# Patent

## Title
GIPs, a family of polypeptides with transcription factor activity that interact with goodpasture antigen binding protein

## Abstract

The present invention provides isolated GPBP-interacting 90 and 130 kDa polypeptides, and portions thereof (GIP90/130 polypeptides), antibodies to the GIP90/130 polypeptides, and pharmaceutical compositions thereof. The present invention also provides isolated GIP90/130 nucleic acid sequences, expression vectors comprising the nucleic acid sequences, and host cells transfected with the expression vectors. The invention further provides methods for detecting the GIP90/130 polypeptides or nucleic acid sequences, methods for inhibiting interactions between GPBP and GIP90/130 polypeptides, between pol k76 and GIP90/130 polypeptides or aggregation of GIP90/130 polypeptides, and methods for treating patients with autoimmune disorders or cancer.

## Background
CROSS REFERENCE
This application claims priority to U.S. Provisional Patent Application Nos. 60/338,287 filed Dec. 7, 2001 and 60/382,004 filed May 20, 2002.


FIELD OF THE INVENTION
The present invention is in the general fields of molecular biology, cell biology, protein-protein interactions, autoimmunity, cancer, and drug discovery.
BACKGROUND
Goodpasture antigen binding protein (GPBP) is a ubiquitous protein kinase with a Mr of 80–89 kDa that is preferentially expressed in tissues and cells that are common targets of autoimmune responses, such as the Langerhans islets (type I diabetes); the white matter of the central nervous system (multiple sclerosis); the biliary ducts (primary biliary cirrhosis); the cortical cells of the adrenal gland (Addison disease); striated muscle cells (myasthenia gravis); spermatogonium (male infertility); Purkinje cells of the cerebellum (paraneoplasic cerebellar degeneration syndrome); and intestinal epithelial cells (pernicious anemia, autoimmune gastritis and enteritis).
GPBP is expressed as two isoforms (GPBP and GPBPΔ26) which result from exon alternative splicing of the corresponding pre-mRNA. GPBP is the more active variant, and its expression is still more restricted to histological structures targeted by common autoimmune responses including human alveolar and glomerular basement membranes (Goodpasture disease). GPBP binds to and phosphorylates the human α3 NC1 domain of type IV collagen (α3(IV)NC1) also called the Goodpasture antigen (WO 00/50607), as this domain is the target of the pathogenic autoantibodies mediating the Goodpasture autoimmune response. Phosphorylation activates the α3(IV)NC1 domain for aggregation, a process that is catalyzed at least in part by GPBP and which comprises conformational isomerization reactions and disulfide-bond exchange (WO 02/061430).
An augmented expression of GPBP with respect to GPBPΔ26 has been associated with the production of non-tolerized, aberrant conformational versions of the human α3(IV)NC1 domain (“aberrant conformers”) and the subsequent autoantibody production that causes Goodpasture disease (WO 02/061430). The evidence suggests that a similar pathogenic mechanism is involved in other autoimmune conditions, including cutaneous lupus erythematosus, pemphigus, pemphigoid and lichen planus, and that aberrant GPBP expression and autoimmune pathogenesis are related processes. Furthermore, GPBP is down-regulated in cancer cell lines (WO 00/50607), suggesting that the cell machinery harboring GPBP/GPBPΔ26 is also involved in signaling pathways that decrease cell division or induce cell death. These pathways could be up regulated during autoimmune pathogenesis to cause altered antigen presentation in individuals carrying specific MHC haplotypes, and down regulated during cell transformation to prevent autoimmune attack of the transformed cells during tumor growth.
Based on all of the above, there exists a need in the art to identify methods and reagents for modifying GPBP activity for use in treating autoimmune disorders and cancer.
SUMMARY OF THE INVENTION
In one aspect, the present invention provides isolated GPBP-interacting 90 and 130 kDa polypeptides, and portions thereof (GIP90/130 polypeptides), antibodies to the GIP 90/130 polypeptides, and pharmaceutical compositions thereof. In a further aspect, the present invention provides isolated GIP90/130 nucleic acid sequences, expression vectors comprising the nucleic acid sequences, and host cells transfected with the expression vectors. The invention further provides methods for detecting the GIP90/130 polypeptides or nucleic acid sequences, methods for modifying interactions between GPBP and GIP90/130 polypeptides, aggregation of GIP90/130 polypeptides, and GIP90/130 polypeptide-mediated gene transcription, and methods for treating patients with autoimmune disorders or cancer.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 is a diagram of the exon-intron structure of the GIP90 genomic DNA as determined by BLAST search against Human Genome NCBI in May 20, 2002.
FIG. 2 is a representation of differences between various GIP90/130 mRNA and polypeptide species.
FIG. 3 is a sequence alignment of the full length GIP90/130 polypeptides and DOC1 and DOC1-related protein.
FIG. 4 is the amino acid sequence of I-20. Residues in bold font are those identified as essential for interactions between GIP90/130 and GPBP; in small letters are other residues identified as participating in interaction between GIP90/130 and GPBP, but not essential; and underlined are the residues implicated in GIP90/130 aggregation.



DETAILED DESCRIPTION OF THE INVENTION
Within this application, unless otherwise stated, the techniques utilized may be found in any of several well-known references such as: Molecular Cloning: A Laboratory Manual (Sambrook, et al., 1989, Cold Spring Harbor Laboratory Press), Gene Expression Technology (Methods in Enzymology, Vol. 185, edited by D. Goeddel, 1991. Academic Press, San Diego, Calif.), “Guide to Protein Purification” in Methods in Enzymology (M. P. Deutshcer, ed., (1990) Academic Press, Inc.); PCR Protocols: A Guide to Methods and Applications (Innis, et al. 1990. Academic Press, San Diego, Calif.), Culture of Animal Cells: A Manual of Basic Technique, 2nd Ed. (R. I. Freshney. 1987. Liss, Inc. New York, N.Y.), Gene Transfer and Expression Protocols, pp. 109–128, ed. E. J. Murray, The Humana Press Inc., Clifton, N.J.), and the Ambion 1998 Catalog (Ambion, Austin, Tex.).
As used herein, the term “GIP90/130” and “GIP90/130 polypeptide(s)” refers to the family of GPBP-interacting proteins that includes GIP90, GIP130a, GIP130b, and GIP130c, amino acid sequences derived therefrom, and includes both monomers and oligomers thereof.
As used herein, the term “GIP90” refers to the 90 kDa form of GIP, which consists of the amino acid sequence of SEQ ID NO: 10, and includes both monomers and oligomers thereof.
As used herein, the term “GIP130a” refers to one of the 130 kDa forms of GIP, which consists of the amino acid sequence of SEQ ID NO:12, and includes both monomers and oligomers thereof.
As used herein, the term “GIP130b” refers to one of the 130 kDa forms of GIP, which consists of the amino acid sequence of SEQ ID NO:14, and includes both monomers and oligomers thereof.
As used herein, the term “GIP130c” refers to one of the 130 kDa forms of GIP, which consists of the amino acid sequence of SEQ ID NO:16, and includes both monomers and oligomers thereof.
The numbering of nucleotides and residues used below for GIP proteins refer to the GenBank accession number AF329092.
As used herein, the term “DOC proteins” or “DOC1 proteins” refers to down regulated in ovarian cancer-1 (DOC1) (Genbank accession number NM 014890) and DOC1-related protein (Genbank accession number BC027860). DOC1 and DOC1-related protein are derived from the same gene since they are identical in the homology region at nucleotide and amino acid levels
As used herein, the term “GPBP” refers to Goodpasture antigen binding protein, and includes both monomers and oligomers thereof, as disclosed in WO 00/50607.
As used herein, the term “GPBPΔ26” refers to the Goodpasture antigen binding protein alternatively spliced product deleted for 26 amino acid residues as disclosed in WO 00/50607, and includes both monomers and oligomers thereof.
As used herein pol κ means the primary protein product of the POLK as disclosed in WO 02/46378.
As used herein, pol κ76 means the 76 kDa alternatively spliced isoform product of the POLK as disclosed in WO 02/46378.
As used herein, “aggregation” refers to both self-aggregation of an individual GIP90/130 polypeptide, and aggregation of two or more different GIP90/130 polypeptides.
In one aspect, the present invention provides isolated GIP90/130 polypeptides. In one embodiment, the isolated GIP90/130 polypeptide comprises at least 6 amino acids of the amino acid sequence of SEQ ID NO:2, which is a unique 10 amino acid polypeptide (SYRRILGQLL) that is herein demonstrated to be essential for the interaction between GIP90/130 and GPBP (discussed in detail below), and is not present in DOC proteins. In further embodiments, the isolated GIP90/130 polypeptide comprises at least 7, 8, 9, or 10 amino acids of the amino acid sequence of SEQ ID NO:2. In still further embodiments, the isolated GIP90/130 polypeptide consists of at least 6, 7, 8, 9, or 10 amino acids of the amino acid sequence of SEQ ID NO:2. These polypeptides can be used, for example, to modify interactions between GPBP and GIP90/130 polypeptides or to raise antibodies that interfere with GPBP-GIP90/130 interaction.
In further embodiments, the isolated GIP90/130 polypeptide comprises and/or consists of the amino acid sequence of SEQ ID NO:4, which is the N-terminal region of GIP90/130a/c that is not present in DOC proteins (described in detail below), and which is encoded by exon II–IV and part of exon V (FIG. 3). These polypeptides are thus useful, for example, to develop reagents, such as antibodies, that can distinguish between GIP90/130 and DOC proteins. This polypeptide includes sequences implicated in the interaction between GPBP and GIP90/130 (including SEQ ID NO: 2), and thus can be used (or antibodies to the polypeptides can be used), for example, to modify interactions between GPBP and GIP90/130 polypeptides. This polypeptide also includes sequences implicated in GIP90/130 aggregation, and thus can further be used (or antibodies to the polypeptides can be used) to modify GIP90/130 aggregation. This polypeptide also includes sequences implicated in the transcriptional activity of GIP90/130 and thus the polypeptides, or antibodies derived therefrom, can be further used for modulating specific gene expression.
The polypeptides of the invention also include polypeptides comprising and/or consisting of the amino acid sequence of SEQ ID NO: 6, which is referred to as I-20, a 265 amino acid polypeptide that is described in detail below. This polypeptide interacts more strongly with GPBP and pol κ76 than the full length GIP90/130 polypeptides, and aggregates more efficiently than the full length GIP90/130 polypeptides. Furthermore, I-20 does not induce gene transcription, in contrast to the full length GIP90/130 polypeptides. Therefore this polypeptide can be used (or antibodies to the polypeptides can be used), for example, to modify (a) interactions between GPBP and GIP90/130 polypeptides; (b) interactions between pol κ76 and GIP90/130 polypeptides; (c) GIP90/130 polypeptide aggregation; and (d) other functions of the GIP90/130 polypeptides, such as induction of gene transcription.
The polypeptides of the invention also include polypeptides comprising and/or consisting of the amino acid sequence of SEQ ID NO:8, which consists of the N-terminus of GIP90 to the end of I-20, and is encoded by exons II–IV and part of exon V up to the end of the I-20 coding sequence. This polypeptide includes sequences implicated in (a) the interaction between GPBP and GIP90/130 polypeptides, (b) GIP90/130 polypeptide aggregation, and (c) the transcriptional activity of GIP90/130 polypeptides, and thus the polypeptides, or antibodies derived therefrom, can be used, for example, to modify interactions between GPBP and GIP90/130 polypeptides, to modify GIP90/130 aggregation, and to modulate gene expression.
The polypeptides of the invention also include polypeptides comprising and/or consisting of the amino acid sequence of SEQ ID NO:10 (GIP90), SEQ ID NO:12 (GIP130a), SEQ ID NO:14 (GIP130b), or SEQ ID NO:16 (GIP130c). These full length polypeptides, described in more detail below, interact with GPBP and are capable of aggregation. These polypeptides can be used, for example, to modify GPBP-GIP90/130 interactions, to modify GIP90/130 aggregation, to modulate gene expression, as well as for other purposes described herein.
In a further embodiment, the isolated GIP 90/130 polypeptide comprises at least 8 amino acids of the amino acid sequence of SEQ ID NO:18, which is a unique 15 amino acid peptide that is present at the C-terminus of GIP90 and is not present in DOC proteins, GIP130a, GIP130b, or GIP130c, and thus can be used, for example, to generate reagents, such as antibodies, to distinguish GIP90 from other members of the GIP90/130 polypeptide family. Furthermore, the polypeptides, or antibodies thereto, can be used to specifically modify GIP90 self-aggregation. In further embodiments, the isolated GIP90/130 polypeptide comprises or consists of at least 9, 10, 11, 12, 13, 14, or 15 amino acids of the amino acid sequence of SEQ ID NO:18.
In a further embodiment, the isolated GIP90/130 polypeptide consists of at least 8 amino acids of the amino acid sequence of SEQ ID NO:20, which is a 30 amino acid polypeptide present within I-20 that has been implicated in the interaction of GIP90/130 with GPBP and also in GIP90/130 aggregation. In further embodiments, the isolated GIP90/130 polypeptide consists of at least 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 amino acids the amino acid sequence of SEQ ID NO:20. Thus, these polypeptides, or antibodies to the polypeptides, can be used, for example, to modify interactions between GPBP and GIP90/130 polypeptides. Furthermore, since this polypeptide is present in each of GIP90, GIP130a, GIP130b, GIP130c, and DOC1 proteins, these polypeptides, or antibodies thereto, can be used to generally modify aggregation of the GIP90/130 polypeptides and DOC1 proteins. Despite the fact that DOC1 proteins contain SEQ ID NO:20, they do not interact in a two hybrid assay with GPBP (see below), and thus SEQ ID NO:20, while implicated in the interaction of GIP90/130 polypeptides and GPBP, is not sufficient for GPBP interaction.
In a still further embodiment, the isolated GIP90/130 polypeptide comprises or consists of the amino acid sequence of SEQ ID NO:22, which is a unique 386 amino acid polypeptide that is present at the C-terminus of GIP130a but is not present in GIP90, is not wholly present in DOC1, and includes variations from GIP130b, GIP130c, and DOC1-related protein, and thus can be used, for example, to modify GIP130a aggregation, and to generate reagents, such as antibodies, to distinguish GIP130a from other members of the GIP90/130 polypeptide family, and the DOC proteins. This region contains sequences that down-regulate GIP 90/130 interaction with GPBP which can be used to modify GIP90/130-GPBP interaction, or to generate reagents, such as antibodies for the same purposes.
In a still further embodiment, the isolated GIP90/130 polypeptide comprises or consists of the amino acid sequence of SEQ ID NO:24, which is GIP130a deleted from the N-terminus to the end of I-20. This polypeptide lacks critical regions of the GIP90/130 polypeptides implicated in GPBP interaction and induction of gene expression, and like the C terminus of GIP130b/c contains amino acid sequences that down-regulate interaction with GPPB. Thus, the polypeptides, or antibodies thereto, can be used, for example, to modify GPBP-GIP90/130 polypeptide interactions or to modify GIP90/130 polypeptide aggregation.
In a still further embodiment, the isolated GIP 90/130 polypeptide comprises or consists of the amino acid sequence of SEQ ID NO:26, which is a unique 7 amino acid polypeptide present at the C-terminus of GIP130a, and is not present in any of GIP90, GIP130b, GIP130c, and DOC proteins. Thus, these polypeptides can be used to produce reagents, such as antibodies, that are specific for GIP130a, and which can be used, for example, to specifically modify GIP130a aggregation.
In another embodiment, the isolated GIP90/130 polypeptide comprises at least 6 amino acids of the amino acid sequence of SEQ ID NO:28, which is a unique 10 amino acid polypeptide (LDKVVEKHKE) within I-20 that participates in interactions between GIP90/130 polypeptides and GPBP, is essential for GIP90/130 polypeptide aggregation, and is not present in DOC proteins. In further embodiments, the isolated GIP90/130 polypeptide comprises or consists of at least 7, 8, 9, or 10 amino acids of the amino acid sequence of SEQ ID NO:28. These polypeptides or antibodies raised against them can be used, for example, to modify interactions between GPBP and GIP90/130 polypeptides or to modify GIP90/130 polypeptide aggregation.
In another embodiment, the isolated GIP90/130 polypeptide consists of at least 6 amino acids of the amino acid sequence of SEQ ID NO:30, which is an 10 amino acid polypeptide (EEEQKATRLE) within I-20 that participates in interactions between GIP90/130 polypeptides and GPBP, is essential for GIP90/130 polypeptide aggregation, and is present in DOC proteins. In further embodiments, the isolated GIP90/130 polypeptide consists of at least 7, 8, 9, or 10 amino acids of the amino acid sequence of SEQ ID NO:30. These polypeptides or antibodies raised against them can be used, for example, to modify interactions between GPBP and GIP90/130 polypeptides or to modify GIP90/130 polypeptide aggregation. Furthermore, since this polypeptide is present in each of GIP90, GIP130a, GIP130b, GIP130c, and DOC1 proteins, these polypeptides, or antibodies thereto, can be used to generally modify aggregation of the GIP90/130 polypeptides and DOC1/DOC1-related proteins. Despite the fact that DOC1 proteins contain SEQ ID NO:20, they do not interact in a two hybrid assay with GPBP (see below), and thus SEQ ID NO:20, while implicated in the interaction of GIP90/130 polypeptides and GPBP, is not sufficient for GPBP interaction.
In another embodiment, the isolated GIP90/130 polypeptide comprises at least 8 amino acids of the amino acid sequence of SEQ ID NO:32, which is a unique 20 amino acid polypeptide (LDKVVEKHKESYRRILGQLL) within I-20 that contains essential residues for the interaction between GIP90/130 polypeptides and GPBP and for GIP90/130 polypeptide aggregation, and is not present in DOC proteins. In further embodiments, the isolated GIP90/130 polypeptide comprises or consists of at least 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acids of the amino acid sequence of SEQ ID NO:32. These polypeptides can be used, for example, to modify interactions between GPBP and GIP90/130 polypeptides and to modify GIP90/130 polypeptide aggregation, or to raise antibodies that modify interactions between GPBP and GIP90/130 polypeptides and to modify GIP90/130 polypeptide aggregation.
In another embodiment, the isolated GIP90/130 polypeptide consists of at least 8 amino acids of the amino acid sequence of SEQ ID NO:34, which is a 50 amino acid polypeptide that is contained within I-20, contains regions essential for the interaction between GIP90/130 polypeptides and GPBP and for GIP90/130 polypeptide aggregation, and is present in DOC proteins. In further embodiments, the isolated GIP90/130 polypeptide consists of at least 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 amino acids of the amino acid sequence of SEQ ID NO:34. These polypeptides can be used, for example, to modify interactions between GPBP and GIP90/130 polypeptides and to modify GIP90/130 polypeptide aggregation, or to raise antibodies that modify interactions between GPBP and GIP90/130 polypeptides and to modify GIP90/130 polypeptide aggregation. Furthermore, since this polypeptide is present in each of GIP90, GIP130a, GIP130b, GIP130c, and DOC1 proteins, these polypeptides, or antibodies thereto, can be used to generally modify aggregation of the GIP90/130 polypeptides and DOC1/DOC1-related proteins. Despite the fact that DOC1 proteins contain SEQ ID NO:20, they do not interact in a two hybrid assay with GPBP (see below), and thus SEQ ID NO:20, while inplicated in the interaction of GIP90/130 polypeptides and GPBP, is not sufficient for GPBP interaction.
The polypeptides of the invention also include polypeptides comprising and/or consisting of the amino acid sequence of SEQ ID NO:36, which consists of the first 240 amino acids of the N-terminus of GIP130b, which is not present in DOC1 proteins, and which differs from the corresponding sequence in GIP90, GIP130a, and GIP130c by a single amino acid residue at position 168. This polypeptide includes sequences implicated in (a) the interaction between GPBP and GIP90/130 polypeptides, (b) GIP90/130 polypeptide aggregation, and (c) the transcriptional activity of GIP90/130 polypeptides, and thus the polypeptides, or antibodies derived therefrom, can be used, for example, to modify interactions between GPBP and GIP90/130 polypeptides, to modify GIP90/130 aggregation, and to modulate gene expression.
In a still further embodiment, the isolated GIP 90/130 polypeptide consists of the amino acid sequence of SEQ ID NO:38 which is a unique 384 amino acid polypeptide that is present at the C terminus of GIP130b/c and DOC1-related protein but is not present in GIP90, is not wholly present in DOC1, and includes variations from GIP130a, and thus can be used, for example, to modify GIP130b/c aggregation, and to generate reagents, such as antibodies, to distinguish GIP130b/c and the DOC1-related protein from other members of the GIP90/130 polypeptide family.
As used herein, an “isolated polypeptide” refers to a polypeptide that is substantially free of other proteins, cellular material and culture medium when isolated from cells or produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized. Thus, the protein can either be purified from natural sources, chemically synthesized, or recombinant protein can be purified from the recombinant host cells disclosed below.
Synthetic polypeptides, prepared using the well known techniques of solid phase, liquid phase, or peptide condensation techniques, or any combination thereof, can include natural and unnatural amino acids. Amino acids used for peptide synthesis may be standard Boc (Nα-amino protected Nα-t-butyloxycarbonyl) amino acid resin with the standard deprotecting, neutralization, coupling and wash protocols of the original solid phase procedure of Merrifield (1963, J. Am. Chem. Soc. 85:2149–2154), or the base-labile Nα-amino protected 9-fluorenylmethoxycarbonyl (Fmoc) amino acids first described by Carpino and Han (1972, J. Org. Chem. 37:3403–3409). Both Fmoc and Boc Nα-amino protected amino acids can be obtained from Sigma, Cambridge Research Biochemical, or other chemical companies familiar to those skilled in the art. In addition, the polypeptides can be synthesized with other Nα-protecting groups that are familiar to those skilled in this art.
Solid phase peptide synthesis may be accomplished by techniques familiar to those in the art and provided, for example, in Stewart and Young, 1984, Solid Phase Synthesis, Second Edition, Pierce Chemical Co., Rockford, Ill.; Fields and Noble, 1990, Int. J. Pept. Protein Res. 35:161–214, or using automated synthesizers. The polypeptides of the invention may comprise D-amino acids (which are resistant to L-amino acid-specific proteases in vivo), a combination of D- and L-amino acids, and various “designer” amino acids (e.g., β-methyl amino acids, Cα-methyl amino acids, and Nα-methyl amino acids, etc.) to convey special properties. Synthetic amino acids include omithine for lysine, fluorophenylalanine for phenylalanine, and norleucine for leucine or isoleucine.
In addition, the polypeptides can have peptidomimetic bonds, such as ester bonds, to prepare peptides with novel properties. For example, a peptide may be generated that incorporates a reduced peptide bond, i.e., R1—CH2—NH—R2, where R1 and R2 are amino acid residues or sequences. A reduced peptide bond may be introduced as a dipeptide subunit. Such a polypeptide would be resistant to protease activity, and would possess an extended half-live in vivo.
Alternatively, the proteins are produced by the recombinant host cells disclosed below, and purified using standard techniques. (See for example, Molecular Cloning: A Laboratory Manual (Sambrook, et al., 1989, Cold Spring Harbor Laboratory Press.)) The protein can thus be purified from prokaryotic or eukaryotic sources. In various further preferred embodiments, the protein is purified from bacterial, yeast, or mammalian cells.
The protein may comprise additional sequences useful for promoting purification of the protein, such as epitope tags and transport signals. Examples of such epitope tags include, but are not limited to FLAG (Sigma Chemical, St. Louis, Mo.), myc (9E10) (Invitrogen, Carlsbad, Calif.), 6-His (Invitrogen; Novagen, Madison, Wis.), and HA (Boehringer Manheim Biochemicals). Examples of such transport signals include, but are not limited to, export signals, secretory signals, nuclear localization signals, and plasma membrane localization signals.
In another aspect, the present invention provides antibodies against the GIP90/130 polypeptides disclosed herein. Such antibodies can be used in a manner similar to the polypeptides they recognize in modifying GPBP-GIP90/130 interactions, modifying GIP90/130 aggregation, and/or modifying GIP90/130-mediated transcriptional activity. Furthermore, such antibodies can be used to distinguish between members of the GIP90/130 family, as discussed above.
In one embodiment, the antibodies are directed against an epitope present in a polypeptide of one or more of the amino acid sequences selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:18, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:32, and SEQ ID NO:36. In a further embodiment, the antibodies are directed against an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, and SEQ ID NO:38.
Antibodies can be made by well-known methods, such as described in Harlow and Lane, Antibodies; A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., (1988). In one example, pre-immune serum is collected prior to the first immunization. A peptide portion of the amino acid sequence of a GIP90/130 polypeptide, together with an appropriate adjuvant, is injected into an animal in an amount and at intervals sufficient to elicit an immune response. Animals are bled at regular intervals, preferably weekly, to determine antibody titer. The animals may or may not receive booster injections following the initial immunization. At about 7 days after each booster immunization, or about weekly after a single immunization, the animals are bled, the serum collected, and aliquots are stored at about −20° C. Polyclonal antibodies against GIP90/130 polypeptides can then be purified directly by passing serum collected from the animal through a column to which non-antigen-related proteins prepared from the same expression system without GIP90/130 polypeptides bound.
Monoclonal antibodies can be produced by obtaining spleen cells from the animal. (See Kohler and Milstein, Nature 256, 495–497 (1975)). In one example, monoclonal antibodies (mAb) of interest are prepared by immunizing inbred mice with a GIP90/130 polypeptide, or portion thereof. The mice are immunized by the IP or SC route in an amount and at intervals sufficient to elicit an immune response. The mice receive an initial immunization on day 0 and are rested for about 3 to about 30 weeks. Immunized mice are given one or more booster immunizations of by the intravenous (IV) route. Lymphocytes from antibody positive mice are obtained by removing spleens from immunized mice by standard procedures known in the art. Hybridoma cells are produced by mixing the splenic lymphocytes with an appropriate fusion partner under conditions which will allow the formation of stable hybridomas. The antibody producing cells and fusion partner cells are fused in polyethylene glycol at concentrations from about 30% to about 50%. Fused hybridoma cells are selected by growth in hypoxanthine, thymidine and aminopterin supplemented Dulbecco's Modified Eagles Medium (DMEM) by procedures known in the art. Supernatant fluids are collected from growth positive wells and are screened for antibody production by an immunoassay such as solid phase immunoradioassay. Hybridoma cells from antibody positive wells are cloned by a technique such as the soft agar technique of MacPherson, Soft Agar Techniques, in Tissue Culture Methods and Applications, Kruse and Paterson, Eds., Academic Press, 1973.
To generate such an antibody response, a GIP90/130 polypeptide or portion thereof is typically formulated with a pharmaceutically acceptable carrier for parenteral administration. Such acceptable adjuvants include, but are not limited to, Freund's complete, Freund's incomplete, alum-precipitate, water in oil emulsion containing Corynebacterium parvum and tRNA. The formulation of such compositions, including the concentration of the polypeptide and the selection of the vehicle and other components, is within the skill of the art.
The term antibody as used herein is intended to include antibody fragments thereof which are selectively reactive with GIP90/130 polypeptides. Antibodies can be fragmented using conventional techniques, and the fragments screened for utility in the same manner as described above for whole antibodies. For example, F(ab′)2 fragments can be generated by treating antibody with pepsin. The resulting F(ab′)2 fragment can be treated to reduce disulfide bridges to produce Fab′ fragments.
In another aspect, the present invention provides isolated nucleic acids that encode GIP90/130 polypeptides. In one embodiment, the isolated nucleic acid sequences comprise sequences encoding an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:32, and SEQ ID NO:36. In a further embodiment, the isolated nucleic acid sequences consist of sequences encoding an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO;34, SEQ ID NO:36, and SEQ ID NO:38.
In another embodiment, the isolated nucleic acids comprise sequences that hybridize under high stringency conditions to a nucleic acid sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:17, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31, and SEQ ID NO:35, their complement, or their transcription product. Stringency of hybridization is used herein to refer to conditions under which nucleic acid hybrids are stable. As known to those of skill in the art, the stability of hybrids is reflected in the melting temperature (TM) of the hybrids. TM decreases approximately 1–1.5° C. with every 1% decrease in sequence homology. In general, the stability of a hybrid is a function of sodium ion concentration and temperature. Typically, the hybridization reaction is performed under conditions of lower stringency, followed by washes of varying, but higher, stringency. Reference to hybridization stringency relates to such washing conditions. Thus, as used herein, high stringency refers to conditions that permit hybridization of those nucleic acid sequences that form stable hybrids in 0.1% SSPE at 65° C. It is understood that these conditions may be duplicated using a variety of buffers and temperatures and that they are not necessarily precise. Denhardt's solution and SSPE (see, e.g., Sambrook, Fritsch, and Maniatis, in: Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1989) are well known to those of skill in the art, as are other suitable hybridization buffers.
In another embodiment, the isolated nucleic acids comprise one or more sequences selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:17, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31, and SEQ ID NO:35, their complement, or their transcription product. In a further embodiment, the isolated nucleic acid sequences comprise one or more sequences selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31, and SEQ ID NO:35, their complement, or their transcription product. In a further embodiment, the isolated nucleic acid sequences consist of one or more sequences selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, and SEQ ID NO:37, their complement, or their transcription product.
As used herein, an “isolated nucleic acid sequence” refers to a nucleic acid sequence that is free of gene sequences which naturally flank the nucleic acid in the genomic DNA of the organism from which the nucleic acid is derived (i.e., genetic sequences that are located adjacent to the gene for the isolated nucleic molecule in the genomic DNA of the organism from which the nucleic acid is derived). An “isolated” GIP90/130 nucleic acid sequence according to the present invention may, however, be linked to other nucleotide sequences that do not normally flank the recited sequence, such as a heterologous promoter sequence, or other vector sequences. It is not necessary for the isolated nucleic acid sequence to be free of other cellular material to be considered “isolated”, as a nucleic acid sequence according to the invention may be part of an expression vector that is used to transfect host cells (see below).
In all of these embodiments, the isolated nucleic acid sequence may comprise RNA or DNA, and may be single stranded or double stranded. Such single stranded sequences can comprise the disclosed sequence, its complement, or the transcription product thereof. The isolated sequence may further comprise additional sequences useful for promoting expression and/or purification of the encoded protein, including but not limited to polyA sequences, modified Kozak sequences, and sequences encoding epitope tags, export signals, and secretory signals, nuclear localization signals, and plasma membrane localization signals.
In another embodiment, the present invention provides an expression vector comprising an isolated nucleic acid as described above, operatively linked to a promoter. In a preferred embodiment, the promoter is heterologous (i.e.: is not the naturally occurring GIP90/130 promoter). A promoter and a GIP90/130 nucleic acid sequence are “operatively linked” when the promoter is capable of driving expression of the GIP90/130 DNA into RNA.
As used herein, the term “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a “plasmid”, which refers to a circular double stranded DNA into which additional DNA segments may be cloned. Another type of vector is a viral vector, wherein additional DNA segments may be cloned into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors), are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of nucleic acid sequences to which they are operatively linked. Such vectors are referred to herein as “recombinant expression vectors” or simply “expression vectors”. In the present invention, the expression of any nucleic acid sequence is directed by operatively linking the promoter sequences of the invention to the nucleic acid sequence to be expressed. In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, “plasmid” and “vector” may be used interchangeably as the plasmid is the most commonly used form of vector. However, the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.
The vector may also contain additional sequences, such as a polylinker for subcloning of additional nucleic acid sequences and a polyadenylation signal to effect proper polyadenylation of the transcript. The nature of the polyadenylation signal is not believed to be crucial to the successful practice of the invention, and any such sequence may be employed, including but not limited to the SV40 and bovine growth hormone poly-A sites. The vector may further include a termination sequence, which can serve to enhance message levels and to minimize read through from the construct into other sequences. Finally, expression vectors typically have selectable markers, often in the form of antibiotic resistance genes, that permit selection of cells that carry these vectors.
In a further embodiment, the present invention provides recombinant host cells in which the expression vectors disclosed herein have been introduced. As used herein, the term “host cell” is intended to refer to a cell into which a nucleic acid of the invention, such as a recombinant expression vector of the invention, has been introduced. Such cells may be prokaryotic or eukaryotic.
The terms “host cell” and “recombinant host cell” are used interchangeably herein. It should be understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.
The host cells can be transiently or stably transfected with one or more of the expression vectors of the invention. Such transfection of expression vectors into prokaryotic and eukaryotic cells can be accomplished via any technique known in the art, including but not limited to standard bacterial transformations, calcium phosphate co-precipitation, electroporation, or liposome mediated-, DEAE dextran mediated-, polycationic mediated-, or viral mediated transfection. Alternatively, the host cells can be infected with a recombinant viral vector comprising the GIP90/130 nucleic acid. (See, for example, Molecular Cloning: A Laboratory Manual (Sambrook, et al., 1989, Cold Spring Harbor Laboratory Press; Culture of Animal Cells: A Manual of Basic Technique, 2nd Ed. (R. I. Freshney. 1987. Liss, Inc. New York, N.Y.).
In a further aspect, the invention provides methods for detecting the presence of the GIP90/130 polypeptides in a protein sample, comprising providing a protein sample to be screened, contacting the protein sample to be screened with an antibody against one or more GIP90/130 polypeptides, and detecting the formation of antibody-GIP90/130 polypeptide complexes. The antibody can be either polyclonal or monoclonal, although monoclonal antibodies are preferred. As used herein, the term “protein sample” refers to any sample that may contain GIP90/130 polypeptides, including but not limited to tissues and portions thereof, tissue sections, intact cells, cell extracts, purified or partially purified protein samples, bodily fluids, and nucleic acid expression libraries. Accordingly, this aspect of the present invention may be used to test for the presence of GIP90/130 polypeptides in these various protein samples by standard techniques including, but not limited to, immunolocalization, immunofluorescence analysis, Western blot analysis, ELISAs, and nucleic acid expression library screening, (See for example, Sambrook et al, 1989.) In one embodiment, the techniques may determine only the presence or absence of GIP90/130 polypeptides. Alternatively, the techniques may be quantitative, and provide information about the relative amount of GIP90/130 polypeptides in the sample. For quantitative purposes, ELISAs are preferred.
Detection of immunocomplex formation between GIP90/130 polypeptides and antibodies or fragments thereof directed against GIP90/130 polypeptides can be accomplished by standard detection techniques. For example, detection of immunocomplexes can be accomplished by using labeled antibodies or secondary antibodies. Such methods, including the choice of label are known to those ordinarily skilled in the art. (Harlow and Lane, Supra). Alternatively, the polyclonal or monoclonal antibodies can be coupled to a detectable substance. The term “coupled” is used to mean that the detectable substance is physically linked to the antibody. Suitable detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, β-galactosidase, or acetylcholinesterase. Examples of suitable prosthetic-group complexes include streptavidin/biotin and avidinibiotin. Examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin. An example of a luminescent material includes luminol. Examples of suitable radioactive material include 125I, 131I, 35S or 3H.
Such methods of detection are useful for a variety of purposes, including but not limited to detecting an autoimmune condition, identifying cell division arrest or cell death, detecting GIP90/130 interactions with GPBP or other proteins, immunolocalization of GIP90/130 polypeptides in a tissue sample, Western blot analysis, and screening of expression libraries to find related proteins.
In yet another aspect, the invention provides methods for detecting the presence of nucleic acid sequences encoding GIP90/130 polypeptides in a sample comprising providing a nucleic acid sample to be screened, contacting the sample with a nucleic acid probe derived from the isolated nucleic acid sequences of the invention, or fragments thereof, and detecting complex formation.
As used herein, the term “sample” refers to any sample that may contain a GIP90/130 polypeptide-encoding nucleic acid, including but not limited to tissues and portions thereof, tissue sections, intact cells, cell extracts, purified or partially purified nucleic acid samples, DNA libraries, and bodily fluids. Accordingly, this aspect of the present invention may be used to test for the presence of GIP90/130 polypeptide-encoding mRNA or DNA in these various samples by standard techniques including, but not limited to, in situ hybridization, Northern blotting, Southern blotting, DNA library screening, polymerase chain reaction (PCR) or reverse transcription-PCR (RT-PCR). (See for example, Sambrook et al, 1989.) In one embodiment, the techniques may determine only the presence or absence of the nucleic acid of interest. Alternatively, the techniques may be quantitative, and provide information about the relative amount of the nucleic acid of interest in the sample. For quantitative purposes, quantitative PCR and RT-PCR are preferred. Thus, in one example, RNA is isolated from a sample, and contacted with an oligonucleotide derived from the GIP90/130 polypeptide-encoding nucleic acid sequence, together with reverse transcriptase, under suitable buffer and temperature conditions to produce cDNAs from the GIP90/130 RNA. The cDNA is then subjected to PCR using primer pairs derived from the appropriate nucleic acid sequence disclosed herein. In a preferred embodiment, the primers are designed to detect the presence of the RNA expression product of GIP90/130, and the amount of GIP90/130 gene expression in the sample is compared to the level in a control sample.
For detecting GIP90/130 nucleic acid sequences, standard labeling techniques can be used to label the probe, the nucleic acid of interest, or the complex between the probe and the nucleic acid of interest, including, but not limited to radio-, enzyme-, chemiluminescent-, or avidin or biotin-labeling techniques, all of which are well known in the art. (See, for example, Molecular Cloning: A Laboratory Manual (Sambrook, et al., 1989, Cold Spring Harbor Laboratory Press), Gene Expression Technology (Methods in Enzymology, Vol. 185, edited by D. Goeddel, 1991. Academic Press, San Diego, Calif.); PCR Protocols: A Guide to Methods and Applications (Innis, et al. 1990. Academic Press, San Diego, Calif.)).
Such methods of nucleic acid detection are useful for a variety of purposes, including but not limited to detecting an autoimmune condition, identifying cell division arrest or cell death, identifying cells that express GIP90/130 nucleic acid sequences, in situ hybridization for GIP90/130 gene expression, Northern and Southern blot analysis, and DNA library screening.
As discussed above, GIP90/130 polypeptides are likely to be involved in cell signaling pathways that impair cell division or cause cell death, which are thought to be up-regulated during autoimmune pathogenesis and down-regulated in cancer cells to prevent autoimmune attack during tumor growth. Thus, the detection methods disclosed herein can be used to detect cells that are undergoing such cell death-related processes.
Furthermore, the present invention provides method for treating an autoimmune disorder or cancer comprising modifying the expression or activity of GIP90/130 RNA or GIP90/130 polypeptides, such as by increasing or decreasing their expression or activity. Modifying the expression or activity of GIP90/130 RNA or GIP90/130 polypeptides can be accomplished by using specific inducers or inhibitors of GIP90/130 polypeptide expression or activity, such as GIP90/130 antibodies, polypeptides representing interactive motifs of GIP90/130 such as those disclosed herein, antisense or RNA interference therapy based on the design of antisense oligonucleotides or double stranded RNAs to the GIP90/130 nucleic acid sequences disclosed herein, cell therapy using host cells expressing one or more GIP90/130 polypeptides, or other techniques known in the art. As used herein, “modification of expression or activity” refers to modifying expression or activity of either the RNA or protein product.
For example, knowing that the GIP90/130 gene is a tumor suppressor gene, that aberrantly increased cell death processes are the basis of specific autoimmune pathogenesis (WO 00/50607), and that aggregates of GIP90/130 polypeptides are expressed in a number of human tissues that are common target of autoimmune responses, the administration of GIP90/130 polypeptides or nucleic acids of the invention, particularly those representing essential interactive motifs for GIP90/130 polypeptide aggregation and/or interaction with other cellular components, such as GPBP, would impact pathogenesis and therefore serve as therapeutic agents for autoimmunity. Alternatively, tumor cells express little or no GPBP or GIP90/130, and thus the administration of the GIP90/130 polypeptide or nucleic acid sequences of the invention, particularly the full length GIP90, GIP130a, GIP130b, and/or GIP130c, alone or in combination with GPBP, is expected to provide a therapeutic benefit in patients with cancer.
While not being limited to any specific mechanism of action, it is believed that a therapeutic benefit in cancer patients would be derived by promoting GIP90/130 interactions with other cellular constituents, such as GPBP and/or GIP90/130 aggregation, whereas a therapeutic benefit to autoimmunity patients would be derived by inhibiting these interactions and/or aggregation.
In another aspect, the invention provides methods for modifying GIP90/130 activity comprising contacting cells with an amount effective of one or more of the polypeptides, antibodies, nucleic acids, or pharmaceutical compositions thereof, of the invention to modify GIP90/130 activity. Such cell contacting can be in vitro or in vivo, and “modifying” includes both increasing or decreasing GIP90/130 activity, including transcription-promoting activity.
In another aspect, the invention provides methods for modifying GPBP activity, comprising contacting cells with an amount effective of one or more of the polypeptides, antibodies, nucleic acids, or pharmaceutical compositions thereof, of the invention to modify GPBP activity. Such cell contacting can be in vitro or in vivo, and “modifying” includes both increasing or decreasing GPBP activity. For example, augmented GPBP activity is associated with autoimmunity, and thus the administration of the GIP90/130 polypeptides or antibodies of the invention (or gene therapy by administration of the GIP90/130 nucleic acid sequences or vectors thereof of the invention) would be expected to impact GPBP-GIP90/130 interactions, and to provide a therapeutic benefit in patients with an autoimmune disorder. Alternatively, tumor cells express little or no GPBP, and thus the co-administration of the GIP90/130 polypeptides of the invention, particularly the full length GIP90, GIP130a, GIP130b, and/or GIP130c, in combination with GPBP, would be expected to provide a therapeutic benefit in patients with cancer.
In another aspect, the present invention provides methods for modifying pol κ76 polypeptide activity, comprising contacting cells with an amount effective of one or more of the polypeptides, antibodies, nucleic acids, or pharmaceutical compositions thereof, of the invention to modify pol κ76 activity. Such cell contacting can be in vitro or in vivo, and “modifying” includes both increasing or decreasing pol κ76 activity. For example, augmented pol κ76 activity is associated with autoimmunity (WO 02/46378), and thus the administration of the GIP90/130 polypeptides or antibodies of the invention (or gene therapy by administration of the GIP90/130 nucleic acid sequences or vectors thereof of the invention) would be expected to impact pol κ76-GIP90/130 interactions, and to provide a therapeutic benefit in patients with an autoimmune disorder.
In practicing the therapeutic methods of the invention, the amount or dosage range of the GIP90/130 polypeptides or antibodies thereto generally ranges between about 0.01 μg/kg body weight and about 10 mg/kg body weight, preferably ranging between about 0.10 μg/kg and about 5 mg/kg body weight, and more preferably between about 1 μg/kg and about 5 mg/kg body weight.
In a further aspect, the present invention provides pharmaceutical compositions, comprising an amount effective of the GIP90/130 polypeptides, antibodies thereto, and nucleic acids disclosed herein to carry out one or more of the therapeutic methods of the invention, and a pharmaceutically acceptable carrier. The GIP90/130 polypeptides, or antibodies thereto, may be subjected to conventional pharmaceutical operations such as sterilization and/or may contain conventional adjuvants, such as preservatives, stabilizers, wetting agents, emulsifiers, buffers etc.
For administration, the polypeptides are ordinarily combined with one or more adjuvants appropriate for the indicated route of administration. The compounds may be admixed with lactose, sucrose, starch powder, cellulose esters of alkanoic acids, stearic acid, talc, magnesium stearate, magnesium oxide, sodium and calcium salts of phosphoric and sulphuric acids, acacia, gelatin, sodium alginate, polyvinylpyrrolidine, and/or polyvinyl alcohol, and tableted or encapsulated for conventional administration. Alternatively, the compounds of this invention may be dissolved in saline, water, polyethylene glycol, propylene glycol, carboxymethyl cellulose colloidal solutions, ethanol, corn oil, peanut oil, cottonseed oil, sesame oil, tragacanth gum, and/or various buffers. Other adjuvants and modes of administration are well known in the pharmaceutical art. The carrier or diluent may include time delay material, such as glyceryl monostearate or glyceryl distearate alone or with a wax, or other materials well known in the art.
The polypeptides or pharmaceutical compositions thereof may be administered by any suitable route, including orally, parentally, by inhalation spray, rectally, or topically in dosage unit formulations containing conventional pharmaceutically acceptable carriers, adjuvants, and vehicles. The term parenteral as used herein includes, subcutaneous, intravenous, intra-arterial, intramuscular, intrasternal, intratendinous, intraspinal, intracranial, intrathoracic, infusion techniques or intraperitoneally. In preferred embodiments, the polypeptides are administered intravenously or subcutaneously.
The polypeptides may be made up in a solid form (including granules, powders or suppositories) or in a liquid form (e.g., solutions, suspensions, or emulsions). The polypeptides of the invention may be applied in a variety of solutions. Suitable solutions for use in accordance with the invention are sterile, dissolve sufficient amounts of the polypeptides, and are not harmful for the proposed application.
The present invention may be better understood with reference to the accompanying examples that are intended for purposes of illustration only and should not be construed to limit the scope of the invention, as defined by the claims appended hereto.
EXAMPLES
Identification and Characterization of GIP90/130 Polypeptides
We performed a yeast two-hybrid screening on several human cDNA libraries searching for GPBP-interactive proteins. The screenings were performed using full length GPBP as bait, cloned in vector pGBT9 to generate the GAL4 binding domain-fusion protein. With the resulting construct we transformed yeast HF7c cells to obtain a stably transfected cell line which was subsequently transformed with the different cDNA libraries we have used: Human Skeletal Muscle (pGAD10 vector), Human Kidney (pGAD10), Human Pancreas (pGAD10), Human Brain (pACT2) and Hela (pGADGH) cDNA libraries (all from Clontech). The transformations were carried out according to the supplier's instructions and plated on medium deficient in Trp, Leu and His containing 20 mM 3-amino-1,2,4-triazol. Interactions were assessed following the manufacture's recommendations. Specifically β-galactosidase activity was assayed with X-GAL (0.75 mg/ml) for the lift colony assays and with ortho-nitrophenyl β-D galactopyranoside (0.66 mg/ml) for the in-solution determinations.
We isolated an 800 bp cDNA (“I-20 cDNA”) encompassing an open reading frame (ORF) which encodes a 265 residue polypeptide, I-20 (SEQ ID NO:6); from a human skeletal muscle library. Part of the ORF coincided with the ORF encoding DOC1 (own-regulated in ovarian cancer 1) (GenBank accession NP—055705) (Mok et al., Gynecol. Oncol. 52(2):247–252 (1994)), a polypeptide whose encoding mRNA is not found in ovarian cancer cell lines, but is abundantly expressed in normal ovarian cell lines. For this reason, the DOC-1 gene is considered to be a tumor suppressor gene.
Using the I-20 cDNA, we probed a multi-tissue Northern blot (Clontech) to determine the level of expression of the I-20 encoding mRNA in normal human tissues and in a number of human cancer cell lines. The membranes were hybridized with 32P-α-dCTP labelled I-20 cDNA (SEQ ID NO:5), and specific mRNAs species were identified by autoradiography. We identified four mRNA species of 9, 4.4, 4 and 3 Kb. The species of 9, 4.4 and 3 Kb were more abundant in skeletal muscle, while the 4 Kb species displayed similar expression in skeletal muscle, pancreas and lung, and higher expression in heart tissue. With the exception of heart, which contained traces of the 9, 4.4 and 3 Kb species, the rest of the tissues tested mainly expressed the 4 Kb mRNA species. As expected from previous studies for DOC1, I-20 cDNA did not hybridize significantly to any mRNA species from the individual human cancer cell lines tested (MTN human cancer cell line blot from Clontech), thus confirming I-20 as being encoded by a tumor suppressor gene.
Since the I-20 ORF contained no stop codon and extended 5′ past the ORF proposed for DOC1, we explored the possibility that in skeletal muscle I-20 represents a partial sequence of a larger protein. By probing the corresponding cDNA library with the I-20 cDNA, we isolated and characterized by nucleotide sequencing four overlapping cDNA clones which in total comprise an ORF encoding a predicted 764-amino acid polypeptide of 90 kDa that was named GIP90 (SEQ ID NO:10), for GPBP interacting protein 90 kDa. The existence of GIP90 mRNA was confirmed by isolating and nucleotide sequencing a continuous PCR fragment derived from the same library containing the proposed overlapping ORF. The more remarkable structural features of GIP90 are the presence of two nuclear localization signals (NLS), one in the N terminal region and another at the C terminal region, and a highly predictable coiled-coil formation through most of its sequence including two leucine zippers.
Using the cDNA nucleotide sequence of GIP90 (“GIP90 cDNA”) (SEQ ID NO: 9) we carried out a BLAST search against the human genome and found that GIP90 cDNA matched at chromosome 3 (3q12) (genomic DNA accession numbers NT—030634 for exon I and NT—033050 for the rest of the exons). We determined the exon/intron structure for the GIP90 genomic sequence, which encompass a total of six exons (FIG. 1). Exons I–IV of the GIP90 gene contain 5′ untranslatable sequence and encode the first 201 residues of an N-terminal segment of 240 residues that is absent in DOC1 and DOC1-related protein (GenBank accession number AAH27860). Exon V encodes the remaining 39 residues not present in DOC proteins as well as the additional 524-residues of GIP90, and exon VI contains 3′ untranslatable sequence.
Comparison of the GIP90 cDNA and the GIP90 genomic sequence revealed the existence of an adenine (A) at position 2720 (A2720) in the GIP90 cDNA that was not present in the GIP90 genomic DNA, suggesting that GIP90 cDNA represents either a cDNA artifact, or a native mRNA species that derives from a DNA polymorphism or mRNA editing. Mutational artifacts are generally unique events unlikely to be found in more than one cDNA molecular species. We have identified A2720 in at least two different GIP90 cDNA fragments, representing two different reverse transcription events, and PCR on total cDNA from the human muscle library (Clontech) using a forward primer from exon I and a reverse primer from exon VI, and subsequent direct sequencing, revealed that the resulting cDNA exclusively contained A2720. A homologous nucleotide was also found in a DOC1 encoding sequence, but not in DOC1-related protein encoding sequences. These results indicate that the A2720 in the GIP90 cDNA does not represent an artifact.
In order to further analyze the origin of GIP90 cDNA, we studied the expression of GIP90 in two independent human skeletal muscle tissue samples by RT-PCR. We were unable to amplify GIP90 mRNA from these samples. In contrast, we isolated and characterized a continuous cDNA fragment (SEQ ID NO: 11) representing a related mRNA species that encodes a 130 kDa polypeptide (1135-residues) that we named GIP130a (SEQ ID NO:12). GIP130a results from faithful transcription and translation of the GIP90 genomic sequence (ie: no A2720), suggesting that a specific mechanism for mRNA diversification is responsible for the production of GIP90 encoding mRNA from the GIP90 genomic sequence.
To further explore the mRNA diversification mechanism of the DOC1/GIP90/130 family, we compared the nucleotide sequences encoding DOC1/DOC1-related protein, GIP90, and GIP130a. Several nucleotide differences were identified, namely: (1) DOC-1 and DOC1-related mRNA are devoid of exon I–IV; (2) DOC1 mRNA showed nucleotide deletions of 42- and 18-bp in exon V, and both DOC1 and DOC1-related mRNA contain an additional 276-bp at the 3′ end of this exon, which corresponds to an intron sequence in GIP90/130a; (3) DOC-1 and DOC1-related mRNAs are both devoid of exon VI.
Therefore, it appeared that the expression of exon VI is associated with expression of GIP90/130a mRNAs, and that DOC-1 and DOC1-related mRNAs are exclusively encoded by an intron-extended exon V. The existence of DOC-1 mRNAs containing exons I–IV was then assessed by PCR of mRNA from human skeletal muscle and from human 293 cells. We obtained two different cDNAs (SEQ ID NOS: 13 and 15) both containing exon I–V sequences and DOC-1 exclusive exon V, and diverging with respect to each other in one single nucleotide (A/G) at position 975, which leads to an amino acid change at position 168 (H168/R168). This results in two different 1133-residue long polypeptides (130-kDa) which we named GIP130b (SEQ ID NO: 14) and GIP130c (SEQ ID NO: 16), respectively. A comparison of the amino acid sequences of GIP90/130 polypeptides and the DOC1 polypeptide family is shown in FIG. 3.
The amino acid sequence of rat filamin A-interacting protein (FILFP) (Genbank accession number BAC00851) and hypothetical human KIAA1275 protein (Genbank accession number BAA86589) are highly homologous (approximately 50%) to the GIP90/130 and DOC proteins. This suggests that these genes are related and that FILIP, KIAA1275 and GIP90/130 are likely to share biological functions. Therefore, knowing that FILIP impairs cell migration of cortical neurons (Nature Cell Biology 2002 July; 4(7): 495–501), it is plausible to hypothesize that GIP90/130 polypeptides exert their tumor suppressor activity, at least in part, by impairing cell migration.
The above data demonstrate that the DOC-1/GIP90/130 mRNA family results from a complex diversification mechanism operating on the expression of the corresponding gene (GIP90 genomic sequence). Thus, we have found that the presence of R168 or H168 is the result of a GIP90 genomic sequence polymorphism. The presence of exon V, which is characteristic of GIP90/GIP130a (exon Va), is linked to the expression of exon VI and represents a complex alternative exon splicing in which the alternative use of two 5′ splice sites of an intron is coordinated with the splicing of an alternative 3+ terminal exon. Thus, when the more upstream 5′ splice site is used to yield a shorter exon V (exon Va), the 3′ terminal exon (exon VI) is spliced, whereas when using the more downstream 5′ splice site resulting in a larger exon V (exon Vb), the 3′ terminal exon (exon VI) is not spliced. Regarding A2720, we still are in the process of determining the specific diversification mechanism responsible for its presence. The exon/intron structure of the gene for the DOC-1/GIP90/130 family is shown in FIG. 1 and a scheme for the more relevant features regarding mRNA and protein structure for the GIP family is presented in FIG. 2. Finally, similar genetic diversification mechanisms perhaps are responsible for the deletion of C2708 in DOC1 and an aberrant alternative splicing within long exons (previously described for other genes) appears to account for the 42- and 18-bp deletions found in DOC1 mRNA.
The presence of R168 in GIP90 generates a putative bipartite NLS signal and a consensus for PKA phosphorylation, whereas the presence of A2720 causes a frame-shift in the ORF encoding GIP90, which results in the appearance of a second nuclear localization signal and a premature stop codon. The latter removes a total of 386 residues of the C terminal region that is present in GIP130 proteins. These residues appear to conform to a domain with no predictable coiled-coils containing a number of putative O-glycosylation sites (FIG. 2).
Characterization of GIP90/130 Interactions
Using a yeast two-hybrid system, we found that the four members of the GIP90/130 interact with GPBP, although to a more limited extent than I-20 (SEQ ID NO:6). GIP90 displayed the strongest interaction with GPBP, whereas individual GIP130 proteins interacted similarly with GPBP, although to a lesser extent than GIP90. These data implicate the C-terminal residues of the GIP130 proteins, which are not present in GIP90, and also the C-terminal residues of GIP90 not present in I-20 in a negative modulation of the interaction of GIP90/130 polypeptides with GPBP. Deletion of the N terminal 240-residues of GIP90, GIP130b, and GIP130c resulted in molecular species that do not interact with GPBP, indicating that the N-terminal region contains residues involved in the interaction of GIP90/130 polypeptides with GPBP. All of these findings account for the observation that I-20 (SEQ ID NO: 6), which contains the bulk of this N terminal region (residues 86–240), and does not harbor the inhibitory C terminal regions, displayed the strongest interaction in a two hybrid system with GPBP. The production of additional I-20 deletion mutants and their use in specific two hybrid studies permitted the identification of two specific regions of I-20 that are essential for GPBP interaction as well as the identification of other residues directly involved but not essential for the interaction (FIG. 4).
GIP90/130 polypeptides self-aggregate and aggregate with each other in a yeast two-hybrid assays, indicating that, similarly to GPBP (WO 00/50607), GIP90/130 polypeptides aggregate to form homo and hetero oligomers. No significant differences were found among GIP90/130 full length polypeptides in their ability to self-aggregate. Deletion of the N-terminal 240-residues from GIP130b/c results in DOC1-related protein, which aggregates more efficiently and does not interact with GPBP. Since the deleted residues contain motifs for I-20 self-aggregation, it is conceivable that the deleted region contains residues that are critical for GIP90/130 aggregation, but not for DOC/DOC1-related protein aggregation, and that GIP90/130 polypeptides and DOC1 polypeptides aggregate in a different manner. Since the N terminal 240 residues also contain essential residues for GIP90/130 polypeptide interactions with GPBP, this further suggests that GPBP interaction negatively modulates GIP90/130 polypeptide aggregation but not DOC aggregation. Consistently, two hybrid assays using I-20 deletion mutants show that essential sequences for GIP90/130 interactions with GPBP and for I-20 aggregation overlap extensively (FIG. 4), strongly suggesting that GPBP binding to GIP90/130 polypeptides prevents GIP90/130 polypeptide aggregation but not DOC aggregation. Accordingly, we have observed with a yeast three-hybrid system that GPBP expression efficiently impairs both I-20 and GIP90 aggregation, and that I-20 and GIP90 efficiently impair GPBP aggregation.
Deletion mutants were obtained using specific primers and PCR, followed by cloning of the resulting cDNAs in the pGBT9 and pGAD424 vectors. The assays were performed in SFY526 or HF7c Saccharomyces cerevisiae strains, with pGBT9 as GAL4 binding domain vector and pGAD424 as GAL4 activation domain vector, by the lift colony assay procedure. Briefly, the yeast cells were co-transformed with constructs of both binding domain and activation domain vectors, and the co-transformants were selected in medium deficient in both tryptophan and leucine. After five days of incubation at 30° C. the colonies were tested for the expression of β-galactosidase with X-Gal substrate (0.75 mg/ml). The intensity of the blue color displayed in the assay informed us about the relative strength of the interactions. When the assays were performed with the HF7c strain, the interactions were assessed by the lift colony assay procedure and by growth in medium deficient in histidine, tryptophan and leucine. For yeast three-hybrid system, we used the pBRIDGE vector, which allows the conditional expression of a third protein apart from the usual GAL4 binding and activation domain-fusion proteins of the two-hybrid system. In this case, the expression of GPBP or I-20 or GIP90 was driven by Met25 promoter, active in absence of methionine. In these experiments, the transformed SFY526 cells were plated in medium deficient in tryptophan, leucine and methionine, and subjected to the colony lift assay after five days at 30° C. In the case of the strain HF7c the colonies grown in the cited plates were streaked on medium with the additional deficiency of histidine.
In an attempt to establish the viability of these molecular interactions in human cells, the interaction between GIP90 and GPBP was assessed in a mammalian two-hybrid system using 293 cells. We used the CLONTECH mammalian two hybrid kit, with vectors pM and pRK5-GAL4BD as GAL4 binding domain vectors and pVP16 as activation domain vector. We transfected 293 cells by the calcium phosphate procedure with the appropriate constructs and reporter vectors and the interactions determined by the CAT ELISA kit (Roche), following the manufacturer's instructions.
Finally, using a yeast two hybrid system, we investigated the interactions between pol κ/pol κ76 and GPBP/GPBPΔ26 and we got no positive results. However, when we challenged interaction between pol κ or pol κ76 and I-20, we obtained positive results with pol κ76 but not with pol κ. The positive interaction of I-20 with pol κ76 suggests that GIP90 is a biological bridge between GPBP and pol κ76 and that the three proteins are partners in specific strategies which become deregulated during autoimmune pathogenesis.
From all these data, we conclude that: (1) GIP90/130 polypeptides aggregate in a different manner than DOC/DOC1-related polypeptides; (2) GPBP interacts with GIP90/130 polypeptides and this interaction counteracts GIP90/130 polypeptide aggregation; (3) GPBP does not interact with DOC/DOC1-related proteins, and therefore GPBP is not expected to influence DOC/DOC1-related protein aggregation; (4) I-20 contains essential amino acid sequences involved in GPBP interaction with GIP90/130 polypeptides and in GIP90/130 polypeptide aggregation; (5) the C terminal domain of GIP130 species exerts a negative effect on their interactions with GPBP, and (6) GIP90/130 polypeptides contain sequences not present in I-20 that negatively modulate both GIP90/130 polypeptide interaction with GPBP and GIP90/130 polypeptide aggregation.
Further Characterization of GIP90/130
Given that GPBP is a protein kinase, we assessed the capacity of GPBP to phosphorylate GIP90 in vitro by using purified yeast recombinant counterparts. GIP90 was cloned in pHIL-D2 vector in frame with the FLAG tag at N-terminal position and with a 6 histidine tail at C-terminal position. It was expressed in the Pichia pastoris expression system (Invitrogen) and purified with an affinity resin (Clontech) making profit of the polyhistidine tail, using an 8 M urea-containing breaking buffer, which was eliminated by dialysis against Tris-buffered saline. The purified protein was incubated with yeast recombinant GPBP in a suitable reaction buffer and labelled for 12 hours at 30° C. The phosphorylation mixtures were analysed by Western blot using FLAG-specific antibodies (Sigma) and autoradiography. Incubation of purified GIP90 and GPBP in the presence of [γ32P] ATP resulted in 32P incorporation into GIP90, thus confirming that GPBP interacts with GIP90 and phosphorylates it.
Remarkable structural features of GIP90/130 proteins are (1) the existence of two nuclear localization sequences (NLS) whose presence appears to be regulated by single nucleotide replacement or addition (see above); and (2) the existence of a large number of predictable coiled-coil motifs including two leucine zippers. Consequently we have assayed the ability of GIP90/130 and DOC1-related protein to induce transcription from a heterologous promoter of a reporter gene. This was accomplished by fusing either GIP90, GIP130a, GIP130b or DOC1-related protein to the binding domain of GAL4 transcription factor in a high level expression pAS2-1 vector (Clontech) and transforming SFY526 yeast cells carrying a LacZ reporter gene under the control of a promoter with a GAL4 binding site. Transformants were selected in tryptophan-deficient medium at 30° C. for five days and colony lift assays performed. The GIP90, GIP130a, and GIP130b fusion polypeptides, but not DOC1-related protein fusion polypeptides, efficiently induced expression of LacZ, as estimated by the appearance of β-galactosidase activity.
We have also expressed GIP90 in bacteria, and have used the corresponding recombinant protein to immunize both rabbits and mice to obtain respectively polyclonal and monoclonal antibodies specific for GIP proteins. GIP90 was cloned in pGEX vector, in frame with glutathione-S-transpherase cDNA. The resulting construct was used to transform DH5α cells and expression of the GST-GIP90 fusion protein was induced with IPTG and further purified on glutathione affinity column. GST-GIP90 purified protein was used to immunize both rabbits and mice in order to obtain respectively polyclonal and monoclonal antibodies. These antibodies were used to identify a native protein in 293 cells displaying the same mobility as recombinant GIP130 which likely represents endogenous GIP130b or GIP130c, since exon VI appears to not be expressed in these cells, as determined by specific RT-PCR approaches. One of the monoclonal antibodies (Mab3) maps in the N terminal 240 residues of GIP90, whereas Mab 8 maps within the next 509 residues (i.e.: between residues 241–750).
By indirect immunofluorescence on COS-7 cells transiently expressing recombinant GIP90 we have identified cells that expressed GIP90 in the nucleus, cells expressing GIP90 in the cytosol, and cells that expressed GIP90 in both the nucleus and the cytosol. When these cells co-expressed recombinant GIP90 and GPBP, double indirect immunofluorescence revealed expression of the two proteins at the cytosol and in some cells GIP90 was also detected in the nucleus. We have not seen GIP90 and GPBP being co-expressed in the nucleus. Finally, using confocal microscopy and NIH3T3 or 293 cells, we have confirmed nuclear localization of GIP90 and cytosolic co-localization GIP90/GPBP. These cells do not express detectable levels of GIP90/130 polypeptides, as no significant fluorescence was detected when non-transfected cells were incubated with anti-GIP antibodies and an appropriate secondary antibody. For immunofluorescence and confocal microscopy studies, GIP90 cDNA was cloned in pRK5 mammalian expression vector, and this construct was used alone or co-transfected with GPBP cloned in pCDNA3 vector (Invitrogen), using the DEAE-dextran or calcium phosphate procedures. After 24 hours of incubation at 37° C., the cells were washed with phosphate-buffered saline (PBS), fixed with methanol or methanol:acetone, blocked with 3% BSA in PBS and incubated with a pool of mouse anti-GIP90 monoclonal antibodies and rabbit anti-GPBP polyclonal antibodies. FITC-conjugated anti-mouse IgG and TRITC-conjugated anti-rabbit IgG antibodies were respectively used as secondary antibody.
Finally, we have performed immunohistochemistry studies on paraffin embedded human tissues and have found GIP proteins to localize in a number of cells and structures also expressing GPBP. Immunohistochemistry studies were done on human multi-tissue control slides (Biomeda, Dako), using the ABC peroxidase method. GIP proteins are widely expressed in human tissues, but are more abundantly expressed in some locations. A strong staining is found in smooth muscle cells, particularly in those of vessel walls, with a diffuse cytoplasmic pattern. There is intense expression in alveolar septa, with a linear pattern suggestive of being associated to basement membrane locations, along with cytoplasmic staining of the pneumocytes. The kidneys show expression in the epithelial cells of the tubules, mainly in distant ones, and also in mesangial cells and podocytes of the glomerulus. In the pancreas there is staining in the cells of endocrine Langerhans islets. In the adrenal gland, the cortical cells show higher expression than the medullar cells. In the liver, hepatocytes show expression of the GIP90/130, which is higher at the epithelial cells of the biliary ducts. The white matter of the central nervous system shows diffuse staining with a fibrillar pattern, with presence also found in some neuronal bodies. Expression of the GIP90/130 is also evident at the epithelial cells of the prostate, breast, bronchi and intestine, in striated muscle cells of the myocardium, in secretory cells of the pituitary, and in spermatogonium and Leydig cells in the testicle.
The expression of the GIP90/130 is quite similar to that previously described for GPBP (WO 00/50607), with staining in tissues targeted by autoimmune responses, such as the Langerhans islets (type I diabetes), the white matter of the central nervous system (multiple sclerosis), the biliary ducts (primary biliary cirrhosis), the cortex of the adrenal gland (Addison disease), alveolar septa (Goodpasture syndrome), and spermatogonium (male infertility).
The evidence suggests that GIP90/130 is a family of proteins encoded by a tumor suppressor gene, which display transcription factor activity, and which interact and are phosphorylated by GPBP. Given the role of GPBP in autoimmune pathogenesis and in cancer, GIP90/130 represent a potential therapeutic or therapeutic target in these disorders.

## Claims

1. An isolated polypeptide comprising the amino acid sequence of SEQ ID NO:6.

2. The isolated polypeptide of claim 1 consisting of the amino acid sequence of SEQ ID NO:6.

3. A composition comprising:
a) an isolated polypeptide according to claim 1; and
b) a pharmaceutically acceptable carrier.