) response, (iv) prevent and/or treat autoimmune diseases (e.g., insulitis, uveitis), (v) prevent and/or treat Crohn's disease, rheumatoid arthritis. Such an agent is a polypeptide homologous to HUMTNFRRP_P2 (SEQ ID NO:178), and/or a polynucleotide homologous to SEQ ID NO: 177 or 180 and/or a peptide homologous to SEQ ID NO:179). It will be appreciated that the polypeptide, polynucleotide and/or peptide used according to this aspect of the present can be administered or provided per se, or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
While further reducing the present invention to practice, the present inventor have uncovered that the TNR3 variant of the present invention is overexpressed in various cancers (e.g., stomach tumor) and therefore can be used as a diagnostic marker for such pathologies.
Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the HUMTNFRRP_P2 variant (SEQ ID NO:178), or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 16
Splice Variant of Granulocyte Colony Stimulating Factor Receptor Precursor (G-CSF-R)
Background
The granulocyte colony stimulating factor receptor precursor (G-CSF-R) (CD114 antigen, GCSR_HUMAN; GenBank Accession No. Q99062) is a type I membrane protein which involves in cell adhesion, signal transduction, and defense response.
Clinical Applications
G-CSF-R has been implicated in anaemia, various cancers such as, breast cancer, leukaemia, acute myelogenous, leukaemia, lymphoma, melanoma, sarcoma, chemotherapy-induced injury, bone marrow, bone marrow leucopenia, bone marrow neutropenia, immunodeficiency, and infections.
The G-CSF-R is overexpressed in amniotic cells and placenta and thus can be used as a marker for cell proliferation in these tissues and as a marker for pathological de-differentiation of these tissues.
Splice Variant HSGCSFR2_T14 (SEQ ID NO:181) Encodes a New Secreted Form of the G-CSF-R, HSGCSFR2_P11 (SEQ ID NO:182)
The present inventors have uncovered a new G-CSF-R variant [HSGCSFR2_P11—SEQ ID NO:182; HSGCSFR2_T14—SEQ ID NO:181]. The protein coordinates on the transcript start from nucleotide 551 and end at nucleotide 2320 as set forth in SEQ ID NO:181 (HSGCSFR2_T14 transcript).
Alignment of the new G-CSF-R variant HSGCSFR2_P11—SEQ ID NO:182) with the WT protein (GenBank Accession No. Q99062; GCSR_HUMAN; SEQ ID NO:183) revealed that the new variant includes the first 525 amino acids as of the WT protein (GenBank Accession No. Q99062) followed by a unique 65 amino acid sequence [GLSTIRPLSRILSSLSQGSAWSPAIRSIGNIAFLPYFQPWRGSLPIPW LTLDPYSWTEIRCWDRN (SEQ ID NO:184), FIG. 106]. The new variant uncovered by the present invention lacks the fibronectin type-III domain (IPR003961; amino acids 527-618 in WT; SEQ ID NO:183) and the transmembrane domain (amino acids 628-650 of GenBank Accession No. Q99062; SEQ ID NO:183) of the WT protein and therefore is expected to be a secreted, soluble protein (i.e., extracellular).
Comparison Report Between HSGCSFR2_P11 and GCSR_HUMAN
1. An isolated chimeric polypeptide HSGCSFR2_P11 (SEQ ID NO:182), comprising a first amino acid sequence being at least 90% homologous to MARLGNCSLTWAALIILLLPGSLEECGHISVSAPIVHLGDPITASCIIKQNCSHL DPEPQILWRLGAELQPGGRQQRLSDGTQESIITLPHLNHTQAFLSCCLNWGNS LQILDQVELRAGYPPAIPHNLSCLMNLTTSSLICQWEPGPETHLPTSFTLKSFKS RGNCQTQGDSILDCVPKDGQSHCCIPRKHLLLYQNMGIWVQAENALGTSMSP QLCLDPMDVVKLEPPMLRTMDPSPEAAPPQAGCLQLCWEPWQPGLHINQKC ELRHKPQRGEASWALVGPLPLEALQYELCGLLPATAYTLQIRCIRWPLPGHW SDWSPSLELRTTERAPTVRLDTWWRQRQLDPRTVQLFWKPVPLEEDSGRIQG YVVSWRPSGQAGAILPLCNTTELSCTFHLPSEAQEVALVAYNSAGTSRPTPVV FSESRGPALTRLHAMARDPHSLWVGWEPPNPWPQGYVIEWGLGPPSASNSN KTWRMEQNGRATGFLLKENIRPFQLYEIIVTPLYQDTMGPSQHVYAYSQEM corresponding to amino acids 1-525 of GCSR_HUMAN (SEQ ID NO:183), which also corresponds to amino acids 1-525 of HSGCSFR2_P11 (SEQ ID NO:182), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GLSTIRPLSRILSSLSQGSAWSPAIRSIGNIAFLPYFQPWRGSLPIPWLTLDPYSW TEIRCWDRN (SEQ ID NO:184) corresponding to amino acids 526-590 of HSGCSFR2_P11 (SEQ ID NO:182), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSGCSFR2_P11 (SEQ ID NO:182), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GLSTIRPLSRILSSLSQGSAWSPAIRSIGNIAFLPYFQPWRGSLPIPWLTLDPYSW TEIRCWDRN (SEQ ID NO:184) in HSGCSFR2_P11 (SEQ ID NO:182).
Splice Variant HSGCSFR2_T8 (SEQ ID NO:185) Encodes a New Secreted Form of the G-CSF-R, HSGCSFR2_P7 (SEQ ID NO:186)
The present inventors have uncovered a new G-CSF-R variant [HSGCSFR2_P7—SEQ ID NO:186; HSGCSFR2_T8—SEQ ID NO:185]. The protein coordinates on the transcript start from nucleotide 551 and end at nucleotide 2281 as set forth in SEQ ID NO:185 (HSGCSFR2_T8 transcript).
Alignment of the new G-CSF-R variant (HSGCSFR2_P7—SEQ ID NO:186) with the WT protein (GenBank Accession No. Q99062; SEQ ID NO:183) revealed that the new variant includes the first 574 amino acids as of the WT protein (GenBank Accession No. Q99062) and is missing 66 amino acid sequence [SAILNASSRGFVLHGLEPASLYHIHLMAASQAGATNSTVLTLMTLTPEGSELH IILGLFGLLLLLT (SEQ ID NO:187), FIG. 107]. The new variant uncovered by the present invention exhibits a truncated fibronectin type-III domain (IPR003961; amino acids 527-618 in WT; GenBank Accession No. Q99062) and lacks the transmembrane domain of the WT protein (amino acids 628-650 of GenBank Accession No. Q99062) and therefore is expected to be a secreted, soluble protein (i.e., extracellular).
Comparison Report Between HSGCSFR2_P7 and GCSR_HUMAN
1. An isolated chimeric polypeptide HSGCSFR2_P7, comprising a first amino acid sequence being at least 90% homologous to MARLGNCSLTWAALIILLLPGSLEECGHISVSAPIVHLGDPITASCIIKQNCSHL DPEPQILWRLGAELQPGGRQQRLSDGTQESIITLPHLNHTQAFLSCCLNWGNS LQILDQVELRAGYPPAIPHNLSCLMNLTTSSLICQWEPGPETHLPTSFTLKSFKS RGNCQTQGDSILDCVPKDGQSHCCIPRKHLLLYQNMGIWVQAENALGTSMSP QLCLDPMDVVKLEPPMLRTMDPSPEAAPPQAGCLQLCWEPWQPGLHINQKC ELRHKPQRGEASWALVGPLPLEALQYELCGLLPATAYTLQIRCIRWPLPGHW SDWSPSLELRTTERAPTVRLDTWWRQRQLDPRTVQLFWKPVPLEEDSGRIQG YVVSWRPSGQAGAILPLCNTTELSCTFHLPSEAQEVALVAYNSAGTSRPTPVV FSESRGPALTRLHAMARDPHSLWVGWEPPNPWPQGYVIEWGLGPPSASNSN KTWRMEQNGRATGFLLKENIRPFQLYEIIVTPLYQDTMGPSQHVYAYSQEMA PSHAPELHLKHIGKTWAQLEWVPEPPELGKSPLTHYTIFWTNAQNQSF corresponding to amino acids 1-574 of GCSR_HUMAN (SEQ ID NO:183), which also corresponds to amino acids 1-574 of HSGCSFR2_P7 (SEQ ID NO:186), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence CLC corresponding to amino acids 575-577 of HSGCSFR2_P7 (SEQ ID NO:186), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
Splice Variant HSGCSFR2_T9 (SEQ ID NO:188) Encodes a New Secreted Form of the G-CSF-R, HSGCSFR2_P8 (SEQ ID NO:189)
The present inventors have uncovered a new G-CSF-R variant [HSGCSFR2_P8—SEQ ID NO:189; HSGCSFR2_T9—SEQ ID NO:188]. The protein coordinates on the transcript start from nucleotide 551 and end at nucleotide 2365 as set forth in SEQ ID NO:188 (HSGCSFR2_T9 transcript).
Alignment of the new G-CSF-R variant (HSGCSFR2_P8—SEQ ID NO:189) with the WT protein (GenBank Accession No. Q99062; SEQ ID NO:183) revealed that the new variant includes the first 574 amino acids as of the WT protein (GenBank Accession No. Q99062), followed by 31 amino acid sequence [CESILSSPTAPEGLEGGAQLPRRQLYHPGLC (SEQ ID NO:190), FIG. 108]. The new variant uncovered by the present invention exhibits a truncated fibronectin type-III domain (IPR003961; amino acids 527-618 in WT; GenBank Accession No. Q99062) and lacks the transmembrane domain of the WT protein (amino acids 628-650 of GenBank Accession No. Q99062) and therefore is expected to be a secreted, soluble protein (i.e., extracellular).
Comparison Report Between HSGCSFR2_P8 and GCSR_HUMAN
1. An isolated chimeric polypeptide HSGCSFR2_P8 (SEQ ID NO:189), comprising a first amino acid sequence being at least 90% homologous to MARLGNCSLTWAALIILLLPGSLEECGHISVSAPIVHLGDPITASCIIKQNCSHL DPEPQILWRLGAELQPGGRQQRLSDGTQESIITLPHLNHTQAFLSCCLNWGNS LQILDQVELRAGYPPAIPHNLSCLMNLTTSSLICQWEPGPETHLPTSFTLKSFKS RGNCQTQGDSILDCVPKDGQSHCCIPRKHLLLYQNMGIWVQAENALGTSMSP QLCLDPMDVVKLEPPMLRTMDPSPEAAPPQAGCLQLCWEPWQPGLHINQKC ELRHKPQRGEASWALVGPLPLEALQYELCGLLPATAYTLQIRCIRWPLPGHW SDWSPSLELRTTERAPTVRLDTWWRQRQLDPRTVQLFWKPVPLEEDSGRIQG YVVSWRPSGQAGAILPLCNTTELSCTFHLPSEAQEVALVAYNSAGTSRPTPVV FSESRGPALTRLHAMARDPHSLWVGWEPPNPWPQGYVIEWGLGPPSASNSN KTWRMEQNGRATGFLLKENIRPFQLYEIIVTPLYQDTMGPSQHVYAYSQEMA PSHAPELHLKHIGKTWAQLEWVPEPPELGKSPLTHYTIFWTNAQNQSF corresponding to amino acids 1-574 of GCSR_HUMAN (SEQ ID NO:183), which also corresponds to amino acids 1-574 of HSGCSFR2_P8 (SEQ ID NO:189), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence CESILSSPTAPEGLEGGAQLPRRQLYHPGLC (SEQ ID NO:190) corresponding to amino acids 575-605 of HSGCSFR2_P8 (SEQ ID NO:189), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSGCSFR2_P8 (SEQ ID NO:189), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence CESILSSPTAPEGLEGGAQLPRRQLYHPGLC (SEQ ID NO:190) in HSGCSFR2_P8 (SEQ ID NO:189).
The expected pharmacological activity of the soluble G-CSF-R variants of the present invention (HSGCSFR2_P11, HSGCSFR2_P7 and HSGCSFR2_P8) are agonists of the granulocyte stimulating factor.
These results suggest the use of the new G-CSF-R variants of the present invention [HSGCSFR2_P11 (SEQ ID NO:182), HSGCSFR2_P7 (SEQ ID NO:186), and/or HSGCSFR2_P8 (SEQ ID NO:189)], the polynucleotides encoding same [HSGCSFR2_T14 (SEQ ID NO:181), HSGCSFR2_T8 (SEQ ID NO:185) and/or HSGCSFR2_T9 (SEQ ID NO:188)] and/or the peptides derived from the HSGCSFR2_P11 variant (SEQ ID NO:184) and/or the HSGCSFR2_P8 (SEQ ID NO:190) as a diagnostic marker for amniotic and/or placental cell proliferation or de-differentiation, as well as various tumors. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the G-CSF-R variant (HSGCSFR2_P11—SEQ ID NO:182], nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Moreover, G-CSF-R is implicated in various hematological and immunological conditions. Thus, the present inventors have uncovered that the new soluble form of G-CSF-R which can be used as an antianaemic, anticancer, immunomodulator, anti-infective, immunostimulant, radio or chemoprotective, anti-AIDS therapeutic agent.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 17
Splice Variant of E-Selectin Precursor
Background
E-selectin (CD62E, ELAM-1) is a member of the selectins (CD62) family which also includes L-selectin (CD62L, LECAM-1, LAM-1) and P-selectin (CD62P, GMP140, PADGEM). E-selectin participates in recruiting leukocytes to sites of inflammation. Its expression is restricted in most cases to venules in site of acute and chronic inflammation and it was found to be expressed on cytokine-(TNFα, IL-1) activated endothelial cells. Furthermore, it is rapidly (within 4 hours) expressed on postcapillary venules in animal models of inflammation, supporting a role for this protein in the initial stages of the inflammatory response such as neutrophil recruitment. However, it seems that E-selectin expression is necessary but insufficient for T cell emigration into skin. Furthermore, E-selectin has some functional redundancy with P-selectin as in a model of DTH (T cell-mediated delayed type hypersensitivity) in E-selectin null mice P-selectin can compensate for the inflammatory response. Although upregulated upon stimulation by inflammatory cytokines, constitutive low levels of E-selectin expression appear to play a role in normal leukocyte trafficking.
Structurally, E-selectin contains an N-terminal C-type lectin domain (also designated carbohydrate-recognition domain, CRD), followed by an epidermal growth factor (EGF)-like domain, six short consensus repeats (SCRs, also designated sushi), a transmembrane domain, and a short cytoplasmic tail. The lectin domain of E-selectin is required for carbohydrate binding. However, mutagenesis studies have shown that although the c-lectin and EGF-like domains are the minimal functional unit, the presence of the six SCRs yields the most potent molecule in terms of binding of the E-selectin to cell surface and in inhibition of adhesion (Li et al., 1994).
Several cell types interact with E-selectin-expressing endothelium including myeloid cells, neutrophils, monocytes and certain subsets of lymphocytes (CD4, CD8 and memory). This interaction occurs via the recognition of carbohydrated, usually sialyl Lewis x (SLex)-bearing selectin ligands, including PSGL-1 (P-selectin glycoprotein ligand-1), L-selectin and CLA (cutaneous lymphocyte associated antigen).
Clinical Applications
Chronic inflammation that results from unregulated leukocyte interaction with the endothelium is reported in ischemia-reperfusion, rheumatoid arthritis, asthma, atherosclerosis, and multiple sclerosis. Additionally, E-selectin over expression and/or CLA+ T cell infiltrates have been associated with a number of chronic skin diseases such as atopic dermatitis, psoriasis, allergic contact dermatitis, cutaneous T cell lymphoma and other diseases (Rossiter et al., 1997). The chronic inflammatory response associated with overexpression of selectins is due, at least in part, to increased cytokine production by extravasated T cells that have encountered antigen and became activated Inhibition of extravasation by blocking selectins could prevent the initial accumulation in tissue, thereby preventing the subsequent production of cytokines. Interestingly, studies employing selectin knock out mice have shown that E-selectin null mice lacks a pathogenic phenotype (Frenette and Wagner, 1997).
E-selectin interaction with carbohydrates (mainly sialyl Lewis a but also x) have also been implicated in formation of metastases of several cancer cells. High amounts of sialyl Lewis (a) are present in human adenocarcinomas of the colon, pancreas and stomach. There are several lines of evidence showing that sialyl Lewis (a) is responsible for the adhesion of human cancer cells to endothelium. E-selectin present on endothelial cells mediates these interactions. Thus, E-selectin antagonists might block E-selectin/cancer cell contact and reduce the metastatic potential of the cancer cells (Ugorski and Laskowska, 2002). Additionally, E-selectin expression was shown to be involved in lymphocyte recruitment to the skin of patients with GvHD (Lange et al., 1995).
Elevated serum levels of soluble E-selectin could serve as a diagnostic marker of chronic inflammatory diseases and cancer as high levels of soluble E-selectin have been described in patients suffering from type II diabetes (Matsumoto et al., 2002), rheumatoid arthritis (Klimiuk et al., 2002), asthma (Hamzaoui et al., 2001), lupus, sepsis (Egerer et al., 2000), and colorectal and breast cancer (Ito et al., 2001, Matsuura et al., 1997). Furthermore, suppression of experimental lupus nephritis by elevated expression of soluble E-selectin in transgenic mice was reported (Takahashi et al., 2002), indicating that soluble E-selectin could also serve as a therapeutic protein in inflammation-associated diseases, even if high levels of the soluble molecules are present in the serum of these patients.
Splice Variant Structure
The present inventors uncovered a novel splice variant of E-selectin (HUMELAM1A_P2—SEQ ID NO:65 and HUMELAM1A_T1—SEQ ID NO:66; FIGS. 37b and a, respectively). The splice variant HUMELAM1A_T1 was obtained by the alternative splicing of the E-selectin gene resulting in extension of exon 4 leading to an insertion of a stop codon and the generation of a truncated protein (FIGS. 38-40). This splice variant encodes 189 amino acids long protein (SEQ ID NO:65), which contains 176 amino acids of the wild type sequence, and a unique sequence of 13 amino acids (SKSGSCLFLHLRW; SEQ ID NO:67). It encompasses the C-type lectin domain, the EGF-like domain, but lacks the six SCR (sushi) domains, the TM and the cytoplasmic domain. The variant retains the potential glycosylation sites relevant to the domains it encompasses.
Comparison Report Between HUMELAM1A_P2 (SEQ ID NO:65) and LEM2_HUMAN (SEQ ID NO:139)
1. An isolated chimeric polypeptide HUMELAM1A_P2 (SEQ ID NO:65), comprising a first amino acid sequence being at least 90% homologous to MIASQFLSALTLVLLIKESGAWSYNTSTEAMTYDEASAYCQQRYTHLVAIQN KEEIEYLNSILSYSPSYYWIGIRKVNNVWVWVGTQKPLTEEAKNWAPGEPNN RQKDEDCVEIYIKREKDVGMWNDERCSKKKLALCYTAACTNTSCSGHGECV ETINNYTCKCDPGFSGLKCEQ corresponding to amino acids 1-176 of LEM2_HUMAN (SEQ ID NO:139), which also corresponds to amino acids 1-176 of HUMELAM1A_P2 (SEQ ID NO:65), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence SKSGSCLFLHLRW (SEQ ID NO:67) corresponding to amino acids 177-189 of HUMELAM1A_P2 (SEQ ID NO:65), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMELAM1A_P2 (SEQ ID NO:65), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence SKSGSCLFLHLRW (SEQ ID NO:67) in HUMELAM1A_P2 (SEQ ID NO:65).
Therapeutic Application of the Splice Variant
E-selectin splice variant T1 contains the lectin-like domain and the EGF-like domain. As it lacks the transmembrane domain, it is predicted to be a soluble protein. Mutagenesis studies have shown that the lectin-like domain and the EGF-like domains contain the sites important for ligand binding. Thus, this variant is predicted to serve as an antagonist for E-selectin activity. However, as described above, the presence of the SCR domains elevate the activity of E-selectin constructs. Furthermore, a work by Lo and colleagues have shown that recombinant soluble E-selectin (comprised of the C-lectin, EGF-like and six SCR domains) serves as a chemoattractant for PMN and that immobilization of the recombinant E-selectin result in integrin activation. Taken together, these data demonstrate that the E-selectin variant T1 will be a very weak antagonist for leukocyte-endothelium interaction and might simultaneously serve a weak adhesion molecule if immobilized to the matrix.
Both agonist and antagonist for E-selectin are described in the pharma project. Most antagonists are antibodies and some of them are chemical or synthetic nucleic acid based molecules, which are designed to treat chronic inflammatory diseases and allergies, as well as cancer. The agonist is reported to be on preclinical status for treatment of ischemia.
Thus, the E-selectin variant of the present invention, the polypeptide, HUMELAM1A_P2 (SEQ ID NO:65), the polynucleotide encoding same, HUMELAM1A_T1 (SEQ ID NO:66) and/or the peptide derived from the splice variant of the present invention (SEQ ID NO:67) is an antagonist for leukocyte-endothelium interaction and thereby can be used as a therapeutic agent to treat various disorders such as chronic inflammation (e.g., ischemia-reperfusion, rheumatoid arthritis, asthma, atherosclerosis, and multiple sclerosis), chronic skin diseases (such as atopic dermatitis, psoriasis, allergic contact dermatitis, cutaneous T cell lymphoma).
According to another aspect of the present invention, the E-selectin variant of the present invention, the polypetide, HUMELAM1A_P2 (SEQ ID NO:65), the polynucleotide encoding same, HUMELAM1A_T1 (SEQ ID NO:66) and/or the peptide derived from the splice variant of the present invention (SEQ ID NO:67) is an antagonist for the E-selectin interaction with carbohydrates and thus can be used as a therapeutic agent to prevent the formation of metastases of several cancer cells (e.g., adenocarcinomas of the colon, pancreas and stomach) and/or prevent the adhesion of human cancer cells to endothelium.
Without being bound to any theory, the E-selectin variant of the present invention, the polypetide, HUMELAM1A_P2 (SEQ ID NO:65), the polynucleotide encoding same, HUMELAM1A_T1 (SEQ ID NO:66) and/or the peptide derived from the splice variant of the present invention (SEQ ID NO:67) is an E-selectin agonist and thus can be used as a therapeutic agent for the treatment of ischemia.
It will be appreciated that such agent(s) can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
According to another aspect of the present invention, the E-selectin variant of the present invention, the polypetide, HUMELAM1A_P2 (SEQ ID NO:65), the polynucleotide encoding same, HUMELAM1A_T1 (SEQ ID NO:66) and/or the peptide derived from the splice variant of the present invention (SEQ ID NO:67) are diagnostic marker(s) for chronic inflammatory diseases (e.g., type II diabetes, rheumatoid arthritis, asthma, lupus, sepsis) and cancers (e.g., colorectal and breast cancer).
Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the HUMELAM1A_P2 (SEQ ID NO:65) variant, or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 18
Splice Variant of Integrin Alpha-L Precursor
Background
Integrin αL (CD11a) forms a heterodimer with integrin β2 (CD18) to generate LFA-1. LFA-1 functions as an intercellular adhesion receptor and as a co-stimulatory and signaling molecule. It mediates the interaction between cytotoxic T cells and their targets, and functions in T and B cells as a mitogen, and in B cells as an inducer of B cell aggregation and Ig production. It interacts with ICAM-1 (CD54), ICAM-2 (CD102), ICAM-3 (CD54), ICAM-4 (Landsteiner-Weiner antigen), or ICAM-5 (telencephalin). High levels of LFA-1 are constitutively expressed on lymphocytes and monocytes, and lower levels on neutrophils. The ability of LFA-1 to interact with its ligands and transmit signals across the plasma membrane is regulated by a variety of extracellular and intracellular factors. These include agents that alter integrin affinity or avidity such as divalent cations Mg2+, Ca2+, Mn2+, the state of cell activation, intracellular Ca2+ release, activation of PKC, and ligands themselves. The regulation of LFA-1 activity by these factors avoid inappropriate adhesion while these cells are circulating in blood or migrating in tissues.
Structurally, the extracellular region of LFA-1 contains seven homologues tandem repeats (I-VII) that fold as a β propeller. Domains V-VII contain putative divalent cation binding sites also designated EF-hands. Between repeats II and III there is insertion of  ̃200 amino acids, known as the I domain, which is considered to be functionally implicated in binding of ligands and cations and contains a discontinued MIDAS. The extracellular portion of integrin αL contains 12 potential N-glycosylation sites and seven disulfide bonds.
Mouse knock out model of integrin αL displays defects in T cell proliferation and cytotoxicity and in tumor rejection but lymphocyte homing, leukocyte extravasation and thymic maturation and selection do not seem to be defected (Cabanas and Sanchez-Madrid, 1999).
Clinical Applications
Inhibition of CD11a, LFA-1, or its ligand have been shown to be a useful target for therapy of several inflammatory situations associated with accumulation of leukocytes leading to clot formation or cytotoxicity. Monoclonal Abs to CD11a, ICAM-1, and CD18 were comparably effective in a rabbit model of myocardial reperfusion injury and reduced infract size by 40-50%, but only if administered well before reperfusion. Reducing cytotoxic T cell activity by mAbs to CD11a/CD18, in combination with standard immunosuppressive therapy, improve the survival of bone marrow transplants in children but not in adults. In a mouse model, anti CD11a mAbs increased the survival of allogenic tumor grafts. LFA-1 might also be involved in cancer metastasis as its expression on hematological tumor cells have been shown to alter metastatic capacity and growth (Mazzone and Richevuti, 1995).
Anti CD11a mAb is a registered drug for treatment of psoriasis (Cabanas and Sanchez-Madrid, 1999 J Biol Regul Homeost Agents 13: 126-129; Mazzone and Richevuti, 1995 Hematologic a 80:161-175; Ihanus et al., 2003 Eur J Biochem 270: 1710-1723; McDowell et al., 1998 JBC 273: 27396-27403; Binnerts et al., 1996 JBC 271: 9962-9968.)
Splice Variant Structure
The present inventors uncovered a novel splice variant of integrin αL (T83460_T11—SEQ ID NO:81; T83460_P8—SEQ ID NO:80; FIGS. 49a and b, respectively). The T11 splice variant (T83460_T11) obtained by the alternative splicing of the integrin αL gene result in extension of exon 18 leading to an insertion of a stop codon and the generation of a truncated protein (FIGS. 50-51). This splice variant encodes 750 amino acids long protein (SEQ ID NO:80), which contains 745 amino acids of the wild type sequence, and 5 unique amino acids (VRRDG; SEQ ID NO:82). It encompasses the FG-GAPS I and VII, while lacking the TM and the cytoplasmic domain. It contains seven out of 12 potential N-glycosilation sites and four out of seven disulfide bonds.
Comparison Report Between T83460_P8 (SEQ ID NO:80) and ITAL_HUMAN_V1 (SEQ ID NO:653)
1. An isolated chimeric polypeptide T83460_P8 (SEQ ID NO:80), comprising a first amino acid sequence being at least 90% homologous to MKDSCITVMAMALLSGFFFFAPASSYNLDVRGARSFSPPRAGRHFGYRVLQV GNGVIVGAPGEGNSTGSLYQCQSGTGHCLPVTLRGSNYTSKYLGMTLATDPT DGSILACDPGLSRTCDQNTYLSGLCYLFRQNLQGPMLQGRPGFQECIKGNVD LVFLFDGSMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSYKTEFDFS DYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIII TDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTF EKLKDLFTELQKKIYVIEGTSKQDLTSFNMELSSSGISADLSRGHAVVGAVGA KDWAGGFLDLKADLQDDTFIGNEPLTPEVRAGYLGYTVTWLPSRQKTSLLAS GAPRYQHMGRVLLFQEPQGGGHWSQVQTIHGTQIGSYFGGELCGVDVDQDG ETELLLIGAPLFYGEQRGGRVFIYQRRQLGFEEVSELQGDPGYPLGRFGEAITA LTDINGDGLVDVAVGAPLEEQGAVYIFNGRHGGLSPQPSQRIEGTQVLSGIQW FGRSIHGVKDLEGDGLADVAVGAESQMIVLSSRPVVDMVTLMSFSPAEIPVH EVECSYSTSNKMKEGVNITICFQIKSLIPQFQGRLVANLTYTLQLDGHRTRRRG LFPGGRHELRRNIAVTTSMSCTDFSFHFPVCVQDLISPINVSLNFSLWEEEGTP RDQRA corresponding to amino acids 1-745 of ITAL_HUMAN_V1 (SEQ ID NO:653), which also corresponds to amino acids 1-745 of T83460_P8 (SEQ ID NO:80), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VRRDG (SEQ ID NO:82) corresponding to amino acids 746-750 of T83460_P8 (SEQ ID NO:80), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of T83460_P8 (SEQ ID NO:80), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VRRDG (SEQ ID NO:82) in T83460_P8 (SEQ ID NO:80).
Comparison Report Between T83460_P8 (SEQ ID NO:80) and ITAL_HUMAN (SEQ ID NO:142)
1. An isolated chimeric polypeptide T83460_P8 (SEQ ID NO:80), comprising a first amino acid sequence being at least 90% homologous to MKDSCITVMAMALLSGFFFFAPASSYNLDVRGARSFSPPRAGRHFGYRVLQV GNGVIVGAPGEGNSTGSLYQCQSGTGHCLPVTLRGSNYTSKYLGMTLATDPT DGSILACDPGLSRTCDQNTYLSGLCYLFRQNLQGPMLQGRPGFQECIKGNVD LVFLFDGSMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSYKTEFDFS DYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIII TDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTF EKLKDLFTELQKKIYVIEGTSKQDLTSFNMELSSSGISADLSRGHAVVGAVGA KDWAGGFLDLKADLQDDTFIGNEPLTPEVRAGYLGYTVTWLPSRQKTSLLAS GAPRYQHMGRVLLFQEPQGGGHWSQVQTIHGTQIGSYFGGELCGVDVDQDG ETELLLIGAPLFYGEQRGGRVFIYQRRQLGFEEVSELQGDPGYPLGRFGEAITA LTDINGDGLVDVAVGAPLEEQGAVYIFNGRHGGLSPQPSQRIEGTQVLSGIQW FGRSIHGVKDLEGDGLADVAVGAESQMIVLSSRPVVDMVTLMSFSPAEIPVH EVECSYSTSNKMKEGVNITICFQIKSL corresponding to amino acids 1-659 of ITAL_HUMAN (SEQ ID NO:142), which also corresponds to amino acids 1-659 of T83460_P8 (SEQ ID NO:80), a bridging amino acid I corresponding to amino acid 660 of T83460_P8 (SEQ ID NO:80), a second amino acid sequence being at least 90% homologous to PQFQGRLVANLTYTLQLDGHRTRRRGLFPGGRHELRRNIAVTTSMSCTDFSFH FPVCVQDLISPINVSLNFSLWEEEGTPRDQRA corresponding to amino acids 661-745 of ITAL_HUMAN (SEQ ID NO:142), which also corresponds to amino acids 661-745 of T83460_P8 (SEQ ID NO:80), and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VRRDG (SEQ ID NO:82) corresponding to amino acids 746-750 of T83460_P8 (SEQ ID NO:80), wherein said first amino acid sequence, bridging amino acid, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of T83460_P8 (SEQ ID NO:80), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VRRDG (SEQ ID NO:82) in T83460_P8 (SEQ ID NO:80).
Therapeutic Applications of the Variant
Immobilized recombinant CD11a I-domain fused to GST was shown to bind ICAM-4 positive cells (Ihanus et al., 2003). In addition, McDowell et al. have shown that recombinant soluble form of CD11a I domain inhibits the binding of Mg2+ activated T cells (high affinity binding) but not phorbol ester-activated T cells (low affinity) to ICAM-1. The conclusion drown from this study suggests that the I domain is involved in a conformational change which is necessary for binding activity and that soluble I domain (or its fragments) interferes with interdomain alterations or intersubunit associations and thereby prevent changes in the quarternary structure of LFA-1. Accordingly, T11, which encompass the whole I domain as well as the MIDAS, is predicted to function as an antagonist of LFA-1 activity and to inhibit leukocyte adhesion to LFA-1 substrates. As the I domains for different ligands are overlapping but not identical (Ihanus et al., 2003), the antagonistic activity of T11 will probably be non-ligand specific.
Thus, a soluble αL variant, i.e., a polypeptide homologous to SEQ ID NO:80, a polynucleotide homologous to SEQ ID NO:81, and/or a peptide homologous to SEQ ID NO:82 is an antagonist of LFA-1 activity.
Thus, the present inventors uncovered a therapeutic agent which can be used to: (i) inhibit leukocyte adhesion to LFA-1 substrates, (ii) prevent the interaction between cytotoxic T cell and their targets, (iii) inhibit leukocyte accumulation associated with inflammation. Such an agent can be used (i) in the treatment of reperfusion injury, (ii) as an immunosuppressant (by reducing cytotoxic T cell activity) in transplantations, (iii) in the treatment of psoriasis. Such an agent is a polypeptide homologous to SEQ ID NO:80, and/or a polynucleotide homologous to SEQ ID NO:81 and/or a peptide homologous to SEQ ID NO:82.
Example 19
Splice Variant of Macrophage Inflammatory Protein-2-Beta Precursor
Background
The macrophage inflammatory protein-2-beta precursor (MIP2-beta; CXCL3; Growth regulated protein gamma; GRO-gamma; GRO3; GROG; SCYB3) is a secreted protein exhibiting chemokine activity for neutrophils. MIP2-β may have a role in inflammation and immune response and exerts its effects on endothelial cells in an autocrine fashion. In vitro studies showed that a processed polypeptide having amino acids 5-73 of the WT protein (GenBank Accession NO. P19876) exhibits a 5-fold higher chemotactic activity for neutrophilic granulocytes, suggesting a functional role for this part of the protein.
MIP2-β is overexpressed in lung and can be used as a marker for proliferation of this tissue or as a marker for pathological de-differentiation of this tissue or tissue damage.
Splice Variant T11329_T1 (SEQ ID NO:191) Encodes a New Secreted Form of the MIP2-β, T11329_P2 (SEQ ID NO:192)
The present inventors have uncovered a new MIP2-β variant [T11329_T1-SEQ ID NO:191; T11329_P2—SEQ ID NO:1921. The protein coordinates on the transcript start from nucleotide 84 and end at nucleotide 614 as set forth in SEQ ID NO:191 (T11329_T1 transcript).
Alignment of the new MIP2-β variant (T11329_P2—SEQ ID NO:192) with the WT protein (GenBank Accession No. P19876; SEQ ID NO:193) revealed that the new variant includes additional 103 amino acids [MHKKGSPILGSHTARVAGTSPPALPLLAQLPDASAEPHGPRHALRRPQQS PAPAGGAAAPAPGGRQPARSRWVPAPWGPRAGRGWGGRPAPTAPLNQRVY SSL (SEQ ID NO:88), FIG. 109] followed by amino acids 34-107 of the WT protein (SEQ ID NO:193). The new variant uncovered by the present invention lacks the signal peptide of the WT protein (amino acids 1-35 of GenBank Accession No. P19876) and the IPR001089 Small chemokine, C-X-C subfamily IPR002473 Small chemokine, and C-X-C/Interleukin 8.
Comparison Report Between T11329_P2 (SEQ ID NO:192) and MI2B_HUMAN (SEQ ID NO:193)
1. An isolated chimeric polypeptide T11329_P2 (SEQ ID NO:192), comprising a first amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence MHKKGSPILGSHTARVAGTSPPALPLLAQLPDASAEPHGPRHALRRPQQSPAP AGGAAAPAPGGRQPARSRWVPAPWGPRAGRGWGGRPAPTAPLNQRVYSSL (SEQ ID NO:88) corresponding to amino acids 1-103 of T11329_P2 (SEQ ID NO:192), and a second amino acid sequence being at least 90% homologous to GASVVTELRCQCLQTLQGIHLKNIQSVNVRSPGPHCAQTEVIATLKNGKKACL NPASPMVQKIIEKILNKGSTN corresponding to amino acids 34-107 of MI2B_HUMAN (SEQ ID NO:193), which also corresponds to amino acids 104-177 of T11329_P2 (SEQ ID NO:192), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a head of T11329_P2 (SEQ ID NO:192), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence MHKKGSPILGSHTARVAGTSPPALPLLAQLPDASAEPHGPRHALRRPQQSPAP AGGAAAPAPGGRQPARSRWVPAPWGPRAGRGWGGRPAPTAPLNQRVYS SL (SEQ ID NO:88) of T11329_P2 (SEQ ID NO:192).
These results suggest the use of the new MIP2-13 variant of the present invention (T11329_P2—SEQ ID NO:192), the polynucleotide encoding same (T11329_T1 transcript—SEQ ID NO:191) as a diagnostic marker for lung cell proliferation or de-differentiation, as well as lung cancer. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the MIP2-β variant (T11329_P2—SEQ ID NO:192)], or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 20
Splice Variant of Integrin Beta-7 Precursor
Background
The β7 integrin subfamily has two known members: α4β7 and αEβ7, both of which are involved in localization of leukocytes to mucosal sites.
In the adult, elevated levels of α4β7 are expressed on activated T and B cells. The preferential ligand for integrin α4β7 is MAdCAM-1, which is expressed on the mucosal endothelium of Peyer's patchs, mesenteric lymph nodes, and within the lamina propria of the small and large intestine. α4β7 also interacts with VCAM-1 and with the CS-1 region of fibronectin although both these interactions are of a much lower affinity than the α4β7/MAdCAM-1 interaction (Viney and Fong, 1998).
The affinity/avidity of α4β7 for MAdCAM-1 can be increased several fold upon activation of the leukocyte. This is achieved by conformational changes in the extracellular domains of the receptor and can be influenced by changes in the cytoplasmic domain of β7 (Viney and Fong 1998).
Integrin αEβ7 mediates interaction of T cells with epithelial cells at mucosal surfaces via recognition of E-cadherin. Interaction of αEβ7 with E-cadherin mediates retention, migration and proliferation of intraepithelial T cells (Viney and Fong 1998).
The ligand binding activity of β7 has been mapped to an inserted sequence that has a high homology with the A-domain (also referred to as I-domain) of the von Willebrand factor. This von Willebrand-like domain resides within the extracellular portion of β7, and is common to all β subunits. Together with conserved downstream residues, the von Willebrand-like domain could form a complete metal-ion-dependent adhesion site (MIDAS) (Higgins et al., 2000). The MIDAS accounts for ligand binding as well as ligand specificity and probably involves in the association with the α subunit. Structure-function studies revealed that the ion binding activity resides within amino acids 150-172 of the MIDAS and that binding of Mn2+ or Mg2+ to this site induces a conformational change that is critical for ligand binding (Tidswell et al., 1997). Downstream to the von Willebrand-like domain there are four cystein rich domains, which are also thought to be involved in ligand binding. These are followed by a transmembrane domain and a short, signaling, cytoplasmic domain.
Clinical Applications
Elevated expression of MAdCAM-1 is described in intestinal inflammation in mouse models of experimentally induced and spontaneous colitis. This increase in MAdCAM-1 expression appears to be associated with increased cellular infiltrates. Thus, disruption of the leukocyte receptor interaction with MAdCAM-1 might selectively attenuate trafficking to the intestine during inflammation. Since MAdCAM-1 has a rather restricted tissue expression, selectively blocking the interaction between MAdCAM-1 and α4β7 might be therapeutically beneficial for treating inflammation in the intestine without dramatically affecting immune regulation and trafficking elsewhere in the body. Indeed, neutralizing mAbs to α4β7 and MAdCAM-1 has both been shown to be useful in attenuating inflammation in experimental models of colitis. Furthermore, administration of antibodies to either α4β7 or αEβ7 reduced intestinal inflammation in GVH disease. αEβ7 is likely to have an additional role in rejection of epithelial tissue within allografts (Higgins et al., 2000). Antagonistic mAbs for α4β7 are in phase II of clinical trials for intestinal inflammation associated with colitis, Crohn's disease, and irritable bowl syndrome.
Splice Variant Structure
The present inventors uncovered a novel splice variant of integrin β7 (S80335_T6-SEQ ID NO:90; S80335_P5—SEQ ID NO:89; FIGS. 57a-b). The T6 splice variant obtained by the alternative splicing of the integrin β7 gene result from extension of exon 5 leading to an insertion of a stop codon and the generation of a truncated protein (FIGS. 58-60). This variant encodes 228 amino acids long protein, which contains 192 amino acids of the wild type (ITB7_HUMAN; SEQ ID NO:144) sequence and 36 unique amino acids (EPSAASRPVSPCLFNHCPSLCQHPGLTRAPTCPPSC SEQ ID NO:91). It encompasses about one fifth of the von Willebrand and lacks all the downstream domains.
Comparison Report Between S80335_P5 (SEQ ID NO:89) and ITB7_HUMAN (SEQ ID NO:144)
1. An isolated chimeric polypeptide S80335_P5 (SEQ ID NO:89), comprising a first amino acid sequence being at least 90% homologous to MVALPMVLVLLLVLSRGESELDAKIPSTGDATEWRNPHLSMLGSCQPAPSCQ KCILSHPSCAWCKQLNFTASGEAEARRCARREELLARGCPLEELEEPRGQQEV LQDQPLSQGARGEGATQLAPQRVRVTLRPGEPQQLQVRFLRAEGYPVDLYYL MDLSYSMKDDLERVRQLGHALLVRLQEVTHSVRIG corresponding to amino acids 1-192 of ITB7_HUMAN (SEQ ID NO:144), which also corresponds to amino acids 1-192 of S80335_P5 (SEQ ID NO:89), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence EPSAASRPVSPCLFNHCPSLCQHPGLTRAPTCPPSC (SEQ ID NO:91) corresponding to amino acids 193-228 of S80335_P5 (SEQ ID NO:89), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of S80335_P5 (SEQ ID NO:89), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence EPSAASRPVSPCLFNHCPSLCQHPGLTRAPTCPPSC (SEQ ID NO:91) in S80335_P5 (SEQ ID NO:89).
Therapeutic Application of the Variant
Variant T6 (S80335_P5) is a truncated protein that lacks the TM and the cytoplasmic domain. It is predicted to be a soluble protein and might bind divalent cations. This might result in conformational change and subsequent ligand binding leading to blockage of the interaction between the β7 integrins (α4β7 or αEβ7) and their ligands (MAdCAM-1 and E-cadherin, respectively). However, it is not clear whether ligand could be bound by a non-heterodimeric protein, nonetheless a truncated protein that encompasses only a small part of the von Willebrand domain.
Thus, the integrin β7 variant of the present invention, can be an antagonist of the β7 integrin receptors (e.g., α4β7 or αEβ7) and as such it can be used to prevent the interaction with MAdCAM-1.
The present inventors uncovered a therapeutic agent which can be used to: prevent and/or treat intestinal inflammation (e.g., colitis, GVH disease, Crohn's disease, and irritable bowl syndrome). Such an agent is a polypeptide homologous to the SEQ ID NO:89, and/or a polynucleotide homologous to SEQ ID NO:90, and/or a peptide homologous to SEQ ID NO:91. It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se, or as part of a pharmaceutical composition with a pharmaceutically acceptable carrier (e.g., PEG or liposomes).
Example 21
Splice Variant of Complement C5
Background
Complement is a dynamic self-assembling system of plasma proteins, which constitute a part of the humoral defense system against bacteria and viral pathogens. The fifth component of the complement, CS, is of particular interest since, upon activation, it participates in both cytolytic and inflammatory processes.
C5 is a member of a structural homologous family of proteins, which includes the complement proteins C3 and C4, as well as α2-macroglobulin. Biosynthesis of C5 occurs in hepatocytes, macrophages, fibroblasts, type II alveolar epithelial cells, lung, spleen, and fetal intestine as an intracellular precursor, pro-C5. Pro-C5 is processed, glycosylated, and secreted to the serum as a 190,000 Da glycoprotein composed of disulfate-linked α- and β-chains designated CS.
Activation of the complement system by antigen-antibody complexes (classical pathway), or polysaccharides/microbial surfaces (alternative pathway), initiates a cascade of proteolytic events in which the two chain-CS component is cleaved by C5 convertase. This cleavage occurs on Arg733 of the amino-terminus of the α-chain, and yields the C5a and C5b. C5a is a powerful, 74 amino acid, peptide-mediator of inflammation with anaphylotoxic activity. It elicits its activity via binding to the 7-transmembrane, GPCR, C5a receptor (C5aR), expressed on cells of myeloid origin (neutrophils, eosenophils, and basophils, macrophages and monocytes), epithelial cells, smooth muscle cells and on activated B and T cells. C5aR activation with sub-nanomolar levels of C5a result in chemotaxis of all myeloid lineages, while higher nanomolar concentrations elicit degranulation and activation of NADPH oxidase.
C5b triggers the formation of the membrane-attack complex that can damage certain pathogens. C5b initiates the assembly of the downstream complement components and their insertion into the cell membrane. This process begins with the binding of one C5b molecule to C6. The C5b,6 complex then binds one molecule of C7. This reaction leads to a conformational change in the constituent molecules, with the exposure of a hydrophobic site on C7, which inserts into the lipid bilayer. Similar hydrophobic sites are exposed on the later components, C8 and C9, when they are bound to the complex, allowing these proteins also to insert into the lipid bilayer.
Clinical Applications
Activation of the complement system via either the classical or the alternative pathway results in the generation of C5a and C5b. C5a acts as a very potent anaphylatoxin and can induce human polymorphonuclear leukocytes to migrate in a directed fashion, to degranulate, to undergo a burst of oxidative metabolism, and to aggregate. The in vivo effect of C5a depends on its site of generation: intravascular release of C5a in the general circulation leads to adult respiratory distress syndrome, while its release in tissue spaces result in local inflammatory reaction. Local generation of neutrophil chemoattractants, including C5a, resulting in neutrophil accumulation, was described in chronic obstructive pulmonary disease (COPD) and in inflammatory responses that result from ischemia in myocardial tissues. Expression of the activating and regulatory proteins of the complement, as well as the C3a/C5a receptors, was also reported in the CNS. Recently, complement activation was shown to account for multiple sclerosis and for Alzheimer disease. Excessive complement activation can also lead to tissue injury that mimics that seen in autoimmune disorders. Accordingly, regulation of C5a receptor was shown to be involved in Arthritis. Excessive C5b and C5a activity has also been associated with renal disease and their regulation is important to avoid hemodialysis and ongoing glumerular diseases.
The only CS-related inherited deficiency described to date is Neisseria. Neisseria is associated with increased susceptibility to infection and involves acute bacterial diseases and meningitis. Complement agonist for treating Neisseria has not been described, probably regarding the hazardous potential of such molecules.
Inhibitors for CS designed to serve as anti-inflammatory and neuroprotective agent, and for treatment of adult respiratory distress, cardiovascular reperfusion injury, arthritis, and for urological use, are at phase II of clinical trials.
Additional references which are fully incorporated herein: Haviland et al., 1991. JBC 226: 11818-11825; Pellas et al., 1999. Current Pharmaceutical Design 5:737-755; Gerard et al., 1994. Annu Rev Immunol 12:775-808; That et al., 2003. JI 171:6565-6573; Sandoval et al., 2000. JI 165:1066-1073; Low et al., 1999, JI 162:6580-6588; Vogt, 1986, Complement 3:177-188; Perez, 1984 Crit. Rev Oncol Hematol 1:199-225; Guenther, 1983 J Am Acad Dermatol 9:815-839; Williams et al., 2001, Navartis Found Sypm 234:141-148; Shen et al., 2003, Prog Neurobiol 70:463-472; Barnum, 2002, Immunol Res 26:7-13; Williams, 1996, Pharmacol Ther 72: 1-12; Ito et al., 1990, Blood Cells 145-166; Till et al., 1983, Agents Actions Suppl 12:383-396; Barger, 1990, Rev Infect Dis 4: S401-409; Tsokos et al., 2004, Curr Dir autoimmun 7:149-164; Johnson, 1997, Curr Opin Nephrol Hypertens 6:120-127).
Splice Variants Structure
The present inventors uncovered two novel splice variants of Complement component C5 (SEQ ID NOs:101, 102, 104 and 105; FIGS. 69a-d).
The C5 splice variant T7 (transcript: HUMC5_T7—SEQ ID NO:102; polypeptide: HUMC5_P6—SEQ ID NO:101; FIGS. 69a and b, respectively) results from the alternative splicing of the C5 gene, thus introducing a new exon (exon 20A), leading to insertion of a stop codon and the generation of a truncated protein (FIGS. 70, 71a, 72). C5 T7 contains 854 amino acids of the wild type C5 (CO5_HUMAN; SEQ ID NO:147) and a unique sequence of 48 amino acids at the C-terminus (SLALSPRLECNGKISGQLQVRLPGSSDSPASASQVAGITGTHHHAQPT; SEQ ID NO:103). It contains an intact β-chain comprised of the α2-macroglobulin domain, and a truncated α-chain containing the anaphylotoxin-like domain and lacks most of the α2-macroglobulin and the NTR (Netrin domain).
Comparison Report Between HUMC5_P6 (SEQ ID NO:101) and CO5_HUMAN_V1 (SEQ ID NO:652)
1. An isolated chimeric polypeptide HUMC5_P6 (SEQ ID NO:101), comprising a first amino acid sequence being at least 90% homologous to MGLLGILCFLIFLGKTWGQEQTYVISAPKIPRVGASENIVIQVYGYTEAFDATIS IKSYPDKKFSYSSGHVHLSSENKFQNSAILTIQPKQLPGGQNPVSYVYLEVVSK HFSKSKRMPITYDNGFLFIHTDKPVYTPDQSVKVRVYSLNDDLKPAKRETVLT FIDPEGSEVDMVEEIDHIGIISFPDFKIPSNPRYGMWTIKAKYKEDFSTTGTAYF EVKEYVLPHFSVSIEPEYNFIGYKNFKNPEITIKARYFYNKVVTEADVYITFGIR EDLKDDQKEMMQTAMQNTMLINGIAQVTFDSETAVKELSYYSLEDLNNKYL YIAVTVIESTGGFSEEAEIPGIKYVLSPYKLNLVATPLFLKPGIPYPIKVQVKDS LDQLVGGVPV corresponding to amino acids 1-388 of CO5_HUMAN_V1 (SEQ ID NO:652), which also corresponds to amino acids 1-388 of HUMC5_P6 (SEQ ID NO:101), a bridging amino acid T corresponding to amino acid 389 of HUMC5_P6 (SEQ ID NO:101), a second amino acid sequence being at least 90% homologous to LNAQTIDVNQETSDLDPSKSVTRVDDGVASFVLNLPSGVTVLEFNVKTDAPD LPEENQAREGYRAIAYSSLSQSYLYIDWTDNHKALLVGEHLNIIVTPKSPYIDK ITHYNYLILSKGKIIHFGTREKFSDASYQSINIPVTQNMVPSSRLLVYYIVTGEQ TAELVSDSVWLNIEEKCGNQLQVHLSPDADAYSPGQTVSLNMATGMDSWVA LAAVDSAVYGVQRGAKKPLERVFQFLEKSDLGCGAGGGLNNANVFHLAGLT FLTNANADDSQENDEPCKEILRPRRTLQKKIEEIAAKYKHSVVKKCCYDGAC VNNDETCEQRAARISLGPRCIKAFTECCVVASQLRANISHKDMQLGRLHMKT LLPVSKPEIRSYFPESWLWEVHLVPRRKQLQFALPDSLTTWEIQGVGISNTGIC VADTVKAKVFKDVFLEMNIPYSVVRGEQIQLKGTVYNYRTSGMQ corresponding to amino acids 390-854 of CO5_HUMAN_V1 (SEQ ID NO:652), which also corresponds to amino acids 390-854 of HUMC5_P6 (SEQ ID NO:101), and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence SLALSPRLECNGKISGQLQVRLPGSSDSPASASQVAGITGTHHHAQPT (SEQ ID NO:103) corresponding to amino acids 855-902 of HUMC5_P6 (SEQ ID NO:101), wherein said first amino acid sequence, bridging amino acid, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMC5_P6 (SEQ ID NO:101), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence SLALSPRLECNGKISGQLQVRLPGSSDSPASASQVAGITGTHHHAQPT (SEQ ID NO:103) in HUMC5_P6 (SEQ ID NO:101).
Comparison Report Between HUMC5_P6 (SEQ ID NO:101) and CO5_HUMAN (SEQ ID NO:147)
1. An isolated chimeric polypeptide HUMC5_P6 (SEQ ID NO:101), comprising a first amino acid sequence being at least 90% homologous to MGLLGILCFLIFLGKTWGQEQTYVISAPKIPRVGASENIVIQVYGYTEAFDATIS IKSYPDKKFSYSSGHVHLSSENKFQNSAILTIQPKQLPGGQNPVSYVYLEVVSK HFSKSKRMPITYDNGFLFIHTDKPVYTPDQSVKVRVYSLNDDLKPAKRETVLT FIDPEGSEVDMVEEIDHIGIISFPDFKIPSNPRYGMWTIKAKYKEDFSTTGTAYF EVKEYVLPHFSVSIEPEYNFIGYKNFKNFEITIKARYFYNKVVTEADVYITFGIR EDLKDDQKEMMQTAMQNTMLINGIAQVTFDSETAVKELSYYSLEDLNNKYL YIAVTVIESTGGFSEEAEIPGIKYVLSPYKLNLVATPLFLKPGIPYPIKVQVKDS LDQLVGGVPV corresponding to amino acids 1-388 of CO5_HUMAN (SEQ ID NO:147), which also corresponds to amino acids 1-388 of HUMC5_P6 (SEQ ID NO:101), a bridging amino acid T corresponding to amino acid 389 of HUMC5_P6 (SEQ ID NO:101), a second amino acid sequence being at least 90% homologous to LNAQTIDVNQETSDLDPSKSVTRVDDGVASFVLNLPSGVTVLEFNVKTDAPD LPEENQAREGYRAIAYSSLSQSYLYIDWTDNHKALLVGEHLNIIVTPKSPYIDK ITHYNYLILSKGKIIHFGTREKFSDASYQSINIPVTQNMVPSSRLLVYYIVTGEQ TAELVSDSVWLNIEEKCGNQLQVHLSPDADAYSPGQTVSLNMATGMDSWVA LAAVDSAVYGVQRGAKKPLERVFQFLEKSDLGCGAGGGLNNANVFHLAGLT FLTNANADDSQENDEPCKEILRPRRTLQKKIEEIAAKYKHSVVKKCCYDGAC VNNDETCEQRAARISLGPRCIKAFTECCVVASQLRANISHKDMQLGRLHMKT LLPVSKPEIRSYFPESWLWEVHLVPRRKQLQFALPDSLTTWEIQG corresponding to amino acids 390-801 of CO5_HUMAN (SEQ ID NO:147), which also corresponds to amino acids 390-801 of HUMC5_P6 (SEQ ID NO:101), a bridging amino acid V corresponding to amino acid 802 of HUMC5_P6 (SEQ ID NO:101), a third amino acid sequence being at least 90% homologous to GISNTGICVADTVKAKVFKDVFLEMNIPYSVVRGEQIQLKGTVYNYRTSGMQ corresponding to amino acids 803-854 of CO5_HUMAN (SEQ ID NO:147), which also corresponds to amino acids 803-854 of HUMC5_P6 (SEQ ID NO:101), and a fourth amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence SLALSPRLECNGKISGQLQVRLPGSSDSPASASQVAGITGTHHHAQPT (SEQ ID NO:103) corresponding to amino acids 855-902 of HUMC5_P6 (SEQ ID NO:101), wherein said first amino acid sequence, bridging amino acid, second amino acid sequence, bridging amino acid, third amino acid sequence and fourth amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMC5_P6 (SEQ ID NO:101), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence SLALSPRLECNGKISGQLQVRLPGSSDSPASASQVAGITGTHHHAQPT (SEQ ID NO:103) in HUMC5_P6 (SEQ ID NO:101).
The C5 splice variant T11 (transcript: HUMC5_T11—SEQ ID NO:105; polypeptide: HUMC5_P7—SEQ ID NO:104; FIGS. 69c and d, respectively) results from the alternative splicing of the C5 gene, thus introducing a new exon (exon 8A), leading to insertion of a stop codon and the generation of a truncated protein (FIGS. 70, 71b, 72). C5 T11 consists of amino acids 1-292 of the wild type protein (CO5_HUMAN; SEQ ID NO:147) and a unique sequence of 5 amino acids at the C-terminus (RAEVR; SEQ ID NO:106). It only contains the N-terminal portion of the α2-macroglobulin.
Comparison Report Between HUMC5_PROT_OF_TR11 (SEQ ID NO:105) and CO5_HUMAN
1. An isolated chimeric polypeptide HUMC5_PROT_OF_TR11, comprising a first amino acid sequence being at least 90% homologous to MGLLGILCFLIFLGKTWGQEQTYVISAPKIFRVGASENIVIQVYGYTEAFDATIS IKSYPDKKFSYSSGHVHLSSENKFQNSAILTIQPKQLPGGQNPVSYVYLEVVSK HFSKSKRMPITYDNGFLFIHTDKPVYTPDQSVKVRVYSLNDDLKPAKRETVLT FIDPEGSEVDMVEEIDHIGIISFPDFKIPSNPRYGMWTIKAKYKEDFSTTGTAYF EVKEYVLPHFSVSIEPEYNFIGYKNFKNFEITIKARYFYNKVVTEADVYITFGIR EDLKDDQKEMMQTAMQNTML corresponding to amino acids 1-292 of CO5_HUMAN, which also corresponds to amino acids 1-292 of HUMC5_PROT_OF_TR11, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence RAEVR corresponding to amino acids 293-297 of HUMC5_PROT_OF_TR11, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMC5_PROT_OF_TR11, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence RAEVR in HUMC5_PROT_OF_TR11.
Comparison Report Between HUMC5_P7 (SEQ ID NO:104) and CO5_HUMAN (SEQ ID NO:147)
1. An isolated chimeric polypeptide HUMC5_P7 (SEQ ID NO:104), comprising a first amino acid sequence being at least 90% homologous to MGLLGILCFLIFLGKTWGQEQTYVISAPKIFRVGASENIVIQVYGYTEAFDATIS IKSYPDKKFSYSSGHVHLSSENKFQNSAILTIQPKQLPGGQNPVSYVYLEVVSK HFSKSKRMPITYDNGFLFIHTDKPVYTPDQSVKVRVYSLNDDLKPAKRETVLT FIDPEGSEVDMVEEIDHIGHSFPDFKIPSNPRYGMWTIKAKYKEDFSTTGTAYF EVKEYVLPHFSVSIEPEYNFIGYKNFKNEEITIKARYFYNKVVTEADVYITFGIR EDLKDDQKEMMQTAMQNTML corresponding to amino acids 1-292 of CO5_HUMAN (SEQ ID NO:147), which also corresponds to amino acids 1-292 of HUMC5_P7 (SEQ ID NO:104), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence RAEVR (SEQ ID NO:106) corresponding to amino acids 293-297 of HUMC5_P7 (SEQ ID NO:104), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMC5_P7 (SEQ ID NO:104), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence RAEVR (SEQ ID NO:106) in HUMC5_P7 (SEQ ID NO:104).
Therapeutic Applications for the C5 Splice Variant T7 and T11
CS is activated when a CS-specific convertase cleaves the α-chain in a single site at Arg 733 yielding the C5a fragment and C5b, which is comprised of the remaining larger fragment of the α-chain associated in a S—S bond to the β-chain. However, the major convertase-binding site lies downstream of the cleavage site, within the NTR domain at residues 1600-1620. Other binding sites of CS to CS convertase reside on the β-chain near residues 150-200 and another putative binding sites reside at position 863 of the α-chain.
The complement variant T7 consists of 854 amino acids of the N-terminus of the wild type protein. Thus, it lacks some of the C5 convertase binding sites and will probably not bind properly to the convertase and will not be cleaved. Still, the variant contains the convertase binding site on the β-chain (and maybe other, not yet known, binding sites), and thus, might interfere with the binding of the convertase with the wild type C5, and might serve as a weak antagonist.
The T7 variant will also not bind C6 and C7 of the membrane attack complex as this interaction occurs via the NTR domain.
The Complement component C5 variant T11 harbors a binding site for the CS convertase, which resides at amino acids 150-200. Thus, T11 might interfere with the interaction between C5 convertase and C5 by competing for this binding site, and may thus serve as an antagonist of complement activation, i.e., a therapeutic agent.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
The complement component C5 variants according to the present invention optionally and preferably modulate complement component C5-related processes. Preferably, these variants are weak agonists or mixed antagonist/agonists, or antagonists. Therefore, the variants according to the present invention preferably act as antagonists to such complement component C5 mediated processes as adult respiratory distress syndrome, inflammatory reactions, neutrophil accumulation (optionally related to chronic obstructive pulmonary disease (COPD) and in inflammatory responses that result from ischemia in myocardial tissues), multiple sclerosis and Alzheimer's disease, and/or autoimmune disorders such as arthritis, and/or renal disease, cardiovascular reperfusion injury, arthritis, neuroprotective agents and for urological use.
As weak agonists, such variants may optionally be used to treat Neisseria, for example.
Treatment may optionally be periodic (weekly or monthly for example, or any other period) or daily depending upon the disease and the need of the subject. Treatment modality could easily be determined by one of ordinary skill in the art.
Example 22
Bone Morphogenetic Protein Receptor Type H
Background
Bone morphogenetic proteins (BMPs) are members of the TGF-beta superfamily of polypeptides. More than 20 mammalian BMPs have been identified so far. BMPs regulate cell proliferation and differentiation, apoptosis, neurogenesis, mesoderm patterning, left-right asymmetry, and the development of a number of organs, such as kidney, gut, lung, teeth, limb, amnion, and testis (Wozney et al, 1988, Science 242, 1528-1534; Hogan, 1996 Curr. Opin. Genet. Dev. 6:432-438; Hogan, 1996, Genes Dev. 10:1580-1594). BMPs were originally identified because of their ability to induce endochondral bone and cartilage formation (Wang E A, et al., 1988, PNAS, 85:1-5; Wozney et al, 1988, Science 242, 1528-1534). BMPs are synthesized by skeletal cells, however, their synthesis is not limited to bone, and they are expressed by a variety of extraskelletal tissues, such as monocytes, epithelial cells, mesenchymal cells and neuronal cells (Balemans and Van Hul, 2002, Dev. Biol. 250:231-250), in which they demonstrate broad array of biological activities and play a critical role in development and cell function. BMPs have also been found to promote nerve cell differentiation and to affect hair follicle formation (K. Basler, T. Edlund, T. M. Jessell, and T. Yamada, Cell, 73: 687-702 (1993); V. M. Paralkar, B. S. Weeks, Y. M. Yu, H. K. Klieinman, and A. H. Reddi, J. Cell Biol., 119: 1721-1728 (1992); M. Blessing, L. B. Nanney, L. E. King, C. M. Jones, and B. L. Hogan, Genes Dev., 7: 204-215 (1993)).
A BMP initiates its biological effect on cells by binding to a specific BMP receptor expressed on the plasma membrane of a BMP-responsive cell. The receptors for various members of the TGF-beta superfamily share similar structural features, and they are typically classified into one of two sub-groups, designated as type I and type II, classified as such based on amino acid sequence characteristics. Both the type I and type II receptors possess a relatively small extracellular ligand binding domain, a transmembrane region, and an intracellular protein kinase domain that is predicted to have serine/threonine kinase activity (Lin and Moustakas, Cellular and Molecular Biology, 40: 337-349 (1994); L. S. Mathews, Endocrine Reviews, 15: 310-325 (1994); L. Attisano, J. L. Wrana, F. Lopez-Casillas, and J. Massague, Biochimica et Biophysica Acta, 1222: 71-80 (1994)). There are three type I receptors identified: Alk2, Alk3 (BRIa) and Alk6 (BRIb), and three type II receptors: BRII, ActRII and ActRIIB, which are capable of binding BMPs (Nohe et al, Cellular Signaling, 2004, 16, 291-299; Yamashita et al., 1994, 269:20172-8; Yamashita et al., 1996, 19:569-574). There is also an alternative splice variant of BRII, which lacks most of the C-terminal tail (Massague, Annu Rev Biochem 1998, 67:753-91; Nohe et al, JBC, 2002, 277:5330-8). Signaling by BMPs requires the presence of both type I and type II receptors on the surface of the same cell. Generally, the type I receptors are the high affinity binding receptors, whereas the Type II receptors bind the BMPs alone with low affinity. The Type II receptors are constitutive active serine threonine kinase receptors. The Type I receptor, which is also a serine threonine kinase, is activated by the Type II receptor by phosphorylation at the GS-Box a juxtamembrane domain enriched in glycines and serines. The ligand can bind to the preformed hetero-oligomeric complexes consisting of at least one Type I and one Type II receptor, leading to the recrution of the pathway restricted Smads (R-Smads, Smads 1, 5, or 8). Alternative option is that the BMP ligand binds to the high affinity receptor Alk3 or Alk6 and then recruit BRII into a hetero-oligomeric complex (BMP-induced signaling complex), leading to activation of the MAP kinase pathway mediated by Tak1/Tab1 leading to the activation of P38 pathway. Kinase deficient BRII receptor mutant that is incapable in forming preassembled receptor complexes but recruits into a BMP-induced receptor complex does not interfere with the Smad pathway but does inhibit the induction of alkaline phoshatase as well as P38 phosphorylation (Nohe et al, 2002, JBC, 277:5330-8).
Mutations in Bone morphogenetic protein receptor type II are the cause of primary pulmonary hypertension (PPH1), a rare progressive autosomal dominant disorder, in which widespread occlusion of the smallest pulmonary arteries leads to increased pulmonary vascular resistance, and subsequently right ventricular failure. The mechanism by which BMPR-II mutants disrupt BMP/Smad signalling is heterogeneous and mutation specific. Thus, substitution of cysteine residues within the ligand binding or kinase domain of BMPR-II leads to failure of trafficking of the mutant protein to the cell surface, which may interfere with wild-type receptor trafficking. In contrast, noncysteine mutations within the kinase domain reach the cell surface but fail to activate a Smad-responsive luciferase reporter gene. All mutants transfected into normal mouse epithelial cells demonstrated ligand-independent activation of p38MAPK and enhanced serum-induced proliferation. Thus the reduced cell surface expression of BMPR-II favors activation of p38MAPK-dependent proproliferative pathways, whilst inhibiting Smad-dependent signalling in a mutation specific manner (Eddahibi et al, 2002, Eur Respir J, 20:1559-1572; Rudarakanchana et al, 2002, Human Mol Genet, 11:1517-1525). These alterations in BMPR-II function may provide the trigger for the abnormal vascular remodeling that characterizes primary pulmonary hypertension.
BMPs and agonists of BMP signaling pathway can be used as therapeutic agents for various indications. Among them are stimulation of maturation of chondrocytes and osteoblasts, thereby enhancing the bone-like tissue formation, which can be crucial for orthopedic repair of bone fractures, treatment of degenerative rheumatic and traumatic bone disorders, facial reconstructive surgery, stomatological diseases and dental surgery, bone loss due to osteoporosis, treatment of cartilage defects in joints and for use in bone transplants. Further potential indications for BMP pathway modulators include tissue regeneration in neurology, angiogenesis, burn and wound repair, Parkinson's disease, diabetic and gastrointestinal ulcers.
A recombinant BMP7 growth factor (developed by Curis; Stryker Biotech; Johnson & Johnson), eptoterminalpha, was currently launched for use as a muskuloskeletal osteogenic drug, and it is now under advanced investigation for potential uses for osteoporosis treatment, as well as in urological and stomatological diseases, as a neuroprotective agent and as an antiparkinsonian agent.
Morphogens, such as BMP7, BMP8, BMP2, BMP4, BMP6, are potentially useful for treatment of ischemic or traumatic injury of the central nervous system, in particular, in cases when the central nervous system tissue has been damaged or lost due to stroke or a similar disruption in blood flow, or due to infliction of physical (e.g., mechanical) trauma affecting the central nervous system (U.S. Pat. No. 6,407,060).
BMPs are also potentially useful as therapeutic molecules for protecting the luminal lining of the gastrointestinal tract from ulceration, particularly in individuals at risk for ulcer formation. Specifically they can limit the proliferation of the epithelial cells, inhibit the inflammation normally associated with ulcerative disease, inhibit scar tissue formation, and induce repair and regeneration of the ulcerated tissue (U.S. Pat. Nos. 6,399,569; 5,739,107).
Recently, the involvement of growth factors, such as GDF-9B and BMP6 in oocyte development and follicle growth was demonstrated (Vitt et al, 2002, Biol Reprod, 67:473-80; Gilchrist et al, 2004, Anim Reprod Sci., 82-83:431-46; Shimasaki et al., 2003, Reprod Suppl, 61: 323-37). Bone morphogenetic protein receptor Type II is a receptor for GDF-9, which is secreted by oocyte and is capable of stimulating granulose cell proliferation and inhibiting differentiation (Vitt et al, 2002, Biol Reprod, 67:473-80). Thus the BMP signaling pathway modulators can be for reproductive disorders.
The role of BMPs and it receptors in pathogenesis of allergic asthma and other airway diseases was recently demonstrated (Gronenberg et al, 2004, Exp. Lung Res., 30:223-50; Rosendahl et al., 2002, Am. J. Respir. Cell Mol. Biol. 27:160-169), suggesting the BMP signaling pathway as an important target for future development of new therapeutic strategies for asthma, chronic obstructive pulmonary diseases and airway inflammation. A failure to reconstitute normal lung architecture, and a number of structural changes (including extensive epithelial damage, deposition of ECM, goblet cell metaplasia, smooth muscle hypertrophy, increase in nerves and blood vessels) contribute to the tissue remodeling that is associated with asthma. A mechanistic explanation for the failure of EGF signaling to mediate proper repair has been suggested to be abnormally high signaling from the antagonistic pathways stimulated by members of the TGF-beta family and BMP-stimulated signaling in allergen-challenged airway epithelium. Thus, modulation and preferably downregulation of the BMP signaling pathway may be considered as therapeutic target for asthma, chronic obstructive pulmonary diseases and airway inflammation. BMPs and BMP signaling pathways have also potential utilities as diagnostic, prognostic and therapeutic targets in various cancers, such as osteosarcomas. Osteosarcomas producing BMPs contain less-differentiated mesenchymal cells, resulting in a poorer prognosis for those patients. Among benign bone tumors, BMPs are expressed in osteoid osteomas or osteoblastomas and effect reactive bone formation such as a surrounding sclerosis.
Antagonists of BMP signaling pathway can be potentially used in the treatment of inappropriate bone formation resulting from complications associated with spinal trauma or major burns, for the treatment of post-surgical adhesions and fibrosis, and for treatment of fibrodysplasia ossificans progressive and other disorders of heterotopic ossification (Kan et al; Am J Pathol. 2004 October; 165(4):1107-15; Glasercet al, J Bone Joint Surg Am. 2003 December; 85-A(12):2332-42).
Heterotopic ossification, the formation of bone in soft tissue, requires inductive signaling pathways, inducible osteoprogenitor cells, and a heterotopic environment conducive to osteogenesis. In fibrodysplasia ossificans progressiva, overexpression of BMP4 and underexpression of multiple antagonists of this protein highlight the potential role of a BMP signaling pathway in these disorders and turns it in to a promising therapeutic target (Kaplan et al, J Am Acad Orthop Surg. 2004 March-April; 12(2): 116-25). The delivery of BMP inhibitor Noggin mediated by muscle-derived stem cells successfully inhibited heterotopic ossification caused by BMP-4, demineralized bone matrix, and trauma in an animal model (Hannallah et al, J Bone Joint Surg Am. 2004 January; 86-A(1):80-91). The heterotopic ossification of muscles, tendons, and ligaments is a common problem faced by orthopaedic surgeons. Blocking bone formation is clinically relevant to disorders of heterotopic ossification in humans, such as fibrodysplasia ossificans progressiva. Furthermore, development of BMP antagonists as therapeutic agents may provide modalities for the treatment of other pathologic conditions that arise from aberrant expression of BMPs and/or from a lack of their antagonists.
BMP antagonists, blocking growth factor signaling, were shown to cause a significant reduction of osteophyte formation and synovial thickening during experimental osteoarthritis (Scharstuhl et al., Arthritis Rheum. 2003 December; 48(12):3442-51), which is a joint disease characterized by osteophyte development, fibrosis, and articular cartilage damage. These findings suggest potential therapeutic uses of antagonists of BMP signaling pathway in the osteoarthritis treatment.
Antagonists of BMP signaling pathway can be also potentially used to improve central nervous system (CNS) regeneration after spinal cord injury. Transplantation of neural precursor cells into lesioned adult rat spinal cord results in only partial functional recovery, and most transplanted cells tend to differentiate predominantly into astrocytes. In order to improve functional recovery after transplantation, it is important that transplanted neural precursor cells appropriately differentiate into cell lineages required for spinal cord regeneration. It was demonstrated that gene modification to inhibit BMP signaling by noggin expression promoted differentiation of neural precursor cells into neurons and oligodendrocytes, in addition to astrocytes after transplantation. Furthermore, functional recovery of the recipient mice with spinal cord injury was observed when noggin-expressing neural precursor cells were transplanted (Setoguchi et al., Exp Neurol. 2004 September; 189(1):33-44.).
Bone Morphogenetic Protein Receptor type II (BMR11) Novel Splice Variant
BMRII splice variant of the present invention (HSU20165_T9; SEQ ID NO:121) results from an alternative splicing of the BMRII_HUMAN gene, incorporating an alternative new exon sequence located within the intronic sequence between the original exons 3 and 4 of the BMRII gene. As a result a new truncated BMRII protein is generated, encoding 156 amino acids (HSU20165_P5; SEQ ID NO:120), which shares with the wild type BMRII the 139 N-terminal amino acids, containing the signal peptide sequence (amino acids 1-26), partial extracellular ligand binding domain (amino acids 27-139), including the three potential glycosylation sites. The new protein contains 17 C-terminal unique amino acids. The new protein does not contain the transmembrane domain of the wild type protein, and therefore it is predicted to be secreted. The new protein does not contain the cytoplasmic domain of the wild type protein, including the kinase domain. The sequence alignment between the novel BMRII splice variant of the present invention and the known BMRII is presented in FIG. 90. The schematic drawing of the new variant as compared to the wild type protein is presented in FIG. 91.
Comparison Report Between HSU20165_P5 (SEQ ID NO:120) and BMR2_HUMAN (SEQ ID NO:152)
1. An isolated chimeric polypeptide HSU20165_P5 (SEQ ID NO:120), comprising a first amino acid sequence being at least 90% homologous to MTSSLQRPWRVPWLPWTILLVSTAAASQNQERLCAFKDPYQQDLGIGESRISH ENGTILCSKGSTCYGLWEKSKGDINLVKQGCWSHIGDPQECHYEECVVTTTP PSIQNGTYRFCCCSTDLCNVNFTENFPPPDTTPL corresponding to amino acids 1-139 of BMR2_HUMAN (SEQ ID NO:152), which also corresponds to amino acids 1-139 of HSU20165_P5 (SEQ ID NO:120), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence KTGFHRVSQDGLDLLTS (SEQ ID NO:334) corresponding to amino acids 140-156 of HSU20165_P5 (SEQ ID NO:120), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSU20165_P5 (SEQ ID NO:120), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence KTGFHRVSQDGLDLLTS (SEQ ID NO:334) in HSU20165_P5 (SEQ ID NO:120).
The new secreted splice variant of BMRII (HSU20165_P5 (SEQ ID NO:120) is predicted to have a dominant negative mode of action with antagonistic effects on the BMP signaling pathway. The BMRII splice variant of the present invention has various potential therapeutic and diagnostic implications. Thus a BMRII polypeptide homologous to SEQ ID NO:120, and/or a BMRII polynucleotide homologous to SEQ ID NO:121 and/or a peptide homologous to SEQ ID NO:334 can be used as a negative modulator of the BMP signaling pathway, and hence serve as a potential therapeutic agent in pathological conditions where blocking or reducing the BMP signaling is required, such as in the treatment of inappropriate bone formation resulting from spinal trauma or major burns; the treatment of post-surgical adhesions and fibrosis; treatment of fibrodysplasia ossificans progressive and other disorders of heterotopic ossification, including the heterotopic ossification of muscles, tendons, and ligaments, which is a common problem faced by orthopaedic surgeons; treatment of osteoarthritis; it can be potentially used to improve central nervous system (CNS) regeneration after spinal cord injury; for treatment of asthma, chronic obstructive pulmonary diseases and airway inflammation; and it can be potentially used as diagnostic, prognostic and therapeutic target in various cancers, such as osteosarcomas.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 23
Splice Variant of Vascular Endothelial Growth Factor A Precursor
Background
The Vascular endothelial growth factor A precursor (VEGF-A; VPF; VEGA_HUMAN; SEQ ID NO:196) is a growth factor which is active in angiogenesis, vasculogenesis, endothelial cell growth, heparin binding angiogenesis, regulation of cell cycle and immune response. It acts as an angiogenesis modulator, induces endothelial cell proliferation, promotes cell migration, inhibits apoptosis, and induces permeabilization of blood vessels. VEGF-A binds to the VEGFR1/Flt-1 and VEGFR2/Kdr receptors, heparan sulfate and heparin. Alternative splicing of the VEGF-A precursor results in several VEGF isoforms: VEGF-121, VEGF-148, VEGF-165, VEGF-183, and VEGF-189. Neuropilin-1 binds isoforms VEGF-165 and VEGF-145.
VEGF-A is implicated in various diseases including, atherosclerosis, peripheral vascular disease, ulcer, diabetic, angina, general, rheumatoid arthritis, Buerger's syndrome, ischaemic cardiomyopathy, endometriosis, heart failure, myocardial infarction, ischaemia, macular degeneration, macular oedema, psoriasis, restenosis, diabetic retinopathy, wound healing, as well as in various cancers such as basal cell carcinoma, lung cancer (small cell and non-small cells lung cancer), brain cancer, breast cancer, cervical cancer, colorectal cancer, head and neck cancer, leukaemia, acute myelogenous, lymphoma, non-Hodgkin's lymphoma, melanoma; mesothelioma, myeloma, ovarian cancer, pancreatic cancer, prostate cancer, renal cancer, sarcoma, Kaposi's sarcoma.
Since VEGF-A is overexpressed in various cancers such as AIDS-associated Kaposi's sarcoma (KS) it can be used as a diagnostic marker for cancer. In addition, KS lesional cells express and respond to VEGF and bFGF, thus exhibit an inherent angiogenic phenotype which is crucial for cancer progression. Prior studies have attempted to treat KS lesions by introducing endostatin, a 20 kDA carboxyl-terminal fragment of collagen XVIII, which exhibits potent angiostatic activity (Mallery S R, J Cell Biochem. 2003; 89: 133-43).
Splice Variant HUMEGFAA_T5 (SEQ ID NO:194) Encodes a New Truncated Form of the VEGF-A, HUMEGFAA_P6 (SEQ ID NO:195)
The present inventors have uncovered a new VEGF-A variant [HUMEGFAA_P6—SEQ ID NO:195; HUMEGFAA_T5—SEQ ID NO:194]. The protein coordinates on the transcript start from nucleotide 1040 and end at nucleotide 1582 as set forth in SEQ ID NO:194 (HUMEGFAA_T5 transcript).
Alignment of the new VEGF-A variant (HUMEGFAA_P6—SEQ ID NO:195) with the WT protein (GenBank Accession No. P15692; SEQ ID NO:196) revealed that the new variant includes the first 130 amino acids as of the WT protein (GenBank Accession No. P15692), is missing 52 amino acids [RPKKDRARQEKKSVRGKGKGQKRKRKKSRYKSWSVYVGARCCLMPWSLP GPH (SEQ ID NO:197), FIG. 110] at position 131-182 of the WT protein, and further includes amino acids 183-232 of the WT protein. Thus, the new variant uncovered by the present invention lacks the bipartite nuclear localization signal (IPR001472) of the WT protein and therefore is expected to be an antagonist of VEGF-A.
Comparison Report Between HUMEGFAA_P6 (SEQ ID NO:195) and VEGA_HUMAN (SEQ ID NO:196)
1. An isolated chimeric polypeptide HUMEGFAA_P6 (SEQ ID NO:195), comprising a first amino acid sequence being at least 90% homologous to MNFLLSWVHWSLALLLYLHHAKWSQAAPMAEGGGQNHHEVVKFMDVYQR SYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITM QIMRIKPHQGQHIGEMSFLQHNKCEC corresponding to amino acids 1-130 of VEGA_HUMAN (SEQ ID NO:196), which also corresponds to amino acids 1-130 of HUMEGFAA_P6 (SEQ ID NO:195), a second amino acid sequence bridging amino acid sequence comprising of S, and a third amino acid sequence being at least 90% homologous to PCGPCSERRKHLFVQDPQTCKCSCKNTDSRCKARQLELNERTCRCDKPRR corresponding to amino acids 183-232 of VEGA_HUMAN (SEQ ID NO:196), which also corresponds to amino acids 132-181 of HUMEGFAA_P6 (SEQ ID NO:195), wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for an edge portion of HUMEGFAA_P6 (SEQ ID NO:195), comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise CSP having a structure as follows (numbering according to HUMEGFAA_P6 (SEQ ID NO:195)): a sequence starting from any of amino acid numbers 130-x to 130; and ending at any of amino acid numbers 132+((n−2)−x), in which x varies from 0 to n−2.
Splice Variant HUMEGFAA_T12 (SEQ ID NO:198) Encodes a New Form of the VEGF-A, HUMEGFAA_P8 (SEQ ID NO:199)
The present inventors have uncovered a new VEGF-A variant [HUMEGFAA_T12—SEQ ID NO:198; HUMEGFAA_P8—SEQ ID NO:1991. The protein coordinates on the transcript start from nucleotide 1040 and end at nucleotide 1450 as set forth in SEQ ID NO:198 (HUMEGFAA_T12 transcript).
Alignment of the new VEGF-A variant (HUMEGFAA_P8—SEQ ID NO:199) with the WT protein (GenBank Accession No. P15692; SEQ ID NO:196) revealed that the new variant includes the first 104 amino acids as of the WT protein (GenBank Accession No. P15692), is missing 95 amino acids of the WT (105-199 of SEQ ID NO:196; QIMRIKPHQGQHIGEMSFLQHNKCECRPKKDRARQEKKSVRGKGKGQKRKR KKSRYKSWSVYVGARCCLMPWSLPGPHPCGPCSERRKHLFVQDP (SEQ ID NO:200), FIG. 110], and it further includes amino acids 200-232 of the WT. The new variant uncovered by the present invention lacks the Bipartite nuclear localization signal (IPR001472) and the Platelet-derived growth factor (IPR000072) of the WT protein and therefore is expected to be antagonist of the endogenous VEGF-A protein.
Comparison Report Between HUMEGFAA_P8 (SEQ ID NO:199) and VEGA_HUMAN (SEQ ID NO:196)
1. An isolated chimeric polypeptide HUMEGFAA_P8 (SEQ ID NO:199), comprising a first amino acid sequence being at least 90% homologous to MNFLLSWVHWSLALLLYLHHAKWSQAAPMAEGGGQNHHEVVKFMDVYQR SYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITM corresponding to amino acids 1-104 of VEGA_HUMAN (SEQ ID NO:196), which also corresponds to amino acids 1-104 of HUMEGFAA_P8 (SEQ ID NO:199), and a second amino acid sequence being at least 90% homologous to QTCKCSCKNTDSRCKARQLELNERTCRCDKPRR corresponding to amino acids 200-232 of VEGA_HUMAN (SEQ ID NO:196), which also corresponds to amino acids 105-137 of HUMEGFAA_P8 (SEQ ID NO:199), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HUMEGFAA_P8 (SEQ ID NO:199), comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise MQ, having a structure as follows: a sequence starting from any of amino acid numbers 104-x to 104; and ending at any of amino acid numbers 105+((n−2)−x), in which x varies from 0 to n−2.
Clinical Implications of the VEGF-A Variants of the Present Invention
Since the VEGF-A variants of the present invention lack the nuclear localization signal it can compete with the endogenous VEGF-A and interfere with its various activities.
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:195 or 199 and/or an expressible polynucleotide homologous to SEQ ID NO:194 or 198 which can be used to treat cancer [e.g., basal cell carcinoma, lung cancer (small cell and non-small cells lung cancer), brain cancer, breast cancer, cervical cancer, colorectal cancer, head and neck cancer, leukaemia, acute myelogenous, lymphoma, non-Hodgkin's lymphoma, melanoma; mesothelioma, myeloma, ovarian cancer, pancreatic cancer, prostate cancer, renal cancer, sarcoma, Kaposi's sarcoma], a cardiovascular disease, inflammation, hypolipemia, fungal disease, angina, allergy, asthma, arthritis, psoriasis, atherosclerosis, symptomatic diabetes, menstruation disorder, musculoskeletal, ophthalmological, protozoacide, urological disease. In addition such an agent can be used as a fertility or reproduction enhancer, recombinant growth factor, coronary vasodilator, vulnerary, cardiostimulant, immunostimulant, immunosuppressant, a peripheral vasodilator.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
These results suggest the use of the new VEGF-A variant of the present invention (SEQ ID NO:195) and/or the polynucleotide encoding same (SEQ ID NO:194) as a diagnostic marker for cell proliferation or de-differentiation, as well as various cancers and tumors as is mentioned hereinabove. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the VEGF-A variant [HUMEGFAA_P6—SEQ ID NO:195], or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 24
Splice Variant of Interleukin-1 Receptor, Type I Precursor
Background
Interleukin-1 receptor (IL1R; IL1R1; IL1RA; IL-1R-1; IL-1R-alpha; P80; Antigen CD121a; P14778; IL1R_HUMAN) is a type I membrane protein which can bind interleukin-1 alpha (IL-1α), IL-1β, and interleukin-1 receptor antagonist protein (IL-1RA). Binding of IL-1α or IL-1β involves the formation of a ternary complex containing IL1RAP, TOLLIP, MYD88, IRAK1 or IRAK2 and leads to activation of NF-kappa-B.
IL-1Rα involves in immune and inflammatory responses and has been implicated in various diseases, disorders or conditions such as allergy, amyotrophic lateral sclerosis, rheumatoid arthritis, asthma, infection, inflammation (e.g., inflammatory bowel disease, sepsis, ocular inflammation), bone marrow transplant rejection, Alzheimer's disease, aplastic anaemia, osteo arthritis, cancer (e.g., breast, colorectal, melanoma, myeloma, prostate cancer, sarcoma), chemotherapy-induced injury, colitis, ulcerative, diabetes, fever, glaucoma, head trauma, ischaemia, cerebral myelodysplastic syndrome, nephritis, neuropathy, diabetic ocular disorder, pain, Parkinson's disease, Surgery adjunct, Ulcer decubitus.
IL-1Rα is overexpressed in various cancers and can be used as a marker for diagnosing cancer.
Splice Variant HUMIL1RA_T8 (SEQ ID NO:201) Encodes a New Secreted Form of the IL-1Rα, HUMIL1RA_P3 (SEQ ID NO:202)
The present inventors have uncovered a new IL-1Rα variant [HUMIL1RA_T8—SEQ ID NO:201; HUMIL1RA_P3—SEQ ID NO:202]. The protein coordinates on the transcript start from nucleotide 353 and end at nucleotide 850 as set forth in SEQ ID NO:201 (HUMIL1RA_T8 transcript).
Splice Variant HUMIL1RA_T10 (SEQ ID NO:205) Encodes a New Secreted Form of the IL-1Rα, HUMIL1RA_P3 (SEQ ID NO:202)
The present inventors have uncovered another new IL-1Rα variant [HUMIL1RA_T10—SEQ ID NO:205] which encodes the HUMIL1RA_P3 polypeptide (SEQ ID NO:202) described hereinabove. The protein coordinates on the transcript start from nucleotide 252 and end at nucleotide 749 as set forth in SEQ ID NO:205 (HUMIL1RA_T10 transcript).
Alignment of the new IL-1Rα variant (HUMIL1RA_P3—SEQ ID NO:202) with the WT protein (GenBank Accession No. P14778; SEQ ID NO:203) revealed that the new variant includes the first 162 amino acids as of the WT protein (GenBank Accession No. P14778) followed by a unique 4 amino acid sequence [VILF (SEQ ID NO:204), FIG. 112]. The new variant uncovered by the present invention exhibits a truncated Ig-like C2 type 1 domain (amino acids 118-210 of WT) and lacks the Ig-like C2 type 3 (amino acids 226-328 of WT), two glycosylation sites (amino acids 249 and 297 of WT), the transmembrane domain (amino acids 337-356 of WT), the cytoplasmic domain (amino acids 357-569 of WT), and the TIR domain (amino acids 383-541 of WT) and is therefore expected to be a secreted, soluble protein and extracellular protein.
Comparison Report Between HUMIL1RA_P3 and IL1R_HUMAN
1. An isolated chimeric polypeptide HUMIL1RA_P3 (SEQ ID NO:202), comprising a first amino acid sequence being at least 90% homologous to MKVLLRLICFIALLISSLEADKCKEREEKIILVSSANEIDVRPCPLNPNEHKGTIT WYKDDSKTPVSTEQASRIHQHKEKLWFVPAKVEDSGHYYCVVRNSSYCLRI KISAKFVENEPNLCYNAQAIFKQKLPVAGDGGLVCPYMEFFKNENNELPKLQ WYK corresponding to amino acids 1-162 of IL1R_HUMAN (SEQ ID NO:203), which also corresponds to amino acids 1-162 of HUMIL1RA_P3 (SEQ ID NO:202), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VILF (SEQ ID NO:204) corresponding to amino acids 163-166 of HUMIL1RA_P3 (SEQ ID NO:202), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMIL1RA_P3 (SEQ ID NO:202), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VILF in HUMIL1RA_P3 (SEQ ID NO:202).
Since the IL-1Rα variant of the present invention lacks the TM and TIR domains it can compete with the endogenous IL-1Rα and interfere with its various activities (i.e., Interleukin 1 modulator).
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:202, an expressible polynucleotide homologous to SEQ ID NO:201 and/or a peptide homologous to SEQ ID NO:204 which can be used as an anti-inflammatory (e.g., for GI inflammatory, bowel disorders), antiallergic, antiarthritic, antiasthma, anticancer, immunosuppressant, septic shock treatment, analgesic, NSAID, antianaemic, antibiotic, antidiabetic, antiglaucoma, antiparkinsonian, antipsoriasis, antiulcer, antiviral, anti-HIV (anti AIDS), cardiovascular, cognition enhancer, dermatological, haematological, hepatoprotective, hypolipaemic, antiatherosclerosis, immunomodulator, anti-infective, immunostimulant, multiple sclerosis treatment, neurological, neuroprotective, ophthalmological, osteoporosis treatment, radio/chemoprotective, radio/chemosensitizer, respiratory, stomatological, symptomatic antidiabetic, urological, and vulnerary agent.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
While further reducing the present invention to practice, these results suggest the use of the new IL-1Rα variant of the present invention (HUMIL1RA_P3—SEQ ID NO:202), the polynucleotide encoding same (HUMIL1RA_T8—SEQ ID NO:201) and/or the peptide derived from the HUMIL1RA_P3 variant (VILF—SEQ ID NO:204) as a diagnostic marker for various cancer cells and tumors (e.g., breast colorectal, melanoma, myeloma, prostate cancer, sarcoma). Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the IL-1Rα variant (HUMIL1RA_P3—SEQ ID NO:202], or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 25
Splice Variant of Complement Receptor Type I Precursor
Background
Complement receptor type I (CR1, or CD35, or C3b/C4b receptor) belongs to the family of regulators of complement activation (RCA) that includes also complement receptor type II (CRII; CD21), membrane cofactor protein (MCP; CD46), decay accelerating factor (DAF; CD55), factor H, and CD4b binding protein. RCA proteins accelerate the dissociation of C3 and C5 convertases, an activity known as decay accelerating activity (DAA), and/or serve as cofactors for the factor I-mediated cleavage of C3b and C4b, that result in inactivation of these molecules, and which is known as cofactor activity (CA).
CR1 is expressed by most peripheral blood cells, including erythrocytes, neutrophils, B-lymphocytes, a subset of T lymphocytes, and monocytes but not on platelets, natural killers cells and most T cells. Additionally, CR1 is expressed by glomerular podocytes and dendritic reticular cells. Erythrocytic CR1 has primary function in the clearance of C3b-fixed immune complexes. Lymphocytic and phagocytic CR1 bearing cells aid in the conversion and inactivation of C3b in the presence of factor-I.
Like all members of RCA family, CR1 is composed of  ̃60 amino-acid-long repeating units called complement control protein repeats (CCPs, also designated sushi domains). Of the 30 CCPs in CR1, the first 28 are organized, based on internal homology, into four long homologous repeats (LHRs), A-D, each composed of seven CCPs. Analysis of CR1 derivatives carrying a single LHR revealed that LHR A (CCPs 1-7), B (CCPs 8-14) and C(CCPs 15-21) contain binding sites for C3b and C4b. LHR A, efficiently binds C4b but binds C3b weakly. It possesses DAA but has a barely detectable CA. LHR B and its structural-functional duplicate, LHR C, efficiently bind C3b and C4b and possess CA for their cleavage. Within LHR A, binding sites for C4b were mapped to site 1 (CCPs 1-4). Specifically, structure function studies revealed one amino acid on CCP1 and three amino acids on CCP2 possessing binding activity for C4b. Binding sites for C3b were found on CCP8 and 9, which are included within site 2 (CCPs 8-11) of LHR B.
Structural analysis of the CCP units revealed that conserved two disulfide bridges as well as conserved amino acids within the CCPs form a hydrophobic core, which is similar in all CCPs.
Known polymorphisms for the sequence of this WT or known protein are as shown in Table 21.







TABLE 21







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment





1208
H → R./FTId = VAR_013819.


1408
T → I./FTId = VAR_013820.


1590
K → E (in MCC(b) antigen)./FTId =



VAR_013821.


1601
R → G (in Sl(2)/Vil antigen and Sl(5)



antigen)./FTId = VAR_013822.


1610
S → T (in Sl(5) antigen)./FTId =



VAR_013823.


1615
I → V./FTId = VAR_013824.


1827
P → R./FTId = VAR_013825.


1850
H → D./FTId = VAR_013826.


1876
T → I









Clinical Applications
Erythrocytic CR1 is responsible for the transport of immune complexes (IC) to liver and spleen. CR1 is also a potent inhibitor of complement activation and inflammation as it serves as a cofactor of the C3b cleavage by factor I. In some diseases such as systemic lupus erythematosus, hemolytic anemia, AIDS, and chronic myeloid leukemia, low levels of CR1 on erythrocytes has been observed, leading to an impaired clearance of IC. CR1 agonists are desirable therapeutic agents in such CR1 deficiencies.
Uncontrolled complement activation has been implicated as a pathological process in a number of inflammatory and autoimmune disorders such as rheumatoid arthritis and multiple sclerosis. Antagonistic soluble CR1 (sCR1) have been shown to be effective in experimental models of systemic sclerosis, arthritis, myasthenia gravis, and glomerulonephritis. It has also been shown to suppress ischemia/reperfusion injury, thermal trauma, and immune complex mediated inflammation. Administration of sCR1 in rat model of hyperacute allograft rejection resulted in reduced hemolysis after transplantation an in prolonged graft survival. Thus, Complement inactivation, mediated by sCR1, may prove useful for transplantation. Complement depletion has been shown to affect demyelination and inflammation in models of experimental allergic neuritis. Concomitantly, allergic neuritis was partially inhibited by treatment with sCR1. Thus, sCR1 could also serve as a neuroprotective agent in neuronal inflammation. Many animal models of rheumatoid arthritis are complement dependent and both incidence and progression of disease can be influenced by complement inhibition. Inhibition of complement via CR1 is of a potential therapeutic usage in rheumatoid arthritis.
Additional references which are fully incorporated herein: Krych et al., 1991 PNAS 88: 4353-4357; Krych et al., 1994 JBC 269: 13273-13278; Krych et al., 1998 JBC 273:8623-8629; Krych-Goldberg et al., 1999 JBC 274:31160-31168; Krych-Goldberg et al., 2001 Immunological Reviews 180:112-122; Asghar et al., 2000 Front Biosci 5:E63-81; Vriesendorp et al., Int J Neurosci 92:287-298; Pruitt et al., J Surg Res 50:350-355).
Splice Variant Structure
The cluster (gene) with regard to these variants, termed HSCR1RS, features 5 transcript(s) and 47 segment(s) of interest, the names for which are given in Tables 22 and 23, respectively, the sequences themselves are given in SEQ ID NOs: 206-210; 211-257 and 261-264, for transcripts; segments and proteins, respectively. The selected protein variants are given in Table 24.







TABLE 22







Transcripts of interest










Transcript Name
SEQ ID NO







HSCR1RS_PEA_1_T5
206



HSCR1RS_PEA_1_T9
207



HSCR1RS_PEA_1_T10
208



HSCR1RS_PEA_1_T13
209



HSCR1RS_PEA_1_T14
210

















TABLE 23







Segments of interest










Segment Name
SEQ ID NO:







HSCR1RS_PEA_1_node_1
211



HSCR1RS_PEA_1_node_3
212



HSCR1RS_PEA_1_node_10
213



HSCR1RS_PEA_1_node_12
214



HSCR1RS_PEA_1_node_19
215



HSCR1RS_PEA_1_node_21
216



HSCR1RS_PEA_1_node_27
217



HSCR1RS_PEA_1_node_29
218



HSCR1RS_PEA_1_node_35
219



HSCR1RS_PEA_1_node_37
220



HSCR1RS_PEA_1_node_45
221



HSCR1RS_PEA_1_node_52
222



HSCR1RS_PEA_1_node_54
223



HSCR1RS_PEA_1_node_57
224



HSCR1RS_PEA_1_node_63
225



HSCR1RS_PEA_1_node_65
226



HSCR1RS_PEA_1_node_71
227



HSCR1RS_PEA_1_node_73
228



HSCR1RS_PEA_1_node_79
229



HSCR1RS_PEA_1_node_81
230



HSCR1RS_PEA_1_node_87
231



HSCR1RS_PEA_1_node_89
232



HSCR1RS_PEA_1_node_91
233



HSCR1RS_PEA_1_node_101
234



HSCR1RS_PEA_1_node_0
235



HSCR1RS_PEA_1_node_5
236



HSCR1RS_PEA_1_node_7
237



HSCR1RS_PEA_1_node_8
238



HSCR1RS_PEA_1_node_14
239



HSCR1RS_PEA_1_node_17
240



HSCR1RS_PEA_1_node_23
241



HSCR1RS_PEA_1_node_25
242



HSCR1RS_PEA_1_node_31
243



HSCR1RS_PEA_1_node_33
244



HSCR1RS_PEA_1_node_39
245



HSCR1RS_PEA_1_node_47
246



HSCR1RS_PEA_1_node_50
247



HSCR1RS_PEA_1_node_56
248



HSCR1RS_PEA_1_node_61
249



HSCR1RS_PEA_1_node_67
250



HSCR1RS_PEA_1_node_69
251



HSCR1RS_PEA_1_node_75
252



HSCR1RS_PEA_1_node_77
253



HSCR1RS_PEA_1_node_83
254



HSCR1RS_PEA_1_node_85
255



HSCR1RS_PEA_1_node_93
256



HSCR1RS_PEA_1_node_97
257

















TABLE 24







Proteins of interest













Corresponding


Protein Name
SEQ ID NO:
Protein Length
Transcript(s)





HSCR1RS_PEA_1_P13
261
P1570
HSCR1RS_PEA_1_T5;





HSCR1RS_PEA_1_T14


HSCR1RS_PEA_1_P14
262
P584
HSCR1RS_PEA_1_T9


HSCR1RS_PEA_1_P15
263
P182
HSCR1RS_PEA_1_T10


HSCR1RS_PEA_1_P17
264
P2020
HSCR1RS_PEA_1_T13









The present inventors uncovered a novel splice variant of Complement Receptor CR1 (SEQ ID NOs:107 and 108; FIGS. 73a-b), variant T5. The T5 splice variant obtained by the alternative splicing of the CR1 gene result in extension of exon 4 leading to an insertion of a stop codon and the generation of a truncated protein (FIGS. 74-76). This splice variant encodes 182 amino acids long protein (SEQ ID NO:107), which contains 162 amino acids of the wild type sequence (GenBank Accession No. P17927; SEQ ID NO:148, and a unique C-terminal sequence of 20 amino acids (SELKYPFLFLLPTHSNFSLE—SEQ ID NO:109; FIG. 75). It encompasses the two N-terminal CCP domains (also designated sushi domains).
Comparison Report Between HSCR1RS_P6 (SEQ ID NO:107) and CR1_HUMAN (SEQ ID NO:148)
1. An isolated chimeric polypeptide HSCR1RS_P6, comprising a first amino acid sequence being at least 90% homologous to MGASSPRSPEPVGPPAPGLPFCCGGSLLAVVVLLALPVAWGQCNAPEWLPFA RPTNLTDEFEFPIGTYLNYECRPGYSGRPFSIICLKNSVWTGAKDRCRRKSCRN PPDPVNGMVHVIKGIQFGSQIKYSCTKGYRLIGSSSATCIISGDTVIWDNETPIC D corresponding to amino acids 1-162 of CR1_HUMAN, which also corresponds to amino acids 1-162 of HSCR1RS_P6, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence SELKYPFLFLLPTHSNFSLE (SEQ ID NO:109) corresponding to amino acids 163-182 of HSCR1RS_P6, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSCR1RS_P6, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence SELKYPFLFLLPTHSNFSLE in HSCR1RS_P6.
A more detailed description of these variant proteins and their corresponding nucleic acid sequences is provided below. As noted above, cluster HSCR1RS features 5 transcript(s), which were listed in Table 22 above. These transcript(s) encode for protein(s) which are variant(s) of protein Complement receptor type 1 precursor. Following is a description of each variant protein according to the present invention.
Variant protein HSCR1RS_PEA—1_P13 (SEQ ID NO:261) of the present invention is encoded by transcript(s) HSCR1RS_PEA—1_T5 (SEQ ID NO:206) and HSCR1RS_PEA—1_T14 (SEQ ID NO:210). An alignment of HSCR1RS_PEA—1_P13 with the known protein (Complement receptor type 1 precursor, SEQ ID NO:260) is shown in FIG. 113. One or more alignments to one or more previously published protein sequences are shown in FIGS. 114-116. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSCR1RS_PEA_P13 and CR1_HUMAN_V4 (SEQ ID NO:260)
1. An isolated chimeric polypeptide HSCR1RS_PEA—1_P13, comprising a first amino acid sequence being at least 90% homologous to MGASSPRSPEPVGPPAPGLPFCCGGSLLAVVVLLALPVAWGQCNAPEWLPFA RPTNLTDEFEFPIGTYLNYECRPGYSGRPFSIICLKNSVWTGAKDRCRRKSCRN PPDPVNGMVHVIKGIQFGSQIKYSCTKGYRLIGSSSATCIISGDTVIWDNETPIC DRIPCGLPPTIT corresponding to amino acids 1-173 of CR1_HUMAN_V4 (SEQ ID NO:260), which also corresponds to amino acids 1-173 of HSCR1RS_PEA—1_P13, a second amino acid sequence being at least 90% homologous to NGDFISTNRENFHYGSVVTYRCNPGSGGRKVFELVGEPSIYCTSNDDQVGIWS GPAPQCIIPNKCTPPNVENGILVSDNRSLFSLNEVVEFRCQPGFVMKGPRRVKC QALNKWEPELPSCSRVCQPPPDVLHAERTQRDKDNFSPGQEVFYSCEPGYDL RGAASMRCTPQGDWSPAAPTCEVKSCDDFMGQLLNGRVLFPVNLQLGAKV DFVCDEGFQLKGSSASYCVLAGMESLWNSSVPVCEQIFCPSPPVIPNGRHTGK PLEVFPFGKTVNYTCDPHPDRGTSFDLIGESTIRCTSDPQGNGVWSSPAPRCGI LGHCQAPDHFLFAKLKTQTNASDFPIGTSLKYECRPEYYGRPFSITCLDNLVW SSPKDVCKRKSCKTPPDPVNGMVHVITDIQVGSRINYSCTTGHRLIGHSSAECI LSGNTAHWSTKPPICQRIPCGLPPTIANGDFISTNRENFHYGSVVTYRCNLGSR GRKVFELVGEPSIYCTSNDDQVGIWSGPAPQCIIPNKCTPPNVENGILVSDNRS LFSLNEVVEFRCQPGFVMKGPRRVKCQALNKWEPELPSCSRVCQPPPEILHGE HTPSHQDNFSPGQEVFYSCEPGYDLRGAASLHCTPQGDWSPEAPRCAVKSCD DFLGQLPHGRVLFPLNLQLGAKVSFVCDEGFRLKGSSVSHCVLVGMRSLWN NSVPVCEHIFCPNPPAILNGRHTGTPSGDIPYGKEISYTCDPHPDRGMTFNLIGE STIRCTSDPHGNGVWSSPAPRCELSVRAGHCKTPEQFPFASPTIPINDFEFPVGT SLNYECRPGYFGKMFSISCLENLVWSSVEDNCRRKSCGPPPEPFNGMVHINTD TQFGSTVNYSCNEGFRLIGSPSTTCLVSGNNVTWDKKAPICEIISCEPPPTISNG DFYSNNRTSFHNGTVVTYQCHTGPDGEQLFELVGERSIYCTSKDDQVGVWSS PPPRCISTNKCTAPEVENAIRVPGNRSFFSLTEIIRFRCQPGFVMVGSHTVQCQT NGRWGPKLPHCSRVCQPPPEILHGEHTLSHQDNFSPGQEVFYSCEPSYDLRGA ASLHCTPQGDWSPEAPRCTVKSCDDFLGQLPHGRVLLPLNLQLGAKVSFVCD EGFRLKGRSASHCVLAGMKALWNSSVPVCEQIFCPNPPAILNGRHTGTPFGDI PYGKEISYACDTHPDRGMTFNLIGESSIRCTSDPQGNGVWSSPAPRCELSVPA ACPHPPKIQNGHYIGGHVSLYLPGMTISYICDPGYLLVGKGFIFCTDQGIWSQL DHYCKEVNCSFPLFMNGISKELEMKKVYHYGDYVTLKCEDGYTLEGSPWSQ CQADDRWDPPLAKCTSRAHDALIV corresponding to amino acids 624-1975 of CR1_HUMAN_V4 (SEQ ID NO:260), which also corresponds to amino acids 174-1525 of HSCR1RS_PEA—1_P13 (SEQ ID NO:261), and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence AIMHMKTLKKWLSIYILKEAAAFIPELCKQMKKIAGSFLDKVLYS corresponding to amino acids 1526-1570 of HSCR1RS_PEA—1_P13 (SEQ ID NO:261), wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HSCR1RS_PEA—1_P13, comprising a polypeptide having “n” amino acids, wherein “n” is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise TN, having a structure as follows: a sequence starting from any of amino acid numbers 173-x to 173; and ending at any of amino acid numbers 174+((n−2)−x), in which x varies from 0 to n−2.
3. An isolated polypeptide for a tail of HSCR1RS_PEA—1_P13, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence AIMHMKTLKKWLSIYILKEAAAFIPELCKQMKKIAGSFLDKVLYS in HSCR1RS_PEA—1_P13.
It should be noted that the known protein sequence (CR1_HUMAN—SEQ ID NO:148) has one or more changes compared to CR1_HUMAN_V4 (SEQ ID NO:260). These changes were previously known to occur and are listed in Table 25, hereinbelow.







TABLE 25







Changes to CR1_HUMAN_V4 (SEQ ID NO: 260)








SNP position(s) on



amino acid sequence
Type of change











895
Public SNP replace


1877
Conflict









The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The HSCR1RS_PEA—1_P13 variant protein is expected to be secreted protein based on the prediction of both a signal-peptide and the absence of a trans-membrane region
Variant protein HSCR1RS_PEA—1_P13 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 26, given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSCR1RS_PEA—1_P13 (SEQ ID NO:261) sequence provides support for the deduced sequence of this variant protein according to the present invention.







TABLE 26







Amino acid substitutions









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












105
R → C
Yes


115
V → A
Yes


445
T → A
Yes


758
H → R
Yes


958
T → M
Yes


1160
S → T
Yes


1165
I → V
Yes


1377
P → R
Yes


1426
I → T
No


1519
A → T
Yes









Table 27, hereinbelow, presents the protein domain of HSCR1RS_PEA—1_P13 (SEQ ID NO:261) as determined by using InterPro.







TABLE 27







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR000436
Sushi
HMMPfam
1007-1064, 104-161,



domain/SCR

1069-1135, 1141-1196,



domain/CCP

1200-1256,



module

1261-1319, 1324-1390,





1398-1454, 1459-1515,





166-232, 238-293,





297-353, 358-416,





421-487, 43-99,





493-549, 554-611,





616-682, 688-743,





747-803, 808-866,





871-937, 946-1002


IPR000436
Sushi
HMMSmart
1007-1064, 104-161,



domain/SCR

1069-1135, 1141-1196,



domain/CCP

1200-1256, 1261-1319,



module

1324-1390, 1398-1454,





1459-1515, 166-232,





238-293, 297-353,





358-416, 421-487,





43-99, 493-549,





554-611, 616-682,





688-743, 747-803,





808-866, 871-937,





946-1002


IPR000834
Peptidase M14,
ScanRegExp
432-442



carboxypeptidase A









Variant Protein HSCR1RS_PEA_P13
Variant protein HSCR1RS_PEA—1_P13 (SEQ ID NO:261) is encoded by the following transcript(s): HSCR1RS_PEA—1_T5 (SEQ ID NO:206) and HSCR1RS_PEA—1_T14 (SEQ ID NO:210).
The coding portion of transcript HSCR1RS_PEA—1_T5 (SEQ ID NO:206) starts at position 112 and ends at position 4821. The HSCR1RS_PEA—1_T5 transcript also has the following SNPs as listed in Table 28, given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSCR1RS_PEA—1_P13 sequence provides support for the deduced sequence of this variant protein according to the present invention.







TABLE 28







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












78
A → G
No


79
T → A
No


201
T → C
Yes


213
T → C
Yes


291
A → G
Yes


424
C → T
Yes


455
T → C
Yes


456
G → A
Yes


1440
G → A
Yes


1444
A → G
Yes


1473
A → G
Yes


2384
A → G
Yes


2984
C → T
Yes


3015
C → T
Yes


3589
T → A
Yes


3604
A → G
Yes


4241
C → G
Yes


4388
T → C
No


4666
G → A
Yes


5299
A → G
Yes


5303
G → T
Yes


5324
→ C
No


5596
G → C
No


5597
C → G
No


5652
T → C
Yes


5688
G → T
Yes


5777
T → C
Yes









The coding portion of transcript HSCR1RS_PEA—1_T14 (SEQ ID NO:210) starts at position 112 and ends at position 4821. The HSCR1RS_PEA—1_T14 transcript also has the following SNPs as listed in Table 29, given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSCR1RS_PEA—1_P13 sequence provides support for the deduced sequence of this variant protein according to the present invention.







TABLE 29







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












78
A → G
No


79
T → A
No


201
T → C
Yes


213
T → C
Yes


291
A → G
Yes


424
C → T
Yes


455
T → C
Yes


456
G → A
Yes


1440
G → A
No


1444
A → G
No


2384
A → G
Yes


2984
C → T
Yes


3015
C → T
Yes


3589
T → A
Yes


3604
A → G
Yes


4241
C → G
Yes


4388
T → C
No


4666
G → A
Yes


5299
A → G
Yes


5303
G → T
Yes


5324
→ C
No


5596
G → C
No


5597
C → G
No


5652
T → C
Yes


5688
G → T
Yes


5777
T → C
Yes









Variant Protein HSCR1RS_PEA—1_P14
Variant protein HSCR1RS_PEA—1_P14 (SEQ ID NO:262) is encoded by transcript HSCR1RS_PEA—1_T9 (SEQ ID NO:207). FIG. 114 presents an alignment of HSCR1RS_PEA—1_P14 (SEQ ID NO:262) with the known protein (Complement receptor type 1 precursor; SEQ ID NO:148). One or more alignments to one or more previously published protein sequences are shown in FIGS. 113, 115, and 116. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSCR1RS_PEA—1_P14 (SEQ ID NO:262) and CR1_HUMAN (SEQ ID NO:148)
1. An isolated chimeric polypeptide HSCR1RS_PEA—1_P14, comprising a first amino acid sequence being at least 90% homologous to MGASSPRSPEPVGPPAPGLPFCCGGSLLAVVVLLALPVAWGQCNAPEWLPFA RPTNLTDEFEFPIGTYLNYECRPGYSGRPFSIICLKNSVWTGAKDRCRRKSCRN PPDPVNGMVHVIKGIQFGSQIKYSCTKGYRLIGSSSATCIISGDTVIWDNETPIC DRIPCGLPPTITNGDFISTNRENFHYGSVVTYRCNPGSGGRKVFELVGEPSIYC TSNDDQVGIWSGPAPQCIIPNKCTPPNVENGILVSDNRSLFSLNEVVEFRCQPG FVMKGPRRVKCQALNKWEPELPSCSRVCQPPPDVLHAERTQRDKDNFSPGQE VFYSCEPGYDLRGAASMRCTPQGDWSPAAPTCEVKSCDDFMGQLLNGRVLF PVNLQLGAKVDFVCDEGFQLKGSSASYCVLAGMESLWNSSVPVCEQIFCPSP PVIPNGRHTGKPLEVFPFGKAVNYTCDPHPDRGTSFDLIGESTIRCTSDPQGNG VWSSPAPRCGILGHCQAPDHFLFAKLKTQTNASDFPIGTSLKYECRPEYYGRP FSITCLDNLVWSSPKDVCKRKSCKTPPDPVNGMVHVITDIQVGSRINYSCTTG corresponding to amino acids 1-584 of CR1_HUMAN (SEQ ID NO:148), which also corresponds to amino acids 1-584 of HSCR1RS_PEA—1_P14 (SEQ ID NO:262).
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be a secreted protein due to the prediction of a signal-peptide and the absence of a trans-membrane region.
Variant protein HSCR1RS_PEA—1_P14 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 31, given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSCR1RS_PEA—1_P14 sequence provides support for the deduced sequence of this variant protein according to the present invention.







TABLE 30







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





105
R → C
Yes


115
V → A
Yes









The glycosylation sites of variant protein HSCR1RS_PEA—1_P14, as compared to the known protein Complement receptor type 1 precursor, are described in Table 31 given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein.







TABLE 31







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












1605
NO



1534
NO


56
YES
56


1481
NO


1540
NO


578
YES
578


1908
NO


1763
NO


860
NO


959
NO


1028
NO


897
NO


252
YES
252


1152
NO


410
YES
410


702
NO


509
YES
509


1504
NO


1310
NO


447
YES
447









The phosphorylation sites of variant protein HSCR1RS_PEA—1_P14, as compared to the known protein Complement receptor type 1 precursor, are described in Table 32 given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein.







TABLE 32







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





42
yes
42









The HSCR1RS_PEA—1_P14 variant protein has the following domains, as determined by using InterPro. The domains are described in Table 33, hereinbelow.







TABLE 33







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR000436
Sushi
HMMPfam
104-161, 166-232,



domain/SCR

238-293, 297-353,



domain/CCP

358-416, 421-487,



module

43-99, 493-549


IPR000436
Sushi
HMMSmart
104-161, 166-232,



domain/SCR

238-293, 297-353,



domain/CCP

358-416, 421-487,



module

43-99, 493-549


IPR000834
Peptidase M14,
ScanRegExp
432-442



carboxypeptidase A









Variant protein HSCR1RS_PEA—1_P14 (SEQ ID NO:262) is encoded by HSCR1RS_PEA—1_T9 (SEQ ID NO:207). The coding portion of transcript HSCR1RS_PEA—1_T9 (SEQ ID NO:207) starts at position 112 and ends at position 1863. The HSCR1RS_PEA—1_T9 transcript also has the following SNPs as listed in Table 34 given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSCR1RS_PEA—1_P14 sequence provides support for the deduced sequence of this variant protein according to the present invention.







TABLE 34







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












78
A → G
No


79
T → A
No


201
T → C
Yes


213
T → C
Yes


291
A → G
Yes


424
C → T
Yes


455
T → C
Yes


456
G → A
Yes









Variant Protein HSCR1RS_PEA_P15
Variant protein HSCR1RS_PEA—1_P15 (SEQ ID NO:263) according to the present invention is encoded by transcript HSCR1RS_PEA—1_T10 (SEQ ID NO:208). FIG. 115 depicts an alignment of HSCR1RS_PEA—1_P15 to the known protein (Complement receptor type 1 precursor; SEQ ID NO:148). One or more alignments to one or more previously published protein sequences are given in FIGS. 113, 114, and 116. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSCR1RS_PEA_P15 and CR1_HUMAN
1. An isolated chimeric polypeptide HSCR1RS_PEA—1_P15, comprising a first amino acid sequence being at least 90% homologous to MGASSPRSPEPVGPPAPGLPFCCGGSLLAVVVLLALPVAWGQCNAPEWLPFA RPTNLTDEFEFPIGTYLNYECRPGYSGRPFSIICLKNSVWTGAKDRCRRKSCRN PPDPVNGMVHVIKGIQFGSQIKYSCTKGYRLIGSSSATCIISGDTVIWDNETPIC D corresponding to amino acids 1-162 of CR1_HUMAN (SEQ ID NO:148), which also corresponds to amino acids 1-162 of HSCR1RS_PEA—1_P15 (SEQ ID NO:263), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least % homologous to a polypeptide having the sequence SELKYPFLFLLPTHSNFSLE (SEQ ID NO:654) corresponding to amino acids 163-182 of HSCR1RS_PEA—1_P15, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSCR1RS_PEA—1_P15, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence SELKYPFLFLLPTHSNFSLE (SEQ ID NO:654) in HSCR1RS_PEA—1_P15.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be a secreted protein based on the prediction of a signal peptide and the absence of a trans-membrane region.
Variant protein HSCR1RS_PEA—1_P15 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 35, given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSCR1RS_PEA—1_P15 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 35







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





105
R → C
Yes


115
V → A
Yes









The glycosylation sites of variant protein HSCR1RS_PEA—1_P15, as compared to the known protein Complement receptor type 1 precursor, are described in Table 36 given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein.







TABLE 36







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












1605
NO



1534
NO


56
YES
56


1481
NO


1540
NO


578
NO


1908
NO


1763
NO


860
NO


959
NO


1028
NO


897
NO


252
NO


1152
NO


410
NO


702
NO


509
NO


1504
NO


1310
NO


447
NO









The phosphorylation sites of variant protein HSCR1RS_PEA—1_P15, as compared to the known protein Complement receptor type 1 precursor, are described in Table 37 given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein.







TABLE 37







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





42
yes
42









The variant protein has the following domains, as determined by using InterPro and presented in Table 38 hereinbelow.







TABLE 38







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR000436
Sushi domain/SCR
HMMPfam
104-161, 43-99



domain/CCP module


IPR000436
Sushi domain/SCR
HMMSmart
104-161, 43-99



domain/CCP module









Variant protein HSCR1RS_PEA—1_P15 is encoded by the following transcript: HSCR1RS_PEA—1_T10 (SEQ ID NO:208). The coding portion of transcript HSCR1RS_PEA—1_T10 (SEQ ID NO:208) starts at position 112 and ends at position 657. The transcript also has the following SNPs as listed in Table 39 given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSCR1RS_PEA—1_P15 sequence provides support for the deduced sequence of this variant protein according to the present invention.







TABLE 39







Nucleic acid SNPs









SNP position on

Previously known


nucleotide sequence
Alternative nucleic acid
SNP?












78
A → G
No


79
T → A
No


201
T → C
Yes


213
T → C
Yes


291
A → G
Yes


424
C → T
Yes


455
T → C
Yes


456
G → A
Yes









Variant Protein HSCR1RS_PEA—1_P17
Variant protein HSCR1RS_PEA—1_P17 (SEQ ID NO:264) is encoded by transcript HSCR1RS_PEA—1_T13 (SEQ ID NO:209). FIG. 116 presents an alignment of HSCR1RS_PEA—1_P17 to the known protein (Complement receptor type 1 precursor; SEQ ID NO:259). One or more alignments to one or more previously published protein sequences are given in FIGS. 113-115. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows.
Comparison Report Between HSCR1RS_PEA—1_P17 and CR1_HUMAN_V1 (SEQ ID NO:259)
1. An isolated chimeric polypeptide HSCR1RS_PEA—1_P17, comprising a first amino acid sequence being at least 90% homologous to MGASSPRSPEPVGPPAPGLPFCCGGSLLAVVVLLALPVAWGQCNAPEWLPFA RPTNLTDEFEFPIGTYLNYECRPGYSGRPFSIICLKNSVWTGAKDRCRRKSCRN PPDPVNGMVHVIKGIQFGSQIKYSCTKGYRLIGSSSATCIISGDTVIWDNETPIC DRIPCGLPPTITNGDFISTNRENFHYGSVVTYRCNPGSGGRKVFELVGEPSIYC TSNDDQVGIWSGPAPQCIIPNKCTPPNVENGILVSDNRSLFSLNEVVEFRCQPG FVMKGPRRVKCQALNKWEPELPSCSRVCQPPPDVLHAERTQRDKDNFSPGQE VFYSCEPGYDLRGAASMRCTPQGDWSPAAPTCEVKSCDDFMGQLLNGRVLF PVNLQLGAKVDFVCDEGFQLKGSSASYCVLAGMESLWNSSVPVCEQIFCPSP PVIPNGRHTGKPLEVFPFGK corresponding to amino acids 1-444 of CR1_HUMAN_V1, which also corresponds to amino acids 1-444 of HSCR1RS_PEA—1_P17 (SEQ ID NO:264), a bridging amino acid T corresponding to amino acid 445 of HSCR1RS_PEA—1_P17, a second amino acid sequence being at least 90% homologous to VNYTCDPHPDRGTSFDLIGESTIRCTSDPQGNGVWSSPAPRCGILGHCQAPDH FLFAKLKTQTNASDFPIGTSLKYECRPEYYGRPFSITCLDNLVWSSPKDVCKR KSCKTPPDPVNGMVHVITDIQVGSRINYSCTTGHRLIGHSSAECILSGNAAHW STKPPICQRIPCGLPPTIANGDFISTNRENFHYGSVVTYRCNPGSGGRKVFELV GEPSIYCTSNDDQVGIWSGPAPQCIIPNKCTPPNVENGILVSDNRSLFSLNEVVE FRCQPGFVMKGPRRVKCQALNKWEPELPSCSRVCQPPPDVLHAERTQRDKD NFSPGQEVFYSCEPGYDLRGAASMRCTPQGDWSPAAPTCEVKSCDDFMGQL LNGRVLFPVNLQLGAKVDFVCDEGFQLKGSSASYCVLAGMESLWNSSVPVC EQIFCPSPPVIPNGRHTGKPLEVFPFGKAVNYTCDPHPDRGTSFDLIGESTIRCT SDPQGNGVWSSPAPRCGILGHCQAPDHFLFAKLKTQTNASDFPIGTSLKYECR PEYYGRPFSITCLDNLVWSSPKDVCKRKSCKTPPDPVNGMVHVITDIQVGSRI NYSCTTGHRLIGHSSAECILSGNTAHWSTKPPICQRIPCGLPPTIANGDFISTNR ENFHYGSVVTYRCNLGSRGRKVFELVGEPSIYCTSNDDQVGIWSGPAPQCIIP NKCTPPNVENGILVSDNRSLFSLNEVVEFRCQPGFVMKGPRRVKCQALNKWE PELPSCSRVCQPPPEILHGEHTPSHQDNFSPGQEVFYSCEPGYDLRGAASLHCT PQGDWSPEAPRCAVKSCDDFLGQLPHGRVLFPLNLQLGAKVSFVCDEGFRLK GSSVSHCVLVGMRSLWNNSVPVCEHIFCPNPPAILNGRHTGTPSGDIPYGKEIS YTCDPHPDRGMTFNLIGESTIRCTSDPHGNGVWSSPAPRCELSVRAGHCKTPE QFPFASPTIPINDFEFPVGTSLNYECRPGYFGKMFSISCLENLVWSSVEDNCRR KSCGPPPEPFNGMVHINTDTQFGSTVNYSCNEGFRLIGSPSTTCLVSGNNVTW DKKAPICEIISCEPPPTISNGDFYSNNRTSFHNGTVVTYQCHTGPDGEQLFELV GERSIYCTSKDDQVGVWSSPPPRCISTNKCTAPEVENAIRVPGNRSFFSLTEIIR FRCQPGFVMVGSHTVQCQTNGRWGPKLPHCSRVCQPPPEILHGEHTLSHQDN FSPGQEVFYSCEPSYDLRGAASLHCTPQGDWSPEAPRCTVKSCDDFLGQLPH GRVLLPLNLQLGAKVSFVCDEGFRLKGRSASHCVLAGMKALWNSSVPVCEQI FCPNPPAILNGRHTGTPFGDIPYGKEISYACDTHPDRGMTFNLIGESSIRCTSDP QGNGVWSSPAPRCELSVPAACPHPPKIQNGHYIGGHVSLYLPGMTISYICDPG YLLVGKGFIFCTDQGIWSQLDHYCKEVNCSFPLFMNGISKELEMKKVYHYGD YVTLKCEDGYTLEGSPWSQCQADDRWDPPLAKCTSRAHDALIV corresponding to amino acids 446-1975 of CR1_HUMAN_V1 (SEQ ID NO:259), which also corresponds to amino acids 446-1975 of HSCR1RS_PEA—1_P17 (SEQ ID NO:264), and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence AIMHMKTLKKWLSIYILKEAAAFIPELCKQMKKIAGSFLDKVLYS corresponding to amino acids 1976-2020 of HSCR1RS_PEA—1_P17, wherein said first amino acid sequence, bridging amino acid, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSCR1RS_PEA—1_P17, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence AIMHMKTLKKWLSIYILKEAAAFIPELCKQMKKIAGSFLDKVLYS (SEQ ID NO:655) in HSCR1RS_PEA—1_P17.
It should be noted that the known protein sequence (CR1_HUMAN—SEQ ID NO:148) has one or more changes compared to CR1_HUMAN_V1 (SEQ ID NO:259). These changes were previously known to occur and are listed in Table 40, hereinbelow.







TABLE 40







Changes to CR1_HUMAN_V1










SNP position(s) on amino




acid sequence
Type of change







1877
Conflict










The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is predicted to be secreted based on the prediction of a signal-peptide and the absence of a trans-membrane region.
Variant protein HSCR1RS_PEA—1_P17 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 41, given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSCR1RS_PEA—1_P17 sequence provides support for the deduced sequence of this variant protein according to the present invention.







TABLE 41







Amino acid substitutions









SNP position(s) on
Alternative amino
Previously known


amino acid sequence
acid(s)
SNP?












105
R → C
Yes


115
V → A
Yes


445
T → A
No


1208
H → R
Yes


1408
T → M
Yes


1610
S → T
Yes


1615
I → V
Yes


1827
P → R
Yes


1876
I → T
No


1969
A → T
Yes









The HSCR1RS_PEA—1_P17 variant protein has the following domains, as determined by using InterPro and presented in Table 42, hereinbelow.







TABLE 42







InterPro domain(s)











Domain




InterPro ID
description
Analysis type
Position(s) on protein





IPR000436
Sushi
HMMPfam
1004-1061, 104-161,



domain/SCR

1066-1132, 1138-1193,



domain/CCP

1197-1253, 1258-1316,



module

1321-1387, 1396-1452,





1457-1514, 1519-1585,





1591-1646, 1650-1706,





166-232, 1711-1769,





1774-1840, 1848-1904,





1909-1965, 238-293,





297-353, 358-416, 421-487,





43-99, 493-549,





554-611, 616-682, 688-743,





747-803, 808-866,





871-937, 943-999


IPR000436
Sushi
HMMSmart
1004-1061, 104-161,



domain/SCR

1066-1132, 1138-1193,



domain/CCP

1197-1253, 1258-1316,



module

1321-1387, 1396-1452,





1457-1514, 1519-1585,





1591-1646, 1650-1706,





166-232, 1711-1769,





1774-1840, 1848-1904,





1909-1965, 238-293,





297-353, 358-416, 421-487,





43-99, 493-549,





554-611, 616-682, 688-743,





747-803, 808-866,





871-937, 943-999


IPR000834
Peptidase
ScanRegExp
432-442, 882-892



M14,



carboxy-



peptidase A









Variant protein HSCR1RS_PEA—1_P17 is encoded by the following transcript: HSCR1RS_PEA—1_T13 (SEQ ID NO:209). The coding portion of transcript HSCR1RS_PEA—1_T13 (SEQ ID NO:209) starts at position 112 and ends at position 6171. The transcript also has the following SNPs as listed in Table 43 given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSCR1RS_PEA—1_P17 sequence provides support for the deduced sequence of this variant protein according to the present invention.







TABLE 43







Nucleic acid SNPs









SNP position on

Previously known


nucleotide sequence
Alternative nucleic acid
SNP?












78
A → G
No


79
T → A
No


201
T → C
Yes


213
T → C
Yes


291
A → G
Yes


424
C → T
Yes


455
T → C
Yes


456
G → A
Yes


1440
G → A
No


1444
A → G
No


3734
A → G
Yes


4334
C → T
Yes


4365
C → T
Yes


4939
T → A
Yes


4954
A → G
Yes


5591
C → G
Yes


5738
T → C
No


6016
G → A
Yes


6649
A → G
Yes


6653
G → T
Yes


6674
→ C
No


6946
G → C
No


6947
C → G
No


7002
T → C
Yes


7038
G → T
Yes


7127
T → C
Yes









Therapeutic Applications for the CR1 Splice Variant of the Present Invention
Since splice variant T5 (SEQ ID NO:206) of the CR1 encodes a truncated protein that contains only the two N-terminal CCPs (CCPS 1,2), to which binding activity of C4b is attributed, it is predicted to bind C4b and to inhibit complement activation by preventing the assembly of C3 convertases. Indeed, works by Krych and colleagues demonstrated that a truncated CR1 containing only LHR A (CCPs 1-3) prevents hemolysis induced by the classical pathway C3 convertase. The inhibition of hemolysis is referred to the DAA possessed by CR1. In such assays, LHR A possesses 60-100% DAA relative to sCR1. This inhibitory activity was attributed to LHR A only when classical pathway C3 convertase was assayed but not for alternative pathway C3 convertase (which is composed of C3b and Bb rather then C2b and C4b in the classical pathway). Altogether, these data indicate that the CR1 splice variant discussed here might inhibit classical pathway complement activation.
A soluble form of the full-length receptor (sCR1) has been widely described as an antagonist for complement activation. Moreover, antagonists for CR1 are reported to be on phase II clinical trials in treatment of reperfusion injury, respiratory distress syndrome, rheumatoid arthritis and general transplant rejection.
Thus, the present inventors uncovered a therapeutic agent which can be used to: inhibit complement activation by preventing the assembly of C3 convertases and thus treat disorders, disease or conditions such as reperfusion injury, respiratory distress syndrome, rheumatoid arthritis and general transplant rejection. Such an agent is a polypeptide homologous to SEQ ID NO:107, and/or a polynucleotide homologous to SEQ ID NO:108 or 206.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 26
Splice Variant of Complement Cis Component Precursor (C1 Esterase)
Background
The classical pathway of complement activation is initiated by the first component of the complement system, C1. C1 is a multimolecular enzyme complex resulting from the noncovalent association of two distinct entities: the recognition protein C1q, and the catalytic subunit, which is a Ca2+ dependent tetramer: C1s-C1r-C1r-C1s. C1s and C1r are the proteases responsible for the activation of proteolytic activity of the C1 complex of complement. They share a similar overall structural organization and are composed of five nonenzymatic protein modules (two CUB modules surrounding a single EGF module, and a pair of CCP modules) followed by a serine protease domain. The N-terminal region of both proteases possess high affinity binding site for Ca2+ ions which enables them to associate with each other within the tetramer, and to interact with C1q upon C1 assembly.
The role of C1s incorporated in the C1 complex is to mediate the proteolitic function of C1, i.e. to cleave first C4 and then C2 during complement activation. These cleavages occur in a cascade in which active C1s cleaves C4 (to generate C4a and C4b), thus exposes a reactive group on C4b that allows it to bind covalently to the pathogen surface. C4b then binds C2, making it susceptible to cleavage by C1s. The cleavage of C2 results in the formation of C2a and C2b. A complex composed of C2b and C4b generates C3 convertase. In the classical pathway, C2b is the active protease component of C3 convertase, however, C3 convertase is also formed (by other proteins) in the other pathways of complement activation. C3 convertase cleaves many molecules of C3 to produce C3a and C3b. In the MB-lectin pathway, C3b binds to the bacteria cell membrane, thus opsonizes the bacteria and enables phagocytes to internalize them, while C3a serves as an inflammatory mediator. A complex composed of C3b and C3 convertase (=C4b+C2b) acts as C5 convertase. C5 binds this complex through C3b and its cleavage generates C5b and C5a. C5a serves as a powerful peptide mediator of inflammation, while C5b triggers the late events of complement activation, in which the terminal components of complement assemble into membrane-attack complex that can damage certain pathogens.
Clinical Application
Unwanted or uncontrolled activation of C1s can contribute to the pathogenesis of several diseases. The harmful effect of complement activation is suspected in the inflammatory events occurring in ischemia and reperfusion. It has been demonstrated that mice which are homozygous deficient in C3 or C4 were equally protected against reperfusion injury. In addition, C1s inhibitors are being synthesized for therapeutic use in cardiovascular diseases. Hereditary angioedema (HAE) result from deficient function or depletion of the C1 inhibitor. Accordingly, C1s inhibitors are at phase II in treatment of this disease. Uncontrolled activation of C1s could also account for neurodegenerative diseases in the CNS. For example, abnormal levels of C1s are expressed by pyramidal neurons and senile plaques of Alzheimer patients. There are also possible implications of C1s in non-complement related diseases; Human C1s is also implicated in the cleavage of type I and type II collagens. It was hypothesized therefore that C1s participates in the metabolism of cartilage matrix and possibly in the pathogenesis of rheumatoid arthritis and downregulation of the immune response. In addition, C1s can cleave insulin-like growth factor-binding protein-5 (IGFBP-5). IGFBP-5 regulates the action of insulin-like growth factor-I (IGF-I) through tight binding. The cleavage of IGFBP-5 by C1s result in the release of IGF-I to receptors. IGF-I release occurs as a result of acute complement activation during injury and contribute to tissue repair. Thus, this phenomenon could represent a linkage between inflammation and subsequent cellular repair processes.
Deficiency of C1s (as well as C1r) often causes systemic lupus erythematosus-like syndromes and severe pyogenic infections. Selective and complete C1s deficiency accounts for early onset of multiple autoimmune diseases.
Additional references which are fully incorporated herein: Thielens et al. 1999. Immunopharmacology 42: 3-13; Gal et al. 2002. immunobiology 205: 383-394; Terai et al. 1997. Brain Res. 769: 385-390; Sullivan et al. 1996. J Rheumatol. 23: 2063-2067).
Complement Component C1s Splice Variants
The present inventors uncovered two novel splice variants of Complement component C1s (SEQ ID NOs:95, 96, 98, and 99; FIGS. 65a-d).
C1s Splice Variant T7 (HUMC1RS_T7) Structure
C1s splice variant T7 (HUMC1RS_T7—SEQ ID NO:99 and HUMC1RS_P5-SEQ ID NO:98), FIG. 65a and b, respectively) result from alternative splicing of the C1s gene, thus introducing a new exon (exon 11a), causing the insertion of a stop codon, that result in a truncated C1s protein (FIGS. 66, 67a, 68). The variant protein thus created is a 455 amino acids long truncated protein, which contains the N-terminal 423 amino acids of wild type C1s (SEQ ID NO:146), followed by a unique sequence of 32 amino acids (SEQ ID NO:97). It contains the two CUB modules separated by an EGF module, and followed by two CCP modules, but it lacks the whole serine protease domain.
Comparison Report Between HUMC1RS_P5 and C1S_HUMAN
1. An isolated chimeric polypeptide HUMC1RS_P5, comprising a first amino acid sequence being at least 90% homologous to MWCIVLFSLLAWVYAEPTMYGEILSPNYPQAYPSEVEKSWDIEVPEGYGIHL YFTHLDIELSENCAYDSVQIISGDTEEGRLCGQRSSNNPHSPIVEEFQVPYNKL QVIFKSDFSNEERFTGFAAYYVATDINECTDFVDVPCSHFCNNFIGGYFCSCPP EYFLHDDMKNCGVNCSGDVFTALIGEIASPNYPKPYPENSRCEYQIRLEKGFQ VVVTLRREDFDVEAADSAGNCLDSLVFVAGDRQFGPYCGHGFPGPLNIETKS NALDIIFQTDLTGQKKGWKLRYHGDPMPCPKEDTPNSVWEPAKAKYVFRDV VQITCLDGFEVVEGRVGATSFYSTCQSNGKWSNSKLKCQPVDCGIPESIENGK VEDPESTLFGSVIRYTCEEPYYYMENGGGGEYHCAGNGSWVNEVLGPELPKC VP corresponding to amino acids 1-423 of C1S_HUMAN (SEQ ID NO:146), which also corresponds to amino acids 1-423 of HUMC1RS_P5 (SEQ ID NO:98), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GLNSDLPESSSVRWQYHCAVGCQGRGEPPQPH (SEQ ID NO:97) corresponding to amino acids 424-455 of HUMC1RS_P5, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMC1RS_P5, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GLNSDLPESSSVRWQYHCAVGCQGRGEPPQPH (SEQ ID NO:97) in HUMC1RS_P5.
C1s Splice Variant T8 (HUMC1RS_T8) Structure
C1s splice variant T8 (HUMC1RS_T8—SEQ ID NO:96 and HUMC1RS_P6-SEQ ID NO:95, FIG. 65c and d, respectively) result from alternative splicing of the C1s gene, thus leading to the skipping of exon 4 and the generation of a protein lacking amino acids 65-131 of wild type C1s, while introducing one novel amino acid Y in the junction (FIGS. 66, 67b, 68, SEQ ID NO:100). This splice variant encodes a 622 amino acids long protein which contains an incomplete first CUB domain followed by intact EGF, CUB, and two CCP modules, and possess a serine protease domain.
Comparison Report Between HUMC1RS_P6 and C1S_HUMAN
1. An isolated chimeric polypeptide HUMC1RS_P6, comprising a first amino acid sequence being at least 90% homologous to MWCIVLFSLLAWVYAEPTMYGEILSPNYPQAYPSEVEKSWDIEVPEGYGIHL YFTHLDIELSEN corresponding to amino acids 1-64 of C1S_HUMAN (SEQ ID NO:146), which also corresponds to amino acids 1-64 of HUMC1RS_P6 (SEQ ID NO:95), a second amino acid sequence bridging amino acid sequence comprising of Y, and a third amino acid sequence being at least 90% homologous to INECTDFVDVPCSHFCNNFIGGYFCSCPPEYFLHDDMKNCGVNCSGDVFTALI GEIASPNYPKPYPENSRCEYQIRLEKGFQVVVTLRREDFDVEAADSAGNCLDS LVFVAGDRQFGPYCGHGFPGPLNIETKSNALDIIFQTDLTGQKKGWKLRYHG DPMPCPKEDTPNSVWEPAKAKYVFRDVVQITCLDGFEVVEGRVGATSFYSTC QSNGKWSNSKLKCQPVDCGIPESIENGKVEDPESTLFGSVIRYTCEEPYYYME NGGGGEYHCAGNGSWVNEVLGPELPKCVPVCGVPREPFEEKQRIIGGSDADI KNFPWQVFEDNPWAGGALINEYWVLTAAHVVEGNREPTMYVGSTSVQTSRL AKSKMLTPEHVFIHPGWKLLEVPEGRTNFDNDIALVRLKDPVKMGPTVSPICL PGTSSDYNLMDGDLGLISGWGRTEKRDRAVRLKAARLPVAPLRKCKEVKVE KPTADAEAYVFTPNMICAGGEKGMDSCKGDSGGAFAVQDPNDKTKFYAAG LVSWGPQCGTYGLYTRVKNYVDWIMKTMQENSTPRED corresponding to amino acids 132-688 of C1S_HUMAN (SEQ ID NO:146), which also corresponds to amino acids 66-622 of HUMC1RS_P6 (SEQ ID NO:95), wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for an edge portion of HUMC1RS_P6 (SEQ ID NO:95), comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise NYI having a structure as follows (numbering according to HUMC1RS_P6; SEQ ID NO:95): a sequence starting from any of amino acid numbers 64-x to 64; and ending at any of amino acid numbers 66+((n−2)−x), in which x varies from 0 to n−2.
Therapeutic Applications for the C1s Splice Variants of the Present Invention
Using native and recombinant fragments of C1s it has been shown that the CUB-EGF region of C1s contains all the structural elements necessary for C1s to bind to C1r and C1q (Gal et al., 2002). Assembly of such a pseudo-C1 complexes retains their ability of C1r activation, despite the absent catalytic domain of C1s. Thus, the T7 variant that possess intact structure of first five modules but lacks the serine protease domain could serve as an antagonist for C1 activity, it might serve as a therapeutic agent in cases of unwanted or uncontrolled C1 activation such as inflammation resulting from ischemia and reperfusion, Alzheimer disease, rheumatoid arthritis, angioedema, and injury related tissue repair.
Structure-Function studies have shown that the CCP modules are responsible for the binding and proteolysis of C4 and C2 by C1s, while the CUB1-EGF modules are essential for the interaction of C1s with C1r (Gal et al., 2002). Since splice variant T8 has an incomplete first CUB domain, its ability to bind C1r will be harmed and therefore, it will not be active, however, it will still retain its ability to bind C1s substrates, namely C4 and C2. Thus, splice variant T8 will have antagonistic activity and might serve as a therapeutic agent in cases of unwanted or uncontrolled C1 activation as detailed above.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 27
Splice Variant of Interleukin-1 Beta Precursor
Background
Interleukin-1 beta precursor (IL-1 beta; GenBank Accession No. P01584; IL1B_HUMAN) is a cytokine having an interleukin-1 β receptor binding activity and is involved in inflammatory and immune responses. IL-1β is produced by activated macrophages and is involved in thymocyte proliferation, B-cell maturation and proliferation, and fibroblast growth factor activity. IL-1 stimulate the release of prostaglandin and collagenase from synovial cells, can increase the expression of adhesion molecules and induce the production of paracrine IL-6. IL-1β has been implicated in human myeloma (Lust J A and Donovan K A, 1999; Hematol. Oncol. Clin. North. Am. 13: 1117-25). The fact that the IL-1β precursor lacks any specific hydrophobic segments suggests that IL-1 is released by damaged cells or is secreted in a unique mechanism.
IL-1β is overexpressed in immune T-cells and can be used as a marker for proliferation of these cells or as a marker for pathological de-differentiation of such cells.
Clinical Applications
IL-1β has been implicated in various diseases, disorders or conditions such as allergy, amyotrophic lateral sclerosis, rheumatoid arthritis, asthma, infection, inflammation (e.g., inflammatory bowel disease, sepsis, ocular inflammation), bone marrow transplant rejection, Alzheimer's disease, aplastic anaemia, osteo arthritis, cancer (e.g., breast, colorectal, melanoma, myeloma, prostate cancer, sarcoma), chemotherapy-induced injury, colitis, ulcerative, diabetes, fever, glaucoma, head trauma, ischaemia, cerebral myelodysplastic syndrome, nephritis, neuropathy, diabetic ocular disorder, pain, Parkinson's disease, Surgery adjunct, Ulcer decubitus.
Splice Variant HSPROI1B_T4 (SEQ ID NO: 269) Encodes a New Secreted Form of the IL-1,a HSPROI1B_X1 (SEQ ID NO: 270)
The present inventors have uncovered a new IL-1β variant [HSPROI1B_T4—SEQ ID NO: 269; HSPROI1B_X1—SEQ ID NO:2701. The protein coordinates on the transcript start from nucleotide 156 and end at nucleotide 878 as set forth in SEQ ID NO:269 (HSPROI1B_T4 transcript).
Alignment of the new IL-1β variant (HSPROI1B_X1—SEQ ID NO:270) with the WT protein (GenBank Accession No. P01584; SEQ ID NO:265) revealed that the new variant includes the first 199 amino acids as of the WT protein (GenBank Accession No. P01584) followed by a unique 42 amino acid sequence [VSECYGMKPFSASCYHLFPDNHLLPAPIPRKSWEQVYLTILH (SEQ ID NO:266), FIG. 117]. The new variant uncovered by the present invention exhibits 7 out of the 14 β-strand regions and 3 out of 7 hydrogen bond turns of the WT protein. The following interpro domains are missing or reduced in the new variant: IPR000975 Interleukin-1, IPR002348 Interleukin 1/heparin-binding growth factor, IPR003294 Interleukin-1, alpha/beta, IPR003296 Interleukin-1, beta IL1B. The new IL-10 variant of the present invention is expected to be an extracellular interleukin 1 modulator.
Comparison Report Between HSPROI1B_X1 (SEQ ID NO:270) and IL1B_HUMAN_V1 (SEQ ID NO:656)
1. An isolated chimeric polypeptide HSPROI1B_X1 (SEQ ID NO:270), comprising a first amino acid sequence being at least 90% homologous to MAEVPELASEMMAYYSGNEDDLFFEADGPKQMKCSFQDLDLCPLDGGIQLRI SDHHYSKGFRQAASVVVAMDKLRKMLVPCPQTFQENDLSTEEPFIFEEEPIFF DTWDNEAYVHDAPVRSLNCTLRDSQQKSLVMSGPYELKALHLQGQDMEQQ VVFSMSFVQGEESNDKIPVALGLKEKNLYLSCVLKDDKPTLQLE corresponding to amino acids 1-199 of IL1B_HUMAN_V1 (SEQ ID NO:656), which also corresponds to amino acids 1-199 of HSPROI1B_X1 (SEQ ID NO:270), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSECYGMKPFSASCYHLFPDNHLLPAPIPRKSWEQVYLTILH (SEQ ID NO:266) corresponding to amino acids 200-241 of HSPROI1B_X1 (SEQ ID NO:270), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSPROI1B_X1 (SEQ ID NO:270), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSECYGMKPFSASCYHLFPDNHLLPAPIPRKSWEQVYLTILH (SEQ ID NO:266) in HSPROI1B_X1 (SEQ ID NO:270).
Comparison Report Between HSPROI1B_X1 (SEQ ID NO:270) and IL1B_HUMAN (SEQ ID NO:265)
1. An isolated chimeric polypeptide HSPROI1B_X1 (SEQ ID NO:270), comprising a first amino acid sequence being at least 90% homologous to MAEVP corresponding to amino acids 1-5 of IL1B_HUMAN (SEQ ID NO:265), which also corresponds to amino acids 1-5 of HSPROI1B_X1 (SEQ ID NO:270), a bridging amino acid E corresponding to amino acid 6 of HSPROI1B_X1 (SEQ ID NO:270), a second amino acid sequence being at least 90% homologous to LASEMMAYYSGNEDDLFFEADGPKQMKCSFQDLDLCPLDGGIQLRISDHHYS KGERQAASVVVAMDKLRKMLVPCPQTFQENDLSTEEPFIFEEEPIFFDTWDNE AYVHDAPVRSLNCTLRDSQQKSLVMSGPYELKALHLQGQDMEQQVVFSMSF VQGEESNDKIPVALGLKEKNLYLSCVLKDDKPTLQLE corresponding to amino acids 7-199 of IL1B_HUMAN (SEQ ID NO:265), which also corresponds to amino acids 7-199 of HSPROI1B_X1 (SEQ ID NO:270), and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSECYGMKPFSASCYHLFPDNHLLPAPIPRKSWEQVYLTILH (SEQ ID NO:266) corresponding to amino acids 200-241 of HSPROI1B_X1 (SEQ ID NO:270), wherein said first amino acid sequence, bridging amino acid, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSPROI1B_X1 (SEQ ID NO:270), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSECYGMKPFSASCYHLFPDNHLLPAPIPRKSWEQVYLTILH (SEQ ID NO:266) in HSPROI1B_X1 (SEQ ID NO:270).
Since the HSPROI1B_X1 variant of the present invention is a truncated form of IL-1β it can compete with the endogenous IL-1β and interfere with its various activities.
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:270 and/or an expressible polynucleotide homologous to SEQ ID NO:269 and/or a peptide homologous to SEQ ID NO:266 which can be used as an anti-inflammatory (e.g., for GI inflammatory, bowel disorders), antiallergic, antiarthritic, antiasthma, anticancer, immunosuppressant, septic shock treatment, analgesic, NSAID, antianaemic, antibiotic, antidiabetic, antiglaucoma, antiparkinsonian, antipsoriasis, antiulcer, antiviral, anti-HIV (anti AIDS), cardiovascular, cognition enhancer, dermatological, haematological, hepatoprotective, hypolipaemic, antiatherosclerosis, immunomodulator, anti-infective, immunostimulant, multiple sclerosis treatment, neurological, neuroprotective, ophthalmological, osteoporosis treatment, radio/chemoprotective, radio/chemosensitizer, respiratory, stomatological, symptomatic antidiabetic, urological, and vulnerary agent.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
While further reducing the present invention to practice, these results suggest the use of the new IL-1β variant of the present invention (HSPROI1B_X1—SEQ ID NO:270), the polynucleotide encoding same (HSPROI1B_T4—SEQ ID NO:269) and/or the peptide derived from the HSPROI1B_X1 variant (SEQ ID NO:266) as a diagnostic marker for immune T-cells proliferation or de-differentiation, as well as various cancers. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the IL-1βvariant (HSPROI1B_X1—SEQ ID NO:270)], nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 28
Splice Variant of Integrin Alpha-IIb Precursor
Background
Integrin αIIβ (also designated glycoprotein IIb) is a platelet adhesion receptor that forms a heterodimeric receptor with β3 (GPIIIa) subunit. Both subunits must be cosynthesized to be expressed on the cell surface. αIIβ expression is limited to platelets, megakaryocytes, and some transformed cells, and its naturally occurring ligands are fibrinogen, von Willebrand factor, fibronectin and vitronectin (all of which contain RGD sequence). On unstimulated platelets, it exists in a resting conformation, unable to bind large extracellular adhesive ligands and it becomes activated upon platelet stimulation via “inside-out” (cytoplasmic) signaling, or by binding small ligands (such as the RGD peptide). This allows ligand binding that leads to further conformational change and to “outside-in” signaling. Activated αIIβ 3 mediates fibrinogen binding and platelet aggregation. These activities prevent blood loss at sites of vascular injury, however, on ruptured atherosclerotic plaques it contribute directly to myocardial infraction and stroke (Naik and Parise, 1997).
The αIIβ and the β3 subunits are synthesized as single chains and assembled intracellularly into heterodimers, in a Ca2+-dependent process. The αIIβ subunit undergoes proteolytic cleavage, generating a mature disulfide-linked heavy and light chains. The light chain contains the cytoplasmic and the transmembrane domains whereas most of the extracellular domain is obtained by the heavy chain, which forms a large disulfide-linked loop and contains seven FG-GAP domains and four cation binding sites. The ligand specificity of αIIβ is attributed to the first third of the N-terminal portion of the extracellular domain, which includes the first two Ca2+-binding sites (Naik and Parise, 1997).
Clinical Applications
Platelets play an important role in the pathophysiology of acute myocardial infraction, unstable angina, and ischemic stroke. αIIβ3 constitutes the common pathway for platelet aggregation. A number of αIIβ3 antagonists were developed and evaluated in clinical trials. Three of them are approved in the US and other countries: abciximab (antibody Fab fragment), eptifibatide (a cyclic heptapeptide) and tirofiban (a tyrosin-derived non-peptide molecule). The greatest clinical impact of these agents (used in conjunction with heparin and aspirin) has been in the prevention of ischemic complications after percutaneous coronary intervention. Eptifibatide and tirofiban are specific for αIIβ3, whereas abciximab also exhibit cross-reactivity with αvβ3 and αMβ2. Abciximab has been more efficacious than the other agents, probably due to its cross reactivity with the other integrins. Abciximab has also yielded promising results in experimental models of tumor angiogenesis and sickle cell anemia (Leclerc et al., 2002). In addition, it has been described (in the pharma) as a launched drug for unstable angina, restenosis, coronary thrombosis, and surgery adjunct, and in phase III of clinical trials for treatment of Crohn's disease myocardial infraction, and cerebral ischemia.
Another pathogenenesis involving αIIβ3 is chronic immune thrombocytopenia purpura (AITP). Patients with AITP produce autoantibodies, directed mainly against αIIβ3, that cause platelet destruction. Two recombinant anti-idiotypic antibodies have been described to block the interaction of the autoantibodies with αIIβ3 in AITP patients (Escher et al., 2002).
Integrin αIIβ Splice Variants
The present inventors uncovered two novel splice variants of integrin αIIβ3 gene (SEQ ID NOs: 83, 84, 86 and 87; FIGS. 53a-b, 54a-b).
The T8 Splice Variant (HUMGPIIBA_R36—SEQ ID NO:87)
The T8 splice variant (HUMGPIIBA_R36—SEQ ID NO:87; FIG. 54a) was obtained by the alternative splicing of the integrin αIIβ gene, thus leading to skipping of exons 26, 27, 28, 29 and the generation of a new αIIβ variant (HUMGPIIBA_X26—SEQ ID NO:86; FIG. 54b). Alignment of the new αIIβ variant (variant T8; SEQ ID NO:83) with the WT protein (ITAB_HUMAN; SEQ ID NO:143) revealed that the new variant lacks amino acids 867-1019 of wild type αIIβ (FIG. 55b, 56). This splice variant encodes 886 amino acids long protein (SEQ ID NO:86). It encompasses most of the heavy chain, including FG-GAPS I-VH within it, and the cytoplasmic domain, while it lacks the extracellular portion of the light chain and the TM. It contains four out of seven potential N-glycosilation sites and seven out of nine disulfide bonds.
Comparison Report Between HUMGPIIBA_X26 (SEQ ID NO:86) and ITAB_HUMAN (SEQ ID NO:143)
1. An isolated chimeric polypeptide HUMGPIIBA_X26 (SEQ ID NO:86), comprising a first amino acid sequence being at least 90% homologous to MARALCPLQALWLLEWVLLLLGPCAAPPAWALNLDPVQLTFYAGPNGSQFG FSLDFHKDSHGRVAIVVGAPRTLGPSQEETGGVFLCPWRAEGGQCPSLLFDLR DETRNVGSQTLQTFKARQGLGASVVSWSDVIVACAPWQHWNVLEKTEEAEK TPVGSCFLAQPESGRRAEYSPCRGNTLSRIYVENDFSWDKRYCEAGFSSVVTQ AGELVLGAPGGYYFLGLLAQAPVADIFSSYRPGILLWHVSSQSLSFDSSNPEYF DGYWGYSVAVGEFDGDLNTTEYVVGAPTWSWTLGAVEILDSYYQRLHRLR AEQMASYFGHSVAVTDVNGDGRHDLLVGAPLYMESRADRKLAEVGRVYLF LQPRGPHALGAPSLLLTGTQLYGRFGSAIAPLGDLDRDGYNDIAVAAPYGGPS GRGQVLVFLGQSEGLRSRPSQVLDSPFPTGSAFGFSLRGAVDIDDNGYPDLIV GAYGANQVAVYRAQPVVKASVQLLVQDSLNPAVKSCVLPQTKTPVSCFNIQ MCVGATGHNIPQKLSLNAELQLDRQKPRQGRRVLLLGSQQAGTTLNLDLGG KHSPICHTTMAFLRDEADERDKLSPIVLSLNVSLPPTEAGMAPAVVLHGDTHV QEQTRIVLDCGEDDVCVPQLQLTASVTGSPLLVGADNVLELQMDAANEGEG AYEAELAVHLPQGAHYMRALSNVEGFERLICNQKKENETRVVLCELGNPMK KNAQIGIAMLVSVGNLEEAGESVSFQLQIRSKNSQNPNSKIVLLDVPVRAEAQ VELRGNSFPASLVVAAEEGEREQNSLDSWGPKVEHTYELHNNGPGTVNGLH LSIHLPGQSQPSDLLYILDIQPQGGLQCFPQPPVNPL corresponding to amino acids 1-866 of ITAB_HUMAN (SEQ ID NO:143), which also corresponds to amino acids 1-866 of HUMGPIIBA_X26 (SEQ ID NO:86), and a second amino acid sequence being at least 90% homologous to KVGFFKRNRPPLEEDDEEGE corresponding to amino acids 1020-1039 of ITAB_HUMAN (SEQ ID NO:143), which also corresponds to amino acids 867-886 of HUMGPIIBA_X26 (SEQ ID NO:86), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HUMGPIIBA_X26 (SEQ ID NO:86), comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise LK, having a structure as follows: a sequence starting from any of amino acid numbers 866-x to 866; and ending at any of amino acid numbers 867+((n−2)−x), in which x varies from 0 to n−2.
The T9 Splice Variant (HUMGPIIBA_R35—SEQ ID NO:84)
The T9 splice variant (HUMGPIIBA_R35— SEQ ID NO:84; FIG. 53a) was obtained by the alternative splicing of the integrin αIIβ gene, thus leading to skipping of exon 29 and the generation of a of a new αIIβ variant (HUMGPIIBA_X24—SEQ ID NO:83; FIG. 53b). Alignment of the new αIIβ variant protein (variant T9, HUMGPIIBA_X24) with the WT protein (ITAB_HUMAN; SEQ ID NO:143) revealed that the new variant lacks lacking amino acids 982-1020 of wild type αIIβ (FIGS. 55a, 56). This splice variant encodes 1000 amino acids long protein (SEQ ID NO:83). It encompasses the heavy chain including FG-GAPS I-VII within it, part of the extracellular portion of the light chain, and the cytoplasmic domain, while it lacks the TM. It contains all the potential N-glycosilation sites and disulfide bonds.
Comparison Report Between HUMGPIIBA_X24 (SEQ ID NO:83) and ITAB_HUMAN (SEQ ID NO:143)
1. An isolated chimeric polypeptide HUMGPIIBA_X24 (SEQ ID NO:83), comprising a first amino acid sequence being at least 90% homologous to MARALCPLQALWLLEWVLLLLGPCAAPPAWALNLDPVQLTFYAGPNGSQFG FSLDFHKDSHGRVAIVVGAPRTLGPSQEETGGVFLCPWRAEGGQCPSLLFDLR DETRNVGSQTLQTFKARQGLGASVVSWSDVIVACAPWQHWNVLEKTEEAEK TPVGSCFLAQPESGRRAEYSPCRGNTLSRIYVENDFSWDKRYCEAGFSSVVTQ AGELVLGAPGGYYFLGLLAQAPVADIFSSYRPGILLWHVSSQSLSEDSSNPEYF DGYWGYSVAVGEFDGDLNTTEYVVGAPTWSWTLGAVEILDSYYQRLHRLR AEQMASYFGHSVAVTDVNGDGRHDLLVGAPLYMESRADRKLAEVGRVYLF LQPRGPHALGAPSLLLTGTQLYGRFGSAIAPLGDLDRDGYNDIAVAAPYGGPS GRGQVLVFLGQSEGLRSRPSQVLDSPFPTGSAFGFSLRGAVDIDDNGYPDLIV GAYGANQVAVYRAQPVVKASVQLLVQDSLNPAVKSCVLPQTKTPVSCFNIQ MCVGATGHNIPQKLSLNAELQLDRQKPRQGRRVLLLGSQQAGTTLNLDLGG KHSPICHTTMAFLRDEADPRDKLSPIVLSLNVSLPPTEAGMAPAVVLHGDTHV QEQTRIVLDCGEDDVCVPQLQLTASVTGSPLLVGADNVLELQMDAANEGEG AYEAELAVHLPQGAHYMRALSNVEGFERLICNQKKENETRVVLCELGNPMK KNAQIGIAMLVSVGNLEEAGESVSFQLQIRSKNSQNPNSKIVLLDVPVRAEAQ VELRGNSFPASLVVAAEEGEREQNSLDSWGPKVEHTYELHNNGPGTVNGLH LSIHLPGQSQPSDLLYILDIQPQGGLQCFPQPPVNPLKVDWGLPIPSPSPIHPAH HKRDRRQIFLPEPEQPSRLQDPVLVSCDSAPCTVVQCDLQEMARGQRAMVTV LAFLWLPSLYQRPLDQFVLQSHAWFNVSSLPYAVPPLSLPRGEAQ corresponding to amino acids 1-981 of ITAB_HUMAN (SEQ ID NO:143), which also corresponds to amino acids 1-981 of HUMGPIIBA_X24 (SEQ ID NO:83), and a second amino acid sequence being at least 90% homologous to VGFFKRNRPPLEEDDEEGE corresponding to amino acids 1021-1039 of ITAB_HUMAN (SEQ ID NO:143), which also corresponds to amino acids 982-1000 of HUMGPIIBA_X24 (SEQ ID NO:83), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HUMGPIIBA_X24 (SEQ ID NO:83), comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise QV, having a structure as follows: a sequence starting from any of amino acid numbers 981-x to 981; and ending at any of amino acid numbers 982+((n−2)−x), in which x varies from 0 to n−2.
Therapeutic Application of the Variants
Peterson et al. have generated a soluble recombinant form of integrin αIIβ3 (rsαIIbβ3) lacking the transmembrane and the cytoplasmic domains. The high yield of soluble integrin produced in this study is attributed to the inclusion of the entire extracellular region of αIIβ light chain in the construct. rsαIIbβ3 was shown to react spontaneously with fibrinogen, and this interaction was inhibited in the presence of RGD peptides. rsαIIbβ3 reacted with a variety of antibodies specific to platelet αIIbβ3, it is predicted to maintain the ligand binding conformation.
Based on these evidences, T9, which is predicted to be a soluble form of αIIβ can be used for production of a soluble αIIbβ3 when co-expressed with a soluble form of the β3 subunit. Such a heterodimer might antagonize platelet αIIbβ3 interaction with its natural ligands (Peterson at al., 1998; Wang et al., 1997, Esher et al., 1995).
T8 encompass a shorter extracellular region than T9, which completely lacks the light chain. Thus, it might form a heterodimer with β3 and serve as an antagonist for αIIbβ3 interaction with its natural ligands, however, such a construct might be secreted in low amounts.
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:86 or 83 and/or an expressible polynucleotide homologous to SEQ ID NO:87 or 84 which can be used as an antagonist of the platelet αIIbβ3 interaction with its natural ligands and thus prevent and/or treat ischemic complications after percutaneous coronary intervention, unstable angina, restenosis, coronary thrombosis, surgery adjunct, Crohn's disease, myocardial infraction, and cerebral ischemia. In addition, such a therapeutic agent can be used as a target for autoantibodies directed against αIIβ3 [e.g., in the case of chronic immune thrombocytopenia purpura (AITP)] and thus prevent platelet destruction.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 29
Splice Variant of Integrin Alpha-4 Precursor
Background
Integrins are cell surface receptors that mediate cell adhesion to extracellular matrix (ECM) as well as cell-cell adhesion. The integrin family is composed of 19 different α subunits and 8 different β subunits that are associated, in a non-covalent manner, to form 25 different heterodimers with many distinct ligand-binding properties (Humphries, 2000). Integrin α4 can form heterodimers with either α1 or β7. The α4β1 (VLA4) complex is expressed on B and T cells, thymocytes, monocytes, eosenophils, basophils, macrophages, and some melanoma cells, and has several distinct adhesion activities: (i) it binds fibronectin, (ii) it binds activated endothelium via VCAM-1 (vascular cell adhesion molecule-1) (iii) it involves in the intercellular leukocyte interaction (homotypic aggregation), and (iv) may play a role in cytolytic T cell function (Teixido et al., 1992). As a result of its binding activity, VLA4 plays a role in leukocyte recruitment to inflammatory sites. In addition, adhesion of VLA4 bearing tumor cells to VCAM-1 indicates a role for VLA4 during metastasis. As opposed to α4β1, the α4β7 heterodimer is expressed mainly on lymphocytes that home to the intestine and to associated lymphoid tissues such as Peyer's patches. It binds mainly MAdCAM-1 which is expressed on the high endothelial venules (HEV) of Peyer's patches, on mesenteric lymph node HEV and on lamina propria venules within the gut, but it also binds VCAM-1. Both VCAM-1 and MAdCAM-1 are expressed upon inflammation in the gut, however, VCAM-1 is also expressed in peripheral organs while MAdCAM-1 expression is confined to the gut. Thus, MAdCAM-1 is thought to be involved in the recruitment of leukocytes to the gut in chronic inflammatory diseases. The α4β1 and α4β7 integrins have been shown the mediate the initial rolling of immune cells but furthermore, upon chemokine activation, they mediate firm adhesion to cytokine-activated endothelium.
Structurally, integrin α4 is composed of seven N-terminal repeats designated GF-GAPs followed by a sequence with no identified domains, a transmembrane domain and a cytoplasmic tail which is capable of transducing intracellular signals. Integrin α4 encompasses three cation binding sites (also designated EF-hands) within the last three GF-GAP domains. These sites are involved in ligand binding. The α4 subunit can be expressed on cell surface either as an intact form (α4-150) or can be cleaved near the middle of the molecule into non-disulfide-linked fragments of 80 and 70 KDa (Teixido et al., 1992). The cleavage of α4 is a regulated, compartmentalized event, occurring soon after maturation of the β1-associated α4 subunit, and it is supposed to have a role in integrin activation (α6 cleavage mutants are capable of binding matrix but defective in inside-out signaling upon PMA activation) (Blue et al., 1993).
Clinical Applications
Elevated MAdCAM-1 expression in the gastrointestinal tract has been linked with several gastrointestinal autoimmune diseases, including Crohn's disease, ulcerative colitis, and hepatitis C. Expression of VCAM-1 on HEVs in the lung is correlated with asthma and its expression in the synovium and in nervous tissues is thought to be linked to rheumatoid arthritis and multiple sclerosis, respectively. VCAM-1 expression is also associated with inflammatory bowel disease (Jackson, 2002). α4 integrins have also been implicated in the pathogenesis of cardiovascular diseases, most notably atherosclerosis and ischemia reperfusion injury (Liu et al., 2000). In vivo and in vitro studies have shown that blockage of α4β1 inhibits the attachment and recruitment of mononuclear leukocytes during atherosclerosis. In addition to their role in the inflammatory process, binding of α4 integrins to their ligands may also play important roles in stem cell adhesion to bone marrow stromal cells, and in tumor cell metastasis (Jackson, 2002). Furthermore, VLA4 is involved in graft rejection and its blockage by antibodies result in increased survival in mice model of hurt transplant. The pro-survival effect was increased upon combined treatment with antibodies for both VLA4 and VCAM-1 (Isobe et al., 1998). mAbs directed for α4 can also efficiently inhibit Insulin-dependent diabetes mellitus (Michie et al., 1998). As α4 integrins are widely implicated in disease processes, they are attractive targets for the development of antagonists. Such antagonists have been developed in the form of mAbs, peptides, peptidomimetics, proteomimetics, and small molecules, most of which are targeted to block α4β1, however, non-specific α4 inhibitors that will inhibit both α4β1 and α4β7 are thought to afford the greatest benefit for treatment of autoimmune diseases since a generic α4 integrin antagonist would be useful for a broader range of indications (Jackson, 2002).
Splice Variant Structure
The present inventors uncovered a novel splice variant of Integrin α4 (HSINTAL4_T2—SEQ ID NO:111; FIG. 78a). Integrin α4 splice variant T2 result from alternative splicing of the integrin α4 gene, leading to extension of exon 19 due to splicing in an alternative 5′ acceptor site of exon 19 (FIGS. 79-81). This leads to insertion of a stop codon and result in a truncated integrin α4 protein of 703 amino acids (HSINTAL4_P2—SEQ ID NO:110; FIG. 78b). The protein coordinates on the transcript start from nucleotide 1152 and end at nucleotide 3260 as set forth in SEQ ID NO:111 (HSINTAL4_T2 transcript).
Alignment of the new integrin α4 variant (HSINTAL4_P2—SEQ ID NO:110) with the WT protein (GenBank Accession No. P13612; SEQ ID NO:149) revealed that the new that includes 697 wild type amino acids and 6 unique amino acids (LFHFSH; SEQ ID NO:112). It contains the seven N-terminal repeats designated GF-GAPs, and a part of the following sequence with no identified domains; it lacks the transmembrane domain and the cytoplasmic tail. Within this region, it contains the three cation binding motifs (also designated EF-hands), the cleavage site, 6 out of 9 disulfide bonds and 9 out of 11 potential glycosylation sites residing within the extracellular domain.
Comparison Report Between HSINTAL4_P2 (SEQ ID NO:110) and ITA4_HUMAN (SEQ ID NO:149)
1. An isolated chimeric polypeptide HSINTAL4_P2 (SEQ ID NO:110), comprising a first amino acid sequence being at least 90% homologous to MFPTESAWLGKRGANP corresponding to amino acids 1-16 of ITA4_HUMAN (SEQ ID NO:149), which also corresponds to amino acids 1-16 of HSINTAL4_P2 (SEQ ID NO:110), a bridging amino acid A corresponding to amino acid 17 of HSINTAL4_P2 (SEQ ID NO:110), a second amino acid sequence being at least 90% homologous to PEAAVRETVMLLLCLGVPTGRPYNVDTESALLYQGPHNTLFGYSVVLHSHGA NRWLLVGAPTANWLANASVINPGAIYRCRIGKNPGQTCEQLQLGSPNGEPCG KTCLEERDNQWLGVTLSRQPGENGSIVTCGHRWKNIFYIKNENKLPTGGCYG VPPDLRTELSKRIAPCYQDYVKKFGENFASCQAGISSFYTKDLIVMGAPGSSY WTGSLFVYNITTNKYKAFLDKQNQVKFGSYLGYSVGAGHFRSQHTTEVVGG APQHEQIGKAYIFSIDEKELNILHEMKGKKLGSYFGASVCAVDLNADGFSDLL VGAPMQSTIREEGRVFVYINSGSGAVMNAMETNLVGSDKYAARFGESIVNLG DIDNDGEEDVAIGAPQEDDLQGAIYIYNGRADGISSTESQRIEGLQISKSLSMFG QSISGQIDADNNGYVDVAVGAFRSDSAVLLRTRPVVIVDASLSHPESVNRTKF DCVENGWPSVCIDLTLCFSYKGKEVPGYIVLFYNMSLDVNRKAESPPRFYFSS NGTSDVITGSIQVSSREANCRTHQAFMRKDVRDILTPIQIEAAYHLGPHVISKR STEEFPPLQPILQQKKEKDIMKKTINFARFCAHENCSADLQVSAKIGFLKPHEN KTYLAVGSMKTLMLNVSLFNAGDDAYETTLHVKLPVGLYFIKILEL corresponding to amino acids 18-697 of ITA4_HUMAN (SEQ ID NO:149), which also corresponds to amino acids 18-697 of HSINTAL4_P2 (SEQ ID NO:110), and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence LFHFSH (SEQ ID NO:112) corresponding to amino acids 698-703 of HSINTAL4_P2 (SEQ ID NO:110), wherein said first amino acid sequence, bridging amino acid, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSINTAL4_P2 (SEQ ID NO:110), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence LFHFSH (SEQ ID NO:112) in HSINTAL4_P2 (SEQ ID NO:110).
Therapeutic Application of the Splice Variant
Recombinant soluble α4β1 have been previously produced by co-transfecting insect cells with both α and β chains lacking the transmembrane and cytoplasmic domains. These rsα4β1 were able to dimerize, to bind their ligands, and retained specific mAbs epitopes indicating the transmembrane domain and the cytoplasmic tail are not necessary for these activities (Humphries, 2000). Splice variant T2 contains an incomplete extracellular domain that contains many of the sites reported to be important for ligand binding, however, it does not contain Asp-698 and Asp-811 that are reported to be important for LDV binding (but not for RGD binding) (Zeller et al., 1997). Apparently, T2 might bind fibronectin and MAdCAM-1, however it is not clear whether this binding activity could be attributed to α4 which is not dimerized with a β subunit. Moreover, the dimerization process is poorly described and it is not clear whether it is an intracellular process or a membranal process. Antagonists for α4β7 and for α4β1 have been described in phase II of clinical trials for treatment of Crohn's disease, ulcerative colitis, asthma, rheumatoid arthritis, multiple sclerosis and inflammatory bowel disease. α4β1 antagonist was also described for treatment of head trauma.
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:110 and/or an expressible polynucleotide homologous to SEQ ID NO:111 and/or a peptide homologous to SEQ ID NO:112 which can be serve as an antagonist of α4 interaction with either al, β7 or β4, and/or an antagonist for the α4β34 and/or α4β7 receptor. As such, the agent of the present invention can be used treat gastrointestinal autoimmune diseases (e.g., Crohn's disease, ulcerative colitis, and hepatitis C), asthma, rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease, cardiovascular diseases (e.g., atherosclerosis and ischemia reperfusion injury), tumor cell metastasis, graft rejection, and insulin-dependent diabetes mellitus.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 30
Splice Variant of Beta Platelet-Derived Growth Factor Receptor Precursor (PDGF-R-BETA)
Background
The beta platelet-derived growth factor receptor precursor (PDGF-R-β; CD140b antigen; GenBank Accession No. P09619; PGDR_HUMAN; PDGFRB) is a type I transmembrane protein, transmembrane receptor protein tyrosine kinase involves in signaling pathway and cell growth and/or maintenance.
PDGF-R-β has been implicated in decubitus ulcer, diabetic ulcer, various cancers (e.g., leukaemia), hyperlipidaemia, glomerulonephritis and renal failure, restenosis, infection, peripheral vascular disease, tissue regeneration (e.g., bone), thrombocytopenia, and wound healing.
PDGF-R-β is overexpressed in pancreatic tumors it can be used as a marker for these pathologies.
Splice Variant HUMPDGFR_T13 (SEQ ID NO:271) Encodes a New Secreted Form of the PDGF-R-β, HUMPDGFR_P6 (SEQ ID NO:272)
The present inventors have uncovered a new PDGF-R-β variant [HUMPDGFR_T13—SEQ ID NO:271; HUMPDGFR_P6—SEQ ID NO:272]. The protein coordinates on the transcript start from nucleotide 474 and end at nucleotide 2108 as set forth in SEQ ID NO:271 (HUMPDGFR_T13 transcript).
Alignment of the new PDGF-R-β variant (HUMPDGFR_P6—SEQ ID NO:272) with the WT protein (GenBank Accession No. P09619; SEQ ID NO:267) revealed that the new variant includes the first 526 amino acids as of the WT protein (GenBank Accession No. P09619) followed by a unique 19 amino acid sequence [CESPASVAPDDPNPYLNPA (SEQ ID NO:268), FIG. 118]. The new variant uncovered by the present invention lacks the transmembrane domain (amino acids 532-556 of WT), cytoplasmic domain (amino acids 557-1106 of WT), np binding domain (amino acids 606-614 of WT), two phosphotyrosine sites (amino acids 751 and 857 of WT), and the PDGFRB active site (amino acid 826 of WT). Thus, the new PDGF-R-β variant of the present invention lacks the Protein kinase (IPR000719) and Tyrosine protein kinase (IPR001245) domains, as well as the TM domain and thus is expected to be a secreted, extracellular protein. Such a protein can compete with the endogenous PDGF-R-β, interfere with its various activities, and serve as a PDGF-R-β antagonist or a platelet growth factor modulator.
Comparison Report Between HUMPDGFR_P6 (SEQ ID NO:272) and PGDR_HUMAN (SEQ ID NO:267)
1. An isolated chimeric polypeptide HUMPDGFR_P6 (SEQ ID NO:272), comprising a first amino acid sequence being at least 90% homologous to MRLPGAMPALALKGELLLLSLLLLLEPQISQGLVVTPPGPELVLNVSSTFVLTC SGSAPVVWERMSQEPPQEMAKAQDGTFSSVLTLTNLTGLDTGEYFCTHNDSR GLETDERKRLYIFVPDPTVGFLPNDAEELFIFLTEITEITIPCRVTDPQLVVTLHE KKGDVALPVPYDHQRGFSGIFEDRSYICKTTIGDREVDSDAYYVYRLQVSSIN VSVNAVQTVVRQGENITLMCIVIGNEVVNFEWTYPRKESGRLVEPVTDFLLD MPYHIRSILHIPSAELEDSGTYTCNVTESVNDHQDEKAINITVVESGYVRLLGE VGTLQFAELHRSRTLQVVFEAYPPPTVLWFKDNRTLGDSSAGEIALSTRNVSE TRYVSELTLVRVKVAEAGHYTMRAFHEDAEVQLSFQLQINVPVRVLELSESH PDSGEQTVRCRGRGMPQPNIIWSACRDLKRCPRELPPTLLGNSSEEESQLETN VTYWEEEQEFEVVSTLRLQHVDRPLSVRCTLRNAVGQDTQEVIVVPH corresponding to amino acids 1-526 of PGDR_HUMAN (SEQ ID NO:267), which also corresponds to amino acids 1-526 of HUMPDGFR_P6 (SEQ ID NO:272), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence CESPASVAPDDPNPYLNPA (SEQ ID NO:268) corresponding to amino acids 527-545 of HUMPDGFR_P6 (SEQ ID NO:272), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMPDGFR_P6 (SEQ ID NO:272), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence CESPASVAPDDPNPYLNPA (SEQ ID NO:268) in HUMPDGFR_P6 (SEQ ID NO:272).
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:272 and/or an expressible polynucleotide homologous to SEQ ID NO:271 and/or a peptide homologous to SEQ ID NO:268 which can be used to treat decubitus ulcer, diabetic ulcer, various cancers (e.g., leukaemia), hyperlipidaemia, glomerulonephritis and renal failure, restenosis, infection, peripheral vascular disease, tissue regeneration (e.g., bone), thrombocytopenia, and wound healing. Thus is agent can be used in various therapies such as, ophthalmological, stomatological, symptomatic antidiabetic, vulnerary, radio/chemosensitizer, anticancer, cardiovascular; hypolipaemic/Antiatherosclerosis, antihypertensive, urological, antihypertensive, antiulcer, antiviral, cardiovascular, haematological, musculoskeletal, and radio/chemoprotective.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
While further reducing the present invention to practice, these results suggest the use of the new PDGF-R-β variant of the present invention (HUMPDGFR_P6—SEQ ID NO: 272), the polynucleotide encoding same (HUMPDGFR_T13—SEQ ID NO: 271) and/or the peptide derived from the HUMPDGFR_P6 variant (SEQ ID NO: 268) as a diagnostic marker for various cancers such as pancreatic tumors. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the PDGF-R-β variant (HUMPDGFR_P6—SEQ ID NO:272)], or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 31
Splice Variant of Interleukin-13 Receptor Alpha-1 Chain Precursor
Background
IL-13, a pleioytopic immune regulatory cytokine, produced predominantly by activated lymphocytes, especially Th2 cells, mast cells, basophils, NK and dentritic cells. Although IL-13 exhibits only 30% homology with IL-4 in amino acid sequence, it shares a conserved hydrophobic structural core with IL-4 and both of these cytokines share the same receptor subunit. Therefore IL-13 is able to induce nearly all biological responses generated by IL-4 (Terabe et al., 2004). Both cytokines induce IgE class switching in B cells, enhancement of monocyte/macrophage antigen presentation ability, by up-regulation of major histocompatibility complex (MHC) class II and CD23 expression, up-regulation of VCAM-1 molecules on endothelial cells and adhesion molecules on monocytes and mast cells, which contribute to enhances extravasation, mobility and trafficking of these cells. Both cytokines also have important immunosuppressive and anti-inflammatory activities on macrophages and other cells, including inhibition of pro-inflammatory cytokines like IL-1, IL-6, IL-10, IL-12, TNF-a, GM-CSF, G-CSF, and chemokines like IL-8, MIP-1, MCP-3, Eotaxin and RANTES and production of anti-inflammatory molecules. Despite these common functions of the two cytokines, not all biological properties are mutual and overlapping, which is partially due to the differential expression of IL-4 and IL-13 receptor components on various cell types and species. IL-4, but not IL-13, promotes Th2 cell differentiation, which is characterised by secretion of IL-4, IL-5, IL-9, IL-10, and IL-13 and generation of humoral immune responses (Brombacher, 2000). Recently many unique effector functions of IL-13 have been demonstrated, that distinguish it from IL-4. Resistance to most gastrointestinal nematodes is mediated by type-2 cytokine responses, in which IL-13 plays a dominant role. By regulating cell-mediated immunity, IL-13 modulates resistance to intracellular organisms including Leishmania major, Leishmaniamexicana, and Listeria monocytogenes. In the lung, IL-13 is the central mediator of allergic asthma, where it regulates eosinophilic inflammation, mucus secretion, and airway hyperresponsiveness (Wynn, 2003). IL-13 was also shown to be involved in several malignancies. Its effect in tumor growth by an autocrine manner was observed in Hodgkin's lymphoma (Terabe et al., 2004). In addition to the promotion of tumor growth, IL-13 affects the immune response to this tumor. By down-regulating type-1-immune response, IL-13 acts as a major suppressor of immunosurveillance mechanisms which are part of the host defense against tumors. Finally, IL-13 was shown to be involved in the induction of oxazolone colitis (TH2-induced ulcerative colitis), parasite-induced liver and lung fibrosis, and other cases of lung fibrosis (Terabe et al., 2004). The overlapping biological functions of IL-4 and IL-13 on some cell types are due to at least, one shared component of otherwise distinct receptors. The IL-4 receptor (IL-4R) is a heterodimeric complex comprised of an IL-4Rα-chain and the common γ chain (γc), also called the type I IL-4R. IL-4Rα-chain can dimerize with IL-13-Rα1 to form a functional IL-13 receptor, called also the type II IL-4R. This type of receptor expressed on a broad range of cell types, including hematopoitic and non hematopoitic cells, except for T cells, and can bind both IL-13 and IL-4. IL-13Rα1 can bind IL-13 but not IL-4. IL-4Rα can bind only IL-4. IL-13 binds with low affinity to the IL-13Rα1 chain, but by IL-4Rα recruitment forms the high affinity receptor for IL-13. On the other hand, IL-4 first binds to IL-4Rα, which then recruits either the IL-13Rα1 or the IL-2Rγc chain, which increases its binding affinity (Terabe et al., 2004). There is another receptor for IL-13 called IL-13α2. This receptor binds only IL-13 with relatively high affinity and seems to be a decoy. Since the IL-4Rα chain is the only component which has kinase-sensitive tyrosine residues in the cytoplasmic domain, signals from both type I and type II IL-4R are transduced by the IL-4Rα chain. Therefore, IL-13 and IL-4 primarily use the same Janus kinase (JAK)-signal transducer and activator of transcription (Stat6) pathway, although each receptor chain associates with different JAKs. When the type I or type II IL-4R is dimerized, JAKs associated with the receptor components phosphorylate additional tyrosine residues of the IL-4Rα cytoplasmic domain. This phosphorylation recruits Stat6, which is then also phosphorylated, dimerize and migrate to the nucleus to bind to certain promoters (Terabe et al., 2004).
Clinical Application
IL-13 regulates a variety of functions in immune cells. It has been shown to play a prominent role in atopic dermatitis, allergic rhinitis, pulmonary asthma and related lung injury, lung fibrosis, hepatic fibrosis induced by schistosomiasis, TH2-induced ulcerative colitis and susceptibility to Leishmania major infection and malignancies. Therefore, it has been hypothesized that blocking the effect of IL-13 can provide therapeutic benefit in these pathological conditions.
Splice Variant Structure
The present inventors uncovered a novel splice variant of IL-13Rα1 gene (Z40355_T1—SEQ ID NO:93; FIG. 61a). IL-13Rα1 splice variant T1 results from alternative splicing of the IL-13Rα1 gene, thus introducing a novel exon 5a (between exons 5 and 6), leading to an insertion of a stop codon and the generation of a truncated protein (Z40355_P2—SEQ ID NO:92, FIG. 61b and FIGS. 62-64). The protein coordinates on the transcript start from nucleotide 70 and end at nucleotide 789 as set forth in SEQ ID NO:93 (Z40355_T1 transcript). Alignment of the new IL-13Rα1 splice variant (variant T1; SEQ ID NO:92) with the WT protein (GenBank Accession No. P78552; I131_HUMAN; SEQ ID NO:145) revealed that the new variant encodes a 240 amino acids long protein which contains the N-terminal 225 amino acids of the wild type IL-13R, including the signal sequence (residues 1-21), almost the complete cytokine receptor common beta/gamma chain domain (CR1A) and a unique sequence of 15 amino acids at the C-terminus of the protein (GPTSPYCHIGDEVST; SEQ ID NO:94; FIG. 63). It is predicated to be a secreted protein due to the fact that it lacks the transmembrane domain.
Comparison Report Between Z40355_P2 (SEQ ID NO:92) and I131_HUMAN (SEQ ID NO:145)
1. An isolated chimeric polypeptide Z40355_P2 (SEQ ID NO:92), comprising a first amino acid sequence being at least 90% homologous to MEWPARLCGLWALLLCAGGGGGGGGAAPTETQPPVTNLSVSVENLCTVIWT WNPPEGASSNCSLWYFSHFGDKQDKKIAPETRRSIEVPLNERICLQVGSQCST NESEKPSILVEKCISPPEGDPESAVTELQCIWHNLSYMKCSWLPGRNTSPDTNY TLYYWHRSLEKIHQCENIFREGQYFGCSFDLTKVKDSSFEQHSVQIMVKDNA GKIKPSFNIVPLTSR corresponding to amino acids 1-225 of I131_HUMAN (SEQ ID NO:145), which also corresponds to amino acids 1-225 of Z40355_P2 (SEQ ID NO:92), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GPTSPYCHIGDEVST (SEQ ID NO:94) corresponding to amino acids 226-240 of Z40355_P2 (SEQ ID NO:92), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of Z40355_P2 (SEQ ID NO:92), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GPTSPYCHIGDEVST (SEQ ID NO:94) in Z40355_P2 (SEQ ID NO:92).
The Therapeutic Potential of IL-13Rα1 Splice Variants
IL-13Rα1 splice variants, which is a soluble form of the receptor could serve as a powerful antagonists of IL-13-IL-13R interaction. It contains the complete CRIA, which is predicted to constitute the ligand binding region and therefore can inhibit IL-13 signaling by competing with the membrane-bound receptor for IL-13, thus preventing it from binding to the cell surface receptor and activating the membrane receptor.
IL-13 signaling pathway plays a major role in the pathogenesis of allergic diseases. Blocking of this signaling could therefore have an important therapeutic potential for the treatment of asthma, atopic dermatitis and allergic rhinitis. In addition, IL-13 has been shown to play a role in tissue fibrosis such as lung fibrosis and hepatic fibrosis induced by schistosomiasis and in TH2-induced ulcerative colitis. Inhibition of this signaling pathway can provide therapeutic advantage in these pathological conditions. Manipulation of IL-13 effector function may also prove useful in the treatment of some cancers like B-cell chronic lymphocytic leukemia and Hodgkin's disease, where IL-13 modulates apoptosis or tumor cell growth. IL-13 can also inhibit tumor immunosurveillance. As such, inhibitors of IL-13 might be effective as cancer immunotherapeutics.
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:92 and/or an expressible polynucleotide homologous to SEQ ID NO:93 and/or a peptide homologous to SEQ ID NO:94 which can be used to prevent and/or treat allergic diseases (e.g., asthma, atopic dermatitis and allergic rhinitis), tissue fibrosis (e.g., lung fibrosis and hepatic fibrosis induced by schistosomiasis and in TH2-induced ulcerative colitis), cancers (e.g., B-cell chronic lymphocytic leukemia and Hodgkin's disease), tumor immunosurveillance (i.e., serve as an immunotherapeutic agent for cancer treatment).
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 32
Splice Variant of Tissue-Type Plasminogen Activator Precursor (TPA)
Background
Tissue plasminogen activator (tPA) is a serine protease responsible for converting plasminogen into the protease plasmin. Plasmin is involved in a range of biological processes, including fibrinolysis, tissue development, and tumor invasion and metastasis. After converting plasminogen to plasmin, t-PA is subjected to cleavage by plasmin into two di-sulfide-connected chains. Both single and two-chain forms of t-PA posses full biological activity. The reaction between t-PA and fibrinogen is much more effective in the presence of fibrin-bound plasminogen. t-PA exert its enzymatic activity only upon binding fibrin which is bound to plasminogen. The selectivity of t-PA for fibrin-associated plasminogen avoids degradation of circulating fibrinogen. t-PA is abundant in the blood and is also found in organs such as the uterus, prostate, lung, ovary, muscle, heart, spleen, and liver (Robison, A. K., and D. Collen. 1987. Activation of the fibrinolytic system. Cardiol Clin 5:13.). In addition to fibrin, t-PA's enzymatic activity is also modulated by the serpin PAI-1. PAI-1 binds t-PA around amino acid 300 (Bennett, W. F., N. F. Paoni, B. A. Keyt, D. Botstein, A. J. Jones, L. Presta, F. M. Wurm, and M. J. Zoller. 1991. High resolution analysis of functional determinants on human tissue-type plasminogen activator. J Biol Chem 266:5191). Structurally, t-PA consists of an N-terminal heavy chain, which contains a finger (also designated fibronectin-like) domain, an epidermal growth factor (EGF) homologous region, and two “kringle” structures (K1, K2), while the C-terminal light chain consists of a serine protease domain. Fibrin binding has been attributed to the kringle-2 domain and to a lesser extent to the finger and EGF domains (Lee, S. G., N. Kalyan, J. Wilhelm, W. T. Hum, R. Rappaport, S. M. Cheng, S. Dheer, C. Urbano, R. W. Hartzell, M. Ronchetti-Blume, and et al. 1988. Construction and expression of hybrid plasminogen activators prepared from tissue-type plasminogen activator and urokinase-type plasminogen activator genes. J Biol Chem 263:2917). The finger and growth factor domains are also important for clearance by the liver, a process that is also regulated by t-PA glycosylation (Bennett, W. F., N. F. Paoni, B. A. Keyt, D. Botstein, A. J. Jones, L. Presta, F. M. Wurm, and M. J. Zoller. 1991. High resolution analysis of functional determinants on human tissue-type plasminogen activator. J Biol Chem 266:5191).
Clinical Applications
Coronary arterial thrombolysis is becoming an established treatment of acute myocardial infarction. Intravenous recombinant t-PA (also designated alteplase) has been proved to be an efficient therapy for acute myocardial infarction. However, the short half-life of t-PA and complications such as bleeding, especially intracranial, raised the need for developing of new agents. Second and third generation t-PAs resulting from genetic engineering of the t-PA molecule have yielded refinements in thrombolitic therapy (Smalling, R. W. 1996. Molecular biology of plasminogen activators: what are the clinical implications of drug design? Am J Cardiol 78:2). In addition to acute myocardial infarction, t-PA agonists have also been described in the pharma as neuroprotective agents.
t-PA antagonists are of potential therapeutic use in cancer and thrombocytopenia related to chemotherapy-induced injury, as well as psoriasis and hyphemia.
Splice Variants of tPA: HUMUPAA_T6 (variant T6) and HUMUPAA_R56 (Variant T9)
The present inventors uncovered two novel splice variants of the tPA gene: HUMUPAA_T6 (variant T6) and HUMUPAA_R56 (variant T9).
Splice Variant HUMUPAA_T6 (variant T6) Structure
The t-PA splice variant T6 (HUMUPAA_T6—SEQ ID NO:114; HUMUPAA_P4—SEQ ID NO:113; FIGS. 82a and b, respectively) result from alternative splicing of the t-PA gene, which is caused by alternative donor site in exon 4 and alternative acceptor site in exon 6 while skipping of exon 5, and inserting a unique amino acid in the junction (FIGS. 83a, 84a, 85). The resulting protein has a deletion of amino acids 54-134 of the WT protein (TPA_HUMAN; GenBank Accession No. P00750; SEQ ID NO:150). This splice variant encodes a 482 amino acids long protein (SEQ ID NO:113), which lacks part of the finger domain, the EGF domain and part of K1, while including a full K2 and serine protease domains. The variant lacks 6 of 17 potential disulfide-bonds and 1 out of four glycosylation sites.
Comparison Report Between HUMUPAA_P4 and TPA_HUMAN
1. An isolated chimeric polypeptide HUMUPAA_P4 (SEQ ID NO:113), comprising a first amino acid sequence being at least 90% homologous to MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARSYQVICRDEKTQMIYQQ H corresponding to amino acids 1-53 of TPA_HUMAN (SEQ ID NO:150), which also corresponds to amino acids 1-53 of HUMUPAA_P4 (SEQ ID NO:113), a second amino acid sequence bridging amino acid sequence comprising of H, and a third amino acid sequence being at least 90% homologous to YRGTWSTAESGAECTNWNSSALAQKPYSGRRPDAIRLGLGNHNYCRNPDRD SKPWCYVFKAGKYSSEFCSTPACSEGNSDCYFGNGSAYRGTHSLTESGASCLP WNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTW EYCDVPSCSTCGLRQYSQPQERIKGGLFADIASHPWQAAIFAKHRRSPGERFL CGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVH KEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSG YGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGG PQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTN YLDWIRDNMRP corresponding to amino acids 135-562 of TPA_HUMAN (SEQ ID NO:150), which also corresponds to amino acids 55-482 of HUMUPAA_P4 (SEQ ID NO:113), wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for an edge portion of HUMUPAA_P4 (SEQ ID NO:113), comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise HHY having a structure as follows [numbering according to HUMUPAA_P4 (SEQ ID NO:113)]: a sequence starting from any of amino acid numbers 53-x to 53; and ending at any of amino acid numbers 55+((n−2)−x), in which x varies from 0 to n−2.
Splice Variant HUMUPAA_R56 (variant T9) Structure
The t-PA splice variant T9 (HUMUPAA_R56—SEQ ID NO:116; HUMUPAA_X24—SEQ ID NO:115, FIGS. 82c and d, respectively) result from alternative splicing of the t-PA gene, which is caused by alternative acceptor site in exon 8 while skipping exon 7 (FIGS. 83b, 84b, 85). The resulting truncated protein encompasses 208 amino acids (SEQ ID NO:115) of them the first 180 amino acids are identical to the wild type protein (SEQ ID NO:150) and 28 unique amino acids (TPVPRHWAWANIITAGILMGMPSPGATC; SEQ ID NO:117). It contains a complete finger and EGF domains and a partial kringle-1 while lacking K2 and serine protease domains. It has most of the potential disulfide-bonds relevant to the domains it encompasses except for one, and includes the relevant glycosylation sites.
Comparison Report Between HUMUPAA_X24 (SEQ ID NO:115) and TPA_HUMAN (SEQ ID NO:150)
1. An isolated chimeric polypeptide HUMUPAA_X24 (SEQ ID NO:115), comprising a first amino acid sequence being at least 90% homologous to MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARSYQVICRDEKTQMIYQQ HQSWLRPVLRSNRVEYCWCNSGRAQCHSVPVKSCSEPRCFNGGTCQQALYF SDFVCQCPEGFAGKCCEIDTRATCYEDQGISYRGTWSTAESGAECTNWNSSA LAQKPYSGRRPDAIRLGLGNHNYCR corresponding to amino acids 1-180 of TPA_HUMAN (SEQ ID NO:150), which also corresponds to amino acids 1-180 of HUMUPAA_X24 (SEQ ID NO:115), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence TPVPRHWAWANIITAGILMGMPSPGATC (SEQ ID NO:117) corresponding to amino acids 181-208 of HUMUPAA_X24 (SEQ ID NO:115), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMUPAA_X24 (SEQ ID NO:115), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence TPVPRHWAWANIITAGILMGMPSPGATC (SEQ ID NO:117) in HUMUPAA_X24 (SEQ ID NO:115).
Therapeutic Application of the Splice Variant
Studies of deletion mutants of t-PA have demonstrated that the K2 domain and the protease domain are sufficient to exert plasminogen activator activity of t-PA (van Zonneveld, A. J., H. Veerman, and H. Pannekoek. 1986. Autonomous functions of structural domains on human tissue-type plasminogen activator. Proc Natl Acad Sci U S A 83:4670). In addition, the finger and EGF domains, which are involved in fibrin binding to a lesser extent than K2, are also important for t-PA's clearance by the liver (Bennett, W. F., N. F. Paoni, B. A. Keyt, D. Botstein, A. J. Jones, L. Presta, F. M. Wurm, and M. J. Zoller. 1991. High resolution analysis of functional determinants on human tissue-type plasminogen activator. J Biol Chem 266:5191). Concomitantly, new thrombolytic agents have been described: n-PA, which is a deletion mutant lacking the finger and EGF domains and bearing a point mutation on amino acid 152, and r-PA, which lacks the finger, EGF, and K1 domains, have been shown to have an improved lytic activity in animal models and a more extended half-life comparing to t-PA (Smalling, R. W. 1996. Molecular biology of plasminogen activators: what are the clinical implications of drug design? Am J Cardiol 78:2). Based on these findings, the t-PA splice variant T6 (SEQ ID NO:113) is predicted to be able to bind fibrin via K2 and to exert t-PA activity. Furthermore, as it lacks the finger and EGF domains, it is predicted to be less susceptible to clearance in the liver and thus, it might have a longer half-life than the wild type protein. Altogether, these data support a role for T6 as an agonist of t-PA activity, however, similar to n-PA and r-PA, it might have a reduced fibrin affinity (Smalling, R. W. 1996. Molecular biology of plasminogen activators: what are the clinical implications of drug design? Am J Cardiol 78:2).
The T9 variant of t-PA (SEQ ID NO:115) is a truncated protein that posses only the finger and EGF domains. These domains can bind, although with low efficiency, to fibrin (van Zonneveld, A. J., H. Veerman, and H. Pannekoek. 1986. Autonomous functions of structural domains on human tissue-type plasminogen activator. Proc Natl Acad Sci USA 83:4670), however in the absence of the protease domain such binding is unlikely to result in t-PA activity. Accordingly, T9 is predicted to compete for fibrin binding and can serve as a weak antagonist for t-PA.
While reducing the present invention to practice, and without being bound to any theory, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:113 and/or an expressible polynucleotide homologous to SEQ ID NO:114 which can be used as a t-PA agonist to treat acute myocardial infarction and to serve as a neuroprotective agent.
While further reducing the present invention to practice, and without being bound to any theory, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:115 and/or an expressible polynucleotide homologous to SEQ ID NO:116, and/or a peptide homologous to SEQ ID NO:117 which can be used as a t-PA antagonist to prevent and/or treat cancer, thrombocytopenia related to chemotherapy-induced injury, psoriasis and hyphemia.
It will be appreciated that such agents can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 33
Splice Variant of L-Selectin Precursor
Background
L-selectin (CD62L, LECAM-1, LAM-1) is a member of the selectins (CD62) family, which also includes P-selectin (CD62P, GMP140, PADGEM) and E-selectin (CD62E, ELAM-1). The selectins regulate the first reversible interaction between leukocytes and the endothelium, whereas the second and third phases of extravasation are mediated by integrins. L-selectin was originally defined as a lymphocyte membrane molecule which mediates the attachment of lymphocytes to specialized lymph node postcapillary venules (the ‘high endothelial venules’, HEV). Later on, L-selectin was found to be involved also in leukocyte homing to sites of inflammation (Tedder et al. 1993).
Structurally, each member of the selectin family contains an N-terminal C-type lectin domain (also designated carbohydrate-recognition domain, CRD) followed by an epidermal growth factor (EGF)-like domain, short consensus repeat (SCR, also designated sushi, two in L-selectin), a transmembrane domain, and a short cytoplasmic tail. Biochemical studies revealed that L-selectin is heavily glycosylated (Sackstein, 1997).
L-selectin is expressed on the earliest hematopoitic progenitor (CD34+) cells, by very immature thymocytes and early B cell precursors, and by mature B and T lymphocytes and mature granulocytes and monocytes. The expression of L-selectin on the cell surface of leukocytes is tightly regulated: in response to a chemoattractant a transient increase in L-selectin activity (but not cell surface expression) is observed, which is followed by a rapid (within minutes) proteolytic shedding of the molecule from the cell surface (Rosen and Bertozzi, 1994). The shedding is mediated by a cystein metalloprotease, presumably the TNFα converting enzyme (TACE), between Lys321 and Ser322 in a region that links the second CSR and the transmembrane domain (Jasuja et al., 2000; Migaki et al., 1995). Concomitantly, high levels of L-selectin on cell surface are found in peripheral neutrophils while in the inflammatory site its surface level is very low. It was proposed that L-selectin is essential for rolling and firm adhesion of leukocytes, however, its shedding allows the leukocyte to break its tight bonds with the vascular endothelium and proceed with extravasation. Additionally, the shed molecule is present in the extracellular fluid and can inhibit specific cell attachment of lymphocytes to cytokine-activated endothelium and may serve as a regulator of leukocyte attachment to endothelium (Jutila, 1994; Tedder et al., 1993).
The ligands for L-selectin are E-selectin, GlyCAM-1, CD34 and MAdCAM-1 all of which are expressed on endothelial cells. CD34 is expressed also by progenitor cells and its interaction with L-selectin involves in progenitor cell maturation. These molecules have extracellular domains with a mucin organization, i.e. serin/threonin-rich regions that are densely associated with O-linked fucosylaed or sialylated carbohydrate chains. The mucin-associated oligosaccharides are recognized and bound by the selectin (Rosen and Bertozzi, 1994). The avidity of interaction between the selectin and the mucin-like ligand result from oligomerization of the L-selectin molecules on the leukocyte surface and is influenced by the density of the ligand on the opposed cell.
Clinical Applications
Leukocyte-endothelial interactions are critical for host defense; however, in some disease state leukocyte-endothelial interactions may be deleterious to the host. For example, activation signals generated during ischemia may trigger vigorous inflammatory response during reperfusion, provoking greater tissue damage then the initial ischemic insult. In diseases such as rheumatoid arthritis, psoriasis, asthma, atherosclerosis, or multiple sclerosis, mononuclear leukocytes may contribute to secondary tissue damage (Harlan et al., 2002). Downregulation of L-selectin shedding, resulting in continued adherence of leukocytes to endothelium, possibly causing further damage and immune complex deposition, have been described in lupus (Bloom et al., 2002). High levels of soluble L-selectin were found in the blood of ulcerative colitis but not Crohn's patients (Seidelin et al., 1998; Elewaut et al., 1998). L-selectin antagonists were reported to be on phase II of clinical trials for treatment of colitis. Anti-L-selectin antibodies have been implicated in a baboon model of traumatic shock. This resulted in reduced trauma-associated organ damage and mortality, and had beneficial effects on long-term survival (Shlag et al., 1999). Altogether, selectins might be ideal targets for treatment of acute and chronic inflammatory reactions as their primary role appears to be specific as it is restricted to endothelial cells and platelet adhesion to leukocytes during inflammation or leukocyte homing. Additionally, constitutive T cell L-selectin and upregulated L-selectin ligands expression were found in rejected grafts (Jones et al., 2003). Concomitantly, L-selectin antagonist are in phase II of clinical trials for transplant rejection. Another biological process that may involve selectins is the adhesion of circulating tumor cells to endothelium in cancer metastasis of different tumor types. Measurement of selectins could thus be useful for prognosis, and manipulation of their levels could lead to new cancer therapies (Krause and Turner, 1999).
New L-Selectin Structure Splice Variants: T2, T3, and T6
The present inventors uncovered a novel splice variants of L-selectin (SEQ ID NOs: 68, 69, 71, 72, 74 and 75, FIGS. 41a-f).
L-Selectin Splice Variant T2
L-selectin splice variant T2 (MMPLNHR_T2—SEQ ID NO:69; MMPLNHR_P2—SEQ ID NO:68, FIGS. 41a and b, respectively) results from alternative splicing of the L-selectin gene, thus introducing a new exon (exon 5a), causing the insertion of a stop codon, that result in a truncated L-selectin protein (FIGS. 42a, 43a, 44). The variant protein thus created is a 257 amino acids long truncated protein (SEQ ID NO:68), which contains the N-terminal 255 amino acids of wild type L-selectin, followed by 2 unique amino acids (GE; SEQ ID NO: 70). It contains the C-type lectin domain, the EGF-like domain, the first SCRs (also designated sushi domains), while it lacks the second SCR, the TM and the intracellular portion. The variant has all the potential disulfide-bonds and glycosylation sites relevant to the domains it encompasses.
Comparison Report Between MMPLNHR_P2 (SEQ ID NO:68) and LEM—1_HUMAN (SEQ ID NO:140)
1. An isolated chimeric polypeptide MMPLNHR_P2, comprising a first amino acid sequence being at least 90% homologous to MIFPWKCQSTQRDLWNIFKLWGWTMLCCDFLAHHGTDCWTYHYSEKPMN WQRARRFCRDNYTDLVAIQNKAEIEYLEKTLPFSRSYYWIGIRKIGGIWTWVG TNKSLTEEAENWGDGEPNNKKNKEDCVEIYIKRNKDAGKWNDDACHKLKA ALCYTASCQPWSCSGHGECVEIINNYTCNCDVGYYGPQCQFVIQCEPLEAPEL GTMDCTHPLGNFSFSSQCAFSCSEGTNLTGIEETTCGPFGNWSSPEPTCQ corresponding to amino acids 1-255 of LEM1_HUMAN, which also corresponds to amino acids 1-255 of MMPLNHR_P2, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GE corresponding to amino acids 256-257 of MMPLNHR_P2, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
Comparison Report Between MMPLNHR_P2 and LEM1_HUMAN
1. An isolated chimeric polypeptide MMPLNHR_P2, comprising a first amino acid sequence being at least 90% homologous to MIFPWKCQSTQRDLWNIFKLWGWTMLCCDFLAHHGTDCWTYHYSEKPMN WQRARRFCRDNYTDLVAIQNKAEIEYLEKTLPFSRSYYWIGIRKIGGIWTWVG TNKSLTEEAENWGDGEPNNKKNKEDCVEIYIKRNKDAGKWNDDACHKLKA ALCYTASCQPWSCSGHGECVEIINNYTCNCDVGYYGPQCQFVIQCEPLEAPEL GTMDCTHPLGNFSFSSQCAFSCSEGTNLTGIEETTCGPFGNWSSPEPTCQ corresponding to amino acids 1-255 of LEM1_HUMAN, which also corresponds to amino acids 1-255 of MMPLNHR_P2, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GE corresponding to amino acids 256-257 of MMPLNHR_P2, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
L-Selectin Splice Variant T3
L-selectin splice variant T3 (MMPLNHR_T3—SEQ ID NO:72, MMPLNHR_P3—SEQ ID NO:71, FIGS. 41c and d, respectively) result from alternative splicing of the L-selectin, thus leading to the skipping of exon 7 and the generation of a protein lacking amino acids 317-361 of wild type L-selectin, while introducing one novel amino acid in the junction (new edge—SEQ ID NO:73; FIGS. 42, 43b, 44). This splice variant encodes a 329 amino acids long protein which contains the C-type lectin domain, the EGF-like domain, both SCRs, and the intracellular domain, while lacking the TM. The variant has all the potential disulfide-bonds and glycosylation sites relevant to the domains it encompasses.
Comparison Report Between MMPLNHR_P3 and LEM1_HUMAN
1. An isolated chimeric polypeptide MMPLNHR_P3, comprising a first amino acid sequence being at least 90% homologous to MIFPWKCQSTQRDLWNIFKLWGWTMLCCDFLAHHGTDCWTYHYSEKPMN WQRARRFCRDNYTDLVAIQNKAEIEYLEKTLPFSRSYYWIGIRKIGGIWTWVG TNKSLTEEAENWGDGEPNNKKNKEDCVEIYIKRNKDAGKWNDDACHKLKA ALCYTASCQPWSCSGHGECVEIINNYTCNCDVGYYGPQCQFVIQCEPLEAPEL GTMDCTHPLGNFSFSSQCAFSCSEGTNLTGIEETTCGPFGNWSSPEPTCQVIQC EPLSAPDLGIMNCSHPLASFSFTSACTFICSEGTELIGKKKTICESSGIWSNPSPIC Q corresponding to amino acids 1-317 of LEM1_HUMAN, which also corresponds to amino acids 1-317 of MMPLNHR_P3, a second amino acid sequence bridging amino acid sequence comprising of S, and a third amino acid sequence being at least 90% homologous to KKSKRSMNDPY corresponding to amino acids 362-372 of LEM1_HUMAN, which also corresponds to amino acids 319-329 of MMPLNHR_P3, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for an edge portion of MMPLNHR_P3, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise QSK having a structure as follows (numbering according to MMPLNHR_P3): a sequence starting from any of amino acid numbers 317-x to 317; and ending at any of amino acid numbers 319+((n−2)−x), in which x varies from 0 to n−2.
The T6 Splice Variant
The T6 splice variant (MMPLNHR_T6—SEQ ID NO:75; MMPLNHR_P6-SEQ ID NO:74, FIGS. 41e and f, respectively) obtained by the alternative splicing of the L-selectin gene result in extension of exon 6 leading to an insertion of a stop codon and the generation of a truncated protein (FIGS. 42, 43c, 44). This splice variant encodes 319 amino acids long protein, which contains 317 amino acids of the wild type sequence, and 2 unique amino acids (SE—SEQ ID NO:76). It encompasses the C-type lectin domain, the EGF-like domain, and both SCRs while it lacks the TM and the cytoplasmic domain. The variant has all the potential disulfide-bonds and glycosylation sites relevant to the domains it encompasses.
Comparison Report Between MMPLNHR_P6 and LEM1_HUMAN
1. An isolated chimeric polypeptide MMPLNHR_P6, comprising a first amino acid sequence being at least 90% homologous to MIFPWKCQSTQRDLWNIFKLWGWTMLCCDFLAHHGTDCWTYHYSEKPMN WQRARRFCRDNYTDLVAIQNKAEIEYLEKTLPFSRSYYWIGIRKIGGIWTWVG TNKSLTEEAENWGDGEPNNKKNKEDCVEIYIKRNKDAGKWNDDACHKLKA ALCYTASCQPWSCSGHGECVEIINNYTCNCDVGYYGPQCQFVIQCEPLEAPEL GTMDCTHPLGNFSFSSQCAFSCSEGTNLTGIEETTCGPFGNWSSPEPTCQVIQC EPLSAPDLGIMNCSHPLASFSFTSACTFICSEGTELIGKKKTICESSGIWSNPSPIC Q corresponding to amino acids 1-317 of LEM1_HUMAN, which also corresponds to amino acids 1-317 of MMPLNHR_P6, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence SE corresponding to amino acids 318-319 of MMPLNHR_P6, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
Therapeutic Application of the Splice Variants
Splice variant T2 contains the lectin domain, which is responsible for interaction with L-selectin ligands, the EGF-like domain, and the first SCR. It is predicted to be a soluble protein as it lacks the TM domain and will thus serve as an antagonist for L-selectin interaction with its ligands.
Splice variant T3 consists of all the L-selectin domains but lacks the TM and the N-terminus portion of the cytoplasmic domain as a result of exon skipping. It is predicted to be a soluble protein that will antagonize L-selectin function by competing for its ligand.
Splice variant T6 is a truncated protein that lacks the TM and the cytoplasmic domain. It is thus predicted to be a soluble protein that will antagonize L-selectin function by competing for its ligand. The protein resulting from this variant (excluding the 2 unique amino acids) is analogous to the naturally occurring soluble L-selectin that result from the shedding of the membrane bound L-selectin at position 321.
Antagonists for L-selectin activity have been described in phase II of clinical trials for treatment of inflammation, psoriasis, traumatic-shock, asthma, transplant rejection, ulcerative colitis, irritable bowel syndrome, and atopic eczema.
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:68, 71 or 74 and/or an expressible polynucleotide homologous to SEQ ID NO:69, 72 or 75 which can serve as an antagonist of L-selectin function and thus can prevent and/or treat inflammation (e.g., chronic inflammatory), psoriasis, traumatic-shock, asthma, transplant rejection, ulcerative colitis, irritable bowel syndrome, and atopic eczema, rheumatoid arthritis, atherosclerosis, multiple sclerosis, and cancer metastasis.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Since L-selectin involves in the adhesion of circulating tumor cells to endothelium in cancer metastasis of different tumor types, the new L-selectin variants of the present invention (T2, T3 and/or T6; SEQ ID NOs:68, 69, 71, 72, 74, 75) can be used as diagnostic markers for determining prognosis of cancer as well as markers for the efficacy of new cancer therapies. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the L-selectin variants (SEQ ID NO:68, 71 and/or 74], or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 34
Splice Variant of Elastase IIIb Precursor
Background
The elastase IIIB precursor (Protease E; GenBank Accession No. P08861; EL3B_HUMAN; ELAS; ELA3A; ELA3B) is an extracellular protein which belongs to the peptidase S1 family (the elastase subfamily) and exhibits proteolysis, peptidolysis and trypsin activity, although it does not hydrolyze elastin. It exhibits specificity towards Alanine and cleaves the Ala-|-Xaa bond. The elastase IIIB precursor is overexpressed in endocrine tissues and particularly in the pancreas and can be used as a marker for proliferation of this tissue or as a marker for pathological de-differentiation of this tissue or tissue damage. In addition, since elastase IIIB is overexpressed in pancreatic tumors it can be used as a marker for these pathologies.
Clinical Applications
Elastase IIIb has been implicated in various disease, disorders or conditions such as asthma, thrombosis, psoriasis, pancreatitis, cystic fibrosis, general emphysema, infection (e.g., respiratory tract infection. sepsis), reperfusion injury, chronic bronchitis, pulmonary fibrosis, HIV/AIDS, haemorrhage, rheumatoid arthritis, inflammation, peripheral vascular disease, respiratory disease, alpha-1 antitrypsin deficiency, chronic obstructive pulmonary disease.
Splice Variant HUMPRE_T3 (SEQ ID NO:273) Encodes a New Secreted Form of the Elastase IIIB, HUMPRE_P4 (SEQ ID NO:274)
The present inventors have uncovered a new elastase IIIB variant [HUMPRE_T3—SEQ ID NO:273; HUMPRE_P4—SEQ ID NO:274]. The protein coordinates on the transcript start from nucleotide 147 and end at nucleotide 833 as set forth in SEQ ID NO:273 (HUMPRE_T3 transcript).
Alignment of the new elastase IIIB variant (HUMPRE_P4—SEQ ID NO:274) with the WT protein (GenBank Accession No. P08861; SEQ ID NO:328) revealed that the new variant includes the first 214 amino acids as of the WT protein (GenBank Accession No. P08861) followed by a unique 15 amino acid sequence [EAHGVHSSLRLHRLD (SEQ ID NO:329), FIG. 119]. The new variant uncovered by the present invention includes 3 out of 5 potential disulfide bonds and one glycosylation site as in the WT and is lacking the Peptidase 51 chymotrypsin (IPR001254), Peptidase S1A, chymotrypsin (IPR001314) domains of the WT protein and thus is expected to be a non-functional elestase Mb variant.
Comparison Report Between HUMPRE_P4 (SEQ ID NO:274) and EL3B_HUMAN (SEQ ID NO:328)
1. An isolated chimeric polypeptide HUMPRE_P4 (SEQ ID NO:274), comprising a first amino acid sequence being at least 90% homologous to MMLRLLSSLLLVAVASGYGPPSSRPSSRVVNGEDAVPYSWPWQVSLQYEKS GSFYHTCGGSLIAPDWVVTAGHCISSSWTYQVVLGEYDRAVKEGPEQVIPINS GDLFVHPLWNRSCVACGNDIALIKLSRSAQLGDAVQLASLPPAGDILPNETPC YITGWGRLYTNGPLPDKLQEALLPVVDYEHCSRNWWGSSVKKTMVCAGG DIRSGCN corresponding to amino acids 1-214 of EL3B_HUMAN (SEQ ID NO:328), which also corresponds to amino acids 1-214 of HUMPRE_P4 (SEQ ID NO:274), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence EAHGVHSSLRLHRLD (SEQ ID NO:329) corresponding to amino acids 215-229 of HUMPRE_P4 (SEQ ID NO:274), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMPRE_P4 (SEQ ID NO:274), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence EAHGVHSSLRLHRLD (SEQ ID NO:329) in HUMPRE_P4 (SEQ ID NO:274).
Since the elestase Mb variant of the present invention lacks the functional domains it can compete with the endogenous elestase IIIb and interfere with its various activities.
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:274 and/or an expressible polynucleotide homologous to SEQ ID NO:273 and/or a peptide homologous to SEQ ID NO:329 which can be used as an anti-inflammatory, antiasthma, anticoagulant, antithrombotic, cardiovascular. hypolipaemic/antiatherosclerosis, respiratory, septic shock treatment, antiarthritic, antipsoriasis, COPD treatment, cognition enhancer, cystic fibrosis treatment, cytokine, dermatological, GI inflammatory/bowel disorders, haemostatic, lung surfactant, neuroprotective, ophthalmological, stomatological, urological, peripheral vasodilator, systemic vasoprotective, vulnerary agent.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
While further reducing the present invention to practice, these results suggest the use of the new elastase Mb variant of the present invention (HUMPRE_P4—SEQ ID NO:274), the polynucleotide encoding same (HUMPRE_T3—SEQ ID NO:273) and/or the peptide derived from the elastase Mb variant (SEQ ID NO:329) as a diagnostic marker for pancreas proliferation or de-differentiation, as well as pancreatic tumors. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the (HUMPRE_P4 variant (SEQ ID NO:274)], nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 35
Atrial Natriuretic Peptide Receptor B
Background
Atrial natriuretic peptide receptor B, also called ANP-B, ANPRB, GC-B, Guanylate cyclase, NPR-B, encoded by the gene called NPR2 (ANPRB), is one of two integral type I membrane receptors for natriuretic peptides. ANP-B contain five functional domains: an extracellular ligand-binding domain, a single membrane-spanning region, and intracellularly a protein kinase homology domain), an helical hinge region involved in oligomerization, and a carboxyl-terminal guanylyl cyclase catalytic domain. ANP-B is the primary receptor for C-type natriuretic peptide (CNP), which upon ligand binding exhibits greatly increased guanylyl cyclase activity. The receptor is only weakly sensitive to by Brain Natriuretic peptide (BNP) and Atriuretic peptide (ANP) (Vanderheyden et al, 2004, The European J Heart failure, 6:261-168). Guanylyl cyclases (GCs) are enzymes that convert guanosine-5′-triphosphate (GTP) to cyclic guanosine-3′,5′-monophosphate (cGMP). Receptor dimerization is essential for the activation of the catalytic domain. The second messenger cGMP participates in signaling by (1) stimulating the activity of kinases that belong to the protein kinase G family, (2) altering the conductance of cGMP-gated ion channels and (3) changing the activity of cGMP-regulated phosphodiesterases, and thereby modifies cellular functions. The glycosylation of residues located at the N-terminal end of the extracellular domain of the Natriuretic Peptide receptors plays a role in ligand binding (Kuhn, M 2003, Circ. Res, 93:700-709).
Natriuretic peptides and their receptors possess potent natriuretic, diuretic and vasodilating activities, and have important roles in regulation of body fluid and electrolyte homeostasis, and blood pressure control, thereby playing an important role in renal and cardiovascular physiology (Kuhn, 2004, Basic Res. Cardiol, 99:76-82; Vanderheyden et al, 2004 15:261-8). They are also known by their expression and physiological activity in various tissues other than cardiovascular system. The primary ligand of ANP-B, CNP is expressed mostly in the central nervous system and in the vascular endothelium. CNP is produced by most of the major endocrine glands, including the hypothalamus and anterior pituitary. The relative abundance of the ANP-B receptor in these glands suggests that CNP is a local neuroendocrine regulator. CNP is mainly produced by vascular endothelial cells and may act locally as an autocrine/paracrine regulator of vascular tone and cell growth at the vascular and venous levels. It potently inhibits the proliferation of vascular smooth muscle cells but stimulates endothelial cell growth and migration, and might therefore modulate vascular regeneration. CNP is more potent than ANP in eliciting smooth muscle relaxation, but it is less potent inducer of diuresis and natriuresis. Thus in the cardiovascular system CNP is likely to have primary local roles in the blood vessel wall rather than as a circulating natriuretic hormone. In cardiac fibroblasts ANP-B is the predominant receptor that could mediate the antiproliferative response in fibroblasts. CNP has been postulated to be a local regulator of ACE activity, and inhibition of angiotensin II formation reduces vascular hypertrophy and remodeling. CNP infusion in the rat restinosis model resulted in 60% reduction of neointima formation, suggesting its therapeutic potential in restinosis (Tremblay, et al., 2002, MCB, 230:31-47).
Targeted disruption of the murine genes for CNP or cGMP-dependent protein kinase II (PKG II) resulted in severe Dwarfism as a result of impaired endochondral ossification, demonstrating that the CNP/ANP-B system has an essential role in the local stimulation of growth plate chondrocyte proliferation and differentiation, matrix synthesis, and cell hypertrophy through cGMP-mediated activation of PKGII (Chusho et al, 2001, PNAS, 98:4016-4021, Yasoda et al, 2004, Nature Med. 10:80-86). Thus, CNP is a regulatory peptide in the bone, where it activates growth of plate chondrocyte proliferation and differentiation. CNP deletion caused altered endochondral ossification, Dwarfism and early death, while overexpression of CNP in chondrocytes rescued achondroplasia, suggesting that activation of the CNP/ANP-2 system in endochondral bone formation should be considered as a new therapeutic strategy for human achondroplasia (Yasoda et al, 2004, Nature Med, 10:80-86).
The involvement of the CNP and the ANP-B receptor in various reproductive processes in male and female reproductive systems, as well as in embryonic and fetal development was demonstrated (Walther et al, J Endocrinology, 2004, 180:17-22). Both, endocrine function of the testis and the regulation of penile erection are regulated by the CNP/ANP-B axis.
CNP secretion was shown to be suppressed by VEGF, indicating that CNP/ANP-B axis might be involved in regulation of angiogenesis (Doi et al, 1996, Hypertension, 27:811-5).
The NRP-B is expressed in many different tissues, in particular in vascular tissue, bone, high density fibroblasts and in the brain, particularly in the pituitary gland. An extensive analysis of ANP-B deficient mice revealed a complex phenotype with accumulation of white adipose tissue, seizure attacks and infertility (Kuhn, 2004, Basic Res. Cardiol, 99:76-82), suggesting various local physiological roles of ANP-B in tissue remodeling, reproduction and brain function.
Atrial Natriuretic Peptide Receptor B New Variant Structure
Atrial natriuretic peptide receptor B splice variant (HUMGUANCYC_T1—SEQ ID NO:123; HUMGUANCYC_P2—SEQ ID NO:122) of the present invention results from an alternative splicing of the ANPB_HUMAN gene (GenBank Accession No. P20594; SEQ ID NO:153) leading to exon skipping and production of a new truncated atrial natriuretic peptide receptor B protein of 431 amino acids (SEQ ID NO:122), which shares with the wild type atrial natriuretic peptide receptor B the first 406 N-terminal amino acids, containing the signal peptide sequence (amino acids 1-22), partial extracellular ligand binding domain (amino acids 23-406), including all the potential glycosylation sites, but not including the two cysteins potentially involved in the interchain disulfide bonds. The new protein contains 25 C-terminal unique amino acids (LHFQPWQLWLWAQESPSSCLVFPAS; SEQ ID NO:643; FIG. 92). The new protein does not contain the transmembrane domain of the wild type protein, and therefore is predicted to be secreted. Likewise, the new protein does not contain the cytoplasmic domain of the wild type protein, including the kinase-like and the guanylate cuclase domains (see FIG. 93).
Comparison Report Between HUMGUANCYC_P2 and ANPB_HUMAN (SEQ ID NO:153)
1. An isolated chimeric polypeptide HUMGUANCYC_P2, comprising a first amino acid sequence being at least 90% homologous to MALPSLLLLVAALAGGVRPPGARNLTLAVVLPEHNLSYAWAWPRVGPAVAL AVEALGRALPVDLRFVSSELEGACSEYLAPLSAVDLKLYHDPDLLLGPGCVY PAASVARFASHWRLPLLTAGAVASGFSAKNDHYRTLVRTGPSAPKLGEFVVT LHGHFNWTARAALLYLDARTDDRPHYFTIEGVFEALQGSNLSVQHQVYARE PGGPEQATHFIRANGRIVYICGPLEMLHEILLQAQRENLTNGDYVFFYLDVFG ESLRAGPTRATGRPWQDNRTREQAQALREAFQTVLVITYREPPNPEYQEFQN RLLIRAREDFGVELGPSLMNLIAGCFYDGILLYAEVLNETIQEGGTREDGLRIV EKMQGRRYHGVTGLVVMDKNNDRETDFVLWAMGDLDSGDFQ corresponding to amino acids 1-406 of ANPB_HUMAN, which also corresponds to amino acids 1-406 of HUMGUANCYC_P2, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence LHFQPWQLWLWAQESPSSCLVFPAS corresponding to amino acids 407-431 of HUMGUANCYC_P2, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMGUANCYC_P2, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence LHFQPWQLWLWAQESPSSCLVFPAS in HUMGUANCYC_P2.
The new secreted splice variant of atrial natriuretic peptide receptor B is predicted to have an antagonistic mode of action. The atrial natriuretic peptide receptor B splice variant of the present invention has various potential therapeutic and diagnostic implications. It can be used as a negative modulator of the CNP signaling pathway, and hence serve as a potential therapeutic agent in pathological conditions where blocking or reducing the CNP signaling is required, for example, as an anti-angiogenic agent for treatment of solid tumors.
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:122 and/or an expressible polynucleotide homologous to SEQ ID NO:123 and/or a peptide homologous to SEQ ID NO:643 which can be used to treat cancer (e.g., solid tumor).
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
While further reducing the present invention to practice, since CNP is mostly expressed in the central nervous system, vascular endothelium, major endocrine glands (e.g., hypothalamus and anterior pituitary), the new atrial natriuretic peptide receptor B variant of the present invention (HUMGUANCYC_P2—SEQ ID NO:122), the polynucleotide encoding same (HUMGUANCYC_T1—SEQ ID NO:123) and/or the peptide derived from the HUMGUANCYC_P2 variant SEQ ID NO:643) can be used as a diagnostic marker for proliferation or de-differentiation of such tissues, as well as for the tissue related tumors. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the atrial natriuretic peptide receptor B variant (HUMGUANCYC_P2—SEQ ID NO:122)], nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 36
Splice Variant of Somatotropin Precursor
Background
The somatotropin precursor (Growth hormone; GH; CSHL1; GH1; GH-N; Pituitary growth hormone; Growth hormone 1; GenBank Accession No. P01241; SOMA_HUMAN) is an extracellular protein which gives rise to growth hormone. Growth hormone involves in various activities including the stimulation of the liver to secrete IGF-I, stimulation of myoblasts to differentiate and proliferate, as well its effect on amino acid uptake and protein synthesis in muscle and other tissues.
Structurally, the somatotropin precursor can be as a monomer, or form dimers, trimers, tetramers and pentamers via disulfide-linkage (at positions 79 and 191 of GenBank Accession No. P01241) or other non-covalent association. It can form a complex with GHBP or the α2-macroglobulin complex.
Growth hormone deficiency results in idiopathic short stature (ISS) and missense mutations were identified in Kowarski syndrome (Takahashi Y and Chihara K., 1998; Int. J. Mol. Med. 2: 287-291). Thus a substitution of R→C at position 103 resulted in loss of activity and Kowarski syndrome phenotype.
The somatotropin precursor is overexpressed in central nervous system (e.g., brain) and other tissues such as the myocardial tissue, and can be used as a marker for proliferation of this tissue or as a marker for pathological de-differentiation of this tissue or tissue damage.
Clinical Applications
Growth hormone is involved in the pathogenesis of various disease, disorders and conditions such as acromegaly, burns, cachexia, Type II diabetes, lipodystrophy, obesity, osteoporosis, female infertility, sex-chromosome abnormality, Turner's syndrome, short-bowel syndrome, uraemia, various cancers (e.g., brain, breast, pancreatic, prostate), diarrhea, muscular atrophy, ulcer, and venostasis, and has been implicated in the treatment of dwarfism, growth hormone deficiency, bone regeneration, and wound healing.
Splice Variant HSGROW1_T10 (SEQ ID NO: 275) Encodes a New Secreted Form of the Somatotropin Precursor, HSGROW1_P11 (SEQ ID NO: 276)
The present inventors have uncovered a new somatotropin precursor variant [HSGROW1_T10—SEQ ID NO:275; HSGROW1_P11—SEQ ID NO:2761. The protein coordinates on the transcript start from nucleotide 80 and end at nucleotide 523 as set forth in SEQ ID NO: 275 (HSGROW1_T10 transcript).
Alignment of the new somatotropin precursor variant (HSGROW1_P11—SEQ ID NO:276) with the WT protein (GenBank Accession No. P01241; SEQ ID NO:640) revealed that the new variant includes the first 57 amino acids as of the WT protein (GenBank Accession No. P01241), is missing amino acids 58-127 of the WT protein (IPR001400, Somatotropin hormone), and includes amino acids 128-217 of the WT (FIG. 120]. Thus, the new variant uncovered by the present invention is expected to be a growth hormone antagonist, which competes and interferes with the endogenous growth hormone.
Comparison Report Between HSGROW1_μl and SOMA_HUMAN (SEQ ID NO:640)
1. An isolated chimeric polypeptide HSGROW1_P11, comprising a first amino acid sequence being at least 90% homologous to MATGSRTSLLLAFGLLCLPWLQEGSAFPTIPLSRLFDNAMLRAHRLHQLAFDT YQEF corresponding to amino acids 1-57 of SOMA_HUMAN, which also corresponds to amino acids 1-57 of HSGROW1_P11, and a second amino acid sequence being at least 90% homologous to LVYGASDSNVYDLLKDLEEGIQTLMGRLEDGSPRTGQIFKQTYSKFDTNSHN DDALLKNYGLLYCFRKDMDKVETFLRIVQCRSVEGSCGF corresponding to amino acids 127-217 of SOMA_HUMAN, which also corresponds to amino acids 58-148 of HSGROW1_P11, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HSGROW1_P11, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise FL, having a structure as follows: a sequence starting from any of amino acid numbers 57-x to 57; and ending at any of amino acid numbers 58+((n−2)−x), in which x varies from 0 to n−2.
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:276 and/or an expressible polynucleotide homologous to SEQ ID NO:275 which can be used to treat acromegaly, anorecsis, GI inflammatory/bowel disorders, osteoporosis treatment and/or can be used as an alimentary/Metabolic, anabolic, antiobesity, anticancer, antidiabetic, fertility enhancer, hypolipaemic/antiatherosclerosis, musculoskeletal, ophthalmological, reproductive/gonadal, somatostatin, symptomatic antidiabetic, urological, vulnerary, antidiarrheal, haemostatic, peripheral vasodilator agent.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
While further reducing the present invention to practice, these results suggest the use of the new growth hormone variant of the present invention (SEQ ID NO:276), the polynucleotide encoding same (SEQ ID NO:275) as a diagnostic marker for brain and/or myocardial tissue proliferation or de-differentiation, as well as brain and myocardial tumors. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the new growth hormone variant (SEQ ID NO:276)], or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 37
Splice Variant of Lactogen Precursor
Background
The lactogen precursor (Choriomammotropin; Chorionic somatomammotropin; GenBank Accession No. P01243; CSH_HUMAN, which is also known as PLL_HUMAN; CSH1) is a glycoprotein hormone with both lactogenic and growth-promoting activity. Human chorionic somatomammotropin (HCS) is similar to growth hormone and has effects on maternal carbohydrate, fat, and protein metabolism. As maternal utilization of fatty acids increases, available glucose is reserved for the fetus. HCS has its major effect, in conjunction with prolactin, on development of the mammary gland and is involved in cell-cell signaling, pregnancy and signal transduction. Chorionic somatomammotropin is overexpressed in placenta (e.g., in syncytiotrophoblast cells) and can be used as a marker for proliferation of this tissue or as a marker for pathological de-differentiation of this tissue or tissue damage.
Clinical Applications
HCS can be used in the therapeutics in cases in which abortion is feared or for resolving other pathological situations in pregnancy.
In addition, human placental lactogen (hPL) is expressed (positive IHC) in tumor cells of breast cancer with choriocarcinomatous features (Erhan Y, et al., 2002, Breast J. 8: 244-8), thus suggesting HCS as a diagnostic marker for various chorion—related pathologies such as cancer.
Splice Variant HUMCS2_T2 (SEQ ID NO:277) Encodes a New Secreted Form of the Chorionic Somatomammotropin, HUMCS2_P3 (SEQ ID NO:278)
The present inventors have uncovered a new chorionic somatomammotropin variant [HUMCS2_T2—SEQ ID NO:277; HUMCS2_P3—SEQ ID NO:278]. The protein coordinates on the transcript start from nucleotide 139 and end at nucleotide 906 as set forth in SEQ ID NO: 277 (HUMCS2_T2 transcript).
Alignment of the new chorionic somatomammotropin variant (HUMCS2_P3-SEQ ID NO:278) with the WT protein (GenBank Accession No. P01243; SEQ ID NO:330) revealed that the new variant includes the first 152 amino acids as of the WT protein (GenBank Accession No. P01243) followed by a unique 104 amino acid sequence [VRVAPGVTNPGTPLASRAGGEKYCCPLFSSKALTQENSPYSSFRLVNP PGLSLHPEGEGGKWINERGREQCPSAWPLLLFLHFAEAGRRQPPDWADPQ ADLQQV (SEQ ID NO:331), FIG. 121]. The new variant uncovered by the present invention lacks the Somatotropin hormone domain (IPR001400) of the WT protein, and three of the four potential sites for disulfide bonds (amino acids 191, 208 and 215) and is therefore a potential antagonist of chorionic somatomammotropin.
Comparison Report Between HUMCS2_P3 (SEQ ID NO:278) and CSH_HUMAN (SEQ ID NO:330)
1. An isolated chimeric polypeptide HUMCS2_P3 (SEQ ID NO:278), comprising a first amino acid sequence being at least 90% homologous to MAPGSRTSLLLAFALLCLPWLQEAGAVQTVPLSRLFDHAMLQAHRAHQLAID TYQEFEETYIPKDQKYSFLHDSQTSFCFSDSIPTPSNMEETQQKSNLELLRISLL LIESWLEPVRFLRSMFANNLVYDTSDSDDYHLLKDLEEGIQTLMG corresponding to amino acids 1-152 of CSH_HUMAN, which also corresponds to amino acids 1-152 of HUMCS2_P3 (SEQ ID NO:278), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VRVAPGVTNPGTPLASRAGGEKYCCPLFSSKALTQENSPYSSFRLVNPPGLSL HPEGEGGKWINERGREQCPSAWPLLLFLHFAEAGRRQPPDWADPQADLQQV (SEQ ID NO:331) corresponding to amino acids 153-256 of HUMCS2_P3 (SEQ ID NO:278), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMCS2_P3 (SEQ ID NO:278), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VRVAPGVTNPGTPLASRAGGEKYCCPLFSSKALTQENSPYSSFRLVNPPGLSL HPEGEGGKWINERGREQCPSAWPLLLFLHFAEAGRRQPPDWADPQADLQQV (SEQ ID NO:331) in HUMCS2_P3 (SEQ ID NO:278).
Splice Variant HUMCS2_T13 (SEQ ID NO:279) Encodes a New Secreted Form of the Chorionic Somatomammotropin, HUMCS2_P9 (SEQ ID NO:280)
The present inventors have uncovered a new chorionic somatomammotropin variant [HUMCS2_T13—SEQ ID NO:279; HUMCS2_P9—SEQ ID NO:280]. The protein coordinates on the transcript start from nucleotide 139 and end at nucleotide 741 as set forth in SEQ ID NO:279 (HUMCS2_T13 transcript).
Alignment of the new chorionic somatomammotropin variant (HUMCS2_P9-SEQ ID NO:280) with the WT protein (GenBank Accession No. P01243; SEQ ID NO:330) revealed that the new variant includes the first 152 amino acids as of the WT protein (GenBank Accession No. P01243) followed by a unique 49 amino acid sequence [VRVAPGVTNPGTPLASRAGGEKYCCPLFSKAGRRQPPDWADPQADLQQV (SEQ ID NO:641), FIG. 122]. The new variant uncovered by the present invention lacks the Somatotropin hormone domain (IPR001400) of the WT protein, and three of the four potential sites for disulfide bonds (amino acids 191, 208 and 215) and is therefore a potential antagonist of chorionic somatomammotropin.
Comparison Report Between HUMCS2_P9 and CSH_HUMAN (GenBank Accession No. P01243)
1. An isolated chimeric polypeptide HUMCS2_P9 (SEQ ID NO:280), comprising a first amino acid sequence being at least 90% homologous to MAPGSRTSLLLAFALLCLPWLQEAGAVQTVPLSRLFDHAMLQAHRAHQLAID TYQEFEETYIPKDQKYSFLHDSQTSFCFSDSIPTPSNMEETQQKSNLELLRISLL LIESWLEPVRFLRSMFANNLVYDTSDSDDYHLLKDLEEGIQTLMG corresponding to amino acids 1-152 of CSH_HUMAN (GenBank Accession No. P01243; SEQ ID NO:330), which also corresponds to amino acids 1-152 of HUMCS2_P9 (SEQ ID NO:280), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VRVAPGVTNPGTPLASRAGGEKYCCPLFSKAGRRQPPDWADPQADLQQV (SEQ ID NO:641) corresponding to amino acids 153-201 of HUMCS2_P9 (SEQ ID NO:280), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMCS2_P9 (SEQ ID NO:280), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VRVAPGVTNPGTPLASRAGGEKYCCPLFSKAGRRQPPDWADPQADLQQV (SEQ ID NO:641) in HUMCS2_P9 (SEQ ID NO:280).
Since the HUMCS2_P3 and HUMCS2_P9 variants of the present invention lacks the Somatotropin hormone domain they can compete with the endogenous chorionic somatomammotropin and interfere with its various activities.
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:278 or 280 and/or an expressible polynucleotide homologous to SEQ ID NO:277 or 279 and/or a peptide homologous to SEQ ID NO:331 or 641 which can be used to treat chorion-related cancer such as breast cancer with choriocarcinomatous features.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
While further reducing the present invention to practice, and without being bound to any theory, these results suggest the use of the new Somatotropin variant of the present invention SEQ ID NO:278 or 280), the polynucleotide encoding same (SEQ ID NO:277 or 279) and/or the peptide derived from the new Somatotropin variants (SEQ ID NO:331 or 641) as a diagnostic marker for chorion-related cancer (e.g., breast cancer with choriocarcinomatous features). Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the HUMCS2_P9 or HUMCS2_P3 variants (SEQ ID NO:278 or 280)], or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 38
Splice Variant of Fibronectin Precursor
Background
Fibronectin (FN; Cold-insoluble globulin; CIG; FN; FN1; GenBank Accession No. P02751; FINC_HUMAN) is a high molecular weight extracellular glycoprotein capable of binding cell surfaces, collagen, fibrin, heparin, DNA, and actin.
Fibronectin is recognized by at least ten cell surface receptors of the integrin family and many cell types in the body can adhere to fibronectin via these receptors. Fibronectins are involved in cell adhesion, cell motility, opsonization, wound, healing, maintenance of cell shape, and acute-phase response. They interact with FBLN1, AMBP and LGALS3BP, form heterodimers or multimers via disulfide bonds.
The extracellular matrix controls cell survival, cell morphology and tissue organization by supporting cell adhesion. Remodeling of the extracellular matrix and cell migration are key processes in the development of properly organized blood vessels, tissues and organs, and have been implicated in pathological processes (Werb, 1997, Cell 91:439-442; Liotta et al., 1991, Cell 64:327-336).
Fibronectin is expressed at the cell surface of many types of differentiated cells and is involved in the attachment of cells to the surrounding extracellular matrix. Soluble plasma fibronectin binds poorly to many cell types, but after deposition onto a suitable substrate, its cell binding avidity is enhanced. The substrates may be collagen in the extracellular matrix or fibrin in peripheral blood. In the extracellular matrix, fibronectin provides signals that control cell shape, migration, proliferation, differentiation, morphogenesis and survival. This makes fibronectin a paradigm adhesive protein, non-reactive in its soluble state, but highly adhesive when insoluble. In the extracellular matrix, adhesive proteins display biologically active cryptic sites that are revealed after structural or conformational alterations. For example, collagen binding may induce a conformational change in fibronectin that disengages the intramolecular interaction of domains I-1/I-2/I-3/I-4/I-5 with III-3 (Pickford A R, et al., EMBO J. 2001, 20: 1519-29). As a result cryptic sites in this gelatin binding domain of fibronectin may be exposed.
More than half of the fibronectin molecule consists of so-called fibronectin type III repeats. Two splice-variants of fibronectin are known. The ED-A splice variant is expressed in some normal tissues and can also be found in the serum and is expression is upregulated in tumor and embryonic tissues. The ED-B splice variant is only expressed in embryonic and tumor tissues and is not detectable in healthy adult tissue.
Clinical Applications
Fibrobectin is been used in the diagnosis of various cancers such as thyroid tumors (Prasad M L, et al., 2005, Mod. Pathol. 18: 48-57), bladder tumor (Mutlu N, et al., 2003, Clin. Chem. Lab, Med. 41: 1069-74), cholangiocarcinoma (Chen C Y, et al., 2003, Hepatogastroenterology, 50: 924-7), malignant ascites (Sood A, et al., 1997. J. Assoc. Physicians. India. 45: 283-5), malignant and benign diseases of the biliary tract (Korner T, et al., Hepatology. 1996 March; 23(3):423-8), as well as in various conditions such as myocardial infarction (Hu B J, et al., 2002, Med. Sci. Law. 42: 195-9), and preterm labour (Grobman W A, et al., 2004, Am. J. Obstet. Gynecol. 191: 235-40).
In addition, fibronectin is accumulated in cases of various injuries such as corneal injury, blood injury and thus can be used as an ophthalmological vulnerary.
Splice Variant HUMFNC_T54 (SEQ ID NO:281) Encodes a New Secreted Form of the Fibronectin, HUMFNC_P54 (SEQ ID NO:282)
The present inventors have uncovered a new fibronectin variant [HUMFNC_T54—SEQ ID NO:281); HUMFNC_P54—SEQ ID NO:2821. The protein coordinates on the transcript start from nucleotide 371 and end at nucleotide 4222 as set forth in SEQ ID NO:281 (HUMFNC_T54 transcript).
Alignment of the new fibronectin variant (HUMFNC_P54—SEQ ID NO: 282) with the WT protein (GenBank Accession No. P02751; SEQ ID NO:644) revealed that the new variant includes the first 1264 amino acids as of the WT protein (GenBank Accession No. P02751) followed by a unique 19 amino acid sequence [GNRKISCYPESDTSNKSGD (SEQ ID NO:645), FIG. 123]. The new variant uncovered by the present invention includes 9 out of 12 fibronectin type I domains (IPR000083), the two fibronectin type II domains, 7 out of 16 fibronectin type III domains (IPR003961), one out of 3 fibrin/heparin binding domains, lacks the connecting strand 3 (CS-3; V region) and the FBLN1 binding domain of the WT protein.
Comparison Report Between HUMFNC_P54 and FINC_HUMAN_V3 (SEQ ID NO:646)
1. An isolated chimeric polypeptide HUMFNC_P54, comprising a first amino acid sequence being at least 90% homologous to MLRGPGPGLLLLAVQCLGTAVPSTGASKSKRQAQQMVQPQSPVAVSQSKPG CYDNGKHYQINQQWERTYLGNALVCTCYGGSRGFNCESKPEAEETCFDKYT GNTYRVGDTYERPKDSMIWDCTCIGAGRGRISCTIANRCHEGGQSYKIGDTW RRPHETGGYMLECVCLGNGKGEWTCKPIAEKCFDHAAGTSYVVGETWEKPY QGWMMVDCTCLGEGSGRITCTSRNRCNDQDTRTSYRIGDTWSKKDNRGNLL QCICTGNGRGEWKCERHTSVQTTSSGSGPFTDVRAAVYQPQPHPQPPPYGHC VTDSGVVYSVGMQWLKTQGNKQMLCTCLGNGVSCQETAVTQTYGGNSNGE PCVLPFTYNGRTFYSCTTEGRQDGHLWCSTTSNYEQDQKYSFCTDHTVLVQT RGGNSNGALCHFPFLYNNHNYTDCTSEGRRDNMKWCGTTQNYDADQKFGF CPMAAHEEICTTNEGVMYRIGDQWDKQHDMGHMMRCTCVGNGRGEWTCI AYSQLRDQCIVDDITYNVNDTFHKRHEEGHMLNCTCFGQGRGRWKCDPVDQ CQDSETGTFYQIGDSWEKYVHGVRYQCYCYGRGIGEWHCQPLQTYPSSSGPV EVFITETPSQPNSHPIQWNAPQPSHISKYILRWRPKNSVGRWKEATIPGHLNSY TIKGLKPGVVYEGQLISIQQYGHQEVTRFDFTTTSTSTPVTSNTVTGETTPFSPL VATSESVTEITASSFVVSWVSASDTVSGFRVEYELSEEGDEPQYLDLPSTATSV NIPDLLPGRKYIVNVYQISEDGEQSLILSTSQTTAPDAPPD corresponding to amino acids 1-816 of FINC_HUMAN_V3, which also corresponds to amino acids 1-816 of HUMFNC_P54, a bridging amino acid T corresponding to amino acid 817 of HUMFNC_P54, a second amino acid sequence being at least 90% homologous to TVDQVDDTSIVVRWSRPQAPITGYRIVYSPSVEGSSTELNLPETANSVTLSDLQ PGVQYNITIYAVEENQESTPVVIQQETTGTPRSDTVPSPRDLQFVEVTDVKVTI MWTPPESAVTGYRVDVIPVNLPGEHGQRLPISRNTFAEVTGLSPGVTYYFKVF AVSHGRESKPLTAQQTTKLDAPTNLQFVNETDSTVLVRWTPPRAQITGYRLT VGLTRRGQPRQYNVGPSVSKYPLRNLQPASEYTVSLVAIKGNQESPKATGVF TTLQPGSSIPPYNTEVTETTIVITWTPAPRIGFKLGVRPSQGGEAPREVTSDSGSI VVSGLTPGVEYVYTIQVLRDGQERDAPIVNKVVTPLSPPTNLHLEANPDTGVL TVSWERSTTPDITGYRITTTPTNGQQGNSLEEVVHADQSSCTFDNLSPGLEYN VSVYTVKDDKESVPISDTIIP corresponding to amino acids 818-1265 of FINC_HUMAN_V3, which also corresponds to amino acids 818-1265 of HUMFNC_P54, and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GNRKISCYPESDTSNKSGD corresponding to amino acids 1266-1284 of HUMFNC_P54, wherein said first amino acid sequence, bridging amino acid, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMFNC_P54, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GNRKISCYPESDTSNKSGD in HUMFNC_P54.
Comparison Report Between HUMFNC_P54 and FINC_HUMAN (SEQ ID NO:644)
1. An isolated chimeric polypeptide HUMFNC_P54, comprising a first amino acid sequence being at least 90% homologous to MLRGPGPGLLLLAVQCLGTAVPSTGASKSKRQAQQMVQPQSPVAVSQSKPG CYDNGKHYQINQQWERTYLGNALVCTCYGGSRGFNCESKPEAEETCFDKYT GNTYRVGDTYERPKDSMIWDCTCIGAGRGRISCTIANRCHEGGQSYKIGDTW RRPHETGGYMLECVCLGNGKGEWTCKPIAEKCFDHAAGTSYVVGETWEKPY QGWMMVDCTCLGEGSGRITCTSRNRCNDQDTRTSYRIGDTWSKKDNRGNLL QCICTGNGRGEWKCERHTSVQTTSSGSGPFTDVRAAVYQPQPHPQPPPYGHC VTDSGVVYSVGMQWLKTQGNKQMLCTCLGNGVSCQETAVTQTYGGNSNGE PCVLPFTYNGRTFYSCTTEGRQDGHLWCSTTSNYEQDQKYSFCTDHTVLVQT corresponding to amino acids 1-410 of FINC_HUMAN, which also corresponds to amino acids 1-410 of HUMFNC_P54, a bridging amino acid R corresponding to amino acid 411 of HUMFNC_P54, a second amino acid sequence being at least 90% homologous to GGNSNGALCHFPFLYNNHNYTDCTSEGRRDNMKWCGTTQNYDADQKFGFC PMAAHEEICTTNEGVMYRIGDQWDKQHDMGHMMRCTCVGNGRGEWTCIA YSQLRDQCIVDDITYNVNDTFHKRHEEGHMLNCTCFGQGRGRWKCDPVDQC QDSETGTFYQIGDSWEKYVHGVRYQCYCYGRGIGEWHCQPLQTYPSSSGPVE VFITETPSQPNSHPIQWNAPQPSHISKYILRWRPKNSVGRWKEATIPGHLNSYT IKGLKPGVVYEGQLISIQQYGHQEVTRFDFTTTSTSTPVTSNTVTGETTPFSPLV ATSESVTEITASSFVVSWVSASDTVSGFRVEYELSEEGDEPQYLDLPSTATSVN IPDLLPGRKYIVNVYQISEDGEQSLILSTSQTTAPDAPPD corresponding to amino acids 412-816 of FINC_HUMAN, which also corresponds to amino acids 412-816 of HUMFNC_P54, a bridging amino acid T corresponding to amino acid 817 of HUMFNC_P54, a third amino acid sequence being at least 90% homologous to TVDQVDDTSIVVRWSRPQAPITGYRIVYSPSVEGSSTELNLPETANSVTLSDLQ PGVQYNITIYAVEENQESTPVVIQQETTGTPRSDTVPSPRDLQFVEVTDVKVTI MWTPPESAVTGYRVDVIPVNLPGEHGQRLPISRNTFAEVTGLSPGVTYYFKVF AVSHGRESKPLTAQQTTKLDAPTNLQFVNETDSTVLVRWTPPRAQITGYRLT VGLTRRGQPRQYNVGPSVSKYPLRNLQPASEYTVSLVAIKGNQESPKATGVF TTLQPGSSIPPYNTEVTETTIVITWTPAPRIGFKLGVRPSQGGEAPREVTSDSGSI VVSGLTPGVEYVYTIQVLRDGQERDAPIVNKVVTPLSPPTNLHLEANPDTGVL TVSWERSTTPDITGYRITTTPTNGQQGNSLEEVVHADQSSCTFDNLSPGLEYN VSVYTVKDDKESVPISDTIIP corresponding to amino acids 818-1265 of FINC_HUMAN, which also corresponds to amino acids 818-1265 of HUMFNC_P54, and a fourth amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GNRKISCYPESDTSNKSGD corresponding to amino acids 1266-1284 of HUMFNC_P54, wherein said first amino acid sequence, bridging amino acid, second amino acid sequence, bridging amino acid, third amino acid sequence and fourth amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMFNC_P54, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GNRKISCYPESDTSNKSGD in HUMFNC_P54.
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:282 and/or an expressible polynucleotide homologous to SEQ ID NO:281 and/or a peptide homologous to SEQ ID NO:645 which can be used in wound healing, in the treatment of corneal injury, blood injury and as an ophthalmological vulnerary.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
While further reducing the present invention to practice, these results suggest the use of the new fibronectin variant of the present invention (HUMFNC_P54—SEQ ID NO:282), the polynucleotide encoding same (HUMFNC_T54—SEQ ID NO:281) and/or the peptide derived from the HUMFNC_P54 variant (GNRKISCYPESDTSNKSGD—SEQ ID NO:645) as a diagnostic marker for thyroid tumors, bladder tumor, cholangiocarcinoma, malignant ascites, malignant and benign diseases of the biliary tract, myocardial infarction, and preterm labour. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the fibronectin variant (HUMFNC_P54—SEQ ID NO:2821, or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 39
Splice Variant of Integrin Alpha-8
Background
The integrin family is composed of 15 α and 8 β subunits that form over twenty different αβ heterodimeric combinations on cell surfaces. Integrins recognize extracellular matrix (ECM) proteins and cell surface immunoglobulin family molecules through short peptide sequences. The integrin-mediated adhesion of cells to the ECM leads to bi-directional intracellular signaling events that can regulate cell survival, proliferation and migration. In contrast, inhibition of integrin-ligands interactions suppresses cellular growth or induces apoptotic cell death.
The integrin alpha-8 subunit (ITGA8; GenBank Accession No. P53668; ITA8_HUMAN; SEQ ID NO:327) is a type I membrane protein composed of heavy and light chains linked by a disulfide bond. Integrin α8 associates with integrin β1 to form the α8β1 integrin receptor for fibronectin and cytotactin, vitronectin, tenascin, and osteopontin. Integrin α8 involves in cell-matrix adhesion, cell-cell adhesion. Integrin α8 is expressed in hippocampal dentate hilar neurons, overexpressed in lung injury, smooth muscle cells and can be used as a marker for proliferation of these cell or as a marker for pathological de-differentiation of these cells and tissues. In addition, since integrin α8 is overexpressed in hepatocellular carcinoma (Liu L X, et al., 2002, World J. Gastroenterol. 8: 631-7) it can be used as a marker for such cancer.
Splice Variant M85929_T2 (SEQ ID NO:283) Encodes a New Secreted Form of the Integrin α8, M85929_P3 (SEQ ID NO:284)
The present inventors have uncovered a new integrin α8 variant [M85929_T2—SEQ ID NO:283; M85929_P3—SEQ ID NO:284]. The protein coordinates on the transcript start from nucleotide 388 and end at nucleotide 2292 as set forth in SEQ ID NO:283 (M85929_T2 transcript).
Alignment of the new integrin α8 variant (M85929_P3—SEQ ID NO:284) with the WT protein (GenBank Accession No. P53708; SEQ ID NO:327) revealed that the new variant includes the first 634 amino acids as of the WT protein (GenBank Accession No. M85929_P3) followed by a unique amino acid R [FIG. 124]. The new variant uncovered by the present invention lacks the integrin α8 light chain (IPR000413; amino acids 907-1063 of WT), the transmembrane domain (amino acids 1013-1033 of WT), the cytoplasmic domain (amino acids 1034-1063 of WT), as well as four potential disulfide bond and six potential glycosylation sites and therefore is expected to be a secreted, soluble protein (i.e., extracellular).
Comparison Report Between M85929_P3 (SEQ ID NO:284) and ITA8_HUMAN (SEQ ID NO:327)
1. An isolated chimeric polypeptide M85929_P3 (SEQ ID NO:284), comprising a first amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence MSPGASRGPRGSQAPLIAPLCCAAAALGMLLWSPACQA corresponding to amino acids 1-38 of M85929_P3 (SEQ ID NO:284), a second amino acid sequence being at least 90% homologous to FNLDVEKL corresponding to amino acids 1-8 of ITA8_HUMAN (SEQ ID NO:327), which also corresponds to amino acids 39-46 of M85929_P3 (SEQ ID NO:284), a bridging amino acid T corresponding to amino acid 47 of M85929_P3 (SEQ ID NO:284), a third amino acid sequence being at least 90% homologous to VYSGPKGSYFGYAVDFHIPDARTASVLVGAPKANTSQPDIVEGGAVYYCPWP AEGSAQCRQIPFDTTNNRKIRVNGTKEPIEFKSNQWFGATVKAHKGKVVACA PLYHWRTLKPTPEK corresponding to amino acids 10-127 of ITA8_HUMAN (SEQ ID NO:327), which also corresponds to amino acids 48-165 of M85929_P3 (SEQ ID NO:284), a bridging amino acid D corresponding to amino acid 166 of M85929_P3 (SEQ ID NO:284), a fourth amino acid sequence being at least 90% homologous to PVGTCYVAIQNFSAYAEFSPC corresponding to amino acids 129-149 of ITA8_HUMAN (SEQ ID NO:327), which also corresponds to amino acids 167-187 of M85929_P3 (SEQ ID NO:284), a bridging amino acid R corresponding to amino acid 188 of M85929_P3, a fifth amino acid sequence being at least 90% homologous to NSNADPEGQGYCQAGFSLDFYKNGDLIVGGPGSFYWQGQVITASVADIIANY SFKDILRKLAGEKQTEVAPASYDDSYLGYSVAAGEFTGDSQQELVAGIPRGA QNFGYVSIINS corresponding to amino acids 151-265 of ITA8_HUMAN (SEQ ID NO:327), which also corresponds to amino acids 189-303 of M85929_P3 (SEQ ID NO:284), a bridging amino acid T corresponding to amino acid 304 of M85929_P3, a sixth amino acid sequence being at least 90% homologous to DMTFIQNFTGEQMASYFGYTVVVSDVNSDGLDDVLVGAPLFMEREFESNPRE VGQIYLYLQVSSLLFRDPQILTGTETFGRFGSAMAHLGDLNQDGYNDIAIGVP FAGKDQRGKVLIYNGNKDGLNTKPSQVLQGVWASHAVPSGFGFTLRGDSDI DKNDYPDLIVGAFGTGKVAVYRARPVVTVDAQLLLHPMIINLENKTCQVPDS MTSAACFSLRVCASVTGQSIANTIVLMAEVQLDSLKQKGAIKRTLFLDNHQA HRVFPLVIKRQKSHQCQDFIVYLRDETEFRDKLSPINISLNYSLDESTFKEGLEV KPILNYYRENIVSEQ corresponding to amino acids 267-596 of ITA8_HUMAN (SEQ ID NO:327), which also corresponds to amino acids 305-634 of M85929_P3 (SEQ ID NO:284), a seventh amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence R corresponding to amino acids 635-635 of M85929_P3 (SEQ ID NO:284), wherein said first amino acid sequence, second amino acid sequence, bridging amino acid, third amino acid sequence, bridging amino acid, fourth amino acid sequence, bridging amino acid, fifth amino acid sequence, bridging amino acid, sixth amino acid sequence and seventh amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a head of M85929_P3 (SEQ ID NO:284), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence MSPGASRGPRGSQAPLIAPLCCAAAALGMLLWSPACQA of M85929_P3 (SEQ ID NO:284).
Since the integrin α8 variant of the present invention lacks the transmembrane domain as well as the integrin α8 light chain it can compete with the endogenous integrin α8 on associating with the integrin β subunits and serve as an antagonist of the integrin α8β1 receptor and interfere with its various activities.
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:284 and/or an expressible polynucleotide homologous to SEQ ID NO:283 which can be used to prevent the association of endogenous integrin α8 with the integrin β1 subunit and/or with an α8 ligand and thus prevent integrin α8β1 activation and treat integrin α8β1-related disease, disorder or condition such as cancer (e.g., hepatocellular carcinoma).
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 40
Splice Variant of Thrombopoietin
Background
Thrombopoietin (TPO, also known as c-Mpl ligand) is a hematopoietic growth factor that mediates megakaryocyte progenitor proliferation and differentiation, and increased platelets production. It is produced constitutively, mainly in the liver with trace amounts being produced in the kidney, it circulates in the bloodstream, and delivered to the bone marrow, where it stimulates the early development of multiple hematopoietic lineages and megakaryocytopoiesis. TPO has multi lineage effects in hematopoiesis, and in addition for stimulating megakaryocytes it also acts in synergy with other cytokines to enhance proliferation and survival of committed erythroid progenitors and primitive hematopoietic stem cells. Elevated TPO levels occur in thrombocytopenia and leads to an increase in megakaryocyte number, size, and ploidy and will result in increased production of platelets. It has been suggested that a feedback mechanism can sense a decrease in platelet mass and cause an increase in TPO activity. c-Mpl, the TPO-receptor, is an oncogene that belongs to the hematopoitic receptor family. TPO activity is probably regulated by the binding and metabolism by c-Mpl-expressing platelets.
The TPO protein is divided into two domains: an amino terminal half (153 amino acids, not including the signal peptide which consists of 21 amino acids) with homology to erythropoietin (epo-like domain) and a unique C-terminal domain (of 182 amino acids) containing multiple potential N-linked glycosylation sites. The epo-like domain alone is sufficient for activation of c-Mpl. TPO-2, a naturally occurring alternative splice variant that result from an alternative acceptor site in exon 6 and in the concomitant deletion of amino acids 133-136 (numbers include the signal peptide) which reside within the epo-like domain, is inactive (Gurney, A. L., W. J. Kuang, M. H. Xie, B. E. Malloy, D. L. Eaton, and F. J. de Sauvage. 1995. Genomic structure, chromosomal localization, and conserved alternative splice forms of thrombopoietin. Blood 85:981.).
Clinical Applications
An obvious clinical indication for the use of TPO is for treatment of thrombocytopenias, especially those resulting from chemo- and irradiation therapy. Non-cancer related thrombocytopenia where TPO might have efficacy is Immunologic thrombocytopenia (ITP) in which premature removal of platelets from the circulation occurs, and HIV-related thrombocitopenia (Lok, S., and D. C. Foster. 1994. The structure, biology and potential therapeutic applications of recombinant thrombopoietin. Stem Cells 12:586.).
As TPO is highly involved in platelet aggregation (Oda, A., Y. Miyakawa, B. J. Druker, K. Ozaki, K. Yabusaki, Y. Shirasawa, M. Handa, T. Kato, H. Miyazaki, A. Shimosaka, and Y. Ikeda. 1996. Thrombopoietin primes human platelet aggregation induced by shear stress and by multiple agonists. Blood 87:4664.), TPO antagonists might be useful in preventing coagulation. In addition TPO antagonist might be useful for treatment of essential thrombocytopenia (ET)—a chronic myeloproliferative syndrome caused by sustained proliferation of megakaryocytes which result in elevated levels of circulating platelets, thrombotic or hemorrhagic episodes and occasional leukaemic transformation.
Splice Variant Structure
The present inventors uncovered two novel splice variant of Thrombopoietin. The new splice variant T8 [HSU11025_T8—SEQ ID NO:119 (FIG. 86a); HSU11025_P6—SEQ ID NO:118 (FIG. 86b)] results from alternative splicing of the thrombopoietin gene, thus introducing an alternative splice acceptor site in exon 6, causing a deletion of amino acids 133-159 of the WT protein (TPO_HUMAN; SEQ ID NO:151). The variant protein thus created is a 327 amino acids long protein (SEQ ID NO:118), which contains the N-terminal epo-like domain with 26 amino acids deletion, and a complete carbohydrate domain (FIGS. 87-89).
Comparison Report Between HSU11025_P6 (SEQ ID NO:118) and TPO_HUMAN (SEQ ID NO:151)
1. An isolated chimeric polypeptide HSU11025_P6 (SEQ ID NO:118), comprising a first amino acid sequence being at least 90% homologous to MELTELLLVVMLLLTARLTLSSPAPPACDLRVLSKLLRDSHVLHSRLSQCPEV HPLPTPVLLPAVDFSLGEWKTQMEETKAQDILGAVTLLLEGVMAARGQLGPT CLSSLLGQLSGQVRLLLGALQSLLGTQ corresponding to amino acids 1-132 of TPO_HUMAN (SEQ ID NO:151), which also corresponds to amino acids 1-132 of HSU11025_P6 (SEQ ID NO:118), and a second amino acid sequence being at least % homologous to VRFLMLVGGSTLCVRRAPPTTAVPSRTSLVLTLNELPNRTSGLLETNFTASAR TTGSGLLKWQQGFRAKIPGLLNQTSRSLDQIPGYLNRIHELLNGTRGLFPGPSR RTLGAPDISSGTSDTGSLPPNLQPGYSPSPTHPPTGQYTLFPLPPTLPTPVVQLH PLLPDPSAPTPTPTSPLLNTSYTHSQNLSQEG corresponding to amino acids 160-353 of TPO_HUMAN (SEQ ID NO:151), which also corresponds to amino acids 133-326 of HSU11025_P6 (SEQ ID NO:118), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HSU11025_P6 (SEQ ID NO:118), comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise QV, having a structure as follows: a sequence starting from any of amino acid numbers 132-x to 132; and ending at any of amino acid numbers 133+((n−2)−x), in which x varies from 0 to n−2.
Therapeutic Applications for the Thrombopoietin Splice Variant
The epo-like domain is sufficient and necessary for TPO activity, thus, as T8 has an impaired epo-like domain, it is predicted to be inactive. In addition, mutating amino acids 153, 154 or 159 resulted in reduced proliferation activity, and their deletion in T8 will probably result in a pronounced reduction of activity (Jagerschmidt, A., V. Fleury, M. Anger-Leroy, C. Thomas, M. Agnel, and P. O'Brien D. 1998. Human thrombopoietin structure-function relationships: identification of functionally important residues. Biochem J 333 (Pt 3):729.). However, it might serve as an antagonist and prevent TPO-induced coagulation.
The variants according to the present invention preferably serve as TPO antagonists and/or partial agonists. They may optionally be used to treat any type of TPO-mediated and/or promoted disease or disorder, including but not limited to, preventing coagulation (for situations in which coagulation is excessive and/or undesirable) or treatment of essential thrombocytopenia (ET), and may optionally be useful for treatment of blood disorders in which blockage or reduction of TPO activity is desirable.
Example 41
Intracellular Adhesion Molecule 2
Background
Intracellular adhesion molecule 2 (ICAM-2, CD102 antigen) is a member of the immunoglobulin superfamily, encompassing two immunoglobulin domains, was originally described as a counterreceptor for the leukocyte integrin leukocyte function antigen-1 (LFA-1). ICAM-2 play a role in lymphocyte recirculation by blocking LFA-1 dependent cell adhesion. It mediates adhesive interactions important for antigen specific immune response, NK-cell mediated clearance, lymphocyte recirculation and other cellular interactions important for immune response and surveillance.
ICAM-2 expression is restricted to endothelial cells and lymphocytes. The surface expression on lymphocytes is up-regulated on activation from low basal levels and, importantly, many malignancies derived from both T and B lymphocytes are ICAM-2 positive. Recent studies have established that mannose-rich carbohydrate structures attached to ICAM-2 interact with the Dendritic Cell (DC)-specific lectin DC-SIGN (CD209), playing, therefore, a potentially important role both in DC-T-cell interactions and DC trafficking through endothelial bathers. DC-SIGN was proposed to be used by viral and bacterial pathogens, including HCV, HIV, Ebola virus, CMV, and Mycobacterium tuberculosis, to facilitate infection. ICAM-2 was shown to ignite a signaling pathway that inhibits programmed cell death (Murillo, et al, 2003, Clin Cancer Res., 9:5454-5464).
The first NH2-terminal immunoglobulin domain of ICAM-2 is important for binding to LFA-1 (CD11a/CD18) and Mac-1 (CD11b/CD18) (Kotovuori et al, 1999, J Immunol, 162:6613-6620). Synthetic 22 amino acid peptide (P1), derived from residues 21-42 of the ICAM-2 protein (numbering without the signal peptide), corresponding to a sequence from the first Ig domain, was shown to be able to bind CD11a/CD18 and CD11b/CD18 and stimulate aggregation of various leukocytes and stimulate the migration and cytotoxicity of NK cells. P1 was further shown to stimulate the adhesion of T-cell lymphocytes to ICAM-1, 2, and 3, and induced increased integrin affinity for ICAMs (Kotovuori et al, 1999, J Immunol, 162:6613-6620; Li, et al 1995, JCB, 129:1143-1153; Li et al, 1993, JBC, 268:21474-21477). The finding that P1 stimulates the binding of leukocytes to fibrinogen raises the intriguing possibility that ICAM-2, which is constitutively expressed on most endothelia have an important role in leukocyte binding during physiological conditions. On the other hand, the capacity of the P1 peptide to inhibit the adhesion of ICAM-2 containing nonleukocytic endothelial cells to CD11a/CD18 was demonstrated as well, supporting the contribution of this peptide to the adhesive interaction itself. P1 also inhibited the binding of B-lymphoblastoid cells to endothelial cells (Li, et al 1995, JCB, 129:1143-1153; Li et al, 1993, JBC, 268:17513-16518).
Soluble ICAM-2Fc proteins, containing either a part of or the entire extracellular region of the molecule, exhibited costimulatory effects of ICAM-2 and were able to induce T lymphocyte adhesion to purified ICAMs (Damle et al, 1992, J Immunol., 148:665-671).
Mutagenesis studies of ICAMSs have shown that four conserved residues are important for adhesive interactions with LFA-1: Glu-37 is the most critical for integrin binding, while Tyr-54, Gln-30 and Gln-75 are also important (Casaanovas, et al, 1997, Nature, 387:312-315).
Inhibition of CD11a, LFA-1, or its ligand have been shown to be a useful target for therapy of several inflammatory situations associated with accumulation of leukocytes leading to clot formation or cytotoxicity. mAbs to CD11a, ICAM-1, and CD18 were comparably effective in a rabbit model of myocardial reperfusion injury and reduced infarct size by 40-50%, but only if administered well before reperfusion. Reducing cytotoxic T cell activity by mAbs to CD11a/CD18, in combination with standard immunosuppressive therapy, improve the survival of bone marrow transplants in children but not in adults. In a mouse model, anti CD11a mAbs increased the survival of allogenic tumor grafts. LFA-1 might also be involved in cancer metastasis as its expression on hematological tumor cells have been shown to alter metastatic capacity and growth (Mazzone and Richevuti, 1995).
Binding of immunotherapeutic mAbs to ICAM-2 enhance its adhesiveness to DC-SIGN, and promotes the survival of activated T lymphocytes that recognize tumor antigens (Murillo, et al, 2003, Clin Cancer Res., 9:5454-5464).
Intracellular Adhesion Molecule-2 Novel Splice Variants HSICAM2_T12 (SEQ ID NO:339) Encodes a New Secreted Form of ICAM-2, HSICAM2_P8 (SEQ ID NO:338)
Intracellular Adhesion Molecule-2 splice variants of the present invention results from an alternative splicing of the ICAM-2 (GenBank Accession No. P13598; ICA2_HUMAN; SEQ ID NO:154). The alternatively spliced new variant HSICAM2-T12 (SEQ ID NO:339) results due to exon 2 extension incorporating into the new mRNA part of the intronic sequence from the intron located originally between exon 2 and 3 in the known wild type sequence, and production of a new truncated Intracellular Adhesion Molecule-2 protein, encoding 149 amino acids (HSICAM2_P8—SEQ ID NO:338), which shares with the wild type Intracellular Adhesion Molecule-2 the first 109 N-terminal amino acids, containing the signal peptide sequence (amino acids 1-21), partial extracellular ligand binding domain (amino acids 22-109 of the ICA2_HUMAN amino acid sequence), including the first Ig-like domain, three out of six potential glycosylation sites, two of the three cysteins, potentially involved in the disulfide bonds. The new protein does not contain the second Ig-like domain, however it retains all four amino acid residues, known to be crucial for integrin binding, Glu-37, Tyr-54, Gln-30 and Gln-75 (numbering on the mature protein). The new protein contains 40 C-terminal unique amino acids (REWLCCGALLSPGTEAVSTECTQSPSVPAPGHCHRGALPP—SEQ ID NO:340). The new protein does not contain the transmembrane domain of the wild type protein, and therefore is predicted to be secreted protein. The new protein does not contain the cytoplasmic domain of the wild type protein. The sequence alignment between the novel Intracellular Adhesion Molecule-2 splice variant HSICAM2-P8 (SEQ ID NO:338) of the present invention and the known Intracellular Adhesion Molecule-2 amino acid sequence is presented in FIG. 94a. The schematic drawing of the new variant as compared to the wild type protein is presented in FIG. 95.
Comparison Report Between HSICAM2_P8 (SEQ ID NO:338) and ICA2_HUMAN ((SEQ ID NO:154)
1. An isolated chimeric polypeptide HSICAM2_P8, comprising a first amino acid sequence being at least 90% homologous to MSSFGYRTLTVALFTLICCPGSDEKVFEVHVRPKKLAVEPKGSLEVNCSTTCN QPEVGGLETSL corresponding to amino acids 1-64 of ICA2_HUMAN, which also corresponds to amino acids 1-64 of HSICAM2_P8, a bridging amino acid D corresponding to amino acid 65 of HSICAM2_P8, a second amino acid sequence being at least 90% homologous to KILLDEQAQWKHYLVSNISHDTVLQCHFTCSGKQESMNSNVSVY corresponding to amino acids 66-109 of ICA2_HUMAN, which also corresponds to amino acids 66-109 of HSICAM2_P8, and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence REWLCCGALLSPGTEAVSTECTQSPSVPAPGHCHRGALPP (SEQ ID NO:340) corresponding to amino acids 110-149 of HSICAM2_P8, wherein said first amino acid sequence, bridging amino acid, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSICAM2_P8, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence REWLCCGALLSPGTEAVSTECTQSPSVPAPGHCHRGALPP in HSICAM2_P8.
Comparison Report Between HSICAM2_P8 and ICA2_HUMAN_V1
1. An isolated chimeric polypeptide HSICAM2_P8, comprising a first amino acid sequence being at least 90% homologous to MSSFGYRTLTVALFTLICCPGSDEKVFEVHVRPKKLAVEPKGSLEVNCSTTCN QPEVGGLETSLDKILLDEQAQWKHYLVSNISHDTVLQCHFTCSGKQESMNSN VSVY corresponding to amino acids 1-109 of ICA2_HUMAN_V1, which also corresponds to amino acids 1-109 of HSICAM2_P8, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence REWLCCGALLSPGTEAVSTECTQSPSVPAPGHCHRGALPP (SEQ ID NO:340) corresponding to amino acids 110-149 of HSICAM2_P8, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSICAM2_P8, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence REWLCCGALLSPGTEAVSTECTQSPSVPAPGHCHRGALPP in HSICAM2_P8.
Intracellular Adhesion Molecule-2 Novel Splice Variants HSICAM2_T8 (SEQ ID NO:336) Encodes a New Secreted Form of ICAM-2, New Variant Encoded by HSICAM2_T8 (SEQ ID NO:335)
The alternatively spliced new variant HSICAM2-T8 (transcript—SEQ ID NO:336, protein—SEQ ID NO:335) results from the incorporation of an alternative exon between the original exons 2 and 3, derived from the intronic sequence located originally between exon 2 and 3 in the known wild type sequence, and production of a new truncated Intracellular Adhesion Molecule-2 (SEQ ID NO:335), comprising 164 amino acids, which shares with the wild type Intracellular Adhesion Molecule-2 (ICA2_HUMAN, SEQ ID NO:154) the 109 N-terminal amino acids, containing the signal peptide sequence (amino acids 1-21), partial extracellular ligand binding domain (amino acids 22-109), including the first Ig-like domain, three out of six potential glycosylation sites, two of the three cysteins, potentially involved in the disulfide bonds. The new protein does not contain the second Ig-like domain, however it retains all four amino acid residues, known to be crucial for integrin binding, Glu-37, Tyr-54, Gln-30 and Gln-75 (according to the sequence of the mature protein). The new protein contains 55 C-terminal unique amino acids (LGCTISEPCPCRHLVTGNHHVCKTTTQSSLHPQLLPSSSLHWSRPGHLLPNRG TP—SEQ ID NO:337). The new protein does not contain the transmembrane domain of the wild type protein, and therefore it is predicted to be secreted. The new protein does not contain the cytoplasmic domain of the wild type protein. The sequence alignment between the novel Intracellular Adhesion Molecule-2 splice variant HSICAM2-P8 (SEQ ID NO:335) of the present invention and the known Intracellular Adhesion Molecule-2 is presented in FIG. 94b. The schematic drawing of the new variant as compared to the wild type protein is presented in FIG. 95.
Clinical Applications of the New Variants
Synthetic 22 amino acid peptide (P1), derived from the first NH2-terminal immunoglobulin domain of the ICAM-2 protein was shown to be able to bind CD11a/CD18 and CD11b/CD18 and stimulate aggregation of various leukocytes as well as stimulate the migration and the cytotoxicity of NK cells. P1 was further shown to stimulate the adhesion of T-cell lymphocytes to ICAM-1, 2, and 3, and induced increased integrin affinity for ICAMs (Kotovuori et al, 1999, J Immunol, 162:6613-6620; Li, et al 1995, JCB, 129:1143-1153; Li et al, 1993, JBC, 268:21474-21477). Soluble ICAM-2Fc protein was also able to induce T lymphocyte adhesion to purified ICAMs. On the other hand, the P1 peptide inhibits the adhesion of ICAM-2 containing nonleukocytic endothelial cells to CD11a/CD18 and inhibits the binding of B-lymphoblastoid cells to endothelial cells (Li, et al 1995, JCB, 129:1143-1153; Li et al, 1993, JBC, 268:17513-16518). The ICAM-2 new variants [(HSICAM2-P8 (SEQ ID NO:335) and HSICAM2-P12 (SEQ ID NO:338)] of the present invention are therefore predicted to be secreted proteins with agonistic mode of action, binding to the integrin receptors and enhancing aggregation of various leukocytes as well as stimulating the migration and the cytotoxicity of NK cells. The new variants of the present invention are predicted to have antagonistic mode of action on endothelial cells.
The ICAM-2 new variants of the present invention can be used as immunostimulatory therapeutic agents for treatment of pathological conditions where immunostimulation can be of therapeutic benefit, such as for treatment of malignant diseases and infectious diseases. The ICAM-2 new variants of the present invention can be also used for potential therapy of cancer metastasis, based on inhibition of adhesive interaction between cancer cells and endothelial cells.
Thus, the present inventors uncovered a therapeutic agent which can be used to treat malignant diseases, infectious diseases, and cancer metastasis. Such an agent is a polypeptide homologous to the ICAM variants of the present invention (SEQ ID NO:338 or 335), and/or a polynucleotide homologous to SEQ ID NO:339 or 336, and/or a peptide homologous to SEQ ID NO:340 or 337.
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
Example 42
Description for Cluster HSEGF01
Cluster HSEGF01 features 4 transcript(s) and 48 segment(s) of interest, the names for which are given in Tables 44 and 45, respectively, the sequences themselves are given in SEQ ID NOs: 371-374; 375-422 and 423-426, for transcript; segments and proteins, respectively. The selected protein variants are given in Table 46.







TABLE 44







Transcripts of interest










Transcript Name
SEQ ID NO







HSEGF01_PEA_1_T12
371



 



HSEGF01 PEA_1_T19
372



 



HSEGF01_PEA 1_T22
373



 



HSEGF01_PEA_1_T27
374

















TABLE 45







Segments of interest










Segment Name
SEQ ID NO







HSEGF01_PEA_1_node_1
375



 



HSEGF01_PEA_1_node_12
376



 



HSEGF01_PEA_1_node_15
377



 



HSEGF01_PEA_1_node_17
378



 



HSEGF01_PEA_1_node_18
379



 



HSEGF01_PEA_1_node_25
380



 



HSEGF01_PEA_1_node_26
381



 



HSEGF01_PEA_1_node_29
382



 



HSEGF01_PEA_1_node_30
383



 



HSEGF01_PEA_1_node_37
384



 



HSEGF01_PEA_1_node_51
385



 



HSEGF01_PEA_1_node_53
386



 



HSEGF01_PEA_1_node_57
387



 



HSEGF01_PEA_1_node_59
388



 



HSEGF01_PEA_1_node_63
389



 



HSEGF01_PEA_1_node_67
390



 



HSEGF01_PEA_1_node_72
391



 



HSEGF01_PEA_1_node_77
392



 



HSEGF01_PEA_1_node_84
393



 



HSEGF01_PEA_1_node_85
394



 



HSEGF01_PEA_1_node_86
395



 



HSEGF01_PEA_1_node_90
396



 



HSEGF01_PEA_1_node_91
397



 



HSEGF01_PEA_1_node_96
398



 



HSEGF01_PEA_1_node_97
399



 



HSEGF01_PEA_1_node_98
400



 



HSEGF01_PEA_1_node_0
401



 



HSEGF01_PEA_1_node_20
402



 



HSEGF01_PEA_1_node_22
403



 



HSEGF01_PEA_1_node_28
404



 



HSEGF01_PEA_1_node_32
405



 



HSEGF01_PEA_1_node_35
406



 



HSEGF01_PEA_1_node_39
407



 



HSEGF01_PEA_1_node_40
408



 



HSEGF01_PEA_1_node_42
409



 



HSEGF01_PEA_1_node_44
410



 



HSEGF01_PEA_1_node_45
411



 



HSEGF01_PEA_1_node_52
412



 



HSEGF01_PEA_1_node_61
413



 



HSEGF01_PEA_1_node_70
414



 



HSEGF01_PEA_1_node_75
415



 



HSEGF01_PEA_1_node_79
416



 



HSEGF01_PEA_1_node_81
417



 



HSEGF01_PEA_1_node_88
418



 



HSEGF01_PEA_1_node_92
419



 



HSEGF01_PEA_1_node_93
420



 



HSEGF01_PEA_1_node_94
421



 



HSEGF01_PEA_1_node_95
422

















TABLE 46







Proteins of interest












SEQ




Protein
ID
Corresponding


Protein Name
Length
NO
Transcript(s)





HSEGF01_PEA_1_P11
P705
423
HSEGF01_PEA_1_T19


 


HSEGF01_PEA_1_P14
P317
424
HSEGF01_PEA_1_T22


 


HSEGF01_PEA_1_P18
P215
425
HSEGF01_PEA_1_T27


 


HSEGF01_PEA_1_P24
P350
426
HSEGF01_PEA_1_T12









These sequences are variants of the known protein Epidermal growth factor receptor precursor (SwissProt accession identifier EGFR_HUMAN (SEQ ID NO: 427); known also according to the synonyms EC 2.7.1.112; Receptor protein-tyrosine kinase ErbB-1), referred to herein as the previously known protein.
Protein Epidermal growth factor receptor precursor is known or believed to have the following function(s): Receptor for EGF, but also for other members of the EGF family, as TGF-alpha, amphiregulin, betacellulin, heparin-binding EGF-like growth factor, GP30 and vaccinia virus growth factor. Is involved in the control of cell growth and differentiation; Isoform 2/truncated isoform may act as an antagonist. The sequence for protein Epidermal growth factor receptor precursor is given in SEQ ID NO: 427, as “Epidermal growth factor receptor precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 47.







TABLE 47







Amino acid mutations for Known Protein










SNP position(s) on amino




acid sequence
Comment







540
N → K










Protein Epidermal growth factor receptor precursor localization is believed to be Type I membrane protein. Isoform 2 is secreted.
It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein or of drugs directed to this protein are as follows: Angiogenesis stimulant; CD8 agonist; Epidermal growth factor agonist; ErbB-1 inhibitor; Fibroblast growth factor agonist; Heparin epidermal growth factor agonist. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Anticancer; Vulnerary; Antiulcer; Ophthalmological; Symptomatic antidiabetic; Stomatological; Cardiovascular; GI inflammatory/bowel disorders; Respiratory;
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: protein amino acid phosphorylation; EGF receptor signaling pathway; cell proliferation, which are annotation(s) related to Biological Process; receptor; epidermal growth factor receptor; ATP binding which are annotation(s) related to Molecular Function; and plasma membrane; integral plasma membrane protein, which are annotation(s) related to Cellular Component. The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
As noted above, cluster HSEGF01 features 4 transcript(s), which were listed in Table 44 above. These transcript(s) encode for protein(s) which are variant(s) of protein Epidermal growth factor receptor precursor. A description of each variant protein according to the present invention is now provided.
Ariant protein HSEGF01_PEA—1_P11 (SEQ ID NO:423) is encoded by transcript(s) HSEGF01_PEA—1_T19 (SEQ ID NO: 272). An alignment is given to the known protein (Epidermal growth factor receptor precursor; SEQ ID NO:427) in FIG. 148. One or more alignments to one or more previously published protein sequences are given in FIGS. 149-151. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSEGF01_PEA—1_P11 (SEQ ID NO: 423) and EGFR_HUMAN (SEQ ID NO: 427):
1. An isolated chimeric polypeptide HSEGF01_PEA—1_P11 (SEQ ID NO: 423), comprising a first amino acid sequence being at least 90% homologous to MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQ RMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQI IRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALC NVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGEENCQ KLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATC KDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRAC GADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTS ISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHA FENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANT INWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSC RNVSRGRECVDKCNLLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNC IQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNCTYG corresponding to amino acids 1-627 of EGFR_HUMAN, which also corresponds to amino acids 1-627 of HSEGF01_PEA—1_P11 (SEQ ID NO: 423), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence PGNESLKAMLFCLFKLSSCNQSNDGSVSHQSGSPAAQESCLGWIPSLLPSEFQL GWGGCSHLHAWPSASVIITASSCH corresponding to amino acids 628-705 of HSEGF01_PEA—1_P11 (SEQ ID NO: 423), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSEGF01_PEA—1_P11 (SEQ ID NO: 423), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence PGNESLKAMLFCLFKLSSCNQSNDGSVSHQSGSPAAQESCLGWIPSLLPSEFQL GWGGCSHLHAWPSASVIITASSCH in HSEGF01_PEA—1_P11 (SEQ ID NO: 423).
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSEGF01_PEA—1_P11 (SEQ ID NO: 423) also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 48, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSEGF01_PEA—1_P11 (SEQ ID NO: 423) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 48







Amino acid mutations









SNP position(s) on amino
Alternative



acid sequence
amino acid(s)
Previously known SNP?





141
Q → *
No


234
N → S
No









The glycosylation sites of variant protein HSEGF01_PEA—1_P11 (SEQ ID NO: 423), as compared to the known protein Epidermal growth factor receptor precursor, are described in Table 49 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 49







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












56
yes
56


568
yes
568


128
yes
128


413
yes
413


603
yes
603


352
yes
352


361
yes
361


175
yes
175


444
yes
444


528
yes
528









The phosphorylation sites of variant protein HSEGF01_PEA—1_P11, as compared to the known protein Epidermal growth factor receptor precursor, are described in Table 50 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 50







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












1197
no



678
no


1110
no


1172
no


1092
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 51:







TABLE 51







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR001450
4Fe—4S ferredoxin,
FPrintScan
548-559,



iron-sulfur binding

590-601



domain


IPR006211
Furin-like cysteine rich
HMMPfam
184-338



region


IPR000494
Epidermal growth-factor
HMMPfam
361-481,



receptor (EGFR), L

57-168



domain


IPR006212
Furin-like repeat
HMMSmart
228-270,





496-547,





552-601


IPR000345
Cytochrome c heme-
ScanRegExp
555-560



binding site









Variant protein HSEGF01_PEA—1_P11 (SEQ ID NO: 423) is encoded by the HSEGF01_PEA—1_T19 (SEQ ID NO:372). The coding portion of transcript HSEGF01_PEA—1_T19 (SEQ ID NO: 372) starts at position 504 and ends at position 2618. The transcript also has the following SNPs as listed in Table 52 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSEGF01_PEA—1_P11 (SEQ ID NO: 423) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 52







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












288
G → T
No


313
C → A
No


352
G →
No


758
G → T
No


924
C → T
No


977
T → C
No


1204
A → G
No


3258
T → A
No









Variant protein HSEGF01_PEA—1_P14 (SEQ ID NO: 424) is encoded by transcript(s) HSEGF01_PEA—1_T22 (SEQ ID NO: 373). An alignment is given to the known protein (Epidermal growth factor receptor precursor; SEQ ID NO:427) is presented in FIG. 149. One or more alignments to one or more previously published protein sequences are given in FIGS. 148, 150 and 151. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSEGF01_PEA_P14 (SEQ ID NO: 424) and EGFR_HUMAN (SEQ ID NO: 427):
1. An isolated chimeric polypeptide HSEGF01_PEA—1_P14 (SEQ ID NO: 424), comprising a first amino acid sequence being at least 90% homologous to MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQ RMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQI IRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALC NVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGEENCQ KLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATC KDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPR corresponding to amino acids 1-297 of EGFR_HUMAN, which also corresponds to amino acids 1-297 of HSEGF01_PEA—1_P14 (SEQ ID NO: 424), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence ESSSVGPLTGQASLSRSVSC corresponding to amino acids 298-317 of HSEGF01_PEA—1_P14 (SEQ ID NO: 424), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSEGF01_PEA—1_P14 (SEQ ID NO: 424), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence ESSSVGPLTGQASLSRSVSC in HSEGF01_PEA—1_P14 (SEQ ID NO: 424).
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSEGF01_PEA—1_P14 (SEQ ID NO: 424) also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 53, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSEGF01_PEA—1_P14 (SEQ ID NO: 424) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 53







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





141
Q → *
No


234
N → S
No









The glycosylation sites of variant protein HSEGF01_PEA—1_P14 (SEQ ID NO: 424), as compared to the known protein Epidermal growth factor receptor precursor, are described in Table 54 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 54







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












56
yes
56


568
no


128
yes
128


413
no


603
no


352
no


361
no


175
yes
175


444
no


528
no









The phosphorylation sites of variant protein HSEGF01_PEA—1_P14 (SEQ ID NO: 424), as compared to the known protein Epidermal growth factor receptor precursor, are described in Table 55 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 55







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












1197
no



678
no


1110
no


1172
no


1092
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 56:







TABLE 56







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR006211
Furin-like cysteine rich
HMMPfam
184-317



region


IPR000494
Epidermal growth-factor
HMMPfam
57-168



receptor (EGFR), L



domain


IPR006212
Furin-like repeat
HMMSmart
228-270









Variant protein HSEGF01_PEA—1_P14 (SEQ ID NO:424) is encoded by the following transcript(s): HSEGF01_PEA—1_T22 (SEQ ID NO:373). The coding portion of transcript HSEGF01_PEA—1_T22 (SEQ ID NO:373) starts at position 504 and ends at position 1454. The transcript also has the following SNPs as listed in Table 57 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSEGF01_PEA—1_P14 (SEQ ID NO:424) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 57







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












288
G → T
No


313
C → A
No


352
G →
No


758
G → T
No


924
C → T
No


977
T → C
No


1204
A →
No









Variant protein HSEGF01_PEA—1_P18 (SEQ ID NO:425) according to the present invention is encoded by transcript(s) HSEGF01_PEA—1_T27 (SEQ ID NO:374). An alignment is given to the known protein (Epidermal growth factor receptor precursor) in FIG. 150. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSEGF01_PEA—1_P18 (SEQ ID NO:425) and EGFR_HUMAN (SEQ ID NO:427):
1. An isolated chimeric polypeptide HSEGF01_PEA—1_P18 (SEQ ID NO:425), comprising a first amino acid sequence being at least 90% homologous to MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQ RMFNNCEVVLGNLEITYVQRNYDLSELKTIQEVAGYVLIALNTVERIPLENLQI IRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALC NVESIQWRDIVSSDFLSNMSMDFQNHLGSC corresponding to amino acids 1-187 of EGFR_HUMAN (SEQ ID NO:427), which also corresponds to amino acids 1-187 of HSEGF01_PEA—1_P18 (SEQ ID NO:425), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence KCRIHTISASSSYGGQLYSTGAGERSHV corresponding to amino acids 188-215 of HSEGF01_PEA—1_P18 (SEQ ID NO:425), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSEGF01_PEA—1_P18 (SEQ ID NO:425), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence KCRIHTISASSSYGGQLYSTGAGERSHV in HSEGF01_PEA—1_P18 (SEQ ID NO:425).
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSEGF01_PEA—1_P18 (SEQ ID NO:425) also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 58, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSEGF01_PEA—1_P18 (SEQ ID NO:425) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 58







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





141
Q → *
No









The glycosylation sites of variant protein HSEGF01_PEA—1_P18 (SEQ ID NO:425), as compared to the known protein Epidermal growth factor receptor precursor, are described in Table 59 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 59







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












56
yes
56


568
no


128
yes
128


413
no


603
no


352
no


361
no


175
yes
175


444
no


528
no









The phosphorylation sites of variant protein HSEGF01_PEA—1_P18 (SEQ ID NO:425), as compared to the known protein Epidermal growth factor receptor precursor, are described in Table 60 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 60







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












1197
No



678
No


1110
No


1172
No


1092
No









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 61:







TABLE 61







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR000494
Epidermal growth-factor
HMMPfam
57-168



receptor (EGFR), L



domain









Variant protein HSEGF01_PEA—1_P18 (SEQ ID NO:425) is encoded by the following transcript(s): HSEGF01_PEA—1_T27 (SEQ ID NO:374). The coding portion of transcript HSEGF01_PEA—1_T27 (SEQ ID NO:374) is starts at position 504 and ends at position 1148. The transcript also has the following SNPs as listed in Table 62 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSEGF01_PEA—1_P18 (SEQ ID NO:425) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 62







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












288
G → T
No


313
C → A
No


352
G →
No


758
G → T
No


924
C → T
No


977
T → C
No


1276
T → G
No


1317
A → G
No


1440
C → T
No


1503
A → G
No









Variant protein HSEGF01_PEA—1_P24 (SEQ ID NO:426) according to the present invention is encoded by transcript(s) HSEGF01_PEA—1_T12 (SEQ ID NO:371). An alignment is given to the known protein (Epidermal growth factor receptor precursor) in FIG. 151. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSEGF01_PEA—1_P24 (SEQ ID NO:426) and EGFR_HUMAN (SEQ ID NO:427):
1. An isolated chimeric polypeptide HSEGF01_PEA—1_P24 (SEQ ID NO:426), comprising a first amino acid sequence being at least 90% homologous to MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQ RMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQI IRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALC NVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGEENCQ KLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATC KDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRAC GADSYEMEEDGVRKCKKCEGPCRK corresponding to amino acids 1-335 of EGFR_HUMAN (SEQ ID NO:427), which also corresponds to amino acids 1-335 of HSEGF01_PEA—1_P24 (SEQ ID NO:426), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GRKPAGVRTRLVLGC corresponding to amino acids 336-350 of HSEGF01_PEA—1_P24 (SEQ ID NO:426), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSEGF01_PEA—1_P24 (SEQ ID NO:426), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GRKPAGVRTRLVLGC in HSEGF01_PEA—1_P24 (SEQ ID NO:426).
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSEGF01_PEA—1_P24 (SEQ ID NO:426) also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 63, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSEGF01_PEA—1_P24 (SEQ ID NO:426) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 63







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





141
Q → *
No


234
N → S
No









The glycosylation sites of variant protein HSEGF01_PEA—1_P24 (SEQ ID NO:426), as compared to the known protein Epidermal growth factor receptor precursor, are described in Table 64 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 64







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












56
yes
56


568
no


128
yes
128


413
no


603
no


352
no


361
no


175
yes
175


444
no


528
no









The phosphorylation sites of variant protein HSEGF01_PEA—1_P24 (SEQ ID NO:426), as compared to the known protein Epidermal growth factor receptor precursor, are described in Table 65 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 65







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












1197
no



678
no


1110
no


1172
no


1092
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 66:







TABLE 66







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR006211
Furin-like cysteine rich
HMMPfam
184-338



region


IPR000494
Epidermal growth-factor
HMMPfam
57-168



receptor (EGFR), L



domain


IPR006212
Furin-like repeat
HMMSmart
228-270









Variant protein HSEGF01_PEA—1_P24 (SEQ ID NO:426) is encoded by the following transcript(s): HSEGF01_PEA—1_T12 (SEQ ID NO:371). The coding portion of transcript HSEGF01_PEA—1_T12 (SEQ ID NO:371) starts at position 504 and ends at position 1553. The transcript also has the following SNPs as listed in Table 67 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSEGF01_PEA—1_P24 (SEQ ID NO:426) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 67







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












288
G → T
No


313
C → A
No


352
G →
No


758
G → T
No


924
C → T
No


977
T → C
No


1204
A → G
No


2976
T → A
No


3095
G → T
No


3450
G → A
No


3798
C → T
No


4410
T → C
No


4418
A → G
No


4805
G →
No


4960
T →
No


4971
A → T
No


5496
T → C
No


6894
G → A
No


7422
G → A
No


7801
G → C
No


7979
T → C
No


8799
C → T
No


9038
C → G
No


9376
G → A
No


9934
C → G
No


9934
C → T
No


10264
C → A
No


10264
C → G
No


10332
→ C
No


10332
→ G
No


10369
T → G
No


10692
A → C
No









FIG. 34 presents the domain structure of the variants described hereinabove.
Example 43
Splice Variant of Insulin-Like Growth Factor Binding Protein 3 Precursor
Background
The insulin-like growth factor system, which includes insulin-like growth factors (IGF-I and IGF-II), IGF receptors (IGF-IR and IGF-IIR) and IGF binding proteins (IGFBPs), plays an important role in epithelial growth, anti-apoptosis and mitogenesis. The IGFs are not stored within cells of a specific tissue but are present at very high levels throughout the body. They circulate at total concentrations approximately 1000 times higher than that of most peptide hormones and although tissue levels are somewhat lower, they are still present in vast excess compared to that required for maximal cellular stimulation. These high levels are maintained due to their association with the IGFBPs, which dramatically slow their clearance. The IGFBPs bind the IGFs with greater affinity than their cell surface receptors, enabling them to tightly control tissue activity. The IGFBP proteases modify the IGFBPs, lowering the affinity with which they bind IGFs. In the tissues the IGFs are important regulators of cell survival, growth, metabolism and differentiated function; the complex system confers specificity on these actions. The complex of IGF-I and IGFBP-3 (“binary complex” or “IGF-I/IGFBP-3”) is considerably different from uncomplexed IGF-I, both physically and chemically. The binary complex is approximately 5 times larger than uncomplexed IGF-I, has a different overall pI, and has a different overall hydrophobicity. These differences cause the binary complex to behave quite differently than IGF-I.
Due to its wide range of activities, IGF-I has been developed as a treatment for a variety of conditions, including amyotrophic lateral sclerosis (commonly known as Lou Gehrig's disease) and diabetes. Unfortunately, the administration of IGF-I is accompanied by a variety of undesirable side effects, including hypoglycemia, edema (which can cause Bell's palsy, carpal tunnel syndrome, and a variety of other deleterious conditions), hypophosphatemia (low serum phosphorus), and hypernatermia (excessive serum sodium). Administration of IGF-I as a complex of IGF-I and IGFBP-3 can reduce or eliminate these undesirable side effects (Adams et al., 1996, Prog. Growth Factor Res. 6:2-4).
While administration of IGF-I/IGFBP-3 complex may be desirable, the complex, like many proteins, has very limited stability (shelf life) in most formulations. The formulations thus disclosed for IGF-I/IGFBP-3 have been unsatisfactory due to poor stability of the proteins. Formulations which can be stored at normal refrigerator temperatures or higher while still providing a long shelf life are critical to the commercial development of IGF-I/IGFBP for use as a therapeutic.
Catabolic conditions in which debilitating nitrogen wasting or protein wasting occurs include, but are not limited to, chronic obstructive pulmonary disease, gastrointestinal tract resections or disorders, illnesses requiring corticosteroid therapy, diabetes, trauma, pneumonia, heart failure, stroke, cancer cachexia, and AIDS cachexia. Severe loss of body protein substantially increases chances for dying and/or prolonged hospitalization and major medical expenses. An additional group of patients who are at risk of negative nitrogen balance are patients in hospitals or nursing homes who are convalescing from acute illnesses.
Administration of IGFBP-3 or IGF/IGFBP-3 complex has been proposed for a variety of conditions and diseases, for example, for wound healing and systemic tissue repair in burns, trauma, ulcers, surgery, etc (U.S. Pat. No. 5,407,913 to Sommer et al); for renal disease, renal toxicity, autoimmune nephropathy, and renal dysfunction (U.S. Pat. No. 5,723,441 to Higley et al); for protein wasting and other catabolic disease (U.S. Pat. No. 5,643,867 to Maack et al) and for increasing low sex steroid levels in the elderly (U.S. Pat. No. 6,025,332 to Mascarenhas).
There is a growing body of evidence showing that IGFs control growth and proliferation of several types of cancer. The growth promoting effects of IGF-I and IGF-II on cancer cells are mediated through the IGF-IR, which is a tyrosine kinase. Cancer cells with a strong tendency to metastasize have a higher expression of the IGF-IR. Most of the IGFs in circulation are bound to the IGFBPs, which regulate the bioavailability of the IGFs. All IGFBPs inhibit IGF action by high affinity binding, while some of them also potentiate the effects of IGFs. Some cancer cells produce specific proteases that degrade the IGFBP so that the IGF will be free to act on the cancer cell in an autocrine manner. Therefore, the IGFBPs play a crucial role in the development of cancer. The correlation of high IGF and low IGFBP-3 levels in prostate and other cancers has lead to the development of cancer diagnostic methods for prostate cancer (U.S. Pat. No. 6,645,770 to Pollack et al) and breast cancer. Rechler et al (Endocrinol. 2000 138:2645-47) have proposed treatment of breast cancer with IGFBP-3, to inhibit the mitogenic effects of IGF.
IGF/IGFBP-3 complex is critical for musculoskeletal growth and development, and IGFBP-3 may both inhibit, or potentiate effects of IGF on growth (Oksbjerg et al Domestic Anim Endocrinology 1996 27; 219-240). Thus, measurement of IGF or IGFBP-3 has been proposed for indicating feed conversion, growth rate and reproductive capacity in the selection of livestock (U.S. Pat. No. 6,090,569 to Owens et al.).
Splice Variants S56205_T7 (SEQ ID NO:286) and S56205_T15 (SEQ ID NO:288) Encode New Secreted Forms of Insulin-Like Growth Factor Binding Protein 3 Precursor (IGFBP-3) S56205_P7 (SEQ ID NO:285) and S56205_P15 (SEQ ID NO:287), Respectively.
S56205_P7 (SEQ ID NO:285)
The present inventors have uncovered a new IGFBP-3 precursor variant [S56205_P7 (SEQ ID NO:285), S56205_T7 (SEQ ID NO:286). The protein coordinates on the transcript start from nucleotide 151 and end at nucleotide 1042, as set forth in SEQ ID NO: 286.
Alignment of the new IGFBP-3 precursor variant [S56205_P2 (SEQ ID NO:285] with the WT Insulin-like growth factor binding protein 3 precursor (GenBank Accession NO. P17936; IBP3_HUMAN (SEQ ID NO:647), as shown in FIG. 125, revealed the presence of a unique amino acid sequence (PPAPGE, SEQ ID NO:659). The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having IGF binding properties and useful in the treatment and diagnosis of all musculoskeletal disorders, amyotrophic lateral sclerosis (ALS), burns, cachexia, cancers of all types, Type I and Type II diabetes, dwarfism, Growth hormone (GH) deficiency, hormone replacement therapy (HRT), general neuropathy, osteoporosis, bone regeneration, wound healing, psoriasis, cerebral ischaemia, prostate and breast cancer, sexual dysfunction, neurological and opthalmalogical disorders, and for selection and breeding of livestock.
Comparison Report Between S56205_P7 and IBP3_HUMAN (SEQ ID NO:647)
1. An isolated chimeric polypeptide S56205_P7, comprising a first amino acid sequence being at least 90% homologous to MQRARPTLWAAALTLLVLLRGPPVARAGASSGGLGPVVRCEPCDARALAQC APPPAVCAELVREPGCGCCLTCALSEGQPCGIYTERCGSGLRCQPSPDEARPL QALLDGRGLCVNASAVSRLRAYLLPA corresponding to amino acids 1-130 of IBP3_HUMAN, which also corresponds to amino acids 1-130 of S56205_P7, a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence PPAPGE (SEQ ID NO:659) corresponding to amino acids 131-136 of S56205_P7, and a third amino acid sequence being at least 90% homologous to PPAPGNASESEEDRSAGSVESPSVSSTHRVSDPKFHPLHSKIIIIKKGHAKDSQR YKVDYESQSTDTQNFSSESKRETEYGPCRREMEDTLNHLKFLNVLSPRGVHIP NCDKKGFYKKKQCRPSKGRKRGFCWCVDKYGQPLPGYTTKGKEDVHCYSM QSK corresponding to amino acids 131-291 of IBP3_HUMAN, which also corresponds to amino acids 137-297 of S56205_P7, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for an edge portion of S56205_P7, comprising an amino acid sequence being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence encoding for PPAPGE, corresponding to S56205_P7.
S56205_P15 (SEQ ID NO:287)
The present inventors have uncovered a new IGFBP-3 precursor variant [S56205_P15 (SEQ ID NO:287), S56205_T15 (SEQ ID NO:288). The protein coordinates on the transcript start from nucleotide 134 and end at nucleotide 1019, as set forth in SEQ ID NO: 288.
Alignment of the new IGFBP-3 precursor variant [S56205_P15 (SEQ ID NO:287)] with the WT Insulin-like growth factor binding protein 3 precursor (IBP3_HUMAN; SEQ ID NO:647), as shown in FIG. 126, revealed that the interpro domain(s) Thyroglobulin type-1 repeat IPR000716 (amino acids 212-281 of GenBank Accession No. P17936, SEQ ID NO:647) is missing, and that the new IGFBP-3 precursor variant has an additional 10 cysteine (Cys) residues. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having IGF binding properties and useful in the treatment and diagnosis of all musculoskeletal disorders, amyotrophic lateral sclerosis (ALS), burns, cachexia, cancers of all types, Type I and Type II diabetes, dwarfism, Growth hormone (GH) deficiency, hormone replacement therapy (HRT), general neuropathy, osteoporosis, bone regeneration, wound healing, psoriasis, cerebral ischaemia, prostate and breast cancer, sexual dysfunction, neurological and opthalmalogical disorders, and for selection and breeding of livestock.
Comparison Report Between S56205_P15 and IBP3_HUMAN (SEQ ID NO:647)
1. An isolated chimeric polypeptide S56205_P15, comprising a first amino acid sequence being at least 90% homologous to MQRARPTLWAAALTLLVLLRGPPVARAGASS corresponding to amino acids 1-31 of IBP3_HUMAN, which also corresponds to amino acids 1-31 of S56205_P15, a bridging amino acid A corresponding to amino acid 32 of S56205_P15, a second amino acid sequence being at least 90% homologous to GLGPVVRCEPCDARALAQCAPPPAVCAELVREPGCGCCLTCALSEGQPCGIY TERCGSGLRCQPSPDEARPLQALLDGRGLCVNASAVSRLRAYLLPAPPAP corresponding to amino acids 33-134 of IBP3_HUMAN, which also corresponds to amino acids 33-134 of S56205_P15, and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence AARLGRQMRALRLGAEDQPLPAWIPQLRAVYCRPIPARPACQAACPGCRRHA AGATHALGRCADSAGAAPRAAGGAGWRELGGLGSRGALRDRCRRCWTAA GSASTLVPSAACAPTCCQRRQLQEMLVSRRKTAAPAVWRARPSPARTGCLIP SSTPSIQR (SEQ ID NO:660) corresponding to amino acids 135-295 of S56205_P15, wherein said first amino acid sequence, bridging amino acid, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of S56205_P15, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence AARLGRQMRALRLGAEDQPLPAWIPQLRAVYCRPIPARPACQAACPGCRRHA AGATHALGRCADSAGAAPRAAGGAGWRELGGLGSRGALRDRCRRCWTAA GSASTLVPSAACAPTCCQRRQLQEMLVSRRKTAAPAVWRARPSPARTGCLIP SSTPSIQR in S56205_P15.
Clinical Applications of the Insulin-Like Growth Factor Binding Protein 3 Precursor Variants of the Present Invention
Native (WT) IGFBP-3 (GenBank Accession No. P17936, SEQ ID NO:647) comprises numerous functions, such as IGF binding, protease sensitivity, and nuclear localization, which, when combined, provide IGFBP-3 the capability to carefully regulate effective levels of IGF. It will be appreciated that alterations in amino acid sequence of the type disclosed herein for the IGFBP-3 precursor variants of the present invention [S56205_P7 (SEQ ID NO:285) and S56205_P15 (SEQ ID NO:287)] can result in increase or decrease of many of the IGFBP-3 activities, and as such the new variants can compete with the endogenous IGFBP-3 protein and related peptides, and interfere with their various activities, most importantly, IGF binding and exchange, and, indirectly, effect IGF-IGF receptor binding.
Alteration in IGFBP-3 protein sequence has been used for diagnostic and therapeutic applications. Rechler et al (U.S. patent application Ser. No. 10/499,379) discloses IGFBP-3 mutants without IGF binding capability, for inhibition of DNA synthesis and induction of apoptosis. Mascarenhas (U.S. patent application Ser. Nos. 10/264,672 an 09/956,508) teaches the use of IGFBP-3 derived peptides having anti-inflammatory, proapoptotic, anti-angiogenic, cardiovascular, metal-binding, ECM-binding, cell internalization, protease inhibitory, transcription inhibitory, and other activity. IGFBP-3 having altered protease resistance and nuclear localization have also been disclosed.
For example, since the IGFBP-3 precursor variants of the present invention lack the Thyroglobulin type-1 repeat IPR000716 of the WT IGFBP-3 protein (GenBank Accession No. P17936, SEQ ID NO:647), the new IGFBP-3 variants of the present invention might function as an IGF inhibitor.
The IGFBP-3 variants of the present invention can also interfere with the binding of IGF to IGF receptors by increased or diminished affinity to IGF. Thus, the new variants of IGFBP-3 precursor of the present invention can be used as IGF agonists and antagonists for the treatment of musculoskeletal, cancer, inflammatory, endocrine, wound healing, and tissue proliferative conditions. Further, the IGFBP-3 precursor variants, and the polynucleotides encoding same, can be used in the treatment of inborn errors of metabolism, such as dwarfism, via, for example, transient or stable expression of a polynucleotide encoding one or more IGFBP-3 precursor variants in a subject in need thereof.
Thus, the present inventors have uncovered therapeutic agents, polypeptide homologous to SEQ ID NOs:285 and 287 and/or an expressible polynucleotide homologous to SEQ ID NO:286 and 288 and/or a peptide homologous to SEQ ID NO:659 or 660, which can be used to treat a variety of IGFBP-3 and IGF-related conditions, such as all musculoskeletal disorders, amyotrophic lateral sclerosis (ALS), burns, cachexia, cancers of all types, Type I and Type II diabetes, dwarfism, Growth hormone (GH) deficiency, hormone replacement therapy (HRT), general neuropathy, osteoporosis, bone regeneration, wound healing, psoriasis, cerebral ischaemia, prostate and breast cancer, sexual dysfunction, neurological and opthalmalogical disorders, and for selection and breeding of livestock. Since WT IGFBP-3 is the key protein in regulation of circulating IGF levels, important for all cell growth in development and adult life, IGFBP-3 precursor variants such as S56205_P7 (SEQ ID NO:285) and S56205_P15 (SEQ ID NO:287), which can act as agonists and/or antagonists of IGFBP-3 and IGF activity can be useful in upregulating or downregulating a variety of growth and IGF related conditions, such as ALS, autoimmune disease and renal function. The new IGFBP-3 variants of the present invention can also be used to produce novel anti-IGFBP-3 antibodies which can be used for in-vivo therapy of IGFBP-3 and IGF-related disorders and as antagonists and/or agonists of specific IGF and IGFBP-3-related receptor(s), and as diagnostic tools for proliferation of tissue, preferably musculoskeletal tissues, or as a marker for pathological de-differentiation or tissue damage in all systems.
It will be appreciated that such agents can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes). One preferred method of administration of variant IGFBP-3 polypeptides and/or polynucleotides expressing same, of the present invention, is intravenous administration.
It will be appreciated that the new IGFBP-3 precursor variants of the present invention can be used as a marker for proliferative disorders of tissues, preferably of the musculoskeletal system, such as growth, sarcomas and bone cancer, or as a marker for pathological de-differentiation and/or tissue damage in all tissues. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the IGFBP-3 precursor variants [S56205_P7 edited protein (SEQ ID NO:285) and/or S56205_P15 (SEQ ID NO:287)], or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 44
Splice Variant of Renin-Binding Protein
Background
N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase; N-acetyl-D-glucosamine 2-epimerase; Renin-binding protein; RNBP; GenBank Accession No. P51606; RNBP_HUMAN (SEQ ID NO:648) is a bifunctional enzyme critical to the synthesis of sialic acid groups. Sialic acids are widely expressed as terminal carbohydrates on glycoconjugates of eukaryotic cells. Sialylation is crucial for a variety of cellular functions, such as cell adhesion or signal recognition, and regulates the biological stability of glycoproteins. The key enzyme of sialic acid biosynthesis is the bifunctional UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase (UDP-GlcNAc 2-epimerase), which catalyzes the first two steps of sialic acid biosynthesis in the cytosol. It has been reported that inactivation of the UDP-GlcNAc 2-epimerase by gene targeting causes early embryonic lethality in mice, thereby emphasizing the fundamental role of this bifunctional enzyme and sialylation during development.
N-Acetylneuraminic acid (NeuAc) is an important molecule in biological recognition systems. NeuAc is known to be biosynthesized either from UDP-N-acetyl-D-glucosamine by an action of UDP-N-acetyl-D-glucosamine 2-epimerase or from N-acetyl-D-glucosamine by N-acyl-D-glucosamine 2-epimerase (GlcNAc 2-epimerase). The GlcNAc 2-epimerase enzyme and its gene were isolated. Sequence analysis indicated that the gene was capable of synthesizing a 46.5-kDa protein (402 amino acids) with a conserved leucine zipper motif. Homology search for the cloned gene revealed that the GlcNAc 2-epimerase was identical with renin-binding protein (RnBP) in porcine kidney (Inoue, H., Fukui, K., Takahashi, S., and Miyake, Y. (1990) J. Biol. Chem. 265, 6556-6561). Targeted mutagenesis revealed that residue Cys 380 is essential for enzymatic activity of the GlcNAc 2-epimerase. Further mutational analysis of multi-cysteine/serine mutants revealed that cysteines 41 and 390 were critical for the activity or stabilization of the enzyme, while cysteine residues in the middle of the enzyme, cysteines 125, 210, 239, and 302, had no essential function in relation to the activity. Studies with recombinant GlcNAc 2-epimerase have revealed that the middle domain of the GlcNAc 2-epimerase molecule participates in the specificity for and binding of nucleotides, and that nucleotides are essential to form the catalytic domain of the enzyme. GlcNAc 2-epimerase can serve a catabolic role, diverting metabolic flux away from the sialic acid pathway.
The causative molecular defect in the inborn human disease sialuria, is a single amino-acid substitution in the region of the allosteric site (codons 263-266), causing a loss of feedback inhibition by CMP-Neu5Ac), resulting in overproduction of ManNAc, thereby competitively excluding ManLev from the pathway and abolishing SiaLev expression on the cell surface. Because flux of the natural substrate, ManNAc, continues through the pathway, there is no change in cell-surface glycan expression in the absence of ManLev. Only three mutations have been characterized from human patients, because the disease is rare.
Sialuria is characterized by variable and transient signs and symptoms, especially in infancy. These include prolonged neonatal jaundice, equivocal or mild hepatomegaly and general organomegaly, coarse facial features, microcytic anemia, frequent upper respiratory infections, and episodes of gastroenteritis sometimes leading to failure to thrive. Mild developmental delay and hypotonia have been reported. Learning difficulty and seizures have been observed later in childhood. Mutations in the GNE gene specifically affecting one of a small number of adjacent nucleotides encoding the putative allosteric site in UDP-GlcNAc 2-epimerase/ManNac kinase, the bifunctional rate-limiting enzyme in the biosynthesis pathway of sialic acid, can be detected by mutation scanning and/or sequence analysis.
Splice Variants HUMREBP_T1 (SEQ ID NO:290), HUMREBP_Skippingexon—10_T (SEQ ID NO:292), HUMREBP_T4 (SEQ ID NO:294), HUMREBP_T5 (SEQ ID NO:296), and HUMREBP_T5 (SEQ ID NO:298) Encode New Secreted Forms of N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase): HUMREBP_P2 (SEQ ID NO:289), HUMREBP_Skippingexon_P_P (SEQ ID NO:291), HUMREBP_P3 (SEQ ID NO:293), HUMREBP_P4 (SEQ ID NO:295), and HUMREBP_P1 (SEQ ID NO:297), Respectively.
HUMREBP_P2 (SEQ ID NO:289)
The present inventors have uncovered a new GlcNAc 2-epimerase variant [HUMREBP_P2—SEQ ID NO:289, HUMREBP_T1—SEQ ID NO:290). The protein coordinates on the transcript start from nucleotide 201 and end at nucleotide 1265, as set forth in SEQ ID NO: 290.
Alignment of the new GlcNAc-2 epimerase variant [HUMREBP_P2—SEQ ID NO:289] with the WT N-acylglucosamine 2-epimerase (GenBank Accession No. P51606; SEQ ID NO:648), as shown in FIG. 127, revealed that the interpro domain N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) IPR008928 and IPR010819 are missing. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having endopeptidase inhibitor activity, isomerase activity, and rennin binding activity, useful as a cardiostimulant, antihypertensive, peripheral vasodilator, antihypertensive, and further as stimulant of the renin system, and a hypertensive agent (blood pressure stimulator) (CPR).
Comparison Report Between HUMREBP_P2 (SEQ ID NO:289) and RNBP_HUMAN (SEQ ID NO:648)
1. An isolated chimeric polypeptide HUMREBP_P2, comprising a first amino acid sequence being at least 90% homologous to MEKERETLQAWKERVGQELDRVVAFWMEHSHDQEHGGFFTCLGREGRVYD DLKYVWLQGRQVWMYCRLYRTFERFRHAQLLDAAKAGGEFLLRYARVAPP GKKCAFVLTRDGRPVKVQRTIFSECFYTMAMNELWRATGEVRYQTEAVEM MDQIVHWVQEDASGLGRPQLQGAPAAEPMAVPMMLLNLVEQLGEADEELA GKYAELGDWCARRILQHVQRDGQAVLENVSEGGKELPGCLGRQQNPGHTLE AGWFLLRHCIRKGDPELRAHVIDKFLLLPFHSGWDPDHGGLFYFQDADNFCP TQLEWAMKLWWPHSEAMIAFLMGYSDSGDPVLLRLFYQVAEYTFRQ corresponding to amino acids 1-349 of RNBP_HUMAN, which also corresponds to amino acids 1-349 of HUMREBP_P2, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GLYRPG (SEQ ID NO:661) corresponding to amino acids 350-355 of HUMREBP_P2, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMREBP_P2, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GLYRPG in HUMREBP_P2.
HUMREB Skipping exon—10_P (SEQ ID NO:291),
The present inventors have uncovered a new GlcNAc 2-epimerase variant [HUMREBP Skippingexon—10_P—SEQ ID NO:291, HUMREBP Skippingexon 10_T—SEQ ID NO:292. The protein coordinates on the transcript start from nucleotide 1 and end at nucleotide 1072, as set forth in SEQ ID NO: 292.
Alignment of the new GlcNAc-2 epimerase variant [HUMREBP Skippingexon—10_P2—SEQ ID NO:2911 with the WT N-acylglucosamine 2-epimerase (GenBank Accession No. P51606; SEQ ID NO:648), as shown in FIG. 128, revealed that the interpro domain N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) IPR008928 and IPR010819 are missing. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having endopeptidase inhibitor activity, isomerase activity, and rennin binding activity, useful as a cardiostimulant; antihypertensive; peripheral vasodilator, antihypertensive, and further as stimulant of the renin system, and a hypertensive agent (blood pressure stimulator) (CPR).
Comparison Report Between HUMREBP_Skippingexon—10_P (SEQ ID NO:291) and RNBP_HUMAN (SEQ ID NO:648)
1. An isolated chimeric polypeptide HUMREBP_Skippingexon—10_P, comprising a first amino acid sequence being at least 90% homologous to MEKERETLQAWKERVGQELDRVVAFWMEHSHDQEHGGFFTCLGREGRVYD DLKYVWLQGRQVWMYCRLYRTFERFRHAQLLDAAKAGGEFLLRYARVAPP GKKCAFVLTRDGRPVKVQRTIFSECFYTMAMNELWRATGEVRYQTEAVEM MDQIVHWVQEDASGLGRPQLQGAPAAEPMAVPMMLLNLVEQLGEADEELA GKYAELGDWCARRILQHVQRDGQAVLENVSEGGKELPGCLGRQQNPGHTLE AGWFLLRHCIRKGDPELRAHVIDKFLLLPFHSGWDPDHGGLFYFQDADNFCP TQLEWAMKLWWPHSEAMIAFLMGYSDSGDPVLLRLFYQVAEYTFRQ corresponding to amino acids 1-349 of RNBP_HUMAN, which also corresponds to amino acids 1-349 of HUMREBP_Skippingexon—10_P, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence AASTCRGA (SEQ ID NO:662) corresponding to amino acids 350-357 of HUMREBP_Skippingexon—10_P, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMREBP_Skippingexon—10_P, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence AASTCRGA in HUMREBP_Skippingexon—10_P.
HUMREB_P3 (SEQ ID NO:293)
The present inventors have uncovered a new GlcNAc 2-epimerase variant [HUMREBP_P3—SEQ ID NO:293, HUMREBP_T4—SEQ ID NO:294. The protein coordinates on the transcript start from nucleotide 201 and end at nucleotide 877, as set forth in SEQ ID NO: 294.
Alignment of the new GlcNAc-2 epimerase variant [HUMREBP_P3—SEQ ID NO:2931 with the WT N-acylglucosamine 2-epimerase (GenBank Accession No. P51606; SEQ ID NO:648), as shown in FIG. 129, revealed that the interpro domain N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) IPR008928 and IPR010819 are missing. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having endopeptidase inhibitor activity, isomerase activity, and rennin binding activity, useful as a cardiostimulant; antihypertensive; peripheral vasodilator, antihypertensive, and further as stimulant of the renin system, and a hypertensive agent (blood pressure stimulator) (CPR).
Comparison Report Between HUMREBP_P3 (SEQ ID NO:293) and RNBP_HUMAN (SEQ ID NO:648)
1. An isolated chimeric polypeptide HUMREBP_P3, comprising a first amino acid sequence being at least 90% homologous to MEKERETLQAWKERVGQELDRVVAFWMEHSHDQEHGGFFTCLGREGRVYD DLKYVWLQGRQVWMYCRLYRTFERFRHAQLLDAAKAGGEFLLRYARVAPP GKKCAFVLTRDGRPVKVQRTIFSECFYTMAMNELWRATGEVRYQTEAVEM MDQIVHWVQEDASGLGRPQLQGAPAAEPMAVPMMLLNLVEQLGEADEELA GKYAELGDWCARRILQHVQ corresponding to amino acids 1-219 of RNBP_HUMAN, which also corresponds to amino acids 1-219 of HUMREBP_P3, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence ARAGRGGSCL (SEQ ID NO:663) corresponding to amino acids 220-229 of HUMREBP_P3, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMREBP_P3, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence ARAGRGGSCL in HUMREBP_P3.
HUMREB_P4 (SEQ ID NO:295)
The present inventors have uncovered a new GlcNAc 2-epimerase variant [HUMREBP_P4—SEQ ID NO:295, HUMREBP_T5—SEQ ID NO:296. The protein coordinates on the transcript start from nucleotide 201 and end at nucleotide 877, as set forth in SEQ ID NO: 296.
Alignment of the new GlcNAc-2 epimerase variant [HUMREBP_P4 (SEQ ID NO:295)] with the WT N-acylglucosamine 2-epimerase (GenBank Accession No. P51606; SEQ ID NO:648), as shown in FIG. 130, revealed that the interpro domain N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) IPR008928 and IPR010819 are missing. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having endopeptidase inhibitor activity, isomerase activity, and rennin binding activity, useful as a cardiostimulant; antihypertensive; peripheral vasodilator, antihypertensive, and further as stimulant of the renin system, and a hypertensive agent (blood pressure stimulator) (CPR).
Comparison Report Between HUMREBP_P4 (SEQ ID NO:295) and RNBP_HUMAN (SEQ ID NO:648)
1. An isolated chimeric polypeptide HUMREBP_P4, comprising a first amino acid sequence being at least 90% homologous to MEKERETLQAWKERVGQELDRVVAFWMEHSHDQEHGGFFTCLGREGRVYD DLKYVWLQGRQVWMYCRLYRTFERFRHAQLLDAAKAGGEFLLRYARVAPP GKKCAFVLTRDGRPVKVQRTIFSECFYTMAMNELWRATGEVRY corresponding to amino acids 1-143 of RNBP_HUMAN, which also corresponds to amino acids 1-143 of HUMREBP_P4, a second amino acid sequence being at least 90% homologous to QEDASGLGRPQLQGAPAAEPMAVPMMLLNLVEQLGEADEELAGKYAELGD WCARRILQHVQ corresponding to amino acids 159-219 of RNBP_HUMAN, which also corresponds to amino acids 144-204 of HUMREBP_P4, and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence ATRWKPAGFCSVIAFGKATPNFEPT corresponding to amino acids 205-229 of HUMREBP_P4, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric edge portion of HUMREBP_P4, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise YQ, having a structure as follows: a sequence starting from any of amino acid numbers 143-x to 143; and ending at any of amino acid numbers 144+((n−2)−x), in which x varies from 0 to n−2.
3. An isolated polypeptide for a tail of HUMREBP_P4, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence ATRWKPAGFCSVIAFGKATPNFEPT in HUMREBP_P4.
HUMREB_P1 (SEQ ID NO:297),
The present inventors have uncovered a new GlcNAc 2-epimerase variant [HUMREBP_P1—SEQ ID NO:297, HUMREBP_T2—SEQ ID NO:298. The protein coordinates on the transcript start from nucleotide 201 and end at nucleotide 1553, as set forth in SEQ ID NO: 298.
Alignment of the new GlcNAc-2 epimerase variant [HUMREBP_P1—SEQ ID NO:2971 with the WT N-acylglucosamine 2-epimerase (GenBank Accession No. P51606; SEQ ID NO:648), as shown in FIG. 131, revealed that the interpro domain N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) IPR008928 and IPR010819 are missing. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having endopeptidase inhibitor activity, isomerase activity, and rennin binding activity, useful as a cardiostimulant; antihypertensive; peripheral vasodilator, antihypertensive, and further as stimulant of the renin system, and a hypertensive agent (blood pressure stimulator) (CPR).
Comparison Report Between HUMREBP_P1 (SEQ ID NO:297) and RNBP_HUMAN (SEQ ID NO:648)
1. An isolated chimeric polypeptide HUMREBP_P1, comprising a first amino acid sequence being at least 90% homologous to MEKERETLQAWKERVGQELDRVVAFWMEHSHDQEHGGFFTCLGREGRVYD DLKYVWLQGRQVWMYCRLYRTFERFRHAQLLDAAKAGGEFLLRYARVAPP GKKCAFVLTRDGRPVKVQRTIFSECFYTMAMNELWRATGEVRYQTEAVEM MDQIVHWVQEDASGLGRPQLQGAPAAEPMAVPMMLLNLVEQLGEADEELA GKYAELGDWCARRILQHVQRDGQAVLENVSEGGKELPGCLGRQQNPGHTLE AGWFLLRHCIRKGDPELRAHVIDKFLLLPFHSGWDPDHGGLFYFQDADNFCP TQLEWAMKLWWPHSEAMIAFLMGYSDSGDPVLLRLFYQVAEYTFR corresponding to amino acids 1-348 of RNBP_HUMAN, which also corresponds to amino acids 1-348 of HUMREBP_P1, a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence QAGAQWRDLSSLQPPPPVFKLFSRLSLPSILLGL (SEQ ID NO:664) corresponding to amino acids 349-382 of HUMREBP_P1, and a third amino acid sequence being at least 90% homologous to QFRDPEYGEWFGYLSREGKVALSIKGGPFKGCFHVPRCLAMCEEMLGALLSR PAPAPSPAPTPACRGAE corresponding to amino acids 349-417 of RNBP_HUMAN, which also corresponds to amino acids 383-451 of HUMREBP_P1, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated edge portion of HUMREBP_P1, comprising an amino acid sequence being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence encoding for QAGAQWRDLSSLQPPPPVFKLFSRLSLPSILLGL, corresponding to HUMREBP_P1.
Clinical Applications of the N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) Variant of the Present Invention
Since the N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) variants of the present invention lack the IPR008928 and IPR010819 domains of the WT N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) protein (GenBank Accession No. P51606, SEQ ID NO:648), they can compete with the endogenous N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) protein and related peptides, and interfere with their various activities. For example, the new N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) variants of the present invention might inactivate Renin, without performing the reduced N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) function, and thus can act as a potent renin inhibitor in the renin-angiotensin-aldosterone system, causing reduction in aldosterone and water retention.
The N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) variants of the present invention can also inactivate (by dominant negative effect) the normal renin binding function of the normal N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) (RENBP) by heterodimer formation, and thus act as a renin stimulator. Thus, the new variants of N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) of the present invention can be used as N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) agonists and antagonists for the treatment of hypertension and other disorders of renal function, as stimulants in cardiac disorders, as peripheral vasodilators, and as a blood pressure stimulator (CPR). Further, the new N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) variants, and the polynucleotides encoding same, can be used in the treatment of inborn errors of metabolism, such as sialuria, via, for example, transient or stable expression of a polynucleotide encoding one or more N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) variants in a subject in need thereof.
Thus, the present inventors have uncovered therapeutic agents, polypeptide homologous to SEQ ID NOs:289, 291, 293, 295 and 297 and/or an expressible polynucleotide homologous to SEQ ID NO:290, 292, 294, 296 and 298 which can be used to treat a variety of N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)-related conditions, such as renal and cardiac disease, hypertension and hypotension (shock), and as a peripheral vasodilator. Since WT N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) is the key enzyme in the sialylation pathways important for cell adhesion and cell recognition, and for biological stability of glycoproteins, and is considered crucial in embryonic viability, and in the functioning of the renin-angiotensin-aldosterone pathway, N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) variants such as HUMREBP_T1 (SEQ ID NO:290), HUMREBP_Skippingexon—10_T (SEQ ID NO:292), HUMREBP_T4 (SEQ ID NO:294), HUMREBP_T5 (SEQ ID NO:296), and HUMREBP_T5 (SEQ ID NO:298), which can act as agonists and/or antagonists of N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) activity can be useful in upregulating or downregulating a variety of N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) and sialylation-related conditions, such as hypertension and/or cardiac insufficiency. The new N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) variants of the present invention can also be used to produce novel anti-N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) antibodies which can be used for in-vivo therapy of N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)-related disorders and as antagonists and/or agonists of specific N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)-related receptor(s), and as diagnostic tools for proliferation of skin tissue, or as a marker for pathological de-differentiation or tissue damage in the skin.
It will be appreciated that such agents can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes). One preferred method of administration of variant N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) polypeptides and/or polynucleotides expressing same, of the present invention, is intravenous administration.
It will be appreciated that, since the new N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) variants of the present invention are overexpressed in the skin, the new N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) variants can be used as a marker for proliferative disorders of the skin, such as psoriasis and keloids, or as a marker for pathological de-differentiation and/or tissue damage in the skin. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) variants (SEQ ID NO:289, 291, 293, 295, or 297], or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 45
Splice Variant of Hepatocyte Growth Factor Precursor
Background
Hepatocyte growth factor precursor (Scatter factor; SF; Hepatopoeitin A; GenBank Accession No. P14210; HGF_HUMAN (SEQ ID NO:649); HGF precursor) is cleaved into HGF, a mesenchyme-derived pleiotropic factor, which regulates cell growth, cell motility, and morphogenesis of various types of cells and is thus considered a humoral mediator of epithelial-mesenchymal interactions responsible for morphogenic tissue interactions during embryonic development and organogenesis.
Growing evidence indicates that HGF is also an endogenous renoprotective factor that possesses a potent antifibrotic ability. HGF prevents the initiation and progression of chronic renal fibrosis and inhibits transforming growth factor (TGF)-beta(1) expression in a wide variety of animal models, and can be used for inhibition of renal fibrosis.
Although HGF was originally identified as a potent mitogen for hepatocytes, it has also been identified as a member of angiogenic growth factors. Interestingly, the presence of its specific receptor, c-met, is also observed in vascular cells and cardiac myocytes. Among growth factors, the mitogenic action of HGF on human endothelial cells was most potent. Recent studies have demonstrated the potential application of HGF to treat cardiovascular diseases such as peripheral vascular disease, myocardial infarction and cerebrovascular disease.
HGF polypeptides are able to induce a variety of biological effects besides cell proliferation. The main biological activities of these molecules are: stimulation of cell division (mitogenesis); stimulation of motility (scattering); induction of polarisation and cell differentiation; induction of tubule formation (branched morphogenesis), increase of cell survival (protection from apoptosis). The tissues that respond to HGF and MSP stimulation are those containing cells that express the respective Met (HGF) and Ron (MSP) receptors. The most important target tissues of these factors are epithelia of different organs, such as liver, kidney, lung, breast, pancreas and stomach, and some cells of the hematopoietic and nervous systems.
Examples of the therapeutic and diagnostic use of HGF and agonists and antagonists of HGF and HGF receptor abound. Schwall et al (U.S. Pat. Nos. 6,214,344 and 6,207,152) teach the use of anti HGF mAbs and HGF receptor agonists for the treatment of cancer (breast, lung, prostate, colon, pancreatic, lung cancer); Morishita et al (U.S. Pat. No. 6,248,722) teach the use of HGF for treatment of arterial disease. U.S. Pat. No. 6,319,899 teaches the use of specific domains of HGF for the stimulation of mitogenesis and motility, induction of cell polarization and differentiation, morphogenesis and increased cell survival in the epithelia of organs such as liver, kidney, lung, breast, pancreas, stomach, and cells of the hematopoietic and nervous systems. US Patent Application 0040138120 to Kirchhofer et al teaches HGF precursor polypeptides having novel kallekrein or FXIa cleavage sites for generation of HGF variants or fragments for the treatment of a wide variety of cancer and inflammatory diseases.
Splice Variants HSHGFR_Skipping_exon—3_T (SEQ ID NO:300), HSHGFR_Skipping_exon—4_T (SEQ ID NO:302), HSHGFR_Skipping_exon—7_T (SEQ ID NO:304) and HSHGFR_Skipping_exon—9_T (SEQ ID NO:306) Encode New Secreted Forms of Hepatocyte Growth Factor (HGF) Precursor HSHGFR_Skipping_exon—3_P (SEQ ID NO:299), HSHGFR_Skipping_exon—4_P (SEQ ID NO:301), HSHGFR_Skipping_exon—7_P (SEQ ID NO:303) and HSHGFR_Skipping_exon—9_P (SEQ ID NO:305, Respectively).
HSHGFR_Skipping_exon—3_P
The present inventors have uncovered a new Hepatocyte Growth Factor precursor variant [HSHGFR_Skippingexon—3_P—SEQ ID NO:299, HSHGFR_Skippingexon—3_T—SEQ ID NO:3001. The protein coordinates on the transcript start from nucleotide 168 and end at nucleotide 428, as set forth in SEQ ID NO: 300.
Alignment of the new HGF precursor variant [HSHGFR_Skippingexon—3_P—SEQ ID NO:2991 with the WT HGF precursor protein [GenBank Accession No. P14210; HGF_HUMAN—SEQ ID NO:6491, as shown in FIGS. 132 and 20a, revealed that the interpro domain IPR001254—Trypsin, four kringle domains—IPR000001 (amino acids 126-207, 208-289, 302-384 and 388-470 of GenBank Accession No. P14210, SEQ ID NO:649) and a PAN domain—IPR003014 or IPR003609 are missing in the new variant. The new variant contains a SP IPR003609 (amino acids 1-28 of GenBank Accession No. P14210, SEQ ID NO:649) and a reduced PAN domain—IPR003609 (amino acids 32-83 of GenBank Accession No. P14210, SEQ ID NO:649), and 2 unique amino acids. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having HGF receptor binding and MET protooncogene receptor antagonist activity.
Comparison Report Between HSHGFR_Skipping_exon—3_P and HGF_HUMAN (SEQ ID NO:649)
1. An isolated chimeric polypeptide HSHGFR_Skipping_exon—3_P, comprising a first amino acid sequence being at least 90% homologous to MWVTKLLPALLLQHVLLHLLLLPIAIPYAEGQRKRRNTIHEFKKSAKTTLIKID PALKIKTKKVNTADQCANRCTRNKGLPFTCK corresponding to amino acids 1-85 of HGF_HUMAN, which also corresponds to amino acids 1-85 of HSHGFR_Skipping_exon—3_P, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence LH corresponding to amino acids 86-87 of HSHGFR_Skipping_exon—3_P, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
HSHGFR_Skipping_exon—4_P
The present inventors have uncovered a new Hepatocyte Growth Factor precursor variant [HSHGFR_Skippingexon—4_P—SEQ ID NO:301, HSHGFR_Skippingexon—4_T—SEQ ID NO:302]. The protein coordinates on the transcript start from nucleotide 168 and end at nucleotide 686, as set forth in SEQ ID NO: 302.
Alignment of the new HGF precursor variant [HSHGFR_Skippingexon—4_P—SEQ ID NO:3011 with the WT HGF precursor protein [GenBank Accession No. P14210—SEQ ID NO:649, as shown in FIGS. 133 and 20b, revealed that the interpro domain IPR001254—Trypsin, four kringle domains—IPR000001 (amino acids 126-207, 208-289, 302-384 and 388-470 of GenBank Accession No. P14210, SEQ ID NO:649) and a PAN domain—IPR003014 or IPR003609 are missing in the new variant. The new variant contains a SP IPR003609 (amino acids 1-28 of GenBank Accession No. P14210, SEQ ID NO:649) and a reduced PAN domain—IPR003609 (amino acids 32-120 of GenBank Accession No. P14210, SEQ ID NO: 649), and 51 unique amino acids. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having HGF receptor binding and MET protooncogene receptor antagonist activity.
Comparison Report Between HSHGFR_Skipping_exon—4_P and HGF_HUMAN
1. An isolated chimeric polypeptide HSHGFR_Skipping_exon—4_P, comprising a first amino acid sequence being at least 90% homologous to MWVTKLLPALLLQHVLLHLLLLPIAIPYAEGQRKRRNTIHEFKKSAKTTLIKID PALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSS GVKKEFGHEFDLYENK corresponding to amino acids 1-122 of HGF_HUMAN, which also corresponds to amino acids 1-122 of HSHGFR_Skipping_exon—4_P, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence AFCLRAIGVKTYRKTTVEILEGKKGDPGVSQAIQRYATKSVTFLSVQKLNA (SEQ ID NO:665) corresponding to amino acids 123-173 of HSHGFR_Skipping_exon—4_P, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSHGFR_Skipping_exon—4_P, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence AFCLRAIGVKTYRKTTVEILEGKKGDPGVSQAIQRYATKSVTFLSVQKLNA in HSHGFR_Skipping_exon—4_P.
HSHGFR_Skipping_exon—7_P
The present inventors have uncovered a new Hepatocyte Growth Factor precursor variant [HSHGFR_Skippingexon—7_P—SEQ ID NO:303, HSHGFR_Skippingexon—7_T—SEQ ID NO:304]. The protein coordinates on the transcript start from nucleotide 168 and end at nucleotide 941, as set forth in SEQ ID NO: 304.
Alignment of the new HGF precursor variant [HSHGFR_Skippingexon—7_P—SEQ ID NO:303] with the WT HGF precursor protein [HGF_HUMAN—SEQ ID NO:649], as shown in FIGS. 20c and 134, revealed that the interpro domain IPR001254—Trypsin and three kringle domains—IPR000001 are missing in the new variant. The new variant contains a SP IPR003609 (amino acids 1-28 of GenBank Accession No. P14210, SEQ ID NO:649) a PAN domain—IPR003609 (amino acids 32-127 of GenBank Accession No. P14210, SEQ ID NO:649), one full Kringle IPR000001 domain (amino acids 128-206 of GenBank Accession No. P14210, SEQ ID NO: 649) and a portion of a second Kringle IPR000001 domain (amino acids 211-247 of GenBank Accession No. P14210, SEQ ID NO:649). The new variant has a single unique amino acid. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having HGF receptor binding and MET protooncogene receptor antagonist activity, MET inhibitor, anticancer, anti-proliferative activity. The new variant is expected to be a partial agonist of MET (much like the NK2 known variant—antagonizing growth but facilitates metastasis), a hepatoprotective agent and a proliferative agent (wound healing).
Comparison Report Between HSHGFR_Skipping_exon—7_P and HGF_HUMAN
1. An isolated chimeric polypeptide HSHGFR_Skipping_exon—7_P, comprising a first amino acid sequence being at least 90% homologous to MWVTKLLPALLLQHVLLHLLLLPIAIPYAEGQRKRRNTIHEFKKSAKTTLIKID PALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSS GVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEH SFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEVECMT CNGESYRGLMDHTESGKICQRWDHQTPHRHKFLPE corresponding to amino acids 1-248 of HGF_HUMAN, which also corresponds to amino acids 1-248 of HSHGFR_Skipping_exon—7_P, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence S corresponding to amino acids 249-249 of HSHGFR_Skipping_exon—7_P, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
RT-PCR Validation of the Novel Splice Variant of HGF, Skipping Exon 7
While reducing the present invention to practice, tissue samples from various organs were assayed, using RT-PCR, for expression of the novel splice variant of HGF, skipping exon 7. RT-PCR analysis results for identification of the novel exon 7 skipping splice variant of Hepatocyte Growth Factor are shown in FIG. 21. Primers were taken from exon 6 (0 and 8 (r). The predicted product of the full length transcription product was 302 bp, which was found in all tissue samples (FIG. 21). Skipping exon 7 (predicted 163 bp) was found exclusively in samples of Colon tissue (lane 6-arrowhead). A larger product (probably a novel exon) was found in samples of Breast tissue (lane 5). Tissue type cDNA pools: 1—Cervix+HeLa; 2—Uterus; 3—Ovary; 4—Placenta; 5—Breast; 6—Colon; 7—Pancreas; 8—Liver+Spleen; 9—Brain; 10—Prostate; 11—Testis; 12—Kidney; 13—Thyroid; 14—As sorted Cell-lines (5). M=1 kb ladder marker; H=H2O negative control.
Materials and Experimental Methods
RT-PCR conditions: RT was done on Total RNA samples (see source on mark 9). The reaction was done using random hexamer primer mix (Invitrogen) and Superscript II Reverse transcriptase (Invitrogen).
Conditions:

    
    
        (i) Denaturation at 70° C. (5 min)
        (ii) Annealing on ice
        (iii) RT at 37° C. (1 hour).
    
    


PCR conditions: For all reactions, “Hot-Star” Taq polymerase (Qiagen) was used.
Some reactions required addition of Q solution (Qiagen) to enhance the reaction.
Reaction Composition:
Total Volume 25 μl

    
    
        Taq Buffer ×10—2.5 μl
        DNTP's (mix of 4) ×12.5—2 μl
        Primers—0.5 μl of each (total 1 μl)
        cDNA—1 μl
        Taq Enzyme—0.5 μl
        Q solution (optional) ×5—5 μl
        H2O—To add up to 25 μl
    
    


Reaction Conditions:













1-Activation of HotStar Taq
95° C. for 5 min's


2-Denaturation
94° C. for 45 sec.


3-Annealing
Tm (specific for primer set) - 4-5° C.



for 45 sec.


4-Extension
72° C. for 1 min.







5-Repeat stages 2-4 for 34 more times.








6-Gap filling
72° C. for 10 min's.


7-Storage
10° C. (indefinitely).









Reaction product was separated on a 2% agarose gel in TBEx5 at  ̃150V. DNA was extracted from gel using a Qiaquick (Qiagen) kit, and DNA was used for direct sequencing using the same primers.
Primers used are:









Forward:
5′ GGATCATCAGACACCACACCGGC 3′
TM = 67







Predicted Product size: 302 bp (183 bp without


exon).









Reverse:
5′ CGTGAGGATACTGAGAATCCCAACGC 3′
TM = 67






Source of the tissue samples used for the RT-PCR:
Sample 1: Cervix pool—A pool of 3 RNA samples of mixed origin from cervical tissue (Tumor and Normal), and samples of mRNA from a HeLa cell-line (cervical cancer).
Sample 2: Uterus pool—A pool of 3 RNA samples of mixed origin from uterine tissue (Tumor and Normal).
Sample 3: Ovary pool—A pool of 5 RNA samples from ovarian tissue (Biochain—Normal), added with two samples of mixed origin (Tumor and Normal).
Sample 4: Placenta—One sample of RNA from placental tissue (Biochain—Normal).
Sample 5: Breast Pool—A pool of 3 RNA samples of breast tissue of mixed origin (2 from tumor and one from normal).
Sample 6: Colon and intestine—A pool of 5 RNA samples of colon and of mix origin (Tumor and Normal), with one intestine (Normal) derived RNA sample.
Sample 7: Pancreas—One sample of RNA of pancreas tissue (Biochain—Normal).
Sample 8: Liver and Spleen—One sample of RNA from liver tissue (Biochain—Normal), one sample of RNA from Spleen tissue (Biochain—Normal), added with—One sample of RNA from HepG2 cell line (Liver tumor).
Sample 9: Brain pool—A pool of RNA samples from brain tissue (Biochain—Normal).
Sample 10: Prostate pool—A pool of RNA samples from prostate tissue (Biochain—Normal).
Sample 11: Testis pool—A pool of RNA samples from Testis (Biochain—Normal).
Sample 12: Kidney pool—A pool of RNA samples from kidney tubules (Biochain—Normal).
Sample 13: Thyroid pool—A pool of RNA samples from thyroid tissue (Biochain—Normal).
Sample 14: Assorted cell-line pool—A pool of RNA samples from cells of the cell-lines: DLD, MiaPaCa, HT29, THP1, MCF7 (ATCC).
HSHGFR_Skipping_exon—9_P
The present inventors have uncovered a new Hepatocyte Growth Factor precursor variant [HSHGFR_Skippingexon—9_P—SEQ ID NO:305, HSHGFR_Skippingexon—9_T—SEQ ID NO:306]. The protein coordinates on the transcript start from nucleotide 168 and end at nucleotide 1337, as set forth in SEQ ID NO: 306.
Alignment of the new HGF precursor variant [HSHGFR_Skippingexon—9_P—SEQ ID NO:305] with the WT HGF precursor protein [GenBank Accession No. P14210; HGF_HUMAN—SEQ ID NO:649], as shown in FIGS. 135 and 20d, revealed that the interpro domain IPR001254—Trypsin and three kringle domains—IPR000001 are missing in the new variant. The new variant contains a SP IPR003609 (amino acids 1-28 of GenBank Accession No. P14210, SEQ ID NO:649) a PAN domain—IPR003609 (amino acids 32-127 of GenBank Accession No. P14210, SEQ ID NO:649), two full Kringle IPR000001 domain (amino acids 128-206 and 211-288 of GenBank Accession No. P14210, SEQ ID NO:649) and a portion of a third Kringle IPR000001 domain (amino acids 305-345 of GenBank Accession No. P14210, SEQ ID NO:649). The new variant has 43 unique amino acids. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having HGF receptor binding and MET protooncogene receptor antagonist activity, MET inhibitor, anticancer, anti-proliferative activity. The new variant is expected to be a partial agonist of MET (much like the NK2 known variant—antagonizing growth but facilitates metastasis), a hepatoprotective agent and a proliferative agent (wound healing).
Comparison Report Between HSHGFR_Skipping_exon—9_P and HGF_HUMAN
1. An isolated chimeric polypeptide HSHGFR_Skipping_exon—9_P, comprising a first amino acid sequence being at least 90% homologous to MWVTKLLPALLLQHVLLHLLLLPIAIPYAEGQRKRRNTIHEFKKSAKTTLIKID PALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSS GVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEH SFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEVECMT CNGESYRGLMDHTESGKICQRWDHQTPHRHKFLPERYPDKGFDDNYCRNPD GQPRPWCYTLDPHTRWEYCAIKTCADNTMNDTDVPLETTECIQGQGEGYRG TVNTIWNGIPCQRWDSQYPHEHDMTPENFKCK corresponding to amino acids 1-347 of HGF_HUMAN, which also corresponds to amino acids 1-347 of HSHGFR_Skipping_exon—9_P, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence LLSWEWQKLYGQLIPNKIWTNMFNVGQEHGRLTSSYLLGTRCK (SEQ ID NO:666) corresponding to amino acids 348-390 of HSHGFR_Skipping_exon—9_P, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSHGFR_Skipping_exon—9_P, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence LLSWEWQKLYGQLIPNKIWTNMFNVGQEHGRLTSSYLLGTRCK in HSHGFR_Skipping_exon—9_P.
Clinical Applications of the HGF Precursor Variant of the Present Invention
Since the HGF precursor variants of the present invention lack the Trypsin, and significant portions of the Kringle and PAN domains of the WT HGF precursor protein (GenBank Accession No. P14210, SEQ ID NO:649), they can compete with the endogenous HGF precursor protein and related peptides, and interfere with their various activities. For example, the new variants of HGF precursor proteins of the present invention can be used as HGF and HGF receptor agonists and antagonists for the treatment of cancer (breast, lung, prostate, colon, pancreatic, lung cancer), arterial disease, for the stimulation of mitogenesis and motility, induction of cell polarization and differentiation, morphogenesis and increased cell survival in the epithelia of organs such as liver, kidney, lung, breast, pancreas, stomach, and cells of the hematopoietic and nervous systems.
Thus, the present inventors have uncovered therapeutic agents, polypeptide homologous to SEQ ID NOs:299, 301, 303 and 305 and/or an expressible polynucleotide homologous to SEQ ID NO:300, 302, 304 and 306 which can be used to treat a variety of HGF-related conditions, such as hepatic, vascular, gastrointestinal, pulmonary, renal and cardiac disease, hematopoietic and nervous disorders, and cancers of various origins, and their metastatic development. Since HGF and component peptides effect cell growth, cell motility, and morphogenesis of various types of cells and WT HGF is considered a humoral mediator of epithelial-mesenchymal interactions responsible for morphogenic tissue interactions during embryonic development and organogenesis, HGF precursor variants such as HSHGFR_Skippingexon—3_P (SEQ ID NO:299), HSHGFR_Skippingexon—4_P (SEQ ID NO: 301), HSHGFR_Skippingexon—7_P (SEQ ID NO:303) and HSHGFR_Skippingexon—9_P (SEQ ID NO:305), which can act as agonists and/or antagonists of specific HGF receptor(s) can be useful in upregulating or downregulating a variety of HGF-related conditions, such as cancer of the breast, colon, pancreas, etc, and other Met-receptor related malignancies. The new HGF precursor variants of the present invention can also be used to produce novel anti-HGF peptide antibodies which can be used for in-vivo therapy of HGF-related disorders and as antagonists and/or agonists of specific HGF-related receptor(s), and as diagnostic tools for proliferation of endothelial and other system tissue, or as a marker for pathological vascular and/or nervous system de-differentiation or tissue damage. Agonist peptides can be used for tissue regeneration in organs in need, such as regenerating liver following resection, trauma or disease, while antagonist peptides can be used for treatment of proliferative and hyperproliferative disease such as cancer.
It will be appreciated that such agents can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes). One preferred method of administration of variant HGF precursor polypeptides and/or polynucleotides expressing same, of the present invention, is intravenous administration.
While further reducing the present invention to practice, tissue specific expression of the HGF precursor variant HSHGFR_Skippingexon—7_P (SEQ ID NO:303) was detected, using the methods and compositions taught herein, in tissue samples from Colon, while only WT HGF precursor transcripts were detected in samples from other tissues (FIG. 21). These results suggest the use of the new HGF precursor precursor variants of the present invention [HSHGFR_Skippingexon—3_P (SEQ ID NO:299), HSHGFR_Skippingexon—4_P (SEQ ID NO: 301), HSHGFR_Skippingexon—7_P (SEQ ID NO: 303) and HSHGFR_Skippingexon—9_P (SEQ ID NO: 305)], the polynucleotides encoding same [HSHGFR_Skippingexon—3_T (SEQ ID NO:300), HSHGFR_Skippingexon—4_T (SEQ ID NO: 302), HSHGFR_Skippingexon—7_T (SEQ ID NO: 304) and HSHGFR_Skippingexon—9_T (SEQ ID NO: 306)] as diagnostic markers for disorders such as hepatic disease, cancer progression, cell growth and migration and cell proliferation (mostly in metastasis). Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the HGF precursor variants ([HSHGFR_Skippingexon—3_P (SEQ ID NO:299), HSHGFR_Skippingexon—4_P (SEQ ID NO: 301), HSHGFR_Skippingexon—7_P (SEQ ID NO: 303) and HSHGFR_Skippingexon—9_P (SEQ ID NO: 305)], or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 46
Splice Variant of Cocaine- and Amphetamine-Regulated Transcript Protein Precursor
Background
Cocaine- and amphetamine-regulated transcript (CART) encodes a neuropeptide precursor protein that is highly abundant in cells of the hypothalamus. COCAINE- AND AMPHETAMINE-REGULATED transcript (CART) cDNA was originally isolated from rat brain by PCR differential screening of transcripts up-regulated after the administration of cocaine or amphetamine. CART Cocaine- and amphetamine-regulated transcript protein precursor [Contains: CART(1-39); CART(32-89)] gi|2833274|sp|Q165681CART_HUMAN, SEQ ID NO:650] and its translated peptide are found throughout the central nervous system and peripheral tissues. CART is one of the most abundant mRNAs in the hypothalamus, highly expressed in the arcuate nucleus (ARC), paraventricular nucleus (PVN), dorsomedial nucleus (DMN) and ventromedial nucleus (VMN). Cocaine- and amphetamine-regulated transcript (CART) and CART peptide are abundant in hypothalamic nuclei controlling anterior pituitary function, having established roles in the regulation of feeding.
Two C-terminal CART-derived peptides, CART 42-89 and CART 49-89, have been isolated from rat hypothalamus and arcuate nucleus as well as the pituitary. Both peptides result from proteolytic cleavage events at dibasic residues (KR and KK, respectively) within the CART peptide precursor and thus represent potential biologically active neuropeptides.
CART has been implicated in the control of feeding behavior. CART mRNA and peptide are colocalized with the anorectic peptide αMSH in the ARC and with the orexigenic peptide melanin-concentrating hormone in the lateral hypothalamic area (LHA). Nerve terminals immunoreactive for the orexigenic peptide NPY are closely apposed with CART peptide-containing cell bodies in the PVN, ARC, LHA, and DMN. Intracerebroventricular (icy) injection of the active fragment of CART, CART(55-102), has been shown to activate the immediate early gene c-fos in the PVN, DMN, ARC, and supraoptic nucleus (SON) of the hypothalamus. Intracerebroventricular (ICV) injection of CART peptide results in neuronal activation in the paraventricular nucleus (PVN), rich in corticotrophin-releasing factor (CRH) and thyrotrophin-releasing factor (TRH) immunoreactive neurons. CART peptides have also been detected in the peripheral nervous system, such as the myenteric plexus (Couceryo et al, Synapse 1998; 30:1-8). Both anorexigenic, and orexigenic activities have been ascribed to the CART peptides (Abbott et al Endocrinology 2001; 142:3457-63), in addition to modulation of psychostimulant effects such as abuse and dependent behaviour, locomotor activity associated with mesolimbic dopamine (Jaworski et al Life Sciences 2003; 73:741-47). A specific CART peptide receptor is postulated.
Soluble forms of CART peptide neurotransmitters have been detected in central and peripheral nervous system, and in body fluids. Since the CART peptides have extensive psychostimulant and behavioural activity, ligands constituting agonists and antagonists of specific CART receptor(s), and/or anti-CART peptide antibodies can be useful in upregulating or downregulating a variety of CART-related behaviours, such as abuse and dependency, feeding, etc. Further, since CART peptides are overexpressed in the brain and other nervous system tissue, CART peptides and their homologues can be used as diagnostic markers for proliferation of nervous system tissue or as a marker for pathological nervous system de-differentiation or tissue damage.
Splice Variant HSU16826_Skippingexon—2_T(SEQ ID NO:308) Encodes a New Secreted Form of Cocaine and Amphetamine Regulated Transcript (CART) Protein Precursor HSU16826_Skippingexon—2_P (SEQ ID NO:307).
The present inventors have uncovered a new CART protein precursor variant [HSU16826_Skippingexon—2_P-SEQ ID NO:307; HSU16826_Skippingexon—2_T—SEQ ID NO:308]. The protein coordinates on the transcript start from nucleotide 1 and end at nucleotide 247.
Alignment of the new CART protein precursor variant [HSU16826_Skippingexon—2_P—SEQ ID NO:307] with the WT CART Cocaine- and amphetamine-regulated transcript protein precursor [GenBank Accession No. Q16568|CART_HUMAN, SEQ ID NO:650], as shown in FIGS. 22 and 136, revealed that 28 consecutive amino acids (amino acids 54-81 of GenBank Accession No. Q16568, SEQ ID NO:650) are missing in the new variant. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having neuropeptide hormone activity in synaptic transmission and neuropeptide signaling pathways.
Comparison Report Between HSU16826_Skippingexon—2_P and CART_HUMAN (SEQ ID NO:650)
1. An isolated chimeric polypeptide HSU16826_Skippingexon—2_P, comprising a first amino acid sequence being at least 90% homologous to MESSRVRLLPLLGAALLLMLPLLGTRAQEDAELQPRALDIYSAVDDASHEKE L corresponding to amino acids 1-53 of CART_HUMAN, which also corresponds to amino acids 1-53 of HSU16826_Skippingexon—2_P, and a second amino acid sequence being at least 90% homologous to CDAGEQCAVRKGARIGKLCDCPRGTSCNSFLLKCL corresponding to amino acids 82-116 of CART_HUMAN, which also corresponds to amino acids 54-88 of HSU16826_Skippingexon—2_P, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric edge portion of HSU16826_Skippingexon—2_P, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise LC, having a structure as follows: a sequence starting from any of amino acid numbers 53-x to 53; and ending at any of amino acid numbers 54+((n−2)−x), in which x varies from 0 to n−2.
Clinical Applications of the CART Protein Precursor Variant of the Present Invention
Since the CART protein precursor variant of the present invention lacks the amino acids 52-81 of the WT CART protein precursor (GenBank Accession No. Q16568, SEQ ID NO:650) it can compete with the endogenous CART protein and related peptides, and interfere with their various activities. The WT CART protein and component peptides have been implicated in regulation of pituitary and hypothalamo-pituitary-adrenal axis function, and regulation of levels of endocrine hormones such as Prolactin, ACTH and GH (Stanley et al, Brain Res 2001 893:186-94). Further, it has been demonstrated that the CART peptide comprising amino acids 42-89, or smaller synthetic fragments thereof, when applied intervertebrocerebroventricularly (i.v.c.), cause a significant, and reversible repression of feeding behaviour, and reduction in body weight (Larsen et al, Obesity Res 2000; 8:590-96).
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:307 and/or an expressible polynucleotide homologous to SEQ ID NO:308 which can be used to treat a variety of CART-related conditions, such as endocrine imbalance (e.g. diabetes, metabolic dysfunction), abuse and dependency, and feeding behaviours, etc. Since the CART peptides have extensive endocrine and psychostimulant and behavioural activity, CART protein precursor variants such as HSU16826_Skippingexon—2_P (SEQ ID NO:307) which can act as an agonist and/or antagonist of specific CART receptor(s) can be useful in upregulating or downregulating a variety of CART-related behaviours, such as obesity and drug addition, etc. The new CART protein precursor variant of the present invention can also be used to produce novel anti-CART peptide antibodies which can be used for in-vivo therapy of CART-related disorders and as antagonists and/or agonists of specific CART-related receptor(s), and as diagnostic tools for proliferation of nervous system tissue or as a marker for pathological nervous system de-differentiation or tissue damage.
It will be appreciated that such agents can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes). One preferred method of administration of variant CART protein precursor polypeptides and/or polynucleotides expressing same, of the present invention, is i.v.c. administration (directly to the brain) or other direct administration to the central or peripheral nervous system using an indwelling minipump (ALZET Labs).
While further reducing the present invention to practice, these results suggest the use of the new CART protein precursor variant of the present invention (HSU16826_Skippingexon—2_P—SEQ ID NO:307), the polynucleotide encoding same (HSU16826_Skippingexon—2_T SEQ ID NO:308) as diagnostic markers for nervous system, and specifically neuroendocrine, disorders such as obesity, diabetes and dependency behaviour, neuroendocrine proliferation or de-differentiation, as well as brain and neural tissue tumors. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the CART protein precursor variant (HSU16826_Skippingexon—2_P-SEQ ID NO:307)], or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 47
Splice Variants of Dipeptidyl Peptidase IV
Background
Dipeptidyl Peptidase (DPP IV; T-cell activation antigen CD26; TP103; Adenosine deaminase complexing protein-2; ADABP; GenBank Accession No. P27487; DPP4_HUMAN; SEQ ID NO:651) cleaves two amino acids from the N-terminus of the intact, biologically active forms of both so-called incretin hormones, glucagon-like peptide-1 and glucose-dependent insulinotropic polypeptide (formerly known as gastric inhibitory polypeptide), resulting in truncated metabolites, which are largely inactive. Human dipeptidyl peptidase IV (DPP-IV) is a ubiquitously expressed type II transmembrane serine protease. It cleaves the penultimate positioned prolyl bonds at the N terminus of physiologically important peptides such as the incretin hormones glucagon-like peptide 1 and glucose-dependent insulinotropic peptide.
Dipeptidyl peptidase IV (DPPIV/CD26) has a unique enzymatic specificity in cleaving dipeptides from neuropeptides, chemokines, and hormones, and is thus potentially involved in the regulation of functions of the immune, endocrine, and nervous systems. Dipeptidyl peptidase IV deficient rats were found to have behavioural abnormalities, such as increased pain sensitivity and decreased susceptibility to alcohol sedation (Karl et al, Physiol Behav 2003; 80:123-34), and improved glucose tolerance and blunted natural killer cell function (Karl et al., Regul Peptid 2003; 15:81-90), and reduced susceptibility to tumor adhesion and metastatic development (Shingu et al, Cancer Immunol Immunother, 2003, May 8), suggesting that Dipeptidyl peptidase IV is associated with metastatic development, especially lung metastases of breast cancer (Cheng et al, Clin Exp Metastasis 1999; 17:609-15).
Apart from its catalytic activity, it interacts with several proteins, for instance, adenosine deaminase, the HIV gp120 protein, fibronectin, collagen, the chemokine receptor CXCR4, and the tyrosine phosphatase CD45. DPP IV is expressed on a specific set of T lymphocytes, where it is up-regulated after activation. It is also expressed in a variety of tissues, primarily on endothelial and epithelial cells. A soluble form is present in plasma and other body fluids. DPP IV can be used as a diagnostic or prognostic marker for various tumors, hematological malignancies, immunological, inflammatory, psychoneuroendocrine disorders, and viral infections (Lambier, et al, Crit Rev Clin Lab 2003, 40:209-94), particularly for T-cell related pathologies and conditions associated with it's upregulation in activated T lymphocytes.
Splice Variants HSPCHDP7_Skippingexon—7_T (SEQ ID NO:310), HSPCHDP7_Skippingexon—9_T (SEQ ID NO:312), HSPCHDP7_Skippingexon—19_T (SEQ ID NO:314), HSPCHDP7_Skippingexon—21_T (SEQ ID NO:316), HSPCHDP_Skippingexon—22_T (SEQ ID NO:318), HSPCHDP7_Skippingexon—24_T (SEQ ID NO:320), HSPCHDP7_Skippingexon—25_T (SEQ ID NO:322), HSPCHDP7_skippingexon—24—25_T (SEQ ID NO:324) of Dipeptidyl Peptidase IV Encode New Secreted Forms of Dipeptidyl Peptidase IV (DPP IV), HSPCHDP7_Skippingexon—7_P (SEQ ID NO309), HSPCHDP7_Skippingexon—9_P (SEQ ID NO:311), HSPCHDP7_Skippingexon—19_P (SEQ ID NO:313), HSPCHDP7_Skippingexon—21_P (SEQ ID NO:315), HSPCHDP_Skippingexon—22_P (SEQ ID NO:317), HSPCHDP7_Skippingexon—24_P (SEQ ID NO:319), HSPCHDP7_Skippingexon—25_P (SEQ ID NO:321), HSPCHDP7_skippingexon—24—25_P (SEQ ID NO:323), respectively.
HSPCHDP7_Skippingexon—7 Variant Structure
The present inventors have uncovered a new Dipeptidyl peptidase variant [HSPCHDP7_Skippingexon—7_P—SEQ ID NO:309, HSPCHDP7_Skippingexon—7_T—SEQ ID NO:309]. The protein coordinates on the transcript start from nucleotide 561 and end at nucleotide 1064, as set forth in SEQ ID NO: 310.
Alignment of the new Dipeptidyl peptidase IV variant [HSPCHDP7_Skippingexon—7_P—SEQ ID NO:309] with the WT DPP IV protein [GenBank Accession No. P27487; DPP4_HUMAN—SEQ ID NO:651], as shown in FIGS. 23a and 137 revealed that the interpro domain IPR002469 Dipeptidylpeptidase IV (CD26) N-terminal (amino acids 43-554 of GenBank Accession No. P27487, SEQ ID NO:651) is reduced, and that the interpro domains ESTERASE—IPR000379 (Peptidase_S9—IPR001375) (amino acids 558-635 of GenBank Accession No. P27487, SEQ ID NO:651) and PRO_ENDOPEP_SER—IPR002471 are missing in the new variant. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having proteolytic and peptidolytic prolyl oligopeptidase activity.
Comparison Report Between HSPCHDP7_Skippingexon—7_P and DPP4_HUMAN
1. An isolated chimeric polypeptide HSPCHDP7_Skippingexon—7_P, comprising a first amino acid sequence being at least 90% homologous to MKTPWKVLLGLLGAAALVTIITVPVVLLNKGTDDATADSRKTYTLTDYLKNT YRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDY SISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKR corresponding to amino acids 1-140 of DPP4_HUMAN, which also corresponds to amino acids 1-140 of HSPCHDP7_Skippingexon—7_P, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence HMFGTMTFMLKLNQIYQVTESHGRGKKI (SEQ ID NO:667) corresponding to amino acids 141-168 of HSPCHDP7_Skippingexon—7_P, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSPCHDP7_Skippingexon—7_P, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence HMFGTMTFMLKLNQIYQVTESHGRGKKI in HSPCHDP7_Skippingexon—7_P.
HSPCHDP7_Skippingexon—9 Variant Structure
The present inventors have uncovered a new Dipeptidyl peptidase variant [HSPCHDP7_Skippingexon—9_P—SEQ ID NO:311, HSPCHDP7_Skippingexon—7_T—SEQ ID NO:312]. The protein coordinates on the transcript start from nucleotide 561 and end at nucleotide 1301, as set forth in SEQ ID NO: 312.
Alignment of the new Dipeptidyl peptidase IV variant [HSPCHDP7_Skippingexon—9_P—SEQ ID NO:311] with the WT DPP IV protein [GenBank Accession No. P27487; DPP4_HUMAN—SEQ ID NO:651], as shown in FIGS. 23b and 138, revealed that the interpro domain IPR002469 Dipeptidylpeptidase IV (CD26) N-terminal (amino acids 43-554 of GenBank Accession No. P27487, SEQ ID NO:651) is reduced, and that the interpro domains ESTERASE—IPR000379 (Peptidase_S9—IPR001375) (amino acids 558-635 of GenBank Accession No. P27487, SEQ ID NO:651) and PRO_ENDOPEP_SER—IPR002471 are missing in the new variant. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having proteolytic and peptidolytic prolyl oligopeptidase activity.
Comparison Report Between HSPCHDP7_Skippingexon—9_P and DPP4_HUMAN
1. An isolated chimeric polypeptide HSPCHDP7_Skippingexon—9_P, comprising a first amino acid sequence being at least 90% homologous to MKTPWKVLLGLLGAAALVTIITVPVVLLNKGTDDATADSRKTYTLTDYLKNT YRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDY SISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWS PVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYE corresponding to amino acids 1-204 of DPP4_HUMAN, which also corresponds to amino acids 1-204 of HSPCHDP7_Skippingexon—9_P, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GRSCESNCKVLCCKYRLSQLSHQCNFHTNHCSCFYVDRGSLLV (SEQ ID NO:668) corresponding to amino acids 205-247 of HSPCHDP7_Skippingexon—9_P, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSPCHDP7_Skippingexon—9_P, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GRSCESNCKVLCCKYRLSQLSHQCNFHTNHCSCFYVDRGSLLV in HSPCHDP7_Skippingexon—9_P.
HSPCHDP7_Skippingexon—19 Variant Structure
The present inventors have uncovered a new Dipeptidyl peptidase variant [HSPCHDP7_Skippingexon—19_P—SEQ ID NO:313, HSPCHDP7_Skippingexon—19_T—SEQ ID NO:314]. The protein coordinates on the transcript start from nucleotide 561 and end at nucleotide 2171, as set forth in SEQ ID NO: 314.
Alignment of the new Dipeptidyl peptidase IV variant [HSPCHDP7_Skippingexon—19_P—SEQ ID NO:313] with the WT DPP IV protein [GenBank Accession No. P27487; DPP4_HUMAN—SEQ ID NO:651], as shown in FIGS. 23c and 139, revealed that the interpro domains ESTERASE—IPR000379 (Peptidase_S9—IPR001375) (amino acids 558-635 of GenBank Accession No. P27487, SEQ ID NO:651) and PRO_ENDOPEP_SER—IPR002471 are missing in the new variant. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having proteolytic and peptidolytic prolyl oligopeptidase activity.
Comparison Report Between HSPCHDP7—Skippingexon—19_P and DPP4_HUMAN
1. An isolated chimeric polypeptide HSPCHDP7_Skippingexon—19_P, comprising a first amino acid sequence being at least 90% homologous to MKTPWKVLLGLLGAAALVTIITVPVVLLNKGTDDATADSRKTYTLTDYLKNT YRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDY SISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWS PVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAY SALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVN PTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWL RRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRPRPSEPHFTLDG NSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYK GMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGP GLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNET corresponding to amino acids 1-522 of DPP4_HUMAN, which also corresponds to amino acids 1-522 of HSPCHDP7_Skippingexon—19_P, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence SMQAHVVKKQTLSSD (SEQ ID NO:669) corresponding to amino acids 523-537 of HSPCHDP7_Skippingexon—19_P, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSPCHDP7_Skippingexon—19_P, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence SMQAHVVKKQTLSSD in HSPCHDP7_Skippingexon—19_P.
HSPCHDP7_Skippingexon—21 Variant Structure
The present inventors have uncovered a new Dipeptidyl peptidase variant [HSPCHDP7_Skippingexon—21_P—SEQ ID NO:315, HSPCHDP7_Skippingexon—21_T—SEQ ID NO:316]. The protein coordinates on the transcript start from nucleotide 561 and end at nucleotide 2408, as set forth in SEQ ID NO: 316.
Alignment of the new Dipeptidyl peptidase IV variant [HSPCHDP7_Skippingexon—21_P—SEQ ID NO:315] with the WT DPP IV protein [GenBank Accession No. P27487; DPP4_HUMAN—SEQ ID NO:651], as shown in FIGS. 23d and 140, revealed that the interpro domains ESTERASE—IPR000379 (Peptidase_S9—IPR001375) (amino acids 558-635 of GenBank Accession No. P27487, SEQ ID NO:651) and PRO_ENDOPEP_SER—IPR002471 are missing in the new variant. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having proteolytic and peptidolytic prolyl oligopeptidase activity.
Comparison Report Between HSPCHDP7_Skippingexon—21_P and DPP4_HUMAN
1. An isolated chimeric polypeptide HSPCHDP7_Skippingexon—21_P, comprising a first amino acid sequence being at least 90% homologous to MKTPWKVLLGLLGAAALVTIITVPVVLLNKGTDDATADSRKTYTLTDYLKNT YRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDY SISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWS PVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAY SALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVN PTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWL RRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRPRPSEPHFTLDG NSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYK GMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGP GLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQ MILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDG RGSGYQGDKIMHAINRRLGTFEVEDQIEAA corresponding to amino acids 1-610 of DPP4_HUMAN, which also corresponds to amino acids 1-610 of HSPCHDP7_Skippingexon—21_P, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence SHMEGT (SEQ ID NO:670) corresponding to amino acids 611-616 of HSPCHDP7_Skippingexon—21_P, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSPCHDP7_Skippingexon—21_P, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence SHMEGT in HSPCHDP7_Skippingexon—21_P.
HSPCHDP_Skippingexon—22 Variant Structure
The present inventors have uncovered a new Dipeptidyl peptidase variant [HSPCHDP_Skippingexon—22_P—SEQ ID NO:317, HSPCHDP_Skippingexon—22_T—SEQ ID NO:318]. The protein coordinates on the transcript start from nucleotide 561 and end at nucleotide 2525, as set forth in SEQ ID NO: 318.
Alignment of the new Dipeptidyl peptidase IV variant [HSPCHDP_Skippingexon—22_P—SEQ ID NO:317] with the WT DPP IV protein [GenBank Accession No. P27487; DPP4_HUMAN—SEQ ID NO:651], as shown in FIGS. 23e and 141, revealed that the interpro domains ESTERASE—IPR000379 (Peptidase_S9—IPR001375) (amino acids 558-635 of GenBank Accession No. P27487, SEQ ID NO:651) and PRO_ENDOPEP_SER—IPR002471 are missing in the new variant. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having proteolytic and peptidolytic prolyl oligopeptidase activity.
Comparison Report Between HSPCHDP_Skippingexon—22_P and DPP4_HUMAN
1. An isolated chimeric polypeptide HSPCHDP_Skippingexon—22_P, comprising a first amino acid sequence being at least 90% homologous to MKTPWKVLLGLLGAAALVTIITVPVVLLNKGTDDATADSRKTYTLTDYLKNT YRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDY SISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWS PVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDHYNGITDWVYEEEVFSAY SALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVN PTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWL RRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRERPSEPHFTLDG NSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYK GMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGP GLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQ MILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDG RGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGW corresponding to amino acids 1-629 of DPP4_HUMAN, which also corresponds to amino acids 1-629 of HSPCHDP_Skippingexon—22_P, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence TQCTQNVTWVSQLQKTTLTITEIQQS (SEQ ID NO:671) corresponding to amino acids 630-655 of HSPCHDP_Skippingexon—22_P, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSPCHDP_Skippingexon—22_P, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence TQCTQNVTWVSQLQKTTLTITEIQQS in HSPCHDP_Skippingexon—22_P.
HSPCHDP7_Skippingexon—24 Variant Structure
The present inventors have uncovered a new Dipeptidyl peptidase variant [HSPCHDP7_Skippingexon—24_P—SEQ ID NO:319, HSPCHDP7_Skippingexon—24_T—SEQ ID NO:320]. The protein coordinates on the transcript start from nucleotide 561 and end at nucleotide 2711, as set forth in SEQ ID NO:320.
Alignment of the new Dipeptidyl peptidase IV variant [HSPCHDP7_Skippingexon—24_P—SEQ ID NO:319] with the WT DPP IV protein [GenBank Accession No. P27487; DPP4_HUMAN—SEQ ID NO:651], as shown in FIGS. 23a and 142, revealed that the two most C-terminal active sites are missing in the new variant. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having proteolytic and peptidolytic prolyl oligopeptidase activity.
Comparison Report Between HSPCHDP7_Skippingexon—24_P and DPP4_HUMAN
1. An isolated chimeric polypeptide HSPCHDP7_Skippingexon—24_P, comprising a first amino acid sequence being at least 90% homologous to MKTPWKVLLGLLGAAALVTIITVPVVLLNKGTDDATADSRKTYTLTDYLKNT YRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDY SISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWS PVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDHYNGITDWVYEEEVFSAY SALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVN PTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWL RRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRERPSEPHFTLDG NSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYK GMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGP GLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQ MILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDG RGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYG GYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHY R corresponding to amino acids 1-684 of DPP4_HUMAN, which also corresponds to amino acids 1-684 of HSPCHDP7_Skippingexon—24_P, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence ITFTFSSQLRSPKPWSMLEWISRQCGILMKTME (SEQ ID NO:672) corresponding to amino acids 685-717 of HSPCHDP7_Skippingexon—24_P, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSPCHDP7_Skippingexon—24_P, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence ITFTFSSQLRSPKPWSMLEWISRQCGILMKTME in HSPCHDP7_Skippingexon—24_P.
HSPCHDP7_Skippingexon—25 Variant Structure
The present inventors have uncovered a new Dipeptidyl peptidase variant [HSPCHDP7_Skippingexon—25_P—SEQ ID NO:321, HSPCHDP7_Skippingexon—25_T—SEQ ID NO:322]. The protein coordinates on the transcript start from nucleotide 561 and end at nucleotide 2693, as set forth in SEQ ID NO: 322.
Alignment of the new Dipeptidyl peptidase IV variant [HSPCHDP7_Skippingexon—25_P—SEQ ID NO:321] with the WT DPP IV protein [GenBank Accession No. P27487; DPP4_HUMAN—SEQ ID NO:651], as shown in FIGS. 23g and 143, revealed that the most C-terminal active site of the WT DPP IV protein is missing in the new variant. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having proteolytic and peptidolytic prolyl oligopeptidase activity.
Comparison Report Between HSPCHDP7_Skippingexon—25_P and DPP4_HUMAN
1. An isolated chimeric polypeptide HSPCHDP7_Skippingexon—25_P, comprising a first amino acid sequence being at least 90% homologous to MKTPWKVLLGLLGAAALVTIITVPVVLLNKGTDDATADSRKTYTLTDYLKNT YRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDY SISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWS PVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAY SALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVN PTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWL RRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRPRPSEPHFTLDG NSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYK GMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGP GLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQ MILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDG RGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYG GYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHY RNSTVMSRAENFKQVEYLLIHGTAD corresponding to amino acids 1-708 of DPP4_HUMAN, which also corresponds to amino acids 1-708 of HSPCHDP7_Skippingexon—25_P, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VVY (SEQ ID NO:673) corresponding to amino acids 709-711 of HSPCHDP7_Skippingexon—25_P, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
HSPCHDP7_Skippingexon—24—25 Variant Structure
The present inventors have uncovered a new Dipeptidyl peptidase variant [HSPCHDP7_Skippingexon—24—25_P—SEQ ID NO:323, HSPCHDP7_Skippingexon—24—25_T—SEQ ID NO:324]. The protein coordinates on the transcript start from nucleotide 561 and end at nucleotide 2711, as set forth in SEQ ID NO: 324.
Alignment of the new Dipeptidyl peptidase IV variant [HSPCHDP7_Skippingexon—24—25_P—SEQ ID NO:323] with the WT DPP IV protein [GenBank Accession No. P27487; DPP4_HUMAN—SEQ ID NO:651], as shown in FIGS. 23h and 144, revealed that the two most C-terminal active sites of the WT DPP IV protein are missing in the new variant. The new variant uncovered by the present invention is expected to be a secreted, extracellular protein having proteolytic and peptidolytic prolyl oligopeptidase activity.
Comparison Report Between HSPCHDP7_skippingexon—24—25_P and DPP4_HUMAN
1. An isolated chimeric polypeptide HSPCHDP7_skippingexon—24—25_P, comprising a first amino acid sequence being at least 90% homologous to MKTPWKVLLGLLGAAALVTIITVPVVLLNKGTDDATADSRKTYTLTDYLKNT YRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDY SISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWS PVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDHYNGITDWVYEEEVFSAY SALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVN PTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWL RRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRPRPSEPHFTLDG NSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYK GMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGP GLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQ MILPPHFDKSKKYPLLLDVYAGPCSQKADTVERLNWATYLASTENIIVASFDG RGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYG GYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHY R corresponding to amino acids 1-684 of DPP4_HUMAN, which also corresponds to amino acids 1-684 of HSPCHDP7_skippingexon—24—25_P, and a second amino acid sequence being at least 90% homologous to WYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLP corresponding to amino acids 734-766 of DPP4_HUMAN, which also corresponds to amino acids 685-717 of HSPCHDP7_skippingexon—24—25_P, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric edge portion of HSPCHDP7_skippingexon—24—25_P, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise RW, having a structure as follows: a sequence starting from any of amino acid numbers 684-x to 684; and ending at any of amino acid numbers 685+((n−2)−x), in which x varies from 0 to n−2.
Clinical Applications of the New Dipeptidyl Peptidase IV Variants of the Present Invention.
Thus the present inventors have uncovered therapeutic agents, a polypeptide homologous to SEQ ID NO:309, 311, 313, 315, 317, 319, 321, or 323 and/or an expressible polynucleotide homologous to SEQ ID NO:310, 312, 314, 316, 318, 320, 322, 324 which can be used to treat conditions associated with reduced DPP IV activity, such as the behavioural abnormalities and reduced NK cell function described above (Karl et al, Physiol Behav 2003; 80:123-34).
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per use or as part of a pharmaceutical composition with a pharmaceutically acceptable carrier (e.g., PEG and liposomes).
While further reducing the present invention to practice, these results suggest the use of the new Dipeptidy peptidase IV variants of the present invention described hereinabove (e.g., SEQ ID NO:309-324) as diagnostic markers for various tumors, hematological malignancies, immunological, inflammatory, psychoneuroendocrine disorders, and viral infections, as well as for proliferation, de-differentiation, and metastatic dissemination of cancer, such as breast cancer. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the Dipeptidyl peptidase IV variants (e.g., SEQ ID NO:309, 311, 313, 315, 317, 319, 321, 323), or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 48
Splice Variants of CD154
Background
CD154, also named CD40L (SwissProt accession: TNF5_HUMAN, SEQ ID NO:136; synonyms: Tumor necrosis factor ligand superfamily member 5; CD40 ligand (CD40L); TRAP; T cell antigen Gp39), engages its receptor, CD40, promoting cell survival and costimulatory protein expression necessary for interaction with T-lymphocytes. CD40 was originally described as a receptor responsible for the activation and differentiation of B-lymphocytes. Thus, interaction of B- and T-cells via the CD40-CD154 system allows mutual activation, with B-cells secreting antibodies and T-cells becoming effector cells producing cytokines (Kehry (1996) J. Immunol. 156: 2345-2348).
The CD40-CD154 system has wider implications than mere activation of B- and T-lymphocytes (Schonbeck and Libby (2001) Cell. Mol. Life Sci. 58: 4-43). CD40 is also expressed by migratory immune cells such as macrophages and dendritic cells, which present antigens and activate T-lymphocytes. Engagement of CD40 by T-lymphocyte CD154 activates these immune cells to express new immune modulators, such as the cytokines IL-1, IL-12 and TNFα (Van Kooten and Banchereau (2000) J. Leukoc. Biol. 67: 2-17).
Recent studies reveal that non-hematopoietic cells, including fibroblasts, endothelial cells, smooth muscle cells and some epithelial cells, constitutively display CD40 on their surface (Schonbeck and Libby, 2001 supra), and that this expression is upregulated following exposure to IFN?. Activation of CD40 signaling in non-hematopoietic cells via CD154 results in new cellular functions, including synthesis of pro-inflammatory cytokines (van Kooten and Banchereau, 2000 supra). CD40 engagement on human fibroblasts and endothelial cells induces synthesis of cyclooxygenase (COX-2) and production of prostaglandins. CD40 engagement on endothelial and vascular smooth muscle cells induces synthesis of matrix matalloproteinases (MMP). These enzymes degrade collagens and other connective tissue proteins crucial for the stability of atherosclerotic plaques and their fibrous caps.
Initially, it was thought that CD154 is expressed only on the surface of T-lymphocytes after their activation. However, CD154 was also found to be expressed by eosinophils and mast cells (Schonbeck and Libby, 2001 supra). In addition, human platelets have preformed CD154 inside them. Once activated by thrombin or other mediators, platelet internal stores of CD154 are exported to the surface where some is secreted (Hen et al., 1998, Nature 391: 591-594). Several other cell types are now known to have CD154 stored within. These include macrophages, B-lymphocytes, endothelial cells and smooth muscle cells.
A number of pathological processes of chronic inflammatory diseases in humans, and several experimental animal models of chronic inflammation, were shown to be dependent upon or involve the CD40-CD154 system. These include graft-versus-host disease, transplant rejection, neurodegenerative disorders, atherosclerosis, pulmonary fibrosis, autoimmune diseases such as lupus nephritis, systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, as well as hematological malignancies and other cancers. A remarkable spectrum of chronic inflammatory conditions can be blocked or substantially reduced by disrupting the CD40-CD154 system. These studies typically employ either mice with targeted disruption of either CD40 or CD154 genes, or use neutralizing monoclonal anti-CD154 antibodies (van Kooten and Banchereau, 2000 supra). These antibodies appear to work by disrupting the communication bridge constructed by CD40-CD154. The animals in these experimental models appear to be no worse for having this system disrupted for extended periods of time.
Splice Variants CD154 skip 3 (SEQ ID NO:657) and CD154 skip 4 (SEQ ID NO:325) Encode New Forms of CD154 (SEQ ID NOs:656 and 326, Respectively)
The present inventors have uncovered 2 new splice variants of CD154 (SwissProt accession: TNF5_HUMAN, SEQ ID NO:136), CD154 skip 3 [CD154 skip 3-SEQ ID NO:656 (FIG. 28b), and CD154 skip4-SEQ ID NO:326 (FIG. 28f)] were uncovered using the methods described above.
CD154 skip 3 Variant Structure
CD154 splice variant skipping exon 3 (CD154 skip 3_P) (SEQ ID NO:656, FIG. 28b) contains 96 N-terminal amino acids identical to the wild type CD154, and 10 unique amino acids at it's C-terminus. The nucleic acid sequence (SEQ ID NO:657) and the amino acid sequence of the CD154 splice variant skip 3 (SEQ ID NO:656) are described in FIGS. 28a and 28b, respectively. Alignment of the new CD154 variant with the WT CD 154 (SwissProt accession: TNF5_HUMAN—SEQ ID NO:136) is shown in FIG. 29.
Six out of ten unique amino acids of the new CD154 splice variant skip 3 appear in the mutated CD154 derived from patients with hyper-IgM syndrome (Ramesh N, et al., Int Immunol. 1993 July; 5(7): 769-73; gi AAD13982, (SEQ ID NO:642, FIG. 28c). Alignment between the mRNA sequence derived from HIgM syndrome and that of the new splice variant CD 154 skip 3 is shown in FIG. 28d. The difference between the two isoforms is due to a single nucleotide deletion in the previously described mRNA derived from the HIgM syndrome (gi: S66178, SEQ ID NO:642, FIG. 28d). Thus, the novel splice variant of CD154 splice variant skip 3 might be involved in the X-linked hyper-IgM syndrome.
CD 154 Skip 4
CD 154 splice variant skipping exon 4 contains an in frame deletion of 21 amino acids at the positions 116-136 of the original wild type CD154 (SwissProt accession: TNF5_HUMAN, SEQ ID NO:136). The nucleic acid sequence (CD skip 4, SEQ ID NO:325) and the amino acid sequence of the novel splice variant (CD154 skip 4_P; SEQ ID NO:326) is presented in FIGS. 28e and 28f, respectively. The splice variant skipping exon 4 (CD 154 skip 4_P, SEQ ID NO:326) of the present invention contains the amino acids involved in CD40 binding, but not the amino acids predicted to be involved in the Integrin α2, βIII binding (FIG. 30). The two domains were predicted to be modular in the three-dimensional structure of the CD154, as can be seen in FIGS. 32a and b, and therefore each domain can function independently. An mRNA encoding a polypeptide similar to the new CD154 splice variant skipping exon 4 was identified in Macaca nemestrina (FIG. 31a, gi|21363028|sp|Q9BDM7|TNF5_MACNE, SEQ ID NO:137), while in other primates, including other types of Macacas, there is a wild type CD154. The alignment of the Macaca protein (SEQ ID NO:137) and the human wild type CD154 (SwissProt accession: TNF5_HUMAN, SEQ ID NO:136) or the novel splice variant of CD154 of the present invention, CD 154 skip 4_P (SEQ ID NO:326, FIG. 28f), is presented in FIGS. 31b and c, respectively. The evolutional conservation of the sequence supports the novel splicing prediction of CD154 skip 4.
Clinical Applications
Since interaction between CD 154 and the CD40 receptor results in the induction of proinflammatory cytokines, splice variants of the CD40 ligand CD154 can be used as CD40 receptor antagonists, as therapeutic agents for the treatment of inflammatory disease such as graft-versus-host disease, transplant rejection, neurodegenerative disorders, atherosclerosis, pulmonary fibrosis, autoimmune diseases such as lupus nephritis, systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, as well as hematological malignancies and other cancers, and other chronic inflammatory conditions. Treatment can effected by providing to an individual suffering from a CD40-CD154 related condition described hereinabove a polypeptide homologous to SEQ ID NOs:656 (CD154 skip 3_P) and/or 326 (CD 154 skip—4) or a polynucleotide homologous to SEQ ID NOs:657 (CD 154 skip 3) or 325 (CD 154 skip 4) to treat the condition. It will be appreciated that such therapeutic agents (i.e., the polypeptide, and or the polynucleotide) or can be administered or provided as part of a pharmaceutical composition with a pharmaceutically acceptable carrier (e.g., PEG and liposomes).
While further reducing the present invention to practice, the present inventors have uncovered that the CD154 skip 3 variant of the present invention (CD154 skip 3_P, SEQ ID NO:656) and the polynucleotide encoding same (SEQ ID NO:657) can be used as diagnostic markers for hyper IgM (HIgM) syndrome.
Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the CD154 skip 3_P, SEQ ID NO:656 variant, or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 49
Description for Cluster HUMEGFAA
Cluster HUMEGFAA features 16 transcript(s) and 51 segment(s) of interest, the names for which are given in Tables 68 and 69, respectively, the sequences themselves are given in SEQ ID NOs 428-443; 444-494 and 495-496, for transcripts; segments and proteins, respectively. The selected protein variants are given in Table 70.







TABLE 68







Transcripts of interest










Transcript Name
SEQ ID NO







HUMEGFAA_PEA_2_T0
428



 



HUMEGFAA_PEA_2_T4
429



 



HUMEGFAA_PEA_2_T6
430



 



HUMEGFAA_PEA_2_T7
431



 



HUMEGFAA_PEA_2_T10
432



 



HUMEGFAA_PEA_2_T11
433



 



HUMEGFAA_PEA_2_T13
434



 



HUMEGFAA_PEA_2_T16
435



 



HUMEGFAA_PEA_2_T17
436



 



HUMEGFAA_PEA_2_T19
437



 



HUMEGFAA_PEA_2_T21
438



 



HUMEGFAA_PEA_2_T22
439



 



HUMEGFAA_PEA_2_T25
440



 



HUMEGFAA_PEA_2_T29
441



 



HUMEGFAA_PEA_2_T43
442



 



HUMEGFAA_PEA_2_T44
443

















TABLE 69







Segments of interest










Segment Name
SEQ ID NO:







HUMEGFAA_PEA_2_node_0
444



 



HUMEGFAA_PEA_2_node_1
445



 



HUMEGFAA_PEA_2_node_2
446



 



HUMEGFAA_PEA_2_node_3
447



 



HUMEGFAA_PEA_2_node_10
448



 



HUMEGFAA_PEA_2_node_13
449



 



HUMEGFAA_PEA_2_node_18
450



 



HUMEGFAA_PEA_2_node_23
451



 



HUMEGFAA_PEA_2_node_25
452



 



HUMEGFAA_PEA_2_node_26
453



 



HUMEGFAA_PEA_2_node_30
454



 



HUMEGFAA_PEA_2_node_34
455



 



HUMEGFAA_PEA_2_node_37
456



 



HUMEGFAA_PEA_2_node_38
457



 



HUMEGFAA_PEA_2_node_41
458



 



HUMEGFAA_PEA_2_node_44
459



 



HUMEGFAA_PEA_2_node_56
460



 



HUMEGFAA_PEA_2_node_58
461



 



HUMEGFAA_PEA_2_node_60
462



 



HUMEGFAA_PEA_2_node_7
463



 



HUMEGFAA_PEA_2_node_12
464



 



HUMEGFAA_PEA_2_node_14
465



 



HUMEGFAA_PEA_2_node_15
466



 



HUMEGFAA_PEA_2_node_16
467



 



HUMEGFAA_PEA_2_node_17
468



 



HUMEGFAA_PEA_2_node_21
469



 



HUMEGFAA_PEA_2_node_22
470



 



HUMEGFAA_PEA_2_node_24
471



 



HUMEGFAA_PEA_2_node_27
472



 



HUMEGFAA_PEA_2_node_28
473



 



HUMEGFAA_PEA_2_node_29
474



 



HUMEGFAA_PEA_2_node_31
475



 



HUMEGFAA_PEA_2_node_32
476



 



HUMEGFAA_PEA_2_node_33
477



 



HUMEGFAA_PEA_2_node_35
478



 



HUMEGFAA_PEA_2_node_36
479



 



HUMEGFAA_PEA_2_node_39
480



 



HUMEGFAA_PEA_2_node_40
481



 



HUMEGFAA_PEA_2_node_42
482



 



HUMEGFAA_PEA_2_node_43
483



 



HUMEGFAA_PEA_2_node_45
484



 



HUMEGFAA_PEA_2_node_46
485



 



HUMEGFAA_PEA_2_node_47
486



 



HUMEGFAA_PEA_2_node_48
487



 



HUMEGFAA_PEA_2_node_49
488



 



HUMEGFAA_PEA_2_node_50
489



 



HUMEGFAA_PEA_2_node_52
490



 



HUMEGFAA_PEA_2_node_53
491



 



HUMEGFAA_PEA_2_node_54
492



 



HUMEGFAA_PEA_2_node_55
493



 



HUMEGFAA_PEA_2_node_57
494

















TABLE 70







Proteins of interest











SEQ





ID
Protein
Corresponding


Protein Name
NO:
Length
Transcript(s)





HUMEGFAA_PEA_2_P3
495
P143
HUMEGFAA_PEA_2_T0;





HUMEGFAA_PEA_2_T4;





HUMEGFAA_PEA_2_T6;





HUMEGFAA_PEA_2_T7;





HUMEGFAA_PEA_2_T10;





HUMEGFAA_PEA_2_T11;





HUMEGFAA_PEA_2_T13;





HUMEGFAA_PEA_2_T16;





HUMEGFAA_PEA_2_T17;





HUMEGFAA_PEA_2_T19;





HUMEGFAA_PEA_2_T21;





HUMEGFAA_PEA_2_T22;





HUMEGFAA_PEA_2_T25;





HUMEGFAA_PEA_2_T29;





HUMEGFAA_PEA_2_T43


 


HUMEGFAA_PEA_2_P14
496
P131
HUMEGFAA_PEA_2_T44









These sequences are variants of the known protein Vascular endothelial growth factor A precursor (SwissProt accession identifier VEGA_HUMAN; known also according to the synonyms VEGF-A; Vascular permeability factor; VPF), SEQ ID NO: 196, referred to herein as the previously known protein.
Protein Vascular endothelial growth factor A precursor is known or believed to have the following function(s): Growth factor active in angiogenesis, vasculogenesis and endothelial cell growth. It induces endothelial cell proliferation, promotes cell migration, inhibits apoptosis, and induces permeabilization of blood vessels. It binds to the VEGFR1/Flt-1 and VEGFR2/Kdr receptors and to heparan sulfate and heparin. Neuropilin-1 binds isoforms VEGF-165 and VEGF-145. The sequence for protein Vascular endothelial growth factor A precursor is given in SEQ ID NO: 196, as “Vascular endothelial growth factor A precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 71.







TABLE 71







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment











87
C → S


210
D → H









Protein Vascular endothelial growth factor A precursor localization is believed to be secreted. The localization of the known splice variants is as follows: VEGF121 is acidic and freely secreted. VEGF165 is more basic, has heparin-binding properties and, although a significant proportion remains cell-associated, most is freely secreted. VEGF189 is very basic; it is cell-associated after secretion and is bound avidly by heparin and the extracellular matrix, although it may be released as a soluble form by heparin, heparinase or plasmin.
It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein or of drugs directed to this protein are as follows: Endothelial growth factor receptor kinase inhibitor; Angiogenesis modulator; Endothelial growth factor modulator. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Symptomatic antidiabetic; Anticancer; Ophthalmological; Vulnerary; Cardiovascular.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: cell cycle control; angiogenesis; stress response; homophilic cell adhesion; signal transduction; cell proliferation; positive control of cell proliferation, which are annotation(s) related to Biological Process; vascular endothelial growth factor receptor ligand; growth factor; heparin binding, which are annotation(s) related to Molecular Function; and extracellular; soluble fraction; membrane, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
As noted above, cluster HUMEGFAA features 16 transcript(s), which were listed in Table 1 above. These transcript(s) encode for protein(s) which are variant(s) of protein Vascular endothelial growth factor A precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HUMEGFAA_PEA—2_P3 (SEQ ID NO:495) according to the present invention is encoded by transcript(s) HUMEGFAA_PEA—2_T0, HUMEGFAA_PEA—2_T4, HUMEGFAA_PEA—2_T6, HUMEGFAA_PEA—2_T7, HUMEGFAA_PEA—2_T10, HUMEGFAA_PEA—2_T11, HUMEGFAA_PEA—2_T13, HUMEGFAA_PEA—2_T16, HUMEGFAA_PEA—2_T17, HUMEGFAA_PEA—2_T19, HUMEGFAA_PEA—2_T21, HUMEGFAA_PEA—2_T22, HUMEGFAA_PEA—2_T25, HUMEGFAA_PEA—2_T29 and HUMEGFAA_PEA—2_T43. An alignment is given to the known protein (Vascular endothelial growth factor A precursor; SEQ ID NO:196) in FIG. 152. One or more alignments to one or more previously published protein sequences in given in FIG. 153. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMEGFAA_PEA—2_P3 and VEGA_HUMAN:
1. An isolated chimeric polypeptide HUMEGFAA_PEA—2_P3, comprising a first amino acid sequence being at least 90% homologous to MNFLLSWVHWSLALLLYLHHAKWSQAAPMAEGGGQNHHEVVKFMDVYQR SYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITM Q corresponding to amino acids 1-105 of VEGA_HUMAN, which also corresponds to amino acids 1-105 of HUMEGFAA_PEA—2_P3, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VGIFGKWGKGGIGRGVTLWEQVVPGRFLARFALSGSCP corresponding to amino acids 106-143 of HUMEGFAA_PEA—2_P3, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMEGFAA_PEA—2_P3, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VGIFGKWGKGGIGRGVTLWEQVVPGRFLARFALSGSCP in HUMEGFAA_PEA—2_P3.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMEGFAA_PEA—2_P3 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 72, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 72







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





122
T → R
Yes









The glycosylation sites of variant protein HUMEGFAA_PEA—2_P3, as compared to the known protein Vascular endothelial growth factor A precursor, are described in Table 73 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 73







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





101
yes
101









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 74, hereinbelow.







TABLE 74







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR000072
Platelet-derived growth
HMMPfam
52-132



factor (PDGF)


IPR000072
Platelet-derived growth
HMMSmart
50-129



factor (PDGF)


IPR000072
Platelet-derived growth
ScanRegExp
75-87



factor (PDGF)


IPR000072
Platelet-derived growth
BlastProDom
43-106



factor (PDGF)


IPR000072
Platelet-derived growth
ProfileScan
39-106



factor (PDGF)









The coding portion of transcript HUMEGFAA_PEA—2_T0 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 75 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 75







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


2729
C → T
Yes


2849
C → T
Yes


2972
C → T
Yes


2979
G → A
Yes


3050
G → A
Yes


3051
G → A
Yes


3166
G → T
Yes


3167
T → C
Yes


3178
T → C
Yes


3224
A → T
Yes


3563
A → G
Yes


3571
G →
No


3573
T →
No


3951
C → G
Yes


3953
G → A
Yes


3959
C → T
Yes


3960
G → A
Yes


4037
C → T
Yes


4042
T → G
Yes


4154
→ C
No


4246
C → T
Yes


4398
C → G
Yes


4398
C → T
Yes


4589
A → G
Yes


4713
C → T
Yes


4766
T → C
Yes


4834
T → C
Yes


5094
G → A
Yes


5117
C → T
Yes


5121
T → C
No


5157
G → A
Yes


5157
G → C
Yes


6095
T → A
Yes


6096
C → G
Yes


6155
G → C
Yes


6160
G → A
Yes


6191
G → C
Yes


6300
C → A
Yes


6641
C → T
Yes


6679
A → G
Yes


6795
G → T
Yes


6963
C → T
Yes


7273
C → G
Yes


7365
T →
No


7533
A → G
Yes


7688
C → T
Yes


7829
G → A
Yes


7901
G → A
No


7901
G → C
No


7907
C → T
No


7943
A →
No


8117
C → A
No


8141
C → T
Yes


8656
C → T
Yes


8743
G →
No


8752
C →
No


8752
C → G
No


8817
G → A
Yes


8852
C → T
Yes


8870
C →
No


8870
C → G
No


8908
T →
No


8930
G → A
Yes


9046
C → T
Yes


9054
C →
No


9054
C → T
No


9198
→ T
No


9293
A →
No


9327
G → A
No


9393
G → A
Yes


9396
C →
No


9470
A → C
No


9478
T →
No


9478
T → A
No


9500
T → C
Yes


9514
→ A
No


9572
A → C
No


9800
T → G
No









The coding portion of transcript HUMEGFAA_PEA—2_T4 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 76 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 76







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


2729
C → T
Yes


2849
C → T
Yes


2972
C → T
Yes


2979
G → A
Yes


3050
G → A
Yes


3051
G → A
Yes


3166
G → T
Yes


3167
T → C
Yes


3178
T → C
Yes


3224
A → T
Yes


3563
A → G
Yes


3571
G →
No


3573
T →
No


3951
C → G
Yes


3953
G → A
Yes


3959
C → T
Yes


3960
G → A
Yes


4037
C → T
Yes


4042
T → G
Yes


4154
→ C
No


4246
C → T
Yes


4398
C → G
Yes


4398
C → T
Yes


4589
A → G
Yes


4713
C → T
Yes


4766
T → C
Yes


4834
T → C
Yes


5094
G → A
Yes


5117
C → T
Yes


5121
T → C
No


5157
G → A
Yes


5157
G → C
Yes


5447
G → A
No


5447
G → C
No


5453
C → T
No


5489
A →
No


5663
C → A
No


5687
C → T
Yes


6202
C → T
Yes


6289
G →
No


6298
C →
No


6298
C → G
No


6363
G → A
Yes


6398
C → T
Yes


6416
C →
No


6416
C → G
No


6454
T →
No


6476
G → A
Yes


6592
C → T
Yes


6600
C →
No


6600
C → T
No


6744
→ T
No


6839
A →
No


6873
G → A
No


6939
G → A
Yes


6942
C →
No


7016
A → C
No


7024
T →
No


7024
T → A
No


7046
T → C
Yes


7060
→ A
No


7118
A → C
No


7346
T → G
No









The coding portion of transcript HUMEGFAA_PEA—2_T6 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 77 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 77







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


2729
C → T
Yes


2849
C → T
Yes


2972
C → T
Yes


2979
G → A
Yes


3050
G → A
Yes


3051
G → A
Yes


3166
G → T
Yes


3167
T → C
Yes


3178
T → C
Yes


3224
A → T
Yes


3563
A → G
Yes


3571
G →
No


3573
T →
No


3951
C → G
Yes


3953
G → A
Yes


3959
C → T
Yes


3960
G → A
Yes


4037
C → T
Yes


4042
T → G
Yes


4294
G → A
No


4294
G → C
No


4300
C → T
No


4336
A →
No


4510
C → A
No


4534
C → T
Yes


5049
C → T
Yes


5136
G →
No


5145
C →
No


5145
C → G
No


5210
G → A
Yes


5245
C → T
Yes


5263
C →
No


5263
C → G
No


5301
T →
No


5323
G → A
Yes


5439
C → T
Yes


5447
C →
No


5447
C → T
No


5591
→ T
No


5686
A →
No


5720
G → A
No


5786
G → A
Yes


5789
C →
No


5863
A → C
No


5871
T →
No


5871
T → A
No


5893
T → C
Yes


5907
→ A
No


5965
A → C
No


6193
T → G
No









The coding portion of transcript HUMEGFAA_PEA—2_T7 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 78 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 78







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


2435
A → G
Yes


2443
G →
No


2445
T →
No


2823
C → G
Yes


2825
G → A
Yes


2831
C → T
Yes


2832
G → A
Yes


2909
C → T
Yes


2914
T → G
Yes


3026
→ C
No


3118
C → T
Yes


3270
C → G
Yes


3270
C → T
Yes


3461
A → G
Yes


3585
C → T
Yes


3638
T → C
Yes


3706
T → C
Yes


3966
G → A
Yes


3989
C → T
Yes


3993
T → C
No


4029
G → A
Yes


4029
G → C
Yes


4967
T → A
Yes


4968
C → G
Yes


5027
G → C
Yes


5032
G → A
Yes


5063
G → C
Yes


5172
C → A
Yes


5513
C → T
Yes


5551
A → G
Yes


5667
G → T
Yes


5835
C → T
Yes


6145
C → G
Yes


6237
T →
No


6405
A → G
Yes


6560
C → T
Yes


6701
G → A
Yes


6773
G → A
No


6773
G → C
No


6779
C → T
No


6815
A →
No


6989
C → A
No


7013
C → T
Yes


7528
C → T
Yes


7615
G →
No


7624
C →
No


7624
C → G
No


7689
G → A
Yes


7724
C → T
Yes


7742
C →
No


7742
C → G
No


7780
T →
No


7802
G → A
Yes


7918
C → T
Yes


7926
C →
No


7926
C → T
No


8070
→ T
No


8165
A →
No


8199
G → A
No


8265
G → A
Yes


8268
C →
No


8342
A → C
No


8350
T →
No


8350
T → A
No


8372
T → C
Yes


8386
→ A
No


8444
A → C
No


8672
T → G
No









The coding portion of transcript HUMEGFAA_PEA—2_T10 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 79 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 79







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


2729
C → T
Yes


2849
C → T
Yes


2972
C → T
Yes


2979
G → A
Yes


3050
G → A
Yes


3051
G → A
Yes


3166
G → T
Yes


3167
T → C
Yes


3178
T → C
Yes


3224
A → T
Yes


3563
A → G
Yes


3571
G →
No


3573
T →
No


3951
C → G
Yes


3953
G → A
Yes


3959
C → T
Yes


3960
G → A
Yes


4037
C → T
Yes


4042
T → G
Yes


4276
G → A
No


4276
G → C
No


4282
C → T
No


4318
A →
No


4492
C → A
No


4516
C → T
Yes


5031
C → T
Yes


5118
G →
No


5127
C →
No


5127
C → G
No


5192
G → A
Yes


5227
C → T
Yes


5245
C →
No


5245
C → G
No


5283
T →
No


5305
G → A
Yes


5421
C → T
Yes


5429
C →
No


5429
C → T
No


5573
→ T
No


5668
A →
No


5702
G → A
No


5768
G → A
Yes


5771
C →
No


5845
A → C
No


5853
T →
No


5853
T → A
No


5875
T → C
Yes


5889
→ A
No


5947
A → C
No


6175
T → G
No









The coding portion of transcript HUMEGFAA_PEA—2_T11 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 80 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 80







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


2729
C → T
Yes


2849
C → T
Yes


2972
C → T
Yes


2979
G → A
Yes


3050
G → A
Yes


3051
G → A
Yes


3166
G → T
Yes


3167
T → C
Yes


3178
T → C
Yes


3224
A → T
Yes


3563
A → G
Yes


3571
G →
No


3573
T →
No


3951
C → G
Yes


3953
G → A
Yes


3959
C → T
Yes


3960
G → A
Yes


4037
C → T
Yes


4042
T → G
Yes


4162
G → A
No


4162
G → C
No


4168
C → T
No


4204
A →
No


4378
C → A
No


4402
C → T
Yes


4917
C → T
Yes


5004
G →
No


5013
C →
No


5013
C → G
No


5078
G → A
Yes


5113
C → T
Yes


5131
C →
No


5131
C → G
No


5169
T →
No


5191
G → A
Yes


5307
C → T
Yes


5315
C →
No


5315
C → T
No


5459
→ T
No


5554
A →
No


5588
G → A
No


5654
G → A
Yes


5657
C →
No


5731
A → C
No


5739
T →
No


5739
T → A
No


5761
T → C
Yes


5775
→ A
No


5833
A → C
No


6061
T → G
No









The coding portion of transcript HUMEGFAA_PEA—2_T13 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 81 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 81







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


3055
T → A
Yes


3056
C → G
Yes


3115
G → C
Yes


3120
G → A
Yes


3151
G → C
Yes


3260
C → A
Yes


3601
C → T
Yes


3639
A → G
Yes


3755
G → T
Yes


3923
C → T
Yes


4233
C → G
Yes


4325
T →
No


4493
A → G
Yes


4648
C → T
Yes


4789
G → A
Yes


4861
G → A
No


4861
G → C
No


4867
C → T
No


4903
A →
No


5077
C → A
No


5101
C → T
Yes


5616
C → T
Yes


5703
G →
No


5712
C →
No


5712
C → G
No


5777
G → A
Yes


5812
C → T
Yes


5830
C →
No


5830
C → G
No


5868
T →
No


5890
G → A
Yes


6006
C → T
Yes


6014
C →
No


6014
C → T
No


6158
→ T
No


6253
A →
No


6287
G → A
No


6353
G → A
Yes


6356
C →
No


6430
A → C
No


6438
T →
No


6438
T → A
No


6460
T → C
Yes


6474
→ A
No


6532
A → C
No


6760
T → G
No









The coding portion of transcript HUMEGFAA_PEA—2_T16 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 82 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 82







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


3127
T → A
Yes


3128
C → G
Yes


3187
G → C
Yes


3192
G → A
Yes


3223
G → C
Yes


3332
C → A
Yes


3673
C → T
Yes


3711
A → G
Yes


3827
G → T
Yes


3995
C → T
Yes


4305
C → G
Yes


4397
T →
No


4565
A → G
Yes


4720
C → T
Yes


4861
G → A
Yes


4933
G → A
No


4933
G → C
No


4939
C → T
No


4975
A →
No


5149
C → A
No


5173
C → T
Yes


5688
C → T
Yes


5775
G →
No


5784
C →
No


5784
C → G
No


5849
G → A
Yes


5884
C → T
Yes


5902
C →
No


5902
C → G
No


5940
T →
No


5962
G → A
Yes


6078
C → T
Yes


6086
C →
No


6086
C → T
No


6230
→ T
No


6325
A →
No


6359
G → A
No


6425
G → A
Yes


6428
C →
No


6502
A → C
No


6510
T →
No


6510
T → A
No


6532
T → C
Yes


6546
→ A
No


6604
A → C
No


6832
T → G
No









The coding portion of transcript HUMEGFAA_PEA—2_T17 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 83 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 83







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


2275
G → A
No


2275
G → C
No


2281
C → T
No


2317
A →
No


2491
C → A
No


2515
C → T
Yes


3030
C → T
Yes


3117
G →
No


3126
C →
No


3126
C → G
No


3191
G → A
Yes


3226
C → T
Yes


3244
C →
No


3244
C → G
No


3282
T →
No


3304
G → A
Yes


3420
C → T
Yes


3428
C →
No


3428
C → T
No


3572
→ T
No


3667
A →
No


3701
G → A
No


3767
G → A
Yes


3770
C →
No


3844
A → C
No


3852
T →
No


3852
T → A
No


3874
T → C
Yes


3888
→ A
No


3946
A → C
No


4174
T → G
No









The coding portion of transcript HUMEGFAA_PEA—2_T19 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 84 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 84







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


2407
G → A
No


2407
G → C
No


2413
C → T
No


2449
A →
No


2623
C → A
No


2647
C → T
Yes


3162
C → T
Yes


3249
G →
No


3258
C →
No


3258
C → G
No


3323
G → A
Yes


3358
C → T
Yes


3376
C →
No


3376
C → G
No


3414
T →
No


3436
G → A
Yes


3552
C → T
Yes


3560
C →
No


3560
C → T
No


3704
→ T
No


3799
A →
No


3833
G → A
No


3899
G → A
Yes


3902
C →
No


3976
A → C
No


3984
T →
No


3984
T → A
No


4006
T → C
Yes


4020
→ A
No


4078
A → C
No


4306
T → G
No









The coding portion of transcript HUMEGFAA_PEA—2_T21 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 85 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 85







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


2479
G → A
No


2479
G → C
No


2485
C → T
No


2521
A →
No


2695
C → A
No


2719
C → T
Yes


3234
C → T
Yes


3321
G →
No


3330
C →
No


3330
C → G
No


3395
G → A
Yes


3430
C → T
Yes


3448
C →
No


3448
C → G
No


3486
T →
No


3508
G → A
Yes


3624
C → T
Yes


3632
C →
No


3632
C → T
No


3776
→ T
No


3871
A →
No


3905
G → A
No


3971
G → A
Yes


3974
C →
No


4048
A → C
No


4056
T →
No


4056
T → A
No


4078
T → C
Yes


4092
→ A
No


4150
A → C
No


4378
T → G
No









The coding portion of transcript HUMEGFAA_PEA—2_T22 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 86 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 86







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


2461
G → A
No


2461
G → C
No


2467
C → T
No


2503
A →
No


2677
C → A
No


2701
C → T
Yes


3216
C → T
Yes


3303
G →
No


3312
C →
No


3312
C → G
No


3377
G → A
Yes


3412
C → T
Yes


3430
C →
No


3430
C → G
No


3468
T →
No


3490
G → A
Yes


3606
C → T
Yes


3614
C →
No


3614
C → T
No


3758
→ T
No


3853
A →
No


3887
G → A
No


3953
G → A
Yes


3956
C →
No


4030
A → C
No


4038
T →
No


4038
T → A
No


4060
T → C
Yes


4074
→ A
No


4132
A → C
No


4360
T → G
No









The coding portion of transcript HUMEGFAA_PEA—2_T25 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 87 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 87







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


2425
G → A
No


2425
G → C
No


2431
C → T
No


2467
A →
No


2641
C → A
No


2665
C → T
Yes


3180
C → T
Yes


3267
G →
No


3276
C →
No


3276
C → G
No


3341
G → A
Yes


3376
C → T
Yes


3394
C →
No


3394
C → G
No


3432
T →
No


3454
G → A
Yes


3570
C → T
Yes


3578
C →
No


3578
C → T
No


3722
→ T
No


3817
A →
No


3851
G → A
No


3917
G → A
Yes


3920
C →
No


3994
A → C
No


4002
T →
No


4002
T → A
No


4024
T → C
Yes


4038
→ A
No


4096
A → C
No


4324
T → G
No









The coding portion of transcript HUMEGFAA_PEA—2_T29 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 88 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 88







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


2729
C → T
Yes


2849
C → T
Yes


2972
C → T
Yes


2979
G → A
Yes


3050
G → A
Yes


3051
G → A
Yes


3166
G → T
Yes


3167
T → C
Yes


3178
T → C
Yes


3224
A → T
Yes


3563
A → G
Yes


3571
G →
No


3573
T →
No


3951
C → G
Yes


3953
G → A
Yes


3959
C → T
Yes


3960
G → A
Yes


4037
C → T
Yes


4042
T → G
Yes


4154
→ C
No


4246
C → T
Yes


4398
C → G
Yes


4398
C → T
Yes


4589
A → G
Yes


4713
C → T
Yes


4766
T → C
Yes


4834
T → C
Yes


5094
G → A
Yes


5117
C → T
Yes


5121
T → C
No


5157
G → A
Yes


5157
G → C
Yes


6095
T → A
Yes


6096
C → G
Yes


6155
G → C
Yes


6160
G → A
Yes


6191
G → C
Yes


6300
C → A
Yes


6641
C → T
Yes


6679
A → G
Yes


6795
G → T
Yes


6963
C → T
Yes


7273
C → G
Yes


7365
T →
No


7533
A → G
Yes


7688
C → T
Yes


7829
G → A
Yes


7901
G → A
No


7901
G → C
No


7907
C → T
No


7943
A →
No


8117
C → A
No


8141
C → T
Yes


8656
C → T
Yes


8743
G →
No


8752
C →
No


8752
C → G
No


8817
G → A
Yes


8852
C → T
Yes


8870
C →
No


8870
C → G
No


8908
T →
No


8930
G → A
Yes


9046
C → T
Yes


9054
C →
No


9054
C → T
No


9198
→ T
No


9293
A →
No


9327
G → A
No


9393
G → A
Yes


9396
C →
No


9470
A → C
No


9478
T →
No


9478
T → A
No


9500
T → C
Yes


9514
→ A
No


9572
A → C
No









The coding portion of transcript HUMEGFAA_PEA—2_T43 starts at position 1041 and ends at position 1469. The transcript also has the following SNPs as listed in Table 89 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 89







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1405
C → G
Yes


1530
C → T
Yes


1828
G → A
Yes


1854
A → T
No


2122
C → T
Yes


2205
A → G
No


2282
G → A
Yes


2317
C → T
Yes


2363
C → T
Yes


2376
A → G
Yes


2424
T → G
Yes


2442
A → G
Yes









Variant protein HUMEGFAA_PEA—2_P14 according to the present invention is encoded by transcript(s) HUMEGFAA_PEA—2_T44. An alignment is given to the known protein (Vascular endothelial growth factor A precursor) in FIG. 153. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMEGFAA_PEA—2_P14 and VEGA_HUMAN:
1. An isolated chimeric polypeptide HUMEGFAA_PEA—2_P14, comprising a first amino acid sequence being at least 90% homologous to MNFLLSWVHWSLALLLYLHHAKWSQAAPMAEGGGQNHHEVVKFMDVYQR SYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITM QIMRIKPHQGQHIGEMSFLQHNKCECR corresponding to amino acids 1-131 of VEGA_HUMAN, which also corresponds to amino acids 1-131 of HUMEGFAA_PEA—2_P14.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMEGFAA_PEA—2_P14 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 90, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P14 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 90







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





124
Q → R
No









The glycosylation sites of variant protein HUMEGFAA_PEA—2_P14, as compared to the known protein Vascular endothelial growth factor A precursor, are described in Table 91 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 91







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





101
yes
101









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 92, hereinbelow.








TABLE 92







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR002400
Growth factor, cystine
FPrintScan
126-130, 79-88



knot


IPR000072
Platelet-derived growth
HMMPfam
52-130



factor (PDGF)


IPR000072
Platelet-derived growth
HMMSmart
50-131



factor (PDGF)


IPR000072
Platelet-derived growth
ScanRegExp
75-87



factor (PDGF)


IPR000072
Platelet-derived growth
BlastProDom
43-129



factor (PDGF)


IPR000072
Platelet-derived growth
ProfileScan
39-131



factor (PDGF)









Variant protein HUMEGFAA_PEA—2_P14 is encoded by the following transcript(s): HUMEGFAA_PEA—2_T44. The coding portion of transcript HUMEGFAA_PEA—2_T44 starts at position 1041 and ends at position 1433. The transcript also has the following SNPs as listed in Table 93 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMEGFAA_PEA—2_P14 sequence provides support for the deduced sequence of this variant protein according to the present invention).








TABLE 93







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












82
G →
No


118
G →
No


407
C → G
Yes


431
G → A
Yes


465
C →
No


1034
C → T
Yes


1035
G → T
No


1036
A → T
No


1322
T → C
No


1411
A → G
No


1488
G → A
Yes


1523
C → T
Yes


1569
C → T
Yes


1582
A → G
Yes


1630
T → G
Yes


1648
A → G
Yes









The variants were found to have the following domain structure as shown in the FIG. 35 in comparison to the known or wild-type (WT) protein.
Example 50
Description for Cluster HSFLT
Cluster HSFLT features 8 transcript(s) and 25 segment(s) of interest, the names for which are given in Tables 94 and 95, respectively, the sequences themselves are given in SEQ ID NOs: 497-504; 505-529 and 531-537, for transcripts, segments and proteins, respectively. The selected protein variants are given in Table 96.







TABLE 94







Transcripts of interest










Transcript Name
SEQ ID NO:







HSFLT_PEA_1_T4
497



 



HSFLT_PEA_1_T5
498



 



HSFLT_PEA_1_T13
499



 



HSFLT_PEA_1_T15
500



 



HSFLT_PEA_1_T16
501



 



HSFLT_PEA_1_T17
502



 



HSFLT_PEA_1_T19
503



 



HSFLT_PEA_1_T25
504

















TABLE 95







Segments of interest










Segment Name
SEQ ID NO:







HSFLT_PEA_1_node_0
505



 



HSFLT_PEA_1_node_8
506



 



HSFLT_PEA_1_node_11
507



 



HSFLT_PEA_1_node_15
508



 



HSFLT_PEA_1_node_17
509



 



HSFLT_PEA_1_node_19
510



 



HSFLT_PEA_1_node_20
511



 



HSFLT_PEA_1_node_24
512



 



HSFLT_PEA_1_node_26
513



 



HSFLT_PEA_1_node_33
514



 



HSFLT_PEA_1_node_42
515



 



HSFLT_PEA_1_node_43
516



 



HSFLT_PEA_1_node_44
517



 



HSFLT_PEA_1_node_46
518



 



HSFLT_PEA_1_node_47
519



 



HSFLT_PEA_1_node_49
520



 



HSFLT_PEA_1_node_51
521



 



HSFLT_PEA_1_node_1
522



 



HSFLT_PEA_1_node_3
523



 



HSFLT_PEA_1_node_6
524



 



HSFLT_PEA_1_node_22
525



 



HSFLT_PEA_1_node_28
526



 



HSFLT_PEA_1_node_35
527



 



HSFLT_PEA_1_node_37
528



 



HSFLT_PEA_1_node_39
529

















TABLE 96







Proteins of interest











SEQ





ID
Protein
Corresponding


Protein Name
NO:
Length
Transcript(s)





HSFLT_PEA_1_P3
531
P567
HSFLT_PEA_1_T4


 


HSFLT_PEA_1_P4
532
P541
HSFLT_PEA_1_T5


 


HSFLT_PEA_1_P10
533
P733
HSFLT_PEA_1_T13


 


HSFLT_PEA_1_P12
534
P718
HSFLT_PEA_1_T15;





HSFLT PEA_1_T17


 


HSFLT_PEA_1_P13
535
P736
HSFLT_PEA_1_T16


 


HSFLT_PEA_1_P14
536
P547
HSFLT_PEA_1_T19


 


HSFLT_PEA_1_P19
537
P365
HSFLT_PEA_1_T25









These sequences are variants of the known protein Vascular endothelial growth factor receptor 1 precursor (SEQ ID NO:530; SwissProt accession identifier VGR1_HUMAN; known also according to the synonyms EC 2.7.1.112; VEGFR-1; Vascular permeability factor receptor; Tyrosine-protein kinase receptor FLT; Flt-1; Tyrosine-protein kinase FRT; Fms-like tyrosine kinase 1), referred to herein as the previously known protein.
Protein Vascular endothelial growth factor receptor 1 precursor is known or believed to have the following function(s): Receptor for VEGF, VEGFB and PGF. Has a tyrosine-protein kinase activity. The VEGF-kinase ligand/receptor signaling system plays a key role in vascular development and regulation of vascular permeability. Isoform SFlt1 may have an inhibitory role in angiogenesis. The sequence for protein Vascular endothelial growth factor receptor 1 precursor is given in SEQ ID NO: 530, as “Vascular endothelial growth factor receptor 1 precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 97.







TABLE 97







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment











914
Y → F: No loss of phosphorylation.


1213
Y → F: Loss of phosphorylation.


1242
Y → F: Loss of phosphorylation.


1327
Y → F: Loss of phosphorylation.


1333
Y → F: Loss of phosphorylation.


779
L → F









Protein Vascular endothelial growth factor receptor 1 precursor localization is believed to be Type I membrane protein (Flt1) and soluble (SFlt1).
It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein or of drugs directed to this protein are as follows: Endothelial growth factor agonist; Endothelial growth factor receptor kinase inhibitor; Angiogenesis modulator. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic and/or indications: Cardiovascular; Vulnerary; Anticancer; Symptomatic antidiabetic; peripheral vascular disease; ulcer; ischaemia.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: angiogenesis; protein amino acid phosphorylation; transmembrane receptor protein tyrosine kinase signaling pathway; pregnancy; positive control of cell proliferation, which are annotation(s) related to Biological Process; receptor; vascular endothelial growth factor receptor; ATP binding; transferase, which are annotation(s) related to Molecular Function; and extracellular space; integral plasma membrane protein, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
As noted above, cluster HSFLT features 8 transcript(s), which were listed in Table 94 above. These transcript(s) encode for protein(s) which are variant(s) of protein Vascular endothelial growth factor receptor 1 precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HSFLT_PEA—1_P3 (SEQ ID NO:531) is encoded by transcript(s) HSFLT_PEA—1_T4. An alignment is given to the known protein (Vascular endothelial growth factor receptor 1 precursor; SEQ ID NO:530) is presented in FIG. 154. One or more alignments to one or more previously published protein sequences are given in FIGS. 155-160. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSFLT_PEA—1_P3 and VGR1_HUMAN:
1. An isolated chimeric polypeptide HSFLT_PEA—1_P3, comprising a first amino acid sequence being at least 90% homologous to MVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQ CRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGF YSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRV TSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHL YKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSY PDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKS VNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKD GLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNV KPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARC DFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYIC IASNKVGTVGRNISFYIT corresponding to amino acids 1-553 of VGR1_HUMAN, which also corresponds to amino acids 1-553 of HSFLT_PEA—1_P3, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence ELSNFECLHPCSQE corresponding to amino acids 554-567 of HSFLT_PEA—1_P3, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSFLT_PEA—1_P3, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence ELSNFECLHPCSQE in HSFLT_PEA—1_P3.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSFLT_PEA—1_P3 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 98, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSFLT_PEA—1_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 98







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





250
L → P
No


284
Q → R
No


343
V → A
No


394
D → G
No









The glycosylation sites of variant protein HSFLT_PEA—1_P3, as compared to the known protein Vascular endothelial growth factor receptor 1 precursor, are described in Table 99 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 99







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





547
yes
547


474
yes
474


620
no


666
no


597
no


100
yes
100


402
yes
402


323
yes
323


251
yes
251


164
yes
164


417
yes
417


625
no


196
yes
196









The phosphorylation sites of variant protein HSFLT_PEA—1_P3, as compared to the known protein Vascular endothelial growth factor receptor 1 precursor, are described in Table 100 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 100







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





1169
no



1213
no


1053
no


1242
no


1333
no


1327
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 101.







TABLE 101







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR009134
Vascular endothelial
FPrintScan
125-136, 184-194,



growth factor receptor,

242-254, 390-407,



VEGFR

448-462, 89-107


IPR009135
Vascular endothelial
FPrintScan
130-155, 224-247,



growth factor receptor 1,

26-41, 273-290,



VEGFR1

350-370, 375-389,





79-93


IPR007110
Immunoglobulin-like
HMMPfam
151-209, 245-313,





359-404, 447-537,





90-109


IPR003598
Immunoglobulin C-2 type
HMMSmart
149-214, 243-318,





348-412


IPR003599
Immunoglobulin subtype
HMMSmart
143-224, 237-329,





344-425, 38-129,





439-553


IPR007110
Immunoglobulin-like
ProfileScan
230-327, 32-107,





349-404, 428-553









Variant protein HSFLT_PEA—1_P3 is encoded by the following transcript(s): HSFLT_PEA—1_T4. The coding portion of transcript HSFLT_PEA—1_T4 starts at position 315 and ends at position 2015. The transcript also has the following SNPs as listed in Table 102 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSFLT_PEA—1_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 102







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












719
C → T
Yes


823
→ C
No


1063
T → C
No


1165
A → G
No


1325
A → G
No


1342
T → C
No


1495
A → G
No


1533
C → T
No


2083
G → A
No


2424
A →
No


2579
C → T
Yes


2605
C → T
Yes


2997
T →
Yes


3339
G → A
Yes


3524
T → A
Yes


3595
A → G
No


3615
A → G
Yes


3679
A →
No


4443
A → G
Yes


5614
T → C
Yes


5689
T → A
Yes


5716
T → C
Yes


5790
T → G
Yes


5814
G → T
Yes


6293
T → G
Yes









Variant protein HSFLT_PEA—1_P4 (SEQ ID NO:532) is encoded by transcript(s) HSFLT_PEA—1_T5. An alignment is given to the known protein (Vascular endothelial growth factor receptor 1 precursor; SEQ ID NO:530) in FIG. 155. One or more alignments to one or more previously published protein sequences are given in FIGS. 154, 156-160. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSFLT_PEA—1_P4 and VGR1_HUMAN:
1. An isolated chimeric polypeptide HSFLT_PEA—1_P4, comprising a first amino acid sequence being at least 90% homologous to MVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQ CRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGF YSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRV TSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHL YKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSY PDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKS VNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKD GLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNV KPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARC DFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNK corresponding to amino acids 1-517 of VGR1_HUMAN, which also corresponds to amino acids 1-517 of HSFLT_PEA—1_P4, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence LPPANSSFMLPPTSFSSNYFHFLP corresponding to amino acids 518-541 of HSFLT_PEA—1_P4, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSFLT_PEA—1_P4, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence LPPANSSFMLPPTSFSSNYFHFLP in HSFLT_PEA—1_P4.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSFLT_PEA—1_P4 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 103, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSFLT_PEA—1_P4 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 103







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





250
L → P
No


284
Q → R
No


343
V → A
No


394
D → G
No









The glycosylation sites of variant protein HSFLT_PEA—1_P4, as compared to the known protein Vascular endothelial growth factor receptor 1 precursor, are described in Table 104 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 104







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





547
no



474
yes
474


620
no


666
no


597
no


100
yes
100


402
yes
402


323
yes
323


251
yes
251


164
yes
164


417
yes
417


625
no


196
yes
196









The phosphorylation sites of variant protein HSFLT_PEA—1_P4, as compared to the known protein Vascular endothelial growth factor receptor 1 precursor, are described in Table 105 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 105







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





1169
no



1213
no


1053
no


1242
no


1333
no


1327
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 106.







TABLE 106







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR009134
Vascular endothelial
FPrintScan
125-136, 184-194,



growth factor receptor,

242-254, 390-407,



VEGFR

448-462, 89-107


IPR009135
Vascular endothelial
FPrintScan
130-155, 224-247,



growth factor receptor 1,

26-41, 273-290,



VEGFR1

350-370, 375-389,





79-93


IPR007110
Immunoglobulin-like
HMMPfam
151-209, 245-313,





359-404, 447-467,





90-109


IPR003598
Immunoglobulin C-2 type
HMMSmart
149-214, 243-318,





348-412


IPR003599
Immunoglobulin subtype
HMMSmart
143-224, 237-329,





344-425, 38-129


IPR007110
Immunoglobulin-like
ProfileScan
230-327, 32-107,





349-404, 428-467









Variant protein HSFLT_PEA—1_P4 is encoded by HSFLT_PEA—1_T5. The coding portion of transcript HSFLT_PEA—1_T5 starts at position 315 and ends at position 1937. The transcript also has the following SNPs as listed in Table 107 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSFLT_PEA—1_P4 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 107







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












719
C → T
Yes


823
→ C
No


1063
T → C
No


1165
A → G
No


1325
A → G
No


1342
T → C
No


1495
A → G
No


1533
C → T
No


2103
G → A
No


2444
A →
No


2599
C → T
Yes


2625
C → T
Yes


3017
T →
Yes


3359
G → A
Yes


3544
T → A
Yes


3615
A → G
No


3635
A → G
Yes


3699
A →
No


4463
A → G
Yes


5634
T → C
Yes


5709
T → A
Yes


5736
T → C
Yes


5810
T → G
Yes


5834
G → T
Yes


6313
T → G
Yes









Variant protein HSFLT_PEA—1_P10 (SEQ ID NO:533) according to the present invention is encoded by transcript(s) HSFLT_PEA—1_T13. An alignment is given to the known protein (Vascular endothelial growth factor receptor 1 precursor; SEQ ID NO:530) is presented in FIG. 155. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSFLT_PEA—1_P10 and VGR1_HUMAN:
1. An isolated chimeric polypeptide HSFLT_PEA—1_P10, comprising a first amino acid sequence being at least 90% homologous to MVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQ CRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGF YSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRV TSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHL YKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSY PDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKS VNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKD GLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNV KPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARC DFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYIC IASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVT WILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNV YTGEEILQKKEITIRDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWF KNNHKIQQEP corresponding to amino acids 1-705 of VGR1_HUMAN, which also corresponds to amino acids 1-705 of HSFLT_PEA—1_P10, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence ELYTSTSPSSSSSSPLSSSSSSSSSSSS corresponding to amino acids 706-733 of HSFLT_PEA—1_P10, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSFLT_PEA—1_P10, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence ELYTSTSPSSSSSSPLSSSSSSSSSSSS in HSFLT_PEA—1_P10.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSFLT_PEA—1_P10 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 108, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSFLT_PEA—1_P10 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 108







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





250
L → P
No


284
Q → R
No


343
V → A
No


394
D → G
No









The glycosylation sites of variant protein HSFLT_PEA—1_P10, as compared to the known protein Vascular endothelial growth factor receptor 1 precursor, are described in Table 109 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 109







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





547
yes
547


474
yes
474


620
yes
620


666
yes
666


597
yes
597


100
yes
100


402
yes
402


323
yes
323


251
yes
251


164
yes
164


417
yes
417


625
yes
625


196
yes
196









The phosphorylation sites of variant protein HSFLT_PEA—1_P10, as compared to the known protein Vascular endothelial growth factor receptor 1 precursor, are described in Table 110 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 110







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





1169
no



1213
no


1053
no


1242
no


1333
no


1327
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 111.







TABLE 111







InterPro domain(s)










InterPro

Analysis
Position(s) on


ID
Domain description
type
protein





IPR003598
Immunoglobulin C-2
HMMSmart
149-214, 243-318,



type

348-412, 568-643,





673-732


IPR003599
Immunoglobulin
HMMSmart
143-224, 237-329,



subtype

344-425, 38-129,





439-553, 562-658


IPR007110
Immunoglobulin-like
ProfileScan
230-327, 32-107,





349-404, 428-553,





556-654, 661-733


IPR009134
Vascular endothelial
FPrintScan
125-136, 184-194,



growth factor receptor,

242-254, 390-407,



VEGFR

448-462, 89-107


IPR009135
Vascular endothelial
FPrintScan
130-155, 224-247,



growth factor receptor

26-41, 273-290,



1, VEGFR1

350-370, 375-389,





79-93


IPR007110
Immunoglobulin-like
HMMPfam
151-209, 245-313,





359-404, 447-537,





570-638, 675-733,





90-109


IPR003596
Immunoglobulin
HMMSmart
247-313, 572-638



V-type









Variant protein HSFLT_PEA—1_P10 is encoded by HSFLT_PEA—1_T13. The coding portion of transcript HSFLT_PEA—1_T13 starts at position 315 and ends at position 2513. The transcript also has the following SNPs as listed in Table 112 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSFLT_PEA—1_P10 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 112







Nucleic acid SNPs









SNP position on
Alternative nucleic
Previously


nucleotide sequence
acid
known SNP?












719
C → T
Yes


823
→ C
No


1063
T → C
No


1165
A → G
No


1325
A → G
No


1342
T → C
No


1495
A → G
No


1533
C → T
No


2018
G → A
No


2375
C → T
Yes


2656
G →
No


2781
G → A
Yes


3301
G → T
Yes









Variant protein HSFLT_PEA—1_P12 according to the present invention is encoded by transcript(s) HSFLT_PEA—1_T15. An alignment is given to the known protein (Vascular endothelial growth factor receptor 1 precursor) in FIG. 157. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSFLT_PEA—1_P12 and VGR1_HUMAN:
1. An isolated chimeric polypeptide HSFLT_PEA—1_P12, comprising a first amino acid sequence being at least 90% homologous to MVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQ CRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGF YSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRV TSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHL YKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSY PDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKS VNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKD GLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNV KPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARC DFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYIC IASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVT WILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNV YTGEEILQKKEITIRDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWF KNNHKIQQEPG corresponding to amino acids 1-706 of VGR1_HUMAN, which also corresponds to amino acids 1-706 of HSFLT_PEA—1_P12, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence SANTAVNKKTEI corresponding to amino acids 707-718 of HSFLT_PEA—1_P12, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSFLT_PEA—1_P12, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence SANTAVNKKTEI in HSFLT_PEA—1_P12.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
The glycosylation sites of variant protein HSFLT_PEA—1_P12, as compared to the known protein Vascular endothelial growth factor receptor 1 precursor, are described in Table 113 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 113







Glycosylation site(s)









Position(s) on known
Present in
Position in


amino acid sequence
variant protein?
variant protein?





547
yes
547


474
yes
474


620
yes
620


666
yes
666


597
yes
597


100
yes
100


402
yes
402


323
yes
323


251
yes
251


164
yes
164


417
yes
417


625
yes
625


196
yes
196









The phosphorylation sites of variant protein HSFLT_PEA—1_P12, as compared to the known protein Vascular endothelial growth factor receptor 1 precursor, are described in Table 114 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 114







Phosphorylation site(s)









Position(s) on




known amino acid
Present in variant
Position in variant


sequence
protein?
protein?





1169
no



1213
no



1053
no



1242
no



1333
no



1327
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 115.







TABLE 115







InterPro domain(s)










InterPro ID
Domain description
Analysis type
Position(s) on protein





IPR009134
Vascular endothelial
FPrintScan
125-136, 184-194, 242-254,



growth factor receptor,

390-407, 448-462,



VEGFR

89-107


IPR009135
Vascular endothelial
FPrintScan
130-155, 224-247, 26-41,



growth factor receptor 1,

273-290, 350-370, 375-389,



VEGFR1

79-93


IPR007110
Immunoglobulin-like
HMMPfam
151-209, 245-313, 359-404,





447-537, 570-638,





675-702, 90-109


IPR003596
Immunoglobulin V-type
HMMSmart
247-313, 572-638


IPR003598
Immunoglobulin C-2 type
HMMSmart
149-214, 243-318, 348-412,





568-643, 673-716


IPR003599
Immunoglobulin subtype
HMMSmart
143-224, 237-329, 344-425,





38-129, 439-553,





562-658


IPR007110
Immunoglobulin-like
ProfileScan
230-327, 32-107, 349-404,





428-553, 556-654, 661-718









Variant protein HSFLT_PEA—1_P12 is encoded by the following transcript(s): HSFLT_PEA—1_T15. The coding portion of transcript HSFLT_PEA—1_T15 starts at position 315 and ends at position 2468. The transcript also has the following SNPs as listed in Table 116 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSFLT_PEA—1_P12 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 116







Nucleic acid SNPs









SNP position on




nucleotide

Previously known


sequence
Alternative nucleic acid
SNP?












719
C → T
Yes


823
→ C
No


1063
T → C
No


1165
A → G
No


1325
A → G
No


1342
T → C
No


1495
A → G
No


1533
C → T
No


2018
G → A
No


2375
C → T
Yes









Variant protein HSFLT_PEA—1_P13 according to the present invention is encoded by transcript(s) HSFLT_PEA—1_T16. An alignment is given to the known protein (Vascular endothelial growth factor receptor 1 precursor) in FIG. 158. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSFLT_PEA—1_P13 and VGR1_HUMAN:
1. An isolated chimeric polypeptide HSFLT_PEA—1_P13, comprising a first amino acid sequence being at least 90% homologous to MVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQ CRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGF YSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRV TSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHL YKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSY PDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKS VNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKD GLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNV KPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARC DFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYIC IASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVT WILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNV YTGEEILQKKEITIRDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWF KNNHKIQQEPG corresponding to amino acids 1-706 of VGR1_HUMAN, which also corresponds to amino acids 1-706 of HSFLT_PEA—1_P13, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence KRLFFLPFIISHLSSAPLSLNSPVTCFQYV corresponding to amino acids 707-736 of HSFLT_PEA—1_P13, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSFLT_PEA—1_P13, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence KRLFFLPFIISHLSSAPLSLNSPVTCFQYV in HSFLT_PEA— 1_P13.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSFLT_PEA—1_P13 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 117, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSFLT_PEA—1_P13 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 117







Amino acid mutations









SNP position(s)




on amino acid

Previously known


sequence
Alternative amino acid(s)
SNP?





250
L → P
No


284
Q → R
No


343
V → A
No


394
D → G
No


728
S → I
Yes









The glycosylation sites of variant protein HSFLT_PEA—1_P13, as compared to the known protein Vascular endothelial growth factor receptor 1 precursor, are described in Table 1118 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 118







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





547
yes
547


474
yes
474


620
yes
620


666
yes
666


597
yes
597


100
yes
100


402
yes
402


323
yes
323


251
yes
251


164
yes
164


417
yes
417


625
yes
625


196
yes
196









The phosphorylation sites of variant protein HSFLT_PEA—1_P13, as compared to the known protein Vascular endothelial growth factor receptor 1 precursor, are described in Table 119 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 119







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





1169
no



1213
no



1053
no



1242
no



1333
no



1327
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 120.







TABLE 120







InterPro domain(s)










InterPro ID
Domain description
Analysis type
Position(s) on protein





IPR009134
Vascular endothelial
FPrintScan
125-136, 184-194, 242-254,



growth factor receptor,

390-407, 448-462,



VEGFR

89-107


IPR009135
Vascular endothelial
FPrintScan
130-155, 224-247, 26-41,



growth factor receptor 1,

273-290, 350-370, 375-389,



VEGFR1

79-93


IPR007110
Immunoglobulin-like
HMMPfam
151-209, 245-313, 359-404,





447-537, 570-638,





675-734, 90-109


IPR003596
Immunoglobulin V-type
HMMSmart
247-313, 572-638


IPR003598
Immunoglobulin C-2 type
HMMSmart
149-214, 243-318, 348-412,





568-643, 673-725


IPR003599
Immunoglobulin subtype
HMMSmart
143-224, 237-329, 344-425,





38-129, 439-553,





562-658


IPR007110
Immunoglobulin-like
ProfileScan
230-327, 32-107, 349-404,





428-553, 556-654, 661-732









Variant protein HSFLT_PEA—1_P13 is encoded by the following transcript(s): HSFLT_PEA—1_T16. The coding portion of transcript HSFLT_PEA—1_T16 starts at position 315 and ends at position 2522. The transcript also has the following SNPs as listed in Table 121 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSFLT_PEA—1_P13 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 121







Nucleic acid SNPs









SNP position on

Previously known


nucleotide sequence
Alternative nucleic acid
SNP?












719
C → T
Yes


823
→ C
No


1063
T → C
No


1165
A → G
No


1325
A → G
No


1342
T → C
No


1495
A → G
No


1533
C → T
No


2018
G → A
No


2375
C → T
Yes


2497
G → T
Yes


2636
G → A
Yes









Variant protein HSFLT_PEA—1_P14 according to the present invention is encoded by transcript(s) HSFLT_PEA—1_T19. An alignment is given to the known protein (Vascular endothelial growth factor receptor 1 precursor) in FIG. 159. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSFLT_PEA—1_P14 and VGR1_HUMAN:
1. An isolated chimeric polypeptide HSFLT_PEA—1_P14, comprising a first amino acid sequence being at least 90% homologous to MVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQ CRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGF YSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRV TSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHL YKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSY PDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKS VNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKD GLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNV KPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARC DFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNK corresponding to amino acids 1-517 of VGR1_HUMAN, which also corresponds to amino acids 1-517 of HSFLT_PEA—1_P14, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence YLDIRTEEQIFSFIQKTQTLKLTVSCKAAF corresponding to amino acids 518-547 of HSFLT_PEA—1_P14, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSFLT_PEA—1_P14, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence YLDIRTEEQIFSFIQKTQTLKLTVSCKAAF in HSFLT_PEA—1_P14.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSFLT_PEA—1_P14 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 122, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSFLT_PEA—1_P14 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 122







Amino acid mutations









SNP position(s) on

Previously known


amino acid sequence
Alternative amino acid(s)
SNP?





250
L → P
No


284
Q → R
No


343
V → A
No


394
D → G
No









The glycosylation sites of variant protein HSFLT_PEA—1_P14, as compared to the known protein Vascular endothelial growth factor receptor 1 precursor, are described in Table 123 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 123







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





547
no



474
yes
474


620
no



666
no



597
no



100
yes
100


402
yes
402


323
yes
323


251
yes
251


164
yes
164


417
yes
417


625
no



196
yes
196









The phosphorylation sites of variant protein HSFLT_PEA—1_P14, as compared to the known protein Vascular endothelial growth factor receptor 1 precursor, are described in Table 124 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 124







Phosphorylation site(s)









Position(s) on




known amino acid
Present in variant
Position in variant


sequence
protein?
protein?





1169
no



1213
no



1053
no



1242
no



1333
no



1327
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 125.







TABLE 125







InterPro domain(s)










InterPro ID
Domain description
Analysis type
Position(s) on protein





IPR003599
Immunoglobulin subtype
HMMSmart
143-224, 237-329, 344-425,





38-129


IPR007110
Immunoglobulin-like
ProfileScan
230-327, 32-107, 349-404,





428-467


IPR003598
Immunoglobulin C-2 type
HMMSmart
348-412


IPR009134
Vascular endothelial
FPrintScan
125-136, 184-194, 242-254,



growth factor receptor,

390-407, 448-462,



VEGFR

89-107


IPR009135
Vascular endothelial
FPrintScan
130-155, 224-247, 26-41,



growth factor receptor 1,

273-290, 350-370, 375-389,



VEGFR1

79-93


IPR007110
Immunoglobulin-like
HMMPfam
151-209, 245-313, 359-404,





447-467, 90-109


IPR003598
Immunoglobulin C-2 type
HMMSmart
149-214, 243-318









Variant protein HSFLT_PEA—1_P14 is encoded by the following transcript(s): HSFLT_PEA—1_T19. The coding portion of transcript HSFLT_PEA—1_T19 starts at position 315 and ends at position 1955. The transcript also has the following SNPs as listed in Table 126 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSFLT_PEA—1_P14 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 126







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












719
C → T
Yes


823
→ C
No


1063
T → C
No


1165
A → G
No


1325
A → G
No


1342
T → C
No


1495
A → G
No


1533
C → T
No


2465
A → G
Yes









Variant protein HSFLT_PEA—1_P19 according to the present invention is encoded by transcript(s) HSFLT_PEA—1_T25. An alignment is given to the known protein (Vascular endothelial growth factor receptor 1 precursor) in FIG. 160. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSFLT_PEA—1_P19 and VGR1_HUMAN:
1. An isolated chimeric polypeptide HSFLT_PEA—1_P19, comprising a first amino acid sequence being at least 90% homologous to MVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQ CRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGF YSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRV TSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHL YKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSY PDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKS VNTSVHIY corresponding to amino acids 1-329 of VGR1_HUMAN, which also corresponds to amino acids 1-329 of HSFLT_PEA—1_P19, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GKHSSALPTHAMLSNHCRCLCSLNKSVFCWPRVTLS corresponding to amino acids 330-365 of HSFLT_PEA—1_P19, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSFLT_PEA—1_P19, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GKHSSALPTHAMLSNHCRCLCSLNKSVFCWPRVTLS in HSFLT_PEA—1_P19. The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSFLT_PEA—1_P19 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 127, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSFLT_PEA—1_P19 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 127







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





250
L → P
No


284
Q → R
No









The glycosylation sites of variant protein HSFLT_PEA—1_P19, as compared to the known protein Vascular endothelial growth factor receptor 1 precursor, are described in Table 128 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 128







Glycosylation site(s)









Position(s) on




known amino acid
Present in variant
Position in variant


sequence
protein?
protein?





547
no



474
no


620
no


666
no


597
no


100
yes
100


402
no


323
yes
323


251
yes
251


164
yes
164


417
no


625
no


196
yes
196









The phosphorylation sites of variant protein HSFLT_PEA—1_P19, as compared to the known protein Vascular endothelial growth factor receptor 1 precursor, are described in Table 129 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 129







Phosphorylation site(s)









Position(s) on




known amino acid
Present in variant
Position in variant


sequence
protein?
protein?





1169
no



1213
no


1053
no


1242
no


1333
no


1327
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 130.







TABLE 130







InterPro domain(s)










InterPro

Analysis
Position(s) on


ID
Domain description
type
protein





IPR009134
Vascular endothelial
FPrintScan
125-136, 184-194,



growth factor receptor,

242-254, 89-107



VEGFR


IPR009135
Vascular endothelial
FPrintScan
130-155, 224-247,



growth factor

26-41, 273-290,



receptor 1, VEGFR1

79-93


IPR003598
Immunoglobulin
HMMSmart
149-214, 243-318



C-2 type


IPR003599
Immunoglobulin
HMMSmart
143-224, 237-329,



subtype

38-129


IPR007110
Immunoglobulin-like
ProfileScan
230-327, 32-107









Variant protein HSFLT_PEA—1_P19 is encoded by the following transcript(s): HSFLT_PEA—1_T25. The coding portion of transcript HSFLT_PEA—1_T25 starts at position 315 and ends at position 1409. The transcript also has the following SNPs as listed in Table 131 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSFLT_PEA—1_P19 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 131







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












719
C → T
Yes


823
→ C
No


1063
T → C
No


1165
A → G
No









The variants were found to have the following domain structure as shown in FIG. 36.
Example 51
Description for cluster HUMKDRZ
Cluster HUMKDRZ features 2 transcript(s) and 15 segment(s) of interest, the names for which are given in Tables 132 and 133, respectively, the sequences themselves are given in SEQ ID NOs: 538-539; 540-554 and 556-557, for transcripts; segments and proteins, respectively. The selected protein variants are given in Table 134.







TABLE 132







Transcripts of interest










Transcript Name
SEQ ID NO:














HUMKDRZ_T12
538



 



HUMKDRZ_T13
539

















TABLE 133







Segments of interest










Segment Name
SEQ ID NO:














HUMKDRZ_node_0
540



 



HUMKDRZ_node_6
541



 



HUMKDRZ_node_8
542



 



HUMKDRZ_node_10
543



 



HUMKDRZ_node_12
544



 



HUMKDRZ_node_14
545



 



HUMKDRZ_node_18
546



 



HUMKDRZ_node_19
547



 



HUMKDRZ_node_21
548



 



HUMKDRZ_node_23
549



 



HUMKDRZ_node_27
550



 



HUMKDRZ_node_28
551



 



HUMKDRZ_node_2
552



 



HUMKDRZ_node_16
553



 



HUMKDRZ_node_25
554

















TABLE 134







Proteins of interest











SEQ
Protein
Corresponding


Protein Name
ID NO:
Length
Transcript(s)













HUMKDRZ_P8
556
P678
HUMKDRZ_T12


 


HUMKDRZ_P9
557
P469
HUMKDRZ_T13









These sequences are variants of the known protein Vascular endothelial growth factor receptor 2 precursor (SEQ ID NO:555; SwissProt accession identifier VGR2_HUMAN; known also according to the synonyms EC 2.7.1.112; VEGFR-2; Kinase insert domain receptor; Protein-tyrosine kinase receptor Flk-1), referred to herein as the previously known protein.
Protein Vascular endothelial growth factor receptor 2 precursor is known or believed to have the following function(s): RECEPTOR FOR VEGF OR VEGF-C. HAS A TYROSINE-PROTEIN KINASE ACTIVITY. THE VEGF-KINASE LIGAND/RECEPTOR SIGNALING SYSTEM PLAYS A KEY ROLE IN VASCULAR DEVELOPMENT AND REGULATION OF VASCULAR PERMEABILITY. The sequence for protein Vascular endothelial growth factor receptor 2 precursor is given in SEQ ID NO:555, as “Vascular endothelial growth factor receptor 2 precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 135.







TABLE 135







Amino acid mutations for Known Protein








SNP position(s) on amino acid



sequence
Comment











2
Q → E


772
A → T


787
R → G


835
K → N


848
V → E


1347
S → T









Protein Vascular endothelial growth factor receptor 2 precursor localization is believed to be Type I membrane protein.
It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein or of drugs directed to this protein are as follows: Endothelial growth factor receptor kinase inhibitor; Angiogenesis modulator; Endothelial growth factor modulator. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Cardiovascular; Vulnerary; Anticancer; Symptomatic antidiabetic.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: angiogenesis; protein amino acid phosphorylation; transmembrane receptor protein tyrosine kinase signaling pathway, which are annotation(s) related to Biological Process; receptor; vascular endothelial growth factor receptor; ATP binding, which are annotation(s) related to Molecular Function; and integral plasma membrane protein, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
As noted above, cluster HUMKDRZ features 2 transcript(s), which were listed in Table 1 above. These transcript(s) encode for protein(s) which are variant(s) of protein Vascular endothelial growth factor receptor 2 precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HUMKDRZ_P8 according to the present invention is encoded by transcript(s) HUMKDRZ_T12. An alignment is given to the known protein (Vascular endothelial growth factor receptor 2 precursor) in FIG. 161. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMKDRZ_P8 and VGR2_HUMAN:
1. An isolated chimeric polypeptide HUMKDRZ_P8, comprising a first amino acid sequence being at least 90% homologous to MQSKVLLAVALWLCVETRAASVGLPSVSLDLPRLSIQKDILTIKANTTLQITCR GQRDLDWLWPNNQSGSEQRVEVTECSDGLFCKTLTIPKVIGNDTGAYKCFYR ETDLASVIYVYVQDYRSPFIASVSDQHGVVYITENKNKTVVIPCLGSISNLNVS LCARYPEKRFVPDGNRISWDSKKGFTIPSYMISYAGMVFCEAKINDESYQSIM YIVVVVGYRIYDVVLSPSHGIELSVGEKLVLNCTARTELNVGIDFNWEYPSSK HQHKKLVNRDLKTQSGSEMKKFLSTLTIDGVTRSDQGLYTCAASSGLMTKK NSTFVRVHEKPFVAFGSGMESLVEATVGERVRIPAKYLGYPPPEIKWYKNGIP LESNHTIKAGHVLTIMEVSERDTGNYTVILTNPISKEKQSHVVSLVVYVPPQIG EKSLISPVDSYQYGTTQTLTCTVYAIPPPHHIHWYWQLEEECANEPSQAVSVT NPYPCEEWRSVEDFQGGNKIEVNKNQFALIEGKNKTVSTLVIQAANVSALYK CEAVNKVGRGERVISFHVTRGPEITLQPDMQPTEQESVSLWCTADRSTFENLT WYKLGPQPLPIHVGELPTPVCKNLDTLWKLNATMFSNSTNDILIMELKNASL QDQGDYVCLAQDRKTKKRHCVVRQLTVL corresponding to amino acids 1-662 of VGR2_HUMAN, which also corresponds to amino acids 1-662 of HUMKDRZ_P8, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GRETILDHCAEAVGMP corresponding to amino acids 663-678 of HUMKDRZ_P8, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMKDRZ_P8, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GRETILDHCAEAVGMP in HUMKDRZ_P8.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMKDRZ_P8 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 136, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMKDRZ_P8 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 136







Amino acid mutations









SNP position(s) on




amino acid
Alternative amino
Previously known


sequence
acid(s)
SNP?












98
T → A
No


244
L → F
No


268
Q → R
No


297
V → I
Yes


305
Y → H
No


349
R → K
Yes


392
D → N
Yes


472
Q → H
Yes


482
C → R
No


523
N → S
No


636
D → G
No









The glycosylation sites of variant protein HUMKDRZ_P8, as compared to the known protein Vascular endothelial growth factor receptor 2 precursor, are described in Table 137 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 137







Glycosylation site(s)









Position(s) on




known amino
Present in variant
Position in variant


acid sequence
protein?
protein?












619
yes
619


46
yes
46


395
yes
395


66
yes
66


675
no


96
yes
96


580
yes
580


143
yes
143


511
yes
511


318
yes
318


245
yes
245


158
yes
158


523
yes
523


613
yes
613


704
no


631
yes
631


721
no


374
yes
374









The phosphorylation sites of variant protein HUMKDRZ_P8, as compared to the known protein Vascular endothelial growth factor receptor 2 precursor, are described in Table 138 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 138







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in


amino acid sequence
protein?
variant protein?





1059
no










The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 139.







TABLE 139







InterPro domain(s)












Analysis
Position(s)


InterPro ID
Domain description
type
on protein





IPR009134
Vascular endothelial
FPrintScan
115-126, 177-187,



growth factor receptor,

236-248, 383-400,



VEGFR

439-453, 85-103


IPR009136
Vascular endothelial
FPrintScan
186-199, 203-224,



growth factor

449-464, 645-663



receptor 2, VEGFR2


IPR007110
Immunoglobulin-like
HMMPfam
239-309, 345-397,





438-532, 46-105,





564-644


IPR003598
Immunoglobulin
HMMSmart
237-314, 343-405,



C-2 type

436-537, 562-649


IPR003599
Immunoglobulin
HMMSmart
135-218, 231-325,



subtype

337-418, 38-119,





430-548, 556-662


IPR007110
Immunoglobulin-like
ProfileScan
224-320, 328-414,





421-548, 551-660









Variant protein HUMKDRZ_P8 is encoded by the following transcript(s): HUMKDRZ_T12. The coding portion of transcript HUMKDRZ_T12 starts at position 303 and ends at position 2336. The transcript also has the following SNPs as listed in Table 140 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMKDRZ_P8 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 140







Nucleic acid SNPs









SNP position on
Alternative
Previously known


nucleotide sequence
nucleic acid
SNP?












32
G → A
Yes


293
G → T
No


594
A → G
No


1034
A → C
No


1105
A → G
No


1191
G → A
Yes


1215
T → C
No


1226
A → G
No


1348
G → A
Yes


1476
G → A
Yes


1718
A → T
Yes


1746
T → C
No


1870
A → G
No


2209
A → G
No


2419
C → T
Yes









Variant protein HUMKDRZ_P9 according to the present invention is encoded by transcript(s) HUMKDRZ_T13. An alignment is given to the known protein (Vascular endothelial growth factor receptor 2 precursor) in FIG. 162. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMKDRZ_P9 and VGR2_HUMAN:
1. An isolated chimeric polypeptide HUMKDRZ_P9, comprising a first amino acid sequence being at least 90% homologous to MQSKVLLAVALWLCVETRAASVGLPSVSLDLPRLSIQKDILTIKANTTLQITCR GQRDLDWLWPNNQSGSEQRVEVTECSDGLFCKTLTIPKVIGNDTGAYKCFYR ETDLASVIYVYVQDYRSPFIASVSDQHGVVYITENKNKTVVIPCLGSISNLNVS LCARYPEKRFVPDGNRISWDSKKGFTIPSYMISYAGMVFCEAKINDESYQSIM YIVVVVGYRIYDVVLSPSHGIELSVGEKLVLNCTARTELNVGIDFNWEYPSSK HQHKKLVNRDLKTQSGSEMKKFLSTLTIDGVTRSDQGLYTCAASSGLMTKK NSTFVRVHEKPFVAFGSGMESLVEATVGERVRIPAKYLGYPPPEIKWYKNGIP LESNHTIKAGHVLTIMEVSERDTGNYTVILTNPISKEKQSHVVSLVVY corresponding to amino acids 1-418 of VGR2_HUMAN, which also corresponds to amino acids 1-418 of HUMKDRZ_P9, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GESIQFSSLPKIYYDTLSSKSAKPPFLCLLLLHSYHGWACVQKSSGVVKLK corresponding to amino acids 419-469 of HUMKDRZ_P9, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMKDRZ_P9, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GESIQFSSLPKIYYDTLSSKSAKPPFLCLLLLHSYHGWACVQKSSGVVKLK in HUMKDRZ_P9.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMKDRZ_P9 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 141, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMKDRZ_P9 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 141







Amino acid mutations









SNP position(s) on
Alternative amino
Previously known


amino acid sequence
acid(s)
SNP?












98
T → A
No


244
L → F
No


268
Q → R
No


297
V → I
Yes


305
Y → H
No


349
R → K
Yes


392
D → N
Yes









The glycosylation sites of variant protein HUMKDRZ_P9, as compared to the known protein Vascular endothelial growth factor receptor 2 precursor, are described in Table 142 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 142







Glycosylation site(s)









Position(s) on known
Present in
Position in variant


amino acid sequence
variant protein?
protein?












619
no



46
yes
46


395
yes
395


66
yes
66


675
no


96
yes
96


580
no


143
yes
143


511
no


318
yes
318


245
yes
245


158
yes
158


523
no


613
no


704
no


631
no


721
no


374
yes
374









The phosphorylation sites of variant protein HUMKDRZ_P9, as compared to the known protein Vascular endothelial growth factor receptor 2 precursor, are described in Table 143 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 143







Phosphorylation site(s)









Position(s) on known
Present in
Position in variant


amino acid sequence
variant protein?
protein?





1059
no










The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 144.







TABLE 144







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR009134
Vascular endothelial
FPrintScan
115-126, 177-187,



growth factor receptor,

236-248, 383-400,



VEGFR

85-103


IPR009136
Vascular endothelial
FPrintScan
186-199, 203-224



growth factor receptor 2,



VEGFR2


IPR007110
Immunoglobulin-like
HMMPfam
239-309, 345-397,





46-105


IPR003598
Immunoglobulin C-2 type
HMMSmart
237-314, 343-405


IPR003599
Immunoglobulin subtype
HMMSmart
135-218, 231-325,





337-418, 38-119


IPR007110
Immunoglobulin-like
ProfileScan
224-320, 328-414









Variant protein HUMKDRZ_P9 is encoded by the following transcript(s): HUMKDRZ_T13. The coding portion of transcript HUMKDRZ_T13 starts at position 303 and ends at position 1709. The transcript also has the following SNPs as listed in Table 145 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMKDRZ_P9 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 145







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












32
G → A
Yes


293
G → T
No


594
A → G
No


1034
A → C
No


1105
A → G
No


1191
G → A
Yes


1215
T → C
No


1226
A → G
No


1348
G → A
Yes


1476
G → A
Yes


1676
C → T
Yes


1959
G → A
Yes









FIG. 203 presents the domain structure of the variants described hereinabove in comparison to the known or wild-type (WT) protein.
Example 52
Description for Cluster HUMCTLA4B













W.T






 


P678






 


P469













Cluster HUMCTLA4B features 1 transcript(s) and 5 segment(s) of interest, the names for which are given in Tables 146 and 147, respectively, the sequences themselves are given in SEQ ID NOs: 558; 559-563 and 565, for transcript, segments and proteins, respectively. The selected protein variants are given in Table 148.







TABLE 146







Transcripts of interest










Transcript Name
SEQ ID NO:







HUMCTLA4B_PEA_1_T5
558

















TABLE 147







Segments of interest










Segment Name
SEQ ID NO:














HUMCTLA4B_PEA_1 node_0
559



 



HUMCTLA4B_PEA_1_node_4
560



 



HUMCTLA4B_PEA_1_node_10
561



 



HUMCTLA4B_PEA_1_node_13
562



 



HUMCTLA4B_PEA_1_node_1
563

















TABLE 148







Proteins of interest











SEQ
Protein
Corresponding


Protein Name
ID NO:
Length
Transcript(s)





HUMCTLA4B_PEA_1_P3
565
P174
HUMCTLA4B_PEA_1_T5









These sequences are variants of the known protein Cytotoxic T-lymphocyte protein 4 precursor (SEQ ID NO:564; SwissProt accession identifier CTL4_HUMAN; known also according to the synonyms Cytotoxic T-lymphocyte-associated antigen 4; CTLA-4; CD152 antigen), referred to herein as the previously known protein.
Protein Cytotoxic T-lymphocyte protein 4 precursor is known or believed to have the following function(s): Possibly involved in T-cell activation. Binds to B7-1 (CD80) and B7-2 (CD86). The sequence for protein Cytotoxic T-lymphocyte protein 4 precursor is in SEQ ID NO:564, as “Cytotoxic T-lymphocyte protein 4 precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 149.







TABLE 149







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment











17
T → A (in dbSNP: 231775)./



FTId = VAR_013577.


147
T → A









Protein Cytotoxic T-lymphocyte protein 4 precursor localization is believed to be Type I membrane protein.
The previously known protein also has the following indication(s) and/or potential therapeutic use(s): Thrombocytopenic purpura; Transplant rejection, bone marrow. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein are as follows: CD28 antagonist; CTLA4 inhibitor; Immunosuppressant. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Antiviral, anti-HIV; Anticancer; Antipruritic/inflamm, allergic; Immunosuppressant; Multiple sclerosis treatment; Haematological; Neurological; Immunostimulant.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: immune response, which are annotation(s) related to Biological Process; and integral plasma membrane protein, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
As noted above, cluster HUMCTLA4B features 1 transcript(s), which were listed in Table 1 above. These transcript(s) encode for protein(s) which are variant(s) of protein Cytotoxic T-lymphocyte protein 4 precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HUMCTLA4B_PEA—1_P3 according to the present invention is encoded by transcript(s) HUMCTLA4B_PEA—1_T5. An alignment is given to the known protein (Cytotoxic T-lymphocyte protein 4 precursor) in FIG. 163. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMCTLA4B_PEA—1_P3 and CTL4 HUMAN:
1. An isolated chimeric polypeptide HUMCTLA4B_PEA—1_P3, comprising a first amino acid sequence being at least 90% homologous to MACLGFQRHKAQLNLATRTWPCTLLFFLLFIPVFCKAMHVAQPAVVLASSRG IASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNELTFLDDSICT GTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVI corresponding to amino acids 1-152 of CTL4_HUMAN, which also corresponds to amino acids 1-152 of HUMCTLA4B_PEA—1_P3, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence AKEKKPSYNRGLCENAPNRARM corresponding to amino acids 153-174 of HUMCTLA4B_PEA—1_P3, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMCTLA4B_PEA—1_P3, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence AKEKKPSYNRGLCENAPNRARM in HUMCTLA4B_PEA—1_P3.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMCTLA4B_PEA—1_P3 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 150, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMCTLA4B_PEA—1_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 150







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





17
T → A
Yes


91
M → T
Yes









The glycosylation sites of variant protein HUMCTLA4B_PEA—1_P3, as compared to the known protein Cytotoxic T-lymphocyte protein 4 precursor, are described in Table 151 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 151







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





113
yes
113









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 152.







TABLE 152







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR008096
Cytotoxic T-
FPrintScan
110-122, 17-34,



lymphocyte

36-62, 78-92



antigen 4


IPR003596
Immunoglobulin
HMMSmart
53-131



V-type


IPR003599
Immunoglobulin
HMMSmart
43-152



subtype









Variant protein HUMCTLA4B_PEA—1_P3 is encoded by the following transcript(s): HUMCTLA4B_PEA—1_T5. The coding portion of transcript HUMCTLA4B_PEA—1_T5 starts at position 420 and ends at position 941. The transcript also has the following SNPs as listed in Table 153 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMCTLA4B_PEA—1_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 153







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












101
C → T
Yes


414
A →
No


415
A → T
No


468
A → G
Yes


691
T → C
Yes


1005
C →
No


1006
C → A
No


1356
G → A
Yes









Example 53
Description for Cluster HSTNFR1A
Cluster HSTNFR1A features 13 transcript(s) and 52 segment(s) of interest, the names for which are given in Tables 154 and 155, respectively, the sequences themselves are given in SEQ ID NOs: 566-578; 579-630 and 632-639, for transcripts, segments and proteins, respectively. The selected protein variants are given in Table 156.







TABLE 154







Transcripts of interest










Transcript Name
SEQ ID NO:







HSTNFR1A_PEA_1_T8
566



 



HSTNFR1A_PEA_1_T9
567



 



HSTNFR1A_PEA_1_T12
568



 



HSTNFR1A_PEA_1_T13
569



 



HSTNFR1A_PEA_1_T15
570



 



HSTNFR1A_PEA_1_T18
571



 



HSTNFR1A_PEA_1_T20
572



 



HSTNFR1A_PEA_1_T25
573



 



HSTNFR1A_PEA_1_T26
574



 



HSTNFR1A_PEA_1_T28
575



 



HSTNFR1A_PEA_1_T29
576



 



HSTNFR1A_PEA_1_T30
577



 



HSTNFR1A_PEA_1_T37
578

















TABLE 155







Segments of interest










Segment Name
SEQ ID NO:







HSTNFR1A_PEA_1_node_12
579



 



HSTNFR1A_PEA_1_node_40
580



 



HSTNFR1A_PEA_1_node_42
581



 



HSTNFR1A_PEA_1_node_47
582



 



HSTNFR1A_PEA_1_node_49
583



 



HSTNFR1A_PEA_1_node_77
584



 



HSTNFR1A_PEA_1_node_81
585



 



HSTNFR1A_PEA_1_node_11
586



 



HSTNFR1A_PEA_1_node_13
587



 



HSTNFR1A_PEA_1_node_14
588



 



HSTNFR1A_PEA_1_node_15
589



 



HSTNFR1A_PEA_1_node_26
590



 



HSTNFR1A_PEA_1_node_27
591



 



HSTNFR1A_PEA_1_node_28
592



 



HSTNFR1A_PEA_1_node_29
593



 



HSTNFR1A_PEA_1_node_32
594



 



HSTNFR1A_PEA_1_node_33
595



 



HSTNFR1A_PEA_1_node_34
596



 



HSTNFR1A_PEA_1_node_35
597



 



HSTNFR1A_PEA_1_node_36
598



 



HSTNFR1A_PEA_1_node_38
599



 



HSTNFR1A_PEA_1_node_39
600



 



HSTNFR1A_PEA_1_node_41
601



 



HSTNFR1A_PEA_1_node_44
602



 



HSTNFR1A_PEA_1_node_45
603



 



HSTNFR1A_PEA_1_node_46
604



 



HSTNFR1A_PEA_1_node_48
605



 



HSTNFR1A_PEA_1_node_50
606



 



HSTNFR1A_PEA_1_node_51
607



 



HSTNFR1A_PEA_1_node_52
608



 



HSTNFR1A_PEA_1_node_55
609



 



HSTNFR1A_PEA_1_node_58
610



 



HSTNFR1A_PEA_1_node_59
611



 



HSTNFR1A_PEA_1_node_60
612



 



HSTNFR1A_PEA_1_node_61
613



 



HSTNFR1A_PEA_1_node_62
614



 



HSTNFR1A_PEA_1_node_63
615



 



HSTNFR1A_PEA_1_node_64
616



 



HSTNFR1A_PEA_1_node_65
617



 



HSTNFR1A_PEA_1_node_66
618



 



HSTNFR1A_PEA_1_node_67
619



 



HSTNFR1A_PEA_1_node_68
620



 



HSTNFR1A_PEA_1_node_70
621



 



HSTNFR1A_PEA_1_node_71
622



 



HSTNFR1A_PEA_1_node_72
623



 



HSTNFR1A_PEA_1_node_73
624



 



HSTNFR1A_PEA_1_node_74
625



 



HSTNFR1A_PEA_1_node_75
626



 



HSTNFR1A_PEA_1_node_76
627



 



HSTNFR1A_PEA_1_node_78
628



 



HSTNFR1A_PEA_1_node_79
629



 



HSTNFR1A_PEA_1_node_80
630

















TABLE 156







Proteins of interest














Corresponding



Protein Name
SEQ ID NO:
Protein Length
Transcript(s)





HSTNFR1A_PEA_1_P11
632
P291
HSTNFR1A_PEA_1_T13



 


HSTNFR1A_PEA_1_P15
633
P228
HSTNFR1A_PEA_1_T18


 


HSTNFR1A_PEA_1_P19
634
P404
HSTNFR1A_PEA_1_T25


 


HSTNFR1A_PEA_1_P20
635
P218
HSTNFR1A_PEA_1_T8;





HSTNFR1A_PEA_1_T9;





HSTNFR1A_PEA_1_T12;





HSTNFR1A_PEA_1_T15;





HSTNFR1A_PEA_1_T20;





HSTNFR1A_PEA_1_T26


 


HSTNFR1A_PEA_1_P22
636
P247
HSTNFR1A_PEA_1_T28


 


HSTNFR1A_PEA_1_P23
637
P242
HSTNFR1A_PEA_1_T29


 


HSTNFR1A_PEA_1_P24
638
P219
HSTNFR1A_PEA_1_T30


 


HSTNFR1A_PEA_1_P28
639
P184
HSTNFR1A_PEA_1_T37









These sequences are variants of the known protein Tumor necrosis factor receptor superfamily member 1A precursor (SEQ ID NO:631; SwissProt accession identifier TR1A_HUMAN; known also according to the synonyms p60; TNF-R1; TNF-RI; p55; CD120a; TBPI), referred to herein as the previously known protein.
Protein Tumor necrosis factor receptor superfamily member 1A precursor is known or believed to have the following function(s): Receptor for TNFSF2/TNF-alpha and homotrimeric TNFSF1/lymphotoxin-alpha. The adaptor molecule FADD recruits caspase-8 to the activated receptor. The resulting death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation which initiates the subsequent cascade of caspases (aspartate-specific cysteine proteases) mediating apoptosis. Contributes to the induction of noncytocidal TNF effects including anti-viral state and activation of the acid sphingomyelinase. The sequence for protein Tumor necrosis factor receptor superfamily member 1A precursor is given in SEQ ID NO: 631, as “Tumor necrosis factor receptor superfamily member 1A precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 157.







TABLE 157







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment











59
C → R (in FHF)./FTId = VAR_013410.


62
C → Y (in FHF)./FTId = VAR_013411.


79
T → M (in FHF)./FTId = VAR_013412.


81
C → F (in FHF)./FTId = VAR_013413.


117
C → R (in FHF)./FTId = VAR_013414.


117
C → Y (in FHF)./FTId = VAR_013415.


305
P → T (in dbSNP: 1804532)./FTId =



VAR_011813.


412
Missing


443-446
GPAA → APP









Protein Tumor necrosis factor receptor superfamily member 1A precursor localization is believed to be Type I membrane protein and secreted.
The previously known protein also has the following indication(s) and/or potential therapeutic use(s): Infection, hepatitis-C virus; Ankylosing spondylitis; Arthritis, rheumatoid; Asthma; Chronic obstructive pulmonary disease; Diabetes; Fibrosis, pulmonary; Granulomatous disease; Psoriasis; Uveitis; Arthritis, psoriatic; Multiple sclerosis; Sepsis. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein or of drugs directed against this protein are as follows: Tumour necrosis factor modulator; Tumour necrosis factor alpha modulator. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Immunosuppressant; Antidiabetic; Antipsoriasis; Immunomodulator, anti-infective; Antiasthma; Ophthalmological; COPD treatment; Antiarthritic, Septic shock treatment; Multiple sclerosis treatment; Antiarthritic; Anticancer; Cytokine; Cardiovascular.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: apoptosis; signal transduction, which are annotation(s) related to Biological Process; receptor; tumor necrosis factor receptor, type I, which are annotation(s) related to Molecular Function; and extracellular; integral plasma membrane protein, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
This protein is one of the major receptors for the tumor necrosis factor-alpha. TNF is produced by T-cells and activated macrophages in response to infection, by ligating TNFR1.
This protein is a type I membrane protein that is secreted. The soluble form is produced from the membrane form by proteolytic processing. Binding of TNF to the extracellular domain leads to homotrimerization. This complex activates at least two distinct signaling cascades, apoptosis and NF-kappa-B signaling.
Germline mutations of the extracellular domains of this receptor were found to be associated with the autosomal dominant periodic fever syndrome.
As noted above, cluster HSTNFR1A features 13 transcript(s), which were listed in Table 1 above. These transcript(s) encode for protein(s) which are variant(s) of protein Tumor necrosis factor receptor superfamily member 1A precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HSTNFR1A_PEA—1_P11 according to the present invention is encoded by transcript(s) HSTNFR1A_PEA—1_T13. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 1A precursor) in FIG. 164. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSTNFR1A_PEA—1_P11 and TR1A_HUMAN:
1. An isolated chimeric polypeptide HSTNFR1A_PEA—1_P11, comprising a first amino acid sequence being at least 90% homologous to MGLSTVPDLLLPLVLLELLVGIYPSGVIGLVPHLGDREKRDSVCPQGKYIHPQ NNSICCTKCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLRHCLSCSKCR KEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLS C corresponding to amino acids 1-158 of 1A_HUMAN, which also corresponds to amino acids 1-158 of HSTNFR1A_PEA—1_P11, a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence ERSSPEAKPSPHPRGWPLPHAVALPFLPPPVFCGSDNQLLSGRPHPVPRHFLCP VGWGCRRFSFSCAALLPTG corresponding to amino acids 159-231 of HSTNFR1A_PEA—1_P11, a third amino acid sequence being at least 90% homologous to QEKQNTVCTCHAGFFLRENECVSCS corresponding to amino acids 159-183 of TR1A_HUMAN, which also corresponds to amino acids 232-256 of HSTNFR1A_PEA—1_P11, and a fourth amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence KVLLCRPGWNAVARSRLTATSASQIQAILLLQPPK corresponding to amino acids 257-291 of HSTNFR1A_PEA—1_P11, wherein said first amino acid sequence, second amino acid sequence, third amino acid sequence and fourth amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for an edge portion of HSTNFR1A_PEA—1_P11, comprising an amino acid sequence being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence encoding for ERSSPEAKPSPHPRGWPLPHAVALPFLPPPVFCGSDNQLLSGRPHPVPRHFLCP VGWGCRRFSFSCAALLPTG, corresponding to HSTNFR1A_PEA—1_P11.
3. An isolated polypeptide for a tail of HSTNFR1A_PEA—1_P11, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence KVLLCRPGWNAVARSRLTATSASQIQAILLLQPPK in HSTNFR1A_PEA—1_P11.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSTNFR1A_PEA—1_P11 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 158, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P11 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 158







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












45
P → S
No


75
P → L
Yes


121
R → Q
Yes


179
A → V
Yes


185
L → R
Yes


220
F → S
Yes


223
S → N
Yes









The glycosylation sites of variant protein HSTNFR1A_PEA—1_P11, as compared to the known protein Tumor necrosis factor receptor superfamily member 1A precursor, are described in Table 159 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 159







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












54
yes
54


151
yes
151


145
yes
145









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 160.







TABLE 160







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR001368
TNFR/CD27/30/40/
HMMPfam
44-81, 84-125



95 cysteine-rich



region


IPR001368
TNFR/CD27/30/40/
HMMSmart
127-165, 241-269,



95 cysteine-rich

44-81, 84-125



region


IPR000345
Cytochrome c heme-
ScanRegExp
59-64



binding site


IPR001368
TNFR/CD27/30/40/
ScanRegExp
44-81, 84-125



95 cysteine-rich



region


IPR006209
EGF-like domain
ScanRegExp
239-252


IPR001368
TNFR/CD27/30/40/
ProfileScan
43-81, 83-125



95 cysteine-rich



region









Variant protein HSTNFR1A_PEA—1_P11 is encoded by the following transcript(s): HSTNFR1A_PEA—1_T13. The coding portion of transcript HSTNFR1A_PEA—1_T13 starts at position 282 and ends at position 1154. The transcript also has the following SNPs as listed in Table 161 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P11 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 161







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












102
T →
No


267
C → T
No


317
A → G
Yes


414
C → T
No


505
C → T
Yes


643
G → A
Yes


817
C → T
Yes


835
T → G
Yes


940
T → C
Yes


949
G → A
Yes


1526
A → G
Yes


1703
A → T
Yes


2363
C →
No


2480
C → A
Yes


2867
C → T
Yes


2943
C →
No


3130
G → A
Yes


3268
G → A
Yes


3470
A → T
Yes









Variant protein HSTNFR1A_PEA—1_P15 according to the present invention is encoded by transcript(s) HSTNFR1A_PEA—1_T18. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 1A precursor) in FIG. 165. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSTNFR1A_PEA—1_P15 and TR1A_HUMAN:
1. An isolated chimeric polypeptide HSTNFR1A_PEA—1_P15, comprising a first amino acid sequence being at least 90% homologous to MGLSTVPDLLLPLVLLELLVGIYPSGVIGLVPHLGDREKRDSVCPQGKYIHPQ NNSICCTKCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLRHCLSCSKCR KEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLS CQEKQNTVCTCHAGFFLRENECVSCS corresponding to amino acids 1-183 of TR1A_HUMAN, which also corresponds to amino acids 1-183 of HSTNFR1A_PEA—1_P15, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence KHHSAVAPGHFLWSLPFIPPLHWFNVSLPTVEVQALLHCLWEIDT corresponding to amino acids 184-228 of HSTNFR1A_PEA—1_P15, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSTNFR1A_PEA—1_P15, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence KHHSAVAPGHFLWSLPFIPPLHWFNVSLPTVEVQALLHCLWEIDT in HSTNFR1A_PEA—1_P15.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSTNFR1A_PEA—1_P15 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 162, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P15 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 162







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












45
P → S
No


75
P → L
Yes


121
R → Q
Yes









The glycosylation sites of variant protein HSTNFR1A_PEA—1_P15, as compared to the known protein Tumor necrosis factor receptor superfamily member 1A precursor, are described in Table 163 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 163







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












54
yes
54


151
yes
151


145
yes
145









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 164.







TABLE 164







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR001368
TNFR/CD27/30/40/
HMMPfam
127-166, 44-81,



95 cysteine-rich

84-125



region


IPR001368
TNFR/CD27/30/40/
HMMSmart
127-166, 44-81,



95 cysteine-rich

84-125



region


IPR000345
Cytochrome c heme-
ScanRegExp
59-64



binding site


IPR001368
TNFR/CD27/30/40/
ScanRegExp
127-166, 44-81,



95 cysteine-rich

84-125



region


IPR006209
EGF-like domain
ScanRegExp
166-179


IPR001368
TNFR/CD27/30/40/
ProfileScan
126-166, 43-81,



95 cysteine-rich

83-125



region









Variant protein HSTNFR1A_PEA—1_P15 is encoded by the following transcript(s): HSTNFR1A_PEA—1_T18. The coding portion of transcript HSTNFR1A_PEA—1_T18 starts at position 282 and ends at position 965. The transcript also has the following SNPs as listed in Table 165 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P15 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 165







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












102
T →
No


267
C → T
No


317
A → G
Yes


414
C → T
No


505
C → T
Yes


643
G → A
Yes


1003
C →
No


1120
C → A
Yes


1507
C → T
Yes


1583
C →
No


1770
G → A
Yes


1908
G → A
Yes


2110
A → T
Yes









Variant protein HSTNFR1A_PEA—1_P19 according to the present invention is encoded by transcript(s) HSTNFR1A_PEA—1_T25. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 1A precursor) in FIG. 166. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSTNFR1A_PEA—1_P19 and TR1A_HUMAN:
1. An isolated chimeric polypeptide HSTNFR1A_PEA—1_P19, comprising a first amino acid sequence being at least 90% homologous to MGLSTVPDLLLPLVLLELLVGIYPSGVIGLVPHLGDREKRDSVCPQGKYIHPQ NNSICCTKCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLRHCLSCSKCR KEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLS CQEKQNTVCTCHAGFFLRENECVSCSNCKKSLECTKLCLPQIENVKGTEDSGT TVLL corresponding to amino acids 1-214 of TR1A_HUMAN, which also corresponds to amino acids 1-214 of HSTNFR1A_PEA—1_P19, and a second amino acid sequence being at least 90% homologous to PLAPNPSFSPTPGFTPTLGFSPVPSSTFTSSSTYTPGDCPNFAAPRREVAPPYQG ADPILATALASDPIPNPLQKWEDSAHKPQSLDTDDPATLYAVVENVPPLRWK EFVRRLGLSDHEIDRLELQNGRCLREAQYSMLATWRRRTPRREATLELLGRV LRDMDLLGCLEDIEEALCGPAALPPAPSLLR corresponding to amino acids 266-455 of TR1A_HUMAN, which also corresponds to amino acids 215-404 of HSTNFR1A_PEA—1_P19, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric edge portion of HSTNFR1A_PEA—1_P19, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise LP, having a structure as follows: a sequence starting from any of amino acid numbers 214-x to 214; and ending at any of amino acid numbers 215+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSTNFR1A_PEA—1_P19 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 166, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P19 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 166







Amino acid mutations









SNP position(s)




on amino


acid sequence
Alternative amino acid(s)
Previously known SNP?












45
P → S
No


75
P → L
Yes


121
R → Q
Yes


254
P → T
Yes









glycosylation sites of variant protein HSTNFR1A_PEA—1_P19, as compared to the known protein Tumor necrosis factor receptor superfamily member 1A precursor, are described in Table 167 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 167







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












54
yes
54


151
yes
151


145
yes
145









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 168.







TABLE 168







InterPro domain(s)












Analysis
Position(s)


InterPro ID
Domain description
type
on protein





IPR001368
TNFR/CD27/30/40/95
HMMPfam
127-166, 44-81,



cysteine-rich region

84-125


IPR000488
Death domain
HMMPfam
306-390


IPR000488
Death domain
HMMSmart
294-390


IPR001368
TNFR/CD27/30/40/95
HMMSmart
127-166, 168-195,



cysteine-rich region

44-81, 84-125


IPR000345
Cytochrome c heme-
ScanRegExp
59-64



binding site


IPR001368
TNFR/CD27/30/40/95
ScanRegExp
127-166, 44-81,



cysteine-rich region

84-125


IPR006209
EGF-like domain
ScanRegExp
166-179


IPR000488
Death domain
ProfileScan
305-390


IPR001368
TNFR/CD27/30/40/95
ProfileScan
126-166, 43-81,



cysteine-rich region

83-125









Variant protein HSTNFR1A_PEA—1_P19 is encoded by the following transcript(s): HSTNFR1A_PEA—1_T25. The coding portion of transcript HSTNFR1A_PEA—1_T25 starts at position 282 and ends at position 1493. The transcript also has the following SNPs as listed in Table 169 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P19 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 169







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












102
T →
No


267
C → T
No


317
A → G
Yes


414
C → T
No


505
C → T
Yes


643
G → A
Yes


1041
C → A
Yes


1428
C → T
Yes


1504
C →
No


1691
G → A
Yes


1829
G → A
Yes


2031
A → T
Yes









Variant protein HSTNFR1A_PEA—1_P20 according to the present invention is encoded by transcript(s) HSTNFR1A_PEA—1_T8, HSTNFR1A_PEA—1_T9, HSTNFR1A_PEA—1_T12, HSTNFR1A_PEA—1_T15, HSTNFR1A_PEA—1_T20 and HSTNFR1A_PEA—1_T26. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 1A precursor) in FIG. 167. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSTNFR1A_PEA—1_P20 and TR1A_HUMAN:
1. An isolated chimeric polypeptide HSTNFR1A_PEA—1_P20, comprising a first amino acid sequence being at least 90% homologous to MGLSTVPDLLLPLVLLELLVGIYPSGVIGLVPHLGDREKRDSVCPQGKYIHPQ NNSICCTKCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLRHCLSCSKCR KEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLS CQEKQNTVCTCHAGFFLRENECVSCS corresponding to amino acids 1-183 of TR1A_HUMAN, which also corresponds to amino acids 1-183 of HSTNFR1A_PEA—1_P20, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence KVLLCRPGWNAVARSRLTATSASQIQAILLLQPPK corresponding to amino acids 184-218 of HSTNFR1A_PEA—1_P20, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSTNFR1A_PEA—1_P20, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence KVLLCRPGWNAVARSRLTATSASQIQAILLLQPPK in HSTNFR1A_PEA—1_P20.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSTNFR1A_PEA—1_P20 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 170, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P20 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 170







Amino acid mutations









SNP position(s)




on amino


acid sequence
Alternative amino acid(s)
Previously known SNP?












45
P → S
No


75
P → L
Yes


121
R → Q
Yes









The glycosylation sites of variant protein HSTNFR1A_PEA—1_P20, as compared to the known protein Tumor necrosis factor receptor superfamily member 1A precursor, are described in Table 171 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 171







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












54
yes
54


151
yes
151


145
yes
145









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 172.







TABLE 172







InterPro domain(s)












Analysis
Position(s)


InterPro ID
Domain description
type
on protein





IPR001368
TNFR/CD27/30/40/95
HMMPfam
127-166, 44-81,



cysteine-rich region

84-125


IPR001368
TNFR/CD27/30/40/95
HMMSmart
127-166, 168-196,



cysteine-rich region

44-81, 84-125


IPR000345
Cytochrome c heme-
ScanRegExp
59-64



binding site


IPR001368
TNFR/CD27/30/40/95
ScanRegExp
127-166, 44-81,



cysteine-rich region

84-125


IPR006209
EGF-like domain
ScanRegExp
166-179


IPR001368
TNFR/CD27/30/40/95
ProfileScan
126-166, 43-81,



cysteine-rich region

83-125









Variant protein HSTNFR1A_PEA—1_P20 is encoded by the following transcript(s): HSTNFR1A_PEA—1_T8, HSTNFR1A_PEA—1_T9, HSTNFR1A_PEA—1_T12, HSTNFR1A_PEA—1_T15 and HSTNFR1A_PEA—1_T20.
The coding portion of transcript HSTNFR1A_PEA—1_T8 starts at position 282 and ends at position 935. The transcript also has the following SNPs as listed in Table 173 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P20 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 173







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












102
T →
No


267
C → T
No


317
A → G
Yes


414
C → T
No


505
C → T
Yes


643
G → A
Yes


1195
C →
No


1312
C → A
Yes


1699
C → T
Yes


1775
C →
No


1962
G → A
Yes


2100
G → A
Yes


2302
A → T
Yes









The coding portion of transcript HSTNFR1A_PEA—1_T9 starts at position 282 and ends at position 935. The transcript also has the following SNPs as listed in Table 174 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P20 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 174







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












102
T →
No


267
C → T
No


317
A → G
Yes


414
C → T
No


505
C → T
Yes


643
G → A
Yes


1307
A → G
Yes


1484
A → T
Yes


2144
C →
No


2261
C → A
Yes


2648
C → T
Yes


2724
C →
No


2911
G → A
Yes


3049
G → A
Yes


3251
A → T
Yes









The coding portion of transcript HSTNFR1A_PEA—1_T12 starts at position 282 and ends at position 935. The transcript also has the following SNPs as listed in Table 175 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P20 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 175







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












102
T →
No


267
C → T
No


317
A → G
Yes


414
C → T
No


505
C → T
Yes


643
G → A
Yes


1307
A → G
Yes


1484
A → T
Yes


1983
G → A
Yes


2086
C → T
Yes


2285
C →
No


2402
C → A
Yes


2789
C → T
Yes


2865
C →
No


3052
G → A
Yes


3190
G → A
Yes


3392
A → T
Yes









The coding portion of transcript HSTNFR1A_PEA—1_T15 starts at position 282 and ends at position 935. The transcript also has the following SNPs as listed in Table 176 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P20 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 176







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












102
T →
No


267
C → T
No


317
A → G
Yes


414
C → T
No


505
C → T
Yes


643
G → A
Yes


1199
C →
No


1316
C → A
Yes


1703
C → T
Yes


1779
C →
No


1966
G → A
Yes


2104
G → A
Yes


2306
A → T
Yes









The coding portion of transcript HSTNFR1A_PEA—1_T20 starts at position 282 and ends at position 935. The transcript also has the following SNPs as listed in Table 177 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P20 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 177







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












102
T →
No


267
C → T
No


317
A → G
Yes


414
C → T
No


505
C → T
Yes


643
G → A
Yes


1121
C →
No


1238
C → A
Yes


1625
C → T
Yes


1701
C →
No


1888
G → A
Yes


2026
G → A
Yes


2228
A → T
Yes









Variant protein HSTNFR1A_PEA—1_P20 is encoded by the following transcript(s): HSTNFR1A_PEA—1_T26. The coding portion of transcript HSTNFR1A_PEA—1_T26 starts at position 282 and ends at position 935. The transcript also has the following SNPs as listed in Table 178 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P20 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 178







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












102
T →
No


267
C → T
No


317
A → G
Yes


414
C → T
No


505
C → T
Yes


643
G → A
Yes


1195
C →
No


1275
C → A
Yes


1662
C → T
Yes


1738
C →
No


1925
G → A
Yes


2063
G → A
Yes


2265
A → T
Yes









Variant protein HSTNFR1A_PEA—1_P22 according to the present invention is encoded by transcript(s) HSTNFR1A_PEA—1_T28. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 1A precursor) in FIG. 168. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSTNFR1A_PEA—1_P22 and TR1A_HUMAN:
1. An isolated chimeric polypeptide HSTNFR1A_PEA—1_P22, comprising a first amino acid sequence being at least 90% homologous to MGLSTVPDLLLPLVLLELLVGIYPSGVIGLVPHLGDREKRDSVCPQGKYIHPQ NNSICCTKCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLRHCLSCSKCR KEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLS CQEKQNTVCTCHAGFFLRENECVSCSNCKKSLECTKLCLPQIENVKGTEDS corresponding to amino acids 1-208 of TR1A_HUMAN, which also corresponds to amino acids 1-208 of HSTNFR1A_PEA—1_P22, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence ERWHHPIRGLTPSLRQPSPPTPSPTPFRSGRTAPTSHRA corresponding to amino acids 209-247 of HSTNFR1A_PEA—1_P22, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSTNFR1A_PEA—1_P22, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence ERWHHPIRGLTPSLRQPSPPTPSPTPFRSGRTAPTSHRA in HSTNFR1A_PEA—1_P22.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSTNFR1A_PEA—1_P22 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 179, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P22 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 179







Amino acid mutations









SNP position(s)




on amino


acid sequence
Alternative amino acid(s)
Previously known SNP?












45
P → S
No


75
P → L
Yes


121
R → Q
Yes









The glycosylation sites of variant protein HSTNFR1A_PEA—1_P22, as compared to the known protein Tumor necrosis factor receptor superfamily member 1A precursor, are described in Table 180 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 180







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












54
yes
54


151
yes
151


145
yes
145









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 181.








TABLE 181







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR001368
TNFR/CD27/30/40/
HMMPfam
127-166, 44-81,



95 cysteine-rich

84-125



region


IPR001368
TNFR/CD27/30/40/
HMMSmart
127-166, 168-195,



95 cysteine-rich

44-81, 84-125



region


IPR000345
Cytochrome c heme-
ScanRegExp
59-64



binding site


IPR001368
TNFR/CD27/30/40/
ScanRegExp
127-166, 44-81,



95 cysteine-rich

84-125



region


IPR006209
EGF-like domain
ScanRegExp
166-179


IPR001368
TNFR/CD27/30/40/
ProfileScan
126-166, 43-81,



95 cysteine-rich

83-125



region









Variant protein HSTNFR1A_PEA—1_P22 is encoded by the following transcript(s): HSTNFR1A_PEA—1_T28. The coding portion of transcript HSTNFR1A_PEA—1_T28 starts at position 282 and ends at position 1022. The transcript also has the following SNPs as listed in Table 182 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P22 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 182







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












102
T →
No


267
C → T
No


317
A → G
Yes


414
C → T
No


505
C → T
Yes


643
G → A
Yes


1271
C → T
Yes


1347
C →
No


1534
G → A
Yes


1672
G → A
Yes


1874
A → T
Yes









Variant protein HSTNFR1A_PEA—1_P23 according to the present invention is encoded by transcript(s) HSTNFR1A_PEA—1_T29. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 1A precursor) in FIG. 169. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSTNFR1A_PEA—1_P23 and TR1A_HUMAN:
1. An isolated chimeric polypeptide HSTNFR1A_PEA—1_P23, comprising a first amino acid sequence being at least 90% homologous to MGLSTVPDLLLPLVLLELLVGIYPSGVIGLVPHLGDREKRDSVCPQGKYIHPQ NNSICCTKCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLRHCLSCSKCR KEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLS CQEKQNTVCTCHAGFFLRENECVSCS corresponding to amino acids 1-183 of TR1A_HUMAN, which also corresponds to amino acids 1-183 of HSTNFR1A_PEA—1_P23, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence KVLLCRPGWNAVARSRLTATSASQIQAILLLQPPKLHPHPGLQSRAQFHLHLQ LHLYPR corresponding to amino acids 184-242 of HSTNFR1A_PEA—1_P23, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSTNFR1A_PEA—1_P23, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence KVLLCRPGWNAVARSRLTATSASQIQAILLLQPPKLHPHPGLQSRAQFHLHLQ LHLYPR in HSTNFR1A_PEA—1_P23.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSTNFR1A_PEA—1_P23 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 183, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P23 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 183







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












45
P → S
No


75
P → L
Yes


121
R → Q
Yes









The glycosylation sites of variant protein HSTNFR1A_PEA—1_P23, as compared to the known protein Tumor necrosis factor receptor superfamily member 1A precursor, are described in Table 184 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 184







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












54
yes
54


151
yes
151


145
yes
145









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 185.







TABLE 185







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR001368
TNFR/CD27/30/40/
HMMPfam
127-166, 44-81,



95 cysteine-rich

84-125



region


IPR001368
TNFR/CD27/30/40/
HMMSmart
127-166, 168-196,



95 cysteine-rich

44-81, 84-125



region


IPR000345
Cytochrome c heme-
ScanRegExp
59-64



binding site


IPR001368
TNFR/CD27/30/40/
ScanRegExp
127-166, 44-81,



95 cysteine-rich

84-125



region


IPR006209
EGF-like domain
ScanRegExp
166-179


IPR001368
TNFR/CD27/30/40/
ProfileScan
126-166, 43-81,



95 cysteine-rich

83-125



region









Variant protein HSTNFR1A_PEA—1_P23 is encoded by the following transcript(s): HSTNFR1A_PEA—1_T29. The coding portion of transcript HSTNFR1A_PEA—1_T29 starts at position 282 and ends at position 1007. The transcript also has the following SNPs as listed in Table 186 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P23 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 186







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












102
T →
No


267
C → T
No


317
A → G
Yes


414
C → T
No


505
C → T
Yes


643
G → A
Yes


1015
C → A
Yes


1402
C → T
Yes


1478
C →
No


1665
G → A
Yes


1803
G → A
Yes


2005
A → T
Yes









Variant protein HSTNFR1A_PEA—1_P24 according to the present invention is encoded by transcript(s) HSTNFR1A_PEA—1_T30. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 1A precursor) in FIG. 170. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSTNFR1A_PEA—1_P24 and TR1A_HUMAN:
1. An isolated chimeric polypeptide HSTNFR1A_PEA—1_P24, comprising a first amino acid sequence being at least 90% homologous to MGLSTVPDLLLPLVLLELLVGIYPSGVIGLVPHLGDREKRDSVCPQGKYIHPQ NNSICCTKCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLRHCLSCSKCR KEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLS CQEKQNTVCTCHAGFFLRENECVSCSNCKKSLECTKLCLPQIENVKGTEDSGT TVLLPLV corresponding to amino acids 1-217 of TR1A_HUMAN, which also corresponds to amino acids 1-217 of HSTNFR1A_PEA—1_P24, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence RP corresponding to amino acids 218-219 of HSTNFR1A_PEA—1_P24, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSTNFR1A_PEA—1_P24 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 187, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P24 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 187







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












45
P → S
No


75
P → L
Yes


121
R → Q
Yes









The glycosylation sites of variant protein HSTNFR1A_PEA—1_P24, as compared to the known protein Tumor necrosis factor receptor superfamily member 1A precursor, are described in Table 188 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 188







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












54
yes
54


151
yes
151


145
yes
145









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 189.







TABLE 189







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR001368
TNFR/CD27/30/40/
HMMPfam
127-166, 44-81,



95 cysteine-rich

84-125



region


IPR001368
TNFR/CD27/30/40/
HMMSmart
127-166, 168-195,



95 cysteine-rich

44-81, 84-125



region


IPR000345
Cytochrome c heme-
ScanRegExp
59-64



binding site


IPR001368
TNFR/CD27/30/40/
ScanRegExp
127-166, 44-81,



95 cysteine-rich

84-125



region


IPR006209
EGF-like domain
ScanRegExp
166-179


IPR001368
TNFR/CD27/30/40/
ProfileScan
126-166, 43-81,



95 cysteine-rich

83-125



region









Variant protein HSTNFR1A_PEA—1_P24 is encoded by the following transcript(s): HSTNFR1A_PEA—1_T30. The coding portion of transcript HSTNFR1A_PEA—1_T30 starts at position 282 and ends at position 938. The transcript also has the following SNPs as listed in Table 190 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P24 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 190







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












102
T →
No


267
C → T
No


317
A → G
Yes


414
C → T
No


505
C → T
Yes


643
G → A
Yes


956
G → A
Yes


1158
A → T
Yes


1389
C → T
Yes









Variant protein HSTNFR1A_PEA—1_P28 according to the present invention is encoded by transcript(s) HSTNFR1A_PEA—1_T37. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 1A precursor) in FIG. 171. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSTNFR1A_PEA—1_P28 and TR1A_HUMAN:
1. An isolated chimeric polypeptide HSTNFR1A_PEA—1_P28, comprising a first amino acid sequence being at least 90% homologous to MGLSTVPDLLLPLVLLELLVGIYPSGVIGLVPHLGDREKRDSVCPQGKYIHPQ NNSICCTKCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLRHCLSCSKCR KEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLS CQEKQNTVCTCHAGFFLRENECVSCS corresponding to amino acids 1-183 of TR1A_HUMAN, which also corresponds to amino acids 1-183 of HSTNFR1A_PEA—1_P28, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence K corresponding to amino acids 184-184 of HSTNFR1A_PEA—1_P28, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSTNFR1A_PEA—1_P28 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 191, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P28 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 191







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












45
P → S
No


75
P → L
Yes


121
R → Q
Yes









The glycosylation sites of variant protein HSTNFR1A_PEA—1_P28, as compared to the known protein Tumor necrosis factor receptor superfamily member 1A precursor, are described in Table 192 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 192







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












54
yes
54


151
yes
151


145
yes
145









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 193.







TABLE 193







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR001368
TNFR/CD27/30/40/
HMMPfam
127-166, 44-81,



95 cysteine-rich

84-125



region


IPR001368
TNFR/CD27/30/40/
HMMSmart
127-166, 44-81,



95 cysteine-rich

84-125



region


IPR000345
Cytochrome c heme-
ScanRegExp
59-64



binding site


IPR001368
TNFR/CD27/30/40/
ScanRegExp
127-166, 44-81,



95 cysteine-rich

84-125



region


IPR006209
EGF-like domain
ScanRegExp
166-179


IPR001368
TNFR/CD27/30/40/
ProfileScan
126-166, 43-81,



95 cysteine-rich

83-125



region









Variant protein HSTNFR1A_PEA—1_P28 is encoded by the following transcript(s): HSTNFR1A_PEA—1_T37. The coding portion of transcript HSTNFR1A_PEA—1_T37 starts at position 282 and ends at position 833. The transcript also has the following SNPs as listed in Table 194 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTNFR1A_PEA—1_P28 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 194







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












102
T →
No


267
C → T
No


317
A → G
Yes


414
C → T
No


505
C → T
Yes


643
G → A
Yes


1066
A → G
Yes


1207
G → T
Yes


1444
T → C
Yes


1444
T → G
Yes


1445
G → C
Yes


1558
C → T
Yes


1719
G → C
Yes









FIG. 204 presents the domain structure of the variants described hereinabove by a comparison to the known or wild-type (WT) protein:
Example 54
Description for Cluster HUMC5
Cluster HUMC5 features 3 transcript(s) and 24 segment(s) of interest, the names for which are given in Tables 195 and 196, respectively, the sequences themselves are given in SEQ ID NOs: 700-702; 703-726 and 727-729, for transcripts; segments and proteins, respectively. The selected protein variants are given in Table 197.







TABLE 195







Transcripts of interest










Transcript Name
SEQ ID NO:







HUMC5_PEA_3_T11
700



 



HUMC5_PEA_3_T14
701



 



HUMC5_PEA_3_T16
702

















TABLE 196







Segments of interest










Segment Name
SEQ ID NO:







HUMC5_PEA_3_node_6
703



 



HUMC5_PEA_3_node_8
704



 



HUMC5_PEA_3_node_21
705



 



HUMC5_PEA_3_node_23
706



 



HUMC5_PEA_3_node_27
707



 



HUMC5_PEA_3_node_29
708



 



HUMC5_PEA_3_node_30
709



 



HUMC5_PEA_3_node_32
710



 



HUMC5_PEA_3_node_34
711



 



HUMC5_PEA_3_node_36
712



 



HUMC5_PEA_3_node_40
713



 



HUMC5_PEA_3_node_47
714



 



HUMC5_PEA_3_node_49
715



 



HUMC5_PEA_3_node_4
716



 



HUMC5_PEA_3_node_10
717



 



HUMC5_PEA_3_node_13
718



 



HUMC5_PEA_3_node_15
719



 



HUMC5_PEA_3_node_17
720



 



HUMC5_PEA_3_node_19
721



 



HUMC5_PEA_3_node_25
722



 



HUMC5_PEA_3_node_38
723



 



HUMC5_PEA_3_node_42
724



 



HUMCS_PEA_3_node_44
725



 



HUMC5_PEA_3_node_45
726

















TABLE 197







Proteins of interest












Protein
Corresponding


Protein Name
SEQ ID NO:
Length
Transcript(s)





HUMC5_PEA_3_P12
727
P902
HUMC5_PEA_3_T11


 


HUMC5_PEA_3_P13
728
P505
HUMC5_PEA_3_T14


 


HUMC5_PEA_3_P15
729
P297
HUMC5_PEA_3_T16









These sequences are variants of the known protein Complement C5 precursor (SEQ ID NO:730) [Contains: C5a anaphylatoxin] (SwissProt accession identifier CO5_HUMAN SEQ ID NO:730)), referred to herein as the previously known protein.
Protein Complement C5 precursor (SEQ ID NO:730) [Contains: C5a anaphylatoxin] is known or believed to have the following function(s): Activation of C5 by a C5 convertase initiates the spontaneous assembly of the late complement components, C5-C9, into the membrane attack complex. C5b has a transient binding site for C6. The C5b-C6 complex is the foundation upon which the lytic complex is assembled; Derived from proteolytic degradation of complement C5, C5 anaphylatoxin is a mediator of local inflammatory process. It induces the contraction of smooth muscle, increases vascular permeability and causes histamine release from mast cells and basophilic leukocytes. C5a also stimulates the locomotion of polymorphonuclear leukocytes (chemokinesis) and direct their migration toward sites of inflammation (chemotaxis). The sequence for protein Complement C5 precursor (SEQ ID NO:730) [Contains: C5a anaphylatoxin] is given in SEQ ID NO: 730, as “Complement C5 precursor [Contains: C5a anaphylatoxin] amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 198.







TABLE 198







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment











518
F → S. /FTId = VAR_001996.


802
I → V (in dbSNP: 17611). /FTId = VAR_014574.


1053
M → L (in dbSNP: 17609). /FTId = VAR_014575.


1310
S → N (in dbSNP: 17610). /FTId = VAR_014576.


1437
E → D (in dbSNP: 17612). /FTId = VAR_014577.









The previously known protein also has the following indication(s) and/or potential therapeutic use(s): Inflammation; Asthma; Haemorrhage; Anaemia; Pemphigus; Psoriasis; Nephritis; Lupus nephritis; Arthritis, rheumatoid; Infarction, myocardial; Ischaemia, cerebral. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein or of drugs directed against this protein are as follows: C5a inhibitor; Complement factor C5 stimulant. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Dermatological; Antipsoriasis; Urological; Immunosuppressant; Antiarthritic; Septic shock treatment; Respiratory; antibody; Anti-inflammatory; Haemostatic; Cardiovascular; Antiasthma; Neuroprotective.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: activation of MAPK; chemotaxis; stress response; inflammatory response; complement activation, alternative pathway; complement activation, classical pathway; G-protein coupled receptor protein signaling pathway; response to pathogenic bacteria, which are annotation(s) related to Biological Process; antibacterial peptide; proteinase inhibitor; ligand; chemokine, which are annotation(s) related to Molecular Function; and membrane attack complex; extracellular space, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
As noted above, cluster HUMC5 features 3 transcript(s), which were listed in Table 195 above. These transcript(s) encode for protein(s) which are variant(s) of protein Complement C5 precursor [Contains: C5a anaphylatoxin]. A description of each variant protein according to the present invention is now provided.
Variant protein HUMC5_PEA—3_P12 (SEQ ID NO:727) according to the present is encoded by transcript(s) HUMC5_PEA—3_T11 (SEQ ID NO:700). An alignment is given to the known protein (Complement C5 precursor [Contains: C5a anaphylatoxin]) in FIG. 172. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMC5_PEA—3_P12 (SEQ ID NO:727) and CO5_HUMAN_V1 (SEQ ID NO:730):
1. An isolated chimeric polypeptide HUMC5_PEA—3_P12 (SEQ ID NO:727), comprising a first amino acid sequence being at least 90% homologous to MGLLGILCFLIFLGKTWGQEQTYVISAPKIFRVGASENIVIQVYGYTEAFDATIS IKSYPDKKFSYSSGHVHLSSENKFQNSAILTIQPKQLPGGQNPVSYVYLEVVSK HFSKSKRMPITYDNGFLFIHTDKPVYTPDQSVKVRVYSLNDDLKPAKRETVLT FIDPEGSEVDMVEEIDHIGIISFPDFKIPSNPRYGMWTIKAKYKEDFSTTGTAYF EVKEYVLPHFSVSIEPEYNFIGYKNFKNFEITIKARYFYNKVVTEADVYITFGIR EDLKDDQKEMMQTAMQNTMLINGIAQVTFDSETAVKELSYYSLEDLNNKYL YIAVTVIESTGGFSEEAEIPGIKYVLSPYKLNLVATPLFLKPGIPYPIKVQVKDS LDQLVGGVPV corresponding to amino acids 1-388 of CO5_HUMAN_V1, which also corresponds to amino acids 1-388 of HUMC5_PEA—3_P12 (SEQ ID NO:727), a bridging amino acid T corresponding to amino acid 389 of HUMC5_PEA—3_P12 (SEQ ID NO:727), a second amino acid sequence being at least 90% homologous to LNAQTIDVNQETSDLDPSKSVTRVDDGVASFVLNLPSGVTVLEFNVKTDAPD LPEENQAREGYRAIAYSSLSQSYLYIDWTDNHKALLVGEHLNIIVTPKSPYIDK ITHYNYLILSKGKIIHFGTREKFSDASYQSINIPVTQNMVPSSRLLVYYIVTGEQ TAELVSDSVWLNIEEKCGNQLQVHLSPDADAYSPGQTVSLNMATGMDSWVA LAAVDSAVYGVQRGAKKPLERVFQFLEKSDLGCGAGGGLNNANVFHLAGLT FLTNANADDSQENDEPCKEILRPRRTLQKKIEEIAAKYKHSVVKKCCYDGAC VNNDETCEQRAARISLGPRCIKAFTECCVVASQLRANISHKDMQLGRLHMKT LLPVSKPEIRSYFPESWLWEVHLVPRRKQLQFALPDSLTTWEIQGVGISNTGIC VADTVKAKVFKDVFLEMNIPYSVVRGEQIQLKGTVYNYRTSGMQ corresponding to amino acids 390-854 of CO5_HUMAN_V1 (SEQ ID NO:730), which also corresponds to amino acids 390-854 of HUMC5_PEA—3_P12 (SEQ ID NO:727), and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence SLALSPRLECNGKISGHCKLRLPGSSDSPASASQVAGITGTHHHAQPT corresponding to amino acids 855-902 of HUMC5_PEA—3_P12 (SEQ ID NO:727), wherein said first amino acid sequence, bridging amino acid, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMC5_PEA—3_P12 (SEQ ID NO:727), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence SLALSPRLECNGKISGHCKLRLPGSSDSPASASQVAGITGTHHHAQPT in HUMC5_PEA—3_P12 (SEQ ID NO:727).
It should be noted that the known protein sequence (CO5_HUMAN SEQ ID NO:730) has one or more changes than the sequence given in SEQ ID NO: 731 and named as being the amino acid sequence for CO5_HUMAN_V1. These changes were previously known to occur and are listed in the Table below.







TABLE 199







Changes to CO5_HUMAN_V1








SNP position(s) on



amino acid sequence
Type of change





802
variant









The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMC5_PEA—3_P12 (SEQ ID NO:727) also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 200, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC5_PEA—3_P12 (SEQ ID NO:727) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 200







Amino acid mutations









SNP position(s) on amino
Alternative



acid sequence
amino acid(s)
Previously known SNP?












74
S → P
No


449
R → G
Yes


691
K → *
No


777
V → I
Yes


802
V → I
Yes









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 201:







TABLE 201







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR001840
Complement
FPrintScan
694-703,



C3a/C4a/C5a

710-721,



anaphylatoxin

723-734


IPR000020
Anaphylatoxin/fibulin
HMMPfam
698-732


IPR002890
Alpha-2-macroglobulin,
HMMPfam
3-633



N-terminal




IPR000020
Anaphylatoxin/fibulin
HMMSmart
698-732


IPR000020
Anaphylatoxin/fibulin
ScanRegExp
698-732


IPR000020
Anaphylatoxin/fibulin
BlastProDom
684-751


IPR000020
Anaphylatoxin/fibulin
ProfileScan
698-732









Variant protein HUMC5_PEA—3_P12 (SEQ ID NO:727) is encoded by the following transcript(s): HUMC5_PEA—3_T11 (SEQ ID NO:700). The coding portion of transcript HUMC5_PEA—3_T11 (SEQ ID NO:700) starts at position 32 and ends at position 2737. The transcript also has the following SNPs as listed in Table 202 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC5_PEA—3_P12 (SEQ ID NO:727) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 202







Nucleic acid SNPs









SNP position on
Alternative
Previously


nucleotide sequence
nucleic acid
known SNP?












1
A → T
No


251
T → C
No


1186
A → G
Yes


1376
A → G
Yes


1492
C → T
Yes


1513
C → T
Yes


1564
C → T
Yes


1663
C → T
Yes


1756
G → A
Yes


2102
A → T
No


2360
G → A
Yes


2435
G → A
Yes


2602
C → T
Yes









Variant protein HUMC5_PEA—3_P13 (SEQ ID NO:728) according to the present is encoded by transcript(s) HUMC5_PEA—3_T14 (SEQ ID NO:701). An alignment is given to the known protein (Complement C5 precursor [Contains: C5a anaphylatoxin]) in FIG. 173. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMC5_PEA—3_P13 (SEQ ID NO:728) and CO5_HUMAN (SEQ ID NO:730):
1. An isolated chimeric polypeptide HUMC5_PEA—3_P13 (SEQ ID NO:728), comprising a first amino acid sequence being at least 90% homologous to MGLLGILCFLIFLGKTWGQEQTYVISAPKIFRVGASENIVIQVYGYTEAFDATIS IKSYPDKKFSYSSGHVHLSSENKFQNSAILTIQPKQLPGGQNPVSYVYLEVVSK HFSKSKRMPITYDNGFLFIHTDKPVYTPDQSVKVRVYSLNDDLKPAKRETVLT FIDPEGSEVDMVEEIDHIGIISFPDFKIPSNPRYGMWTIKAKYKEDFSTTGTAYF EVKEYVLPHFSVSIEPEYNFIGYKNFKNFEITIKARYFYNKVVTEADVYITFGIR EDLKDDQKEMMQTAMQNTMLINGIAQVTFDSETAVKELSYYSLEDLNNKYL YIAVTVIESTGGFSEEAEIPGIKYVLSPYKLNLVATPLFLKPGIPYPIKVQVKDS LDQLVGGVPV corresponding to amino acids 1-388 of CO5_HUMAN (SEQ ID NO:730), which also corresponds to amino acids 1-388 of HUMC5_PEA—3_P13 (SEQ ID NO:728), a bridging amino acid T corresponding to amino acid 389 of HUMC5_PEA—3_P13 (SEQ ID NO:728), a second amino acid sequence being at least 90% homologous to LNAQTIDVNQETSDLDPSKSVTRVDDGVASFVLNLPSGVTVLEFNVKTDAPD LPEENQAREGYRAIAYSSLSQSYLYIDWTDNHKALLVGEHLNIIVTPKSPYIDK ITHYNYL corresponding to amino acids 390-502 of CO5_HUMAN (SEQ ID NO:730), which also corresponds to amino acids 390-502 of HUMC5_PEA—3_P13 (SEQ ID NO:728), and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VST corresponding to amino acids 503-505 of HUMC5_PEA—3_P13 (SEQ ID NO:728), wherein said first amino acid sequence, bridging amino acid, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMC5_PEA—3_P13 (SEQ ID NO:728), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VST in HUMC5_PEA—3_P13 (SEQ ID NO:728).
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMC5_PEA—3_P13 (SEQ ID NO:728) also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 203, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC5_PEA—3_P13 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 203







Amino acid mutations









SNP position(s) on amino
Alternative



acid sequence
amino acid(s)
Previously known SNP?












74
S → P
No


449
R → G
Yes









The glycosylation sites of variant protein HUMC5_PEA—3_P13 (SEQ ID NO:728), as compared to the known protein Complement C5 precursor (SEQ ID NO:730) [Contains: C5a anaphylatoxin], are described in Table 204 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 204







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












1630
no



911
no



741
no



1115
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 205:







TABLE 205







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR002890
Alpha-2-macroglobulin,
HMMPfam
3-505



N-terminal









Variant protein HUMC5_PEA—3_P13 (SEQ ID NO:728) is encoded by the following transcript(s): HUMC5_PEA—3_T14 (SEQ ID NO:701). The coding portion of transcript HUMC5_PEA—3_T14 (SEQ ID NO:701) starts at position 32 and ends at position 1546. The transcript also has the following SNPs as listed in Table 206 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC5_PEA—3_P13 (SEQ ID NO:728) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 206







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












1
A → T
No


251
T → C
No


1186
A → G
Yes


1376
A → G
Yes


1492
C → T
Yes


1513
C → T
Yes


1653
G → A
Yes


2021
C → T
Yes









Variant protein HUMC5_PEA—3_P15 (SEQ ID NO:729) according to the present invention is encoded by transcript(s) HUMC5_PEA—3_T16 (SEQ ID NO:702). An alignment is given to the known protein (Complement C5 precursor [Contains: C5a anaphylatoxin]) in FIG. 174. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison report between HUMC5_PEA—3_P15 (SEQ ID NO:729) and CO5_HUMAN (SEQ ID NO:730):
1. An isolated chimeric polypeptide HUMC5_PEA—3_P15 (SEQ ID NO:729), comprising a first amino acid sequence being at least 90% homologous to MGLLGILCFLIFLGKTWGQEQTYVISAPKIPRVGASENIVIQVYGYTEAFDATIS IKSYPDKKFSYSSGHVHLSSENKFQNSAILTIQPKQLPGGQNPVSYVYLEVVSK HFSKSKRMPITYDNGFLFIHTDKPVYTPDQSVKVRVYSLNDDLKPAKRETVLT FIDPEGSEVDMVEEIDHIGIISFPDFKIPSNPRYGMWTIKAKYKEDFSTTGTAYF EVKEYVLPHFSVSIEPEYNFIGYKNFKNFEITIKARYFYNKVVTEADVYITFGIR EDLKDDQKEMMQTAMQNTML corresponding to amino acids 1-292 of CO5_HUMAN (SEQ ID NO:730), which also corresponds to amino acids 1-292 of HUMC5_PEA—3_P15 (SEQ ID NO:729), and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence RAEVR corresponding to amino acids 293-297 of HUMC5_PEA—3_P15 (SEQ ID NO:729), wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMC5_PEA—3_P15 (SEQ ID NO:729), comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence RAEVR in HUMC5_PEA—3_P15 (SEQ ID NO:729).
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMC5_PEA—3_P15 (SEQ ID NO:729) also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 207, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC5_PEA—3_P15 (SEQ ID NO:729) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 207







Amino acid mutations









SNP position(s) on amino
Alternative



acid sequence
amino acid(s)
Previously known SNP?





74
S → P
No









The glycosylation sites of variant protein HUMC5_PEA—3_P15 (SEQ ID NO:729), as compared to the known protein Complement C5 precursor [Contains: C5a anaphylatoxin], are described in Table 208 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 208







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












1630
no



911
no



741
no



1115
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 209:







TABLE 209







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR002890
Alpha-2-macroglobulin,
HMMPfam
3-297



N-terminal









Variant protein HUMC5_PEA—3_P15 (SEQ ID NO:729) is encoded by the following transcript(s): HUMC5_PEA—3_T16 (SEQ ID NO:702). The coding portion of transcript HUMC5_PEA—3_T16 (SEQ ID NO:702) starts at position 32 and ends at position 922. The transcript also has the following SNPs as listed in Table 210 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC5_PEA—3_P15 (SEQ ID NO:729) sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 210







Nucleic acid SNPs









SNP position on
Alternative



nucleotide sequence
nucleic acid
Previously known SNP?












1
A → T
No


251
T → C
No









FIG. 189 depicts the variants domain structure in comparison to the known or wild-type (WT) protein.
Structure of C5 and its Variants




T11 contains the convertase binding site on the β-chain (and maybe other, not yet known, binding sites), and thus, might interfere with the binding of the convertase with the wild type C5, and might serve as an antagonist.

T16, T14 might compete with C5 on its interaction with C5 convertase, and may thus serve as an antagonist of complement activation.

Example 55
Description for Cluster HUMFVIII
Cluster HUMFVIII features 4 transcript(s) and 30 segment(s) of interest, the names for which are given in Tables 211 and 212, respectively, the sequences themselves are given in SEQ ID NOs: 731-734; 735-764 and 765-768, for transcripts; segments and proteins, respectively. The selected protein variants are given in table 213.







TABLE 211







Transcripts of interest










Transcript Name
SEQ ID NO:







HUMFVIII_PEA_1_T2
731



 



HUMFVIII_PEA_1_T3
732



 



HUMFVIII_PEA_1_T6
733



 



HUMFVIII_PEA_1_T11
734

















TABLE 212







Segments of interest










Segment Name
SEQ ID NO:







HUMFVIII_PEA_1_node_0
735



 



HUMFVIII_PEA_1_node_3
736



 



HUMFVIII_PEA_1_node_6
737



 



HUMFVIII_PEA_1_node_8
738



 



HUMFVIII_PEA_1_node_10
739



 



HUMFVIII_PEA_1_node_15
740



 



HUMFVIII_PEA_1_node_17
741



 



HUMFVIII_PEA_1_node_19
742



 



HUMFVIII_PEA_1_node_21
743



 



HUMFVIII_PEA_1_node_25
744



 



HUMFVIII_PEA_1_node_27
745



 



HUMFVIII_PEA_1_node_29
746



 



HUMFVIII_PEA_1_node_31
747



 



HUMFVIII_PEA_1_node_33
748



 



HUMFVIII_PEA_1_node_35
749



 



HUMFVIII_PEA_1_node_37
750



 



HUMFVIII_PEA_1_node_39
751



 



HUMFVIII_PEA_1_node_46
752



 



HUMFVIII_PEA_1_node_47
753



 



HUMFVIII_PEA_1_node_49
754



 



HUMFVIII_PEA_1_node_51
755



 



HUMFVIII_PEA_1_node_55
756



 



HUMFVIII_PEA_1_node_4
757



 



HUMFVIII_PEA_1_node_12
758



 



HUMFVIII_PEA_1_node_14
759



 



HUMFVIII_PEA_1_node_23
760



 



HUMFVIII_PEA_1_node_41
761



 



HUMFVIII_PEA_1_node_43
762



 



HUMFVIII_PEA_1_node_52
763



 



HUMFVIII_PEA_1_node_54
764

















TABLE 213







Proteins of interest














Corresponding



Protein Name
SEQ ID NO:
Protein Length
Transcript(s)













HUMFVIII_PEA_1_P9
765
P300 
HUMFVIII_PEA_1_T11


 


HUMFVIII_PEA_1_P10
766
P2316
HUMFVIII_PEA_1_T2


 


HUMFVIII_PEA_1_P11
767
P2345
HUMFVIII_PEA_1_T3


 


HUMFVIII_PEA_1_P13
768
P265
HUMFVIII_PEA_1_T6









These sequences are variants of the known protein Coagulation factor VIII precursor (SwissProt accession identifier FA8_HUMAN; SEQ ID NO:769; known also according to the synonyms Procoagulant component; Antihemophilic factor; AHF), referred to herein as the previously known protein.
Protein Coagulation factor VIII precursor is known or believed to have the following function(s): Factor VIII, along with calcium and phospholipid, acts as a cofactor for factor IXa when it converts factor X to the activated form, factor Xa. The sequence for protein Coagulation factor VIII precursor is given in SEQ ID NO: 769, as “Coagulation factor VIII precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 214.







TABLE 214







Amino acid mutations for Known Protein








SNP



position(s)



on amino



acid



sequence
Comment











26
L → R (in HEMA; severe). /FTId = VAR_001045.


30
E → V (in HEMA; mild). /FTId = VAR_001046.


41
G → C (in HEMA; severe/moderate). /FTId = VAR_001047.


48
R → C (in HEMA; severe). /FTId = VAR_001048.


72
E → K (in HEMA; moderate). /FTId = VAR_017330.


75
D → V (in dbSNP: 1800288). /FTId = VAR_001049.


89
G → D (in HEMA; severe). /FTId = VAR_001050.


89
G → V (in HEMA; mild). /FTId = VAR_001051.


97
A → P (in HEMA). /FTId = VAR_017331.


99
V → D (in HEMA; severe). /FTId = VAR_001052.


104
V → D (in HEMA; mild). /FTId = VAR_001053.


108
K → T (in HEMA; mild). /FTId = VAR_001054.


110
M → V (in HEMA; moderate). /FTId = VAR_001055.


117
L → R (in HEMA; severe). /FTId = VAR_001056.


129
E → V (in HEMA; severe). /FTId = VAR_001057.


130
G → R (in HEMA; severe). /FTId = VAR_001058.


132
E → D (in HEMA; severe). /FTId = VAR_001059.


133
Y → C (in HEMA; mild). /FTId = VAR_001060.


135
D → G (in HEMA; severe). /FTId = VAR_001061.


137
T → I (in HEMA; moderate). /FTId = VAR_001062.


155
Y → H (in HEMA; moderate). /FTId = VAR_017332.


164
G → V (in HEMA; mild). /FTId = VAR_001063.


165
P → S (in HEMA; severe). /FTId = VAR_001064.


181
V → M (in HEMA; moderate). /FTId = VAR_001065.


181
V → E (in HEMA; mild). /FTId = VAR_017333.


185
K → T (in HEMA; mild). /FTId = VAR_001066.


189
S → L (in HEMA; moderate). /FTId = VAR_001067.


202
S → R (in HEMA; mild). /FTId = VAR_008123.


222
D → V (in HEMA; moderate). /FTId = VAR_001068.


224
G → W (in HEMA; moderate). /FTId = VAR_001069.


253
V → F (in HEMA; severe). /FTId = VAR_001070.


254
N → I (in HEMA; severe). /FTId = VAR_017334.


255
G → V (in HEMA; severe). /FTId = VAR_015127.


266
G → E (in HEMA; severe). /FTId = VAR_001071.


278
G → R (in HEMA; severe). /FTId = VAR_001072.


285
V → G (in HEMA; mild). /FTId = VAR_001073.


291
E → G (in HEMA; mild). /FTId = VAR_001074.


294
T → I (in HEMA; moderate). /FTId = VAR_001075.


299
N → I (in HEMA; mild). /FTId = VAR_001076.


301
R → H (in HEMA; severe). /FTId = VAR_001077.


301
R → L (in HEMA; severe). /FTId = VAR_001078.


308
S → L (in HEMA; moderate). /FTId = VAR_001079.


312
F → S (in HEMA; moderate). /FTId = VAR_001080.


314
T → A (in HEMA; mild). /FTId = VAR_001081.


314
T → I (in HEMA; moderate). /FTId = VAR_001082.


323
G → E (in HEMA; severe). /FTId = VAR_015128.


327
L → P (in HEMA; severe). /FTId = VAR_001083.


331
I → V (in HEMA; mild). /FTId = VAR_001084.


345
V → L (in HEMA; severe). /FTId = VAR_001085.


348
C → R (in HEMA; severe). /FTId = VAR_001086.


348
C → S (in HEMA; moderate). /FTId = VAR_001087.


348
C → Y (in HEMA; severe). /FTId = VAR_001088.


391
R → C (in HEMA; Okayama; moderate; abolishes the



normal cleavage by thrombin). /FTId = VAR_001089.


391
R → H (in HEMA; Kumamoto; moderate; abolishes the



normal cleavage by thrombin). /FTId = VAR_001090.


391
R → P (in HEMA; severe; abolishes the normal cleavage



by thrombin). /FTId = VAR_001091.


392
S → L (in HEMA; mild; abolishes normal cleavage by



thrombin). /FTId = VAR_001092.


392
S → P (in HEMA; mild). /FTId = VAR_001093.


405
I → S (in HEMA; severe). /FTId = VAR_001094.


409
E → G (in HEMA; severe/moderate). /FTId = VAR_001095.


431
L → F (in HEMA; moderate). /FTId = VAR_001096.


439
G → V (in HEMA; severe). /FTId = VAR_001097.


439
G → S (in HEMA; moderate). /FTId = VAR_017335.


444
K → R (in HEMA; severe). /FTId = VAR_001098.


450
Y → N (in HEMA; moderate). /FTId = VAR_001099.


474
G → R (in HEMA; severe). /FTId = VAR_001100.


488
A → G (in HEMA; moderate). /FTId = VAR_001101.


492
Y → H (in HEMA; mild). /FTId = VAR_001102.


492
Y → C (in HEMA; moderate). /FTId = VAR_001103.


494
I → T (in HEMA; mild). /FTId = VAR_001104.


498
G → R (in HEMA; severe/moderate). /FTId = VAR_001105.


529
K → E (in HEMA; moderate). /FTId = VAR_017336.


544
D → N (in HEMA; moderate). /FTId = VAR_001106.


546
R → W (in HEMA; mild). /FTId = VAR_001107.


550
R → C (in HEMA; moderate). /FTId = VAR_001108.


550
R → G (in HEMA; mild). /FTId = VAR_001109.


550
R → H (in HEMA; mild). /FTId = VAR_001110.


554
S → G (in HEMA; mild). /FTId = VAR_001111.


556
V → D (in HEMA; moderate). /FTId = VAR_001112.


561
D → Y (in HEMA; severe). /FTId = VAR_008967.


567
I → T (in HEMA; mild). /FTId = VAR_017337.


577
S → F (in HEMA; mild). /FTId = VAR_001113.


584
Q → K (in HEMA; moderate). /FTId = VAR_001114.


585
I → T (in HEMA; severe/moderate). /FTId = VAR_001115.


586
M → V (in HEMA; mild). /FTId = VAR_015129.


596
S → P (in HEMA; severe). /FTId = VAR_001116.


603
S → I (in HEMA). /FTId = VAR_001117.


604
W → C (in HEMA; severe). /FTId = VAR_001118.


605
Y → S (in HEMA; severe). /FTId = VAR_001119.


612
R → C (in HEMA; moderate). /FTId = VAR_001120.


631
N → K (in HEMA; severe). /FTId = VAR_001121.


631
N → S (in HEMA). /FTId = VAR_001122.


644
L → V (in HEMA; mild). /FTId = VAR_001123.


653
V → A (in HEMA; mild). /FTId = VAR_001124.


653
V → M (in HEMA; severe). /FTId = VAR_001125.


663
A → V (in HEMA; mild). /FTId = VAR_001126.


671
Missing (in HEMA; severe). /FTId = VAR_001127.


677
F → L (in HEMA; moderate). /FTId = VAR_001128.


699
M → V (in HEMA; severe). /FTId = VAR_001129.


717
R → W (in HEMA; mild). /FTId = VAR_001130.


720
G → D (in HEMA; severe/moderate).



/FTId = VAR_001131.


723
A → T (in HEMA; moderate). /FTId = VAR_001132.


727
V → F (in HEMA; severe). /FTId = VAR_001133.


739
E → K (in HEMA; mild). /FTId = VAR_001134.


1057
E → K (in HEMA; moderate). /FTId = VAR_001135.


1260
D → E (in dbSNP: 1800291). /FTId = VAR_001136.


1481
L → P (in dbSNP: 1800294). /FTId = VAR_001137.


1699
Y → C (in HEMA; severe). /FTId = VAR_001138.


1699
Y → F (in HEMA; moderate). /FTId = VAR_001139.


1708
R → C (in HEMA; East Hartford; severe/moderate;



abolishes thrombin cleavage at the light chain).



/FTId = VAR_001140.


1708
R → H (in HEMA; mild; abolishes thrombin cleavage at



the light chain). /FTId = VAR_001141.


1715
R → G (in HEMA; mild). /FTId = VAR_001142.


1723
E → K (in HEMA; severe). /FTId = VAR_001143.


1728
Y → C (in HEMA; moderate). /FTId = VAR_001144.


1769
G → R (in HEMA; mild). /FTId = VAR_001145.


1775
L → V (in HEMA; moderate). /FTId = VAR_001146.


1775
L → F (in HEMA; mild). /FTId = VAR_001147.


1779
G → E (in HEMA; severe). /FTId = VAR_001148.


1791
M → T (in HEMA; severe). /FTId = VAR_001149.


1800
R → H (in HEMA; moderate). /FTId = VAR_001150.


1800
R → C (in HEMA; moderate). /FTId = VAR_001151.


1800
R → G (in HEMA; mild). /FTId = VAR_001152.


1803
S → Y (in HEMA; severe). /FTId = VAR_001153.


1804
F → S (in HEMA; severe). /FTId = VAR_017338.


1808
L → F (in HEMA; mild). /FTId = VAR_001154.


1842
M → I (in HEMA; moderate). /FTId = VAR_001155.


1844
P → S (in HEMA; mild). /FTId = VAR_001156.


1845
T → P (in HEMA; mild). /FTId = VAR_001157.


1853
A → T (in HEMA; severe). /FTId = VAR_001158.


1853
A → V (in HEMA; mild). /FTId = VAR_001159.


1865
D → N (in HEMA; severe). /FTId = VAR_001160.


1865
D → Y (in HEMA; severe). /FTId = VAR_001161.


1867
H → R (in HEMA; moderate). /FTId = VAR_001162.


1869
G → V (in HEMA; severe). /FTId = VAR_001163.


1873
P → R (in HEMA; severe). /FTId = VAR_001164.


1888
R → I (in HEMA; severe). /FTId = VAR_001165.


1894
E → G (in HEMA; moderate). /FTId = VAR_001166.


1904
E → K (in HEMA; severe). /FTId = VAR_001167.


1941
N → D (in HEMA; severe/moderate).



/FTId = VAR_001168.


1941
N → S (in HEMA; severe/moderate). /FTId = VAR_001169.


1942
G → A (in HEMA; moderate). /FTId = VAR_015130.


1960
R → Q (in HEMA; moderate). /FTId = VAR_001170.


1960
R → L (in HEMA; moderate). /FTId = VAR_001171.


1963
L → P (in HEMA; severe). /FTId = VAR_015131.


1967
G → D (in HEMA; moderate). /FTId = VAR_001172.


1979
G → V (in HEMA; moderate). /FTId = VAR_001173.


1980
H → Y (in HEMA; mild). /FTId = VAR_001174.


2016
R → W (in HEMA; severe/moderate).



/FTId = VAR_001175.


2036
Y → C (in HEMA; moderate). /FTId = VAR_015132.


2038
N → S (in HEMA; moderate). /FTId = VAR_001176.


2051
I → S (in HEMA; severe). /FTId = VAR_017339.


2065
W → R (in HEMA; moderate). /FTId = VAR_001177.


2088
S → F (in HEMA; severe). /FTId = VAR_001178.


2093
D → G (in HEMA; mild). /FTId = VAR_001179.


2105
T → N (in HEMA; moderate). /FTId = VAR_001180.


2107
G → S (in HEMA; severe). /FTId = VAR_001181.


2120
F → L (in HEMA; mild). /FTId = VAR_001182.


2124
Y → C (in HEMA; mild). /FTId = VAR_001183.


2135
R → P (in HEMA; severe). /FTId = VAR_001184.


2138
S → Y (in HEMA; moderate). /FTId = VAR_001185.


2141
T → N (in HEMA; severe). /FTId = VAR_017340.


2148
N → S (in HEMA; moderate). /FTId = VAR_001186.


2169
R → H (in HEMA; severe/mild). /FTId = VAR_001187.


2172
P → Q (in HEMA; moderate). /FTId = VAR_001188.


2172
P → R (in HEMA; severe). /FTId = VAR_015133.


2173
T → I (in HEMA; mild). /FTId = VAR_001189.


2178
R → C (in HEMA; mild). /FTId = VAR_001190.


2178
R → H (in HEMA; mild). /FTId = VAR_001191.


2178
R → L (in HEMA; mild). /FTId = VAR_001192.


2182
R → C (in HEMA; severe/moderate). /FTId = VAR_001193.


2182
R → H (in HEMA; severe/moderate). /FTId = VAR_001194.


2183
M → V (in HEMA; mild). /FTId = VAR_001195.


2185
L → S (in HEMA; severe). /FTId = VAR_001196.


2193
C → G (in HEMA). /FTId = VAR_017341.


2204
I → T (in HEMA; mild). /FTId = VAR_001197.


2209
I → N (in HEMA; moderate). /FTId = VAR_001198.


2211
A → P (in HEMA; moderate). /FTId = VAR_001199.


2223
Missing (in HEMA; severe/moderate).



/FTId = VAR_001200.


2228
R → G (in HEMA; severe). /FTId = VAR_001201.


2228
R → L (in HEMA; moderate). /FTId = VAR_001202.


2228
R → Q (in HEMA; severe/moderate). /FTId = VAR_001203.


2242
V → M. /FTId = VAR_001204.


2248
W → C (in HEMA; moderate). /FTId = VAR_001205.


2262
V → VQ (in HEMA; moderate). /FTId = VAR_017342.


2265
Q → R (in HEMA; moderate). /FTId = VAR_001206.


2307
D → A (in HEMA; moderate). /FTId = VAR_015134.


2319
P → L (in HEMA; mild/severe). /FTId = VAR_001207.


2319
P → S (in HEMA; mild). /FTId = VAR_001208.


2323
R → C (in HEMA; severe; may cause reduced phospholipid



binding). /FTId = VAR_001209.


2323
R → H (in HEMA; mild; may cause reduced phospholipid



binding). /FTId = VAR_001210.


2326
R → L (in HEMA; severe/moderate; may cause reduced



phospholipid binding). /FTId = VAR_001211.


2326
R → Q (in HEMA; moderate; may cause reduced



phospholipid binding). /FTId = VAR_001212.


2344
G → C (in HEMA; moderate). /FTId = VAR_008968.


768
P → R


1922
C → S









Protein Coagulation factor VIII precursor localization is believed to be Extracellular.
The previously known protein also has the following indication(s) and/or potential therapeutic use(s): Haemophilia A; Haemophilia. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein are as follows: Factor VIII agonist; Factor VIIIc agonist. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Haemostatic; Blood fraction; Antifibrinolytic.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: acute-phase response; cell adhesion; blood coagulation, which are annotation(s) related to Biological Process; and blood coagulation factor; copper binding, which are annotation(s) related to Molecular Function.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
Factor VIII (F8) is a cofactor for F9a (intrinsic pathway). Along with calcium and phospholipid, it acts as a cofactor for factor IXa when it converts factor X to the activated form, factor Xa. Factor VIII becomes activated by Thrombin (F2) which cleaves its activation peptide. Defects in F8 cause hemophilia A: Incidence=1-2 in 10,000 males.
FIGS. 190, 191, 192 depict, Factor VIII launched products, related development and clinical preclinical developments, respectively.
As noted above, cluster HUMFVIII features 4 transcript(s), which were listed in Table 211 above. These transcript(s) encode for protein(s) which are variant(s) of protein Coagulation factor VIII precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HUMFVIII_PEA—1_P9 according to the present invention is encoded by transcript(s) HUMFVIII_PEA—1_T11. An alignment is given to the known protein (Coagulation factor VIII precursor) in FIG. 175. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison report between HUMFVIII_PEA—1_P9 and FA8_HUMAN:
1. An isolated chimeric polypeptide HUMFVIII_PEA—1_P9, comprising a first amino acid sequence being at least 90% homologous to MQIELSTCFFLCLLRFCFSATRRYYLGAVELSWDYMQSDLGELPVDARFPPRV PKSFPFNTSVVYKKTLFVEFTDHLFNIAKPRPPWMGLLGPTIQAEVYDTVVITL KNMASHPVSLHAVGVSYWKASEGAEYDDQTSQREKEDDKVFPGGSHTYVW QVLKENGPMASDPLCLTYSYLSHVDLVKDLNSGLIGALLVCREGSLAKEKTQ TLHKFILLFAVFDEGKSWHSETKNSLMQDRDAASARAWPKMHTVNGYVNRS LPG corresponding to amino acids 1-263 of FA8_HUMAN, which also corresponds to amino acids 1-263 of HUMFVIII_PEA—1_P9, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence MYTPAQQSSGSSKFSTRVLYFSSQTARHLRGYSPLNT corresponding to amino acids 264-300 of HUMFVIII_PEA—1_P9, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMFVIII_PEA—1_P9, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence MYTPAQQSSGSSKFSTRVLYFSSQTARHLRGYSPLNT in HUMFVIII_PEA—1_P9.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMFVIII_PEA—1_P9 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 215, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMFVIII_PEA—1_P9 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 215







Amino acid mutations









SNP position(s) on amino
Alternative



acid sequence
amino acid(s)
Previously known SNP?












75
D → V
Yes


210
T → P
Yes









Variant protein HUMFVIII_PEA—1_P9 is encoded by the following transcript(s): HUMFVIII_PEA—1_T11. The coding portion of transcript HUMFVIII_PEA—1_T11 starts at position 173 and ends at position 1072. The transcript also has the following SNPs as listed in Table 216 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMFVIII_PEA—1_P9 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 216







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?





274
C → T
Yes


396
A → T
Yes


800
A → C
Yes









Variant protein HUMFVIII_PEA—1_P10 according to the present invention is encoded by transcript(s) HUMFVIII_PEA—1_T2. An alignment is given to the known protein (Coagulation factor VIII precursor) in FIG. 176. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMFVIII_PEA—1_P10 and FA8_HUMAN:
1. An isolated chimeric polypeptide HUMFVIII_PEA—1_P10, comprising a first amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence MHRDARAQKASRG corresponding to amino acids 1-13 of HUMFVIII_PEA—1_P10, and a second amino acid sequence being at least 90% homologous to FPPRVPKSFPFNTSVVYKKTLFVEFTDHLFNIAKPRPPWMGLLGPTIQAEVYDT VVITLKNMASHPVSLHAVGVSYWKASEGAEYDDQTSQREKEDDKVFPGGSH TYVWQVLKENGPMASDPLCLTYSYLSHVDLVKDLNSGLIGALLVCREGSLA KEKTQTLHKFILLFAVFDEGKSWHSETKNSLMQDRDAASARAWPKMHTVNG YVNRSLPGLIGCHRKSVYWHVIGMGTTPEVHSIFLEGHTFLVRNHRQASLEIS PITFLTAQTLLMDLGQFLLFCHISSHQHDGMEAYVKVDSCPEEPQLRMKNNE EAEDYDDDLTDSEMDVVRFDDDNSPSFIQIRSVAKKHPKTWVHYIAAEEEDW DYAPLVLAPDDRSYKSQYLNNGPQRIGRKYKKVRFMAYTDETFKTREAIQHE SGILGPLLYGEVGDTLLIIFKNQASRPYNIYPHGITDVRPLYSRRLPKGVKHLK DFPILPGEIFKYKWTVTVEDGPTKSDPRCLTRYYSSFVNMERDLASGLIGPLLI CYKESVDQRGNQIMSDKRNVILFSVFDENRSWYLTENIQRFLPNPAGVQLEDP EFQASNIMHSINGYVFDSLQLSVCLHEVAYWYILSIGAQTDFLSVFFSGYTFKH KMVYEDTLTLFPFSGETVFNISMENPGLWILGCHNSDFRNRGMTALLKVSSCD KNTGDYYEDSYEDISAYLLSKNNAIEPRSFSQNSRHPSTRQKQFNATTIPENDI EKTDPWFAHRTPMPKIQNVSSSDLLMLLRQSPTPHGLSLSDLQEAKYETFSDD PSPGAIDSNNSLSEMTHFRPQLHHSGDMVFTPESGLQLRLNEKLGTTAATELK KLDFKVSSTSNNLISTIPSDNLAAGTDNTSSLGPPSMPVHYDSQLDTTLFGKKS SPLTESGGPLSLSEENNDSKLLESGLMNSQESSWGKNVSSTESGRLFKGKRAH GPALLTKDNALFKVSISLLKTNKTSNNSATNRKTHIDGPSLLIENSPSVWQNIL ESDTEFKKVTPLIHDRMLMDKNATALRLNHMSNKTTSSKNMEMVQQKKEGP IPPDAQNPDMSFFKMLFLPESARWIQRTHGKNSLNSGQGPSPKQLVSLGPEKS VEGQNFLSEKNKVVVGKGEFTKDVGLKEMVFPSSRNLFLTNLDNLHENNTH NQEKKIQEEIEKKETLIQENVVLPQIHTVTGTKNFMKNLFLLSTRQNVEGSYD GAYAPVLQDFRSLNDSTNRTKKHTAHFSKKGEEENLEGLGNQTKQIVEKYAC TTRISPNTSQQNFVTQRSKRALKQFRLPLEETELEKRIIVDDTSTQWSKNMKH LTPSTLTQIDYNEKEKGAITQSPLSDCLTRSHSIPQANRSPLPIAKVSSFPSIRPIY LTRVLFQDNSSHLPAASYRKKDSGVQESSHFLQGAKKNNLSLAILTLEMTGD QREVGSLGTSATNSVTYKKVENTVLPKPDLPKTSGKVELLPKVHIYQKDLFPT ETSNGSPGHLDLVEGSLLQGTEGAIKWNEANRPGKVPFLRVATESSAKTPSKL LDPLAWDNHYGTQIPKEEWKSQEKSPEKTAFKKKDTILSLNACESNHAIAAIN EGQNKPEIEVTWAKQGRTERLCSQNPPVLKRHQREITRTTLQSDQEEIDYDDT ISVEMKKEDFDIYDEDENQSPRSFQKKTRHYFIAAVERLWDYGMSSSPHVLR NRAQSGSVPQFKKVVFQEFTDGSFTQPLYRGELNEHLGLLGPYIRAEVEDNIM VTFRNQASRPYSFYSSLISYEEDQRQGAEPRKNFVKPNETKTYFWKVQHHMA PTKDEFDCKAWAYFSDVDLEKDVHSGLIGPLLVCHTNTLNPAHGRQVTVQEF ALFFTIFDETKSWYFTENMERNCRAPCNIQMEDPTFKENYRFHAINGYIMDTL PGLVMAQDQRIRWYLLSMGSNENIHSIHFSGHVFTVRKKEEYKMALYNLYPG VFETVEMLPSKAGIWRVECLIGEHLHAGMSTLFLVYSNKCQTPLGMASGHIR DFQITASGQYGQWAPKLARLHYSGSINAWSTKEPFSWIKVDLLAPMIIHGIKT QGARQKFSSLYISQFIIMYSLDGKKWQTYRGNSTGTLMVFFGNVDSSGIKHNI FNPPIIARYIRLHPTHYSIRSTLRMELMGCDLNSCSMPLGMESKAISDAQITASS YFTNMFATWSPSKARLHLQGRSNAWRPQVNNPKEWLQVDFQKTMKVTGVT TQGVKSLLTSMYVKEFLISSSQDGHQWTLFFQNGKVKVFQGNQDSFTPVVNS LDPPLLTRYLRIHPQSWVHQIALRMEVLGCEAQDLY corresponding to amino acids 49-2351 of FA8_HUMAN, which also corresponds to amino acids 14-2316 of HUMFVIII_PEA—1_P10, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a head of HUMFVIII_PEA—1_P10, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence MHRDARAQKASRG of HUMFVIII_PEA—1_P10.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: intracellularly. The protein localization is believed to be intracellularly because neither of the trans-membrane region prediction programs predicted a trans-membrane region for this protein. In addition both signal-peptide prediction programs predict that this protein is a non-secreted protein.
Variant protein HUMFVIII_PEA—1_P10 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 217, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMFVIII_PEA—1_P10 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 217







Amino acid mutations









SNP position(s) on amino
Alternative



acid sequence
amino acid(s)
Previously known SNP?












40
D → V
Yes


175
T → P
Yes


760
R → G
Yes


1225
D → E
Yes


1446
L → P
Yes


1887
C → S
Yes


1887
C → W
Yes


2199
R → G
No


2199
R → W
No


2222
M → V
Yes


2240
Y → C
No









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 218:







TABLE 218







InterPro domain(s)










InterPro ID
Domain description
Analysis type
Position(s) on protein





IPR001117
Multicopper oxidase, type 1
HMMPfam
183-314


IPR000421
Coagulation factor 5/8
HMMPfam
2008-2150, 2161-2307



type C domain (FA58C)


IPR000421
Coagulation factor 5/8
HMMSmart
2004-2153, 2157-2310



type C domain (FA58C)


IPR001117
Multicopper oxidase, type 1
ScanRegExp
1978-1998, 288-308, 670-690


IPR000421
Coagulation factor 5/8
ScanRegExp
2045-2072, 2202-2231



type C domain (FA58C)


IPR000421
Coagulation factor 5/8
ScanRegExp
2137-2153, 2294-2310



type C domain (FA58C)


IPR000421
Coagulation factor 5/8
ProfileScan
2005-2153, 2158-2310



type C domain (FA58C)









Variant protein HUMFVIII_PEA—1_P10 is encoded by the following transcript(s): HUMFVIII_PEA—1_T2. The coding portion of transcript HUMFIII_PEA—1_T2 starts at position 124 and ends at position 7071. The transcript also has the following SNPs as listed in Table 219 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMFVIII_PEA—1_P10 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 219







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












242
A → T
Yes


646
A → C
Yes


1104
G → A
Yes


1884
T → C
Yes


2401
A → G
Yes


3798
C → G
Yes


3882
A → C
Yes


3939
A → C
Yes


4460
T → C
Yes


4539
A → C
Yes


5310
G → A
Yes


5783
G → C
Yes


5784
C → G
Yes


6660
C → T
Yes


6718
A → G
No


6718
A → T
No


6787
A → G
Yes


6842
A → G
No


7103
C → T
Yes


7776
T →
Yes


8259
C → T
Yes


8366
G → A
Yes


8602
C → A
Yes


8746
A → G
Yes









Variant protein HUMFVIII_PEA—1_P11 according to the present invention is encoded by transcript(s) HUMFVIII_PEA—1_T3. An alignment is given to the known protein (Coagulation factor VIII precursor) in FIG. 177. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMFVIII_PEA—1_μl and FA8_HUMAN:
1. An isolated chimeric polypeptide HUMFVIII_PEA—1_P11, comprising a first amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence MHRDARAQKASRG corresponding to amino acids 1-13 of HUMFVIII_PEA—1_P11, and a second amino acid sequence being at least 90% homologous to ATRRYYLGAVELSWDYMQSDLGELPVDARFPPRVPKSFPFNTSVVYKKTLFV EFTDHLFNIAKPRPPWMGLLGPTIQAEVYDTVVITLKNMASHPVSLHAVGVS YWKASEGAEYDDQTSQREKEDDKVFPGGSHTYVWQVLKENGPMASDPLCL TYSYLSHVDLVKDLNSGLIGALLVCREGSLAKEKTQTLHKFILLFAVFDEGKS WHSETKNSLMQDRDAASARAWPKMHTVNGYVNRSLPGLIGCHRKSVYWHV IGMGTTPEVHSIFLEGHTFLVRNHRQASLEISPITFLTAQTLLMDLGQFLLFCHI SSHQHDGMEAYVKVDSCPEEPQLRMKNNEEAEDYDDDLTDSEMDVVRFDD DNSPSFIQIRSVAKKHPKTWVHYIAAEEEDWDYAPLVLAPDDRSYKSQYLNN GPQRIGRKYKKVRFMAYTDETFKTREAIQHESGILGPLLYGEVGDTLLIIFKNQ ASRPYNIYPHGITDVRPLYSRRLPKGVKHLKDFPILPGEIFKYKWTVTVEDGPT KSDPRCLTRYYSSFVNMERDLASGLIGPLLICYKESVDQRGNQIMSDKRNVIL FSVFDENRSWYLTENIQRFLPNPAGVQLEDPEFQASNIMHSINGYVFDSLQLS VCLHEVAYWYILSIGAQTDFLSVFFSGYTFKHKMVYEDTLTLFPFSGETVFMS MENPGLWILGCHNSDFRNRGMTALLKVSSCDKNTGDYYEDSYEDISAYLLSK NNAIEPRSFSQNSRHPSTRQKQFNATTIPENDIEKTDPWFAHRTPMPKIQNVSS SDLLMLLRQSPTPHGLSLSDLQEAKYETFSDDPSPGAIDSNNSLSEMTHFRPQL HHSGDMVFTPESGLQLRLNEKLGTTAATELKKLDFKVSSTSNNLISTIPSDNLA AGTDNTSSLGPPSMPVHYDSQLDTTLFGKKSSPLTESGGPLSLSEENNDSKLLE SGLMNSQESSWGKNVSSTESGRLFKGKRAHGPALLTKDNALFKVSISLLKTN KTSNNSATNRKTHIDGPSLLIENSPSVWQNILESDTEFKKVTPLIHDRMLMDK NATALRLNHMSNKTTSSKNMEMVQQKKEGPIPPDAQNPDMSFFKMLFLPES ARWIQRTHGKNSLNSGQGPSPKQLVSLGPEKSVEGQNFLSEKNKVVVGKGEF TKDVGLKEMVFPSSRNLFLTNLDNLHENNTHNQEKKIQEEIEKKETLIQENVV LPQIHTVTGTKNFMKNLFLLSTRQNVEGSYDGAYAPVLQDFRSLNDSTNRTK KHTAHFSKKGEEENLEGLGNQTKQIVEKYACTTRISPNTSQQNFVTQRSKRAL KQFRLPLEETELEKRIIVDDTSTQWSKNMKHLTPSTLTQIDYNEKEKGAITQSP LSDCLTRSHSIPQANRSPLPIAKVSSFPSIRPIYLTRVLFQDNSSHLPAASYRKK DSGVQESSHFLQGAKKNNLSLAILTLEMTGDQREVGSLGTSATNSVTYKKVE NTVLPKPDLPKTSGKVELLPKVHIYQKDLFPTETSNGSPGHLDLVEGSLLQGT EGAIKWNEANRPGKVPFLRVATESSAKTPSKLLDPLAWDNHYGTQIPKEEWK SQEKSPEKTAFKKKDTILSLNACESNHAIAAINEGQNKPEIEVTWAKQGRTER LCSQNPPVLKRHQREITRTTLQSDQEEIDYDDTISVEMKKEDFDIYDEDENQSP RSFQKKTRHYFIAAVERLWDYGMSSSPHVLRNRAQSGSVPQFKKVVFQEFTD GSFTQPLYRGELNEHLGLLGPYIRAEVEDNIMVTFRNQASRPYSFYSSLISYEE DQRQGAEPRKNFVKPNETKTYFWKVQHHMAPTKDEFDCKAWAYFSDVDLE KDVHSGLIGPLLVCHTNTLNPAHGRQVTVQEFALFFTIFDETKSWYFTENMER NCRAPCNIQMEDPTFKENYRFHAINGYIMDTLPGLVMAQDQRIRWYLLSMGS NENIHSIHFSGHVFTVRKKEEYKMALYNLYPGVFETVEMLPSKAGIWRVECLI GEHLHAGMSTLFLVYSNKCQTPLGMASGHIRDFQITASGQYGQWAPKLARL HYSGSINAWSTKEPFSWIKVDLLAPMIIHGIKTQGARQKFSSLYISQFIIMYSLD GKKWQTYRGNSTGTLMVFFGNVDSSGIKHNIFNPPIIARYIRLHPTHYSIRSTL RMELMGCDLNSCSMPLGMESKAISDAQITASSYFTNMFATWSPSKARLHLQG RSNAWRPQVNNPKEWLQVDFQKTMKVTGVTTQGVKSLLTSMYVKEFLISSS QDGHQWTLFFQNGKVKVFQGNQDSFTPVVNSLDPPLLTRYLRIHPQSWVHQI ALRMEVLGCEAQDLY corresponding to amino acids 20-2351 of FA8_HUMAN, which also corresponds to amino acids 14-2345 of HUMFVIII_PEA—1_P11, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a head of HUMFVIII_PEA—1_P11, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence MHRDARAQKASRG of HUMFVIII_PEA—1_P11.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: intracellularly. The protein localization is believed to be intracellularly because neither of the trans-membrane region prediction programs predicted a trans-membrane region for this protein. In addition both signal-peptide prediction programs predict that this protein is a non-secreted protein.
Variant protein HUMFVIII_PEA—1_P11 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 210, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMFVIII_PEA—1_P11 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 210







Amino acid mutations









SNP position(s) on amino
Alternative



acid sequence
amino acid(s)
Previously known SNP?












69
D → V
Yes


204
T → P
Yes


789
R → G
Yes


1254
D → E
Yes


1475
L → P
Yes


1916
C → S
Yes


1916
C → W
Yes


2228
R → G
No


2228
R → W
No


2251
M → V
Yes


2269
Y → C
No









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 211:







TABLE 211







InterPro domain(s)










InterPro ID
Domain description
Analysis type
Position(s) on protein





IPR001117
Multicopper oxidase, type 1
HMMPfam
212-343


IPR000421
Coagulation factor 5/8
HMMPfam
2037-2179, 2190-2336



type C domain (FA58C)


IPR000421
Coagulation factor 5/8
HMMSmart
2033-2182, 2186-2339



type C domain (FA58C)


IPR001117
Multicopper oxidase, type 1
ScanRegExp
2007-2027, 317-337, 699-719


IPR000421
Coagulation factor 5/8
ScanRegExp
2074-2101, 2231-2260



type C domain (FA58C)


IPR000421
Coagulation factor 5/8
ScanRegExp
2166-2182, 2323-2339



type C domain (FA58C)


IPR000421
Coagulation factor 5/8
ProfileScan
2034-2182, 2187-2339



type C domain (FA58C)









Variant protein HUMFVIII_PEA—1_P11 is encoded by the following transcript(s): HUMFVIII_PEA—1_T3. The coding portion of transcript HUMFVIII_PEA—1_T3 starts at position 124 and ends at position 7158. The transcript also has the following SNPs as listed in Table 212 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMFVIII_PEA—1_P11 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 212







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












207
C → T
Yes


329
A → T
Yes


733
A → C
Yes


1191
G → A
Yes


1971
T → C
Yes


2488
A → G
Yes


3885
C → G
Yes


3969
A → C
Yes


4026
A → C
Yes


4547
T → C
Yes


4626
A → C
Yes


5397
G → A
Yes


5870
G → C
Yes


5871
C → G
Yes


6747
C → T
Yes


6805
A → G
No


6805
A → T
No


6874
A → G
Yes


6929
A → G
No


7190
C → T
Yes


7863
T →
Yes


8346
C → T
Yes


8453
G → A
Yes


8689
C → A
Yes


8833
A → G
Yes









Variant protein HUMFVIII_PEA—1_P13 according to the present invention is encoded by transcript(s) HUMFVIII_PEA—1_T6. An alignment is given to the known protein (Coagulation factor VIII precursor) at the end in FIG. 178 of the application. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMFVIII_PEA—1_P13 and FA8_HUMAN:
1. An isolated chimeric polypeptide HUMFVIII_PEA—1_P13, comprising a first amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence MHRDARAQKASRG corresponding to amino acids 1-13 of HUMFVIII_PEA—1_P13, a second amino acid sequence being at least 90% homologous to FPPRVPKSFPFNTSVVYKKTLFVEFTDHLFNIAKPRPPWMGLLGPTIQAEVYDT VVITLKNMASHPVSLHAVGVSYWKASEGAEYDDQTSQREKEDDKVFPGGSH TYVWQVLKENGPMASDPLCLTYSYLSHVDLVKDLNSGLIGALLVCREGSLA KEKTQTLHKFILLFAVFDEGKSWHSETKNSLMQDRDAASARAWPKMHTVNG YVNRSLPG corresponding to amino acids 49-263 of FA8_HUMAN, which also corresponds to amino acids 14-228 of HUMFVIII_PEA—1_P13, and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence MYTPAQQSSGSSKFSTRVLYFSSQTARHLRGYSPLNT corresponding to amino acids 229-265 of HUMFVIII_PEA—1_P13, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a head of HUMFVIII_PEA—1_P13, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence MHRDARAQKASRG of HUMFVIII_PEA—1_P13.
3. An isolated polypeptide for a tail of HUMFVIII_PEA—1_P13, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence MYTPAQQSSGSSKFSTRVLYFSSQTARHLRGYSPLNT in HUMFVIII_PEA—1_P13.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: intracellularly. The protein localization is believed to be intracellularly because neither of the trans-membrane region prediction programs predicted a trans-membrane region for this protein. In addition both signal-peptide prediction programs predict that this protein is a non-secreted protein.
Variant protein HUMFVIII_PEA—1_P13 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 213, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMFVIII_PEA—1_P13 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 213







Amino acid mutations









SNP position(s) on amino
Alternative



acid sequence
amino acid(s)
Previously known SNP?












40
D → V
Yes


175
T → P
Yes









Variant protein HUMFVIII_PEA—1_P13 is encoded by the following transcript(s): HUMFVIII_PEA—1_T6. The coding portion of transcript HUMFVIII_PEA—1_T6 starts at position 124 and ends at position 918. The transcript also has the following SNPs as listed in Table 214 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMFVIII_PEA—1_P13 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 214







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?





242
A → T
Yes


646
A → C
Yes









FIG. 193 depict the domain structure of the variants described hereinabove in comparison to the known or wild-type (WT) protein (Factor VIII).
Example 56
Description for Cluster HUMC1RS
Cluster HUMC1RS features 5 transcript(s) and 41 segment(s) of interest, the names for which are given in Tables 215 and 216, respectively, the sequences themselves are given in SEQ ID NOs: 770-774; 775-815 and 816-820, for transcripts, segments and proteins, respectively. The selected protein variants are given in table 217.







TABLE 215







Transcripts of interest










Transcript Name
SEQ ID NO:







HUMC1RS_PEA_1_T2
770



 



HUMC1RS_PEA_1_T3
771



 



HUMC1RS_PEA_1_T10
772



 



HUMC1RS_PEA_1_T29
773



 



HUMC1RS_PEA_1_T34
774

















TABLE 216







Segments of interest










Segment Name
SEQ ID NO:







HUMC1RS_PEA_1_node_0
775



 



HUMCIRS_PEA_1_node_12
776



 



HUMC1RS_PEA_1_node_16
777



 



HUMC1RS_PEA_1_node_19
778



 



HUMC1RS_PEA_1_node_21
779



 



HUMC1RS_PEA_1_node_24
780



 



HUMC1RS_PEA_1_node_25
781



 



HUMC1RS_PEA_1_node_33
782



 



HUMC1RS_PEA_1_node_44
783



 



HUMC1RS_PEA_1_node_51
784



 



HUMC1RS_PEA_1_node_61
785



 



HUMC1RS_PEA_1_node_62
786



 



HUMC1RS_PEA_1_node_1
787



 



HUMC1RS_PEA_1_node_7
788



 



HUMC1RS_PEA_1_node_8
789



 



HUMC1RS_PEA_1_node_9
790



 



HUMC1RS_PEA_1_node_13
791



 



HUMC1RS_PEA_1_node_26
792



 



HUMC1RS_PEA_1_node_27
793



 



HUMC1RS_PEA_1_node_28
794



 



HUMC1RS_PEA_1_node_31
795



 



HUMC1RS_PEA_1_node_32
796



 



HUMC1RS_PEA_1_node_36
797



 



HUMC1RS_PEA_1_node_37
798



 



HUMC1RS_PEA_1_node_38
799



 



HUMC1RS_PEA_1_node_39
800



 



HUMC1RS_PEA_1_node_42
801



 



HUMC1RS_PEA_1_node_46
802



 



HUMC1RS_PEA_1_node_47
803



 



HUMC1RS_PEA_1_node_48
804



 



HUMC1RS_PEA_1_node_49
805



 



HUMC1RS_PEA_1_node_50
806



 



HUMC1RS_PEA_1_node_52
807



 



HUMC1RS_PEA_1_node_53
808



 



HUMC1RS_PEA_1_node_54
809



 



HUMC1RS_PEA_1_node_55
810



 



HUMC1RS_PEA_1_node_56
811



 



HUMC1RS_PEA_1_node_57
812



 



HUMC1RS_PEA_1_node_58
813



 



HUMC1RS_PEA_1_node_59
814



 



HUMC1RS_PEA_1_node_60
815

















TABLE 217







Proteins of interest














Corresponding



Protein Name
SEQ ID NO:
Protein Length
Transcript(s)





HUMC1RS_PEA_1_P8
816
P455
HUMC1RS_PEA_1_T10



 


HUMC1RS_PEA_1_P21
817
P405
HUMC1RS_PEA_1_T29


 


HUMC1RS_PEA_1_P22
818
P622
HUMC1RS_PEA_1_T34


 


HUMC1RS_PEA_1_P23
819
P292
HUMC1RS_PEA_1_T2


 


HUMC1RS_PEA_1_P24
820
P330
HUMC1RS_PEA_1_T3









These sequences are variants of the known protein Complement C1s component precursor (SwissProt accession identifier C1S_HUMAN; SEQ ID NO:821; known also according to the synonyms EC 3.4.21.42; C1 esterase), referred to herein as the previously known protein.
Protein Complement C1s component precursor is known or believed to have the following function(s): C1s B chain is a serine protease that combines with Clq and C1s to form C1, the first component of the classical pathway of the complement system. C1r activates C1s so that it can, in turn, activate C2 and C4. The sequence for protein Complement C1s component precursor is given in SEQ ID NO: 821, as “Complement C1s component precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 218.







TABLE 218







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment





383
R → H (in dbSNP: 20573). /FTId = VAR_014565.


294
C → K


513
G → GG


573
T → A


645-646
TK → GR









It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein or of drugs directed against the protein are as follows: Complement factor 1s inhibitor. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Cardiovascular; Anti-inflammatory.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: proteolysis and peptidolysis; complement activation, classical pathway, which are annotation(s) related to Biological Process; and complement component C1s; chymotrypsin; trypsin; calcium binding; serine-type peptidase; hydrolase, which are annotation(s) related to Molecular Function. The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
FIG. 194 depicts the complement pathway (see for example U.S. Pat. No. 6,010,873).
The first component of complement, C1, comprises two homologous serine proteases, C1r and C1s, assembled with C1q in a tetramer: C1s-C1r-C1r-C1s:C1q
C1s and C1r are the proteases responsible for activating the classical pathway via activating the proteolytic activity of the C1 complex: C1r autoactivation, cleavage of C1s by active C1r, cleavage of C4 and C2 by active C1s, generation of C3 convertase.
Uncontrolled activation of C1s can contribute to the pathogenesis of several diseases, including but not limited to ischemia and reperfusion, angioedema, and injury related tissue damage, neurodegenerative diseases (Alzheimer), rheumatoid arthritis.
Deficiency of C1s (as well as C1r) often causes systemic lupus erythematosus-like syndromes, severe pyogenic infections, and accounts for multiple autoimmune diseases.
Complement component C5 participates in both cytolytic and inflammatory processes. Pro-05 is composed of disulfate-linked a- and b-chains designated C5. Activation of the complement system initiates a cascade of proteolytic events in which the two chain-C5 component is cleaved by C5 convertase, and yields the C5a and C5b.
C5a is a powerful mediator of inflammation with anaphylotoxic activity. It elicits its activity via binding to the 7-transmembrane, GPCR, C5a receptor (C5aR), expressed on cells of myeloid origin (neutrophils, eosenophils, and basophils, macrophages and monocytes), epithelial cells, smooth muscle cells and on activated B and T cells. C5aR activation with sub-nanomolar levels of C5a result in chemotaxis of all myeloid lineages, while higher nanomolar concentrations elicit degranulation and activation of NADPH oxidase. C5b triggers the formation of the membrane-attack complex that can damage certain pathogens.
Unregulated C5a production is involved in the following non-limiting list of diseases: adult respiratory distress syndrome, local inflammation, chronic obstructive pulmonary disease (COPD), myocardial ischemia multiple sclerosis, Alzheimer disease, autoimmune disease-related tissue injury, and renal disease.
Complement receptor type I (CR1, or CD35, or C3b/C4b receptor) belongs to the family of regulators of complement activation (RCA). These receptors accelerate the dissociation of C3 and C5 convertases, an activity known as decay accelerating activity (DAA), and/or serve as cofactors for the factor I-mediated cleavage of C3b and C4b, that result in inactivation of these molecules, and which is known as cofactor activity (CA). CR1 is expressed by most peripheral blood cells, but not on platelets, natural killer cells and most T cells.
FIGS. 195, 196, 197 and 198 depict CS-clinical developments, CS, preclinical developments, CR1 clinical development, C1s-clinical developments, respectively.
As noted above, cluster HUMC1RS features 5 transcript(s), which were listed in Table 215 above. These transcript(s) encode for protein(s) which are variant(s) of protein Complement C1s component precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HUMC1RS_PEA—1_P8 according to the present invention is encoded by transcript(s) HUMC1RS_PEA—1_T10. An alignment is given to the known protein (Complement C1s component precursor) in FIG. 179. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMC1RS_PEA—1_P8 and C1S_HUMAN:
1. An isolated chimeric polypeptide HUMC1RS_PEA—1_P8, comprising a first amino acid sequence being at least 90% homologous to MWCIVLFSLLAWVYAEPTMYGEILSPNYPQAYPSEVEKSWDIEVPEGYGIHL YFTHLDIELSENCAYDSVQIISGDTEEGRLCGQRSSNNPHSPIVEEFQVPYNKL QVIFKSDFSNEERFTGFAAYYVATDINECTDFVDVPCSHFCNNFIGGYFCSCPP EYFLHDDMKNCGVNCSGDVFTALIGEIASPNYPKPYPENSRCEYQIRLEKGFQ VVVTLRREDFDVEAADSAGNCLDSLVFVAGDRQFGPYCGHGFPGPLNIETKS NALDIIFQTDLTGQKKGWKLRYHGDPMPCPKEDTPNSVWEPAKAKYVFRDV VQITCLDGFEVVEGRVGATSFYSTCQSNGKWSNSKLKCQPVDCGIPESIENGK VEDPESTLFGSVIRYTCEEPYYYMENGGGGEYHCAGNGSWVNEVLGPELPKC VP corresponding to amino acids 1-423 of C1S_HUMAN, which also corresponds to amino acids 1-423 of HUMC1RS_PEA—1_P8, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GLNSDLPESSSVRWQYHCAVGCQGRGEPPQPH corresponding to amino acids 424-455 of HUMC1RS_PEA—1_P8, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMC1RS_PEA—1_P8, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GLNSDLPESSSVRWQYHCAVGCQGRGEPPQPH in HUMC1RS_PEA—1_P8.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMC1RS_PEA—1_P8 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 219, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC1RS_PEA—1_P8 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 219







Amino acid mutations









SNP position(s) on amino
Alternative



acid sequence
amino acid(s)
Previously known SNP?





119
R → H
Yes


327
V → L
Yes


334
A →
No


396
G → R
No









The glycosylation sites of variant protein HUMC1RS_PEA—1_P8, as compared to the known protein Complement C1s component precursor, are described in Table 220 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 220







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





174
yes
174


406
yes
406









The phosphorylation sites of variant protein HUMC1RS_PEA—1_P8, as compared to the known protein Complement C1s component precursor, are described in Table 221 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 221







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





149
yes
149









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 222:







TABLE 222







InterPro domain(s)










InterPro ID
Domain description
Analysis type
Position(s) on protein





IPR006209
EGF-like domain
HMMPfam
135-171


IPR000436
Sushi domain/SCR
HMMPfam
294-354, 359-421



domain/CCP module


IPR000859
CUB
HMMPfam
175-287, 18-127


IPR000436
Sushi domain/SCR
HMMSmart
294-354, 359-421



domain/CCP module


IPR000859
CUB
HMMSmart
175-290, 9-130


IPR001881
EGF-like calcium-binding
HMMSmart
131-172


IPR000152
Aspartic acid and
ScanRegExp
147-158



asparagine hydroxylation



site


IPR001881
EGF-like calcium-binding
ScanRegExp
131-156


IPR000859
CUB
ProfileScan
175-290, 3-130









Variant protein HUMC1RS_PEA—1_P8 is encoded by the following transcript(s): HUMC1RS_PEA—1_T10. The coding portion of transcript HUMC1RS_PEA—1_T10 starts at position 713 and ends at position 2077. The transcript also has the following SNPs as listed in Table 223 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC1RS_PEA—1_P8 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 223







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












417
G → T
No


693
G →
No


1068
G → A
Yes


1074
→ A
No


1074
→ G
No


1153
C → T
Yes


1691
G → C
Yes


1714
A →
No


1879
A → G
Yes


1898
G → A
No


1898
G → C
No


2644
A → C
No


2678
C → G
No


2768
C → T
No


2789
G → A
No


2863
A → T
Yes


2889
C → T
No


3058
G → T
Yes


3081
A → G
Yes


3099
C → T
Yes


3117
C → T
Yes


3132
G → C
Yes


3189
G → C
Yes


3247
C → T
Yes


3254
C → T
Yes


3340
A → C
Yes









Variant protein HUMC1RS_PEA—1_P21 according to the present invention is encoded by transcript(s) HUMC1RS_PEA—1_T29. An alignment is given to the known protein (Complement C1s component precursor) in FIG. 180. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMC1RS_PEA—1_P21 and C1S_HUMAN:
1. An isolated chimeric polypeptide HUMC1RS_PEA—1_P21, comprising a first amino acid sequence being at least 90% homologous to MWCIVLFSLLAWVYAEPTMYGEILSPNYPQAYPSEVEKSWDIEVPEGYGIHL YFTHLDIELSENCAYDSVQIISGDTEEGRLCGQRSSNNPHSPIVEEFQVPYNKL QVIFKSDFSNEERFTGFAAYYVATDINECTDFVDVPCSHFCNNFIGGYFCSCPP EYFLHDDMKNCGVNCSGDVFTALIGEIASPNYPKPYPENSRCEYQIRLEKGFQ VVVTLRREDFDVEAADSAGNCLDSLVFVAGDRQFGPYCGHGFPGPLNIETKS NALDIIFQTDLTGQKKGWKLRYHGDPMPCPKEDTPNSVWEPAKAKYVFRDV VQITCLDGFEVVEGRVGATSFYSTCQSNGKWSNSKLKCQ corresponding to amino acids 1-355 of C1S_HUMAN, which also corresponds to amino acids 1-355 of HUMC1RS_PEA—1_P21, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence RMCLFKVEVFLFLSERMERSAHQNSNAWFPLRHVREWVGFLKGSQSWKLF corresponding to amino acids 356-405 of HUMC1RS_PEA—1_P21, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMC1RS_PEA—1_P21, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence RMCLFKVEVFLFLSERMERSAHQNSNAWFPLRHVREWVGFLKGSQSWKLF in HUMC1RS_PEA—1_P21.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMC1RS_PEA—1_P21 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 224, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC1RS_PEA—1_P21 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 224







Amino acid mutations









SNP position(s) on amino
Alternative



acid sequence
amino acid(s)
Previously known SNP?





119
R → H
Yes


327
V → L
Yes


334
A →
No









The glycosylation sites of variant protein HUMC1RS_PEA—1_P21, as compared to the known protein Complement C1s component precursor, are described in Table 225 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 225







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





174
yes
174


406
no









The phosphorylation sites of variant protein HUMC1RS_PEA—1_P21, as compared to the known protein Complement C1s component precursor, are described in Table 226 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 226







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





149
yes
149









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 227:







TABLE 227







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR006209
EGF-like domain
HMMPfam
135-171


IPR000436
Sushi domain/SCR
HMMPfam
294-354



domain/CCP module


IPR000859
CUB
HMMPfam
175-287, 18-127


IPR000436
Sushi domain/SCR
HMMSmart
294-354



domain/CCP module


IPR000859
CUB
HMMSmart
175-290, 9-130


IPR001881
EGF-like calcium-
HMMSmart
131-172



binding


IPR000152
Aspartic acid and
ScanRegExp
147-158



asparagine



hydroxylation



site


IPR001881
EGF-like calcium-
ScanRegExp
131-156



binding


IPR000859
CUB
ProfileScan
175-290, 3-130









Variant protein HUMC1RS_PEA—1_P21 is encoded by the following transcript(s): HUMC1RS_PEA—1_T29. The coding portion of transcript HUMC1RS_PEA—1_T29 starts at position 713 and ends at position 1927. The transcript also has the following SNPs as listed in Table 228 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC1RS_PEA—1_P21 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 228







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












417
G → T
No


693
G →
No


1068
G → A
Yes


1074
→ A
No


1074
→ G
No


1153
C → T
Yes


1691
G → C
Yes


1714
A →
No









Variant protein HUMC1RS_PEA—1_P22 according to the present invention is encoded by transcript(s) HUMC1RS_PEA—1_T34. An alignment is given to the known protein (Complement C1s component precursor) in FIG. 181. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMC1RS_PEA—1_P22 and C1S_HUMAN:
1. An isolated chimeric polypeptide HUMC1RS_PEA—1_P22, comprising a first amino acid sequence being at least 90% homologous to MWCIVLFSLLAWVYAEPTMYGEILSPNYPQAYPSEVEKSWDIEVPEGYGIHL YFTHLDIELSEN corresponding to amino acids 1-64 of C1S_HUMAN, which also corresponds to amino acids 1-64 of HUMC1RS_PEA—1_P22, a second amino acid sequence bridging amino acid sequence comprising of Y, and a third amino acid sequence being at least 90% homologous to INECTDFVDVPCSHFCNNFIGGYFCSCPPEYFLHDDMKNCGVNCSGDVFTALI GEIASPNYPKPYPENSRCEYQIRLEKGFQVVVTLRREDFDVEAADSAGNCLDS LVFVAGDRQFGPYCGHGFPGPLNIETKSNALDIIFQTDLTGQKKGWKLRYHG DPMPCPKEDTPNSVWEPAKAKYVFRDVVQITCLDGFEVVEGRVGATSFYSTC QSNGKWSNSKLKCQPVDCGIPESIENGKVEDPESTLFGSVIRYTCEEPYYYME NGGGGEYHCAGNGSWVNEVLGPELPKCVPVCGVPREPFEEKQRIIGGSDADI KNFPWQVFFDNPWAGGALINEYWVLTAAHVVEGNREPTMYVGSTSVQTSRL AKSKMLTPEHVFIHPGWKLLEVPEGRTNFDNDIALVRLKDPVKMGPTVSPICL PGTSSDYNLMDGDLGLISGWGRTEKRDRAVRLKAARLPVAPLRKCKEVKVE KPTADAEAYVFTPNMICAGGEKGMDSCKGDSGGAFAVQDPNDKTKFYAAG LVSWGPQCGTYGLYTRVKNYVDWIMKTMQENSTPRED corresponding to amino acids 132-688 of C1S_HUMAN, which also corresponds to amino acids 66-622 of HUMC1RS_PEA—1_P22, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated edge portion of HUMC1RS_PEA—1_P22, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise NYI having a structure as follows (numbering according to HUMC1RS_PEA—1_P22): a sequence starting from any of amino acid numbers 64-x to 64; and ending at any of amino acid numbers 66+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMC1RS_PEA—1_P22 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 229, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC1RS_PEA—1_P22 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 229







Amino acid mutations









SNP position(s) on amino
Alternative



acid sequence
amino acid(s)
Previously known SNP?





261
V → L
Yes


268
A →
No


330
G → R
No


507
T → P
No


518
A → G
No


548
P → L
No


555
G → E
No


580
K → *
Yes









The glycosylation sites of variant protein HUMC1RS_PEA—1_P22, as compared to the known protein Complement C1s component precursor, are described in Table 230 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 230







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





174
yes
108


406
yes
340









The phosphorylation sites of variant protein HUMC1RS_PEA—1_P22, as compared to the known protein Complement C1s component precursor, are described in Table 231 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 231







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





149
yes
83









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 232:







TABLE 232







InterPro domain(s)










InterPro ID
Domain description
Analysis type
Position(s) on protein





IPR001254
Peptidase S1,
ProfileScan
372-614



chymotrypsin


IPR001314
Peptidase S1A,
FPrintScan
395-410, 459-473, 559-571



chymotrypsin


IPR006209
EGF-like domain
HMMPfam
69-105


IPR000436
Sushi domain/SCR
HMMPfam
228-288, 293-355



domain/CCP module


IPR001254
Peptidase S1,
HMMPfam
372-609



chymotrypsin


IPR000859
CUB
HMMPfam
109-221


IPR001254
Peptidase S1,
HMMSmart
371-609



chymotrypsin


IPR000436
Sushi domain/SCR
HMMSmart
228-288, 293-355



domain/CCP module


IPR000859
CUB
HMMSmart
109-224, 9-104


IPR001881
EGF-like calcium-binding
HMMSmart
66-106


IPR000152
Aspartic acid and
ScanRegExp
81-92



asparagine hydroxylation



site


IPR001254
Peptidase S1,
ScanRegExp
560-571



chymotrypsin


IPR000859
CUB
ProfileScan
109-224, 3-91









Variant protein HUMC1RS_PEA—1_P22 is encoded by the following transcript(s): HUMC1RS_PEA—1_T34. The coding portion of transcript HUMC1RS_PEA—1_T34 starts at position 713 and ends at position 2578. The transcript also has the following SNPs as listed in Table 233 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC1RS_PEA—1_P22 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 233







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












417
G → T
No


693
G →
No


955
C → T
Yes


1493
G → C
Yes


1516
A →
No


1681
A → G
Yes


1700
G → A
No


1700
G → C
No


2231
A → C
No


2265
C → G
No


2355
C → T
No


2376
G → A
No


2450
A → T
Yes


2476
C → T
No


2645
G → T
Yes


2668
A → G
Yes


2686
C → T
Yes


2704
C → T
Yes


2719
G → C
Yes


2776
G → C
Yes


2834
C → T
Yes


2841
C → T
Yes


2927
A → C
Yes









Variant protein HUMC1RS_PEA—1_P23 according to the present invention is encoded by transcript(s) HUMC1RS_PEA—1_T2. An alignment is given to the known protein (Complement C1s component precursor) in FIG. 182. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMC1RS_PEA—1_P23 and C1S_HUMAN:
1. An isolated chimeric polypeptide HUMC1RS_PEA—1_P23, comprising a first amino acid sequence being at least 90% homologous to MWCIVLFSLLAWVYAEPTMYGEILSPNYPQAYPSEVEKSWDIEVPEGYGIHL YFTHLDIELSENCAYDSVQIISGDTEEGRLCGQRSSNNPHSPIVEEFQVPYNKL QVIFKSDFSNEERFTGFAAYYVATDINECTDFVDVPCSHFCNNFIGGYFCSCPP EYFLHDDMKNCGVNCSGDVFTALIGEIASPNYPKPYPENSRCEYQIRLEKGFQ VVVTLRREDFDVEAADSAGNCLDSLVFVAGDRQFGPYCGHGFPGPLNIETKS NALDIIFQTDLTGQKKGWKLRYHGD corresponding to amino acids 1-290 of C1S_HUMAN, which also corresponds to amino acids 1-290 of HUMC1RS_PEA—1_P23, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence RE corresponding to amino acids 291-292 of HUMC1RS_PEA—1_P23, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMC1RS_PEA—1_P23 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 234, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC1RS_PEA—1_P23 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 234







Amino acid mutations









SNP position(s) on amino
Alternative



acid sequence
amino acid(s)
Previously known SNP?





119
R → H
Yes









The glycosylation sites of variant protein HUMC1RS_PEA—1_P23, as compared to the known protein Complement C1s component precursor, are described in Table 235 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 235







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





174
yes
174


406
no









The phosphorylation sites of variant protein HUMC1RS_PEA—1_P23, as compared to the known protein Complement C1s component precursor, are described in Table 236 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 236







Phosphorylation site(s)









Position(s) on known
Present in



amino acid sequence
variant protein?
Position in variant protein?





149
yes
149









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 237:







TABLE 237







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR006209
EGF-like domain
HMMPfam
135-171


IPR000859
CUB
HMMPfam
16-127, 175-287


IPR001881
EGF-like calcium-
HMMPfam
131-171



binding


IPR000859
CUB
HMMSmart
175-290, 9-130


IPR001881
EGF-like calcium-
HMMSmart
131-172



binding


IPR000152
Aspartic acid and
ScanRegExp
147-158



asparagine



hydroxylation



site


IPR001881
EGF-like calcium-
ScanRegExp
131-156



binding


IPR000859
CUB
ProfileScan
175-290, 3-130









Variant protein HUMC1RS_PEA—1_P23 is encoded by the following transcript(s): HUMC1RS_PEA—1_T2. The coding portion of transcript HUMC1RS_PEA—1_T2 starts at position 713 and ends at position 1588. The transcript also has the following SNPs as listed in Table 238 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC1RS_PEA—1_P23 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 238







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












417
G → T
No


693
G →
No


1068
G → A
Yes


1074
→ A
No


1074
→ G
No


1153
C → T
Yes


2238
G → C
Yes


2261
A →
No


2426
A → G
Yes


2445
G → A
No


2445
G → C
No


2976
A → C
No


3010
C → G
No


3100
C → T
No


3121
G → A
No


3195
A → T
Yes


3221
C → T
No


3390
G → T
Yes


3413
A → G
Yes


3431
C → T
Yes


3449
C → T
Yes


3464
G → C
Yes


3521
G → C
Yes


3579
C → T
Yes


3586
C → T
Yes


3672
A → C
Yes









Variant protein HUMC1RS_PEA—1_P24 according to the present invention is encoded by transcript(s) HUMC1RS_PEA—1_T3. An alignment is given to the known protein (Complement C1s component precursor) in FIG. 183. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMC1RS_PEA—1_P24 and C1S_HUMAN:
1. An isolated chimeric polypeptide HUMC1RS_PEA—1_P24, comprising a first amino acid sequence being at least 90% homologous to MWCIVLFSLLAWVYAEPTMYGEILSPNYPQAYPSEVEKSWDIEVPEGYGIHL YFTHLDIELSENCAYDSVQIISGDTEEGRLCGQRSSNNPHSPIVEEFQVPYNKL QVIFKSDFSNEERFTGFAAYYVATDINECTDFVDVPCSHFCNNFIGGYFCSCPP EYFLHDDMKNCGVNCSGDVFTALIGEIASPNYPKPYPENSRCEYQIRLEKGFQ VVVTLRREDFDVEAADSAGNCLDSLVFVAGDRQFGPYCGHGFPGPLNIETKS NALDIIFQTDLTGQKKGWKLRYHGDPMPCPKEDTPNSVWEPAKAKYVFRDV VQITCLDGFEVVE corresponding to amino acids 1-329 of C1S_HUMAN, which also corresponds to amino acids 1-329 of HUMC1RS_PEA—1_P24, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence K corresponding to amino acids 330-330 of HUMC1RS_PEA—1_P24, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMC1RS_PEA—1_P24 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 239, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC1RS_PEA—1_P24 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 239







Amino acid mutations









SNP position(s) on amino

Previously known


acid sequence
Alternative amino acid(s)
SNP?





119
R → H
Yes


327
V → L
Yes









The glycosylation sites of variant protein HUMC1RS_PEA—1_P24, as compared to the known protein Complement C1s component precursor, are described in Table 240 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 240







Glycosylation site(s)









Position(s) on known
Present in variant



amino acid sequence
protein?
Position in variant protein?





174
yes
174


406
no









The phosphorylation sites of variant protein HUMC1RS_PEA—1_P24, as compared to the known protein Complement C1s component precursor, are described in Table 241 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 241







Phosphorylation site(s)









Position(s) on known
Present in variant



amino acid sequence
protein?
Position in variant protein?





149
yes
149









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 242:







TABLE 242







InterPro domain(s)












Analysis
Position(s)


InterPro ID
Domain description
type
on protein





IPR006209
EGF-like domain
HMMPfam
135-171


IPR000859
CUB
HMMPfam
 16-127,





175-287


IPR001881
EGF-like calcium-binding
HMMPfam
131-171


IPR000859
CUB
HMMSmart
175-290, 9-130


IPR001881
EGF-like calcium-binding
HMMSmart
131-172


IPR000152
Aspartic acid and
ScanRegExp
147-158



asparagine hydroxylation



site


IPR001881
EGF-like calcium-binding
ScanRegExp
131-156


IPR000859
CUB
ProfileScan
175-290, 3-130









Variant protein HUMC1RS_PEA—1_P24 is encoded by the following transcript(s): HUMC1RS_PEA—1_T3. The coding portion of transcript HUMC1RS_PEA—1_T3 starts at position 713 and ends at position 1702. The transcript also has the following SNPs as listed in Table 243 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMC1RS_PEA—1_P24 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 243







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












417
G → T
No


693
G →
No


1068
G → A
Yes


1074
→ A
No


1074
→ G
No


1153
C → T
Yes


1691
G → C
Yes


1744
A →
No


1909
A → G
Yes


1928
G → A
No


1928
G → C
No


2459
A → C
No


2493
C → G
No


2583
C → T
No


2604
G → A
No


2678
A → T
Yes


2704
C → T
No


2873
G → T
Yes


2896
A → G
Yes


2914
C → T
Yes


2932
C → T
Yes


2947
G → C
Yes


3004
G → C
Yes


3062
C → T
Yes


3069
C → T
Yes


3155
A → C
Yes









FIG. 199 depicts the domain structure of the variants described hereinabove in comparison to the known or wild-type (WT) protein
Example 57
Description for Cluster HSGROW1
Cluster HSGROW1 features 5 transcript(s) and 22 segment(s) of interest, the names for which are given in Tables 244 and 245, respectively, the sequences themselves are given in SEQ ID NOs: 822-826; 827-848 and 851-855, for transcripts, segments and proteins, respectively. The selected protein variants are given in table 246.







TABLE 244







Transcripts of interest










Transcript Name
SEQ ID NO:







HSGROW1_PEA_1_T6
822



 



HSGROW1_PEA_1_T10
823



 



HSGROW1_PEA_1_T11
824



 



HSGROW1_PEA_1_T12
825



 



HSGROW1_PEA_1_T18
826

















TABLE 245







Segments of interest










Segment Name
SEQ ID NO:







HSGROW1_PEA_1_node_2
827



 



HSGROW1 PEA_1_node_16
828



 



HSGROW1_PEA_1_node_22
829



 



HSGROW1_PEA_1_node_0
830



 



HSGROW1_PEA_1_node_4
831



 



HSGROW1_PEA_1_node_5
832



 



HSGROW1 PEA_1_node_6
833



 



HSGROW1_PEA_1_node_7
834



 



HSGROW1_PEA_1_node_9
835



 



HSGROW1_PEA_1_node_10
836



 



HSGROW1_PEA_1_node_11
837



 



HSGROW1_PEA_1_node_12
838



 



HSGROW1_PEA_1_node_13
839



 



HSGROW1_PEA_1_node_14
840



 



HSGROW1_PEA_1_node_15
841



 



HSGROW1_PEA_1_node_17
842



 



HSGROW1 PEA_1_node_18
843



 



HSGROW1_PEA_1_node_19
844



 



HSGROW1_PEA_1_node_20
845



 



HSGROW1_PEA_1_node_21
846



 



HSGROW1_PEA_1_node_23
847



 



HSGROW1 PEA_1_node_24
848

















TABLE 246







Proteins of interest











Corresponding


Protein Name
SEQ ID NO:
Transcript(s)





HSGROW1_PEA_1_P7
851
HSGROW1_PEA_1_T6


 


HSGROW1_PEA_1_P11
852
HSGROW1_PEA_1_T10


 


HSGROW1_PEA_1_P12
853
HSGROW1_PEA_1_T11


 


HSGROW1_PEA_1_P18
854
HSGROW1_PEA_1_T18


 


HSGROW1_PEA_1_P21
855
HSGROW1_PEA_1_T12









These sequences are variants of the known protein Somatotropin precursor (SwissProt accession identifier SOMA_HUMAN; SEQ ID NO:850; known also according to the synonyms Growth hormone; GH; GH-N; Pituitary growth hormone; Growth hormone 1), referred to herein as the previously known protein.
Protein Somatotropin precursor is known or believed to have the following function(s): Plays an important role in growth control. Its major role in stimulating body growth is to stimulate the liver and other tissues to secrete IGF-1. It stimulates both the differentiation and proliferation of myoblasts. It also stimulates amino acid uptake and protein synthesis in muscle and other tissues. The sequence for protein Somatotropin precursor is given in SEQ ID NO: 850, as “Somatotropin precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 247.







TABLE 247







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment











3
T → A (in IGHD IB; dbSNP: 2001345).



/FTId = VAR_011917.


16
L → P (in IGHD IB; supresses secretion).



/FTId = VAR_015801.


37
D → N (in IGHD IB). /FTId = VAR_015802.


42
R → C (in IGHD IB; reduced secretion).



/FTId = VAR_015803.


53
T → I (in IGHD IB; reduced ability to activate the



JAK/STAT pathway). /FTId = VAR_015804.


67
K → R (in IGHD IB; reduced ability to activate the



JAK/STAT pathway). /FTId = VAR_015805.


73
N → D (in IGHD IB; reduced ability to activate the



JAK/STAT pathway). /FTId = VAR_015806.


97
S → F (in IGHD IB; reduced ability to activate the



JAK/STAT pathway). /FTId = VAR_015807.


100
E → K (in IGHD IB). /FTId = VAR_015808.


103
R → C (in Kowarski syndrome; loss of activity).



/FTId = VAR_015809.


105
S → C (in dbSNP: 6174). /FTId = VAR_011918.


117
Q → L (in IGHD IB; reduced secretion).



/FTId = VAR_015810.


134
S → C (in IGHD IB). /FTId = VAR_015811.


134
S → R (in IGHD IB; reduced ability to activate the



JAK/STAT pathway). /FTId = VAR_015812.


136
V → I (in dbSNP: 5388). /FTId = VAR_011919.


138
D → G (in Kowarski syndrome; loss of activity).



/FTId = VAR_015813.


201
T → A (in IGHD IB; reduced ability to activate the



JAK/STAT pathway). /FTId = VAR_015814.


209
R → H (in IGHD II). /FTId = VAR_015815.


35
L → P


40
M → S









Protein Somatotropin precursor localization is believed to be Secreted.
The previously known protein also has the following indication(s) and/or potential therapeutic use(s): Diabetes, Type II; Acromegaly; Sex-chromosome abnormality, Turner's syndrome; Growth hormone deficiency; Dwarfism; Burns; Cachexia; Osteoporosis; Uraemia; Short-bowel syndrome; Lipodystrophy; Infertility, female; Regeneration, bone; Wound healing. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein are as follows: Growth factor agonist; Growth hormone releasing factor agonist; Growth hormone modulator. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Antidiabetic; Symptomatic antidiabetic; Urological; Somatostatin; Anticancer; Ophthalmological; Growth hormone; Reproductive/gonadal, general; Musculoskeletal; Gene therapy; GI inflammatory/bowel disorders; Hypolipaemic/Antiatherosclerosis; Anabolic; Fertility enhancer; Vulnerary; Releasing hormone; Alimentary/Metabolic; Anorectic/Antiobesity.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: signal transduction, which are annotation(s) related to Biological Process; and hormone; peptide hormone, which are annotation(s) related to Molecular Function.
The GO assignment relies on information from one or more of the SwissProt/TremBl Protein knowledgebase, or Locuslink.
Growth Hormone (GH) plays an important role in growth with (among others) the following important activities: stimulates the production of IGF-1 and stimulates amino acid uptake and protein synthesis in muscles and other tissues. Receptor Binding occurs through dimerization-GH first binds via site 1 to GH receptor and through site 2 to another GH hormone receptor forming the complex GHR/GH/GHR. Clinical use includes (among other indications) pituitary dwarfism and Turner's syndrome (agonist); and acromelagy—a disease that affects middle aged adults in which there is excess GH, which causes overgrowth of bone and cartilage (antagonist).
FIG. 200 depicts GH antagonists-launched products and FIG. 201 depicts GH antagonists-clinical development.
As noted above, cluster HSGROW1 features 5 transcript(s), which were listed in Table 244 above. These transcript(s) encode for protein(s) which are variant(s) of protein Somatotropin precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HSGROW1_PEA—1_P7 according to the present invention is encoded by transcript(s) HSGROW1_PEA—1_T6. An alignment is given to the known protein (Somatotropin precursor) in FIG. 184. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSGROW1_PEA—1_P7 and SOMA_HUMAN:
1. An isolated chimeric polypeptide HSGROW1_PEA—1_P7, comprising a first amino acid sequence being at least 90% homologous to MATGSRTSLLLAFGLLCLPWLQEGSAFPTIPLSRLFDNAMLRAHRLHQLAFDT YQEF corresponding to amino acids 1-57 of SOMA_HUMAN, which also corresponds to amino acids 1-57 of HSGROW1_PEA—1_P7, and a second amino acid sequence being at least 90% homologous to TSLCFSESIPTPSNREETQQKSNLELLRISLLLIQSWLEPVQFLRSVFANSLVYG ASDSNVYDLLKDLEEGIQTLMGRLEDGSPRTGQIFKQTYSKFDTNSHNDDAL LKNYGLLYCFRKDMDKVETFLRIVQCRSVEGSCGF corresponding to amino acids 76-217 of SOMA_HUMAN, which also corresponds to amino acids 58-199 of HSGROW1_PEA—1_P7, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HSGROW1_PEA—1_P7, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise FT, having a structure as follows: a sequence starting from any of amino acid numbers 57-x to 57; and ending at any of amino acid numbers 58+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because of manual inspection of known protein localization and/or gene structure. Variant protein HSGROW1_PEA—1_P7 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 248, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSGROW1_PEA—1_P7 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 248







Amino acid mutations









SNP position(s) on amino

Previously known


acid sequence
Alternative amino acid(s)
SNP?












12
A → S
Yes


12
A → P
Yes


59
S →
No


59
S → F
No


69
P → T
No


79
S →
No


84
L →
No


91
I →
No


106
A →
No


121
L →
No


174
F → C
Yes


174
F → Y
Yes









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 249:







TABLE 249







InterPro domain(s)












Analysis
Position(s)


InterPro ID
Domain description
type
on protein





IPR001400
Somatotropin hormone
FPrintScan
161-177, 177-191,





61-74, 83-101


IPR001400
Somatotropin hormone
HMMPfam
 9-197


IPR001400
Somatotropin hormone
ScanRegExp
61-94


IPR001400
Somatotropin hormone
ScanRegExp
173-190









Variant protein HSGROW1_PEA—1_P7 is encoded by the following transcript(s): HSGROW1_PEA—1_T6. The coding portion of transcript HSGROW1_PEA—1_T6 starts at position 109 and ends at position 705. The transcript also has the following SNPs as listed in Table 250 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSGROW1_PEA—1_P7 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 250







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












32
C → A
Yes


32
C → G
Yes


66
C → G
No


73
C →
No


142
G → C
Yes


142
G → T
Yes


284
C →
No


284
C → T
No


313
C → A
No


344
C →
No


358
C →
No


381
C →
No


381
C → A
No


425
C →
No


471
C →
No


471
C → T
No


629
T → A
Yes


629
T → G
Yes


675
G → A
No


750
C →
No


750
C → T
Yes


767
C →
No


767
C → G
No


772
C →
No


772
C → T
No


797
→ A
No









Variant protein HSGROW1_PEA—1_P11 according to the present invention is encoded by transcript(s) HSGROW1_PEA—1_T10. An alignment is given to the known protein (Somatotropin precursor) in FIG. 185. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSGROW1_PEA—1_μl and SOMA_HUMAN:
1. An isolated chimeric polypeptide HSGROW1_PEA—1_P11, comprising a first amino acid sequence being at least 90% homologous to MATGSRTSLLLAFGLLCLPWLQEGSAFPTIPLSRLFDNAMLRAHRLHQLAFDT YQEFEEAYIPKEQKYSFLQNPQTSLCFSESIPTPSNREETQQKSNLELLRISLLLI QSWLEPVQFLRSVFANSLVYGASDSNVYDLLKDLEEGIQTLMG corresponding to amino acids 1-152 of SOMA_HUMAN, which also corresponds to amino acids 1-152 of HSGROW1_PEA—1_P11, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VRVAPGVPNPGAPLTLRAVLEKHCCPLFSSQALTQENSPYSSFPLVNPPGLSLH PEGEGGK corresponding to amino acids 153-213 of HSGROW1_PEA—1_P11, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSGROW1_PEA—1_P11, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VRVAPGVPNPGAPLTLRAVLEKHCCPLFSSQALTQENSPYSSFPLVNPPGLSLH PEGEGGK in HSGROW1_PEA—1_P11.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because of manual inspection of known protein localization and/or gene structure. Variant protein HSGROW1_PEA—1_P11 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 251, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSGROW1_PEA—1_P11 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 251







Amino acid mutations









SNP position(s) on amino

Previously known


acid sequence
Alternative amino acid(s)
SNP?












12
A → P
Yes


12
A → S
Yes


63
P →
No


77
S →
No


77
S → F
No


87
P → T
No


97
S →
No


102
L →
No


109
I →
No


124
A →
No


139
L →
No









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 252:







TABLE 252







InterPro domain(s)












Analysis
Position(s)


InterPro ID
Domain description
type
on protein





IPR001400
Somatotropin hormone
FPrintScan
101-119, 79-92


IPR001400
Somatotropin hormone
HMMPfam
 9-176


IPR001400
Somatotropin hormone
ScanRegExp
79-112









Variant protein HSGROW1_PEA—1_P11 is encoded by the following transcript(s): HSGROW1_PEA—1_T10. The coding portion of transcript HSGROW1_PEA—1_T10 starts at position 109 and ends at position 747. The transcript also has the following SNPs as listed in Table 253 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSGROW1_PEA—1_μl sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 253







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












32
C → A
Yes


32
C → G
Yes


66
C → G
No


73
C →
No


142
G → C
Yes


142
G → T
Yes


297
A →
No


297
A → C
No


338
C →
No


338
C → T
No


367
C → A
No


398
C →
No


412
C →
No


435
C →
No


435
C → A
No


479
C →
No


525
C →
No


525
C → T
No


936
T → A
Yes


936
T → G
Yes


982
G → A
No


1057
C →
No


1057
C → T
Yes


1074
C →
No


1074
C → G
No


1079
C →
No


1079
C → T
No


1104
→ A
No









Variant protein HSGROW1_PEA—1_P12 according to the present invention is encoded by transcript(s) HSGROW1_PEA—1_T11. An alignment is given to the known protein (Somatotropin precursor) in FIG. 186. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSGROW1_PEA—1_P12 and SOMA_HUMAN:
1. An isolated chimeric polypeptide HSGROW1_PEA—1_P12, comprising a first amino acid sequence being at least 90% homologous to MATGSRTSLLLAFGLLCLPWLQEGSAFPTIPLSRLFDNAMLRAHRLHQLAFDT YQEFEEAYIPKEQKYSFLQNPQTSLCFSESIPTPSNREETQQKSNLELLRISLLLI QSWLEPVQFLRSVFANSLVYGASDSNVYDLLKDLEEGIQTLMG corresponding to amino acids 1-152 of SOMA_HUMAN, which also corresponds to amino acids 1-152 of HSGROW1_PEA—1_P12, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence AGRWQPPDWADLQADLQQVRHKLTQR corresponding to amino acids 153-178 of HSGROW1_PEA—1_P12, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSGROW1_PEA—1_P12, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence AGRWQPPDWADLQADLQQVRHKLTQR in HSGROW1_PEA—1_P12.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because of manual inspection of known protein localization and/or gene structure. Variant protein HSGROW1_PEA—1_P12 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 254, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSGROW1_PEA—1_P12 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 254







Amino acid mutations









SNP position(s) on amino

Previously known


acid sequence
Alternative amino acid(s)
SNP?












12
A → P
Yes


12
A → S
Yes


63
P →
No


77
S →
No


77
S → F
No


87
P → T
No


97
S →
No


102
L →
No


109
I →
No


124
A →
No


139
L →
No









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 255:







TABLE 255







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR001400
Somatotropin hormone
FPrintScan
101-119, 79-92


IPR001400
Somatotropin hormone
HMMPfam
 9-178


IPR001400
Somatotropin hormone
ScanRegExp
79-112









Variant protein HSGROW1_PEA—1_P12 is encoded by the following transcript(s): HSGROW1_PEA—1_T11. The coding portion of transcript HSGROW1_PEA—1_T11 starts at position 109 and ends at position 642. The transcript also has the following SNPs as listed in Table 256 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSGROW1_PEA—1_P12 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 256







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












32
C → A
Yes


32
C → G
Yes


66
C → G
No


73
C →
No


142
G → C
Yes


142
G → T
Yes


297
A →
No


297
A → C
No


338
C →
No


338
C → T
No


367
C → A
No


398
C →
No


412
C →
No


435
C →
No


435
C → A
No


479
C →
No


525
C →
No


525
C → T
No


681
T → A
Yes


681
T → G
Yes


727
G → A
No


802
C →
No


802
C → T
Yes


819
C →
No


819
C → G
No


824
C →
No


824
C → T
No


849
→ A
No









Variant protein HSGROW1_PEA—1_P18 according to the present invention is encoded by transcript(s) HSGROW1_PEA—1_T18. An alignment is given to the known protein (Somatotropin precursor) in FIG. 187. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSGROW1_PEA—1_P18 and SOMA_HUMAN:
1. An isolated chimeric polypeptide HSGROW1_PEA—1_P18, comprising a first amino acid sequence being at least 90% homologous to MATGSRTSLLLAFGLLCLPWLQEGSAFPTIPLSRLFDNAMLRAHRLHQLAFDT YQEF corresponding to amino acids 1-57 of SOMA_HUMAN, which also corresponds to amino acids 1-57 of HSGROW1_PEA—1_P18, and a second amino acid sequence being at least 90% homologous to RLEDGSPRTGQIFKQTYSKFDTNSHNDDALLKNYGLLYCFRKDMDKVETFLR IVQCRSVEGSCGF corresponding to amino acids 153-217 of SOMA_HUMAN, which also corresponds to amino acids 58-122 of HSGROW1_PEA—1_P18, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HSGROW1_PEA—1_P18, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise FR, having a structure as follows: a sequence starting from any of amino acid numbers 57-x to 57; and ending at any of amino acid numbers 58+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because of manual inspection of known protein localization and/or gene structure. Variant protein HSGROW1_PEA—1_P18 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 257, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSGROW1_PEA—1_P18 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 257







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





12
A → P
Yes


12
A → S
Yes


97
F → C
Yes


97
F → Y
Yes









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 258:







TABLE 258







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR001400
Somatotropin hormone
FPrintScan
100-114, 84-100


IPR001400
Somatotropin hormone
HMMPfam
9-120


IPR001400
Somatotropin hormone
ScanRegExp
96-113









Variant protein HSGROW1_PEA—1_P18 is encoded by the following transcript(s): HSGROW1_PEA—1_T18. The coding portion of transcript HSGROW1_PEA—1_T18 starts at position 109 and ends at position 474. The transcript also has the following SNPs as listed in Table 259 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSGROW1_PEA—1_P18 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 259







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












32
C → A
Yes


32
C → G
Yes


66
C → G
No


73
C →
No


142
G → C
Yes


142
G → T
Yes


398
T → A
Yes


398
T → G
Yes


444
G → A
No


519
C →
No


519
C → T
Yes


536
C →
No


536
C → G
No


541
C →
No


541
C → T
No


566
→ A
No









Variant protein HSGROW1_PEA—1_P21 according to the present invention is encoded by transcript(s) HSGROW1_PEA—1_T12. An alignment is given to the known protein (Somatotropin precursor) in FIG. 188. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSGROW1_PEA—1_P21 and SOMA_HUMAN:
1. An isolated chimeric polypeptide HSGROW1_PEA—1_P21, comprising a first amino acid sequence being at least 90% homologous to MATGSRTSLLLAFGLLCLPWLQEGSAFPTIPLSRLFDNAMLRAHRLHQLAFDT YQEF corresponding to amino acids 1-57 of SOMA_HUMAN, which also corresponds to amino acids 1-57 of HSGROW1_PEA—1_P21, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence PGVRRL corresponding to amino acids 58-63 of HSGROW1_PEA—1_P21, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSGROW1_PEA—1_P21, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence PGVRRL in HSGROW1_PEA—1_P21.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because of manual inspection of known protein localization and/or gene structure. Variant protein HSGROW1_PEA—1_P21 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 260, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSGROW1_PEA—1_P21 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 260







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





12
A → P
Yes


12
A → S
Yes









Variant protein HSGROW1_PEA—1_P21 is encoded by the following transcript(s): HSGROW1_PEA—1_T12. The coding portion of transcript HSGROW1_PEA—1_T12 starts at position 109 and ends at position 297. The transcript also has the following SNPs as listed in Table 261 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSGROW1_PEA—1_P21 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 261







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












32
C → A
Yes


32
C → G
Yes


66
C → G
No


73
C →
No


142
G → C
Yes


142
G → T
Yes


319
C →
No


319
C → T
No


477
T → A
Yes


477
T → G
Yes


523
G → A
No


598
C →
No


598
C → T
Yes


615
C →
No


615
C → G
No


620
C →
No


620
C → T
No


645
→ A
No









FIG. 202 depicts the domain structure of the variants described hereinabove in comparison to WT.
Example 58
Splice Variant of Pulmonary Surfactant-Associated Protein D Precursor
Background
Pulmonary surfactant covers the peripheral airway and consists of 90% lipid and 10% protein. The protein fraction contains 4 surfactant-associated proteins: SP-A and SP-D are glycoproteins which bind Collagen (i.e., collagenous proteins) and SP-B and SP-C are small hydrophobic proteins. Pulmonary surfactant contributes to the lung's defense against inhaled microorganisms.
Clinical Application
Surfactant deficiency has been implicated in various diseases. Adult Respiratory Distress Syndrome (ARDS) includes a large number of acute, diffuse infiltrative pulmonary lesions of differing etiology which are associated with a severe gas exchange disorder (in particular arterial hypoxemia). In ARDS, the lung surfactant malfunction can be caused by acute lung injury, diffuse pulmonary infections (e.g. due to viruses, bacteria, fungi), aspiration of, for example, gastric juice or in the case of near-drowning, inhalation of toxins or irritants (e.g. chlorine gas, nitrogen oxides, smoke), direct or indirect trauma (e.g. multiple fractures or pulmonary contusion), systemic reactions to inflammations outside the lung (e.g. hemorrhagic pancreatitis, gram-negative septicemia), transfusions of high blood volumes or alternatively after cardiopulmonary bypass.
In a similar, yet distinctive syndrome, Infant Respiratory Distress Syndrome (IRDS), the lung surfactant deficiency is caused by premature birth.
Surfactant abnormalities of differing severity are also reported for a number of other disease conditions, for example in obstructive pulmonary disorders such as asthma, bronchiolitis, COPD (Chronic Obstructive Pulmonary Disease) and after lung transplantation or alternatively after cardiopulmonary bypass. Macnaughton et al. (Chest 1994; 106: 421425) and DoCampo et al. (Lancet 1994; 343: 482) describe the administration of exogenous surfactant after cardiopulmonary bypass. McBrien et al. (Lancet 1993, 342:1485-1486) and Suzuki et al. (Eur. J. Pediatr. 1996; 155: 383-384) describe the administration of surfactant after near-drowning. Struber et al. (Cardiovasc. Surg. 1995; 110; 563-564) describe the administration of surfactant after lung transplantation.
Presently, therapy of ARDS consists mainly in the earliest possible application of different forms of ventilation. However, it is known in the art, that surfactant preparations can be used in the treatment of IRDS or ARDS.
The Pulmonary Surfactant-Associated Protein D Precursor
The Pulmonary surfactant-associated protein D precursor (SP-D; PSP-D; GenBank Accession No. P35247; PSPD_HUMAN; PSPD; SFTP4; SFTPD) is an extracellular glycoprotein which binds maltose residues, mannose and other alpha-glucosyl moieties. It participates in the extracellular reorganization or turnover of pulmonary surfactant and involves in respiratory gaseous exchange and heterophilic cell adhesion.
Splice Variant D45608_T2 (SEQ ID NO:856) Encodes a New Form of the PSPD, D45608_P3 (SEQ ID NO:857)
The present inventors have uncovered a new PSPD variant [D45608_T2—SEQ ID NO:856; D45608_P3—SEQ ID NO:857]. The protein coordinates on the transcript start from nucleotide 172 and end at nucleotide 1179 as set forth in SEQ ID NO: 856.
Alignment of the new PSPD variant D45608_P3—SEQ ID NO:857) with the WT protein (GenBank Accession No. P35247; PSPD_HUMAN; SEQ ID NO:858) revealed that the new variant is missing amino acids 121-159 of the WT protein (GenBank Accession No. P35247; FIG. 205), thus creating a new edge SG for this protein. The new variant uncovered by the present invention lacks part of the Collagen-like domain (amino acids 46-222 of the WT protein; IPR008160 Collagen triple helix repeat).
Comparison Report Between D45608_P3 (SEQ ID NO:857) and PSPD_HUMAN (SEQ ID NO:858)
1. An isolated chimeric polypeptide D45608_P3, comprising a first amino acid sequence being at least 90% homologous to MLLFLLSALVLLTQPLGYLEAEMKTYSHRTMPSACTLVMCSSVESGLPGRDG RDGREGPRGEKGDPGLPGAAGQAGMPGQAGPVGPKGDNGSVGEPGPKGDT GPS corresponding to amino acids 1-105 of PSPD_HUMAN, which also corresponds to amino acids 1-105 of D45608_P3, and a second amino acid sequence being at least 90% homologous to GEVGAPGMQGSAGARGLAGPKGERGVPGERGVPGNTGAAGSAGAMGPQGS PGARGPPGLKGDKGIPGDKGAKGESGLPDVASLRQQVEALQGQVQHLQAAF SQYKKVELFPNGQSVGEKIFKTAGFVKPFTEAQLLCTQAGGQLASPRSAAEN AALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGEPNDDGGS EDCVEIFTNGKWNDRACGEKRLVVCEF corresponding to amino acids 145-375 of PSPD_HUMAN, which also corresponds to amino acids 106-336 of D45608_P3, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric edge portion of D45608_P3, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise SG, having a structure as follows: a sequence starting from any of amino acid numbers 105-x to 105; and ending at any of amino acid numbers 106+((n−2)−x), in which x varies from 0 to n−2.
Clinical Applications of the New PSDS Variant
The new PSDS variant of the present invention D45608_P3 (SEQ ID NO:857), can be used as either a diagnostic marker for surfactant destruction in various clinical conditions such as acute lung injury, diffuse pulmonary infections (e.g. due to viruses, bacteria, fungi), aspiration of gastric juice, inhalation of toxins or irritants (e.g. chlorine gas, nitrogen oxides, smoke), a trauma (e.g. multiple fractures or pulmonary contusion), systemic reactions to inflammations outside the lung (e.g. hemorrhagic pancreatitis, gram-negative septicemia), transfusions of high blood volumes or alternatively after cardiopulmonary bypass, Infant Respiratory Distress Syndrome (IRDS) and/or Adult Respiratory Distress Syndrome (ARDS). Alternatively or additionally, the new PSPD variant uncovered by the present inventors can be used in the treatment of any of the diseases, disorders or conditions described hereinabove.
Thus, the present inventors have uncovered a therapeutic agent, a polypeptide homologous to SEQ ID NO:857 and/or an expressible polynucleotide homologous to SEQ ID NO:856 which can be used to treat a surfactant deficiency—related disease, disorder of condition, e.g., acute lung injury, diffuse pulmonary infections (e.g. due to viruses, bacteria, fungi), aspiration of gastric juice, inhalation of toxins or irritants (e.g. chlorine gas, nitrogen oxides, smoke), a trauma (e.g. multiple fractures or pulmonary contusion), systemic reactions to inflammations outside the lung (e.g. hemorrhagic pancreatitis, gram-negative septicemia), transfusions of high blood volumes or alternatively after cardiopulmonary bypass, Infant Respiratory Distress Syndrome (IRDS) and/or Adult Respiratory Distress Syndrome (ARDS).
It will be appreciated that such an agent can be administered or provided to an individual in need thereof per se or as part of a pharmaceutical composition with a pharmaceutical acceptable carrier (e.g., PEG and liposomes).
While further reducing the present invention to practice, these results suggest the use of the new PSDS variant of the present invention (SEQ ID NO:857), the polynucleotide encoding same (SEQ ID NO:856) as a diagnostic marker for a surfactant deficiency—related disease as described hereinabove. Diagnosis according to this aspect of the present invention is effected using immunological assays [e.g., Western Blot, immunohistochemistry, FACS analysis, radio immuno assay (RIA), immunofluorescence, and the like using an antibody directed against the PSDS variant (SEQ ID NO:857)], or by nucleic acid techniques (NAT) such as RT-PCR, Northern Blot, in situ hybridization, in situ RT-PCR.
Example 59
Description for Cluster HUMTNFRII
Cluster HUMTNFRII features 6 transcript(s) and 19 segment(s) of interest, the names for which are given in Tables 262 and 263, respectively. The selected protein variants are given in table 264.







TABLE 262







Transcripts of interest










Transcript Name
SEQ ID NO:






HUMTNFRII_PEA_1_T4
138


 



HUMTNFRII_PEA_1_T7
332


 



HUMTNFRII_PEA_1_T8
333


 



HUMTNFRII_PEA_1_T9
370


 



HUMTNFRII_PEA_1_T10
675


 



HUMTNFRII_PEA_1_T11
676
















TABLE 263







Segments of interest










Segment Name
SEQ ID NO:






HUMTNFRII_PEA_1_node_0
677


 



HUMTNFRII_PEA_1_node_8
678


 



HUMTNFRII_PEA_1_node_15
679


 



HUMTNFRII_PEA_1_node_18
680


 



HUMTNFRII_PEA_1_node_32
681


 



HUMTNFRII_PEA_1_node_37
682


 



HUMTNFRII_PEA_1_node_38
683


 



HUMTNFRII_PEA_1_node_39
684


 



HUMTNFRII_PEA_1_node_40
685


 



HUMTNFRII_PEA_1_node_12
686


 



HUMTNFRII_PEA_1_node_17
687


 



HUMTNFRII_PEA_1_node_20
688


 



HUMTNFRII_PEA_1_node_21
689


 



HUMTNFRII_PEA_1_node_23
690


 



HUMTNFRII_PEA_1_node_24
691


 



HUMTNFRII_PEA_1_node_25
692


 



HUMTNFRII_PEA_1_node_27
693


 



HUMTNFRII_PEA_1_node_28
694


 



HUMTNFRII_PEA_1_node_30
695
















TABLE 264







Proteins of interest











Corresponding


Protein Name
SEQ ID NO:
Transcript(s)





HUMTNFRII_PEA_1_P7
696
HUMTNFRII_PEA_1_T11


 


HUMTNFRII_PEA_1_P15
697
HUMTNFRII_PEA_1_T4


 


HUMTNFRII_PEA_1_P16
698
HUMTNFRII_PEA_1_T7


 


HUMTNFRII_PEA_1_P17
699
HUMTNFRII_PEA_1_T8


 


HUMTNFRII_PEA_1_P18
860
HUMTNFRII_PEA_1_T9


 


HUMTNFRII_PEA_1_P19
861
HUMTNFRII_PEA_1_T10









These sequences are variants of the known protein Tumor necrosis factor receptor superfamily member 1B precursor (SwissProt accession identifier TR1B_HUMAN; known also according to the synonyms Tumor necrosis factor receptor 2; p80; TNF-R2; p75; CD120b; Etanercept; TBPII), referred to herein as the previously known protein.
Protein Tumor necrosis factor receptor superfamily member 1B precursor is known or believed to have the following function(s): Receptor with high affinity for TNFSF2/TNF-alpha and approximately 5-fold lower affinity for homotrimeric TNFSF1/lymphotoxin-alpha. The TRAF1/TRAF2 complex recruits the apoptotic suppressors BIRC2 and BIRC3 to TNFRSF1B/TNFR2. The TNF receptor 2 mediates most of the metabolic effects of TNF-alpha. The sequence for protein Tumor necrosis factor receptor superfamily member 1B precursor is given in SEQ ID NO:862, as “Tumor necrosis factor receptor superfamily member 1B precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 265.







TABLE 265







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment





187
V → M (in dbSNP: 5746025)./FTId = VAR_017176.


196
M → R (frequent polymorphism; seems to be associated



with hyperandrogenism, polycystic ovary syndrome



(PCOS) and systemic lupus erythematosus;



dbSNP: 1061622)./FTId = VAR_015434.


232
E → K (in dbSNP: 5746026)./FTId = VAR_015435.


236
A → T (in dbSNP: 5746027)./FTId = VAR_017177.


264
L → P (in dbSNP: 5746031)./FTId = VAR_017178.


269
T → P./FTId = VAR_017179.


295
Q → R (in dbSNP: 5746032)./FTId = VAR_017180.


301
P → R./FTId = VAR_017181.


141
R → P


363
A → T









Protein Tumor necrosis factor receptor superfamily member 1B precursor localization is believed to be Type I membrane protein and secreted.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: apoptosis, which are annotation(s) related to Biological Process; receptor; tumor necrosis factor receptor, which are annotation(s) related to Molecular Function; and integral membrane protein, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebaseor Locuslink.
TNFR1B is a receptor with high affinity for TNF-alpha lymphotoxin-alpha and mediates most of the metabolic effects of TNF-alpha. It is strongly expressed on stimulated T and B lymphocytes. TNFR2 is the main TNF receptor found on circulating T cells and is the major mediator of autoregulatory apoptosis in CD8+ cells. It is a type I membrane protein (isoform 1); secreted (isoform 2 and TBP-II). A soluble form (tumor necrosis factor binding protein 2) is produced from the membrane form by proteolytic processing. Isoform 2 blocks TNF-alpha-induced apoptosis. One currently available therapeutic based on this protein is Enbrel (Immunex and Wyeth-Ayerst), which is used to treat moderate to servere rheumatoid arthritis (RA).
As noted above, cluster HUMTNFRII features 6 transcript(s), which were listed in Table 262 above. These transcript(s) encode for protein(s) which are variant(s) of protein Tumor necrosis factor receptor superfamily member 1B precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HUMTNFRII_PEA—1_P7 according to the present invention is encoded by transcript(s) HUMTNFRII_PEA—1_T11. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 1B precursor) in FIG. 206. One or more alignments to one or more previously published protein sequences are given in FIGS. 207-210. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMTNFRII_PEA—1_P7 and TR1B_HUMAN:
1. An isolated chimeric polypeptide HUMTNFRII_PEA—1_P7, comprising a first amino acid sequence being at least 90% homologous to MAPVAVWAALAVGLELWAAAHALPAQVAFTPYAPEPGSTCRLREYYDQTA QMCCSKCSPGQHAKVFCTKTSDTVCDSCEDSTYTQLWNWVPECLSCGSRCSS DQVETQACTREQNRICTCRPGWYCALSKQEGCRLCAPLRKCRPGFGVARPGT ETSDVVCKPCAPGTFSNTTSSTDICRPHQICNVVAIPGNASMDAVCTSTSPTRS MAPGAVHLPQPVSTRSQHTQPTPEPSTAPSTSFLLPMGPSPPAEGSTGDFALPV corresponding to amino acids 1-262 of TR1B_HUMAN, which also corresponds to amino acids 1-262 of HUMTNFRII_PEA—1_P7, and a second amino acid sequence being at least 90% homologous to DSSPGGHGTQVNVTCIVNVCSSSDHSSQCSSQASSTMGDTDSSPSESPKDEQV PFSKEECAFRSQLETPETLLGSTEEKPLPLGVPDAGMKPS corresponding to amino acids 369-461 of TR1B_HUMAN, which also corresponds to amino acids 263-355 of HUMTNFRII_PEA—1_P7, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric edge portion of HUMTNFRII_PEA—1_P7, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise VD, having a structure as follows: a sequence starting from any of amino acid numbers 262-x to 262; and ending at any of amino acid numbers 263+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMTNFRII_PEA—1_P7 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 266, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRII_PEA—1_P7 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 266







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












25
A →
No


47
D → G
No


61
Q → R
No


81
S → G
No


116
R → H
No


119
T → A
No


153
G → E
No


171
N →
No


187
V → M
Yes


196
M →
No


196
M → R
Yes


232
E → K
Yes


236
A → T
Yes


243
L →
No


254
S → C
No


259
A → V
No


296
S → N
No


333
T →
No


342
P → H
No


342
P →
No









The glycosylation sites of variant protein HUMTNFRII_PEA—1_P7, as compared to the known protein Tumor necrosis factor receptor superfamily member 1B precursor, are described in Table 267 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 267







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





171
yes
171


193
yes
193









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 268:







TABLE 268







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR001368
TNFR/CD27/30/40/
HMMPfam
40-75, 78-118



95 cysteine-rich



region


IPR001368
TNFR/CD27/30/40/
HMMSmart
120-161, 164-200,



95 cysteine-rich

40-75, 78-118



region


IPR001368
TNFR/CD27/30/40/
ScanRegExp
40-75, 78-118



95 cysteine-rich



region


IPR001368
TNFR/CD27/30/40/
ProfileScan
119-161, 39-75,



95 cysteine-rich

77-118



region









Variant protein HUMTNFRII_PEA—1_P7 is encoded by the following transcript(s): HUMTNFRII_PEA—1_T11. The coding portion of transcript HUMTNFRII_PEA—1_T11 starts at position 108 and ends at position 1172. The transcript also has the following SNPs as listed in Table 269 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRII_PEA—1_P7 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 269







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












33
G → T
Yes


49
C → T
Yes


181
C →
No


247
A → G
No


275
A → G
Yes


289
A → G
No


290
A → G
No


348
A → G
No


454
G → A
No


462
A → G
No


565
G → A
No


604
→ C
No


604
→ G
No


618
A →
No


650
C → T
Yes


666
G → A
Yes


694
T →
No


694
T → G
Yes


801
G → A
Yes


813
G → A
Yes


815
T → C
No


836
C →
No


867
A → T
No


883
C → T
No


994
G → A
No


1105
C →
No


1131
C →
No


1132
C →
No


1132
C → A
No


1188
G → A
No


1189
G → A
No


1189
G → C
No


1363
G → A
Yes


1368
T → G
Yes


1390
T → C
Yes


1495
C → T
No


1548
C →
No


1562
C → A
Yes


1600
C → T
Yes


1628
A → G
Yes


1647
T → C
Yes


1653
C → G
Yes


1835
C → T
Yes


2013
C → G
Yes


2069
→ A
No


2097
C → T
Yes


2255
C → T
Yes


2347
C → T
No


2352
C → T
Yes


2440
C → T
Yes


2593
T → C
Yes


2597
G → A
Yes


2669
A → G
Yes


2728
C → A
Yes


2735
C → T
Yes


2819
G → A
Yes


2935
G → A
Yes









Variant protein HUMTNFRII_PEA—1_P15 according to the present invention is encoded by transcript(s) HUMTNFRII_PEA—1_T4. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 1B precursor) in FIG. 207. One or more alignments to one or more previously published protein sequences are given in FIGS. 206, and 208-210. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMTNFRII_PEA—1_P15 and TR1B_HUMAN:
1. An isolated chimeric polypeptide HUMTNFRII_PEA—1_P15, comprising a first amino acid sequence being at least 90% homologous to MAPVAVWAALAVGLELWAAAHALPAQ corresponding to amino acids 1-26 of TR1B_HUMAN, which also corresponds to amino acids 1-26 of HUMTNFRII_PEA—1_P15, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GFAAH corresponding to amino acids 27-31 of HUMTNFRII_PEA—1_P15, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMTNFRII_PEA—1_P15, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GFAAH in HUMTNFRII_PEA—1_P15.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMTNFRII_PEA—1_P15 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 270, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRII_PEA—1_P15 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 270







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





25
A →
No









The glycosylation sites of variant protein HUMTNFRII_PEA—1_P15, as compared to the known protein Tumor necrosis factor receptor superfamily member 1B precursor, are described in Table 271 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 271







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





171
no



193
no









Variant protein HUMTNFRII_PEA—1_P15 is encoded by the following transcript(s): HUMTNFRII_PEA—1_T4. The coding portion of transcript HUMTNFRII_PEA—1_T4 starts at position 108 and ends at position 200. The transcript also has the following SNPs as listed in Table 272 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRII_PEA—1_P15 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 272







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












33
G → T
Yes


49
C → T
Yes


181
C →
No


421
A → G
No


449
A → G
Yes


463
A → G
No


464
A → G
No


522
A → G
No


628
G → A
No


636
A → G
No


739
G → A
No


778
→ C
No


778
→ G
No


792
A →
No


824
C → T
Yes


840
G → A
Yes


868
T →
No


868
T → G
Yes


975
G → A
Yes


987
G → A
Yes


989
T → C
No


1010
C →
No


1041
A → T
No


1057
C → T
No


1072
T → C
Yes


1122
T → C
No


1124
T →
No


1124
T → C
No


1165
A → G
Yes


1184
T → C
No


1195
C → T
No


1206
C → T
No


1270
C →
No


1365
→ A
No


1365
→ G
No


1366
G → A
No


1486
G → A
No


1597
C →
No


1623
C →
No


1624
C →
No


1624
C → A
No


1680
G → A
No


1681
G → A
No


1681
G → C
No


1855
G → A
Yes


1860
T → G
Yes


1882
T → C
Yes


1987
C → T
No


2040
C →
No


2054
C → A
Yes


2092
C → T
Yes


2120
A → G
Yes


2139
T → C
Yes


2145
C → G
Yes


2327
C → T
Yes


2505
C → G
Yes


2561
→ A
No


2589
C → T
Yes


2747
C → T
Yes


2839
C → T
No


2844
C → T
Yes


2932
C → T
Yes


3085
T → C
Yes


3089
G → A
Yes


3161
A → G
Yes


3220
C → A
Yes


3227
C → T
Yes


3311
G → A
Yes


3427
G → A
Yes









Variant protein HUMTNFRII_PEA—1_P16 according to the present invention is encoded by transcript(s) HUMTNFRII_PEA—1_T7. The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMTNFRII_PEA—1_P16 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 273, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRII_PEA—1_P16 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 273







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





25
A →
No


28
N → D
No


28
N → S
No









Variant protein HUMTNFRII_PEA—1_P16 is encoded by the following transcript(s): HUMTNFRII_PEA—1_T7. The coding portion of transcript HUMTNFRII_PEA—1_T7 starts at position 108 and ends at position 287. The transcript also has the following SNPs as listed in Table 274 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRII_PEA—1_P16 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 274







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












33
G → T
Yes


49
C → T
Yes


181
C →
No


189
A → G
No


190
A → G
No


248
A → G
No


354
G → A
No


362
A → G
No


465
G → A
No


504
→ C
No


504
→ G
No


518
A →
No


550
C → T
Yes


566
G → A
Yes


594
T →
No


594
T → G
Yes


701
G → A
Yes


713
G → A
Yes


715
T → C
No


736
C →
No


767
A → T
No


783
C → T
No


798
T → C
Yes


848
T → C
No


850
T →
No


850
T → C
No


891
A → G
Yes


910
T → C
No


921
C → T
No


932
C → T
No


996
C →
No


1091
→ A
No


1091
→ G
No


1092
G → A
No


1212
G → A
No


1323
C →
No


1349
C →
No


1350
C →
No


1350
C → A
No


1406
G → A
No


1407
G → A
No


1407
G → C
No


1581
G → A
Yes


1586
T → G
Yes


1608
T → C
Yes


1713
C → T
No


1766
C →
No


1780
C → A
Yes


1818
C → T
Yes


1846
A → G
Yes


1865
T → C
Yes


1871
C → G
Yes


2053
C → T
Yes


2231
C → G
Yes


2287
→ A
No


2315
C → T
Yes


2473
C → T
Yes


2565
C → T
No


2570
C → T
Yes


2658
C → T
Yes


2811
T → C
Yes


2815
G → A
Yes


2887
A → G
Yes


2946
C → A
Yes


2953
C → T
Yes


3037
G → A
Yes


3153
G → A
Yes









Variant protein HUMTNFRII_PEA—1_P17 according to the present invention is encoded by transcript(s) HUMTNFRII_PEA—1_T8. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 1B precursor) in FIG. 208. One or more alignments to one or more previously published protein sequences are given in FIGS. 206-207 and 209-210. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMTNFRII_PEA—1_P17 and TR1B_HUMAN (SEQ ID NO:862):
1. An isolated chimeric polypeptide HUMTNFRII_PEA—1_P17, comprising a first amino acid sequence being at least 90% homologous to MAPVAVWAALAVGLELWAAAHALPAQVAFTPYAPEPGSTCRLREYYDQTA QMCCSKCSPGQHAKVFCTKTSDTVCDSCEDSTYTQLWNWVPECLSCGSRCSS DQVETQACTREQNRICTCRPGWYCALSKQEGCRLCAPLRKCRPGFGVARP corresponding to amino acids 1-152 of TR1B_HUMAN, which also corresponds to amino acids 1-152 of HUMTNFRII_PEA—1_P17, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence DLS corresponding to amino acids 153-155 of HUMTNFRII_PEA—1_P17, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMTNFRII_PEA—1_P17 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 275, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRII_PEA—1_P17 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 275







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












25
A →
No


47
D → G
No


61
Q → R
No


81
S → G
No


116
R → H
No


119
T → A
No









The glycosylation sites of variant protein HUMTNFRII_PEA—1_P17, as compared to the known protein Tumor necrosis factor receptor superfamily member 1B precursor, are described in Table 276 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 276







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





171
no



193
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 277:







TABLE 277







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR001368
TNFR/CD27/30/40/
HMMPfam
40-75, 78-118



95 cysteine-rich



region


IPR001368
TNFR/CD27/30/40/
HMMSmart
120-155, 40-75,



95 cysteine-rich

78-118



region


IPR001368
TNFR/CD27/30/40/
ScanRegExp
40-75, 78-118



95 cysteine-rich



region


IPR001368
TNFR/CD27/30/40/
ProfileScan
39-75, 77-118



95 cysteine-rich



region









Variant protein HUMTNFRII_PEA—1_P17 is encoded by the following transcript(s): HUMTNFRII_PEA—1_T8. The coding portion of transcript HUMTNFRII_PEA—1_T8 starts at position 108 and ends at position 572. The transcript also has the following SNPs as listed in Table 278 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRII_PEA—1_P17 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 278







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












33
G → T
Yes


49
C → T
Yes


181
C →
No


247
A → G
No


275
A → G
Yes


289
A → G
No


290
A → G
No


348
A → G
No


454
G → A
No


462
A → G
No


648
G → A
No


687
→ C
No


687
→ G
No


701
A →
No


733
C → T
Yes


749
G → A
Yes


777
T →
No


777
T → G
Yes


884
G → A
Yes


896
G → A
Yes


898
T → C
No


919
C →
No


950
A → T
No


966
C → T
No


981
T → C
Yes


1031
T → C
No


1033
T →
No


1033
T → C
No


1074
A → G
Yes


1093
T → C
No


1104
C → T
No


1115
C → T
No


1179
C →
No


1274
→ A
No


1274
→ G
No


1275
G → A
No


1395
G → A
No


1506
C →
No


1532
C →
No


1533
C →
No


1533
C → A
No


1589
G → A
No


1590
G → A
No


1590
G → C
No


1764
G → A
Yes


1769
T → G
Yes


1791
T → C
Yes


1896
C → T
No


1949
C →
No


1963
C → A
Yes


2001
C → T
Yes


2029
A → G
Yes


2048
T → C
Yes


2054
C → G
Yes


2236
C → T
Yes


2414
C → G
Yes


2470
→ A
No


2498
C → T
Yes


2656
C → T
Yes


2748
C → T
No


2753
C → T
Yes


2841
C → T
Yes


2994
T → C
Yes


2998
G → A
Yes


3070
A → G
Yes


3129
C → A
Yes


3136
C → T
Yes


3220
G → A
Yes


3336
G → A
Yes









Variant protein HUMTNFRII_PEA—1_P18 according to the present invention is encoded by transcript(s) HUMTNFRII_PEA—1_T9. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 1B precursor) in FIG. 209. One or more alignments to one or more previously published protein sequences are given in FIGS. 206-208 and 210. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMTNFRII_PEA—1_P18 and TR1B_HUMAN:
1. An isolated chimeric polypeptide HUMTNFRII_PEA—1_P18, comprising a first amino acid sequence being at least 90% homologous to MAPVAVWAALAVGLELWAAAHALPAQVAFTPYAPEPGSTCRLREYYDQTA QMCCSKCSPGQHAKVFCTKTSDTVCDSCEDSTYTQLWNWVPECLSCGSRCSS corresponding to amino acids 1-102 of TR1B_HUMAN, which also corresponds to amino acids 1-102 of HUMTNFRII_PEA—1_P18, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GGNSSLHSGTEPHLHLQARLVLRAEQAGGVPAVRAAAQVPPGLRRGQTRN corresponding to amino acids 103-152 of HUMTNFRII_PEA—1_P18, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMTNFRII_PEA—1_P18, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GGNSSLHSGTEPHLHLQARLVLRAEQAGGVPAVRAAAQVPPGLRRGQTRN in HUMTNFRII_PEA—1_P18.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMTNFRII_PEA—1_P18 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 279, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRII_PEA—1_P18 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 279







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












25
A →
No


47
D → G
No


61
Q → R
No


81
S → G
No


117
H → R
No









The glycosylation sites of variant protein HUMTNFRII_PEA—1_P18, as compared to the known protein Tumor necrosis factor receptor superfamily member 1B precursor, are described in Table 280 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 280







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





171
no



193
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 281:







TABLE 281







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR001368
TNFR/CD27/30/40/
HMMPfam
40-75, 78-103



95 cysteine-rich



region


IPR001368
TNFR/CD27/30/40/
HMMSmart
40-75, 78-113



95 cysteine-rich



region


IPR007087
Zn-finger, C2H2 type
ScanRegExp
93-115


IPR001368
TNFR/CD27/30/40/
ScanRegExp
40-75



95 cysteine-rich



region


IPR001368
TNFR/CD27/30/40/
ProfileScan
39-75



95 cysteine-rich



region









Variant protein HUMTNFRII_PEA—1_P18 is encoded by the following transcript(s): HUMTNFRII_PEA—1_T9. The coding portion of transcript HUMTNFRII_PEA—1_T9 starts at position 108 and ends at position 563. The transcript also has the following SNPs as listed in Table 282 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRII_PEA—1_P18 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 282







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












33
G → T
Yes


49
C → T
Yes


181
C →
No


247
A → G
No


275
A → G
Yes


289
A → G
No


290
A → G
No


348
A → G
No


449
G → A
No


457
A → G
No


560
G → A
No


599
→ C
No


599
→ G
No


613
A →
No


645
C → T
Yes


661
G → A
Yes


689
T →
No


689
T → G
Yes


796
G → A
Yes


808
G → A
Yes


810
T → C
No


831
C →
No


862
A → T
No


878
C → T
No


893
T → C
Yes


943
T → C
No


945
T →
No


945
T → C
No


986
A → G
Yes


1005
T → C
No


1016
C → T
No


1027
C → T
No


1091
C →
No


1186
→ A
No


1186
→ G
No


1187
G → A
No


1307
G → A
No


1418
C →
No


1444
C →
No


1445
C →
No


1445
C → A
No


1501
G → A
No


1502
G → A
No


1502
G → C
No


1676
G → A
Yes


1681
T → G
Yes


1703
T → C
Yes


1808
C → T
No


1861
C →
No


1875
C → A
Yes


1913
C → T
Yes


1941
A → G
Yes


1960
T → C
Yes


1966
C → G
Yes


2148
C → T
Yes


2326
C → G
Yes


2382
→ A
No


2410
C → T
Yes


2568
C → T
Yes


2660
C → T
No


2665
C → T
Yes


2753
C → T
Yes


2906
T → C
Yes


2910
G → A
Yes


2982
A → G
Yes


3041
C → A
Yes


3048
C → T
Yes


3132
G → A
Yes


3248
G → A
Yes









Variant protein HUMTNFRII_PEA—1_P19 according to the present invention is encoded by transcript(s) HUMTNFRII_PEA—1_T10. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 1B precursor) in FIG. 210. One or more alignments to one or more previously published protein sequences are given in FIGS. 206-209. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMTNFRII_PEA—1_P19 and TR1B_HUMAN:
1. An isolated chimeric polypeptide HUMTNFRII_PEA—1_P19, comprising a first amino acid sequence being at least 90% homologous to MAPVAVWAALAVGLELWAAAHALPAQVAFTPYAPEPGSTCRLREYYDQTA QMCCSKCSPGQHAKVFCTKTSDTVCDSCEDSTYTQLWNWVPECLSCGSRCSS DQVETQACTREQNRICTCRPGWYCALSKQEGCRLCAPLRKCRPGFGVARPGT ETSDVVCKPCAPGTFSNTTSSTDICRPHQICNVVAIPGNASMDAVCTSTSPTRS MAPGAVHLPQPVSTRSQHTQPTPEPSTAPSTSFLLPMGPSPPAEGSTGDFALPV corresponding to amino acids 1-262 of TR1B_HUMAN, which also corresponds to amino acids 1-262 of HUMTNFRII_PEA—1_P19, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence ASLACR corresponding to amino acids 263-268 of HUMTNFRII_PEA—1_P19, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMTNFRII_PEA—1_P19, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence ASLACR in HUMTNFRII_PEA—1_P19.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMTNFRII_PEA—1_P19 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 283, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRII_PEA—1_P19 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 283







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












25
A →
No


47
D → G
No


61
Q → R
No


81
S → G
No


116
R → H
No


119
T → A
No


153
G → E
No


171
N →
No


187
V → M
Yes


196
M →
No


196
M → R
Yes


232
E → K
Yes


236
A → T
Yes


243
L →
No


254
S → C
No


259
A → V
No


264
S → P
No









The glycosylation sites of variant protein HUMTNFRII_PEA—1_P19, as compared to the known protein Tumor necrosis factor receptor superfamily member 1B precursor, are described in Table 284 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 284







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





171
yes
171


193
yes
193









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 285:







TABLE 285







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR001368
TNFR/CD27/30/40/
HMMPfam
40-75, 78-118



95 cysteine-rich



region


IPR001368
TNFR/CD27/30/40/
HMMSmart
120-161, 164-200,



95 cysteine-rich

40-75, 78-118



region


IPR001368
TNFR/CD27/30/40/
ScanRegExp
40-75, 78-118



95 cysteine-rich



region


IPR001368
TNPR/CD27/30/40/
ProfileScan
119-161, 39-75,



95 cysteine-rich

77-118



region









Variant protein HUMTNFRII_PEA—1_P19 is encoded by the following transcript(s): HUMTNFRII_PEA—1_T10. The coding portion of transcript HUMTNFRII_PEA—1_T10 starts at position 108 and ends at position 911. The transcript also has the following SNPs as listed in Table 286 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRII_PEA—1_P19 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 286







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












33
G → T
Yes


49
C → T
Yes


181
C →
No


247
A → G
No


275
A → G
Yes


289
A → G
No


290
A → G
No


348
A → G
No


454
G → A
No


462
A → G
No


565
G → A
No


604
→ C
No


604
→ G
No


618
A →
No


650
C → T
Yes


666
G → A
Yes


694
T →
No


694
T → G
Yes


801
G → A
Yes


813
G → A
Yes


815
T → C
No


836
C →
No


867
A → T
No


883
C → T
No


897
T → C
No


908
C → T
No


919
C → T
No


983
C →
No


1078
→ A
No


1078
→ G
No


1079
G → A
No


1199
G → A
No


1310
C →
No


1336
C →
No


1337
C →
No


1337
C → A
No


1393
G → A
No


1394
G → A
No


1394
G → C
No


1568
G → A
Yes


1573
T → G
Yes


1595
T → C
Yes


1700
C → T
No


1753
C →
No


1767
C → A
Yes


1805
C → T
Yes


1833
A → G
Yes


1852
T → C
Yes


1858
C → G
Yes


2040
C → T
Yes


2218
C → G
Yes


2274
→ A
No


2302
C → T
Yes


2460
C → T
Yes


2552
C → T
No


2557
C → T
Yes


2645
C → T
Yes


2798
T → C
Yes


2802
G → A
Yes


2874
A → G
Yes


2933
C → A
Yes


2940
C → T
Yes


3024
G → A
Yes


3140
G → A
Yes









The variants were found to have the following domain structure as shown in FIG. 211 in comparison to the known or wild-type (WT) protein:
Example 60
Description For Cluster HUMTNFRRP
Cluster HUMTNFRRP features 3 transcript(s) and 32 segment(s) of interest, the names for which are given in Tables 287 and 288, respectively. The selected protein variants are given in table 289.







TABLE 287







Transcripts of interest










Transcript Name
SEQ ID NO:











HUMTNFRRP_T2
863


 


HUMTNFRRP_T6
864


 


HUMTNFRRP_T18
865
















TABLE 288







Segments of interest










Segment Name
SED ID NO:






HUMTNFRRP_node_3
866


 



HUMTNFRRP_node_18
867


 



HUMTNFRRP_node_19
868


 



HUMTNFRRP_node_23
869


 



HUMTNFRRP_node_25
870


 



HUMTNFRRP_node_26
871


 



HUMTNFRRP_node_28
872


 



HUMTNFRRP_node_30
873


 



HUMTNFRRP_node_31
874


 



HUMTNFRRP_node_33
875


 



HUMTNFRRP_node_34
876


 



HUMTNFRRP_node_36
877


 



HUMTNFRRP node_37
878


 



HUMTNFRRP_node_42
879


 



HUMTNFRRP_node_4
880


 



HUMTNFRRP_node_5
881


 



HUMTNFRRP_node_6
882


 



HUMTNFRRP_node_7
883


 



HUMTNFRRP_node_10
884


 



HUMTNFRRP_node_13
885


 



HUMTNFRRP_node_14
886


 



HUMTNFRRP_node_16
887


 



HUMTNFRRP_node_17
888


 



HUMTNFRRP_node_20
889


 



HUMTNFRRP_node_22
890


 



HUMTNFRRP_node_24
891


 



HUMTNFRRP_node_27
892


 



HUMTNFRRP_node_29
893


 



HUMTNFRRP_node_38
894


 



HUMTNFRRP_node_39
895


 



HUMTNFRRP_node_40
896


 



HUMTNFRRP_node_41
897
















TABLE 289







Proteins of interest












Protein
Corresponding


Protein Name
SEQ ID NO:
Length
Transcript(s)





HUMTNFRPP_P2
898
P166
HUMTNFRRP_T2


 


HUMTNFRRP_P4
899
p255
HUMTNFRRP_T6


 


HUMTNFRRP_P9
900
P181
HUMTNFRRP_T18









These sequences are variants of the known protein Tumor necrosis factor receptor superfamily member 3 precursor (SwissProt accession identifier TNR3_HUMAN; SEQ ID NO:129; known also according to the synonyms Lymphotoxin-beta receptor; Tumor necrosis factor receptor 2 related protein; Tumor necrosis factor C receptor), referred to herein as the previously known protein.
Protein Tumor necrosis factor receptor superfamily member 3 precursor is known or believed to have the following function(s): Receptor for the heterotrimeric lymphotoxin containing LTA and LTB, and for TNFS14/LIGHT. Promotes apoptosis via TRAF3 and TRAF5. May play a role in the development of lymphoid organs. The sequence for protein Tumor necrosis factor receptor superfamily member 3 precursor is given in SEQ ID NO: 129, as “Tumor necrosis factor receptor superfamily member 3 precursor amino acid sequence”. Protein Tumor necrosis factor receptor superfamily member 3 precursor localization is believed to be Type I membrane protein.
It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein are as follows: Immunosuppressant; Leucotriene modulator. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Immunosuppressant.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: apoptosis; immune response; signal transduction, which are annotation(s) related to Biological Process; transmembrane receptor; protein binding, which are annotation(s) related to Molecular Function; and integral membrane protein, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
Tumor necrosis factor receptor-3 (TNR3) Lymphotoxin-β receptor (LT-βR) binds specifically to two ligands: the membrane form of lymphotoxin, LT-α1/β2, and LIGHT, which are expressed only on activated lymphoid cells and activated T cells respectively. LT-βR stimulation leads to induction of inflammatory response and is involved in normal development of lymphoid organs. In addition its stimulation can induce cell death, chemokine secretion, and activation of NFκB. In vivo blockade of LIGHT and LT1β2 by administration of soluble LTβR-Ig inhibited CTL response and ameliorated lethal GVHD in a B6 to BDF1 mouse model. Treatment of rodents with the fusion protein, LT-βR-Ig prevents the development of autoimmune diseases including but not limited to insulitis and uveitis.
FIG. 212 depicts the clinical trials involve TNR3-lymphotoxin beta.
As noted above, cluster HUMTNFRRP features 3 transcript(s), which were listed in Table 287 above. These transcript(s) encode for protein(s) which are variant(s) of protein Tumor necrosis factor receptor superfamily member 3 precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HUMTNFRRP_P2 according to the present is encoded by transcript(s) HUMTNFRRP_T2. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 3 precursor; SEQ ID NO:129) in FIG. 213. One or more alignments to one or more previously published protein sequences are given in FIGS. 214-215. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMTNFRRP_P2 and TNR3_HUMAN:
1. An isolated chimeric polypeptide HUMTNFRRP_P2, comprising a first amino acid sequence being at least 90% homologous to MLLPWATSAPGLAWGPLVLGLFGLLAASQPQAVPPYASENQTCRDQEKEYY EPQHRICCSRCPPGTYVSAKCSRIRDTVCATCAENSYNEHWNYLTICQLCRPC DPVMGLEEIAPCTSKRKTQCRCQPGMFCAAWALECTHCELLSDCPPGTEAEL K corresponding to amino acids 1-157 of TNR3_HUMAN, which also corresponds to amino acids 1-157 of HUMTNFRRP_P2, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GQRSLRGWM corresponding to amino acids 158-166 of HUMTNFRRP_P2, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMTNFRRP_P2, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GQRSLRGWM in HUMTNFRRP_P2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMTNFRRP_P2 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 290, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRRP_P2 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 290







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





92
W → C
Yes









The glycosylation sites of variant protein HUMTNFRRP_P2, as compared to the known protein Tumor necrosis factor receptor superfamily member 3 precursor, are described in Table 291 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 291







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












40
yes
40


177
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 292:







TABLE 292







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR008063
Fas receptor
FPrintScan
115-142, 61-75,





97-113


IPR001368
TNFR/CD27/30/40/
HMMPfam
43-80, 83-124



95 cysteine-rich



region


IPR001368
TNFR/CD27/30/40/
HMMSmart
126-160, 43-80,



95 cysteine-rich

83-124



region


IPR001368
TNFR/CD27/30/40/
ScanRegExp
43-80, 83-126



95 cysteine-rich



region


IPR001368
TNFR/CD27/30/40/
ProfileScan
42-80, 82-124



95 cysteine-rich



region









Variant protein HUMTNFRRP_P2 is encoded by the following transcript(s): HUMTNFRRP_T2. The coding portion of transcript HUMTNFRRP_T2 starts at position 261 and ends at position 758. The transcript also has the following SNPs as listed in Table 293 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRRP_P2 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 293







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












87
G → A
Yes


87
G → T
No


108
C →
No


416
G → A
Yes


486
C → A
No


536
G → T
Yes


1463
A → C
Yes


2125
G → A
Yes


3262
C → T
Yes


3263
A → G
Yes


3520
T → A
Yes


3743
C → T
No


3752
C → T
No


4666
A → G
Yes


4699
C → G
Yes


4738
A → G
Yes


4780
C → T
Yes


5237
T → C
No


5366
C → T
Yes


5466
G →
No


5475
A → G
Yes


5672
G → A
Yes


5790
G → T
Yes


5887
C → G
Yes


5973
T → C
Yes


6134
G → T
Yes


6413
A → C
Yes









Variant protein HUMTNFRRP_P4 according to the present invention is encoded by transcript(s) HUMTNFRRP_T6. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 3 precursor) in FIG. 214. One or more alignments to one or more previously published protein sequences are given in Figures XX. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMTNFRRP_P4 and TNR3_HUMAN:
1. An isolated chimeric polypeptide HUMTNFRRP_P4, comprising a first amino acid sequence being at least 90% homologous to MLLPWATSAPGLAWGPLVLGLFGLLAASQPQAVPPYASENQTCRDQEKEYY EPQHRICCSRCPPGTYVSAKCSRIRDTVCATCAENSYNEHWNYLTICQLCRPC DPVMGLEEIAPCTSKRKTQCRCQPGMFCAAWALECTHCELLSDCPPGTEAEL KDEVGKGNNHCVPCKAGHFQNTSSPSARCQPHTRCENQGLVEAAPGTAQSD TTCKNPLEPLPPEMS corresponding to amino acids 1-222 of TNR3_HUMAN, which also corresponds to amino acids 1-222 of HUMTNFRRP_P4, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence EPALSKGVENLQALLYQAATGSSEASFPTLSPL corresponding to amino acids 223-255 of HUMTNFRRP_P4, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMTNFRRP_P4, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence EPALSKGVENLQALLYQAATGSSEASFPTLSPL in HUMTNFRRP_P4.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMTNFRRP_P4 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 294, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRRP_P4 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 294







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





92
W → C
Yes









The glycosylation sites of variant protein HUMTNFRRP_P4, as compared to the known protein Tumor necrosis factor receptor superfamily member 3 precursor, are described in Table 295 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 295







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












40
yes
40


177
yes
177









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 296:







TABLE 296







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR008063
Fas receptor
FPrintScan
115-142, 61-75,





97-113


IPR001368
TNFR/CD27/30/40/
HMMPfam
43-80, 83-124



95 cysteine-rich



region


IPR001368
TNFR/CD27/30/40/
HMMSmart
126-167, 170-210,



95 cysteine-rich

43-80, 83-124



region


IPR001368
TNFR/CD27/30/40/
ScanRegExp
43-80, 83-126



95 cysteine-rich



region


IPR001368
TNFR/CD27/30/40/
ProfileScan
169-210, 42-80,



95 cysteine-rich

82-124



region









Variant protein HUMTNFRRP_P4 is encoded by the following transcript(s): HUMTNFRRP_T6. The coding portion of transcript HUMTNFRRP_T6 starts at position 261 and ends at position 1025. The transcript also has the following SNPs as listed in Table 297 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRRP_P4 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 297







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












87
G → A
Yes


87
G → T
No


108
C →
No


416
G → A
Yes


486
C → A
No


536
G → T
Yes


776
A → C
Yes


1136
T → A
Yes


1359
C → T
No


1368
C → T
No


2282
A → G
Yes


2315
C → G
Yes


2354
A → G
Yes


2396
C → T
Yes


2853
T → C
No


2982
C → T
Yes


3082
G →
No


3091
A → G
Yes


3288
G → A
Yes


3406
G → T
Yes


3503
C → G
Yes


3589
T → C
Yes


3750
G → T
Yes


4029
A → C
Yes









Variant protein HUMTNFRRP_P9 according to the present invention is encoded by transcript(s) HUMTNFRRP_T18. An alignment is given to the known protein (Tumor necrosis factor receptor superfamily member 3 precursor) in FIG. 215. One or more alignments to one or more previously published protein sequences are given in FIGS. 213-214. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMTNFRRP_P9 and TNR3_HUMAN:
1. An isolated chimeric polypeptide HUMTNFRRP_P9, comprising a first amino acid sequence being at least 90% homologous to MLLPWATSAPGLAWGPLVLGLFGLLAASQPQAVPPYASENQTCRDQEKEYY EPQHRICCSRCPPGTYVSAKCSRIRDTVCATCAENSYNEHWNYLTICQLCRPC DPVMGLEEIAPCTSKRKTQCRCQPGMFCAAWALECTHCELLSDCPPGTEAEL K corresponding to amino acids 1-157 of TNR3_HUMAN, which also corresponds to amino acids 1-157 of HUMTNFRRP_P9, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GVRTKVWWRQLQALPSPTQPAKIH corresponding to amino acids 158-181 of HUMTNFRRP_P9, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMTNFRRP_P9, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GVRTKVWWRQLQALPSPTQPAKIH in HUMTNFRRP_P9.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMTNFRRP_P9 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 298, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRRP_P9 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 298







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





92
W → C
Yes









The glycosylation sites of variant protein HUMTNFRRP_P9, as compared to the known protein Tumor necrosis factor receptor superfamily member 3 precursor, are described in Table 299 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 299







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












40
yes
40


177
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 300:







TABLE 300







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR008063
Fas receptor
FPrintScan
115-142, 61-75,





97-113


IPR001368
TNFR/CD27/30/40/
HMMPfam
43-80, 83-124



95 cysteine-rich region


IPR001368
TNFR/CD27/30/40/
HMMSmart
126-160, 43-80,



95 cysteine-rich region

83-124


IPR001368
TNFR/CD27/30/40/
ScanRegExp
43-80, 83-126



95 cysteine-rich region


IPR001368
TNFR/CD27/30/40/
ProfileScan
42-80, 82-124



95 cysteine-rich region









Variant protein HUMTNFRRP_P9 is encoded by the following transcript(s): HUMTNFRRP_T18. The coding portion of transcript HUMTNFRRP_T18 starts at position 261 and ends at position 803. The transcript also has the following SNPs as listed in Table 301 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFRRP_P9 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 301







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












87
G → A
Yes


87
G → T
No


108
C →
No


416
G → A
Yes


486
C → A
No


536
G → T
Yes


1007
C → T
No


1016
C → T
No


1930
A → G
Yes


1963
C → G
Yes


2002
A → G
Yes


2044
C → T
Yes


2501
T → C
No


2630
C → T
Yes


2730
G →
No


2739
A → G
Yes


2936
G → A
Yes


3054
G → T
Yes


3151
C → G
Yes


3237
T → C
Yes


3398
G → T
Yes


3677
A → C
Yes









FIG. 216 depicts the domain structure of the TNFRRP variants in comparison to the known or wild-type (WT) protein.
Example 61
Description for Cluster HUMCLMF35
Cluster HUMCLMF35 features 6 transcript(s) and 20 segment(s) of interest, the names for which are given in Tables 302 and 303, respectively. The selected protein variants are given in table 304.







TABLE 302







Transcripts of interest










Transcript Name
SEQ ID NO:






HUMCLMF35_PEA_1_PEA_2_T1
901


 



HUMCLMF35_PEA_1_PEA_2_T5
902


 



HUMCLMF35_PEA_1_PEA_2_T6
903


 



HUMCLMF35_PEA_1_PEA_2_T7
904


 



HUMCLMF35_PEA_1_PEA_2_T10
905


 



HUMCLMF35_PEA_1_PEA_2_T12
906
















TABLE 303







Segments of interest










Segment Name
SEQ ID NO:













HUMCLMF35_PEA_1_PEA_2_node_0
907


 



HUMCLMF35_PEA_1_PEA_2_node_15
908


 



HUMCLMF35_PEA_1_PEA_2_node_20
909


 










HUMCLMF35_PEA_1_PEA_2_node_22
910


 



HUMCLMF35_PEA_1_PEA_2_node_1
911


 



HUMCLMF35_PEA_1_PEA_2_node_2
912


 



HUMCLMF35_PEA_1_PEA_2_node_3
913


 



HUMCLMF35_PEA_1_PEA_2_node_4
914


 



HUMCLMF35_PEA_1_PEA_2_node_5
915


 



HUMCLMF35_PEA_1_PEA_2_node_6
916


 



HUMCLMF35_PEA_1_PEA_2_node_8
917


 



HUMCLMF35_PEA_1_PEA_2_node_9
918


 



HUMCLMF35_PEA_1_PEA_2_node_10
919


 



HUMCLMF35_PEA_1_PEA_2_node_11
920


 



HUMCLMF35_PEA_1_PEA_2_node_13
921


 



HUMCLMF35_PEA_1_PEA_2_node_14
922


 



HUMCLMF35_PEA_1_PEA_2_node_16
923


 



HUMCLMF35_PEA 1_PEA_2_node_17
924


 



HUMCLMF35_PEA_1_PEA_2_node_18
925


 



HUMCLMF35_PEA_1_PEA_2_node_19
926
















TABLE 304







Proteins of interest












Protein
Corresponding


Protein Name
SEQ ID NO:
Length
Transcript(s)





HUMCLMF35_PE
927
P130
HUMCLMF35_PE


A_1_PEA_2_P14


A_1_PEA_2_T1


 


HUMCLMF35_PE
928
P93
HUMCLMF35_PE


A_1_PEA_2_P15


A_1_PEA_2_T5


 


HUMCLMF35_PE
929
P205
HUMCLMF35_PE


A_1_PEA_2_P16


A_1_PEA_2_T6


 


HUMCLMF35_PE
930
P181
HUMCLMF35_PE


A_1_PEA_2_P17


A_1_PEA_2_T7


 


HUMCLMF35_PE
931
P153
HUMCLMF35_PE


A_1_PEA_2_P20


A_1_PEA_2_T10


 


HUMCLMF35_PE
932
P171
HUMCLMF35_PE


A_1_PEA_2_P22


A_1_PEA_2_T12









These sequences are variants of the known protein Interleukin-12 alpha chain precursor (SwissProt accession identifier I12A_HUMAN; known also according to the synonyms IL-12A; Cytotoxic lymphocyte maturation factor 35 kDa subunit; CLMF p35; NK cell stimulatory factor chain 1; NKSF1), SEQ ID NO:933, referred to herein as the previously known protein.
Protein Interleukin-12 alpha chain precursor is known or believed to have the following function(s): Cytokine that can act as a growth factor for activated T and NK cells, enhance the lytic activity of NK/lymphokine-activated Killer cells, and stimulate the production of IFN-gamma by resting PBMC. The sequence for protein Interleukin-12 alpha chain precursor is given in SEQ ID NO: 933, as “Interleukin-12 alpha chain precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 305.







TABLE 305







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment





213
M → T









Protein Interleukin-12 alpha chain precursor localization is believed to be Secreted.
The previously known protein also has the following indication(s) and/or potential therapeutic use(s): Cancer; Infection, HIV/AIDS; Infection, hepatitis-C virus; Cancer, sarcoma, Kaposi's; Cancer, renal; Cancer, melanoma; Cancer, general; Cancer, head and neck, Cancer, ovarian. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein or of drugs directed against this protein are as follows. Immunostimulant; Interleukin 12 agonist; Interleukin 2 agonist; Natural killer cell stimulant; T cell stimulant. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Cytokine; Anticancer; Antipsoriasis; Immunomodulator, anti-infective; Immunosuppressant; Ophthalmological.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: immune response; antimicrobial humoral response (sensu Vertebrata), which are annotation(s) related to Biological Process; defense/immunity protein; signal transducer; cytokine; interleukin-12 receptor ligand, which are annotation(s) related to Molecular Function; and extracellular; extracellular space, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
IL-12 (p70) is a heterodimeric pro-inflammatory cytokine, composed of disulfide-linked p40 and p35 subunits. It is secreted by DCs and phagocytes in response to pathogens during infection. It induces the production IFNg (from T cells and NKs), favors the differentiation of Th1cells. IL-12R is a heterodimer composed of IL-12Rb1 and IL-12Rb2. Individually, each subunit binds IL-12 (p70) with low affinity while interaction with the heterodimer allows high affinity IL-12 binding.
p40 homodimer acts as IL-12 antagonist. Signaling will not occur upon p40 binding to IL-12Rb1.
p35 (IL-12A) may be described as follows. Structurally, mature p35 forms a four-helix bundle. Important residues for dimerization: R211-p35-p40 interaction, C96-disulfide bond with p40. Free p35 is not secreted (without wishing to be limited to a single hypothesis, it is probably unstable in the absence of p40). Glycosylation of p35 is a regulatory step in heterodimer assembly and secretion.
Figure depicts IL12 clinical developments.
As noted above, cluster HUMCLMF35 features 6 transcript(s), which were listed in Table 302 above. These transcript(s) encode for protein(s) which are variant(s) of protein Interleukin-12 alpha chain precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HUMCLMF35_PEA—1_PEA—2_P14 according to the present invention is encoded by transcript(s) HUMCLMF35_PEA—1_PEA—2_T1. An alignment is given to the known protein (Interleukin-12 alpha chain precursor; SEQ ID NO:933) in FIG. 218. One or more alignments to one or more previously published protein sequences are given in FIGS. 219-223. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMCLMF35_PEA_PEA—2_P14 and I12A_HUMAN (SEQ ID NO:933):
1. An isolated chimeric polypeptide HUMCLMF35_PEA—1_PEA—2_P14, comprising a first amino acid sequence being at least 90% homologous to MCPARSLLLVATLVLLDHLSLARNLPVATPDPGMFPCLHHSQNLLRAVSNML QKARQTLEFYPCTSEEIDHEDITKDKTSTVEACLPLELTKNESCLNSRETSFIT corresponding to amino acids 1-106 of I12A_HUMAN, which also corresponds to amino acids 1-106 of HUMCLMF35_PEA—1_PEA—2_P14, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSQKMKSFSLYDEFISLMSDYFFL corresponding to amino acids 107-130 of HUMCLMF35_PEA—1_PEA—2_P14, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMCLMF35_PEA—1_PEA—2_P14, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSQKMKSFSLYDEFISLMSDYFFL in HUMCLMF35_PEA—1_PEA—2_P14.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMCLMF35_PEA—1_PEA—2_P14 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 306, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMCLMF35_PEA—1_PEA—2_P14 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 306







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












82
V → A
No


123
L → V
Yes









The glycosylation sites of variant protein HUMCLMF35_PEA—1_PEA—2_P14, as compared to the known protein Interleukin-12 alpha chain precursor, are described in Table 307 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 307







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












107
no



93
yes
93









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 308:







TABLE 308







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR004281
Interleukin-12 alpha
HMMPfam
1-127



subunit









Variant protein HUMCLMF35_PEA—1_PEA—2_P14 is encoded by the following transcript(s): HUMCLMF35_PEA—1_PEA—2_T1. The coding portion of transcript HUMCLMF35_PEA—1_PEA—2_T1 starts at position 414 and ends at position 803. The transcript also has the following SNPs as listed in Table 309 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMCLMF35_PEA—1_PEA—2_P14 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 309







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












207
T → C
No


208
T → A
No


658
T → C
No


752
T → C
No


780
C → G
Yes


953
A → G
Yes


1118
T → C
Yes


1126
T → C
Yes


1165
A →
No


1239
G → A
Yes


1255
T → C
Yes


1262
T → A
No


1269
G → A
Yes









Variant protein HUMCLMF35_PEA—1_PEA—2_P15 according to the present invention is encoded by transcript(s) HUMCLMF35_PEA—1_PEA—2_T5. An alignment is given to the known protein (Interleukin-12 alpha chain precursor) in FIG. 219. One or more alignments to one or more previously published protein sequences are given in FIGS. 218, 220-223. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMCLMF35_PEA—1_PEA—2_P15 and I12A_HUMAN:
1. An isolated chimeric polypeptide HUMCLMF35_PEA—1_PEA—2_P15, comprising a first amino acid sequence being at least 90% homologous to MCPARSLLLVATLVLLDHLSLARNLPVATPDPGMFPCLHHSQNLLRAVSNML QKARQTLEFYPCTSEEIDHEDITKDKTSTVEACLPLELTK corresponding to amino acids 1-92 of I12A_HUMAN, which also corresponds to amino acids 1-92 of HUMCLMF35_PEA—1_PEA—2_P15, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence V corresponding to amino acids 93-93 of HUMCLMF35_PEA—1_PEA—2_P15, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMCLMF35_PEA—1_PEA—2_P15 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 310, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMCLMF35_PEA—1_PEA—2_P15 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 310







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





82
V → A
No









The glycosylation sites of variant protein HUMCLMF35_PEA—1_PEA—2_P15, as compared to the known protein Interleukin-12 alpha chain precursor, are described in Table 311 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 311







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












107
no



93
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 312:







TABLE 312







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR004281
Interleukin-12 alpha
HMMPfam
1-93



subunit









Variant protein HUMCLMF35_PEA—1_PEA—2_P15 is encoded by the following transcript(s): HUMCLMF35_PEA—1_PEA—2_T5. The coding portion of transcript HUMCLMF35_PEA—1_PEA—2_T5 starts at position 414 and ends at position 692. The transcript also has the following SNPs as listed in Table 313 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMCLMF35_PEA—1_PEA—2_P15 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 313







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












207
T → C
No


208
T → A
No


658
T → C
No


760
A → G
Yes


769
G → A
Yes


857
T → A
Yes


1077
T → C
No


1105
C → G
Yes


1369
A → G
Yes


1534
T → C
Yes


1542
T → C
Yes


1581
A →
No


1655
G → A
Yes


1671
T → C
Yes


1678
T → A
No


1685
G → A
Yes









Variant protein HUMCLMF35_PEA—1_PEA—2_P16 according to the present invention is encoded by transcript(s) HUMCLMF35_PEA—1_PEA—2_T6. An alignment is given to the known protein (Interleukin-12 alpha chain precursor) in FIG. 220. One or more alignments to one or more previously published protein sequences are given in FIGS. 218-219 and 221-223. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMCLMF35_PEA—1_PEA—2_P16 and I12A_HUMAN:
1. An isolated chimeric polypeptide HUMCLMF35_PEA—1_PEA—2_P16, comprising a first amino acid sequence being at least 90% homologous to MCPARSLLLVATLVLLDHLSLARNLPVATPDPGMFPCLHHSQNLLRAVSNML QKARQTLEFYPCTSEEIDHEDITKDKTSTVEACLPLELTK corresponding to amino acids 1-92 of I12A_HUMAN, which also corresponds to amino acids 1-92 of HUMCLMF35_PEA—1_PEA—2_P16, and a second amino acid sequence being at least 90% homologous to NGSCLASRKTSFMMALCLSSIYEDLKMYQVEFKTMNAKLLMDPKRQIFLDQ NMLAVIDELMQALNFNSETVPQKSSLEEPDFYKTKIKLCILLHAFRIRAVTIDR VMSYLNAS corresponding to amino acids 107-219 of I12A_HUMAN, which also corresponds to amino acids 93-205 of HUMCLMF35_PEA—1_PEA—2_P16, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric edge portion of HUMCLMF35_PEA—1_PEA—2_P16, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise KN, having a structure as follows: a sequence starting from any of amino acid numbers 92-x to 92; and ending at any of amino acid numbers 93+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMCLMF35_PEA—1_PEA—2_P16 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 314, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMCLMF35_PEA—1_PEA—2_P16 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 314







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












82
V → A
No


199
M → T
Yes









The glycosylation sites of variant protein HUMCLMF35_PEA—1_PEA—2_P16, as compared to the known protein Interleukin-12 alpha chain precursor, are described in Table 315 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 315







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












107
yes
93


93
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 316:







TABLE 316







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR004281
Interleukin-12 alpha
HMMPfam
1-205



subunit









Variant protein HUMCLMF35_PEA—1_PEA—2_P16 is encoded by the following transcript(s): HUMCLMF35_PEA—1_PEA—2_T6. The coding portion of transcript HUMCLMF35_PEA—1_PEA—2_T6 starts at position 414 and ends at position 1028. The transcript also has the following SNPs as listed in Table 317 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMCLMF35_PEA—1_PEA—2_P16 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 317







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












207
T → C
No


208
T → A
No


658
T → C
No


836
A → G
Yes


1001
T → C
Yes


1009
T → C
Yes


1048
A →
No


1122
G → A
Yes


1138
T → C
Yes


1145
T → A
No


1152
G → A
Yes









Variant protein HUMCLMF35_PEA—1_PEA—2_P17 according to the present invention is encoded by transcript(s) HUMCLMF35_PEA—1_PEA—2_T7. An alignment is given to the known protein (Interleukin-12 alpha chain precursor) in FIG. 221. One or more alignments to one or more previously published protein sequences are given in FIGS. 218-220 and 222-223. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMCLMF35_PEA—1_PEA—2_P17 and I12A_HUMAN:
1. An isolated chimeric polypeptide HUMCLMF35_PEA—1_PEA—2_P17, comprising a first amino acid sequence being at least 90% homologous to MCPARSLLLVATLVLLDHLSLARNLPVATPDPGMFPCLHHSQNLLRAVSNML Q corresponding to amino acids 1-53 of I12A_HUMAN, which also corresponds to amino acids 1-53 of HUMCLMF35_PEA—1_PEA—2_P17, and a second amino acid sequence being at least 90% homologous to KNESCLNSRETSFITNGSCLASRKTSFMMALCLSSIYEDLKMYQVEFKTMNAK LLMDPKRQIFLDQNMLAVIDELMQALNFNSETVPQKSSLEEPDFYKTKIKLCI LLHAFRIRAVTIDRVMSYLNAS corresponding to amino acids 92-219 of I12A_HUMAN, which also corresponds to amino acids 54-181 of HUMCLMF35_PEA—1_PEA—2_P17, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric edge portion of HUMCLMF35_PEA—1_PEA—2_P17, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise QK, having a structure as follows: a sequence starting from any of amino acid numbers 53-x to 53; and ending at any of amino acid numbers 54+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMCLMF35_PEA—1_PEA—2_P17 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 318, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMCLMF35_PEA—1_PEA—2_P17 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 318







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





175
M → T
Yes









The glycosylation sites of variant protein HUMCLMF35_PEA—1_PEA—2_P17, as compared to the known protein Interleukin-12 alpha chain precursor, are described in Table 319 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 319







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












107
yes
69


93
yes
55









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 320:







TABLE 320







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR004281
Interleukin-12 alpha
HMMPfam
1-181



subunit









Variant protein HUMCLMF35_PEA—1_PEA—2_P17 is encoded by the following transcript(s): HUMCLMF35_PEA—1_PEA—2_T7. The coding portion of transcript HUMCLMF35_PEA—1_PEA—2_T7 starts at position 414 and ends at position 956. The transcript also has the following SNPs as listed in Table 321 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMCLMF35_PEA—1_PEA—2_P17 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 321







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












207
T → C
No


208
T → A
No


764
A → G
Yes


929
T → C
Yes


937
T → C
Yes


976
A →
No


1050
G → A
Yes


1066
T → C
Yes


1073
T → A
No


1080
G → A
Yes









Variant protein HUMCLMF35_PEA—1_PEA—2_P20 according to the present invention is encoded by transcript(s) HUMCLMF35_PEA—1_PEA—2_T10. An alignment is given to the known protein (Interleukin-12 alpha chain precursor) in FIG. 222. One or more alignments to one or more previously published protein sequences are given in FIGS. 218-221 and 223. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMCLMF35_PEA—1_PEA—2_P20 and I12A_HUMAN:
1. An isolated chimeric polypeptide HUMCLMF35_PEA—1_PEA—2_P20, comprising a first amino acid sequence being at least 90% homologous to MCPARSLLLVATLVLLDHLSLARNLPVATPDPGMFPCLHHSQNLLRAVSNML QK corresponding to amino acids 1-54 of I12A_HUMAN, which also corresponds to amino acids 1-54 of HUMCLMF35_PEA—1_PEA—2_P20, and a second amino acid sequence being at least 90% homologous to ALCLSSIYEDLKMYQVEFKTMNAKLLMDPKRQIFLDQNMLAVIDELMQALN ENSETVPQKSSLEEPDFYKTKIKLCILLHAFRIRAVTIDRVMSYLNAS corresponding to amino acids 121-219 of I12A_HUMAN, which also corresponds to amino acids 55-153 of HUMCLMF35_PEA—1_PEA—2_P20, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HUMCLMF35_PEA—1_PEA—2_P20, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise KA, having a structure as follows: a sequence starting from any of amino acid numbers 54-x to 54; and ending at any of amino acid numbers 55+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMCLMF35_PEA—1_PEA—2_P20 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 322, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMCLMF35_PEA—1_PEA—2_P20 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 322







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





147
M → T
Yes









The glycosylation sites of variant protein HUMCLMF35_PEA—1_PEA—2_P20, as compared to the known protein Interleukin-12 alpha chain precursor, are described in Table 323 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 323







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












107
no



93
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 324:







TABLE 324







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR004281
Interleukin-12 alpha
HMMPfam
1-153



subunit









Variant protein HUMCLMF35_PEA—1_PEA—2_P20 is encoded by the following transcript(s): HUMCLMF35_PEA—1_PEA—2_T10. The coding portion of transcript HUMCLMF35_PEA—1_PEA—2_T10 starts at position 414 and ends at position 872. The transcript also has the following SNPs as listed in Table 325 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMCLMF35_PEA—1_PEA—2_P20 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 325







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?





207
T → C
No


208
T → A
No


680
A → G
Yes


845
T → C
Yes


853
T → C
Yes


892
A →
No


966
G → A
Yes


982
T → C
Yes


989
T → A
No


996
G → A
Yes









Variant protein HUMCLMF35_PEA—1_PEA—2_P22 according to the present invention is encoded by transcript(s) HUMCLMF35_PEA—1_PEA—2_T12. An alignment is given to the known protein (Interleukin-12 alpha chain precursor) in FIG. 223. One or more alignments to one or more previously published protein sequences are given in FIGS. 218-222. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMCLMF35_PEA—1_PEA—2_P22 and I12A_HUMAN:
1. An isolated chimeric polypeptide HUMCLMF35_PEA—1_PEA—2_P22, comprising a first amino acid sequence being at least 90% homologous to MCPARSLLLVATLVLLDHLSLARNLPVATPDPGMFPCLHHSQNLLRAVSNML QKARQTLEFYPCTSEEIDHEDITKDKTSTVEACLPLELTKNESCLNSRETSFITN GSCLASRKTSFMM corresponding to amino acids 1-120 of I12A_HUMAN, which also corresponds to amino acids 1-120 of HUMCLMF35_PEA—1_PEA—2_P22, and a second amino acid sequence being at least 90% homologous to ALNFNSETVPQKSSLEEPDFYKTKIKLCILLHAFRIRAVTIDRVMSYLNAS corresponding to amino acids 169-219 of I12A_HUMAN, which also corresponds to amino acids 121-171 of HUMCLMF35_PEA—1_PEA—2_P22, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HUMCLMF35_PEA—1_PEA—2_P22, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise MA, having a structure as follows: a sequence starting from any of amino acid numbers 120-x to 120; and ending at any of amino acid numbers 121+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMCLMF35_PEA—1_PEA—2_P22 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 326, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMCLMF35_PEA—1_PEA—2_P22 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 326







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












82
V → A
No


165
M → T
Yes









The glycosylation sites of variant protein HUMCLMF35_PEA—1_PEA—2_P22, as compared to the known protein Interleukin-12 alpha chain precursor, are described in Table 327 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 327







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












107
yes
107


93
yes
93









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 328:







TABLE 328







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR004281
Interleukin-12 alpha
HMMPfam
1-171



subunit









Variant protein HUMCLMF35_PEA—1_PEA—2_P22 is encoded by the following transcript(s): HUMCLMF35_PEA—1_PEA—2_T12. The coding portion of transcript HUMCLMF35_PEA—1_PEA—2_T12 starts at position 414 and ends at position 926. The transcript also has the following SNPs as listed in Table 329 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMCLMF35_PEA—1_PEA—2_P22 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 329







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












207
T → C
No


208
T → A
No


658
T → C
No


899
T → C
Yes


907
T → C
Yes


946
A →
No


1020
G → A
Yes


1036
T → C
Yes


1043
T → A
No


1050
G → A
Yes









FIG. 224 depicts the domain structure of the HUMCLMF35 variants in comparison to the known or wild-type (WT) IL12 protein.
Example 62
Description for Cluster S56892
Cluster S56892 features 4 transcript(s) and 18 segment(s) of interest, the names for which are given in Tables 330 and 331, respectively. The selected protein variants are given in table 332.







TABLE 330







Transcripts of interest










Transcript Name
SEQ ID NO:






S56892_PEA_1_PEA_1_T9
934


 



S56892_PEA_1_PEA_1_T10
935


 



S56892_PEA_1_PEA_1_T13
936


 



S56892_PEA_1 PEA_1_T14
937
















TABLE 331







Segments of interest










Segment Name
SEQ ID NO:






S56892_PEA_1_PEA_1_node_0
938


 



S56892_PEA_1 PEA_1_node_10
939


 



S56892_PEA_1_PEA_1_node_18
940


 



S56892_PEA_1_PEA_1_node_21
941


 



S56892_PEA_1 PEA_1_node_3
942


 



S56892_PEA_1_PEA_1_node_4
943


 



S56892_PEA_1_PEA_1_node_7
944


 



S56892_PEA_1 PEA_1_node_8
945


 



S56892_PEA_1_PEA_1_node_9
946


 



S56892_PEA_1_PEA_1_node_12
947


 



S56892_PEA_1_PEA_1_node_13
948


 



S56892_PEA_1 PEA_1_node_14
949


 



S56892_PEA_1 PEA_1_node_16
950


 



S56892_PEA_1_PEA_1 node_17
951


 



S56892_PEA_1_PEA_1_node_19
952


 



S56892_PEA_1_PEA_1_node_20
953


 



S56892_PEA_1_PEA_1_node_22
954


 



S56892_PEA_1_PEA_1_node_23
956
















TABLE 332







Proteins of interest










SEQ




ID
Cooresponding


Protein Name
NO:
Transcript(s)





S56892_PEA_1_PEA_1_P8
956
S56892_PEA_1_PEA_1_T9


 


S56892_PEA_1_PEA_1_P9
957
S56892_PEA_1_PEA_1_T10


 


S56892_PEA_1_PEA_1_P11
958
S56892_PEA_1_PEA_1_T13









These sequences are variants of the known protein Interleukin-6 precursor (SwissProt accession identifier IL6_HUMAN (SEQ ID NO:959); known also according to the synonyms IL-6; B-cell stimulatory factor 2; BSF-2; Interferon beta-2; Hybridoma growth factor; CTL differentiation factor; CDF), referred to herein as the previously known protein.
Protein Interleukin-6 precursor is known or believed to have the following function(s): IL-6 is a cytokine with a wide variety of biological functions: it plays an essential role in the final differentiation of B-cells into Ig-secreting cells, it induces myeloma and plasmacytoma growth, it induces nerve cells differentiation, in hepatocytes it induces acute phase reactants. The sequence for protein Interleukin-6 precursor is given in SEQ ID NO: 959, as “Interleukin-6 precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 333.







TABLE 333







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment











32
P → S./FTId = VAR_013075.


162
D → V./FTId = VAR_013076.


173
A → V: ALMOST NO LOSS OF ACTIVITY.


185
W → R: NO LOSS OF ACTIVITY.


204
S → P: 87% LOSS OF ACTIVITY.


210
R → K, E, Q, T, A, P: LOSS OF ACTIVITY.


212
M → T, N, S, R: LOSS OF ACTIVITY.









Protein Interleukin-6 precursor localization is believed to be Secreted.
The previously known protein also has the following indication(s) and/or potential therapeutic use(s): Chemotherapy-induced injury; Cancer, sarcoma, Kaposi s; Cancer, myeloma; Chemotherapy-induced injury, bone marrow, thrombocytopenia; Thrombocytopenia; Infection, HIV/AIDS; Chemotherapy-induced injury, bone marrow, neutropenia; Cancer, breast; Cancer, colorectal; Cancer, leukaemia, acute myelogenous; Cancer, melanoma; Myelodysplastic syndrome; Hepatic dysfunction. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein are as follows: Interleukin 1 antagonist; Interleukin 2 agonist; Interleukin 6 modulator. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Radio/chemoprotective; Anticancer; Cytokine; Haematological; Anti-inflammatory; Antianaemic; Antiviral, interferon; Anabolic; Hepatoprotective; Antiarthritic, immunological.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: skeletal development; acute-phase response; humoral defense mechanism; cell surface receptor linked signal transduction; cell-cell signaling; developmental processes; cell proliferation; positive control of cell proliferation; negative control of cell proliferation, which are annotation(s) related to Biological Process; cytokine; interleukin-6 receptor ligand, which are annotation(s) related to Molecular Function; and extracellular space, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
Interleukin-6 is a pleiotropic cytokine with a wide range of biological activities in immune regulation, hematopoiesis, inflammation and oncogenesis. It acts through two different receptors: IL-6R and a 130 kDa common signal transducer-gp130 to generate a high-affinity complex of IL-6/IL-6R/gp130. It has pathological roles in various disease conditions, including but not limited to inflammatory-mesangial proliferative glomerulonephritis, autoimmune-RA, Psoriasis and malignant diseases-multiple myeloma/plasmacytoma, Kaposi's sarcoma.
FIG. 225 depicts IL6 clinical developments.
As noted above, cluster S56892 features 4 transcript(s), which were listed in Table 330 above. These transcript(s) encode for protein(s) which are variant(s) of protein Interleukin-6 precursor. A description of each variant protein according to the present invention is now provided.
Variant protein S56892_PEA—1_PEA—1_P8 according to the present invention is encoded by transcript(s) S56892_PEA—1_PEA—1_T9. An alignment is given to the known protein (Interleukin-6 precursor) in FIG. 227. One or more alignments to one or more previously published protein sequences are given in FIGS. 228-229. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between S56892_PEA—1_PEA—1_P8 and IL6_HUMAN:
1. An isolated chimeric polypeptide S56892_PEA—1_PEA—1_P8, comprising a first amino acid sequence being at least 90% homologous to MNSFSTSAFGPVAFSLGLLLVLPAAFPAPVPPGEDSKDVAAPHRQPLTSSERID KQIRYILDGISALRKETCNKSNMCESSKEALAENNLNLPKMAEKDGCFQSGEN EETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKK corresponding to amino acids 1-157 of IL6_HUMAN, which also corresponds to amino acids 1-157 of S56892_PEA—1_PEA—1_P8, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VGVSSFPQLGVGEDRLKDSVLDNSGMQCHFQKRRLHVNKRV corresponding to amino acids 158-198 of S56892_PEA—1_PEA—1_P8, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of S56892_PEA—1_PEA—1_P8, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VGVSSFPQLGVGEDRLKDSVLDNSGMQCHFQKRRLHVNKRV in S56892_PEA—1_PEA—1_P8.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
The glycosylation sites of variant protein S56892_PEA—1_PEA—1_P8, as compared to the known protein Interleukin-6 precursor, are described in Table 334 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 334







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





73
yes
73









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 335:







TABLE 335







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
FPrintScan
101-126, 56-71,



CSF/MGF

72-95


IPR003574
Interleukin-6
FPrintScan
101-122, 56-72,





78-100


IPR003573
Interleukin-6/G-
HMMPfam
57-158



CSF/MGF


IPR003573
Interleukin-6/G-
HMMSmart
57-198



CSF/MGF


IPR003573
Interleukin-6/G-
ScanRegExp
101-126



CSF/MGF


IPR003574
Interleukin-6
BlastProDom
46-157









Variant protein S56892_PEA—1_PEA—1_P8 is encoded by the following transcript(s): S56892_PEA—1_PEA—1_T9. The coding portion of transcript S56892_PEA—1_PEA—1_T9 starts at position 458 and ends at position 1051. The transcript also has the following SNPs as listed in Table 336 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein S56892_PEA—1_PEA—1_P8 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 336







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












407
A → T
No


408
G → T
No


544
A → G
No


1798
A → G
Yes


2257
G → A
Yes


2711
C →
No


2731
A → G
No


2792
G →
No


2805
C → T
No


3177
→ A
No


3177
→ T
No









Variant protein S56892_PEA—1_PEA—1_P9 according to the present invention is encoded by transcript(s) S56892_PEA—1_PEA—1_T10. An alignment is given to the known protein (Interleukin-6 precursor) in FIG. 228. One or more alignments to one or more previously published protein sequences are given in FIGS. 227 and 229. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between S56892_PEA—1_PEA—1_P9 and IL6_HUMAN:
1. An isolated chimeric polypeptide S56892_PEA—1_PEA—1_P9, comprising a first amino acid sequence being at least 90% homologous to MNSFSTSAFGPVAFSLGLLLVLPAAFPAPVPPGEDSKDVAAPHRQPLTSSERID KQIRYILDGISALRKETCNKSNMCESSKEALAENNLNLPKMAEKDGCFQSGEN E corresponding to amino acids 1-108 of IL6_HUMAN, which also corresponds to amino acids 1-108 of S56892_PEA—1_PEA—1_P9, and a second amino acid sequence being at least 90% homologous to AKNLDAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALR QM corresponding to amino acids 158-212 of IL6_HUMAN, which also corresponds to amino acids 109-163 of S56892_PEA—1_PEA—1_P9, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of S56892_PEA—1_PEA—1_P9, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise EA, having a structure as follows: a sequence starting from any of amino acid numbers 108-x to 108; and ending at any of amino acid numbers 109+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein S56892_PEA—1_PEA—1_P9 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 337, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein S56892_PEA—1_PEA—1_P9 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 337







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





121
T →
No


128
T → A
No


148
S →
No









The glycosylation sites of variant protein S56892_PEA—1_PEA—1_P9, as compared to the known protein Interleukin-6 precursor, are described in Table 338 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 338







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





73
yes
73









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 339:







TABLE 339







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
FPrintScan
101-126, 56-71,



CSF/MGF

72-95


IPR003574
Interleukin-6
FPrintScan
101-122, 56-72,





78-100


IPR003573
Interleukin-6/G-
HMMPfam
110-161, 57-109



CSF/MGF


IPR003573
Interleukin-6/G-
HMMSmart
57-161



CSF/MGF


IPR003574
Interleukin-6
BlastProDom
46-163









Variant protein S56892_PEA—1_PEA—1_P9 is encoded by the following transcript(s): S56892_PEA—1_PEA—1_T10. The coding portion of transcript S56892_PEA—1_PEA—1_T10 starts at position 113 and ends at position 601. The transcript also has the following SNPs as listed in Table 340 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein S56892_PEA—1_PEA—1_P9 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 340







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












62
A → T
No


63
G → T
No


199
A → G
No


474
C →
No


494
A → G
No


555
G →
No


568
C → T
No


940
→ A
No


940
→ T
No









Variant protein S56892_PEA—1_PEA—1_P11 according to the present invention is encoded by transcript(s) S56892_PEA—1_PEA—1_T13. An alignment is given to the known protein (Interleukin-6 precursor) in FIG. 229. One or more alignments to one or more previously published protein sequences are given in FIGS. 227-228. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between S56892_PEA—1_PEA—1_P11 and IL6_HUMAN:
1. An isolated chimeric polypeptide S56892_PEA—1_PEA—1_P11, comprising a first amino acid sequence being at least 90% homologous to MNSFSTSAFGPVAFSLGLLLVLPAAFPAPVPPGEDSKDVAAPHRQPLTSSERID KQIRYILDGISALRKETCNKSN corresponding to amino acids 1-76 of IL6_HUMAN, which also corresponds to amino acids 1-76 of S56892_PEA—1_PEA—1_P11, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence IWLKKMDASNLDSMRRLAW corresponding to amino acids 77-95 of S56892_PEA—1_PEA—1_P11, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of S56892_PEA—1_PEA—1_P11, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence IWLKKMDASNLDSMRRLAW in S56892_PEA—1_PEA—1_P11.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
The glycosylation sites of variant protein S56892_PEA—1_PEA—1_P11, as compared to the known protein Interleukin-6 precursor, are described in Table 341 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 341







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





73
yes
73









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 342:







TABLE 342







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
HMMPfam
57-76



CSF/MGF


IPR003574
Interleukin-6
BlastProDom
46-77









Variant protein S56892_PEA—1_PEA—1_P11 is encoded by the following transcript(s): S56892_PEA—1_PEA—1_T13. The coding portion of transcript S56892_PEA—1_PEA—1_T13 starts at position 459 and ends at position 739. The transcript also has the following SNPs as listed in Table 343 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein S56892_PEA—1_PEA—1_P11 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 343







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












407
A → T
No


408
G → T
No


544
A → G
No


914
C →
No


934
A → G
No


995
G →
No


1008
C → T
No


1380
→ A
No


1380
→ T
No









FIG. 226 depicts the domain structure of the variants described hereinabove in comparison to the known or wild-type (WT) IL6 protein.
Example 63
Description for Cluster HUMTGFBIIR
Cluster HUMTGFBIIR features 2 transcript(s) and 10 segment(s) of interest, the names for which are given in Tables 344 and 345, respectively. The selected protein variants are given in table 346.







TABLE 344







Transcripts of interest










Transcript Name
SEQ ID NO:






HUMTGFBIIR_PEA_1T4
960


 



HUMTGFBIIR_PEA_1_T11
961
















TABLE 345







Segments of interest










Segment Name
SEQ ID NO:






HUMTGFBIIR_PEA_1_node_1
962


 



HUMTGFBIIR_PEA_1_node_2
963


 



HUMTGFBIIR_PEA_1_node_14
964


 



HUMTGFBIIR_PEA_1_node_17
965


 



HUMTGFBIIR_PEA_1_node_18
966


 



HUMTGFBIIR_PEA_1_node_20
967


 



HUMTGFBIIR_PEA_1_node_25
968


 



HUMTGFBIIR_PEA_1_node_28
969


 



HUMTGFBIIR_PEA_1_node_31
970


 



HUMTGFBIIR_PEA_1_node_33
971
















TABLE 346







Proteins of interest











SEQ
Protein
Corresponding


Protein Name
ID NO:
Length
Transcript(s)





HUMTGFBIIR_PEA_1_P9
972
P176
HUMTGFBIIR_PE





A_1_T11


 


HUMTGFBIIR_PEA_1_P14
973
P156
HUMTGFBIIR_PE





A_1_T4









These sequences are variants of the known protein TGF-beta receptor type II precursor (SwissProt accession identifier TGR2_HUMAN SEQ ID NO:974; known also according to the synonyms EC 2.7.1.37; TGFR-2; TGF-beta type II receptor), referred to herein as the previously known protein.
Protein TGF-beta receptor type II precursor is known or believed to have the following function(s): Type I/type II TGF-beta receptors form an heteromeric complex after binding TGF-beta at the cell surface and act as signal transducers. The sequence for protein TGF-beta receptor type II precursor is given in SEQ ID NO: 974, as “TGF-beta receptor type II precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 347.







TABLE 347







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment





191
V → I./FTId = VAR_017606.


315
T → M (in HNPCC6)./FTId = VAR_008156.


526
E → Q (in esophageal cancer)./FTId =



VAR_015816.


277
K → R: Abolishes kinase activity, TGF-beta



signaling and interaction with DAXX.


381
K → N









Protein TGF-beta receptor type II precursor localization is believed to be Type I membrane protein.
The previously known protein also has the following indication(s) and/or potential therapeutic use(s): Cancer, breast; Cancer, colorectal; Multiple sclerosis; Eczema; Lupus erythematosus; Psoriasis. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein or of drugs directed against this protein are as follows: Transforming growth factor beta 3 agonist; Transforming growth factor beta agonist. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Vulnerary; Cytokine; Musculoskeletal; Anticancer; Antidiabetic; Antipruritic/inflamm, allergic; Antipsoriasis; Multiple sclerosis.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: protein amino acid phosphorylation; transmembrane receptor protein serine/threonine kinase signaling pathway; TGFbeta ligand binding to type II receptor; positive control of cell proliferation, which are annotation(s) related to Biological Process; receptor; type II transforming growth factor beta receptor; ATP binding; transferase, which are annotation(s) related to Molecular Function; and integral membrane protein, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
As noted above, cluster HUMTGFBIIR features 2 transcript(s), which were listed in Table 344 above. These transcript(s) encode for protein(s) which are variant(s) of protein TGF-beta receptor type II precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HUMTGFBIIR_PEA—1_P9 according to the present invention is encoded by transcript(s) HUMTGFBIIR_PEA—1_T11. An alignment is given to the known protein (TGF-beta receptor type II precursor) in FIG. 230. One or more alignments to one or more previously published protein sequences are given in FIG. 231. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMTGFBIIR_PEA—1_P9 and TGR2_HUMAN:
1. An isolated chimeric polypeptide HUMTGFBIIR_PEA—1_P9, comprising a first amino acid sequence being at least 90% homologous to MGRGLLRGLWPLHIVLWTRIASTIPPHVQKSVNNDMIVTDNNGAVKFPQLCK FCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPK LPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSE corresponding to amino acids 1-151 of TGR2_HUMAN, which also corresponds to amino acids 1-151 of HUMTGFBIIR_PEA—1_P9, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GEFSSLKGVGPEICANFLYPWSAVS corresponding to amino acids 152-176 of HUMTGFBIIR_PEA—1_P9, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMTGFBIIR_PEA—1_P9, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GEFSSLKGVGPEICANFLYPWSAVS in HUMTGFBIIR_PEA—1_P9.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMTGFBIIR_PEA—1_P9 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 348, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTGFBIIR_PEA—1_P9 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 348







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












8
G → C
No


8
G → S
No


125
E →
No









The glycosylation sites of variant protein HUMTGFBIIR_PEA—1_P9, as compared to the known protein TGF-beta receptor type II precursor, are described in Table 349 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 349







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












94
yes
94


70
yes
70


154
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 350:







TABLE 350







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR000472
TGF-beta receptor/activin
ProfileScan
77-147



receptor, type I/II









Variant protein HUMTGFBIIR_PEA—1_P9 is encoded by the following transcript(s): HUMTGFBIIR_PEA—1_T11. The coding portion of transcript HUMTGFBIIR_PEA—1_T11 starts at position 432 and ends at position 959. The transcript also has the following SNPs as listed in Table 351 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTGFBIIR_PEA—1_P9 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 351







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












46
A → T
No


301
C → G
Yes


453
G → A
No


453
G → T
No


805
A →
No


959
A → G
Yes


1051
G → C
Yes


1152
T → C
Yes


1163
C → T
Yes


1364
T → C
Yes


1384
C → T
Yes









Variant protein HUMTGFBIIR_PEA—1_P14 according to the present invention is encoded by transcript(s) HUMTGFBIIR_PEA—1_T4. An alignment is given to the known protein (TGF-beta receptor type II precursor) in FIG. 231. One or more alignments to one or more previously published protein sequences are given in FIG. 230. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMTGFBIIR_PEA—1_P14 and TGR2_HUMAN:
1. An isolated chimeric polypeptide HUMTGFBIIR_PEA—1_P14, comprising a first amino acid sequence being at least 90% homologous to MGRGLLRGLWPLHIVLWTRIASTIPPHVQKSVNNDMIVTDNNGAVKFPQLCK FCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPK LPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSE corresponding to amino acids 1-151 of TGR2_HUMAN, which also corresponds to amino acids 1-151 of HUMTGFBIIR_PEA—1_P14, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence DFLMK corresponding to amino acids 152-156 of HUMTGFBIIR_PEA—1_P14, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMTGFBIIR_PEA—1_P14, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence DFLMK in HUMTGFBIIR_PEA—1_P14.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMTGFBIIR_PEA—1_P14 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 352, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTGFBIIR_PEA—1_P14 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 352







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












8
G → C
No


8
G → S
No


125
E →
No









The glycosylation sites of variant protein HUMTGFBIIR_PEA—1_P14, as compared to the known protein TGF-beta receptor type II precursor, are described in Table 353 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 353







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












94
yes
94


70
yes
70


154
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 354:







TABLE 354







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR000472
TGF-beta receptor/activin
ProfileScan
77-147



receptor, type I/II









Variant protein HUMTGFBIIR_PEA—1_P14 is encoded by the following transcript(s): HUMTGFBIIR_PEA—1_T4. The coding portion of transcript HUMTGFBIIR_PEA—1_T4 starts at position 432 and ends at position 899. The transcript also has the following SNPs as listed in Table 355 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTGFBIIR_PEA—1_P14 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 355







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












46
A → T
No


301
C → G
Yes


453
G → A
No


453
G → T
No


805
A →
No


1037
T → G
No


1138
C → T
No


1227
C →
No


1454
A → T
No


1455
G → T
No


1502
A → T
Yes


1554
A → G
Yes


1705
A →
No


1705
A → C
No


1722
C → T
Yes


1821
A → G
Yes


1871
T → C
Yes


1903
A → G
No


1930
T → G
No


1944
A → C
No


2587
C → A
Yes


2932
T → C
No


3004
C → G
Yes


3611
C → T
Yes


3778
G → A
Yes


3946
A → T
Yes


4066
A → G
Yes


4090
A → C
Yes


4137
G → A
Yes


4143
G → T
Yes


4322
C → T
Yes


4342
T → A
Yes


4394
→ C
No


4486
T →
No


4504
→ T
No


4561
→ T
No


4573
C → G
Yes


4633
A → C
No


4708
T → G
No









FIG. 232 depicts the domain structure of the variants described hereinabove in comparison to the known or wild-type (WT) TGR2_HUMAN protein.
Example 64
Description for Cluster HUMGCSF
Cluster HUMGCSF features 14 transcript(s) and 11 segment(s) of interest, the names for which are given in Tables 356 and 357, respectively, the sequences themselves are given in the sequence listing. The selected protein variants are given in Table 358.







TABLE 356







Transcripts of interest










Transcript Name
SEQ ID NO:







HUMGCSF_PEA_1_T4
975



 



HUMGCSF_PEA_1_T5
976



 



HUMGCSF PEA_1_T6
977



 



HUMGCSF_PEA_1_T7
978



 



HUMGCSF_PEA_1_T8
979



 



HUMGCSF_PEA_1_T13
980



 



HUMGCSF_PEA_1_T14
981



 



HUMGCSF_PEA_1_T16
982



 



HUMGCSF_PEA_1_T17
983



 



HUMGCSF_PEA_1_T18
984



 



HUMGCSF_PEA_1_T19
985



 



HUMGCSF_PEA_1_T20
986



 



HUMGCSF_PEA_1_T21
987



 



HUMGCSF_PEA_1_T22
988

















TABLE 357







Segments of interest










Segment Name
SEQ ID NO:







HUMGCSF_PEA_1_node_0
989



 



HUMGCSF_PEA_1_node_1
990



 



HUMGCSF_PEA_1_node_2
991



 



HUMGCSF_PEA_1_node_8
992



 



HUMGCSF_PEA_1_node_9
993



 



HUMGCSF_PEA_1_node_11
994



 



HUMGCSF_PEA_1_node_13
995



 



HUMGCSF_PEA_1_node_3
996



 



HUMGCSF_PEA_1_node_7
997



 



HUMGCSF_PEA_1_node_10
998



 



HUMGCSF_PEA_1_node_12
999

















TABLE 358







Proteins of interest











SEQ
Protein
Corresponding


Protein Name
ID NO:
Length
Transcript(s)





HUMGCSF_PEA_1_P5
1000
P151
HUMGCSF_PEA_1_T4


 


HUMGCSF_PEA_1_P6
1001
P110
HUMGCSF_PEA_1_T5


 


HUMGCSF_PEA_1_P7
1002
P190
HUMGCSF_PEA_1_T6


 


HUMGCSF_PEA_1_P8
1003
P147
HUMGCSF_PEA_1_T7


 


HUMGCSF_PEA_1_P9
1004
P168
HUMGCSF_PEA_1_T8;





HUMGCSF_PEA_1_T21


 


HUMGCSF_PEA_1_P13
1005
P171
HUMGCSF_PEA_1_T13;





HUMGCSF_PEA_1_T20


 


HUMGCSF_PEA_1_P14
1006
P103
HUMGCSF_PEA_1_T14


 


HUMGCSF_PEA_1_P16
1007
P154
HUMGCSF_PEA_1_T16


 


HUMGCSF_PEA_1_P18
1008
P187
HUMGCSF_PEA_1_T18


 


HUMGCSF_PEA_1_P19
1009
P150
HUMGCSF_PEA_1_T19


 


HUMGCSF_PEA_1_P20
1010
P106
HUMGCSF_PEA_1_T22


 


HUMGCSF_PEA_1_P21
1011
P107
HUMGCSF_PEA_1_T17









These sequences are variants of the known protein Granulocyte colony-stimulating factor precursor (SwissProt accession identifier CSF3_HUMAN; SEQ ID NO:128; known also according to the synonyms G-CSF; Pluripoietin; Filgrastim; Lenograstim), referred to herein as the previously known protein.
Protein Granulocyte colony-stimulating factor precursor is known or believed to have the following function(s): Granulocyte/macrophage colony-stimulating factors are cytokines that act in hematopoiesis by controlling the production, differentiation, and function of 2 related white cell populations of the blood, the granulocytes and the monocytes-macrophages. This CSF induces granulocytes. The sequence for protein Granulocyte colony-stimulating factor precursor is set forth in SEQ ID NO:128, as “Granulocyte colony-stimulating factor precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 359.







TABLE 359







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment





157
L → M./FTId = VAR_013073.


174
A → T./FTId = VAR_013074.









Protein Granulocyte colony-stimulating factor precursor localization is believed to be Secreted.
The previously known protein also has the following indication(s) and/or potential therapeutic use(s): Anaemia; Chemotherapy-induced injury, bone marrow; Chemotherapy-induced injury, bone marrow, neutropenia; Neutropenia; Chemotherapy-induced injury, bone marrow, leucopenia; Leucopenia; Cancer. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein or of drugs directed against this protein are as follows: Colony stimulating factor agonist; Granulocyte stimulating factor agonist. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Radio/chemoprotective; Cytokine; Immunomodulator, anti-infective; Haematological; Antianaemic; Anticancer; Immunostimulant, anti-AIDS.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: immune response; cellular defense response; cell surface receptor linked signal transduction; cell-cell signaling; developmental processes; positive control of cell proliferation, which are annotation(s) related to Biological Process; cytokine; granulocyte colony stimulating factor receptor ligand; interleukin-6 receptor ligand, which are annotation(s) related to Molecular Function; and extracellular; extracellular space, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
G-CSF Granulocyte Colony-Stimulating Factor has the following biological activities (intended as non-limiting examples only): stimulation of granulocyte proliferation, differentiation and survival; mobilization of hematopoietic stem cells into the peripheral blood circulation. It is secreted mainly by monocytes and macrophages but also by fibroblasts, endothelial cells, T-lymphocytes and polymorphonuclear granulocytes
The GCSF Receptor is a type I receptor that functions as a homodimer; it does not posses TK activity and is primarily expressed on neutrophilic progenitors and mature neutrophils.
FIGS. 233-235 depict the GCSF launched products (FIG. 233), GCSF clinical developments (FIG. 234) and GCSF preclinical developments (FIG. 235).
As noted above, cluster HUMGCSF features 14 transcript(s), which were listed in Table 1 above. These transcript(s) encode for protein(s) which are variant(s) of protein Granulocyte colony-stimulating factor precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HUMGCSF_PEA—1_P5 (SEQ ID NO:1000) is encoded by transcript(s) HUMGCSF_PEA—1_T4. An alignment is given to the known protein (Granulocyte colony-stimulating factor precursor; SEQ ID NO:128) in FIG. 237. One or more alignments to one or more previously published protein sequences are given in FIGS. 237-251. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMGCSF_PEA—1_P5 and CSF3_HUMAN:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P5, comprising a first amino acid sequence being at least 90% homologous to MAGPATQSPMKLMALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQV RKIQGDGAALQEK corresponding to amino acids 1-64 of CSF3_HUMAN, which also corresponds to amino acids 1-64 of HUMGCSF_PEA—1_P5, a second amino acid sequence being at least 90% homologous to LAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQ corresponding to amino acids 104-153 of CSF3_HUMAN, which also corresponds to amino acids 65-114 of HUMGCSF_PEA—1_P5, and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSLVGQGGQGRAGILGTTAGPVYGPCPCCQPPAFPHL corresponding to amino acids 115-151 of HUMGCSF_PEA—1_P5, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HUMGCSF_PEA—1_P5, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise KL, having a structure as follows: a sequence starting from any of amino acid numbers 64-x to 64; and ending at any of amino acid numbers 65+((n−2)−x), in which x varies from 0 to n−2.
3. An isolated polypeptide for a tail of HUMGCSF_PEA—1_P5, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSLVGQGGQGRAGILGTTAGPVYGPCPCCQPPAFPHL in HUMGCSF_PEA—1_P5.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMGCSF_PEA—1_P5 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 360, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P5 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 360







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












31
T →
No


60
A → P
No


60
A →
No


80
Q →
No


94
G → C
No


109
T → A
No


112
W → R
No


134
G → R
Yes


145
P → A
Yes









The glycosylation sites of variant protein HUMGCSF_PEA—1_P5, as compared to the known protein Granulocyte colony-stimulating factor precursor, are described in Table 361 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 361







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





166
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 362:







TABLE 362







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
HMMSmart
51-137



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
33-112



stimulating/myelo-



monocytic growth



factor









Variant protein HUMGCSF_PEA—1_P5 is encoded by the following transcript(s): HUMGCSF_PEA—1_T4 (SEQ ID NO:975). The coding portion of transcript HUMGCSF_PEA—1_T4 starts at position 115 and ends at position 567. The transcript also has the following SNPs as listed in Table 363 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P5 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 363







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












55
C → G
Yes


99
A → G
Yes


206
C →
No


292
G →
No


292
G → C
No


354
G →
No


394
G → T
No


439
A → G
No


448
T → C
No


514
G → A
Yes


547
C → G
Yes


622
T → C
No


630
C → A
Yes


662
G →
No


681
G → A
Yes


716
A → G
Yes


842
G → A
No


926
C → T
Yes


1007
A → G
Yes


1058
T → C
No


1062
C →
No


1238
C →
No


1278
C →
No


1310
C → T
Yes


1365
T → C
Yes


1405
G → A
Yes


1475
C → T
Yes









Variant protein HUMGCSF_PEA—1_P6 (SEQ ID NO:1001) according to the present invention is encoded by transcript(s) HUMGCSF_PEA—1_T5. An alignment is given to the known protein (Granulocyte colony-stimulating factor precursor) in FIG. 238. One or more alignments to one or more previously published protein sequences are given in FIGS. 237-251. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMGCSF_PEA—1_P6 and CSF3_HUMAN:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P6, comprising a first amino acid sequence being at least 90% homologous to MAGPATQSPMKLMALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQV RKIQGDGAALQEKLVSECATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQL corresponding to amino acids 1-104 of CSF3_HUMAN, which also corresponds to amino acids 1-104 of HUMGCSF_PEA—1_P6, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSVRKG corresponding to amino acids 105-110 of HUMGCSF_PEA—1_P6, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMGCSF_PEA—1_P6, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSVRKG in HUMGCSF_PEA—1_P6.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMGCSF_PEA—1_P6 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 364, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P6 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 364







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





31
T →
No


60
A →
No


60
A → P
No









The glycosylation sites of variant protein HUMGCSF_PEA—1_P6, as compared to the known protein Granulocyte colony-stimulating factor precursor, are described in Table 365 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 365







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





166
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 366:







TABLE 366







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
FPrintScan
50-65, 69-92



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
81-104



stimulating/myelo-



monocytic growth



factor









Variant protein HUMGCSF_PEA—1_P6 is encoded by the following transcript(s): HUMGCSF_PEA—1_T5. The coding portion of transcript HUMGCSF_PEA—1_T5 starts at position 115 and ends at position 444. The transcript also has the following SNPs as listed in Table 367 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P6 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 367







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












55
C → G
Yes


99
A → G
Yes


206
C →
No


292
G →
No


292
G → C
No


615
G →
No


655
G → T
No


700
A → G
No


709
T → C
No


775
G → A
Yes


808
C → G
Yes


883
T → C
No


891
C → A
Yes


923
G →
No


942
G → A
Yes


977
A → G
Yes


1103
G → A
No


1187
C → T
Yes


1268
A → G
Yes


1319
T → C
No


1323
C →
No


1499
C →
No


1539
C →
No


1571
C → T
Yes


1626
T → C
Yes


1666
G → A
Yes


1736
C → T
Yes









Variant protein HUMGCSF_PEA—1_P7 (SEQ ID NO:1002) according to the present invention is encoded by transcript(s) HUMGCSF_PEA—1_T6. An alignment is given to the known protein (Granulocyte colony-stimulating factor precursor) in FIG. 239. One or more alignments to one or more previously published protein sequences are given in FIGS. 237-251. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMGCSF_PEA—1_P7 and CSF3_HUMAN:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P7, comprising a first amino acid sequence being at least 90% homologous to MAGPATQSPMKLMALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQV RKIQGDGAALQEKLVSECATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQL AGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQ corresponding to amino acids 1-153 of CSF3_HUMAN, which also corresponds to amino acids 1-153 of HUMGCSF_PEA—1_P7, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSLVGQGGQGRAGILGTTAGPVYGPCPCCQPPAFPHL corresponding to amino acids 154-190 of HUMGCSF_PEA—1_P7, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMGCSF_PEA—1_P7, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSLVGQGGQGRAGILGTTAGPVYGPCPCCQPPAFPHL in HUMGCSF_PEA—1_P7.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMGCSF_PEA—1_P7 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 368, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P7 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 368







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












31
T →
No


60
A →
No


60
A → P
No


119
Q →
No


133
G → C
No


148
T → A
No


151
W → R
No


173
G → R
Yes


184
P → A
Yes









The glycosylation sites of variant protein HUMGCSF_PEA—1_P7, as compared to the known protein Granulocyte colony-stimulating factor precursor, are described in Table 369 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 369







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





166
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 370:







TABLE 370







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
FPrintScan
50-65, 69-92,



CSF/MGF

97-122


IPR003573
Interleukin-6/G-
HMMPfam
51-176



CSF/MGF


IPR003573
Interleukin-6/G-
HMMSmart
51-176



CSF/MGF


IPR003573
Interleukin-6/G-
ScanRegExp
97-122



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
81-151



stimulating/myelo-



monocytic growth



factor









Variant protein HUMGCSF_PEA—1_P7 is encoded by the following transcript(s): HUMGCSF_PEA—1_T6. The coding portion of transcript HUMGCSF_PEA—1_T6 starts at position 115 and ends at position 684. The transcript also has the following SNPs as listed in Table 371 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P7 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 371







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












55
C → G
Yes


99
A → G
Yes


206
C →
No


292
G →
No


292
G → C
No


471
G →
No


511
G → T
No


556
A → G
No


565
T → C
No


631
G → A
Yes


664
C → G
Yes


739
T → C
No


747
C → A
Yes


779
G →
No


798
G → A
Yes


833
A → G
Yes


959
G → A
No


1043
C → T
Yes


1124
A → G
Yes


1175
T → C
No


1179
C →
No


1355
C →
No


1395
C →
No


1427
C → T
Yes


1482
T → C
Yes


1522
G → A
Yes


1592
C → T
Yes









Variant protein HUMGCSF_PEA—1_P8 (SEQ ID NO:1003) according to the present invention is encoded by transcript(s) HUMGCSF_PEA—1_T7. An alignment is given to the known protein (Granulocyte colony-stimulating factor precursor) in FIG. 240. One or more alignments to one or more previously published protein sequences are given in FIGS. 237-251. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMGCSF_PEA—1_P8 and CSF3_HUMAN:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P8, comprising a first amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence MSPEPALSP corresponding to amino acids 1-9 of HUMGCSF_PEA—1_P8, a second amino acid sequence being at least 90% homologous to ALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQVRKIQGDGAALQEK corresponding to amino acids 14-64 of CSF3_HUMAN, which also corresponds to amino acids 10-60 of HUMGCSF_PEA—1_P8, a third amino acid sequence being at least 90% homologous to LAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQ corresponding to amino acids 104-153 of CSF3_HUMAN, which also corresponds to amino acids 61-110 of HUMGCSF_PEA—1_P8, and a fourth amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSLVGQGGQGRAGILGTTAGPVYGPCPCCQPPAFPHL corresponding to amino acids 111-147 of HUMGCSF_PEA—1_P8, wherein said first amino acid sequence, second amino acid sequence, third amino acid sequence and fourth amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a head of HUMGCSF_PEA—1_P8, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence MSPEPALSP of HUMGCSF_PEA—1_P8.
3. An isolated chimeric polypeptide for an edge portion of HUMGCSF_PEA—1_P8, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise KL, having a structure as follows: a sequence starting from any of amino acid numbers 60-x to 60; and ending at any of amino acid numbers 61+((n−2)−x), in which x varies from 0 to n−2.
4. An isolated polypeptide for a tail of HUMGCSF_PEA—1_P8, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSLVGQGGQGRAGILGTTAGPVYGPCPCCQPPAFPHL in HUMGCSF_PEA—1_P8.
Comparison Report Between HUMGCSF_PEA—1_P8 and Q8N4W3:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P8, comprising a first amino acid sequence being at least 90% homologous to MSPEPALSPALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQVRKIQGD GAALQEK corresponding to amino acids 1-60 of Q8N4W3, which also corresponds to amino acids 1-60 of HUMGCSF_PEA—1_P8, a second amino acid sequence being at least 90% homologous to LAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQ corresponding to amino acids 97-146 of Q8N4W3, which also corresponds to amino acids 61-110 of HUMGCSF_PEA—1_P8, and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSLVGQGGQGRAGILGTTAGPVYGPCPCCQPPAFPHL corresponding to amino acids 111-147 of HUMGCSF_PEA—1_P8, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HUMGCSF_PEA—1_P8, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise KL, having a structure as follows: a sequence starting from any of amino acid numbers 60-x to 60; and ending at any of amino acid numbers 61+((n−2)−x), in which x varies from 0 to n−2.
3. An isolated polypeptide for a tail of HUMGCSF_PEA—1_P8, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSLVGQGGQGRAGILGTTAGPVYGPCPCCQPPAFPHL in HUMGCSF_PEA—1_P8.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMGCSF_PEA—1_P8 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 372, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P8 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 372







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












27
T →
No


56
A → P
No


56
A →
No


76
Q →
No


90
G → C
No


105
T → A
No


108
W → R
No


130
G → R
Yes


141
P → A
Yes









The glycosylation sites of variant protein HUMGCSF_PEA—1_P8, as compared to the known protein Granulocyte colony-stimulating factor precursor, are described in Table 373 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 373







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





166
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 374:







TABLE 374







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
HMMSmart
47-133



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
29-108



stimulating/myelo-



monocytic growth



factor









Variant protein HUMGCSF_PEA—1_P8 is encoded by the following transcript(s): HUMGCSF_PEA—1_T7. The coding portion of transcript HUMGCSF_PEA—1_T7 starts at position 303 and ends at position 743. The transcript also has the following SNPs as listed in Table 375 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P8 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 375







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












55
C → G
Yes


99
A → G
Yes


382
C →
No


468
G →
No


468
G → C
No


530
G →
No


570
G → T
No


615
A → G
No


624
T → C
No


690
G → A
Yes


723
C → G
Yes


798
T → C
No


806
C → A
Yes


838
G →
No


857
G → A
Yes


892
A → G
Yes


1018
G → A
No


1102
C → T
Yes


1183
A → G
Yes


1234
T → C
No


1238
C →
No


1414
C →
No


1454
C →
No


1486
C → T
Yes


1541
T → C
Yes


1581
G → A
Yes


1651
C → T
Yes









Variant protein HUMGCSF_PEA—1_P9 (SEQ ID NO:1004) according to the present invention is encoded by transcript(s) HUMGCSF_PEA—1_T8 and HUMGCSF_PEA—1_T21. An alignment is given to the known protein (Granulocyte colony-stimulating factor precursor) in FIG. 242. One or more alignments to one or more previously published protein sequences are given in FIGS. 237-251. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMGCSF_PEA—1_P9 and CSF3_HUMAN:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P9, comprising a first amino acid sequence being at least 90% homologous to MAGPATQSPMKLMALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQV RKIQGDGAALQEK corresponding to amino acids 1-64 of CSF3_HUMAN, which also corresponds to amino acids 1-64 of HUMGCSF_PEA—1_P9, and a second amino acid sequence being at least 90% homologous to LAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQMEE LGMAPALQPTQGAMPAFASAFQRRAGGVLVASHLQSFLEVSYRVLRHLAQP corresponding to amino acids 104-207 of CSF3_HUMAN, which also corresponds to amino acids 65-168 of HUMGCSF_PEA—1_P9, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HUMGCSF_PEA—1_P9, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise KL, having a structure as follows: a sequence starting from any of amino acid numbers 64-x to 64; and ending at any of amino acid numbers 65+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMGCSF_PEA—1_P9 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 376, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P9 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 376







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












31
T →
No


60
A → P
No


60
A →
No


80
Q →
No


94
G → C
No


109
T → A
No


112
W → R
No


115
M → T
No


118
L → M
Yes


128
Q →
No


135
A → T
Yes









The glycosylation sites of variant protein HUMGCSF_PEA—1_P9, as compared to the known protein Granulocyte colony-stimulating factor precursor, are described in Table 377 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 377







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





166
yes
127









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 378







TABLE 378







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
FPrintScan
147-163, 58-83



CSF/MGF


IPR003573
Interleukin-6/G-
HMMPfam
51-163



CSF/MGF


IPR003573
Interleukin-6/G-
HMMSmart
51-163



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
33-168



stimulating/myelo-



monocytic growth



factor


IPR003573
Interleukin-6/G-
FPrintScan
147-163, 58-83



CSF/MGF


IPR003573
Interleukin-6/G-
HMMPfam
51-163



CSF/MGF


IPR003573
Interleukin-6/G-
HMMSmart
51-163



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
33-168



stimulating/myelo-



monocytic growth



factor


IPR003573
Interleukin-6/G-
FPrintScan
147-163, 58-83



CSF/MGF


IPR003573
Interleukin-6/G-
HMMPfam
51-163



CSF/MGF


IPR003573
Interleukin-6/G-
HMMSmart
51-163



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
33-168



stimulating/myelo-



monocytic growth



factor


IPR003573
Interleukin-6/G-
FPrintScan
147-163, 58-83



CSF/MGF


IPR003573
Interleukin-6/G-
HMMPfam
51-163



CSF/MGF


IPR003573
Interleukin-6/G-
HMMSmart
51-163



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
33-168



stimulating/myelo-



monocytic growth



factor









Variant protein HUMGCSF_PEA—1_P9 is encoded by the following transcript(s): HUMGCSF_PEA—1_T8 and HUMGCSF_PEA—1_T21.
The coding portion of transcript HUMGCSF_PEA—1_T8 starts at position 115 and ends at position 618. The transcript also has the following SNPs as listed in Table 379 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P9 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 379







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












55
C → G
Yes


99
A → G
Yes


206
C →
No


292
G →
No


292
G → C
No


354
G →
No


394
G → T
No


439
A → G
No


448
T → C
No


458
T → C
No


466
C → A
Yes


498
G →
No


517
G → A
Yes


552
A → G
Yes


678
G → A
No


762
C → T
Yes


843
A → G
Yes


894
T → C
No


898
C →
No


1074
C →
No


1114
C →
No


1146
C → T
Yes


1201
T → C
Yes


1241
G → A
Yes


1311
C → T
Yes









The coding portion of transcript HUMGCSF_PEA—1_T21 starts at position 115 and ends at position 618. The transcript also has the following SNPs as listed in Table 380 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P9 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 380







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












55
C → G
Yes


99
A → G
Yes


206
C →
No


292
G →
No


292
G → C
No


354
G →
No


394
G → T
No


439
A → G
No


448
T → C
No


458
T → C
No


466
C → A
Yes


498
G →
No


517
G → A
Yes


552
A → G
Yes


678
G → A
No


762
C → T
Yes


843
A → G
Yes


894
T → C
No


898
C →
No


1074
C →
No


1114
C →
No


1146
C → T
Yes


1201
T → C
Yes


1241
G → A
Yes


1311
C → T
Yes









Variant protein HUMGCSF_PEA—1_P13 (SEQ ID NO:1005) according to the present invention is encoded by transcript(s) HUMGCSF_PEA—1_T13 and HUMGCSF_PEA—1_T20. An alignment is given to the known protein (Granulocyte colony-stimulating factor precursor) in FIG. 243. One or more alignments to one or more previously published protein sequences are given in FIGS. 237-251. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMGCSF_PEA—1_P13 and CSF3_HUMAN:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P13, comprising a first amino acid sequence being at least 90% homologous to MAGPATQSPMKLMALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQV RKIQGDGAALQEKLVSE corresponding to amino acids 1-68 of CSF3_HUMAN, which also corresponds to amino acids 1-68 of HUMGCSF_PEA—1_P13, and a second amino acid sequence being at least 90% homologous to AGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQMEEL GMAPALQPTQGAMPAFASAFQRRAGGVLVASHLQSFLEVSYRVLRHLAQP corresponding to amino acids 105-207 of CSF3_HUMAN, which also corresponds to amino acids 69-171 of HUMGCSF_PEA—1_P13, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HUMGCSF_PEA—1_P13, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise EA, having a structure as follows: a sequence starting from any of amino acid numbers 68-x to 68; and ending at any of amino acid numbers 69+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMGCSF_PEA—1_P13 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 381, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P13 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 381







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












31
T →
No


60
A → P
No


60
A →
No


83
Q →
No


97
G → C
No


112
T → A
No


115
W → R
No


118
M → T
No


121
L → M
Yes


131
Q →
No


138
A → T
Yes









The glycosylation sites of variant protein HUMGCSF_PEA—1_P13, as compared to the known protein Granulocyte colony-stimulating factor precursor, are described in Table 382 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 382







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





166
yes
130









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 383:







TABLE 383







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
FPrintScan
150-166, 61-86



CSF/MGF


IPR003573
Interleukin-6/G-
HMMPfam
51-166



CSF/MGF


IPR003573
Interleukin-6/G-
HMMSmart
51-166



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
69-171



stimulating/myelo-



monocytic growth



factor


IPR003573
Interleukin-6/G-
FPrintScan
150-166, 61-86



CSF/MGF


IPR003573
Interleukin-6/G-
HMMPfam
51-166



CSF/MGF


IPR003573
Interleukin-6/G-
HMMSmart
51-166



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
69-171



stimulating/myelo-



monocytic growth



factor


IPR003573
Interleukin-6/G-
FPrintScan
150-166, 61-86



CSF/MGF


IPR003573
Interleukin-6/G-
HMMPfam
51-166



CSF/MGF


IPR003573
Interleukin-6/G-
HMMSmart
51-166



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
69-171



stimulating/myelo-



monocytic growth



factor


IPR003573
Interleukin-6/G-
FPrintScan
150-166, 61-86



CSF/MGF


IPR003573
Interleukin-6/G-
HMMPfam
51-166



CSF/MGF


IPR003573
Interleukin-6/G-
HMMSmart
51-166



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
69-171



stimulating/myelo-



monocytic growth



factor









Variant protein HUMGCSF_PEA—1_P13 is encoded by the following transcript(s): HUMGCSF_PEA—1_T13 and HUMGCSF_PEA—1_T20.
The coding portion of transcript HUMGCSF_PEA—1_T13 starts at position 115 and ends at position 627. The transcript also has the following SNPs as listed in Table 384 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P13 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 384







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












55
C → G
Yes


99
A → G
Yes


206
C →
No


292
G →
No


292
G → C
No


363
G →
No


403
G → T
No


448
A → G
No


457
T → C
No


467
T → C
No


475
C → A
Yes


507
G →
No


526
G → A
Yes


561
A → G
Yes


687
G → A
No


771
C → T
Yes


852
A → G
Yes


903
T → C
No


907
C →
No


1083
C →
No


1123
C →
No


1155
C → T
Yes


1210
T → C
Yes


1250
G → A
Yes


1320
C → T
Yes









The coding portion of transcript HUMGCSF_PEA—1_T20 starts at position 115 and ends at position 627. The transcript also has the following SNPs as listed in Table 385 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P13 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 385







Nucleic acid SNPs -









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












55
C → G
Yes


99
A → G
Yes


206
C →
No


292
G →
No


292
G → C
No


363
G →
No


403
G → T
No


448
A → G
No


457
T → C
No


467
T → C
No


475
C → A
Yes


507
G →
No


526
G → A
Yes


561
A → G
Yes


687
G → A
No


771
C → T
Yes


852
A → G
Yes


903
T → C
No


907
C →
No


1083
C →
No


1123
C →
No


1155
C → T
Yes


1210
T → C
Yes


1250
G → A
Yes


1320
C → T
Yes









Variant protein HUMGCSF_PEA—1_P14 (SEQ ID NO:1006) according to the present invention is encoded by transcript(s) HUMGCSF_PEA—1_T14. An alignment is given to the known protein (Granulocyte colony-stimulating factor precursor) in FIG. 244. One or more alignments to one or more previously published protein sequences are given in FIGS. 237-251. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMGCSF_PEA—1_P14 and CSF3_HUMAN:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P14, comprising a first amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence MSPEPALSP corresponding to amino acids 1-9 of HUMGCSF_PEA—1_P14, a second amino acid sequence being at least 90% homologous to ALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQVRKIQGDGAALQEKL corresponding to amino acids 14-65 of CSF3_HUMAN, which also corresponds to amino acids 10-61 of HUMGCSF_PEA—1_P14, a third amino acid sequence being at least 90% homologous to CATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQL corresponding to amino acids 69-104 of CSF3_HUMAN, which also corresponds to amino acids 62-97 of HUMGCSF_PEA—1_P14, and a fourth amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSVRKG corresponding to amino acids 98-103 of HUMGCSF_PEA—1_P14, wherein said first amino acid sequence, second amino acid sequence, third amino acid sequence and fourth amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a head of HUMGCSF_PEA—1_P14, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence MSPEPALSP of HUMGCSF_PEA—1_P14.
3. An isolated chimeric polypeptide for an edge portion of HUMGCSF_PEA—1_P14, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise LC, having a structure as follows: a sequence starting from any of amino acid numbers 61-x to 61; and ending at any of amino acid numbers 62+((n−2)−x), in which x varies from 0 to n−2.
4. An isolated polypeptide for a tail of HUMGCSF_PEA—1_P14, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSVRKG in HUMGCSF_PEA—1_P14.
Comparison Report Between HUMGCSF_PEA—1_P14 and Q8N4W3:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P14, comprising a first amino acid sequence being at least 90% homologous to MSPEPALSPALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQVRKIQGD GAALQEKLCATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQL corresponding to amino acids 1-97 of Q8N4W3, which also corresponds to amino acids 1-97 of HUMGCSF_PEA—1_P14, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSVRKG corresponding to amino acids 98-103 of HUMGCSF_PEA—1_P14, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMGCSF_PEA—1_P14, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSVRKG in HUMGCSF_PEA—1_P14.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMGCSF_PEA—1_P14 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 386, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P14 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 386







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





27
T →
No


56
A →
No


56
A → P
No









The glycosylation sites of variant protein HUMGCSF_PEA—1_P14, as compared to the known protein Granulocyte colony-stimulating factor precursor, are described in Table 387 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 387







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





166
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 388:







TABLE 388







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
FPrintScan
46-61, 62-85



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
74-97



stimulating/myelo-



monocytic growth



factor









Variant protein HUMGCSF_PEA—1_P14 is encoded by the following transcript(s): HUMGCSF_PEA—1_T14. The coding portion of transcript HUMGCSF_PEA—1_T14 starts at position 303 and ends at position 611. The transcript also has the following SNPs as listed in Table 389 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P14 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 389







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












55
C → G
Yes


99
A → G
Yes


382
C →
No


468
G →
No


468
G → C
No


782
G →
No


822
G → T
No


867
A → G
No


876
T → C
No


886
T → C
No


894
C → A
Yes


926
G →
No


945
G → A
Yes


980
A → G
Yes


1106
G → A
No


1190
C → T
Yes


1271
A → G
Yes


1322
T → C
No


1326
C →
No


1502
C →
No


1542
C →
No


1574
C → T
Yes


1629
T → C
Yes


1669
G → A
Yes


1739
C → T
Yes









Variant protein HUMGCSF_PEA—1_P16 (SEQ ID NO:1007) according to the present invention is encoded by transcript(s) HUMGCSF_PEA—1_T16. An alignment is given to the known protein (Granulocyte colony-stimulating factor precursor) in FIG. 246. One or more alignments to one or more previously published protein sequences are given in FIGS. 237-251. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMGCSF_PEA—1_P16 and CSF3_HUMAN:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P16, comprising a first amino acid sequence being at least 90% homologous to MAGPATQSPMKLMALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQV RKIQGDGAALQEKLVSE corresponding to amino acids 1-68 of CSF3_HUMAN, which also corresponds to amino acids 1-68 of HUMGCSF_PEA—1_P16, a second amino acid sequence being at least 90% homologous to AGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQ corresponding to amino acids 105-153 of CSF3_HUMAN, which also corresponds to amino acids 69-117 of HUMGCSF_PEA—1_P16, and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSLVGQGGQGRAGILGTTAGPVYGPCPCCQPPAFPHL corresponding to amino acids 118-154 of HUMGCSF_PEA—1_P16, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HUMGCSF_PEA—1_P16, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise EA, having a structure as follows: a sequence starting from any of amino acid numbers 68-x to 68; and ending at any of amino acid numbers 69+((n−2)−x), in which x varies from 0 to n−2.
3. An isolated polypeptide for a tail of HUMGCSF_PEA—1_P16, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSLVGQGGQGRAGILGTTAGPVYGPCPCCQPPAFPHL in HUMGCSF_PEA—1_P16.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMGCSF_PEA—1_P16 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 390, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P16 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 390







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












31
T →
No


60
A → P
No


60
A →
No


83
Q →
No


97
G → C
No


112
T → A
No


115
W → R
No


137
G → R
Yes


148
P → A
Yes









The glycosylation sites of variant protein HUMGCSF_PEA—1_P16, as compared to the known protein Granulocyte colony-stimulating factor precursor, are described in Table 391 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 391







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





166
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 392:







TABLE 392







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
HMMSmart
51-140



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
69-115



stimulating/myelo-



monocytic growth



factor









Variant protein HUMGCSF_PEA—1_P16 is encoded by the following transcript(s): HUMGCSF_PEA—1_T16. The coding portion of transcript HUMGCSF_PEA—1_T16 starts at position 115 and ends at position 576. The transcript also has the following SNPs as listed in Table 393 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P16 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 393







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












55
C → G
Yes


99
A → G
Yes


206
C →
No


292
G →
No


292
G → C
No


363
G →
No


403
G → T
No


448
A → G
No


457
T → C
No


523
G → A
Yes


556
C → G
Yes


631
T → C
No


639
C → A
Yes


671
G →
No


690
G → A
Yes


725
A → G
Yes


851
G → A
No


935
C → T
Yes


1016
A → G
Yes


1067
T → C
No


1071
C →
No


1247
C →
No


1287
C →
No


1319
C → T
Yes


1374
T → C
Yes


1414
G → A
Yes


1484
C → T
Yes









Variant protein HUMGCSF_PEA—1_P18 (SEQ ID NO:1008) according to the present invention is encoded by transcript(s) HUMGCSF_PEA—1_T18. An alignment is given to the known protein (Granulocyte colony-stimulating factor precursor; CSF3_HUMAN (SEQ ID NO:128) in FIG. 247. One or more alignments to one or more previously published protein sequences are given in FIGS. 237-251. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMGCSF_PEA—1_P18 and CSF3_HUMAN:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P18, comprising a first amino acid sequence being at least 90% homologous to MAGPATQSPMKLMALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQV RKIQGDGAALQEKL corresponding to amino acids 1-65 of CSF3_HUMAN, which also corresponds to amino acids 1-65 of HUMGCSF_PEA—1_P18, a second amino acid sequence being at least 90% homologous to CATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQLAGCLSQLHSGLFLYQGL LQALEGISPELGPTLDTLQLDVADFATTIWQQ corresponding to amino acids 69-153 of CSF3_HUMAN, which also corresponds to amino acids 66-150 of HUMGCSF_PEA—1_P18, and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSLVGQGGQGRAGILGTTAGPVYGPCPCCQPPAFPHL corresponding to amino acids 151-187 of HUMGCSF_PEA—1_P18, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HUMGCSF_PEA—1_P18, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise LC, having a structure as follows: a sequence starting from any of amino acid numbers 65-x to 65; and ending at any of amino acid numbers 66+((n−2)−x), in which x varies from 0 to n−2.
3. An isolated polypeptide for a tail of HUMGCSF_PEA—1_P18, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSLVGQGGQGRAGILGTTAGPVYGPCPCCQPPAFPHL in HUMGCSF_PEA—1_P18.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMGCSF_PEA—1_P18 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 394, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P18 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 394







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












31
T →
No


60
A →
No


60
A → P
No


116
Q →
No


130
G → C
No


145
T → A
No


148
W → R
No


170
G → R
Yes


181
P → A
Yes









The glycosylation sites of variant protein HUMGCSF_PEA—1_P18, as compared to the known protein Granulocyte colony-stimulating factor precursor, are described in Table 395 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 395







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





166
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 396:







TABLE 396







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
FPrintScan
50-65, 66-89,



CSF/MGF

94-119


IPR003573
Interleukin-6/G-
HMMPfam
51-173



CSF/MGF


IPR003573
Interleukin-6/G-
HMMSmart
51-173



CSF/MGF


IPR003573
Interleukin-6/G-
ScanRegExp
94-119



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
78-148



stimulating/myelo-



monocytic growth



factor









Variant protein HUMGCSF_PEA—1_P18 is encoded by the following transcript(s): HUMGCSF_PEA—1_T18. The coding portion of transcript HUMGCSF_PEA—1_T18 starts at position 115 and ends at position 675. The transcript also has the following SNPs as listed in Table 397 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P18 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 397







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












55
C → G
Yes


99
A → G
Yes


206
C →
No


292
G →
No


292
G → C
No


462
G →
No


502
G → T
No


547
A → G
No


556
T → C
No


622
G → A
Yes


655
C → G
Yes


730
T → C
No


738
C → A
Yes


770
G →
No


789
G → A
Yes


824
A → G
Yes


950
G → A
No


1034
C → T
Yes


1115
A → G
Yes


1166
T → C
No


1170
C →
No


1346
C →
No


1386
C →
No


1418
C → T
Yes


1473
T → C
Yes


1513
G → A
Yes


1583
C → T
Yes









Variant protein HUMGCSF_PEA—1_P19 (SEQ ID NO:1009) according to the present invention is encoded by transcript(s) HUMGCSF_PEA—1_T19. An alignment is given to the known protein (Granulocyte colony-stimulating factor precursor) in FIG. 248. One or more alignments to one or more previously published protein sequences are given in FIGS. 237-251. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMGCSF_PEA—1_P19 and CSF3_HUMAN:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P19, comprising a first amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence MSPEPALSP corresponding to amino acids 1-9 of HUMGCSF_PEA—1_P19, a second amino acid sequence being at least 90% homologous to ALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQVRKIQGDGAALQEKL VSE corresponding to amino acids 14-68 of CSF3_HUMAN, which also corresponds to amino acids 10-64 of HUMGCSF_PEA—1_P19, a third amino acid sequence being at least 90% homologous to AGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQ corresponding to amino acids 105-153 of CSF3_HUMAN, which also corresponds to amino acids 65-113 of HUMGCSF_PEA—1_P19, and a fourth amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSLVGQGGQGRAGILGTTAGPVYGPCPCCQPPAFPHL corresponding to amino acids 114-150 of HUMGCSF_PEA—1_P19, wherein said first amino acid sequence, second amino acid sequence, third amino acid sequence and fourth amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a head of HUMGCSF_PEA—1_P19, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence MSPEPALSP of HUMGCSF_PEA—1_P19.
3. An isolated chimeric polypeptide for an edge portion of HUMGCSF_PEA—1_P19, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise EA, having a structure as follows: a sequence starting from any of amino acid numbers 64-x to 64; and ending at any of amino acid numbers 65+((n−2)−x), in which x varies from 0 to n−2.
4. An isolated polypeptide for a tail of HUMGCSF_PEA—1_P19, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSLVGQGGQGRAGILGTTAGPVYGPCPCCQPPAFPHL in HUMGCSF_PEA—1_P19.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMGCSF_PEA—1_P19 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 398, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P19 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 398







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












27
T →
No


56
A → P
No


56
A →
No


79
Q →
No


93
G → C
No


108
T → A
No


111
W → R
No


133
G → R
Yes


144
P → A
Yes









The glycosylation sites of variant protein HUMGCSF_PEA—1_P19, as compared to the known protein Granulocyte colony-stimulating factor precursor, are described in Table 399 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 399







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





166
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 400:







TABLE 400







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
HMMSmart
47-136



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
65-111



stimulating/myelo-



monocytic growth



factor









Variant protein HUMGCSF_PEA—1_P19 is encoded by the following transcript(s): HUMGCSF_PEA—1_T19. The coding portion of transcript HUMGCSF_PEA—1_T19 starts at position 303 and ends at position 752. The transcript also has the following SNPs as listed in Table 401 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P19 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 401







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












55
C → G
Yes


99
A → G
Yes


382
C →
No


468
G →
No


468
G → C
No


539
G →
No


579
G → T
No


624
A → G
No


633
T → C
No


699
G → A
Yes


732
C → G
Yes


807
T → C
No


815
C → A
Yes


847
G →
No


866
G → A
Yes


901
A → G
Yes


1027
G → A
No


1111
C → T
Yes


1192
A → G
Yes


1243
T → C
No


1247
C →
No


1423
C →
No


1463
C →
No


1495
C → T
Yes


1550
T → C
Yes


1590
G → A
Yes


1660
C → T
Yes









Variant protein HUMGCSF_PEA—1_P20 (SEQ ID NO:1010) according to the present invention is encoded by transcript(s) HUMGCSF_PEA—1_T22. An alignment is given to the known protein (Granulocyte colony-stimulating factor precursor) in FIG. 249. One or more alignments to one or more previously published protein sequences are given in FIGS. 237-251. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMGCSF_PEA—1_P20 and CSF3_HUMAN:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P20, comprising a first amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence MSPEPALSP corresponding to amino acids 1-9 of HUMGCSF_PEA—1_P20, a second amino acid sequence being at least 90% homologous to ALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQVRKIQGDGAALQEKL VSECATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQL corresponding to amino acids 14-104 of CSF3_HUMAN, which also corresponds to amino acids 10-100 of HUMGCSF_PEA—1_P20, and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSVRKG corresponding to amino acids 101-106 of HUMGCSF_PEA—1_P20, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a head of HUMGCSF_PEA—1_P20, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence MSPEPALSP of HUMGCSF_PEA—1_P20.
3. An isolated polypeptide for a tail of HUMGCSF_PEA—1_P20, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSVRKG in HUMGCSF_PEA—1_P20.
Comparison Report Between HUMGCSF_PEA—1_P20 and Q8N4W3:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P20, comprising a first amino acid sequence being at least 90% homologous to MSPEPALSPALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQVRKIQGD GAALQEKL corresponding to amino acids 1-61 of Q8N4W3, which also corresponds to amino acids 1-61 of HUMGCSF_PEA—1_P20, a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSE corresponding to amino acids 62-64 of HUMGCSF_PEA—1_P20, a third amino acid sequence being at least 90% homologous to CATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQL corresponding to amino acids 62-97 of Q8N4W3, which also corresponds to amino acids 65-100 of HUMGCSF_PEA—1_P20, and a fourth amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSVRKG corresponding to amino acids 101-106 of HUMGCSF_PEA—1_P20, wherein said first amino acid sequence, second amino acid sequence, third amino acid sequence and fourth amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for an edge portion of HUMGCSF_PEA—1_P20, comprising an amino acid sequence being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence encoding for VSE, corresponding to HUMGCSF_PEA—1_P20.
3. An isolated polypeptide for a tail of HUMGCSF_PEA—1_P20, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSVRKG in HUMGCSF_PEA—1_P20.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HUMGCSF_PEA—1_P20 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 402, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P20 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 402







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





27
T →
No


56
A →
No


56
A → P
No









The glycosylation sites of variant protein HUMGCSF_PEA—1_P20, as compared to the known protein Granulocyte colony-stimulating factor precursor, are described in Table 403 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 403







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





166
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 404:







TABLE 404







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
FPrintScan
46-61, 65-88



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
77-100



stimulating/myelo-



monocytic growth



factor









Variant protein HUMGCSF_PEA—1_P20 is encoded by the following transcript(s): HUMGCSF_PEA—1_T22. The coding portion of transcript HUMGCSF_PEA—1_T22 starts at position 303 and ends at position 620. The transcript also has the following SNPs as listed in Table 405 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P20 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 405







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












55
C → G
Yes


99
A → G
Yes


382
C →
No


468
G →
No


468
G → C
No


791
G →
No


831
G → T
No


876
A → G
No


885
T → C
No


895
T → C
No


903
C → A
Yes


935
G →
No


954
G → A
Yes


989
A → G
Yes


1115
G → A
No


1199
C → T
Yes


1280
A → G
Yes


1331
T → C
No


1335
C →
No


1511
C →
No


1551
C →
No


1583
C → T
Yes


1638
T → C
Yes


1678
G → A
Yes


1748
C → T
Yes









Variant protein HUMGCSF_PEA—1_P21 (SEQ ID NO:1011) according to the present invention is encoded by transcript(s) HUMGCSF_PEA—1_T17. An alignment is given to the known protein (Granulocyte colony-stimulating factor precursor) in FIG. 251. One or more alignments to one or more previously published protein sequences are given in FIGS. 237-251. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMGCSF_PEA—1_P21 and CSF3_HUMAN:
1. An isolated chimeric polypeptide HUMGCSF_PEA—1_P21, comprising a first amino acid sequence being at least 90% homologous to MAGPATQSPMKLMALQLLLWHSALWTVQEATPLGPASSLPQSFLLKCLEQV RKIQGDGAALQEKL corresponding to amino acids 1-65 of CSF3_HUMAN, which also corresponds to amino acids 1-65 of HUMGCSF_PEA—1_P21, a second amino acid sequence being at least 90% homologous to CATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQL corresponding to amino acids 69-104 of CSF3_HUMAN, which also corresponds to amino acids 66-101 of HUMGCSF_PEA—1_P21, and a third amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSVRKG corresponding to amino acids 102-107 of HUMGCSF_PEA—1_P21, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HUMGCSF_PEA—1_P21, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise LC, having a structure as follows: a sequence starting from any of amino acid numbers 65-x to 65; and ending at any of amino acid numbers 66+((n−2)−x), in which x varies from 0 to n−2.
3. An isolated polypeptide for a tail of HUMGCSF_PEA—1_P21, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSVRKG in HUMGCSF_PEA—1_P21.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because of manual inspection of known protein localization and/or gene structure.
Variant protein HUMGCSF_PEA—1_P21 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 406, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P21 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 406







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





31
T →
No


60
A →
No


60
A → P
No









The glycosylation sites of variant protein HUMGCSF_PEA—1_P21, as compared to the known protein Granulocyte colony-stimulating factor precursor, are described in Table 407 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 407







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





166
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 408:







TABLE 408







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003573
Interleukin-6/G-
FPrintScan
50-65, 66-89



CSF/MGF


IPR003629
Granulocyte colony-
BlastProDom
78-101



stimulating/myelo-



monocytic growth



factor









Variant protein HUMGCSF_PEA—1_P21 is encoded by the following transcript(s): HUMGCSF_PEA—1_T17. The coding portion of transcript HUMGCSF_PEA—1_T17 starts at position 115 and ends at position 435. The transcript also has the following SNPs as listed in Table 409 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMGCSF_PEA—1_P21 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 409







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












55
C → G
Yes


99
A → G
Yes


206
C →
No


292
G →
No


292
G → C
No


606
G →
No


646
G → T
No


691
A → G
No


700
T → C
No


766
G → A
Yes


799
C → G
Yes


874
T → C
No


882
C → A
Yes


914
G →
No


933
G → A
Yes


968
A → G
Yes


1094
G → A
No


1178
C → T
Yes


1259
A → G
Yes


1310
T → C
No


1314
C →
No


1490
C →
No


1530
C →
No


1562
C → T
Yes


1617
T → C
Yes


1657
G → A
Yes


1727
C → T
Yes









FIG. 236 depicts the domain structure of the variants described hereinabove in comparison to the known or wild-type (WT) GCSF protein.
Example 65
Description for Cluster HSTGFB1
Cluster HSTGFB1 features 6 transcript(s) and 24 segment(s) of interest, the names for which are given in Tables 410 and 411, respectively. The selected protein variants are given in Table 412.







TABLE 410







Transcripts of interest










Transcript Name
SEQ ID NO:







HSTGFB1_PEA_1_T5
1013



 



HSTGFB1_PEA_1_T6
1014



 



HSTGFB1_PEA_1_T8
1015



 



HSTGFB1_PEA_1_T9
1016



 



HSTGFB1_PEA_1_T11
1017



 



HSTGFB1_PEA_1_T14
1018

















TABLE 411







Segments of interest










Segment Name
SEQ ID NO:







HSTGFB1_PEA_1_node_0
1019



 



HSTGFB1_PEA_1_node_2
1020



 



HSTGFB1_PEA_1_node_3
1021



 



HSTGFB1_PEA_1_node_4
1022



 



HSTGFB1_PEA_1_node_7
1023



 



HSTGFB1_PEA_1_node_9
1024



 



HSTGFB1_PEA_1_node_15
1025



 



HSTGFB1_PEA_1_node_22
1026



 



HSTGFB1_PEA_1_node_26
1027



 



HSTGFB1_PEA_1_node_28
1028



 



HSTGFB1_PEA_1_node_31
1029



 



HSTGFB1_PEA_1_node_33
1030



 



HSTGFB1_PEA_1_node_1
1031



 



HSTGFB1_PEA_1_node_5
1032



 



HSTGFB1_PEA_1_node_11
1033



 



HSTGFB1_PEA_1_node_14
1034



 



HSTGFB1_PEA_1_node_16
1035



 



HSTGFB1_PEA_1_node_17
1036



 



HSTGFB1_PEA_1_node_18
1037



 



HSTGFB1_PEA_1_node_19
1038



 



HSTGFB1_PEA_1_node_23
1039



 



HSTGFB1_PEA_1_node_25
1040



 



HSTGFB1_PEA_1_node_27
1041



 



HSTGFB1_PEA_1_node_30
1042

















TABLE 412







Proteins of interest











SEQ
Protein
Corresponding


Protein Name
ID NO:
Length
Transcript(s)





HSTGFB1_PEA_1_P2
1043
P248
HSTGFB1_PEA_1_T5


 


HSTGFB1_PEA_1_P3
1044
P363
HSTGFB1_PEA_1_T6


 


HSTGFB1_PEA_1_P5
1045
P357
HSTGFB1_PEA_1_T8;





HSTGFB1_PEA_1_T9


 


HSTGFB1_PEA_1_P7
1046
P332
HSTGFB1_PEA_1_T11


 


HSTGFB1_PEA_1_P10
1047
P370
HSTGFB1_PEA_1_T14









These sequences are variants of the known protein Transforming growth factor beta 1 precursor (SwissProt accession identifier TGF1_HUMAN, SEQ ID NO:1048; known also according to the synonyms TGF-beta 1), referred to herein as the previously known protein.
Protein Transforming growth factor beta 1 precursor is known or believed to have the following function(s): Multifunctional peptide that controls proliferation, differentiation, and other functions in many cell types. Many cells synthesize TGF-beta 1 and essentially all of them have specific receptors for this peptide. TGF-beta 1 regulates the actions of many other peptide growth factors and determines a positive or negative direction of their effects. Play an important role in bone remodelling. It is a potent stimulator of osteoblastic bone formation, causing chemotaxis, proliferation and differentiation in committed osteoblasts (By similarity). The sequence for protein Transforming growth factor beta 1 precursor is set forth by SEQ ID NO:1048, as “Transforming growth factor beta 1 precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 413.







TABLE 413







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment











10
L → P (associated with higher bone mineral density and



lower frequency of vertebral fractures in Japanese post-



menopausal women; dbSNP: 1982073)./FTId = VAR_016171.


25
R → P (in dbSNP: 1800471)./FTId = VAR_016172.


81
Y → H (in CED; leads to TGF-beta 1 intracellular



accumulation)./FTId = VAR_017607.


218
R → C (in CED; higher levels of active TGF-beta 1 in the



culture medium; enhances osteoclast formation in vitro)./



FTId = VAR_017608.


218
R → H (in CED)./FTId = VAR_017609.


222
H → D (in CED; sporadic case; higher levels of active



TGF-beta 1 in the culture medium)./FTId = VAR_017610.


225
C → R (in CED; higher levels of active TGF-beta 1 in the



culture medium)./FTId = VAR_017611.


263
T → I (in dbSNP: 1800472)./FTId = VAR_016173.


159
R → RR









Protein Transforming growth factor beta 1 precursor localization is believed to be Secreted.
The previously known protein also has the following indication(s) and/or potential therapeutic use(s): Cancer, breast; Cancer, colorectal; Multiple sclerosis; Eczema; Lupus erythematosus; Psoriasis. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein or of drugs directed against this protein are as follows: Immunosuppressant; Transforming growth factor beta agonist. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Vulnerary; Cytokine; Immunosuppressant; Anticancer; Antidiabetic; Antipruritic/inflamm, allergic; Antipsoriasis; Multiple sclerosis.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: cell cycle control; anti-apoptosis; TGFbeta receptor signaling pathway; cell-cell signaling; cell proliferation; cell growth; growth, which are annotation(s) related to Biological Process; and transforming growth factor beta receptor ligand, which are annotation(s) related to Molecular Function.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
This protein belongs to the ‘TGF-β superfamily’ which regulates epithelial cell growth, differentiation, motility, organization, apoptosis and tumorogenesis. Some members participate in early embryogenesis, while others play an important role in bone formation and remodelling.
There are three isoforms of TGF-β: TGF-β1, TGF-β2 and TGF-β3, which all bind to the same Type II receptor, TGFBR2. Almost every cell produces TGF-β1 and its receptor. TGF-β1 is secreted in an inactive form, consisting of TGF-β1 non-covalently linked to its propeptide-LAP. After its secretion most TGF-β is stored in the ECM as a complex of TGF-β, LAP and a latent TGF-β-binding protein. Activation of TGF-β requires its release by MMPs or plasmin.
In normal cells TGF-beta acts as a tumor suppressor. In the initial stages of tumorigenesis, the cell loses its TGF-β-mediated growth inhibition, resulting in uncontrolled proliferation. The TGF-β-resistant cancer cells then increase their production of TGF-β. This TGF-β, by acting on the surrounding stromal cells, immune cells and endothelial and smooth-muscle cells, causes immunosuppression and angiogenesis and increases the invasiveness of the tumor.
FIG. 252 depicts TGF beta clinical studies and FIG. 253 depicts TGF beta preclinical studies.
As noted above, cluster HSTGFB1 features 6 transcript(s), which were listed in Table 1 above. These transcript(s) encode for protein(s) which are variant(s) of protein Transforming growth factor beta 1 precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HSTGFB1_PEA—1_P2 (SEQ ID NO:1043) according to the present invention is encoded by transcript(s) HSTGFB1—1_PEA—1_T5. An alignment is given to the known protein (Transforming growth factor beta 1 precursor) in FIG. 255. One or more alignments to one or more previously published protein sequences are given in FIGS. 255-259. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSTGFB1_PEA—1_P2 and TGF1_HUMAN:
1. An isolated chimeric polypeptide HSTGFB1_PEA—1_P2, comprising a first amino acid sequence being at least 90% homologous to MPPSGLRLLLLLLPLLWLLVLTPGRPAAGLSTCKTIDMELVKRKRIEAIRGQIL SKLRLASPPSQGEVPPGPLPEAVLALYNSTRDRVAGESAEPEPEPEADYYAKE VTRVLMVETHNEIYDKFKQSTHSIYMFFNTSELREAVPEPVLLSRAELRLLRL KLKVEQHVELYQKYSNNSWRYLSNRLLAPSDSPEWLSEDVTGVVRQWLSRG GEIEGFRLSAHCSCDSRDNTLQVDING corresponding to amino acids 1-238 of TGF1_HUMAN, which also corresponds to amino acids 1-238 of HSTGFB1_PEA—1_P2, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence EACFPGHAQL corresponding to amino acids 239-248 of HSTGFB1_PEA—1_P2, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSTGFB1_PEA—1_P2, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence EACFPGHAQL in HSTGFB1_PEA—1_P2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSTGFB1_PEA—1_P2 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 414, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTGFB1_PEA—1_P2 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 414







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












10
L → P
Yes


25
R → P
Yes


47
E → G
Yes


65
Q →
No


136
N → H
No


230
N → Y
No


230
N →
No









The glycosylation sites of variant protein HSTGFB1_PEA—1_P2, as compared to the known protein Transforming growth factor beta 1 precursor, are described in Table 415 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 415







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












82
yes
82


136
yes
136


176
yes
176









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 416:







TABLE 416







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003911
Transforming growth
FPrintScan
163-177, 17-36,



factor beta TGFb

178-193, 195-209,





72-84


IPR003939
Transforming growth
FPrintScan
12-31, 135-154,



factor, beta 1

166-177, 207-219,





34-43


IPR001111
Transforming growth
HMMPfam
33-238



factor beta (TGFb),



N-terminal









Variant protein HSTGFB1_PEA—1_P2 is encoded by the following transcript(s): HSTGFB1_PEA—1_T5. The coding portion of transcript HSTGFB1_PEA—1_T5 starts at position 1038 and ends at position 1781. The transcript also has the following SNPs as listed in Table 417 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTGFB1_PEA—1_P2 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 417







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












181
C → A
Yes


205
C → T
Yes


206
T → A
Yes


211
G → C
Yes


214
G →
No


289
C →
No


390
G → C
Yes


585
G → A
Yes


651
C → T
Yes


762
C → A
Yes


789
C → A
Yes


896
C → T
Yes


1024
G → A
Yes


1030
C →
No


1030
C → T
No


1066
T → C
Yes


1111
G → C
Yes


1177
A → G
Yes


1232
G →
No


1443
A → C
No


1725
A →
No


1725
A → T
No


1964
C → T
Yes


2139
C → T
Yes


2148
G → A
Yes


2149
C →
No


2254
G →
No


2254
G → C
No


2255
C →
No


2255
C → G
No


2286
G →
No


2317
A →
No


2317
A → C
No


2353
C → T
No


2408
C → T
No









Variant protein HSTGFB1_PEA—1_P3 (SEQ ID NO:1044) according to the present invention is encoded by transcript(s) HSTGFB1_PEA—1_T6. An alignment is given to the known protein (Transforming growth factor beta 1 precursor) in FIG. 256. One or more alignments to one or more previously published protein sequences are given in FIGS. 255-259. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSTGFB1_PEA—1_P3 and TGF1_HUMAN:
1. An isolated chimeric polypeptide HSTGFB1_PEA—1_P3, comprising a first amino acid sequence being at least 90% homologous to MPPSGLRLLLLLLPLLWLLVLTPGRPAAGLSTCKTIDMELVKRKRIEAIRGQIL SKLRLASPPSQGEVPPGPLPEAVLALYNSTRDRVAGESAEPEPEPEADYYAKE VTRVLMVETHNEIYDKFKQSTHSIYMFFNTSELREAVPEPVLLSRAELRLLRL KLKVEQHVELYQKYSNNSWRYLSNRLLAPSDSPEWLSFDVTGVVRQWLSRG GEIEGFRLSAHCSCDSRDNTLQVDINGFTTGRRGDLATIHGMNRPFLLLMATP LERAQHLQSSRHRRALDTNYCFSSTEKNCCVRQLYIDFRKDLGWKWIHEPKG YHANFCLGPCPYIWSLDTQYSKV corresponding to amino acids 1-339 of TGF1_HUMAN, which also corresponds to amino acids 1-339 of HSTGFB1_PEA—1_P3, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence RLAHRATRCAWGEPGRRKRREKEK corresponding to amino acids 340-363 of HSTGFB1_PEA—1_P3, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSTGFB1_PEA—1_P3, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence RLAHRATRCAWGEPGRRKRREKEK in HSTGFB1_PEA—1_P3.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSTGFB1_PEA—1_P3 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 418, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTGFB1_PEA—1_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 418







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












10
L → P
Yes


25
R → P
Yes


47
E → G
Yes


65
Q →
No


136
N → H
No


230
N → Y
No


230
N →
No


263
T → I
Yes


325
P →
No









The glycosylation sites of variant protein HSTGFB1_PEA—1_P3, as compared to the known protein Transforming growth factor beta 1 precursor, are described in Table 419 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 419







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












82
yes
82


136
yes
136


176
yes
176









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 420:







TABLE 420







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003911
Transforming growth
FPrintScan
163-177, 17-36,



factor beta TGFb

178-193, 195-209,





72-84


IPR003939
Transforming growth
FPrintScan
12-31, 135-154,



factor, beta 1

166-177, 207-219,





264-275, 34-43


IPR001839
Transforming growth
HMMPfam
290-341



factor beta


IPR001111
Transforming growth
HMMPfam
33-252



factor beta (TGFb),



N-terminal


IPR001839
Transforming growth
HMMSmart
293-351



factor beta


IPR001839
Transforming growth
ScanRegExp
311-326



factor beta


IPR001839
Transforming growth
BlastProDom
279-339



factor beta


IPR001839
Transforming growth
ProfileScan
289-328



factor beta









Variant protein HSTGFB1_PEA—1_P3 is encoded by the following transcript(s): HSTGFB1_PEA—1_T6. The coding portion of transcript HSTGFB1_PEA—1_T6 starts at position 1038 and ends at position 2126. The transcript also has the following SNPs as listed in Table 421 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTGFB1_PEA—1_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 421







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












181
C → A
Yes


205
C → T
Yes


206
T → A
Yes


211
G → C
Yes


214
G →
No


289
C →
No


390
G → C
Yes


585
G → A
Yes


651
C → T
Yes


762
C → A
Yes


789
C → A
Yes


896
C → T
Yes


1024
G → A
Yes


1030
C →
No


1030
C → T
No


1066
T → C
Yes


1111
G → C
Yes


1177
A → G
Yes


1232
G →
No


1443
A → C
No


1725
A →
No


1725
A → T
No


1825
C → T
Yes


2000
C → T
Yes


2009
G → A
Yes


2010
C →
No


2203
G →
No


2203
G → C
No


2204
C →
No


2204
C → G
No


2235
G →
No


2266
A →
No


2266
A → C
No


2302
C → T
No


2357
C → T
No









Variant protein HSTGFB1_PEA—1_P5 (SEQ ID NO:1045) according to the present invention is encoded by transcript(s) HSTGFB1_PEA—1_T8. An alignment is given to the known protein (Transforming growth factor beta 1 precursor) in FIG. 257. One or more alignments to one or more previously published protein sequences are given in FIGS. 255-259. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSTGFB1_PEA—1_P5 and TGF1_HUMAN:
1. An isolated chimeric polypeptide HSTGFB1_PEA—1_P5, comprising a first amino acid sequence being at least 90% homologous to MPPSGLRLLLLLLPLLWLLVLTPGRPAAGLSTCKTIDMELVKRKRIEAIRGQIL SKLRLASPPSQGEVPPGPLPEAVLALYNSTRDRVAGESAEPEPEPEADYYAKE VTRVLMVETHNEIYDKFKQSTHSIYMFFNTSELREAVPEPVLLSRAELRLLRL KLKVEQHVELYQKYSNNSWRYLSNRLLAPSDSPEWLSFDVTGVVRQWLSRG GEIEGFRLSAHCSCDSRDNTLQVDINGFTTGRRGDLATIHGMNRPFLLLMATP LERAQHLQSSRHRRALDTNYCFSSTEKNCCVRQLYIDFRKDLGWKWIHEPKG YHANFCLGPCPYIWSLDTQYSK corresponding to amino acids 1-338 of TGF1_HUMAN, which also corresponds to amino acids 1-338 of HSTGFB1_PEA—1_P5, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence LNEQNLIQEVPNIWQREVG corresponding to amino acids 339-357 of HSTGFB1_PEA—1_P5, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSTGFB1_PEA—1_P5, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence LNEQNLIQEVPNIWQREVG in HSTGFB1_PEA—1_P5.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
The glycosylation sites of variant protein HSTGFB1_PEA—1_P5, as compared to the known protein Transforming growth factor beta 1 precursor, are described in Table 422 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 422







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












82
yes
82


136
yes
136


176
yes
176









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 423:







TABLE 423







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003911
Transforming growth
FPrintScan
163-177, 17-36,



factor beta TGFb

178-193, 195-209,





72-84


IPR003939
Transforming growth
FPrintScan
12-31, 135-154,



factor, beta 1

166-177, 207-219,





264-275, 34-43


IPR001839
Transforming growth
HMMPfam
290-338



factor beta


IPR001111
Transforming growth
HMMPfam
33-252



factor beta (TGFb),



N-terminal


IPR001839
Transforming growth
HMMSmart
293-357



factor beta


IPR001839
Transforming growth
ScanRegExp
311-326



factor beta


IPR001839
Transforming growth
BlastProDom
279-339



factor beta


IPR001839
Transforming growth
ProfileScan
289-328



factor beta


IPR003911
Transforming growth
FPrintScan
163-177, 17-36,



factor beta TGFb

178-193, 195-209,





72-84


IPR003939
Transforming growth
FPrintScan
12-31, 135-154,



factor, beta 1

166-177, 207-219,





264-275, 34-43


IPR001839
Transforming growth
HMMPfam
290-338



factor beta


IPR001111
Transforming growth
HMMPfam
33-252



factor beta (TGFb),



N-terminal


IPR001839
Transforming growth
HMMSmart
293-357



factor beta


IPR001839
Transforming growth
ScanRegExp
311-326



factor beta


IPR001839
Transforming growth
BlastProDom
279-339



factor beta


IPR001839
Transforming growth
ProfileScan
289-328



factor beta









Variant protein HSTGFB1_PEA—1_P5 is encoded by the following transcript(s): HSTGFB1_PEA—1_T8. The coding portion of transcript HSTGFB1_PEA—1_T8 starts at position 1038 and ends at position 2108. The transcript also has the following SNPs as listed in Table 424 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTGFB1_PEA—1_P5 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 424







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












181
C → A
Yes


205
C → T
Yes


206
T → A
Yes


211
G → C
Yes


214
G →
No


289
C →
No


390
G → C
Yes


585
G → A
Yes


651
C → T
Yes


762
C → A
Yes


789
C → A
Yes


896
C → T
Yes


1024
G → A
Yes


1030
C →
No


1030
C → T
No


1066
T → C
Yes


1111
G → C
Yes


1177
A → G
Yes


1232
G →
No


1443
A → C
No


1725
A →
No


1725
A → T
No


1825
C → T
Yes


2000
C → T
Yes


2009
G → A
Yes


2010
C →
No









Variant protein HSTGFB1_PEA—1_P7 (SEQ ID NO:1046) according to the present invention is encoded by transcript(s) HSTGFB1_PEA—1_T11. An alignment is given to the known protein (Transforming growth factor beta 1 precursor) in FIG. 258. One or more alignments to one or more previously published protein sequences are given in FIGS. 255-259. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSTGFB1_PEA—1_P7 and TGF1A_HUMAN:
1. An isolated chimeric polypeptide HSTGFB1_PEA—1_P7, comprising a first amino acid sequence being at least 90% homologous to MPPSGLRLLLLLLPLLWLLVLTPGRPAAGLSTCKTIDMELVKRKRIEAIRGQIL SKLRLASPPSQGEVPPGPLPEAVLALYNSTRDRVAGESAEPEPEPEADYYAKE VTRVLMVETHNEIYDKFKQSTHSIYMFFNTSELREAVPEPVLLSRAELRLLRL KLKVEQHVELYQKYSNNSWRYLSNRLLAPSDSPEWLSEDVTGVVRQWLSRG GEIEGFRLSAHCSCDSRDNTLQVDIN corresponding to amino acids 1-237 of TGF1_HUMAN, which also corresponds to amino acids 1-237 of HSTGFB1_PEA—1_P7, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence APRRRTAACGSCTLTSARTSAGSGSTSPRATMPTSASGPAPTFGAWTRSTARS WPCTTSITRAPRRRRAACRRRWSRCPSCTTWAASPRWSSCPT corresponding to amino acids 238-332 of HSTGFB1_PEA—1_P7, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HSTGFB1_PEA—1_P7, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence APRRRTAACGSCTLTSARTSAGSGSTSPRATMPTSASGPAPTFGAWTRSTARS WPCTTSITRAPRRRRAACRRRWSRCPSCTTWAASPRWSSCPT in HSTGFB1_PEA—1_P7.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSTGFB1_PEA—1_P7 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 425, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTGFB1_PEA—1_P7 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 425







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












10
L → P
Yes


25
R → P
Yes


47
E → G
Yes


65
Q →
No


136
N → H
No


230
N → Y
No


230
N →
No


272
S → F
Yes


275
G → D
Yes


275
G →
No


310
R → S
No


310
R →
No


311
R →
No


311
R → G
No


321
W →
No


331
P →
No









The glycosylation sites of variant protein HSTGFB1_PEA—1_P7, as compared to the known protein Transforming growth factor beta 1 precursor, are described in Table 426 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 426







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












82
yes
82


136
yes
136


176
yes
176









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 427:







TABLE 427







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003911
Transforming growth
FPrintScan
163-177, 17-36,



factor beta TGFb

178-193, 195-209,





72-84


IPR003939
Transforming growth
FPrintScan
12-31, 135-154,



factor, beta 1

166-177, 207-219,





34-43


IPR001111
Transforming growth
HMMPfam
33-236



factor beta (TGFb),



N-terminal









Variant protein HSTGFB1_PEA—1_P7 is encoded by the following transcript(s): HSTGFB1_PEA—1_T11. The coding portion of transcript HSTGFB1_PEA—1_T11 starts at position 1038 and ends at position 2033. The transcript also has the following SNPs as listed in Table 428 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTGFB1_PEA—1_P7 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 428







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












181
C → A
Yes


205
C → T
Yes


206
T → A
Yes


211
G → C
Yes


214
G →
No


289
C →
No


390
G → C
Yes


585
G → A
Yes


651
C → T
Yes


762
C → A
Yes


789
C → A
Yes


896
C → T
Yes


1024
G → A
Yes


1030
C →
No


1030
C → T
No


1066
T → C
Yes


1111
G → C
Yes


1177
A → G
Yes


1232
G →
No


1443
A → C
No


1725
A →
No


1725
A → T
No


1852
C → T
Yes


1861
G → A
Yes


1862
C →
No


1967
G →
No


1967
G → C
No


1968
C →
No


1968
C → G
No


1999
G →
No


2030
A →
No


2030
A → C
No


2066
C → T
No


2121
C → T
No









Variant protein HSTGFB1_PEA—1_P10 (SEQ ID NO:1047) according to the present invention is encoded by transcript(s) HSTGFB1_PEA—1_T14. An alignment is given to the known protein (Transforming growth factor beta 1 precursor) in FIG. 259. One or more alignments to one or more previously published protein sequences are given in FIGS. 255-259. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HSTGFB1_PEA—1_P10 and TGF1_HUMAN
1. An isolated chimeric polypeptide HSTGFB1_PEA—1_P10, comprising a first amino acid sequence being at least 90% homologous to MPPSGLRLLLLLLPLLWLLVLTPGRPAAGLSTCKTIDMELVKRKRIEAIRGQIL SKLRLASPPSQGEVPPGPLPEAVLALYNSTRDRVAGESAEPEPEPEADYYAKE VTRVLMVETHNEIYDKFKQSTHSIYMFFNTSELREAVPEPVLLSRAELRLLRL KLKVEQHVELYQKYSNNSWRYLSNRLLAPSDSPEWLSFDVTGVVRQWLSRG GEIEGFRLSAHCSCDSRDNTLQVDIN corresponding to amino acids 1-237 of TGF1_HUMAN, which also corresponds to amino acids 1-237 of HSTGFB1_PEA—1_P10, a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence APRRRTAACGSCTLTSARTSAGSGSTSPRATMPTSASGPAPTFGAWTRSTARY VWPTGLRDALGGSQDGGRGERKRSKVREVLA corresponding to amino acids 238-321 of HSTGFB1_PEA—1_P10, and a third amino acid sequence being at least 90% homologous to LYNQHNPGASAAPCCVPQALEPLPIVYYVGRKPKVEQLSNMIVRSCKCS corresponding to amino acids 342-390 of TGF1_HUMAN, which also corresponds to amino acids 322-370 of HSTGFB1_PEA—1_P10, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HSTGFB1_PEA—1_P10, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise NA, having a structure as follows: a sequence starting from any of amino acid numbers 237-x to 238; and ending at any of amino acid numbers 238+((n−2)−x), in which x varies from 0 to n−2.
3. An isolated polypeptide for an edge portion of HSTGFB1_PEA—1_P10, comprising an amino acid sequence being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence encoding for APRRRTAACGSCTLTSARTSAGSGSTSPRATMPTSASGPAPTFGAWTRSTARY VWPTGLRDALGGSQDGGRGERKRSKVREVLA, corresponding to HSTGFB1_PEA—1_P10.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal-peptide prediction programs predict that this protein has a signal peptide, and neither trans-membrane region prediction program predicts that this protein has a trans-membrane region.
Variant protein HSTGFB1_PEA—1_P10 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 429, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTGFB1_PEA—1_P10 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 429







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












10
L → P
Yes


25
R → P
Yes


47
E → G
Yes


65
Q →
No


136
N → H
No


230
N → Y
No


230
N →
No


272
S → F
Yes


275
G → D
Yes


275
G →
No


340
A →
No


340
A → G
No


340
A → P
No


350
V →
No


361
N →
No


361
N → H
No









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 430:







TABLE 430







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR003911
Transforming growth
FPrintScan
163-177, 17-36,



factor beta TGFb

178-193, 195-209,





72-84


IPR003939
Transforming growth
FPrintScan
12-31, 135-154,



factor, beta 1

166-177, 207-219,





34-43


IPR001839
Transforming growth
HMMPfam
319-370



factor beta


IPR001111
Transforming growth
HMMPfam
33-236



factor beta (TGFb),



N-terminal


IPR001839
Transforming growth
HMMSmart
311-370



factor beta


IPR001839
Transforming growth
BlastProDom
318-370



factor beta


IPR001839
Transforming growth
ProfileScan
319-370



factor beta









Variant protein HSTGFB1_PEA—1_P10 is encoded by the following transcript(s): HSTGFB1_PEA—1_T14. The coding portion of transcript HSTGFB1_PEA—1_T14 starts at position 1038 and ends at position 2147. The transcript also has the following SNPs as listed in Table 431 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HSTGFB1_PEA—1_P10 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 431







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












181
C → A
Yes


205
C → T
Yes


206
T → A
Yes


211
G → C
Yes


214
G →
No


289
C →
No


390
G → C
Yes


585
G → A
Yes


651
C → T
Yes


762
C → A
Yes


789
C → A
Yes


896
C → T
Yes


1024
G → A
Yes


1030
C →
No


1030
C → T
No


1066
T → C
Yes


1111
G → C
Yes


1177
A → G
Yes


1232
G →
No


1443
A → C
No


1725
A →
No


1725
A → T
No


1852
C → T
Yes


1861
G → A
Yes


1862
C →
No


2055
G →
No


2055
G → C
No


2056
C →
No


2056
C → G
No


2087
G →
No


2118
A →
No


2118
A → C
No


2154
C → T
No


2209
C → T
No









FIG. 254 depicts the domain structure of the variants described hereinabove in comparison to the known or wild-type (WT) TGF-beta protein.
Example 66
Description for Cluster HUMUPAA
Cluster HUMUPAA features 3 transcript(s) and 50 segment(s) of interest, the names for which are given in Tables 432 and 433, respectively. The selected protein variants are given in Table 434.







TABLE 432







Transcripts of interest










Transcript Name
SEQ ID NO:







HUMUPAA_T17
1049



 



HUMUPAA_T24
1050



 



HUMUPAA_T27
1051

















TABLE 433







Segments of interest










Segment Name
SEQ ID NO:







HUMUPAA_node_0
1052



 



HUMUPAA_node_73
1053



 



HUMUPAA_node_82
1054



 



HUMUPAA_node_84
1055



 



HUMUPAA_node_85
1056



 



HUMUPAA_node_1
1057



 



HUMUPAA_node_5
1058



 



HUMUPAA_node_10
1059



 



HUMUPAA_node_11
1060



 



HUMUPAA_node_12
1061



 



HUMUPAA_node_15
1062



 



HUMUPAA_node_16
1063



 



HUMUPAA_node_17
1064



 



HUMUPAA_node_18
1065



 



HUMUPAA_node_22
1066



 



HUMUPAA_node_23
1067



 



HUMUPAA_node_24
1068



 



HUMUPAA_node_25
1069



 



HUMUPAA_node_29
1070



 



HUMUPAA_node_30
1071



 



HUMUPAA_node_31
1072



 



HUMUPAA_node_32
1073



 



HUMUPAA_node_33
1074



 



HUMUPAA_node_36
1075



 



HUMUPAA_node_39
1076



 



HUMUPAA_node_40
1077



 



HUMUPAA_node_41
1078



 



HUMUPAA_node_42
1079



 



HUMUPAA_node_43
1080



 



HUMUPAA_node_44
1081



 



HUMUPAA_node_45
1082



 



HUMUPAA_node_46
1083



 



HUMUPAA_node_47
1084



 



HUMUPAA_node_55
1085



 



HUMUPAA_node_56
1086



 



HUMUPAA_node_57
1087



 



HUMUPAA_node_59
1088



 



HUMUPAA_node_60
1089



 



HUMUPAA_node_61
1090



 



HUMUPAA_node_62
1091



 



HUMUPAA_node_63
1092



 



HUMUPAA_node_65
1093



 



HUMUPAA_node_66
1094



 



HUMUPAA_node_68
1095



 



HUMUPAA_node_69
1096



 



HUMUPAA_node_70
1097



 



HUMUPAA_node_79
1098



 



HUMUPAA_node_80
1099



 



HUMUPAA_node_81
1100



 



HUMUPAA_node_83
1101

















TABLE 434







Proteins of interest











SEQ

Corresponding


Protein Name
ID NO:
Protein Length
Transcript(s)





HUMUPAA_P14
1102
P482
HUMUPAA_T17


 


HUMUPAA_P17
1103
P433
HUMUPAA_T24


 


HUMUPAA_P20
1104
P370
HUMUPAA_T27









These sequences are variants of the known protein Tissue-type plasminogen activator precursor (SwissProt accession identifier TPA_HUMAN; SEQ ID NO:150; known also according to the synonyms EC 3.4.21.68; tPA; t-PA; t-plasminogen activator; Alteplase; Reteplase), referred to herein as the previously known protein.
Protein Tissue-type plasminogen activator precursor is known or believed to have the following function(s): Converts the abundant, but inactive, zymogen plasminogen to plasmin by hydrolyzing a single Arg-Val bond in plasminogen. By controlling plasmin-mediated proteolysis, it plays an important role in tissue remodeling and degradation, in cell migration and many other physiopathological events. The sequence for protein Tissue-type plasminogen activator precursor is set forth by SEQ ID NO:150, as “Tissue-type plasminogen activator precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 435.







TABLE 435







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment











164
R → W (in dbSNP: 2020921)./FTId =



VAR_011783.


93
N → T


159-160
KP → NA









Protein Tissue-type plasminogen activator precursor localization is believed to be Secreted; extracellular.
The previously known protein also has the following indication(s) and/or potential therapeutic use(s): Infarction, myocardial; Ischaemia, cerebral; Thrombosis, pulmonary; Thrombosis, cerebral; Thrombosis. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein or of drugs directed against this protein are as follows: Fibrinogen antagonist; Plasminogen activator stimulant; Thrombin inhibitor. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Fibrinolytic; Cardiovascular; Neuroprotective; Respiratory.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: protein modification; proteolysis and peptidolysis; blood coagulation, which are annotation(s) related to Biological Process; chymotrypsin; trypsin; T-plasminogen activator; hydrolase, which are annotation(s) related to Molecular Function; and extracellular, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
Tissue-type plasminogen activator precursor (t-PA) is a serine protease responsible for converting the inactive, zymogen plasminogen to plasmin by specific cleavage of Arg-|-Val bond. It plays an important role in fibrinolysis, tissue remodeling and degradation and cell migration. It is a heterodimer of chain A and chain B held by a disulfide bond. It binds to fibrin with high affinity. This interaction leads to an increase in the catalytic efficiency of the enzyme between 100- and 1000-fold, due to an increase in affinity for plasminogen. It binds to mannose receptor and the low-density lipoprotein receptor-related protein (LRP1). These proteins are involved in TPA clearance. Unidentified interactions on endothelial cells and vascular smooth muscle cells (VSMC) lead to a 100-fold stimulation of plasminogen activation.
Tissue-type plasminogen activator precursor (t-PA) is related to the following diseases; for example, increased activity of TPA causes hyperfibrinolysis, with excessive bleeding as a consequence. Defective release of TPA causes hypofibrinolysis, leading to thrombosis or embolism. Pharmaceutical uses include but are not limited to Acute Myocardial Infarction (AMI), Acute Ischemic Stroke (AIS) and Pulmonary Embolism (PE) to initiates fibrinolysis (see for example Activase (Genentech) and Retavase (Centocor and Roche)).
As noted above, cluster HUMUPAA features 3 transcript(s), which were listed in Table 1 above. These transcript(s) encode for protein(s) which are variant(s) of protein Tissue-type plasminogen activator precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HUMUPAA_P14 (SEQ ID NO:1102) according to the present invention is encoded by transcript(s) HUMUPAA_T17. An alignment is given to the known protein (Tissue-type plasminogen activator precursor) in FIG. 260. One or more alignments to one or more previously published protein sequences are given in FIGS. 260-262. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMUPAA_P14 and TPA_HUMAN:
1. An isolated chimeric polypeptide HUMUPAA_P14, comprising a first amino acid sequence being at least 90% homologous to MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARSYQVICRDEKTQMIYQQ H corresponding to amino acids 1-53 of TPA_HUMAN, which also corresponds to amino acids 1-53 of HUMUPAA_P14, a second amino acid sequence bridging amino acid sequence comprising of H, and a third amino acid sequence being at least 90% homologous to YRGTWSTAESGAECTNWNSSALAQKPYSGRRPDAIRLGLGNHNYCRNPDRD SKPWCYVFKAGKYSSEFCSTPACSEGNSDCYFGNGSAYRGTHSLTESGASCLP WNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTW EYCDVPSCSTCGLRQYSQPQERIKGGLFADIASHPWQAAIFAKHRRSPGERFL CGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVH KEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSG YGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGG PQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTN YLDWIRDNMRP corresponding to amino acids 135-562 of TPA_HUMAN, which also corresponds to amino acids 55-482 of HUMUPAA_P14, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for an edge portion of HUMUPAA_P14, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise
HHY having a structure as follows (numbering according to HUMUPAA_P14): a sequence starting from any of amino acid numbers 53-x to 53; and ending at any of amino acid numbers 55+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because of manual inspection of known protein localization and/or gene structure.
Variant protein HUMUPAA_P14 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 436, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMUPAA_P14 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 436







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












66
A → T
Yes


76
L →
No


84
R → W
Yes


90
R → G
No


108
P →
No


108
P → A
No


125
T →
No


141
S → L
No


154
A → V
No


156
C → S
No


179
L →
No


196
P →
No


198
C →
No


198
C → W
No


203
N → D
No


214
P →
No


214
P → A
No


217
S →
No


254
R →
No


263
G →
No


265
I → V
No


299
V →
No


378
F → L
No


389
R → T
No


420
G →
No


435
G →
No


481
R → *
Yes









The glycosylation sites of variant protein HUMUPAA_P14, as compared to the known protein Tissue-type plasminogen activator precursor, are described in Table 437 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 437







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












483
yes
403


96
no


152
yes
72


219
yes
139









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 438:







TABLE 438







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR000001
Kringle
FPrintScan
135-150, 151-163,





180-200, 205-216


IPR001314
Peptidase S1A,
FPrintScan
263-278, 322-336,



chymotrypsin

426-438


IPR000001
Kringle
HMMPfam
135-216, 55-128


IPR001254
Peptidase S1,
HMMPfam
231-476



chymotrypsin


IPR001254
Peptidase S1,
HMMSmart
230-476



chymotrypsin


IPR000001
Kringle
HMMSmart
133-218, 47-130


IPR000001
Kringle
ScanRegExp
186-198, 98-110


IPR001254
Peptidase S1,
ScanRegExp
273-278



chymotrypsin


IPR001254
Peptidase S1,
ScanRegExp
427-438



chymotrypsin


IPR000001
Kringle
BlastProDom
134-197, 55-109


IPR000001
Kringle
ProfileScan
134-216, 55-128


IPR001254
Peptidase S1,
ProfileScan
231-481



chymotrypsin









Variant protein HUMUPAA_P14 is encoded by the following transcript(s): HUMUPAA_T17. The coding portion of transcript HUMUPAA_T17 starts at position 236 and ends at position 1681. The transcript also has the following SNPs as listed in Table 439 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMUPAA_P14 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 439







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












111
A →
No


163
G →
No


431
G → A
Yes


461
T →
No


485
C → T
Yes


496
T → C
Yes


503
A → G
No


538
C → T
Yes


557
C →
No


557
C → G
No


568
C → T
No


609
C →
No


657
C → T
No


679
C → T
Yes


696
C → T
No


701
T → A
No


772
G →
No


777
→ G
No


821
C →
No


829
C →
No


829
C → G
No


842
A → G
No


856
G → A
Yes


875
C →
No


875
C → G
No


884
T →
No


996
G →
No


1022
G →
No


1028
A → G
No


1057
T → C
No


1063
C → T
No


1132
C →
No


1147
G → A
Yes


1162
C → A
Yes


1162
C → G
Yes


1174
T → C
Yes


1195
T → C
No


1301
C → T
Yes


1363
T → C
Yes


1367
T → C
No


1401
G → C
No


1493
G →
No


1534
G → A
Yes


1540
C →
No


1676
C → T
Yes


1756
C → G
Yes


1946
C →
No


2106
T → C
Yes


2143
C →
No


2166
T → C
Yes


2229
T → C
Yes


2339
C → A
Yes









Variant protein HUMUPAA_P17 (SEQ ID NO:1103) according to the present invention is encoded by transcript(s) HUMUPAA_T24. An alignment is given to the known protein (Tissue-type plasminogen activator precursor) in FIG. 261. One or more alignments to one or more previously published protein sequences are given in FIGS. 260-262. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMUPAA_P17 and TPA_HUMAN:
1. An isolated chimeric polypeptide HUMUPAA_P17, comprising a first amino acid sequence being at least 90% homologous to MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARSYQVICRDEKTQMIYQQ HQSWLRPVLRSNRVEYCWCNSGRAQCHSV corresponding to amino acids 1-81 of TPA_HUMAN, which also corresponds to amino acids 1-81 of HUMUPAA_P17, a second amino acid sequence bridging amino acid sequence comprising of R, and a third amino acid sequence being at least 90% homologous to NSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGK HNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGG LFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLT VILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQE SSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSR CTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRM TLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP corresponding to amino acids 212-562 of TPA_HUMAN, which also corresponds to amino acids 83-433 of HUMUPAA_P17, wherein said first amino acid sequence, second amino acid sequence and third amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for an edge portion of HUMUPAA_P17, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise
VRN having a structure as follows (numbering according to HUMUPAA_P17): a sequence starting from any of amino acid numbers 81-x to 81; and ending at any of amino acid numbers 83+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because of manual inspection of known protein localization and/or gene structure.
Variant protein HUMUPAA_P17 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 440, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMUPAA_P17 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 440







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












56
W →
No


92
S → L
No


105
A → V
No


107
C → S
No


130
L →
No


147
P →
No


149
C →
No


149
C → W
No


154
N → D
No


165
P →
No


165
P → A
No


168
S →
No


205
R →
No


214
G →
No


216
I → V
No


250
V →
No


329
F → L
No


340
R → T
No


371
G →
No


386
G →
No


432
R → *
Yes









The glycosylation sites of variant protein HUMUPAA_P17, as compared to the known protein Tissue-type plasminogen activator precursor, are described in Table 441 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 441







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












483
yes
354


96
no


152
no


219
yes
90









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 442:







TABLE 442







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR000001
Kringle
FPrintScan
102-114, 131-151,





156-167, 86-101


IPR001314
Peptidase S1A,
FPrintScan
214-229, 273-287,



chymotrypsin

377-389


IPR000083
Fibronectin, type I
HMMPfam
41-78


IPR000001
Kringle
HMMPfam
86-167


IPR001254
Peptidase S1,
HMMPfam
182-427



chymotrypsin


IPR001254
Peptidase S1,
HMMSmart
181-427



chymotrypsin


IPR000083
Fibronectin, type I
HMMSmart
41-83


IPR000001
Kringle
HMMSmart
84-169


IPR000001
Kringle
ScanRegExp
137-149


IPR001254
Peptidase S1,
ScanRegExp
224-229



chymotrypsin


IPR001254
Peptidase S1,
ScanRegExp
378-389



chymotrypsin


IPR000083
Fibronectin, type I
ScanRegExp
41-78


IPR000001
Kringle
BlastProDom
85-148


IPR000001
Kringle
ProfileScan
85-167


IPR001254
Peptidase S1,
ProfileScan
182-432



chymotrypsin









Variant protein HUMUPAA_P17 is encoded by the following transcript(s): HUMUPAA_T24. The coding portion of transcript HUMUPAA_T24 starts at position 236 and ends at position 1534. The transcript also has the following SNPs as listed in Table 443 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMUPAA_P17 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 443







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












111
A →
No


163
G →
No


402
G →
No


510
C → T
No


532
C → T
Yes


549
C → T
No


554
T → A
No


625
G →
No


630
→ G
No


674
C →
No


682
C →
No


682
C → G
No


695
A → G
No


709
G → A
Yes


728
C →
No


728
C → G
No


737
T →
No


849
G →
No


875
G →
No


881
A → G
No


910
T → C
No


916
C → T
No


985
C →
No


1000
G → A
Yes


1015
C → A
Yes


1015
C → G
Yes


1027
T → C
Yes


1048
T → C
No


1154
C → T
Yes


1216
T → C
Yes


1220
T → C
No


1254
G → C
No


1346
G →
No


1387
G → A
Yes


1393
C →
No


1529
C → T
Yes


1609
C → G
Yes


1799
C →
No


1959
T → C
Yes


1996
C →
No


2019
T → C
Yes


2082
T → C
Yes


2192
C → A
Yes









Variant protein HUMUPAA_P20 (SEQ ID NO:1104) according to the present invention is encoded by transcript(s) HUMUPAA_T27. An alignment is given to the known protein (Tissue-type plasminogen activator precursor) in FIG. 262. One or more alignments to one or more previously published protein sequences are given in FIGS. 260-262. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMUPAA_P20 and TPA_HUMAN:
1. An isolated chimeric polypeptide HUMUPAA_P20, comprising a first amino acid sequence being at least 90% homologous to MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARSYQ corresponding to amino acids 1-38 of TPA_HUMAN, which also corresponds to amino acids 1-38 of HUMUPAA_P20, a second amino acid sequence bridging amino acid sequence comprising of G, a third amino acid sequence being at least 90% homologous to CSEPRCFNGGTCQQALYFSDFVC corresponding to amino acids 86-108 of TPA_HUMAN, which also corresponds to amino acids 40-62 of HUMUPAA_P20, a fourth amino acid sequence bridging amino acid sequence comprising of H, and a fifth amino acid sequence being at least 90% homologous to AQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYS QPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCF QERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQL KSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKE AHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGP LVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP corresponding to amino acids 256-562 of TPA_HUMAN, which also corresponds to amino acids 64-370 of HUMUPAA_P20, wherein said first amino acid sequence, second amino acid sequence, third amino acid sequence, fourth amino acid sequence and fifth amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for an edge portion of HUMUPAA_P20, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise
QGC having a structure as follows (numbering according to HUMUPAA_P20): a sequence starting from any of amino acid numbers 38-x to 38; and ending at any of amino acid numbers 40+((n−2)−x), in which x varies from 0 to n−2.
3. An isolated polypeptide for an edge portion of HUMUPAA_P20, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise
CHA having a structure as follows (numbering according to HUMUPAA_P20): a sequence starting from any of amino acid numbers 62-x to 62; and ending at any of amino acid numbers 64+((n−2)−x), in which x varies from 0 to n−2.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because of manual inspection of known protein localization and/or gene structure.
Variant protein HUMUPAA_P20 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 444, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMUPAA_P20 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 444







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












61
V → M
No


62
C → R
No


67
L →
No


84
P →
No


86
C →
No


86
C → W
No


91
N → D
No


102
P →
No


102
P → A
No


105
S →
No


142
R →
No


151
G →
No


153
I → V
No


187
V →
No


266
F → L
No


277
R → T
No


308
G →
No


323
G →
No


369
R → *
Yes









The glycosylation sites of variant protein HUMUPAA_P20, as compared to the known protein Tissue-type plasminogen activator precursor, are described in Table 445 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 445







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












483
yes
291


96
yes
50


152
no


219
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 446:







TABLE 446







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR000001
Kringle
FPrintScan
68-88, 93-104


IPR001314
Peptidase S1A,
FPrintScan
151-166, 210-224,



chymotrypsin

314-326


IPR000001
Kringle
HMMPfam
64-104


IPR001254
Peptidase S1,
HMMPfam
119-364



chymotrypsin


IPR001254
Peptidase S1,
HMMSmart
118-364



chymotrypsin


IPR000001
Kringle
HMMSmart
43-106


IPR000001
Kringle
ScanRegExp
74-86


IPR001254
Peptidase S1,
ScanRegExp
161-166



chymotrypsin


IPR001254
Peptidase S1,
ScanRegExp
315-326



chymotrypsin


IPR000001
Kringle
BlastProDom
64-85


IPR000001
Kringle
ProfileScan
71-104


IPR001254
Peptidase S1,
ProfileScan
119-369



chymotrypsin









Variant protein HUMUPAA_P20 is encoded by the following transcript(s): HUMUPAA_T27. The coding portion of transcript HUMUPAA_T27 starts at position 236 and ends at position 1345. The transcript also has the following SNPs as listed in Table 447 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMUPAA_P20 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 447







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












111
A →
No


163
G →
No


416
G → A
No


419
T → C
No


436
G →
No


441
→ G
No


485
C →
No


493
C →
No


493
C → G
No


506
A → G
No


520
G → A
Yes


539
C →
No


539
C → G
No


548
T →
No


660
G →
No


686
G →
No


692
A → G
No


721
T → C
No


727
C → T
No


796
C →
No


811
G → A
Yes


826
C → A
Yes


826
C → G
Yes


838
T → C
Yes


859
T → C
No


965
C → T
Yes


1027
T → C
Yes


1031
T → C
No


1065
G → C
No


1157
G →
No


1198
G → A
Yes


1204
C →
No


1340
C → T
Yes


1420
C → G
Yes


1610
C →
No


1770
T → C
Yes


1807
C →
No


1830
T → C
Yes


1893
T → C
Yes


2003
C → A
Yes









FIG. 263 depicts the domain structure of the variants described hereinabove in comparison to the known or wild-type (WT) TPA_HUMAN protein:
Example 67
Description for Cluster HUMDNASEI
Cluster HUMDNASEI features 5 transcript(s) and 17 segment(s) of interest, the names for which are given in Tables 448 and 449, respectively. The selected protein variants are given in Table 450.







TABLE 448







Transcripts of interest










Transcript Name
SEQ ID NO:







HUMDNASEI_PEA_1_T2
1105



 



HUMDNASEI_PEA_1_T5
1106



 



HUMDNASEI_PEA_1_T7
1107



 



HUMDNASEI_PEA_1_T12
1108



 



HUMDNASEI_PEA_1_T13
1109

















TABLE 449







Segments of interest










Segment Name
SEQ ID NO:







HUMDNASEI_PEA_1_node_0
1110



 



HUMDNASEI_PEA_1_node_1
1111



 



HUMDNASEI_PEA_1_node_4
1112



 



HUMDNASEI_PEA_1_node_6
1113



 



HUMDNASEI_PEA_1_node_26
1114



 



HUMDNASEL PEA_1_node_2
1115



 



HUMDNASEI_PEA_1_node_3
1116



 



HUMDNASEI_PEA_1_node_8
1117



 



HUMDNASEI_PEA_1_node_12
1118



 



HUMDNASEI_PEA_1_node_14
1119



 



HUMDNASEI_PEA_1_node_17
1120



 



HUMDNASEI_PEA_1_node_19
1121



 



HUMDNASEI_PEA_1_node_20
1122



 



HUMDNASET PEA_1_node_21
1123



 



HUMDNASEI_PEA_1_node_23
1124



 



HUMDNASEI_PEA_1_node_24
1125



 



HUMDNASEI_PEA_1_node_25
1126

















TABLE 450







Proteins of interest











SEQ
Protein
Corresponding


Protein Name
ID NO:
Length
Transcript(s)





HUMDNASE1_PEA_1_P3
1127
P213
HUMDNASEI_PEA_1_T2


 


HUMDNASE1_PEA_1_P4
1128
P276
HUMDNASEI_PEA_1_T5;





HUMDNASEI_PEA_1_T12


 


HUMDNASE1_PEA_1_P6
1129
P239
HUMDNASEI_PEA_1_T7


 


HUMDNASEI_PEA_1_P1
1130
P157
HUMDNASEI_PEA_1_T13









These sequences are variants of the known protein Deoxyribonuclease I precursor (SwissProt accession identifier DRN1_HUMAN; SEQ ID NO:1131; known also according to the synonyms EC 3.1.21.1; DNase I; Dornase alfa), referred to herein as the previously known protein.
Protein Deoxyribonuclease I precursor is known or believed to have the following function(s): Among other functions, seems to be involved in cell death by apoptosis. Binds specifically to G-actin and blocks actin polymerization (By similarity). The sequence for protein Deoxyribonuclease I precursor is set forth by SEQ ID NO:1131, as “Deoxyribonuclease I precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 451.







TABLE 451







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment











31
Q → E (in allele DNASE1*4)./FTId =



VAR_002264.


114
V → M (in allele DNASE1*5)./FTId =



VAR_009300.


154
P → A (in allele DNASE1*3; dbSNP: 1799891)./



FTId = VAR_002265.


207
R → C (in allele DNASE1*6)./FTId =



VAR_009301.


244
R → Q (in allele DNASE1*1; dbSNP: 1053874)./



FTId = VAR_002266.


16
L → H









Protein Deoxyribonuclease I precursor localization is believed to be Secretory protein, stored in zymogen granules and found in the nuclear envelope.
The previously known protein also has the following indication(s) and/or potential therapeutic use(s): Cystic fibrosis; Cancer, general. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein are as follows: Deoxyribonuclease 1 stimulant. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Cystic fibrosis treatment; Cancer, general.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: extracellular, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
As noted above, cluster HUMDNASEI features 5 transcript(s), which were listed in Table 1 above. These transcript(s) encode for protein(s) which are variant(s) of protein Deoxyribonuclease I precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HUMDNASEI_PEA—1_P3 (SEQ ID NO:1127) according to the present invention is encoded by transcript(s) HUMDNASEI_PEA—1_T2. An alignment is given to the known protein (Deoxyribonuclease I precursor) in FIG. 264. One or more alignments to one or more previously published protein sequences are given in FIGS. 264-268. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMDNASEI_PEA—1_P3 and DRN1_HUMAN:
1. An isolated chimeric polypeptide HUMDNASEI_PEA—1_P3, comprising a first amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence MPPSSATLCR corresponding to amino acids 1-10 of HUMDNASEI_PEA—1_P3, and a second amino acid sequence being at least 90% homologous to DAPDTYHYVVSEPLGRNSYKERYLFVYRPDQVSAVDSYYYDDGCEPCGNDT ENREPAIVRFFSRFTEVREFAIVPLHAAPGDAVAEIDALYDVYLDVQEKWGLE DVMLMGDFNAGCSYVRPSQWSSIRLWTSPTFQWLIPDSADTTATPTHCAYDR IVVAGMLLRGAVVPDSALPFNFQAAYGLSDQLAQAISDHYPVEVMLK corresponding to amino acids 80-282 of DRN1_HUMAN, which also corresponds to amino acids 11-213 of HUMDNASEI_PEA—1_P3, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a head of HUMDNASEI_PEA—1_P3, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence MPPSSATLCR of HUMDNASEI_PEA—1_P3.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: intracellularly. The protein localization is believed to be intracellularly because of manual inspection of known protein localization and/or gene structure.
Variant protein HUMDNASEI_PEA—1_P3 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 452, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMDNASEI_PEA—1_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 452







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












38
R → G
Yes


48
Y → S
No


58
G → R
Yes


85
P → A
Yes


162
C → Y
Yes


175
R → Q
Yes


177
A → P
Yes


193
G → D
Yes


202
I → N
No









The glycosylation sites of variant protein HUMDNASEI_PEA—1_P3, as compared to the known protein Deoxyribonuclease I precursor, are described in Table 453 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 453







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












128
yes
59


40
no









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 454:







TABLE 454







InterPro domain(s)













Postion(s)


InterPro ID
Domain description
Analysis type
on protein





IPR008185
Deoxyribonuclease I
FPrintScan
108-137, 138-167,





167-189, 190-210,





33-62, 78-107


IPR005135
Endonuclease/
HMMPfam
6-212



exonuclease/



phosphatase


IPR008185
Deoxyribonuclease I
HMMSmart
1-213


IPR008185
Deoxyribonuclease I
ScanRegExp
120-127


IPR008185
Deoxyribonuclease I
ScanRegExp
83-103









Variant protein HUMDNASEI_PEA—1_P3 is encoded by the following transcript(s): HUMDNASEI_PEA—1_T2. The coding portion of transcript HUMDNASEI_PEA—1_T2 starts at position 1181 and ends at position 1819. The transcript also has the following SNPs as listed in Table 455 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMDNASEI_PEA—1_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 455







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












487
A → C
No


917
G →
No


1031
G → A
Yes


1068
G → T
Yes


1106
C →
No


1116
G →
No


1158
A → C
Yes


1240
C → G
Yes


1292
A → G
Yes


1323
A → C
No


1352
G → A
Yes


1433
C → G
Yes


1501
C → G
Yes


1540
C → T
Yes


1597
G → A
Yes


1665
G → A
Yes


1704
G → A
Yes


1709
G → C
Yes


1758
G → A
Yes


1785
T → A
No


1827
C → A
No


1828
C → A
No


1839
C → G
Yes









Variant protein HUMDNASEI_PEA—1_P4 (SEQ ID NO:1128) according to the present invention is encoded by transcript(s) HUMDNASEI_PEA—1_T5. An alignment is given to the known protein (Deoxyribonuclease I precursor) in FIG. 265. One or more alignments to one or more previously published protein sequences are given in FIGS. 264-268. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMDNASEI_PEA—1_P4 and DRN1_HUMAN:
1. An isolated chimeric polypeptide HUMDNASEI_PEA—1_P4, comprising a first amino acid sequence being at least 90% homologous to MRGMKLLGALLALAALLQGAVSLKIAAFNIQTFGETKMSNATLVSYIVQILSR YDIALVQEVRDSHLTAVGKLLDNLNQDAPDTYHYVVSEPLGRNSYKERYLF VYRPDQVSAVDSYYYDDGCEPCGNDTFNREPAIVRFFSRFTEVREFAIVPLHA APGDAVAEIDALYDVYLDVQEKWGLEDVMLMGDFNAGCSYVRPSQWSSIRL WTSPTFQWLIPDSADTTATPTHCAYDRIVVAGMLLRGAVVPDSALPFNFQAA YGLSDQL corresponding to amino acids 1-267 of DRN1_HUMAN, which also corresponds to amino acids 1-267 of HUMDNASEI_PEA—1_P4, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VCVLPCTAT corresponding to amino acids 268-276 of HUMDNASEI_PEA—1_P4, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMDNASEI_PEA—1_P4, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VCVLPCTAT in HUMDNASEI_PEA—1_P4. The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because of manual inspection of known protein localization and/or gene structure.
The glycosylation sites of variant protein HUMDNASEI_PEA—1_P4, as compared to the known protein Deoxyribonuclease I precursor, are described in Table 456 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 456







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












128
yes
128


40
yes
40









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 457:







TABLE 457







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR008185
Deoxyribonuclease I
FPrintScan
102-131, 147-176,





177-206, 207-236,





236-258, 259-276,





33-62, 63-92


IPR005135
Endonuclease/
HMMPfam
23-271



exonuclease/



phosphatase


IPR008185
Deoxyribonuclease I
HMMSmart
6-268


IPR008185
Deoxyribonuclease I
ScanRegExp
189-196


IPR008185
Deoxyribonuclease I
ScanRegExp
152-172


IPR008185
Deoxyribonuclease I
FPrintScan
102-131, 147-176,





177-206, 207-236,





236-258, 259-276,





33-62, 63-92


IPR005135
Endonuclease/
HMMPfam
23-271



exonuclease/



phosphatase


IPR008185
Deoxyribonuclease I
HMMSmart
6-268


IPR008185
Deoxyribonuclease I
ScanRegExp
189-196


IPR008185
Deoxyribonuclease I
ScanRegExp
152-172









Variant protein HUMDNASEI_PEA—1_P4 is encoded by the following transcript(s): HUMDNASEI_PEA—1_T5. The coding portion of transcript HUMDNASEI_PEA—1_T5 starts at position 1063 and ends at position 1890. The transcript also has the following SNPs as listed in Table 458 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMDNASEI_PEA—1_P4 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 458







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












487
A → C
No


917
G →
No


1031
G → A
Yes


1068
G → T
Yes


1106
C →
No


1116
G →
No


1158
A → C
Yes


1329
C → G
Yes


1381
A → G
Yes


1412
A → C
No


1441
G → A
Yes


1522
C → G
Yes


1590
C → G
Yes


1629
C → T
Yes


1686
G → A
Yes


1754
G → A
Yes


1793
G → A
Yes


1798
G → C
Yes


1847
G → A
Yes


1877
C → G
Yes


1894
G → A
Yes


1896
A → G
Yes


1938
C → T
Yes


1963
T → A
No


2005
C → A
No


2006
C → A
No


2017
C → G
Yes









Variant protein HUMDNASEI_PEA—1_P6 (SEQ ID NO:1129) according to the present invention is encoded by transcript(s) HUMDNASEI_PEA—1_T7. An alignment is given to the known protein (Deoxyribonuclease I precursor) in FIG. 266. One or more alignments to one or more previously published protein sequences are given in FIGS. 264-268. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMDNASEI_PEA—1_P6 and DRN1_HUMAN:
1. An isolated chimeric polypeptide HUMDNASEI_PEA—1_P6, comprising a first amino acid sequence being at least 90% homologous to MRGMKLLGALLALAALLQGAVSLKIAAFNIQTFGETKMSNATLVSYIVQILSR YDIALVQEVRDSHLTAVGKLLDNLNQDAPDTYHYVVSEPLGRNSYKERYLF VYRPDQVSAVDSYYYDDGCEPCGNDTFNREPAIVRFFSRFTEVREFAIVPLHA APGDAVAEIDALYDVYLDVQEKWGLEDVMLMGDFNAGCSYVRPSQWSSIRL WTSPTFQWLIPDSADTTATPTHCAYDR corresponding to amino acids 1-235 of DRN1_HUMAN, which also corresponds to amino acids 1-235 of HUMDNASEI_PEA—1_P6, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence LPMA corresponding to amino acids 236-239 of HUMDNASEI_PEA—1_P6, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMDNASEI_PEA—1_P6, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence LPMA in HUMDNASEI_PEA—1_P6.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because of manual inspection of known protein localization and/or gene structure.
Variant protein HUMDNASEI_PEA—1_P6 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 459, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMDNASEI_PEA—1_P6 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 459







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












2
R → S
Yes


15
A →
No


18
Q →
No


107
R → G
Yes


117
Y → S
No


127
G → R
Yes


154
P → A
Yes


231
C → Y
Yes


239
A → T
Yes









The glycosylation sites of variant protein HUMDNASEI_PEA—1_P6, as compared to the known protein Deoxyribonuclease I precursor, are described in Table 460 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 460







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












128
yes
128


40
yes
40









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 461:







TABLE 461







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR008185
Deoxyribonuclease I
FPrintScan
102-131, 147-176,





177-206, 207-236,





33-62, 63-92


IPR005135
Endonuclease/
HMMPfam
23-236



exonuclease/



phosphatase


IPR008185
Deoxyribonuclease I
HMMSmart
6-239


IPR008185
Deoxyribonuclease I
ScanRegExp
189-196


IPR008185
Deoxyribonuclease I
ScanRegExp
152-172









Variant protein HUMDNASEI_PEA—1_P6 is encoded by the following transcript(s): HUMDNASEI_PEA—1_T7. The coding portion of transcript HUMDNASEI_PEA—1_T7 starts at position 1063 and ends at position 1779. The transcript also has the following SNPs as listed in Table 462 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMDNASEI_PEA—1_P6 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 462







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












487
A → C
No


917
G →
No


1031
G → A
Yes


1068
G → T
Yes


1106
C →
No


1116
G →
No


1158
A → C
Yes


1329
C → G
Yes


1381
A → G
Yes


1412
A → C
No


1441
G → A
Yes


1522
C → G
Yes


1590
C → G
Yes


1629
C → T
Yes


1686
G → A
Yes


1754
G → A
Yes


1777
G → A
Yes


1804
T → A
No


1846
C → A
No


1847
C → A
No


1858
C → G
Yes









Variant protein HUMDNASEI_PEA—1_P10 (SEQ ID NO:1130) according to the present invention is encoded by transcript(s) HUMDNASEI_PEA—1_T13. An alignment is given to the known protein (Deoxyribonuclease I precursor) in FIG. 267. One or more alignments to one or more previously published protein sequences are given in FIGS. 264-267. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMDNASEI_PEA—1_P10 and DRN1_HUMAN:
1. An isolated chimeric polypeptide HUMDNASEI_PEA—1_P10, comprising a first amino acid sequence being at least 90% homologous to MRGMKLLGALLALAALLQGAVSLKIAAFNIQTFGETKMSNATLVSYIVQILSR YDIALVQEVRDSHLTAVGKLLDNLNQDAPDTYHYVVSEPLGRNSYKERYLF VYRPDQVSAVDSYYYDDGCEPCGNDTFNREPAIVRFFSRFT corresponding to amino acids 1-145 of DRN1_HUMAN, which also corresponds to amino acids 1-145 of HUMDNASEI_PEA—1_P10, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GPQAAFPGRTSC corresponding to amino acids 146-157 of HUMDNASEI_PEA—1_P10, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMDNASEI_PEA—1_P10, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GPQAAFPGRTSC in HUMDNASEI_PEA—1_P10.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because of manual inspection of known protein localization and/or gene structure.
Variant protein HUMDNASEI_PEA—1_P10 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 463, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMDNASEI_PEA—1_P10 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 463







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












2
R → S
Yes


15
A →
No


18
Q →
No


107
R → G
Yes


117
Y → S
No


127
G → R
Yes









The glycosylation sites of variant protein HUMDNASEI_PEA—1_P10, as compared to the known protein Deoxyribonuclease I precursor, are described in Table 464 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the glycosylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 464







Glycosylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?












128
yes
128


40
yes
40









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 465:







TABLE 465







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR008185
Deoxyribonuclease I
FPrintScan
102-131, 33-62,





63-92


IPR008185
Deoxyribonuclease I
HMMSmart
6-157









Variant protein HUMDNASEI_PEA—1_P10 is encoded by the following transcript(s): HUMDNASEI_PEA—1_T13. The coding portion of transcript HUMDNASEI_PEA—1_T13 starts at position 1063 and ends at position 1533. The transcript also has the following SNPs as listed in Table 466 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMDNASEI_PEA—1_P10 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 466







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












487
A → C
No


917
G →
No


1031
G → A
Yes


1068
G → T
Yes


1106
C →
No


1116
G →
No


1158
A → C
Yes


1329
C → G
Yes


1381
A → G
Yes


1412
A → C
No


1441
G → A
Yes


1500
G → C
Yes


1541
C → T
Yes


1598
G → A
Yes


1666
G → A
Yes


1705
G → A
Yes


1710
G → C
Yes


1759
G → A
Yes


1786
T → A
No


1828
C → A
No


1829
C → A
No


1840
C → G
Yes









Example 68
Description for Cluster HUMTNFAA
Cluster HUMTNFAA features 3 transcript(s) and 9 segment(s) of interest, the names for which are given in Tables 467 and 468, respectively. The selected protein variants are given in Table 469.







TABLE 467







Transcripts of interest










Transcript Name
SEQ ID NO:







HUMTNFAA_PEA_1_T1
1132



 



HUMTNFAA_PEA_1_T2
1133



 



HUMTNFAA_PEA_1_T5
1134

















TABLE 468







Segments of interest










Segment Name
SEQ ID NO:







HUMTNFAA_PEA_1_node_0
1135



 



HUMTNFAA_PEA_1_node_2
1136



 



HUMTNFAA_PEA_1_node_3
1137



 



HUMTNFAA_PEA_1_node_5
1138



 



HUMTNFAA_PEA_1_node_7
1139



 



HUMTNFAA_PEA_1_node_8
1140



 



HUMTNFAA_PEA_1_node_9
1141



 



HUMTNFAA_PEA_1_node_4
1142



 



HUMTNFAA_PEA_1_node_6
1143

















TABLE 469







Proteins of interest











SEQ
Protein
Corresponding


Protein Name
ID NO:
Length
Transcripts(s)





HUMTNFAA_PEA_1_P6
1144
P143
HUMTNFAA_PEA_1_T1


 


HUMTNFAA_PEA_1_P7
1145
P73
HUMTNFAA_PEA_1_T2


 


HUMTNTAA_PEA_1_P8
1146
P217
HUMTNFAA_PEA_1_T5









These sequences are variants of the known protein Tumor necrosis factor precursor (SwissProt accession identifier TNFA_HUMAN; SEQ ID NO:1155; known also according to the synonyms TNF-alpha; Tumor necrosis factor ligand superfamily member 2; TNF-a; Cachectin), referred to herein as the previously known protein.
Protein Tumor necrosis factor precursor is known or believed to have the following function(s): Cytokine that binds to TNFRSF1A/TNFR1 and TNFRSF1B/TNFBR. It is mainly secreted by macrophages and can induce cell death of certain tumor cell lines. It is potent pyrogen causing fever by direct action or by stimulation of interleukin 1 secretion and is implicated in the induction of cachexia, Under certain conditions it can stimulate cell proliferation and induce cell differentiation. The sequence for protein Tumor necrosis factor precursor is seqt forth by SEQ ID NO:1147, as “Tumor necrosis factor precursor amino acid sequence”. Known polymorphisms for this sequence are as shown in Table 470.







TABLE 470







Amino acid mutations for Known Protein








SNP position(s) on



amino acid sequence
Comment











94
A → T (in dbSNP: 1800620)./FTId =



VAR_011927.


105
L → S: Low activity.


108
R → W: Biologically inactive.


112
L → F: Biologically inactive.


160
A → V: Biologically inactive.


162
S → F: Biologically inactive.


167
V → A, D: Biologically inactive.


222
E → K: Biologically inactive.


63
F → S


84-86
PSD → VNR


183
E → R









Protein Tumor necrosis factor precursor localization is believed to be Type II membrane protein. Also exists as an extracellular soluble form.
The previously known protein also has the following indication(s) and/or potential therapeutic use(s): Cancer, head and neck; Cancer, squamous cell; Infection, HIV/AIDS; Cancer, pancreatic; Arthritis, rheumatoid; Multiple sclerosis. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically related or therapeutically related activity or activities of the previously known protein or of drugs directed against this protein are as follows: Tumour necrosis factor modulator; Tumour necrosis factor alpha modulator. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, or part thereof, is used or can be used for a potential therapeutic indication: Anticancer; Radio/chemoprotective; Antiviral; Immunosuppressant; antibody; Antidiabetic; GI inflammatory/bowel disorders; Antipsoriasis; Antiarthritic, immunological; Monoclonal antibody, humanized; Anti-inflammatory; Monoclonal antibody, chimaeric; Septic shock treatment; Cytokine; Cardiovascular; Antiviral, anti-HIV; Anti-infective; Multiple sclerosis treatment; Antimycobacterial.
The following GO Annotation(s) apply to the previously known protein. The following annotation(s) were found: transcription regulation; apoptosis; anti-apoptosis; inflammatory response; immune response; leukocyte cell adhesion; signal transduction; cell-cell signaling; necrosis; response to viruses, which are annotation(s) related to Biological Process; tumor necrosis factor receptor ligand, which are annotation(s) related to Molecular Function; and soluble fraction; integral membrane protein, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the SwissProt/TremB1 Protein knowledgebase, or Locuslink.
As noted above, cluster HUMTNFAA features 3 transcript(s), which were listed in Table 1 above. These transcript(s) encode for protein(s) which are variant(s) of protein Tumor necrosis factor precursor. A description of each variant protein according to the present invention is now provided.
Variant protein HUMTNFAA_PEA—1_P6 (SEQ ID NO:1144) according to the present invention is encoded by transcript(s) HUMTNFAA_PEA—1_T1. An alignment is given to the known protein (Tumor necrosis factor precursor) in FIG. 268. One or more alignments to one or more previously published protein sequences are given in FIGS. 268-270. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMTNFAA_PEA—1_P6 and TNFA_HUMAN
1. An isolated chimeric polypeptide HUMTNFAA_PEA—1_P6, comprising a first amino acid sequence being at least 90% homologous to MSTESMIRDVELAEEALPKKTGGPQGSRRCLFLSLFSFLIVAGATTLFCLLHFG VIGPQREE corresponding to amino acids 1-62 of TNFA_HUMAN, which also corresponds to amino acids 1-62 of HUMTNFAA_PEA—1_P6, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VSAWPAFIHSPTQGEMETQERERDGMGERCALIGRDGEKKTWRKTGMQKE MWQEMGKRERERWRDRMSGTWKVLTKCVWSE corresponding to amino acids 63-143 of HUMTNFAA_PEA—1_P6, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMTNFAA_PEA—1_P6, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VSAWPAFIHSPTQGEMETQERERDGMGERCALIGRDGEKKTWRKTGMQKE MWQEMGKRERERWRDRMSGTWKVLTKCVWSE in HUMTNFAA_PEA—1_P6.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because of manual inspection of known protein localization and/or gene structure.
Variant protein HUMTNFAA_PEA—1_P6 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 471, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFAA_PEA—1_P6 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 471







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?












41
V → M
No


52
H → N
Yes


103
T → S
Yes









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 472:







TABLE 472







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR002959
Tumour necrosis factor
FPrintScan
2-20, 20-35,



alpha/cachectin

43-62









Variant protein HUMTNFAA_PEA—1_P6 (SEQ ID NO:1144) is encoded by the following transcript(s): HUMTNFAA_PEA—1_T1. The coding portion of transcript HUMTNFAA_PEA—1_T1 starts at position 178 and ends at position 606. The transcript also has the following SNPs as listed in Table 473 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFAA_PEA—1_P6 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 473







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












7
C → T
Yes


65
C → G
Yes


150
C → T
Yes


264
G → T
Yes


298
G → A
No


331
C → A
Yes


417
G → A
Yes


484
A → T
Yes


486
G → A
Yes


686
G →
Yes


848
A → G
Yes


884
T → C
Yes


1077
G → A
Yes


1165
T → C
Yes


1221
C → T
Yes


2701
→ C
No









Variant protein HUMTNFAA_PEA—1_P7 (SEQ ID NO:1145) according to the present invention is encoded by transcript(s) HUMTNFAA_PEA—1_T2. An alignment is given to the known protein (Tumor necrosis factor precursor) in FIG. 269. One or more alignments to one or more previously published protein sequences are given in FIGS. 268-270. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMTNFAA_PEA—1_P7 and TNFA_HUMAN:
1. An isolated chimeric polypeptide HUMTNFAA_PEA—1_P7, comprising a first amino acid sequence being at least 90% homologous to MSTESMIRDVELAEEALPKKTGGPQGSRRCLFLSLFSFLIVAGATTLFCLLHFG VIGPQREE corresponding to amino acids 1-62 of TNFA_HUMAN, which also corresponds to amino acids 1-62 of HUMTNFAA_PEA—1_P7, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence QTLKLRGSSSG corresponding to amino acids 63-73 of HUMTNFAA_PEA—1_P7, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide for a tail of HUMTNFAA_PEA—1_P7, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence QTLKLRGSSSG in HUMTNFAA_PEA—1_P7.
The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because of manual inspection of known protein localization and/or gene structure.
Variant protein HUMTNFAA_PEA—1_P7 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 474, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFAA_PEA—1_P7 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 474







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





41
V → M
No


52
H → N
Yes









The phosphorylation sites of variant protein HUMTNFAA_PEA—1_P7, as compared to the known protein Tumor necrosis factor precursor, are described in Table 475 (given according to their position(s) on the amino acid sequence in the first column; the second column indicates whether the phosphorylation site is present in the variant protein; and the last column indicates whether the position is different on the variant protein).







TABLE 475







Phosphorylation site(s)









Position(s) on known
Present in variant
Position in variant


amino acid sequence
protein?
protein?





2
yes
2









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 476:







TABLE 476







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR002959
Tumour necrosis factor
FPrintScan
2-20, 20-35,



alpha/cachectin

43-62









Variant protein HUMTNFAA_PEA—1_P7 is encoded by the following transcript(s): HUMTNFAA_PEA—1_T2. The coding portion of transcript HUMTNFAA_PEA—1_T2 starts at position 178 and ends at position 396. The transcript also has the following SNPs as listed in Table 477 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFAA_PEA—1_P7 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 477







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












7
C → T
Yes


65
C → G
Yes


150
C → T
Yes


264
G → T
Yes


298
G → A
No


331
C → A
Yes


1513
→ C
No









Variant protein HUMTNFAA_PEA—1_P8 (SEQ ID NO:1146) according to the present invention is encoded by transcript(s) HUMTNFAA_PEA—1_T5. An alignment is given to the known protein (Tumor necrosis factor precursor) in FIG. 270. One or more alignments to one or more previously published protein sequences are given in FIGS. 268-270. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows:
Comparison Report Between HUMTNFAA_PEA—1_P8 and TNFA_HUMAN_V1 (SEQ ID NO:1147):
1. An isolated chimeric polypeptide HUMTNFAA_PEA—1_P8, comprising a first amino acid sequence being at least 90% homologous to MSTESMIRDVELAEEALPKKTGGPQGSRRCLFLSLFSFLIVAGATTLFCLLHFG VIGPQREEFPRDLSLISPLAQA corresponding to amino acids 1-76 of TNFA_HUMAN_V1, which also corresponds to amino acids 1-76 of HUMTNFAA_PEA—1_P8, and a second amino acid sequence being at least 90% homologous to VTNPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQ GCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLG GVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL corresponding to amino acids 93-233 of TNFA_HUMAN_V1, which also corresponds to amino acids 77-217 of HUMTNFAA_PEA—1_P8, wherein said first amino acid sequence and second amino acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide for an edge portion of HUMTNFAA_PEA—1_P8, comprising a polypeptide having a length “n”, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise AV, having a structure as follows: a sequence starting from any of amino acid numbers 76-x to 76; and ending at any of amino acid numbers 77+((n−2)−x), in which x varies from 0 to n−2.
It should be noted that the known protein sequence (TNFA_HUMAN) has one or more changes than the sequence set forth by SEQ ID NO:1155 and named as being the amino acid sequence for TNFA_HUMAN_V1 (SEQ ID NO:1147). These changes were previously known to occur and are listed in the Table 478 below.







TABLE 478







Changes to TNFA_HUMAN_V1








SNP position(s) on



amino acid sequence
Type of change





95
variant









The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: membrane. The protein localization is believed to be membrane because the Signalp_hmm software predicts that this protein has a signal anchor region.
Variant protein HUMTNFAA_PEA—1_P8 also has the following non-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 479, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFAA_PEA—1_P8 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 479







Amino acid mutations









SNP position(s) on




amino acid sequence
Alternative amino acid(s)
Previously known SNP?





41
V → M
No


52
H → N
Yes









The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 480:







TABLE 480







InterPro domain(s)













Position(s)


InterPro ID
Domain description
Analysis type
on protein





IPR006053
Tumor necrosis factor
FPrintScan
136-154, 174-197,



alpha, beta and c

205-216, 71-88,





88-106


IPR002959
Tumour necrosis factor
FPrintScan
190-209, 2-20,



alpha/cachectin

20-35, 43-62


IPR006052
Tumor Necrosis Factor
HMMPfam
71-217


IPR006052
Tumor Necrosis Factor
HMMSmart
72-217


IPR006052
Tumor Necrosis Factor
ScanRegExp
108-124


IPR003636
Tumour necrosis factor
BlastProDom
72-217



subfamily


IPR006052
Tumor Necrosis Factor
ProfileScan
74-217









Variant protein HUMTNFAA_PEA—1_P8 is encoded by the following transcript(s): HUMTNFAA_PEA—1_T5. The coding portion of transcript HUMTNFAA_PEA—1_T5 starts at position 178 and ends at position 828. The transcript also has the following SNPs as listed in Table 481 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMTNFAA_PEA—1_P8 sequence provides support for the deduced sequence of this variant protein according to the present invention).







TABLE 481







Nucleic acid SNPs









SNP position on




nucleotide sequence
Alternative nucleic acid
Previously known SNP?












7
C → T
Yes


65
C → G
Yes


150
C → T
Yes


264
G → T
Yes


298
G → A
No


331
C → A
Yes


1559
→ C
No









Example 69
RETT Syndrome
Rett syndrome is a genetic disease which has profound neurological effects. It primarily affects girls. Although seemingly normal at birth and as babies, children affected with this disorder begin to develop symptoms between 6 to 18 months of age. At this point, they cease to play and to communicate, losing speech and both gross and fine motor skills, and instead develop a set of repetitive behaviors. These behaviors include stereotypic hand movements and teeth grinding. Children with this syndrome may also develop seizures and ataxia, and may in fact lose the ability to walk or even to move, and to self-feed. Despite the severity of these symptoms, children affected by the disorder often survive well into adulthood. Typically, the symptoms do not progress in severity beyond that of initial onset.
Rett syndrome has been found to be caused by defects in the MECP2 gene (see MEC2_HUMAN for the SwissProt entry). At least 80% of Rett syndrome patients have been found to carry defects in this gene. This protein binds to methylated DNA, and specifically methylated CpG. DNA methylation involves modifying carbon-5 of the cytosine pyrimidine ring, predominantly at CpG nucleotides. It is involved in silencing of genes during development for example.
Unmethylated genes remain active. Mutations in MECP2 may be involved in other types of retardation as well.
Rett syndrome itself occurs due to mosaicism, as MECP2 is X-linked. Rett syndrome patients therefore have a mosaic of normal and mutated genes, which is presumably why more females are affected by the disease than males: males with the defect typically (although not always) demonstrate much more severe side effects and die within the first two years of life (see Kriaucionis and Bird, Human Molec Genetics, 2003, vol 12, R221-227).
Recent research has found that mutations in this gene, resulting in a defective protein, lead to defects in the three-dimensional folding of chromatin, which in turn leads to Rett syndrome (Horike et al, Nat Genet. 2005 January; 37(1):31-40). Mecp2 was shown to target histone deacetylase 1 to a particular region of DNA that was studied, and to promote repressive histone methylation at this site. Mecp2 (in conjunction with other proteins) enabled a silent chromatin-derived 11-kb chromatin loop to be formed at this locus. Mice lacking the MECP2 gene also lacked this silent chromatin loop. Thus, it is believed that defects in the gene which result in a defective protein prevent silent chromatin loops from forming, thereby leading to Rett syndrome.
The Mecp2 protein has a methyl-CpG binding domain (MBD) at amino acid residues 90-162. Defects in this domain have been shown to be responsible for Rett syndrome in some patients. Another important domain is the transcription repression domain (TRD), which is in two parts at amino acid residues 185-277. Mutations for this domain were also found to be responsible for Rett syndrome in some patients.
A splice variant for Mecp2 has been found, which results in a longer protein (498 amino acids as opposed to 486 amino acids for the known or WT protein; see Mnatzakanian et al, Nature Genetics, vol 36, April 2004, 1-3; accession number MECP2B or AY541280). This protein is translated starting from exon 1, which forms part of the 5′ UTR in normal individuals.
According to preferred embodiments of the present invention, there are provided novel splice variants of Mecp2. These splice variants are either truncation (variant 2, SEQ ID NO:1148 and variant 3, SEQ ID NO:1152) or extension mutations (variant 1, SEQ ID NO:1150). Alignments are shown herein (FIGS. 271-273) with regard to the known or WT form of this protein, which does not result in disease (SEQ ID NO:1154). Each of these variants is described in greater detail. The variants according to the present invention may optionally be used for diagnostic testing of individuals, for example with NAT based testing of biological samples from affected individuals. These variants may also optionally be used as targets for therapeutic agents, such as small molecules, which may optionally be used to treat Rett syndrome, for example. The variants themselves may optionally be useful as therapeutic agents.
Probes associated with these variants, including but not limited to, antibodies or fragments thereof, oligonucleotides capable of specifically hybridizing to the related transcripts or fragments thereof, primer pairs capable of specifically amplifying these transcripts or fragments thereof, or any other such probe, also form preferred embodiments of the present invention. Preferably, the probe is capable of distinguishing between the splice variant and the known protein or known transcript, and optionally and preferably may also be able to distinguish between different splice variants.
Rett Syndrome Variant I (M62144_P2—SEQ ID NO:1150; M62144_T12—SEQ ID NO:1151)
As noted above, variant 1 is an extension mutation, resulting in a longer protein of 508 amino acids (SEQ ID NO:1150). As shown with regard to the alignment (FIG. 272), amino acids 9-486 from the known protein are in the variant amino acid sequence, with an addition of a unique head of 30 amino acids.
Rett Syndrome Variant 2 (M62144_P3—SEQ ID NO:1148; M62144_T13—SEQ ID NO:1149)
As noted above, variant 2 is a truncation mutation, resulting in a protein of 379 amino acids (SEQ ID NO:1148). As shown with regard to the alignment between this variant and the WT or known protein (FIG. 271), this protein is truncated. It features amino acid residues 1-376 that are identical to the known protein and a tail of 3 unique amino acids (TST). It therefore lacks a proline-rich region at amino acids 376-405.
Rett Syndrome Variant 3 (M62144_P4—SEQ ID NO:1152; M62144_T14—SEQ ID NO:1153)
As noted above, variant 3 is a truncation mutation, resulting in a protein of 247 amino acids (SEQ ID NO:1152). As shown with regard to the alignment between this variant and the WT or known protein (FIG. 273), this protein is truncated. It features amino acid residues 1-243 that are identical to the known protein and a tail of 4 unique amino acids (PTST). It therefore lacks part of the TRD (DNA binding) region and the proline-rich region at amino acids 376-405.
It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable subcombination.
Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims. All publications, patents and patent applications mentioned in this specification are herein incorporated in their entirety by reference into the specification, to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference. In addition, citation or identification of any reference in this application shall not be construed as an admission that such reference is available as prior art to the present invention.

## Claims

1. An antibody or binding fragment thereof which specifically binds to the tail portion of the Vascular endothelial growth factor (VEGF) receptor HSFLT PEA-1 P10 of SEQ ID NO:533, wherein the tail portion consisting of the amino acid sequence ELYTSTSPSSSSSSPLSSSSSSSSSSSS corresponding to amino acids 706-733 of SEQ ID NO:533.

2. A kit comprising the antibody of claim 1 and at least one reagent for performing an immunoassay.

3. The kit of claim 2, wherein said immunoassay is selected from the group consisting of an enzyme linked immunosorbent assay (ELISA), an immunoprecipitation assay, an immunofluorescence analysis, FACS analysis, an enzyme immunoassay (EIA), a radioimmunoassay (RIA), and a Western blot analysis.

4. A method of detecting the binding of the antibody of claim 1 to an epitope of a polypeptide comprising the amino acid sequence ELYTSTSPSSSSSSPLSSSSSSSSSSSS, wherein the epitope corresponds to amino acids 706-733 of SEQ ID NO:533, the method comprising the steps of contacting the antibody to a sample from a patient and detecting the binding of said antibody to said polypeptide.

5. The method of claim 4, wherein the patient is suspected of having a disease selected from the group consisting of peripheral vascular disease, ulcers, diabetes, ischemia, and cancer.