# Patent

## Title
Antibodies for oncogenic strains of HPV and methods of their use

## Abstract

The subject invention provides antibodies, including polyclonal and monoclonal antibodies, that bind to E6 proteins from at least three oncogenic strains of HPV. In general, the antibodies bind to amino acids motifs that are conserved between the E6 proteins of different HPV strains, particularly HPV strains 16 and 18. The subject antibodies may be used to detect HPV E6 protein in a sample, and, accordingly, the antibodies find use in a variety of diagnostic applications, including methods of diagnosing cancer. Kits for performing the subject methods and containing the subject antibodies are also provided.

## Background
CROSS-REFERENCE
This application is a continuation application of Ser. No. 13/364,954, filed Feb. 2, 2012, which is a continuation of Ser. No. 12/660,613, filed Mar. 1, 2010, which is a continuation application of Ser. No. 12/156,013, filed May 28, 2008 which is a continuation application Ser. No. 11/021,949, filed Dec. 23, 2004 which claims the benefit of U.S. provisional patent application Ser. No. 60/532,373, filed Dec. 23, 2003, which applications are incorporated herein by reference in their entirety.


SEQUENCE LISTING
The instant application contains a Sequence Lisiting which has been submitted via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCll copy, created on Dec. 17, 2014 is named 34170-702.304_SL.txt and is 316,184 bytes in size.
FIELD OF INVENTION
The present invention relates to detection of oncogenic strains of human papillomavirus (HPV).
BACKGROUND OF THE INVENTION
Cervical cancer is the second most common cancer diagnosis in women and is linked to high-risk human papillomavirus infection 99.7 % of the time. Currently, 12,000 new cases of invasive cervical cancer are diagnosed in US women annually, resulting in 5,000 deaths each year. Furthermore, there are approximately 400,000 cases of cervical cancer and close to 200,000 deaths annually worldwide. Human papillomaviruses (HPVs) are one of the most common causes of sexually transmitted disease in the world. Overall, 50-75 % of sexually active men and women acquire genital HPV infections at some point in their lives. An estimated 5.5 million people become infected with HPV each year in the US alone, and at least 20 million are currently infected. The more than 100 different isolates of HPV have been broadly subdivided into high-risk and low-risk subtypes based on their association with cervical carcinomas or with benign cervical lesions or dysplasias.
A number of lines of evidence point to HPV infections as the etiological agents of cervical cancers. Multiple studies in the 1980's reported the presence of HPV variants in cervical dysplasias, cancer, and in cell lines derived from cervical cancer. Further research demonstrated that the E6-E7 region of the genome from oncogenic HPV 18 is selectively retained in cervical cancer cells, suggesting that HPV infection could be causative and that continued expression of the E6-E7 region is required for maintenance of the immortalized or cancerous state. Further research demonstrated that the E6-E7 genes from HPV 16 were sufficient to immortalize human keratinocytes in culture. It was also demonstrated that although E6-E7 genes from high risk HPVs could transform cell lines, the E6-E7 regions from low risk, or non-oncogenic variants such as HPV 6 and HPV 11 were unable to transform human keratinocytes. HPV 16 and 18 infection was examined by in situ hybridization and E6 protein expression by immunocytochemistry in 623 cervical tissue samples at various stages of tumor progression and found a significant correlation between histological abnormality and HPV infection.
A significant unmet need exists for early and accurate diagnosis of oncogenic HPV infection as well as for treatments directed at the causative HPV infection, preventing the development of cervical cancer by intervening earlier in disease progression. Human papillomaviruses characterized to date are associated with lesions confined to the epithelial layers of skin, or oral, pharyngeal, respiratory, and, most importantly, anogenital mucosae. Specific human papillomavirus types, including HPV 6 and 11, frequently cause benign mucosal lesions, whereas other types such as HPV 16, 18, and a host of other strains, are predominantly found in high-grade lesions and cancer. Individual types of human papillomaviruses (HPV) which infect mucosal surfaces have been implicated as the causative agents for carcinomas of the cervix, breast (Yu et al. (1999) Anticancer Res. 19:55555057-5061; Liu et al. (2001) J. Hum. Virol. 44:329-334), anus, penis, prostate (Dc Villiers et al. (1989) Virology 171:248:253), larynx and the buccal cavity, tonsils (Snijders et al. (1994) J. Gen. Virol. 75 (Pt 10):2769-2775), nasal passage (Trujillo et al. (1996) Virus Genes 12:165-178; Wu et al. (1993) Lancet 341:522-524), skin (Trenfield et al. (1993) Australas. J. Dermatol. 34:71-78), bladder (Baithun et al. (1998) Cancer Surv. 31:17-27), head and neck squamous-cell carcinomas (Braakhuis et al. (2004) J. Natl. Cancer Inst. 96:978-980), occasional periungal carcinomas, as well as benign anogenital warts. The identification of particular HPV types is used for identifying patients with premalignant lesions who are at risk of progression to malignancy. Although visible anogenital lesions are present in some persons infected with human papillomavirus, the majority of individuals with HPV genital tract infection do not have clinically apparent disease, but analysis of cytomorphological traits present in cervical smears can be used to detect HPV infection. Papanicolaou tests are a valuable screening tool, but they miss a large proportion of HPV-infected persons due to the unfortunate false positive and false negative test results. In addition, they are not amenable to worldwide testing because interpretation of results requires trained pathologists.
HPV infection is also associated with Netherton's syndrome (Weber et al. (2001) Br. J. Dermatol. 144:1044-1049) and epidermolysis verruciformis (Rubaie et al. (1998) Int. J. Dermatol. 37:766-771). HPV can also be transmitted to a fetus by the mother (Smith et al. (2004) Sex. Transm. Dis. 31:57-62; Xu et al. (1998) Chin. Med. Sci. J. 13:29-31; Cason et al. (1998) Intervirology 41:213-218).
The detection and diagnosis of disease is a prerequisite for the treatment of disease. Numerous markers and characteristics of diseases have been identified and many are used for the diagnosis of disease. Many diseases are preceded by, and are characterized by, changes in the state of the affected cells. Changes can include the expression of pathogengenes or proteins in infected cells, changes in the expression patterns of genes or proteins in affected cells, and changes in cell morphology. The detection, diagnosis, and monitoring of diseases can be aided by the accurate assessment of these changes. Inexpensive, rapid, early and accurate detection of pathogens can allow treatment and prevention of diseases that range in effect from discomfort to death.
LITERATURE
Literature of interest includes the following references: Zozulya et al., (Genome Biology 2:0018.1-0018.12, 2001; Mombairts (Annu. Rev. Neurosci 22:487-509, 1999); Raming et al., (Nature 361: 353-356, 1993); Belluscio et al., (Neuron 20:69-81, 1988); Ronnet et al., (Annu. Rev. Physiol. 64:189-222, 2002); Lu et al., (Traffic 4:416-533, 2003); Buck (Cell 100:611-618, 2000); Malnic et al., (Cell 96:713-723, 1999); Firestein (Nature 413:211-218, 2001); Zhao et al., (Science 279:237-242, 1998); Touhara et al., (Proc. Natl. Acad. Sci. 96: 4040-4045, 1999); Sklar et al., (J. Biol. Chem 261:15538-15543, 1986); Dryer et al., (TiPS 20:413-417, 1999); Ivic et al., (J Neurobiol. 50:56-68, 2002); Munger (2002) Front. Biosci. 7:d641-9; Glaunsinger (2000) Oncogene 19:5270-80; Gardiol (1999) Oncogene 18:5487-96; Pim (1999) Oncogene 18:7403-8; Meschede (1998) J. Clin. Microbiol. 36:475-80; Kiyono (1997) Proc. Natl. Acad. Sci. 94:11612-6; and Lee (1997) Proc. Natl. Acad. Sci. 94:6670-5; Banks (1987) J. Gen. Virol. 68:1351-1359; Fuchs et al., (Hum. Genet. 108:1-13, 2001); and Giovane et al. (1999) Journal of Molecular Recognition 12:141-152 and published US patent applications 20030143679 and 20030105285; and U.S. Pat. Nos. 6,610,511, 6,492,143 6,410,249, 6,322,794, 6,344,314, 5,415,995, 5753233, 5,876,723, 5,648,459, 6,391,539, 5,665,535 and 4,777,239.
SUMMARY OF THE INVENTION
The subject invention provides antibodies, including polyclonal and monoclonal antibodies, that bind to the E6 proteins from at least three different oncogenic strains of HPV. In general, the antibodies bind to amino acids motifs that are conserved between the E6 proteins of different HPV strains, particularly HPV strains 16 and 18. The subject antibodies may be used to detect HPV E6 protein in a sample, and, accordingly, the antibodies find use in a variety of diagnostic applications, including methods of diagnosing cancer. Kits for performing the subject methods and containing the subject antibodies are also provided.
In certain embodiments, the invention provides an antibody composition comprising a monoclonal antibody that specifically binds to the E6 proteins of at least three (e.g., 4, 5, 6, 7 or 8 or more, usually up to 10 or 12) different oncogenic HPV strains. The antibody composition may comprise a mixture of monoclonal antibodies that specifically bind to the E6 proteins of HPV strains 16, 18, 31, 33 and 45 (e.g., HPV strains 16, 18, 31, 33, 45, 52 and 58, HPV strains 16, 18, 31, 33, 45, 52, 58, 35 and 59 or HPV strains 16, 18, 26, 30, 31, 33, 34, 45, 51, 52, 53, 58, 59, 66, 68 b, 69, 70, 73 and 82, wherein at least one of said monoclonal antibodies specifically binds to the E6 proteins of at least three different oncogenic HPV strains. In certain embodiments, the monoclonal antibody may bind to the E6 proteins of HPV strains 16 and 18, wherein said antibody binds SEQ ID NOS: 1, 3 or 5 of HPV strain 16 E6 and SEQ ID NOS: 2, 4 or 6 of HPV strain 18 E6. In certain embodiments, the monoclonal antibody binds to E6 proteins of HPV strains 16 and 45 or HPV strains 16, 18, 31, 33 and 45.
The invention also provides a method of detecting an HPV E6 protein in a sample. This methods generally involves contacting the subject antibody composition with the sample, and detecting any binding of the antibodies in the composition to the sample, wherein binding of an antibody to the sample indicates the presence of an HPV E6 protein. The sample may be suspected of containing an oncogenic strain of HPV.
The invention also provides a system for detecting the presence of an oncogenic HPV E6 polypeptide in a sample. This system generally comprises a first and a second binding partner for an oncogenic HPV E6 polypeptide, wherein the first binding partner is a PDZ domain protein and said second binding partner is an subject antibody. At least one of said binding partners is attached to a solid support.
The invention also provides a method of detecting the presence of an oncogenic HPV E6 protein in a sample. This method generally comprises: contacting a sample containing an oncogenic HPV E6 protein with a PDZ domain polypeptide; and detecting any binding of the oncogenic HPV E6 protein in said sample to said PDZ domain polypeptide using an subject antibody, wherein binding of the oncogenic HPV E6 protein to said PDZ domain polypeptide indicates the presence of an oncogenic HPV E6 protein in said sample.
The invention also provides a kit containing a subject antibody; and instructions for using the antibody to detect a HPV E6 protein. The kit may also contain a PDZ domain polypeptide.
The invention also provides a peptide of less than 15 amino acids comprising any one of the sequences set forth in Table 1.
INCORPORATION BY REFERENCE
All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.



BRIEF DESCRIPTION OF THE DRAWINGS
The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:
FIG. 1 is an alignment of E6 amino acid sequences from various oncogenic strains of HPV. From top to bottom, the various HPV E6 amino acid sequences are set forth in the sequence listing as SEQ ID NOS: 13-32, respectively. Amino acid sequence from three other oncogenic strains of HPV (strains 34, 67 and 70) are found in the sequence listing as SEQ Ill NOS: 359-361.
FIG. 2 is an alignment of E6 amino acid sequences from a subset of oncogenic strains of HPV shown in FIG. 1. FIG. 2 discloses SEQ ID NOS 15-18, 13 and 28-29, respectively, in order of appearance.
FIG. 3 is a slot western blot showing antibody reactivity with E6 protein.
FIG. 4 is graph showing cross-reactivity of F22-10 D11 monoclonal antibody.



DEFINITIONS
Before the present invention is further described, it is to be understood that this invention is not limited to particular embodiments described, as such may of course vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.
Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.
Throughout this application, various publications, patents and published patent applications are cited. The disclosures of these publications, patents and published patent applications referenced in this application are hereby incorporated by reference in their entirety into the present disclosure. Citation herein by Applicant of a publication, patent, or published patent application is not an admission by Applicant of said publication, patent, or published patent application as prior art.
It must be noted that as used herein and in the appended claims, the singular forms “a”, “and”, and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a sample” includes a plurality of such sample, and reference to “the antibody” includes reference to one or more antibodies and equivalents thereof known to those skilled in the art, and so forth. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely”, “only” and the like in connection with the recitation of claim elements, or the use of a “negative” limitation.
A “biopolymer” is a polymer of one or more types of repeating units, regardless of the source. Biopolymers may be found in biological systems and particularly include polypeptides and polynucleotides, as well as such compounds containing amino acids, nucleotides, or analogs thereof. The term “polynucleotide” refers to a polymer of nucleotides, or analogs thereof, of any length, including oligonucleotides that range from 10-100 nucleotides in length and polynucleotides of greater than 100 nucleotides in length. The term “polypeptide” refers to a polymer of amino acids of any length, including peptides that range from 6-50 amino acids in length and polypeptides that are greater than about 50 amino acids in length.
In most embodiments, the terms “polypeptide” and “protein” are used interchangeably. The term “polypeptide” includes polypeptides in which the conventional backbone has been replaced with non-naturally occurring or synthetic backbones, and peptides in which one or more of the conventional amino acids have been replaced with a non-naturally occurring or synthetic amino acid capable of participating in peptide bonding interactions. The term “fusion protein” or grammatical equivalents thereof is meant a protein composed of a plurality of polypeptide components, that while typically not attached in their native state, typically are joined by their respective amino and carboxyl termini through a peptide linkage to form a single continuous polypeptide. Fusion proteins may be a combination of two, three or even four or more different proteins. The term polypeptide includes fusion proteins, including, but not limited to, fusion proteins with a heterologous amino acid sequence, fusions with heterologous and homologous leader sequences, with or without N-terminal methionine residues; immunologically tagged proteins; fusion proteins with detectable fusion partners, e.g., fusion proteins including as a fusion partner a fluorescent protein, β-galactosidase, luciferase, etc., and the like.
In general, polypeptides may be of any length, e.g., greater than 2 amino acids, greater than 4 amino acids, greater than about 10 amino acids, greater than about 20 amino acids, greater than about 50 amino acids, greater than about 100 amino acids, greater than about 300 amino acids, usually up to about 500 or 1000 or more amino acids. “Peptides” are generally greater than 2 amino acids, greater than 4 amino acids, greater than about 10 amino acids, greater than about 20 amino acids, usually up to about 50 amino acids. In some embodiments, peptides are between 5 and 30 or between 8 and 15 amino acids in length.
The term “capture agent” refers to an agent that binds an analyte through an interaction that is sufficient to permit the agent to bind and concentrate the analyte from a homogeneous mixture of different analytes. The binding interaction is typically mediated by an affinity region of the capture agent. Typical capture agents include any polypeptide, e.g., a PDZ protein, however antibodies may be employed. Capture agents usually “specifically bind” one or more analytes, e.g., an oncogenic E6 protein. Accordingly, the term “capture agent” refers to a molecule or a multi-molecular complex which can specifically bind an analyte, e.g., specifically bind an analyte for the capture agent, with a dissociation constant (KD) of less than about 10−6 M without binding to other targets.
The term “specific binding” refers to the ability of a capture agent to preferentially bind to a particular analyte that is present in a homogeneous mixture of different analytes. Typically, a specific binding interaction will discriminate between desirable and undesirable analytes in a sample, typically more than about 10 to 100-fold or more (e.g., more than about 1000- or 10,000-fold). Typically, the affinity between a capture agent and analyte when they are specifically bound in a capture agent/analyte complex is at least 10−7, at least 10−8 M, at least 10−9 M, usually up to about 10−10 M.
The term “capture agent/analyte complex” is a complex that results from the specific binding of a capture agent with an analyte, i.e., a “binding partner pair”. A capture agent and an analyte for the capture agent will typically specifically bind to each other under “conditions suitable to for specific binding”, where such conditions are those conditions (in terms of salt concentration, pH, detergent, protein concentration, temperature, etc.) which allow for binding to occur between capture agents and analytes to bind in solution. Such conditions, particularly with respect to antibodies and their antigens, are well known in the art (see, e.g., Harlow and Lane (Antibodies: A Laboratory Manual Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989)). Conditions suitable for specific binding typically permit capture agents and target pairs that have a dissociation constant (KD) of less than about 10−6 M to bind to each other, but not with other capture agents or targets.
As used herein, “binding partners” and equivalents refer to pairs of molecules that can be found in a capture agent/analyte complex, i.e., exhibit specific binding with each other.
The phrase “surface-bound capture agent” refers to a capture agent that is immobilized on a surface of a solid substrate, where the substrate can have a variety of configurations, e.g., a sheet, bead, strip, or other structure, such as a plate with wells.
The term “pre-determined” refers to an element whose identity is known prior to its use. For example, a “pre-determined analyte” is an analyte whose identity is known prior to any binding to a capture agent. An element may be known by name, sequence, molecular weight, its function, or any other attribute or identifier. In some embodiments, the term “analyte of interest”, i.e., an known analyte that is of interest, is used synonymously with the term “pre-determined analyte”.
The terms “antibody” and “immunoglobulin” are used interchangeably herein to refer to a type capture agent that has at least an epitope binding domain of an antibody. These terms are well understood by those in the field, and refer to a protein containing one or more polypeptides that specifically binds an antigen. One form of antibody constitutes the basic structural unit of an antibody. This form is a tetramer and consists of two identical pairs of antibody chains, each pair having one light and one heavy chain. In each pair, the light and heavy chain variable regions are together responsible for binding to an antigen, and the constant regions are responsible for the antibody effector functions.
The recognized immunoglobulin polypeptides include the kappa and lambda light chains and the alpha, gamma (IgG1, IgG2, IgG3, IgG4), delta, epsilon and mu heavy chains or equivalents in other species. Full-length immunoglobulin “light chains” (of about 25 kDa or about 214 amino acids) comprise a variable region of about 110 amino acids at the NH2-terminus and a kappa or lambda constant region at the COOH-terminus. Full-length immunoglobulin “heavy chains” (of about 50 kDa or about 446 amino acids), similarly comprise a variable region (of about 116 amino acids) and one of the aforementioned heavy chain constant regions, e.g., gamma (of about 330 amino acids).
The terms “antibodies” and “immunoglobulin” include antibodies or immunoglobulins of any isotype, fragments of antibodies which retain specific binding to antigen, including, but not limited to, Fab, Fv, scFv, and Fd fragments, chimeric antibodies, humanized antibodies, single-chain antibodies, and fusion proteins comprising an antigen-binding portion of an antibody and a non-antibody protein. The antibodies may be detectably labeled, e.g., with a radioisotope, an enzyme which generates a detectable product, a fluorescent protein, and the like. The antibodies may be further conjugated to other moieties, such as members of specific binding pairs, e.g., biotin (member of biotin-avidin specific binding pair), and the like. The antibodies may also be bound to a solid support, including, but not limited to, polystyrene plates or beads, and the like. Also encompassed by the terms are Fab′, Fv, F(ab′)2, and or other antibody fragments that retain specific binding to antigen.
Antibodies may exist in a variety of other forms including, for example, Fv, Fab, and (Fab′)2, as well as bi-functional (i.e. bi-specific) hybrid antibodies (e.g., Lanzavecchia et al., Eur. J. Immunol. 17, 105 (1987)) and in single chains (e.g., Huston et al., Proc. Natl. Acad. Sci. U.S.A., 85, 5879-5883 (1988) and Bird et al., Science, 242, 423-426 (1988), which are incorporated herein by reference). (See, generally, Hood et al, Immunology, Benjamin, N.Y., 2 nd ed. (1984), and Hunkapiller and Hood, Nature, 323, 15-16 (1986). Monoclonal antibodies, polyclonal antibodies, and “phage display” antibodies are well known in the art and encompassed by the term “antibodies”.
The term “mixture”, as used herein, refers to a combination of elements, e.g., capture agents or analytes, that are interspersed and not in any particular order. A mixture is homogeneous and not spatially separable into its different constituents. Examples of mixtures of elements include a number of different elements that are dissolved in the same aqueous solution, or a number of different elements attached to a solid support at random or in no particular order in which the different elements are not specially distinct. In other words, a mixture is not addressable. To be specific, an array of capture agents, as is commonly known in the art, is not a mixture of capture agents because the species of capture agents are spatially distinct and the array is addressable.
“Isolated” or “purified” general refers to isolation of a substance (compound, polynucleotide, protein, polypeptide, polypeptide composition) such that the substance comprises the majority percent of the sample in which it resides. Typically in a sample a substantially purified component comprises 50 %, preferably 80 %-85 %, more preferably 90-95 % of the sample. Techniques for purifying polynucleotides and polypeptides, e.g., antibodies, of interest are well-known in the art and include, for example, ion-exchange chromatography, affinity chromatography and sedimentation according to density.
The term “assessing” refers to any form of measurement, and includes determining if an element is present or not. The terms “determining”, “measuring”, “evaluating”, “assessing” and “assaying” are used interchangeably and include both quantitative and qualitative determinations. Assessing may be relative or absolute. “Assessing the presence of” includes determining the amount of something present, as well as determining whether it is present or absent.
The term ‘marker” or “biological marker”, as used herein, refers to a measurable or detectable entity in a biological sample. Examples or markers include nucleic acids, proteins, or chemicals that are present in biological samples. One example of a marker is the presence of viral or pathogen proteins or nucleic acids in a biological sample from a human source.
The term “sample” as used herein relates to a material or mixture of materials, typically, although not necessarily, in fluid form, i.e., aqueous, containing one or more components of interest. Samples may be derived from a variety of sources such as from food stuffs, environmental materials, a biological sample or solid, such as tissue or fluid isolated from an individual, including but not limited to, for example, plasma, serum, spinal fluid, semen, lymph fluid, the external sections of the skin, respiratory, intestinal, and genitourinary tracts, tears, saliva, milk, blood cells, tumors, organs, and also samples of in vitro cell culture constituents (including but not limited to conditioned medium resulting from the growth of cells in cell culture medium, putatively virally infected cells, recombinant cells, and cell components). The term “biological sample” is meant to distinguish between a sample in a clinical setting from a sample that may be a recombinant sample or derived from a recombinant sample.
Components in a sample are termed “analytes” herein. In many embodiments, the sample is a complex sample containing at least about 102, 5×102, 103, 5×103, 104, 5×104, 105, 5×105, 106, 5×106, 107, 5×107, 108, 109, 1010, 1011, 1012 or more species of analyte.
The term “analyte” is used herein interchangeably and refers to a known or unknown component of a sample, which will specifically bind to a capture agent if the analyte and the capture agent are members of a specific binding pair. In general, analytes are biopolymers, i.e., an oligomer or polymer such as an oligonucleotide, a peptide, a polypeptide, an antibody, or the like. In this case, an “analyte” is referenced as a moiety in a mobile phase (typically fluid), to be detected by a “capture agent” which, in some embodiments, is bound to a substrate, or in other embodiments, is in solution. However, either of the “analyte” or “capture agent” may be the one which is to be evaluated by the other (thus, either one could be an unknown mixture of analytes, e.g., polypeptides, to be evaluated by binding with the other).
A “fusion protein” or “fusion polypeptide” as used herein refers to a composite protein, i.e., a single contiguous amino acid sequence, made up of two (or more) distinct, heterologous polypeptides that are not normally fused together in a single amino acid sequence. Thus, a fusion protein can include a single amino acid sequence that contains two entirely distinct amino acid sequences or two similar or identical polypeptide sequences, provided that these sequences are not normally found together in the same configuration in a single amino acid sequence found in nature. Fusion proteins can generally be prepared using either recombinant nucleic acid methods, i.e., as a result of transcription and translation of a recombinant gene fusion product, which fusion comprises a segment encoding a polypeptide of the invention and a segment encoding a heterologous protein, or by chemical synthesis methods well known in the art.
An “oncogenic HPV strain” is an HPV strain that is known to cause cervical cancer as determined by the National Cancer Institute (NCI, 2001). “Oncogenic E6 proteins” are E6 proteins encoded by the above oncogenic HPV strains. The sequences of exemplary oncogenic E6 proteins of interest are shown in FIG. 1. The sequences of various HPV proteins are also found as database entries at NCBI's Genbank database, as follows: HPV16-E6: GI:9627100; HPV18-E6: GI:9626069; HPV31-E6: GI:9627109; HPV35-E6: GI:9627127; HPV30-E6: GI:9627320; HPV39-E6: GI:9627165; HPV45-E6: GI:9627356; HPV51-E6: GI:9627155; HPV52-E6: 01:9627370; HPV56-E6: GI:9627383; HPV59-E6: GI:9627962; HPV58-E6: GI:9626489; HPV33-E6: GI:9627118; HPV66-E6: GI:9628582; HPV68b-E6: GI:184383; HPV69-E6: GI:9634605; HPV26-E6: GI:396956; HPV53-E6: GI:9627377; HPV73: GI:1491692; HPV82: GI:9634614, HPV34 GI:396989; HPV67 GI:3228267; and HPV70 GI:1173493.
An “oncogenic E6 protein binding partner” can be any molecule that specifically hinds to an oncogenic E6 protein. Suitable oncogenic E6 protein binding partners include a PDZ domain (as described below), antibodies against oncogenic E6 proteins (such as those described below); other proteins that recognize oncogenic E6 protein (e.g., p53, E6-AP or E6-BP); DNA (i.e., cruciform DNA); and other partners such as aptamers. In some embodiments, detection of more than 1 oncogenic E6 protein (e.g., all oncogenic E6 proteins, E6 proteins from HPV strains 16 and 18, or E6 proteins from HPV strains 16 and 45 etc.) is desirable, and, as such, an oncogenic E6 protein binding partner may be antibody that binds to these proteins, as described below, or a mixture of antibodies that each bind to a different proteins. As is known in the art, such binding partners may be labeled to facilitate their detection. In general, binding partner bind E6 with an binding affinity of less then 10−5 M, e.g., less than 10−6, less than 10−7, less than 10−8 M (e.g., less than 10−9 M, 10−10, 10−11, etc.).
As used herein, the term “PDZ domain” refers to protein sequence of less than approximately 90 amino acids, (i.e., about 80-90, about 70-80, about 60-70 or about 50-60 amino acids), characterized by homology to the brain synaptic protein PSD-95, the Drosophila septate junction protein Discs-Large (DLG), and the epithelial tight junction protein ZO1 (ZO1). PDZ domains are also known as Discs-Large homology repeats (“DHRs”) and GLGF(SEQ ID NO: 362) repeats. PDZ domains generally appear to maintain a core consensus sequence (Doyle, D. A., 1996, Cell 85: 1067-76).
PDZ domains are found in diverse membrane-associated proteins including members of the MAGUK family of guanylate kinase homologs, several protein phosphatases and kinases, neuronal nitric oxide synthase, tumor suppressor proteins, and several dystrophin-associated proteins, collectively known as syntrophins.
Exemplary PDZ domain-containing proteins and PDZ domain sequences are shown in TABLE 2 The term “PDZ domain” also encompasses variants (e.g., naturally occurring variants) of the sequences (e.g., polymorphic variants, variants with conservative substitutions, and the like) and domains from alternative species (e.g. mouse, rat). Typically, PDZ domains are substantially identical to those shown in U.S. patent application Ser. Nos. 09/724,553 and 10/938,249), e.g., at least about 70 %, at least about 80 %, or at least about 90 % amino acid residue identity when compared and aligned for maximum correspondence. It is appreciated in the art that PDZ domains can be mutated to give amino acid changes that can strengthen or weaken binding and to alter specificity, yet they remain PDZ domains (Schneider et al., 1998, Nat. Biotech. 17:170-5). Unless otherwise indicated, a reference to a particular PDZ domain (e.g. a MAGI-1 domain 2) is intended to encompass the particular PDZ domain and HPV E6-binding variants thereof. In other words, if a reference is made to a particular PDZ domain, a reference is also made to variants of that PDZ domain that bind oncogenic E6 protein of HPV, as described below. In this respect it is noted that the numbering of PDZ domains in a protein may change. For example, the MAGI-1 domain 2, as referenced herein, may be referenced as MAGI-1 domain 1 in other literature. As such, when a particular PDZ domain of a protein is referenced in this application, this reference should be understood in view of the sequence of that domain, as described herein, particularly in the sequence listing. Table 2 shows the relationship between the sequences of the sequence listing and the names and Genbank accession numbers for various domains, where appropriate. Further description of PDZ proteins, particularly a description of MAGI-1 domain 2 protein, is found in Ser. No. 10/630,590, filed Jul. 29, 2003 and published as US20040018487. This publication is incorporated by reference herein in its entirety for all purposes.
As used herein, the term “PDZ protein” refers to a naturally occurring protein containing a PDZ domain. Exemplary PDZ proteins include CASK, MPP1, DLG1, DLG2, PSD95, NeDLG, TIP-33, SYN1a, LDP, LIM, LIMK1, LIMK2, MPP2, NOS1, AF6, PTN-4, prIL16, 41.8 kD, KIAA0559, RGS12, KIAA0316, DVL1, TIP-40, TIAM1, MINT1, MAGI-1, MAGI-2, MAGI-3, KIAA0303, CBP, MINT3, TIP-2, KIAA0561, and TIP-1.
As used herein, the term “PL protein” or “PDZ Ligand protein” refers to a protein that forms a molecular complex with a PDZ-domain, or to a protein whose carboxy-terminus, when expressed separately from the full length protein (e.g., as a peptide fragment of 4-25 residues, e.g., 8, 10, 12, 14 or 16 residues), forms such a molecular complex. The molecular complex can be observed in vitro using a variety of assays described infra.
As used herein, a “PL sequence” refers to the amino acid sequence of the C-terminus of a PL protein (e.g., the C-terminal 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 20 or 25 residues) (“C-terminal PL sequence”) or to an internal sequence known to bind a PDZ domain (“internal PL sequence”).
As used herein, a “PL fusion protein” is a fusion protein that has a PL sequence as one domain, typically as the C-terminal domain of the fusion protein. An exemplary PL fusion protein is a tat-PL sequence fusion.
In the case of the PDZ domains described herein, a “HPV E6-binding variant” of a particular PDZ domain is a PDZ domain variant that retains HPV E6 PDZ ligand binding activity. Assays for determining whether a PDZ domain variant binds HPV E6 are described in great detail below, and guidance for identifying which amino acids to change in a specific PDZ domain to make it into a variant may be found in a variety of sources. In one example, a PDZ domain may be compared to other PDZ domains described herein and amino acids at corresponding positions may be substituted, for example. In another example, the sequence a PDZ domain of a particular PDZ protein may be compared to the sequence of an equivalent PDZ domain in an equivalent PDZ protein from another species. For example, the sequence of a PDZ domain from a human PDZ protein may be compared to the sequence of other known and equivalent PDZ domains from other species (e.g., mouse, rat, etc.) and any amino acids that are variant between the two sequences may be substituted into the human PDZ domain to make a variant of the PDZ domain. For example, the sequence of the human MAGI-1 PDZ domain 2 may be compared to equivalent MAGI-1 PDZ domains from other species (e.g. mouse Genbank gi numbers 7513782 and 28526157 or other homologous sequences) to identify amino acids that may be substituted into the human MAGI-1-PDZ domain to make a variant thereof. Such method may be applied to any of the MAGI-1 PDZ domains described herein. Minimal MAGI-PDZ domain 2 sequence is provided as SEQ ID NOS:68-76. Particular variants may have 1, up to 5, up to about 10, up to about 15, up to about 20 or up to about 30 or more, usually up to about 50 amino acid changes as compared to a sequence set forth in the sequence listing. Exemplary MAGI-1 PDZ variants include the sequences set forth in SEQ ID NOS: 76-105. In making a variant, if a GFG motif is present in a PDZ domain, in general, it should not be altered in sequence.
In general, variant PDZ domain polypeptides have a PDZ domain that has at least about 70 or 80 %, usually at least about 90 %, and more usually at least about 98 % sequence identity with a variant PDZ domain polypeptide described herein, as measured by BLAST 2.0 using default parameters, over a region extending over the entire PDZ domain.
As used herein, a “detectable label” has the ordinary meaning in the art and refers to an atom (e.g., radionuclide), molecule (e.g., fluorescein), or complex, that is or can be used to detect (e.g., due to a physical or chemical property), indicate the presence of a molecule or to enable binding of another molecule to which it is covalently bound or otherwise associated. The term “label” also refers to covalently bound or otherwise associated molecules (e.g., a biomolecule such as an enzyme) that act on a substrate to produce a detectable atom, molecule or complex. Detectable labels suitable for use in the present invention include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Labels useful in the present invention include biotin for staining with labeled streptavidin conjugate, magnetic beads (e.g., DynabeadsTM), fluorescent dyes (e.g., fluorescein, Texas red, rhodamine, green fluorescent protein, enhanced green fluorescent protein, and the like), radiolabels (e.g., 3 H, 125 I, 35 S, 14 C, or 32 P), enzymes (e.g., hydrolases, particularly phosphatases such as alkaline phosphatase, esterases and glycosidases, or oxidoreductases, particularly peroxidases such as horse radish peroxidase, and others commonly used in ELISAs), substrates, cofactors, inhibitors, chemiluminescent groups, chromogenic agents, and colorimetric labels such as colloidal gold or colored glass or plastic (e.g., polystyrene, polypropylene, latex, etc.) beads. Patents disclosing such labels include U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149; and 4,366,241. Means of detecting such labels are well known to those of skill in the art.
As used herein, the terms “sandwich”, “sandwich ELISA”, “Sandwich diagnostic” and “capture ELISA” all refer to the concept of detecting a biological polypeptide with two different test agents. For example, a PDZ protein could be directly or indirectly attached to a solid support. Test sample could be passed over the surface and the PDZ protein could bind its cognate PL protein(s). A labeled antibody or alternative detection reagent could then be used to determine whether a specific PL protein had bound the PDZ protein.
By “solid phase support” or “carrier” is intended any support capable of binding polypeptide, antigen or antibody. Well-known supports or carriers, include glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides, agaroses, and magnetite. The nature of the carrier can be either soluble to some extent or insoluble for the purposes of the present invention. The support material can have virtually any possible structural configuration so long as the coupled molecule is capable of binding to a PDZ domain polypeptide or an E6 antibody. Thus, the support configuration can be spherical, as in a bead, or cylindrical, as in the inside surface of a test tube, or the external surface of a rod. Alternatively, the surface can be flat, such as a sheet, culture dish, test strip, etc. Those skilled in the art will know many other suitable carriers for binding antibody, peptide or antigen, or can ascertain the same by routine experimentation.
In some embodiments “proteasome inhibitors”, i.e., inhibitors of the proteasome, may be used. These inhibitors, including carbobenzoxyl-leucinyl-leuciny-I norvalinal II (MG 115) or CBZ-LLL, can be purchased from chemical supply companies (e.g., Sigma). As a skilled person would understand, proteasome inhibitors are not protease inhibitors.
As used herein, a “plurality” of components has its usual meaning. In some embodiments, the plurality is at least 5, and often at least 25, at least 40, or at least 60 or more, usually up to about 100 or 1000.
Reference to an “amount” of a E6 protein in these contexts is not intended to require quantitative assessment, and may be either qualitative or quantitative, unless specifically indicated otherwise.
The term “non-naturally occurring” or “recombinant” means artificial or otherwise not found in nature. Recombinant cells usually contain nucleic acid that is not usually found in that cell, recombinant nucleic acid usually contain a fusion of two or more nucleic acids that is not found in nature, and a recombinant polypeptide is usually produced by a recombinant nucleic acid.
“Subject”, “individual,” “host” and “patient” are used interchangeably herein, to refer to any animal, e.g., mammal, human or non-human. Generally, the subject is a mammalian subject. Exemplary subjects include, but are not necessarily limited to, humans, non-human primates, mice, rats, cattle, sheep, goats, pigs, dogs, cats, birds, deer, elk, rabbit, reindeer, deer, and horses, with humans being of particular interest.
DETAILED DESCRIPTION OF THE INVENTION
While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.
The subject invention provides antibodies, including polyclonal and monoclonal antibodies, that bind to E6 proteins from at least three oncogenic strains of HPV. In general, the antibodies bind to amino acid motifs that are conserved between the E6 proteins of different HPV strains, particularly HPV strains 16 and 18. The subject antibodies may be used to detect HPV E6 protein in a sample, and, accordingly, the antibodies find use in a variety of diagnostic applications, including methods of diagnosing cancer. Kits for performing the subject methods and containing the subject antibodies are also provided.
In further describing the invention in greater detail than provided in the Summary and as informed by the Background and Definitions provided above, the subject antibodies are described first, followed by a description of methods in which the subject antibodies find use. Finally, kits for performing the subject methods are described.
Antibody Compositions
The invention provides antibodies, particularly monoclonal antibodies, that bind to E6 proteins of multiple strains of HPV. In other words, the invention provides antibodies that “recognize”, i.e., specifically bind to with KD of 10−6 M or less, multiple E6 proteins. In other words, the subject antibodies each bind to (i.e., cross-react with) a plurality of different E6 proteins (i.e., at least 2, at least 3, at least 4, at least 5, at least 6 or at least 10, usually up to about 12, 15 or 20 or more different E6 proteins) from oncogenic, and, in certain embodiments, non-oncogenic strains of HPV. In general, the subject antibodies bind to amino acid motifs that are conserved between the E6 proteins of different HPV strains, and, accordingly, bind to E6 proteins that have this motif. In many embodiments the antibodies bind at least the E6 proteins of HPV strains 16 and 18 (e.g. the E6 proteins of HPV strains 16, 18, 31, 33 and 45; 16, 18 and 45; or, in other embodiments, the E6 proteins of all of the HPV strains listed in FIG. 1 or 2). In other embodiments, the antibodies bind to at least the E6 proteins from HPV strains 16 and 45. The subject antibodies may bind E6 protein from non-oncogenic strains of HPV (e.g., HPV strains 6 and/or 11) and, accordingly, the subject antibodies may bind to E6 proteins from oncogenic, as well as non-oncogenic, strains of HPV.
The subject antibodies may specifically bind to one of three sequence motifs found in HPV E6 proteins. These motifs are boxed in FIG. 1, and generally correspond to regions of sequence similarity between E6 proteins from different strains of HPV. In general, therefore, a subject antibody binds to peptides having the following sequence: FQDPQERPRKLPQLCTELQTTIHDI (SEQ ID NO:1) and FEDPTRRPYKLPDLCTELNTSLQDI (SEQ ID NO:2), corresponding to a first common sequence motif in the E6 proteins of HPV strains 16 and 18, respectively, LLIRCINCQKPLCPEEKQRHLDK (SEQ ID NO:3) and LLIRCLRCQKPLNPAEKLRHLNE (SEQ ID NO:4), corresponding to a second common sequence motif in the E6 proteins of HPV strains 16 and 18, respectively, or RHLDKKQRFHNIRGRWTGRCMSCC (SEQ ID NO:5) and RHLNEKRRFHNIAGHYRGQCHSCC (SEQ ID NO:6) corresponding to a third common sequence motif in the E6 proteins of HPV strains 16 and 18, respectively. If a subject antibody binds to other E6 proteins, then it usually binds to the other E6 proteins at positions equivalent to those discussed above, or boxed in FIG. 1, where “positions equivalent to” generally means a stretch of contiguous amino acids that correspond to, i.e., are aligned with, the boxed amino acids when the sequence of the other E6 proteins are with those in FIG. 1.
Accordingly, since antibodies generally recognize motifs smaller than those listed above, a subject antibody may recognize peptides that are smaller than and contained within the motifs described above. For example, a subject antibody may bind to a peptide having any 9 contiguous amino acids set forth in any one of SEQ NOS:1-6. In particular, a subject antibody may recognize the sequences RPRKLPQLCTEL (SEQ ID NO:7) and RPYKLPDLCTEL (SEQ ID NO:8), corresponding to sub-sequences of the first common sequences of E6 proteins of HPV strains 16 and 18, described above, LLIRCINCQKPL (SEQ ID NO:9) and LLIRCLRCQKPL (SEQ ID NO:10) corresponding to sub-sequences of the second common sequences of E6 proteins of HPV strains 16 and 18, as described above, or RHLDKKQRFHNI (SEQ ID NO:11) and RHLNEKRRFHNI (SEQ ID NO:12) corresponding to sub-sequences of the third common sequences of E6 proteins of HPV strains 16 and 18, as described above. Since these sub-sequences are generally conserved between different E6 proteins, as discussed above, antibodies that bind to the above-recited sequences generally bind to E6 proteins from other HPV strains.
In certain alternative embodiments, the subject antibodies will bind to E6 proteins from HPV strains 16 and 45. In general, therefore, a subject antibody binds to peptides having the following sequence: FQDPQERPRKLPQLCTELQTTIHDI (SEQ ID NO:1) and FDDPKQRPYKLPDLCTELNTSLQDV (SEQ ID NO:57), corresponding to a first common sequence motif in the E6 proteins of HPV strains 16 and 45, respectively, LLIRCINCQKPLCPEEKQRHLDK (SEQ ID NO:3) and LLIRCLRCQKPLNPAEKRRHLKD (SEQ ID NO: 58), corresponding to a second common sequence motif in the E6 proteins of HPV strains 16 and 45, respectively, or RHLDKKQRFHNIRGRWTGRCMSCC (SEQ ID NO:5) and RHLKDKRRFHSIAGQYRGQCNTCC (SEQ ID NO:59) corresponding to a third common sequence motif in the E6 proteins of HPV strains 16 and 45, respectively. If a subject antibody binds to other E6 proteins, then it usually binds to the other E6 proteins at positions equivalent to those discussed above, or boxed in FIG. 1. For example, the E6 proteins from HPV58, HPV33, HPV52, HPV31, HPV16, HPV18 and HPV45 are shown in FIG. 2, and the above-referenced motifs are boxed therein.
Accordingly, since antibodies generally recognize motifs smaller than those listed above, a subject antibody may recognize peptides that are smaller than and contained within the motifs described above. For example, a subject antibody may bind to a peptide having any 9 contiguous amino acids set forth in any one of SEQ NOS: 1, 3, 5, 57, 58 and 59. In particular, a subject antibody may recognize the sequences RPRKLPQLCTEL (SEQ ID NO:7) and RPYKLPDLCTEL (SEQ ID NO:60), corresponding to sub-sequences of the first common sequences of E6 proteins of HPV strains 16 and 45, described above, LLIRCINCQKPL (SEQ ID NO:9) and LLIRCLRCQKPL (SEQ ID NO: 61) corresponding to sub-sequences of the second common sequences of E6 proteins of HPV strains 16 and 45, as described above, or RHLDKKQRFHNI (SEQ ID NO:11) and RHLKDKRRFHSI (SEQ ID NO: 62) corresponding to sub-sequences of the third common sequences of E6 proteins of HPV strains 16 and 45, as described above. Since these sub-sequences are generally conserved between different E6 proteins, as discussed above, antibodies that bind to the above-recited sequences generally bind to E6 proteins from other HPV strains. In certain embodiments, cysteine residues can be replaced by serine residues to avoid disulfide bridge formation.
Methods for making antibodies, particular monoclonal antibodies, are well known in the art and described in various well known laboratory manuals (e.g., Harlow et al., Antibodies: A Laboratory Manual, First Edition (1988) Cold spring Harbor, N.Y.; Harlow and Lane, Using Antibodies: A Laboratory Manual, CSHL Press (1999) and Ausubel, et al., Short Protocols in Molecular Biology, 3 rd ed., Wiley & Sons, (1995)). Accordingly, given the peptide sequences set forth above and in the accompanying tables, methods for making the subject antibodies do not need to be described herein in any great detail. Any fragment of a longer full-length E6 protein that contains a subject common motif (e.g., the full length protein), a full length E6 protein, or a fusion protein thereof may be used to make the subject antibodies. In certain embodiments, a full length E6 protein, a peptide containing a recited sequence, or a chemically modified (e.g., conjugated) derivative or fusion thereof (e.g., a MBP or GST fusion), may be used as an antigen. In certain embodiments, a nucleic acid encoding the polypeptide may be employed, or a mixture of different polypeptides (e.g., a mixture of E6 polypeptides, each polypeptide from a different HPV strain) may be used as an antigen (Michel (2002) Vaccine 20:A83-A88). Accordingly an antigen is mixed with an adjuvant, and a suitable non-human animal (e.g., a mouse, chicken, goat, rabbit, hamster, horse, rat or guinea pig, etc.) is immunized using standard immunization techniques (e.g., intramuscular injection) and once a specific immune response of the has been established, blood from the animal may be collected and polyclonal antisera that specifically binds to described peptides may be isolated. In many cases, cells from the spleen of the immunized animal are fused with a myeloma cell line, and, after fusion, the cells are grown in selective medium containing e.g., hypoxanthine, aminopterin, and thymidine (HAT), to select for hybridoma growth, and after 2-3 weeks, hybridoma colonies appear. Supernatants from these cultured hybridoma cells are screened for antibody secretion, usually by enzyme-linked immunosorbent assay (ELISA) or the like, and positive clones secreting monoclonal antibodies specific for the antigen can be selected and expanded according to standard procedures.
Exemplary peptides suitable for immunizations are described in Table 1. The peptides are shown as a “consensus” sequence (i.e. peptides in which one of several amino acids may exist at one or more positions) in order to indicate that any one or a mixture of different peptides that are described by the consensus could be used to make the subject antibodies. Accordingly, when a consensus sequence is described, every individual peptide that falls within the consensus should be considered explicitly described. In particular embodiments, exemplary species of peptide encompassed by the consensus sequences have a sequence found in a naturally-occurring HPV E6 protein, such as those described in FIG. 1. Such exemplary sequences can be identified as sequences starting at the amino acid positions defined by the third column of Table 1, “Starting AA” of particular HPV types “HPV type”, and corresponding positions of other HPV E6 proteins (i.e., those positions that are aligned with the positions indicated in Table 1).
Accordingly, peptides having 9, 10, 11, 12, 13, 14, 15 or more, usually up to about 20 or more contiguous amino acids of any of the peptides described above may be used for immunizations. In some embodiments, a recited peptide sequence may be contained within a larger peptide that may be 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more, sometimes up to about 15 or 20 or more amino acids greater in size than a recited polypeptide. Accordingly, a subject peptide may be from about 8 to about 30 amino acids in length. In certain embodiments, a subject peptide is about 9-20 amino acids in length, and usually contains an amino acid sequence described above.
Accordingly, depending on the antibodies desired, a suitable animal is immunized with a subject peptide or a mixture of subject peptides (e.g., a mixture of 2, 3, 4, 5 about 6 or more, about 10 or more or about 15 or more, usually up to about 20 or 30 or more peptides described above). Antibodies are usually isolated from the animal and tested for binding to different HPV E6 proteins using standard methods (e.g., ELISA, western blot, etc.). In many embodiments, therefore, antibodies will be screened for binding to E6 proteins from HPV strains 16 and 18, HPV strains 16, 18, 31, 33 and 45, or, in certain embodiments, all of the HPV strains shown in FIG. 1 or 2, and maybe others. Accordingly, antibodies that bind to, i.e., cross-react with, E6 proteins from more than one strain of HPV may be identified, and permanent cell lines producing those antibodies may be established using known methods. In other words, antibodies are usually tested for binding to more than one antigen, and those antigens are usually E6 proteins from various HPV strains, or fragments thereof. In most embodiments, the antibodies will be tested for binding to antigens in native and denatured states. Antibodies that bind to a plurality of E6 proteins have desirable binding properties, and, accordingly, find use in the subject methods.
As is well known in the art, the subject antibodies may be conjugated to a detectable label, or may be part of a signal generating system, as described above.
Accordingly, using the methods set forth above, an antibody composition for detecting a plurality of HPV E6 proteins is provided. In certain embodiments, a mixture of different antibodies that recognize at least 5, 7, 9, 12, 15, 20 or 24 different strains of HPV may be employed. The composition may contain at least one antibody that recognizes at least 3 different oncogenic E6 proteins. The composition may contain 1, 2, 3, 4, or 5 or more different antibodies, each antibody of the composition recognizing at least one (e.g., 2, 3, about 5, about 10, etc.) E6 protein. Collectively, the antibodies bind to all or a portion of the E6 proteins shown in FIG. 1, and, in certain embodiments, may also bind to non-oncogenic E6 proteins. The antibodies may be mixed, or separate from each other, i.e., in different vessels.
Any of the above-described antibodies may bind to an epitope set forth in Table 1.







TABLE 1







Epitopes










HPV
Starting


Sequence
type
AA












(K/R)-(K/R)-R-F-H-(N/K/S/E/R)-I-(A/S) (SEQ ID NO: 363)
59
124


F-H-(N/K/S/E/R)-I-(A/S)-(G/H)-X-(W/Y)
59
127


H-(N/K/S/E/R)-I-(A/S)-(G/H)-(R/Q)-(W/Y)-(T/K/R)
59
128


P-(E/A/Q)-E-K-(Q/L/K/R)-(R/K/L)-(H/V/I/L)-(V/L/C)
26
112


(G/H)-(R/Q/T/M/G/A/Y/H/S/N/I)-(W/Y/F)-(T/R/K/A)-G-(R/Q/S/L)-C-(R/L/M/A/T)
59
132


(W/Y/F)-(T/R/K/A)-G-(R/Q/S/L)-C-(R/L/M/A/T)-(L/R/A/T)-(N/R/S/A/Q/G)
59
134


G-(R/Q/S/L)-C-(R/L/M/A/T)-(L/R/A/T)-(N/R/S/A/Q/G)-C-(W/C/R)
59
136


(R/K)-P-(R/Y)-(K/T/S)-(L/V)-(H/P)-(D/E/H/Q)-L
59
10


(M/R/L)-F-(E/Q/D/H)-(D/N)-(P/T)-(Q/R/A/E/T)-(E/Q)-(R/K)
59
3


(D/N)-(P/T)-(Q/R/A/E/T)-(E/Q)-(R/K)-(R/K)-P-(R/Y)
59
6


(L/V)-(H/P)-(D/E/Q)-L-(C/S)-(E/T/Q)-(E/V/A/T)-(L/V)-(N/E/D)
59
14


(D/E/N)-(L/V/I)-(Q/E/R/T)-(L/V/I)-(Q/N/D/S/A/N)-C-V-(F/Y/E)-
59
26


L-(L/S)-I-R-C-(I/Y/H/L/M)-(R/I/C)-C (SEQ ID NO: 364)
59
101


(R/I/C)-C-(Q/L)-(K/R)-P-L-(C/T/G/N)-P (SEQ ID NO: 365)
59
107


(K/R)-P-L-(C/T/G/N)-P-(E/A/Q)-E-K (SEQ ID NO: 366)
59
110


P-(E/A/Q)-E-K-(Q/L/K)-(R/L/K)-(H/I)-(L/V/C)
26
112


K-(Q/L/K)-(R/L/K)-(H/I)-(L/V/C)-(D/E/N)-(E/D/Y/L/K/S)-(K/N)
26
115


(L/V/C)-(D/E/N)-(E/D/Y/L/K/S)-(K/N)-(K/R)-R-F-H
26
119


I-(A/S)-(G/H)-(R/Q)-(W/Y)-(T/K/R)-G-(R/Q/L/S)
26
128


(W/Y)-(T/K/R)-G-(R/Q/L/S)-C-(M/A/L/R/T)-(N/S/A/R)-C
26
132









Certain hybridomas that produce the monoclonal antibodies described above and below may be deposited at the ATCC. Any of the deposited hybridomas, the antibodies produced by those hybridomas, as well as other antibodies that bind the same epitopes as the antibodies produced by those hybridomas, are also embodiments of this invention and may be claimed herein. Such antibodies may be employed in any of the methods described herein.
Methods for Detecting an HPV E6 Protein in a Sample
The invention provides a method of detecting an HPV E6 protein in a sample. In general, the methods involve contacting a subject antibody composition with a sample, and assessing any binding of the antibody to the sample. In most embodiments, binding of the antibody to the sample indicates the presence of an HPV E6 protein.
The antibodies of the invention may be screened for immunospecific binding by any method known in the art. The immunoassays which can be used include but are not limited to competitive and non-competitive assay systems using techniques such as western blots, radioimmunoassays, ELISA (enzyme linked immunosorbent assay), “sandwich” immunoassays, immunoprecipitation assays, precipitin reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, complement-fixation assays, immunoradiometric assays, fluorescent immunoassays, protein A immunoassays, and cellular immunostaining (fixed or native) assays to name but a few. Such assays are routine and well known in the art (see, e.g., Ausubel et al., eds, 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc., New York, which is incorporated by reference herein in its entirety). Exemplary immunoassays are described briefly below (but are not intended by way of limitation).
Immunoprecipitation protocols generally involve lysing a population of cells in a lysis buffer such as RIPA buffer (1 % NP-40 or Triton X-100, 1 % sodium deoxycholate, 0.1 % SDS, 0.15 M NaCl, 0.01 M sodium phosphate at pH 7.2, 1 % Trasylol) supplemented with protein phosphatase and/or protease inhibitors (e.g., EDTA, PMSF, aprotinin, sodium vanadate), adding the antibody of interest to the cell lysate, incubating for a period of time (e.g., 1-4 hours) at 4 ° C., adding protein A and/or protein G sepharose beads to the cell lysate, incubating for about an hour or more at 4 ° C., washing the beads in lysis buffer and resuspending the beads in SDS/sample buffer. The ability of the antibody of interest to immunoprecipitate a particular antigen can be assessed by, e.g., western blot analysis. One of skill in the art would be knowledgeable as to the parameters that can be modified to increase the binding of the antibody to an antigen and decrease the background (e.g., pre-clearing the cell lysate with sepharose beads).
Western blot analysis generally involves preparation of protein samples followed by electrophoresis of the protein samples in a polyacrylamide gel (e.g., 8 %-20 % SDS-PAGE depending on the molecular weight of the antigen), and transfer of the separated protein samples from the polyacrylamide gel to a membrane such as nitrocellulose, PVDF or nylon. Following transfer, the membrane is blocked in blocking solution (e.g., PBS with 3 % BSA or non-fat milk), washed in washing buffer (e.g., PBS-Tween 20), and incubated with primary antibody (the antibody of interest) diluted in blocking buffer. After this incubation, the membrane is washed in washing buffer, incubated with a secondary antibody (which recognizes the primary antibody, e.g., an anti-human antibody) conjugated to an enzymatic substrate (e.g., horseradish peroxidase or alkaline phosphatase) or radioactive molecule (e.g., 32 P or 1251), and after a further wash, the presence of the antigen may be detected. One of skill in the art would be knowledgeable as to the parameters that can be modified to increase the signal detected and to reduce the background noise.
ELISAs involve preparing antigen, coating the well of a 96 well multiwell plate with the antigen, adding the antibody of interest conjugated to a detectable compound such as an enzymatic substrate (e.g., horseradish peroxidase or alkaline phosphatase) to the well and incubating for a period of time, and detecting the presence of the antigen. In ELISAs the antibody of interest does not have to be conjugated to a detectable compound; instead, a second antibody (which recognizes the antibody of interest) conjugated to a detectable compound may be added to the well. Further, instead of coating the well with the antigen, the antibody may be coated to the well. In this case, a second antibody conjugated to a detectable compound may be added following the addition of the antigen of interest to the coated well. One of skill in the art would be knowledgeable as to the parameters that can be modified to increase the signal detected as well as other variations of ELISAs known in the art.
The binding affinity of an antibody to an antigen and the off-rate of an antibody-antigen interaction can be determined by competitive binding assays. One example of a competitive binding assay is a radioimmunoassay comprising the incubation of labeled antigen (e.g., 3H or 125 I) with the antibody of interest in the presence of increasing amounts of unlabeled antigen, and the detection of the antibody bound to the labeled antigen. The affinity of the antibody of interest for a particular antigen and the binding off-rates can be determined from the data by scatchard plot analysis. Competition with a second antibody can also be determined using radioimmunoassays. In this case, the antigen is incubated with antibody of interest conjugated to a labeled compound (e.g., 3 H or 125 I) in the presence of increasing amounts of an unlabeled second antibody.
Antibodies of the invention may be screened using immunocytochemistry methods on cells (e.g., mammalian cells, such as CHO cells) transfected with a vector enabling the expression of an antigen or with vector alone using techniques commonly known in the art. Antibodies that bind antigen transfected cells, but not vector-only transfected cells, are antigen specific.
In certain embodiments, however, the assay is an antigen capture assay, and an array or microarray of antibodies may be employed for this purpose. Methods for making and using microarrays of polypeptides are known in the art (see e.g. U.S. Pat. Nos. 6,372,483, 6,352,842, 6,346,416 and 6,242,266).
Systems for Detecting an Oncogenic HPV E6 Protein
The invention provides a system for detecting the presence of an oncogenic HPV E6 polypeptide in a sample. In general, the system comprises a first and a second binding partner for an oncogenic HPV E6 polypeptide. In most embodiments, the first binding partner is a PDZ, domain protein and the second binding partner is a subject antibody.
The subject antibodies may be used along with certain PDZ domain proteins as part of a system for detecting E6 protein from oncogenic strains of HPV. As mentioned above, oncogenic HPV E6 proteins contain a “PDZ-ligand” (“PL”) that is bound by certain PDZ domain polypeptides. Non-oncogenic HPV E6 proteins do not contain such a PDZ-ligand, and, accordingly, are not bound by PDZ-domain polypeptides. Many PDZ domains suitable for use in the subject system are generally described in Table 2, and include MAGI-1 PDZ domain 2, the PDZ domain of TIP-1, and the PDZ domains 1 and 2 of DLG1, and many others. As would be recognized by one of skill in the art, a PDZ domain may be employed as part of a fusion protein, particularly in embodiments in which the PDZ domain polypeptide is anchored to a substrate. Accordingly, the subject system generally contains a suitable PDZ domain polypeptide, which is usually a fusion protein, and a subject antibody.
In certain embodiments, one of the binding partners is attached to a solid support, and the other binding partner may be labeled or part of a signal producing system. Proteins may be covalently bound or noncovalently attached through nonspecific bonding. If covalent bonding between the fusion protein and the surface is desired, the surface will usually be polyfunctional or be capable of being polyfunctionalized. Functional groups which may be present on the surface and used for linking can include carboxylic acids, aldehydes, amino groups, cyano groups, ethylenic groups, hydroxyl groups, mercapto groups and the like. The manner of linking a wide variety of compounds to various surfaces is well known and is amply illustrated in the literature.










TABLE 2





SEQ





ID

GI or



NO.
name
Acc. #
Sequence


















106
AF6 domain 1
430993
LRKEPEIITVTLKKQNGMGLSIVAAKGAGQDKLGIYVK





SVVKGGAADVDGRLAAGDQLLSVDGRSLVGLSQERAAE





LMTRTSSVVTLEVAKQG


 


107
AIPC domain 1
12751451
LIRPSVISIIGLYKEKGKGLGESIAGGRDCIRGQMGIF





VKTIFPNGSAAEDGRLKEGDEILDVNGIPIKGLTFQEA





IHTFKQIRSGLEVLTVRTKLVSPSLTNSS


 


108
AIPC domain 3
12751451
QSENEEDVCFIVLNRKEGSGLGESVAGGTDVEPKSITV





HRVFSQGAASQEGTMNRGDFLLSVNGASLAGLAHGNVL





KVLHQAQLHKDALVVIKKGMDQPRPSNSS


 


109
AIPC domain 2
12751451
GISSLGRKTPGPKDRIVMEVTLNKEPRVGLGIGACCLA





LENSPPGIYIHSLAPGSVAKMESNLSRGDQILEVNSVN





VRHAALSKVHAILSKCPPGPVRLVIGRHPNPKVSEQEM





DEVIARSTYQESKEANSS


 


110
AIPC domain 4
12751451
LGRSVAVHDALCVEVLKESAGLGLSLDGGKSSVTGDGP





LVIKRVYKGGAAEQAGIIEAGDEILAINGKPLVGLMHF





DAWNIMKSVPEGPVQLLIRKHRNSS


 


111
ALP domain 1
2773059
REEGGMPQTVILPGPAPWGFRLSGGIDFNQPLVITRIT





PGSKAAAANLCPGDVILAIDGFGTESMTHADAQDRIKA





AAHQLCLKIDRGETHLWSPNSS


 


112
APXL1 domain 1 
13651263
ILVEVQLSGGAPWGFTLKGGREHGEPLVITKIEEGSKA





AAVDKLLAGDEIVGINDIGLSGFRQEAICLVKGSHKTL





KLVVKRNSS


 


113
CARD11 domain 1
12382772
SVGHVRGPGPSVQHTTLNGDSLTSQLTLLGGNARGSFV





HSVKPGSLAEKAGLREGHQLLLLEGCIRGERQSVPLDT





CTKEEAHWTIQRCSGPVTLHYKVNHEGYRK


 


114
CARD14 domain 1
13129123
RRPARRILSQVTMLAFQGDALLEQISVIGGNLTGIFIH





RVTPGSAADQMALRPGTQIVMVDYEASEPLFKAVLEDT





TLEEAVGLLRRVDGFCCLSVKVNTDGYKR


 


115
CARD14 domain 1
13129123
ILSQVTMLAFQGDALLEQISVIGGNLTGIFIHRVTPGS





AADQMALRPGTQIVMVDYEASEPLFKAVLEDTTLEEAV





GLLRRVDGFCCLSVKVNTDGYKRL


 


116
CASK domain 1
3087815
TRVRLVQFQKNTDEPMGITLKMNELNHCIVARIMHGGM





IHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRG





SITFKIVPSYRTQS


 


117
CNK1 domain 1
3930780
LEQKAVLEQVQLDSPLGLEIHTTSNCQHFVSQVDTQVP





TDSRLQIQPGDEVVQINEQVVVGWPRKNMVRELLREPA





GLSLVLKKIPIP


 


118
Cytohesin binding 
3192908
QRKLVTVEKQDNETFGFEIQSYRPQNQNACSSEMFTLI



Protein domain 1

CKIQEDSPAHCAGLQAGDVLANINGVSTEGFTYKQVVD





LIRSSGNLLTIETLNG


 


119
Densin domain 1
16755892
RCLIQTKGQRSMDGYPEQFCVRIEKNPGLGFSISGGIS





GQGNPFKPSDKGIFVTRVQPDGPASNLLQPGDKILQAN





GHSFVHMEHEKAVLLLKSFQNTVDLVIQRELTV


 


120
DLG 6 splice
AB053303
PTSPEIQELRQMLQAPHFKGATIKRHEMTGDILVARII



variant 2 domain 1

HGGLAERSGLLYAGDKLVEVNGVSVEGLDPEQVIHILA





MSRGTIMFKVVPVSDPPVNSS


 


121
DLG 6 splice
14647140
PTSPEIQELRQMLQAPHFKALLSAHDTIAQKDFEPLLP



variant 1 domain 1

PLPDNIPESEEAMRIVCLVKNQQPLGATIKRHEMTGDI





LVARIIHGGLAERSGLLYAGDKLVEVNGVSVEGLDPEQ





VIHILAMSRGTIMFKVVPVSDPPVNSS


 


122
DLG1 domain 1
475816
IQVNGTDADYEYEEITLERGNSGLGFSIAGGTDNPHIG





DDSSIFITKIITGGAAAQDGRLRVNDCILQVNEVDVRD





VTHSKAVEALKEAGSIVRLYVKRRN


 


123
DLG1 domain 2
475816
IQLIKGPKGLGESIAGGVGNQHIPGDNSIYVTKIIEGG





AAHKDGKLQIGDKLLAVNNVCLEEVTHEEAVTALKNTS





DFVYLKVAKPTSMYMNDGN


 


124
DLG1 domains 1
475816
VNGTDADYEYEEITLERGNSGLGFSIAGGTDNPHIGDD



and 2

SSIFITKIITGGAAAQDGRLRVNDCILQVNEVDVRDVT





HSKAVEALKEAGSIVRLYVKRRKPVSEKIMEIKLIKGP





KGLGFSIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGK





LQIGDKLLAVNNVCLEEVTHEEAVTALKNTSDFVYLKV





AKPTSMYMNDGYA


 


125
DLG1 domain 3
475816
ILHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSGE





LRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVA





QYRPEEYSR


 


126
DLG2 domain 3
12736552
IEGRGILEGEPRKVVLHKGSTGLGFNIVGGEDGEGIFV





SFILAGGPADLSGELQRGDQILSVNGIDLRGASHEQAA





AALKGAGQTVTIIAQHQPEDYARFEAKIHDLNSS


 


127
DLG2 domain 1
12736552
ISYVNGTEIEYEFEEITLERGNSGLGFSIAGGTDNPHI





GIDDPGIFITKIIPGGAAAEDGRLRVNDCILRVNEVDV





SEVSHSKAVEALKEAGSIVRLYVRRR


 


128
DLG2 domain 2
12736552
IPILETVVEIKLFKGPKGLGFSIAGGVGNQHIPGDNSI





YVTKIIDGGAAQKDGRLQVGDRLLMVNNYSLEEVTHEE





AVAILKNTSEVVYLKVGKPTTIYMTDPYGPPNSSLTD


 


129
DLG5 domain 1
3650451
GIPYVEEPRHVKVQKGSEPLGISIVSGEKGGIYVSKVT





VGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIGQ





QCDTITILAQYNPHVHQLRNSSLTD


 


130
DLG5 domain 2
3650451
GILAGDANKKTLEPRVVFIKKSQLELGVHLCGGNLHGV





FVAEVEDDSPAKGPDGLVPGDLILEYGSLDVRNKTVEE





VYVEMLKPRDGVRLKVQYRPEEFIVTD


 


131
DVL1 domain 1
2291005
LNIVTVTLNMERHHFLGISIVGQSNDRGDGGIYIGSIM





KGGAVAADGRIEPGDMLLQVNDVNFENMSNDDAVRVLR





EIVSQTGPISLTVAKCW


 


132
DVL2 domain 1
2291007
LNIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIM





KGGAVAADGRIEPGDMLLQVNDMNFENMSNDDAVRVLR





DIVHKPGPIVLTVAKCWDPSPQNS


 


133
DVL3 domain 1
6806886
IITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIMKG





GAVAADGRIEPGDMLLQVNEINFENMSNDDAVRVLREI





VHKPGPITLTVAKCWDPSP


 


134
EBP50 domain 2
3220018
QQRELRPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVD





PDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRA





GGDETKLLVVDRETDEFFKNSS


 


135
EBP50 domain 1
3220018
GIQMSADAAAGAPLPRLCCLEKGPNGYGFHLHGEKGKL





GQYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQ





QVVSRIRAALNAVRLLVVDPETDEQLQKLGVQVREELL





RAQEAPGQAEPPAAAEVQGAGNENEPREADKSHPEQRE





LRN


 


136
EBP50 domains 1
3220018
GIQMSADAAAGAPLPRLCCLEKGPNGYGFHLHGEKGKL



and 2

GQYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQ





QVVSRIRAALNAVRLLVVDPETDEQLQKLGVQVREELL





RAQEAPGQAEPPAAAEVQGAGNENEFREADKSHPEQRE





LRPRLCTMKKGPSGYGENILHSDKSKPGQFIRSVDPDS





PAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAGGD





ETKLLVVDRETDEFFK


 


137
EBP50 domain 1
3220018
QMSADAAAGAPLPRLCCLEKGPNGYGEFILHGEKGKLG





QYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQQ





VVSRIRAALNAVRLLVVDPETDEQLQKLGVQVREELLR





AQEAPGQAEPPAAAEVQGAGNENEPREADKSHPEQREL





RNSS


 


138
ELFIN 1 domain 1
2957144
LTTQQIDLQGPGPWGFRLVGGKDFEQPLAISRVTPGSK





AALANLCIGDVITAIDGENTSNMTHLEAQNRIKGCTDN





LTLTVARSEHKVWSPLVTNSSW


 


139
ENIGMA domain 1
561636
IFMDSFKVVLEGPAPWGFRLQGGKDFNVPLSISRLTPG





GKAAQAGVAVGDWVLSIDGENAGSLTHIEAQNKIRACG





ERLSLGLSRAQPV


 


140
ERBIN domain 1
8923908
QGHELAKQEIRVRVEKDPELGFSISGGVGGRGNPFRPD





DDGIFVTRVQPEGPASKLLQPGDKIIQANGYSFINIEH





GQAVSLLKTFQNTVELIIVREVSS


 


141
FLJ00011 domain 1
10440352
KNPSGELKTVTLSKMKQSLGISISGGIESKVQPMVKIE





KIFPGGAAFLSGALQAGFELVAVDGENLEQVTHQRAVD





TIRRAYRNKAREPMELVVRVPGPSPRPSPSD


 


142
FLJ11215 domain 1
11436365
EGHSHPRVVELPKTEEGLGFNIMGGKEQNSPIYISRII





PGGIADRHGGLKRGDQLLSVNGVSVEGEHHEKAVELLK





AAQGKVKLVVRYTPKVLEEME


 


143
FLJ12428 domain 1
BC012040
PGAPYARKTFTIVGDAVGWGFVVRGSKPCHIQAVDPSG





PAAAAGMKVCQFVVSVNGLNVLHVDYRTVSNLILTGPR





TIVMEVMEELEC


 


144
FLJ12615 domain 1
10434209
GQYGGETVKIVRIEKARDIPLGATVRNEMDSVIISRIV





KGGAAEKSGLLHEGDEVLEINGIEIRGKDVNEVFDLLS





DMHGTLTFVLIPSQQIKPPPA


 


145
FLJ21687 domain 1
10437836
KPSQASGHFSVELVRGYAGFGLTLGGGRDVAGDTPLAV





RGLLKDGPAQRCGRLEVGDLVLHINGESTQGLTHAQAV





ERIRAGGPQLHLVIRRPLETHPGKPRGV


 


146
FLJ31349 domain 1
AK055911
PVMSQCACLEEVHLPNIKPGEGLGMYIKSTYDGLHVIT





GTTENSPADRSQKIHAGDEVTQVNQQTVVGWQLKNLVK





KLRENPTGVVLLLKKRPTGSFNFTP


 


147
FLJ32798 domain 1
AK057360
IDDEEDSVKIIRLVKNREPLGATIKKDEQTGAIIVARI





MRGGAADRSGLIHVGDELREVNGIPVEDKRPEEIIQIL





AQSQGAITFKIIPGSKEETPS


 


148
GORASP 2
13994253
MGSSQSVEIPGGGTEGYHVLRVQENSPGHRAGLEPFFD



domains 1 and 2

FIVSINGSRLNKDNDTLKDLLKANVEKPVKMLIYSSKT





LELRETSVTPSNLWGGQGLLGVSIRFCSFDGANENVWH





VLEVESNSPAALAGLRPHSDYIIGADTVMNESEDLFSL





IETHEAKPLKLYVYNTDTDNCREVIITPNSAWGGEGSL





GCGIGYGYLHRIPTRPFEEGKKISLPGQMAGTPITPLK





DGFTEVQLSSVNPPSLSPPGTTGIEQSLTGLSISSTPP





AVSSVLSTGVPTVPLLPPQVNQSLTSVPPMNPATTLPG





LMPLPAGLPNLPNLNLNLPAPHIMPGVGLPELVNPGLP





PLPSMPPRNLPGIAPLPLPSEFLPSFPLVPESSSAASS





GELLSSLPPTSNAPSDPATTTAKADAASSLTVDVTPPT





AKAPTTVEDRVGDSTPVSEKPVSAAVDANASESP


 


149
GORASP 2 domain
13994253
NENVWHVLEVESNSPAALAGLRPHSDYHGADTVMNESE



2

DLFSLIETHEAKPLKLYVYNTDTDNCREVIITPNSAWG





GEGSLGCGIGYGYLHRIPTR


 


150
GORASP 2 domain
13994253
MGSSQSVEIPGGGTEGYHVLRVQENSPGHRAGLEPFED



1

FIVSINGSRLNKDNDTLKDLLKANVEKPVKMLIYSSKT





LELRETSVTPSNLWGGQGLLGVSIRFCSFDGANE


 


151
GORASP 1 domain
29826292
RASEQVWHVLDVEPSSPAALAGLRPYTDYVVGSDQILQ



2

ESEDFFTLIESHEGKPLKLMVYNSKSDSCREVTVTPNA





AWGGEGSLGCGIGYGYLHRIPTQ


 


152
GORASP 1 domain
29826292
MGLGVSAEQPAGGAEGFHLHGVQENSPAQQAGLEPYFD



1

FIITIGHSRLNKENDTLKALLKANVEKPVKLEVFNMKT





MRVREVEVVPSNMWGGQGLLGASVRFCSFRRASE


 


153
GORASP 1
29826292
MGLGVSAEQPAGGAEGFHLHGVQENSPAQQAGLEPYFD



domains 1 and 2

FIITIGHSRLNKENDTLKALLKANVEKPVKLEVFNMKT





MRVREVEVVPSNMWGGQGLLGASVRFCSFRRASEQVWH





VLDVEPSSPAALAGLRPYTDYVVGSDQILQESEDFFTL





IESHEGKPLKLMVYNSKSDSCREVTVTPNAAWGGEGSL





GCGIGYGYLHRIPTQPPSYHKKPPGTPPPSALPLGAPP





PDALPPGPTPEDSPSLETGSRQSDYMEALLQAPGSSME





DPLPGPGSPSHSAPDPDGLPHFMETPLQPPPPVQRVMD





PGFLDVSGISLLDNSNASVWPSLPSSTELTTTAVSTSG





PEDICSSSSSHERGGEATWSGSEFEVSFLDSPGAQAQA





DHLPQLTLPDSLTSAASPEDGLSAELLEAQAEEEPAST





EGLDTGTEAEGLDSQAQISTTE


 


154
GRIP 1 domain 6
4539083
IYTVELKRYGGPLGITISGTEEPFDPIIISSLTKGGLA





ERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGET





VTLKIKKQTDAQSA


 


155
GRIP 1 domain 1
4539083
VVELMKKEGTTLGLTVSGGIDKDGKPRVSNLRQGGIAA





RSDQLDVGDYIKAVNGINLAKFRHDEIISLLKNVGERV





VLEVEYE


 


156
GRIP 1 domain 3
4539083
HVATASGPLLVEVAKTPGASLGVALTTSMCCNKQVIVI





DKIKSASIADRCGALHVGDHILSIDGTSMEYCTLAEAT





QFLANTTDQVKLEILPHHQTRLALKGPNSS


 


157
GRIP 1 domain 7
4539083
IMSPTPVELHKVTLYKDSDMEDFGFSVADGLLEKGVYV





KNIRPAGPGDLGGLKPYDRLLQVNHVRTRDFDCCLVVP





LIAESGNKLDLVISRNPLA


 


158
GRIP 1 domain 4
4539083
IYTVELKRYGGPLGITISGTEEPFDPIIISSLTKGGLA





ERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGET





VTLKIKKQTDAQSA


 


159
GRIP 1 domain 5
4539083
IMSPTPVELHKVTLYKDSDMEDFGFSVADGLLEKGVYV





KNIRPAGPGDLGGLKPYDRLLQVNHVRTRIDFDCCLVV





PLIAESGNKLDLVISRNPLA


 


160
GTPase activating
2389008
SRGCETRELALPRDGQGRLGFEVDAEGFVTHVERFTFA



enzyme domain 1

ETAGLRPGARLLRVCGQTLPSLRPEAAAQLLRSAPKVC





VTVLPPDESGRP


 


161
Guanine exchange
6650765
CSVMIFEVVEQAGAIILEDGQELDSWYVILNGTVEISH



factor domain 1

PDGKVENLFMGNSFGITPTLDKQYMHGIVRTKVDDCQF





VCIAQQDYWRILNIIVEKNTHKVEEEGEIVMVH


 


162
HEMBA 1000505
10436367
PRETVKIPDSADGLGFQIRGFGPSVVHAVGRGTVAAAA



domain 2

GLHPGQCIIKVNGINVSKETHASVIAHVTACRKYRRPT





KQDSIQ


 


163
HEMBA 1000505
10436367
LENVIAKSLLIKSNEGSYGFGLEDKNKVPIIKLVEKGS



domain 1

NAEMAGMEVGKKIFAINGDLVFMRPFNEVDCFLKSCLN





SRKPLRVLVSTKP


 


164
HEMBA 1003117
7022001
EDFCYVFTVELERGPSGLGMGLIDGMHTHLGAPGLYIQ



domain 1

TLLPGSPAAADGRLSLGDRILEVNGSSLLGLGYLRAVD





LIRHGGKKMRFLVAKSDVETAKKI


 


165
hShroom domain 1
18652858
IYLEAFLEGGAPWGFTLKGGLEHGEPLIISKVEEGGKA





DTLSSKLQAGDEVVHINEVTLSSSRKEAVSLVKGSYKT





LRLVVRRDVCTDPGH


 


166
HSPC227 domain 1
7106843
NNELTQFLPRTITLKKPPGAQLGFNIRGGKASQLGIFI





SKVIPDSDAHRAGLQEGDQVLAVNDVDFQDIEHSKAVE





ILKTAREISMRVRFFPYNYHRQKE


 


167
HTRA 3 domain 1
AY040094
FLTEFQDKQIKDWKKRFIGIRMRTITPSLVDELKASNP





DFPEVSSGIYVQEVAPNSPSQRGGIQDGDIIVKVNGRP





LVDSSELQEAVLTESPLLLEVRRGNDDLLFS


 


168
HTRA 4 domain 1
AL576444
NKKYLGLQMLSLTVPLSEELKMHYPDFPDVSSGVYVCK





VVEGTAAQSSGLRDHDVIVNINGKPITTTTDVVKALDS





DSLSMAVLRGKDNLLLTV


 


169
INADL domain 3
2370148
PGSDSSLFETYNVELVRKDGQSLGIRIVGYVGTSHTGE





ASGIYVKSIIPGSAAYHNGHIQVNDKIVAVDGVNIQGF





ANHDVVEVLRNAGQVVHLTLVRRKTSSSTSRIHRD


 


170
INADL domain 8
2370148
PATCPIVPGQEMIIEISKGRSGLGLSIVGGKDTPLNAI





VIHEVYEEGAAARDGRLWAGDQILEVNGVDLRNSSHEE





AITALRQTPQKVRLVVY


 


171
INADL domain 2
2370148
LPETVCWGHVEEVELINDGSGLGFGIVGGKTSGVVVRT





IVPGGLADRDGRLQTGDHILKIGGTNVQGMTSEQVAQV





LRNCGNSVRMLVARDPAGDIQSPI


 


172
INADL domain 6
2370148
PNFSHWGPPRIVEIFREPNVSLGISIVVGQTVIKRLKN





GEELKGIFIKQVLEDSPAGKTNALKTGDKILEVSGVDL





QNASHSEAVEAIKNAGNPVVFIVQSLSSTPRVIPNVHN





KANSS


 


173
INADL domain 7
2370148
PGELHIIELEKDKNGLGLSLAGNKDRSRMSIFVVGINP





EGPAAADGRMRIGDELLEINNQILYGRSHQNASAIIKT





APSKVKLVFIRNEDAVNQMANSS


 


174
INADL domain 5
2370148
LSSPEVKIVELVKDCKGLGFSILDYQDPLDPTRSVIVI





RSLVADGVAERSGGLLPGDRLVSVNEYCLDNTSLAEAV





EILKAVPPGLVHLGICKPLVEFIVTD


 


175
INADL domain 1
2370148
IWQIEYIDIERPSTGGLGFSVVALRSQNLGKVDIFVKD





VQPGSVADRDQRLKENDQILAINHTPLDQNISHQQAIA





LLQQTTGSLRLIVAREPVHTKSSTSSSE


 


176
INADL domain 4
2370148
NSDDAELQKYSKLLPIHTLRLGVEVDSFIDGHHYISSI





VSGGPVDTLGLLQPEDELLEVNGMQLYGKSRREAVSFL





KEVPPPFTLVCCRRLFDDEAS


 


177
KIAA0313 domain
7657260
HLRLLNIACAAKAKRRLMTLTKPSREAPLPFILLGGSE



1

KGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENI





QLSKAMEILRNNTHLSITVKTNLFVFKELLTRLSEEKR





NGAP


 


178
KIAA0316 domain
6683123
IPPAPRKVEMRRDPVLGFGFVAGSEKPVVVRSVTPGGP



1

SEGKLIPGDQIVMINDEPVSAAPRERVIDLVRSCKESI





LLTVIQPYPSPK


 


179
KIAA0340 domain
2224620
LNKRTTMPKDSGALLGLKVVGGKMTDLGRLGAFITKVK



1

KGSLADVVGHLRAGDEVLEWNGKPLPGATNEEVYNIIL





ESKSEPQVEIIVSRPIGDIPRIHRD


 


180
KIAA0380 domain
2224700
RCVIIQKDQHGFGFTVSGDRIVLVQSVRPGGAAMKAGV



1

KEGDRIIKVNGTMVTNSSHLEVVKLIKSGAYVALTLLG





S


 


181
KIAA0382 domain
7662087
ILVQRCVIIQKDDNGFGLTVSGDNPVFVQSVKEDGAAM



1

RAGVQTGDRIIKVNGTLVTHSNHLEVVKLIKSGSYVAL





TVQGRPPGNSS


 


182
KIAA0440 domain
2662160
SVEMTLRRNGLGQLGFHVNYEGIVADVEPYGYAWQAGL



1

RQGSRLVEICKVAVATLSHEQMIDLLRTSVTVKVVIIP





PH


 


183
KIAA0545 domain
14762850
LKVMTSGWETVDMTLRRNGLGQLGFHVKYDGTVAEVED



1

YGFAWQAGLRQGSRLVEICKVAVVTLTHDQMIDLLRTS





VTVKVVIIPPFEDGTPRRGW


 


184
KIAA0559 domain
3043641
HYIFPHARIKITRDSKDHTVSGNGLGIRIVGGKEIPGH



1

SGEIGAYIAKILPGGSAEQTGKLMEGMQVLEWNGIPLT





SKTYEEVQSIISQQSGEAEICVRLDLNML


 


185
KIAA0613 domain
3327039
SYSVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAA



1

QSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLS





LTLQKSKNSS


 


186
KIAA0858 domain
4240204
FSDMRISINQTPGKSLDFGFTIKWDIPGIFVASVEAGS



1

PAEFSQLQVDDEIIAINNTKFSYNDSKEWEEAMAKAQE





TGHLVMDVRRYGKAGSPE


 


187
KIAA0902 domain
4240292
QSAHLEVIQLANIKPSEGLGMYIKSTYDGLHVITGTTE



1

NSPADRCKKIHAGDEVIQVNHQTVVGWQLKNLVNALRE





DPSGVILTLKKRPQSMLTSAPA


 


188
KIAA0967 domain
4589577
ILTQTLIPVRHTVKIDKDTLLQDYGFHISESLPLTVVA



1

VTAGGSAHGKLFPGDQILQMNNEPAEDLSWERAVDILR





EAEDSLSITVVRCTSGVPKSSNSS


 


189
KIAA1202 domain
6330421
RSFQYVPVQLQGGAPWGFTLKGGLEHCEPLTVSKIEDG



1

GKAALSQKMRTGDELVNINGTPLYGSRQEALILIKGSF





RILKLIVRRRNAPVS


 


190
KIAA1222 domain
6330610
ILEKLELFPVELEKDEDGLGISIIGMGVGADAGLEKLG



1

IFVKTVTEGGAAQRDGRIQVNDQIVEVDGISLVGVTQN





FAATVLRNTKGNVREVIGREKPGQVSE


 


191
KIAA1284 domain
6331369
KDVNVYVNPKKLTVIKAKEQLKLLEVLVGIIHQTKWSW



1

RRTGKQGDGERLVVHGLLPGGSAMKSGQVLIGDVLVAV





NDVDVTTENIERVLSCIPGPMQVKLTFENAYDVKRET


 


192
KIAA1389 domain
7243158
TRGCETVEMTLRRNGLGQLGFHVNFEGIVADVEPFGFA



1

WKAGLRQGSRLVEICKVAVATLTHEQMIDLLRTSVTVK





VVIIQPHDDGSPRR


 


193
KIAA1415 domain
7243210
VENILAKRLLILPQEEDYGEDIEEKNKAVVVKSVQRGS



1

LAEVAGLQVGRKIYSINEDLVFLRPFSEVESILNQSFC





SRRPLRLLVATKAKEIIKIP


 


194
KIAA1526 domain
5817166
PDSAGPGEVRLVSLRRAKAHEGLGFSIRGGSEHGVGIY



1

VSLVEPGSLAEKEGLRVGDQILRVNDKSLARVTHAEAV





KALKGSKKLVLSVYSAGRIPGGYVTNH


 


195
KIAA1526 domain
5817166
LQGGDEKKVNLVLGDGRSLGLTIRGGAEYGLGIYITGV



2

DPGSEAEGSGLKVGDQILEVNGRSFLNILHDEAVRLLK





SSRHLILTVKDVGRLPHARTTVDE


 


196
KIAA1620 domain
10047316
LRRAELVEIIVETEAQTGVSGINVAGGGKEGIFVRELR



1

EDSPAARSLSLQEGDQLLSARVFFENFKYEDALRLLQC





AEPYKVSFCLKRTVPTGDLALR


 


197
KIAA1719 domain
1267982
IQTTGAVSYTVELKRYGGPLGITISGTEEPFDPIVISG



5

LTKRGLAERTGAIHVGDRILAINNVSLKGRPLSEAIHL





LQVAGETVTLKIKKQLDR


 


198
KIAA1719 domain
1267982
ILEMEELLLPTPLEMHKVTLHKDPMRHDFGFSVSDGLL



6

EKGVYVHTVRPDGPAHRGGLQPFDRVLQVNHVRTRDFD





CCLAVPLLAEAGDVLELIISRKPHTAHSS


 


199
KIAA1719 domain
1267982
IHTVANASGPLMVEIVKTPGSALGISLTTTSLRNKSVI



2

TIDRIKPASVVDRSGALHPGDHILSIDGTSMEHCSLLE





ATKLLASISEKVRLEILPVPQSQRPL


 


200
KIAA1719 domain
1267982
ITVVELIKKEGSTLGLTISGGTDKDGKPRVSNLRPGGL



1

AARSDLLNIGDYIRSVNGIHLTRLRHDEIITLLKNVGE





RVVLEVEY


 


201
KIAA1719 domain
1267982
IQIVIITETTEVVLCGDPLSGFGLQLQGGIFATETLSS



3

PPLVCFIEPDSPAERCGLLQVGDRVLSINGIATEDGTM





EEANQLLRDAALAHKVVLEVEFDVAESV


 


202
KIAA1719 domain
1267982
ILDVSLYKEGNSFGFVLRGGAHEDGHKSRPLVLTYVRP



1

GGPADREGSLKVGDRLLSVDGIPLHGASHATALATLRQ





CSHEALFQVEYDVATP


 


203
KIAA1719 domain
1267982
QFDVAESVIPSSGTFHVKLPKKRSVELGITISSASRKR



4

GEPLIISDIKKGSVAHRTGTLEPGDKLLAIDNIRLDNC





PMEDAVQILRQCEDLVKLKIRKDEDN


 


204
LIM mystique
12734250
MALTVDVAGPAPWGFRITGGRDFHTPIMVTKVAERGKA



domain 1

KDADLRPGDIIVAINGESAEGMLHAEAQSKIRQSPSPL





RLQLDRSQATSPGQT


 


205
LIM protein domain
3108092
SNYSVSLVGPAPWGFRLQGGKDFNMPLTISSLKDGGKA



1

AQANVRIGDVVLSIDGINAQGMTHLEAQNKIKGCTGSL





NMTLQRAS


 


206
LIMK1 domain 1
4587498
TLVEHSKLYCGHCYYQTVVTPVIEQILPDSPGSHLPHT





VTLVSIPASSHGKRGLSVSIDPPHGPPGCGTEHSHTVR





VQGVDPGCMSPDVKNSIHVGDRILEINGTPIRNVPLDE





IDLLIQETSRLLQLTLEHD


 


207
LIMK2 domain 1
1805593
PYSVTLISMPATTEGRRGFSVSVESACSNYATTVQVKE





VNRMHISPNNRNAIHPGDRILEINGTPVRTLRVEEVED





AISQTSQTLQLLIEHD


 


208
LIM-RIL domain 1
1085021
IHSVTLRGPSPWGFRLVGRDFSAPLTISRVHAGSKASL





AALCPGDLIQAINGESTELMTHLEAQNRIKGCHDHLTL





SVSRPE


 


209
LU-1 domain 1
U52111
VCYRTDDEEDLGIYVGEVNPNSIAAKDGRIREGDRIIQ





INGVDVQNREEAVAILSQEENTNISLLVARPESQLA


 


210
MAGI 1 domain 2
3370997
IPATQPELITVHIVKGPMGFGFTIADSPGGGGQRVKQI





VDSPRCRGLKEGDLIVEVNKKNVQALTHNQVVDMLVEC





PKGSEVTLLVQRGGNSS


 


211
MAGI 1 domain 5
3370997
IPDYQEQDIFLWRKETGFGFRILGGNEPGEPIYIGHIV





PLGAADTDGRLRSGDELICVDGTPVIGKSHQLVVQLMQ





QAAKQGHVNLTVRRKVVFAVPKTENSS


 


212
MAGI 1 domain 4
3370997
IPGVVSTVVQPYDVEIRRGENEGFGEVIVSSVSRPEAG





TTFAGNACVAMPHKIGRIIEGSPADRCGKLKVGDRILA





VNGCSITNKSHSDIVNLIKEAGNTVTLRIIPGDESSNA





EFIVTD


 


213
MAGI 1 domain 1
3370997
IPSELKGKFIHTKLRKSSRGFGFTVVGGDEPDEFLQIK





SLVLDGPAALDGKMETGDVIVSVNDTCVLGHTHAQVVK





IFQSIPIGASVDLELCRGYPLPFDPDGIHRD


 


214
MAGI 1 domain 3
3370997
QATQEQDFYTVELERGAKGFGFSLRGGREYNMDLYVLR





LAEDGPAERCGKMRIGDEILEINGETTKNMKHSRAIEL





IKNGGRRVRLFLKRG


 


215
Magi 2 domain 1
2947231
REKPLFTRDASQLKGTFLSTTLKKSNMGFGFTIIGGDE





PDEFLQVKSVIPDGPAAQDGKMETGDVIVYINEVCVLG





HTHADVVKLFQSVPIGQSVNLVLCRGYP


 


216
Magi 2 domain 3
2947231
HYKELDVHLRRMESGFGFRILGGDEPGQPILIGAVIAM





GSADRDGRLHPGDELVYVDGIPVAGKTHRYVIDLMHHA





ARNGQVNLTVRRKVLCG


 


217
Magi 2 domain 4
2947231
EGRGISSHSLQTSDAVIHRKENEGFGFVIISSLNRPES





GSTITVPHKIGRIIDGSPADRCAKLKVGDRILAVNGQS





IINMPHADIVKLIKDAGLSVTLRIIPQEEL


 


218
Magi 2 domain 2
2947231
LSGATQAELMTLTIVKGAQGFGFTIADSPTGQRVKQIL





DIQGCPGLCEGDLIVEINQQNVQNLSHTEVVDILKDCP





IGSETSLIIHRGGFF


 


219
Magi 2 domain 5
2947231
LSDYRQPQDFDYFTVDMEKGAKGFGFSIRGGREYKMDL





YVLRLAEDGPAIRNGRMRVGDQIIEINGESTRDMTHAR





AIELIKSGGRRVRLLLKRGTGQ


 


220
Magi 2 domain 6
2947231
HESVIGRNPEGQLGFELKGGAENGQFPYLGEVKPGKVA





YESGSKLVSEELLLEVNETPVAGLTIRDVLAVIKHCKD





PLRLKCVKQGGIHR


 


221
MAGI 3 domain 2
10047344
ASSGSSQPELVTIPLIKGPKGFGFAIADSPTGQKVKMI





LDSQWCQGLQKGDIIKEIYHQNVQNLTHLQVVEVLKQF





PVGADVPLLILRGGPPSPTKTAKM


 


222
MAGI 3 domain 5
10047344
QNLGCYPVELERGPRGFGFSLRGGKEYNMGLFILRLAE





DGPAIKDGRIHVGDQIVEINGEPTQGITHTRAIELIQA





GGNKVLLLLRPGTGLIPDHGLA


 


223
MAGI 3 domain 3
10047344
LYEDKPPNTKDLDVFLRKQESGFGFRVLGGDGPDQSIY





IGAIIPLGAAEKDGRLRAADELMCIDGIPVKGKSHKQV





LDLMTTAARNGHVLLTVRRKIFYGEKQPEDDS


 


224
MAGI 3 domain 1
10047344
PSQLKGVLVRASLKKSTMGFGFTIIGGDRPDEFLQVKN





VLKDGPAAQDGKIAPGDVIVDINGNCVLGHTHADVVQM





FQLVPVNQYVNLTLCRGYPLPDDSED


 


225
MAGI 3 domain 4
10047344
PAPQEPYDVVLQRKENEGFGFVILTSKNKPPPGVIPHK





IGRVTEGSPADRCGKLKVGDHISAVNGQSIVELSHDNI





VQLIKDAGVTVTLTVIAEEEHHGPPS


 


226
MAST1 domain 1
4589589
GLRSPITIQRSGKKYGFTLRAIRVYMGDTDVYSVHHIV





WHVEEGGPAQEAGLCAGDLITHVNGEPVHGMVHPEVVE





LILKSGNKVAVTTTPFEN


 


227
MAST2 domain 1
3882334
ISALGSMRPPIIIHRAGKKYGFTLRAIRVYMGDSDVYT





VHHMVWHVEDGGPASEAGLRQGDLITHVNGEPVHGLVH





TEVVELILKSGNKVAISTTPLENSS


 


228
MAST3 domain 1
3043645
LCGSLRPPIVIHSSGKKYGFSLRAIRVYMGDSDVYTVH





HVVWSVEDGSPAQEAGLRAGDLITHINGESVLGLVHMD





VVELLLKSGNKISLRTTALENTSIKVG


 


229
MAST4 domain 1
2224546
PHQPIVIHSSGKNYGFTIRAIRVYVGDSDIYTVHHIVW





NVEEGSPACQAGLKAGDLITHINGEPVHGLVHTEVIEL





LLKSGNKVSITTTPF


 


230
MGC5395 domain 1
BC012477
PAKMEKEETTRELLLPNWQGSGSHGLTIAQRDDGVFVQ





EVTQNSPAARTGVVKEGDQIVGATIYFDNLQSGEVTQL





LNTMGHHTVGLKLHRKGDRSPNSS


 


231
MINT1 domain 1
2625024
SENCKdVFIEKQKGEILGVVIVESGWGSILPTVIIANM





MHGGPAEKSGKLNIGDQIMSINGTSLVGLPLSTCQSII





KGLKNQSRVKLNIVRCPPVNSS


 


232
MINT1 domains 1
2625024
SENCKDVFIEKQKGEILGVVIVESGWGSILPTVIIANM



and 2

MHGGPAEKSGKLNIGDQIMSINGTSLVGLPLSTCQSII





KGLENQSRVKLNIVRCPPVTTVLIRRPDLRYQLGFSVQ





NGIICSLMRGGIAERGGVRVGHRIIEINGQSVVATPHE





KIVHILSNAVGEIHMKTMPAAMYRLL


 


233
MINT1 domain 2
2625024
LRCPPVTTVLIRRPDLRYQLGESVQNGIICSLMRGGIA





ERGGVRVGHRIIEINGQSVVATPHEKIVHILSNAVGEI





HMKTMPAAMYRLLNSS


 


234
MINT3 domain 1
3169808
HNGDLDHFSNSDNCREVHLEKRRGEGLGVALVESGWGS





LLPTAVIANLLHGGPAERSGALSIGDRLTAINGTSLVG





LPLAACQAAVRETKSQTSVTLSIVHCPPVT


 


235
MINT3 domain 2
3169808
PVTTAIIHRPHAREQLGFCVEDGIICSLLRGGIAERGG





IRVGHRIIEINGQSVVATPHARIIELLTEAYGEVHIKT





MPAATYRLLTGNSS


 


236
MINT3 domain 1
3169808
LSNSDNCREVHLEKRRGEGLGVALVESGWGSLLPTAVI





ANLLHGGPAERSGALSIGDRLTAINGTSLVGLPLAACQ





AAVRETKSQTSVTLSIVHCPPVTTAIM


 


237
MPP1 domain 1
189785
RKVRLIQFEKVTEEPMGITLKLNEKQSCTVARILHGGM





IHRQGSLHVGDEILEINGTNVTNHSVDQLQKAMKETKG





MISLKVIPNQ


 


238
MPP2 domain 1
939884
PVPPDAVRMVGIRKTAGEHLGVTFRVEGGELVIARILH





GGMVAQQGLLHVGDIIKEVNGQPVGSDPRALQELLRNA





SGSVILKILPNYQ


 


239
MPP3 domain 1
21536463 
NIDEDFDEESVKIVRLVKNKEPLGATIRRDEHSGAVVV





ARIMRGGAADRSGLVHVGDELREVNGIAVLHKRPDEIS





QILAQSQGSITLKIIPATQEEDR


 


240
MUPP1 domain 5
2104784
WEAGIQHIELEKGSKGLGFSILDYQDPIDPASTVIIIR





SLVPGGIAEKDGRLLPGDRLMFVNDVNLENSSLEEAVE





ALKGAPSGTVRIGVAKPLPLSPEE


 


241
MUPP1 domain 12
2104784
LQGLRTVEMKKGPTDSLGISIAGGVGSPLGDVPIFIAM





MHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNL





LKNASGSIEMQVVAGGDVSV


 


242
MUPP1 domain 2
2104784
PVHWQHMETIELYNDGSGLGEGIIGGKATGVIVKTILP





GGVADQHGRLCSGDHILKIGDTDLAGMSSEQVAQVLRQ





CGNRVKLMIARGAIEERTAPT


 


243
MUPP1 domain 3
2104784
QESETEDVELTKNVQGLGITIAGYIGDKKLEPSGIFVK





SITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVE





VLRHTGQTVLLTLMRRGMKQEA


 


244
MUPP1 domain 11
2104784
KEEEVCDTLTIELQKKPGKGLGLSIVGKRNDTGVFVSD





IVKGGIADADGRLMQGDQILMVNGEDVRNATQEAVAAL





LKCSLGTVTLEVGRIKAGPFHS


 


245
MUPP1 domain 8
2104784
LTGELHMIELEKGHSGLGLSLAGNKDRSRMSVFIVGID





PNGAAGKDGRLQIADELLEINGQILYGRSHQNASSIIK





CAPSKVKIIFIRNKDAVNQ


 


246
MUPP1 domain 13
2104784
LGPPQCKSITLERGPDGLGFSIVGGYGSPHGDLPIYVK





TVFAKGAASEDGRLKRGDQIIAVNGQSLEGVTHEEAVA





ILKRTKGTVTLMVLS


 


247
MUPP1 domain 6
2104784
RNVSKESFERTINIAKGNSSLGMTVSANKDGLGMIVRS





IIHGGAISRDGRIAIGDCILSINEESTISVTNAQARAM





LRRHSLIGPDIKITYVPAEHLEE


 


248
MUPP1 domain 1
02104784
LPGCETTIEISKGRTGLGLSIVGGSDTLLGAIIIHEVY





EEGAACKDGRLWAGDQILEVNGIDLRKATHDEAINVLR





QTPQRVRLTLYRDEAPYKE


 


249
MUPP1 domain 7
2104784
LNWNQPRRVELWREPSKSLGISIVGGRGMGSRLSNGEV





MRGIFIKHVLEDSPAGKNGTLKPGDRIVEVDGMDLRDA





SHEQAVEAIRKAGNPVVFMVQSIINRPRKSPLPSLL


 


250
MUPP1 domain 9
2104784
LSSFKNVQHLELPKDQGGLGIATSEEDTLSGVIIKSLT





EHGVAATDGRLKVGDQILAVDDEIVVGYPIEKFISLLK





TAKMTVKLTIHAENPDSQ


 


251
MUPP1 domain 1
2104784
QGRHVEVFELLKPPSGGLGFSVVGLRSENRGELGIFVQ





EIQEGSVAHRDGRLKETDQILAINGQALDQTITHQQAI





SILQKAKDTVQLVIARGSLPQLV


 


252
MUPP1 domain 4
2104784
LNYEIVVAHVSKFSENSGLGISLEATVGHHFIRSVLPE





GPVGHSGKLFSGDELLEVNGITLLGENHQDVVNILKEL





PIEVTMVCCRRTVPPT


 


253
NeDLG domain 2
10863920
ITLLKGPKGLGESIAGGIGNQHIPGDNSIYITKIIEGG





AAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTS





DMVYLKVAKPGSLE


 


254
NeDLG domain 1
10863920
IQYEEIVLERGNSGLGFSIAGGIDNPHVPDDPGIFITK





IIPGGAAAMDGRLGVNDCVLRVNEVEVSEVVHSRAVEA





LKEAGPVVRLVVRRRQN


 


255
NeDLG domain 3
10863920
ILLHKGSTGLGFNIVGGEDGEGIFVSFILAGGPADLSG





ELRRGDRILSVNGVNLRNATHEQAAAALKRAGQSVTIV





AQYRPEEYSRFESKIHDLREQMMNSSMSSGSGSLRTSE





KRSLE


 


256
NeDLG domains 1
10863920
YEEIVLERGNSGLGFSIAGGIDNPHVPDDPGIFITKII



and 2

PGGAAAMDGRLGVNDCVLRVNEVEVSEVVHSRAVEALK





EAGPVVRLVVRRRQPPPETIMEVNLLKGPKGLGFSIAG





GIGNQHIPGDNSIYITKIIEGGAAQKDGRLQIGDRLLA





VNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPGSL


 


257
Neurabin II domain
AJ401189
RVERLELFPVELEKDSEGLGISIIGMGAGADMGLEKLG



1

IFVKTVTEGGAAHRDGRIQVNDLLVEVDGTSLVGVTQS





FAASVLRNTKGRVRCRFMIGRERPGEQSEV


 


258
NOS1 domain 1
642525
QPNVISVRLFKRKVGGLGELVKERVSKPPVIISDLIRG





GAAEQSGLIQAGDIILAVNGRPLVDLSYDSALEVLRGI





ASETHVVLILRGPE


 


259
novel PDZ gene
7228177
PSDTSSEDGVRRIVHLYTTSDDFCLGFNIRGGKEFGLG



domain 2

IYVSKVDHGGLAEENGIKVGDQVLAANGVRFDDISHSQ





AVEVLKGQTHIMLTIKETGRYPAYKEM


 


260
novel PDZ gene
7228177
EANSDESDIIHSVRVEKSPAGRLGFSVRGGSEHGLGIF



domain 1

VSKVEEGSSAERAGLCVGDKITEVNGLSLESTTMGSAV





KVLTSSSRLHMMVRRMGRVPGIKFSKEK


 


261
novel serine
1621243
DKIKKFLTESHDRQAKGKAITKKKYIGIRMMSLTSSKA



protease domain 1

KELKDRHRDEPDVISGAYIIEVIPDTPAEAGGLKENDV





IISINGQSVVSANDVSDVIKRESTLNMVVRRGNEDIMI





TV


 


262
Numb BP domain 2
AK056823
YRPRDDSFHVILNKSSPEEQLGIKLVRKVDEPGVFIFN





ALDGGVAYRHGQLEENDRVLAINGHDLRYGSPESAAHL





IQASERRVHLVVSRQVRQRSPD


 


263
Numb BP domain 3
AK056823
PTITCHEKVVNIQKDPGESLGMTVAGGASHREWDLPIY





VISVEPGGVISRDGRIKTGDILLNVDGVELTEVSRSEA





VALLKRTSSSIVLKALEVKEYEPQ


 


264
Numb BP domain 1
AK056823
PDGEITSIKINRVDPSESLSIRLVGGSETPLVHIIIQH





IYRDGVIARDGRLLPRDIILKVNGMDISNVPHNYAVRL





LRQPCQVLWLTVMREQKFRSR


 


265
Numb BP domain 4
AK056823
PRCLYNCKDIVLRRNTAGSLGFCIVGGYEEYNGNKPFF





IKSIVEGTPAYNDGRIRCGDILLAVNGRSTSGMIHACL





ARLLKELKGRITLTIVSWPGTFL


 


266
outer membrane
7023825
LLTEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIYVS



domain 1

RIKENGAAALDGRLQEGDKILSVNGQDLKNLLHQDAVD





LFRNAGYAVSLRVQHRLQVQNGIHS


 


267
p55T domain 1
12733367
PVDAIRILGIHKRAGEPLGVTFRVENNDLVIARILHGG





MIDRQGLLHVGDIIKEVNGHEVGNNPKELQELLKNISG





SVTLKILPSYRDTITPQQ


 


268
PAR3 domain 2
8037914
GKRLNIQLKKGTEGLGFSITSRDVTIGGSAPIYVKNIL





PRGAAIQDGRLKAGDRLIEVNGVDLVGKSQEEVVSLLR





STKMEGTVSLLVFRQEDA


 


269
PAR3 domain 1
8037914
IPNFSLDDMVKLVEVPNDGGPLGIHVVPFSARGGRTLG





LLVKRLEKGGKAEHENLFRENDCIVRINDGDLRNRRFE





QAQHMFRQAMRTPIIWFHVVPAANKEQYEQ


 


270
PAR3 domain 3
8037914
PREFLTFEVPLNDSGSAGLGVSVKGNRSKENHADLGIF





VKSIINGGAASKDGRLRVNDQLIAVNGESLLGKTNQDA





METLRRSMSTEGNKRGMIQLIVASRISKCNELKSNSS


 


271
PAR3L domain 2
18874467
ISNKNAKKIKIDLKKGPEGLGFTVVTRDSSIHGPGPIF





VKNILPKGAAIKDGRLQSGDRILEVNGRDVTGRTQEEL





VAMLRSTKQGETASLVIARQEGH


 


272
PAR3L domain 3
18874467
ITSEQLTFEIPLNDSGSAGLGVSLKGNKSRETGTDLGI





FIKSIIHGGAAFKDGRLRMNDQLIAVNGESLLGKSNHE





AMETLRRSMSMEGNIRGMIQLVILRRPERP


 


273
PAR3L domain 1
18874467
IPRTKDTLSDMTRTVEISGEGGPLGIHVVPFFSSLSGR





ILGLFIRGIEDNSRSKREGLEHENECIVKINNVDLVDK





TFAQAQDVFRQAMKSPSVLLHVLPPQNR


 


274
PAR6 domain 1
2613011
PETHRRVRLHKHGSDRPLGFYIRDGMSVRVAPQGLERV





PGIFISRLVRGGLAESTGLLAVSDEILEVNGIEVAGKT





LDQVTDMMVANSHNLIVTVKPANQRNNV


 


275
PAR6 beta domain
1353716
IPVSSIIDVDILPETHRRVRLYKYGTEKPLGFYIRDGS



1

SVRVTPHGLEKVPGIFISRLVPGGLAQSTGLLAVNDEV





LEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQRN





NRIHRD


 


276
PAR6 GAMMA
13537118
IDVDLVPETHRRVRLHRHGCEKPLGFYIRDGASVRVTP



domain 1

HGLEKVPGIFISRMVPGGLAESTGLLAVNDEVLEVNGI





EVAGKTLDQVTDMMIANSHNLIVTVKPANQRNNVV


 


277
PDZ-73 domain 3
5031978
PEQIMGKDVRLLRIKKEGSLDLALEGGVDSPIGKVVVS





AVYERGAAERHGGIVKGDEIMAINGKIVTDYTLAEADA





ALQKAWNQGGDWIDLVVAVCPPKEYDD


 


278
PDZ-73 domain 2
5031978
IPGNRENKEKKVFISLVGSRGLGCSISSGPIQKPGIFI





SHVKPGSLSAEVGLEIGDQIVEVNGVDFSNLDHKEAVN





VLKSSRSLTISIVAAAGRELFMTDEF


 


279
PDZ-73 domain 1
5031978
RSRKLKEVRLDRLHPEGLGLSVRGGLEFGCGLFISHLI





KGGQADSVGLQVGDEIVRINGYSISSCTHEEVINLIRT





KKTVSIKVRHIGLIPVKSSPDEFH


 


280
PDZKI domain 2
2944188
RLCYLVKEGGSYGFSLKTVQGKKGVYMTDITPQGVAMR





AGVLADDHLIEVNGENVEDASHEEVVEKVKKSGSRVMF





LLVDKETDKREFIVTD


 


281
PDZK1 domain 3
2944188
QFKRETASLKLLPHQPRIVEMKKGSNGYGEYLRAGSEQ





KGQIIKDIDSGSPAEEAGLKNNDLVVAVNGESVETLDH





DSVVEMIRKGGDQTSLLVVDKETDNMYRLAEFIVTD


 


282
PDZK1 domains 2
2944188
RLCYLVKEGGSYGFSLKTVQGKKGVYMTDITPQGVAMR



and 3 and 4

AGVLADDHLIEVNGENVEDASHEKVVEKVKKSGSRVMF





LLVDKETDKRHVEQKIQFKRETASLKLLPHQPRIVEMK





KGSNGYGFYLRAGSEQKGQIIKDIDSGSPAEEAGLKNN





DLVVAVNGESVETLDHDSVVEMIRKGGDQTSLLVVDKE





TDNMYRLAHFSPFLYYQSQELPNGSVKEAPAPTPTSLE





VSSPPDTTEEVDHKPKLCRLAKGENGYGFHLNAIRGLP





GSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYE





KVVDRIQSSGKNVTLLVCGK


 


283
PDZK1 domain 4
2944188
PDTTEEVDHKPKLCRLAKGENGYGFHLNAIRGLPGSFI





KEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVD





RIQSSGKNVTLLVGKNSS


 


284
PDZK1 domain 1
2944188
LTSTFNPRECKLSKQEGQNYGFFLRIEKDTEGHLVRVV





EKCSPAEKAGLQDGDRVLRINGVFVDKEEHMQVVDLVR





KSGNSVTLLVLDGDSYEKAGSHEPS


 


285
PICK1 domain 1
4678411
LGIPTVPGKVTLQKDAQNLIGISIGGGAQYCPCLYIVQ





VFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKM





IQEVKGEVTIHYNKLQADPKQGM


 


286
PIST domain 1
98374330
SQGVGPIRKVLLLKEDHEGLGISITGGKEHGVPILISE





IHPGQPADRCGGLHVGDAILAVNGVNLRDTKHKEAVTI





LSQQRGEIEFEVVYVAPEVDSD


 


287
prIL16 domain 2
1478492
TAEATVCTVTLEKMSAGLGFSLEGGKGSLHGDKPLTIN





RIFKGAASEQSETVQPGDEILQLGGTAMQGLTRFEAWN





IIKALPDGPVTIVIRRKSLQSK


 


288
prIL16 domain 1
1478492
IHVTILHKEEGAGLGFSLAGGADLENKVITVHRVFPNG





LASQEGTIQKGNEVLSINGKSLKGTTHHDALAILRQAR





EPRQAVIVTRKLTPEEFIVTD


 


289
prIL16 domains 1
1478492
IHVTILHKEEGAGLGFSLAGGADLENKVITVHRVFPNG



and 2

LASQEGTIQKGNEVLSINGKSLKGTTHHDALAILRQAR





EPRQAVIVTRKLTPEAMPDLNSSTDSAASASAASDVSV





ESTAEATVCTVTLEKMSAGLGFSLEGGKGSLHGDKPLT





INRIFKGAASEQSETVQPGDEILQLGGTAMQGLTRFEA





WNIIKALPDGPVTIVIRRKSLQSK


 


290
PSAP domain 1
6409315
IREAKYSGVLSSIGKIFKEEGLLGFFVGLIPHLLGDVV





FLWGCNLLAHFINAYLVDDSVSDTPGGLGNDQNPGSQF





SQALAIRSYTKEVMGIAVSMLTYPFLLVGDLMAVNNCG





LQAGLPPYSPVFKSWIHCWKYLSVQGQLFRGSSLLFRR





VSSGSCFALE


 


291
PSD95 domains 1
3318652
EGEMEYEEITLERGNSGLGFSIAGGTDNPHIGDDPSIF



and 2 and 3

ITKIIPGGAAAQDGRLRVNDSILFVNEVDVREVTHSAA





VEALKEAGSIVRLYVMRRKPPAEKVMEIKLIKGPKGLG





FSIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGRLQIG





DKILAVNSVGLEDVMHEDAVAALKNTYDVVYLKVAKPS





NAYLSDSYAPPDITTSYSQHLDNEISHSSYLGTDYPTA





MTPTSPRRYSPVAKDLLGEEDIPREPRRIVIHRGSTGL





GFNIVGGEDGEGIFISFILAGGPADLSGELRKGDQILS





VNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPE


 


292
PSD95 domain 2
3318652
HVMRRKPPAEKVMEIKLIKGPKGLGFSIAGGVGNQHIP





GDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLED





VMHEDAVAALKNTYDVVYLKVAKPSNAYL


 


293
PSD95 domain 3
3318652
REDIPREPRRIVIHRGSTGLGFNIVGGEDGEGIFISFI





LAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIAL





KNAGQTVTIIAQYKPEFIVTD


 


294
PSD95 domain 1
3318652
LEYEeITLERGNSGLGESIAGGTDNPHIGDDPSIFITK





IIPGGAAAQDGRLRVNDSILFVNEVDVREVTHSAAVEA





LKEAGSIVRLYVMRRKPPAENSS


 


295
PSMD9 domain 1
9184389
RDMAEAHKEAMSRKLGQSESQGPPRAFAKVNSISPGSP





ASIAGLQVDDEIVEFGSVNTQNFQSLHNIGSVVQHSEG





ALAPTILLSVSM


 


296
PTN-3 domain 1
179912
QNDNGDSYLVLIRITPDEDGKFGFNLKGGVDQKMPLVV





SRINPESPADTCIPKLNEGDQIVLINGRDISEHTHDQV





VMFIKASRESHSRELALVIRRRAVRS


 


297
PTN-4 domain 1
190747
IRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADL





CVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERH





SGELMLLVRPNA


 


298
PTPL1 domain 2
515030
GDIFEVELAKNDNSLGISVTGGVNTSVRHGGIYVKAVI





PQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVETLR





NTGQVVHLLLEKGQSPTSK


 


299
PTPL1 domain 1
515030
PEREITLVNLKKDAKYGLGFQIIGGEKMGRLDLGIFIS





SVAPGGPADFHGCLKPGDRLISVNSVSLEGVSHHAAIE





ILQNAPEDVTLVISQPKEKISKVPSTPVHL


 


300
PTPL1 domain 4
515030
ELEVELLITLIKSEKASLGFTVTKGNQRIGCYVHDVIQ





DPAKSDGRLKPGDRLIKVNDTDVTNMTHTDAVNLLRAA





SKTVRLVIGRVLELPRIPMLPH


 


301
PTPL1 domain 3
515030
TEENTFEVKLFKNSSGLGFSFSREDNLIPEQINASIVR





VKKLFAGQPAAESGKIDVGDVILKVNGASLKGLSQQEV





ISALRGTAPEVFLLLCRPPPGVLPEIDT


 


302
PTPL1 domain 5
515030
MLPHLLPDITLTCNKEELGFSLCGGHDSLYQVVYISDI





NPRSVAAIEGNLQLLDVIHYVNGVSTQGMTLEEVNRAL





DMSLPSLVLKATRNDLPV


 


303
RGS 3 domain 1
18644735
VCSERRYRQITIPRGKDGFGFTICCDSPVRVQAVDSGG





PAERAGLQQLDTVLQLNERPVEHWKCVELAHEIRSCPS





EIILLVWRMVPQVKPG


 


304
RGS12 domain 1
3290015
RPSPPRVRSVEVARGRAGYGFTLSGQAPCVLSCVMRGS





PADFVGLRAGDQILAVNEINVKKASHEDVVKLIGKCSG





VLHMVIAEGVGRFESCS


 


305
Rho-GAP 10
50345878
SEDETFSWPGPKTVTLKRTSQGFGFTLRHFIVYPPESA



domain 1

IQFSYKDEENGNRGGKQRNRLEPMDTIFVKQVKEGGPA





FEAGLCTGDRIIKVNGESVIGKTYSQVIALIQNSDTTL





ELSVMPKDED


 


306
Rhophilin domain 1
AY082588
SAKNRWRLVGPVHLTRGEGGFGLTLRGDSPVLIAAVIP





GSQAAAAGLKEGDYIVSVNGQPCRWWRHAEVVTELKAA





GEAGASLQVVSLLPSSRLPS


 


307
Rhophilin-like
AF268032
ISFSANKRWTPPRSIRFTAEEGDLGFTLRGNAPVQVHF



domain 1

LDPYCSASVAGAREGDYIVSIQLVDCKWLTLSEVMKLL





KSFGEDEIEMKVVSLLDSTSSMHNKSAT


 


308
RIM2 domain 1
12734165
TLNEEHSHSDKHPVTWQPSKDGDRLIGRILLNKRLKDG





SVPRDSGAMLGLKVVGGKMTESGRLCAFITKVKKGSLA





DTVGHLRPGDEVLEWNGRLLQGATFEEVYNIILESKPE





PQVELVVSRPIG


 


309
SEMCAP 3 domain
5889526
QEMDREELELEEVDLYRMNSQDKLGLTVCYRTDDEDDI



2

GIYISEIDPNSIAAKDGRIREGDRIIQINGIEVQNREE





AVALLTSEENKNFSLLIARPELQLD


 


310
SEMCAP 3 domain
5889526
QGEETKSLTLVLHRDSGSLGFNIIGGRPSVDNHDGSSS



1

EGIFVSKIVDSGPAAKEGGLQIHDRIIEVNGRDLSRAT





HDQAVEAFKTAKEPIVVQVLRRTPRTKMFTP


 


311
semcap2 domain 1
7019938
ILAHVKGIEKEVNVYKSEDSLGLTITDNGVGYAFIKRI





KDGGVIDSVKTICVGDHIESINGENIVGWRHYDVAKKL





KELKKEELFTMKLIEPKKAFEI


 


312
serine protease
2738914
RGEKKNSSSGISGSQRRYIGVMMLTLSPSILAELQLRE



domain 1

PSFPDVQHGVLIHKVILGSPAHRAGLRPGDVILAIGEQ





MVQNAEDVYEAVRTQSQLAVQIRRGRETLTLYV


 


313
Shank 1 domain 1
6049185
ILEEKTVVLQKKDNEGFGFVLRGAKADTPIEEFTPTPA





FPALQYLESVDEGGVAWQAGLRTGDFLIEVNNENVVKV





GHRQVVNMIRQGGNHLVLKVVTVTRNLDPDDNSS


 


314
Shank 2 domain 1
7025450
ILKEKTVLLQKKDSEGFGFVLRGAKAQTPIEEFTPTPA





FPALQYLESVDEGGVAWRAGLRMGDFLIEVNGQNVVKV





GHRQVVNMIRQGGNTLMVKVVMVTRHPDMDEAVQNSS


 


315
Shank 3 domain 1
*
SDYVIDDKVAVLQKRDHEGFGFVLRGAKAETPIEEFTP





TPAFPALQYLESVDVEGVAWRAGLRTGDFLIEVNGVNV





VKVGHKQVVALIRQGGNRLVMKVVSVTRKPEEDG


 


316
sim to lig of numb
22477649
SNSPREEIFQVALHKRDSGEQLGIKLVRRTDEPGVFIL



px2 domain 2

DLLEGGLAAQDGRLSSNDRVLAINGHDLKYGTPELAAQ





IIQASGERVNLTIARPGKPQPG


 


317
sim to lig of numb
22477649
IQCVTCQEKHITVKKEPHESLGMTVAGGRGSKSGELPI



px2 domain 3

FVTSVPPHGCLARDGRIKRGDVLLNINGIDLTNLSHSE





AVAMLKASAASPAVALKALEVQIVEEAT


 


318
Similar to
14286261
MGLGVSAEQPAGGAEGFHLHGVQENSPAQQAGLEPYFD



GRASP65 domain 1

FIITIGHSRLNKENDTLKALLKANVEKPVKLEVFNMKT





MRVREVEVVPSNMWGGQGLLGASVRFCSFRRASE


 


319
Similar to
14286261
RASEQVWHVLDVEPSSPAALAGLRPYTDYVVGSDQILQ



GRASP65 domain 2

ESEDFFTLIESHEGKPLKLMVYNSKSDSCRESGMWHWL





WVSTPDPNSAPQLPQEATWHPTTFCSTTWCPTT


 


320
Similar to Protein-
21595065
ISVTDGPKFEVKLKKNANGLGFSFVQMEKESCSHLKSD



Tyrosine-

LVRIKRLFPGQPAEENGAIAAGDIILAVNGRSTEGLIF



Phosphatase

QEVLHLLRGAPQEVTLLLCRPPPGA



Homolog domain 1




 


321
SIP1 domain 1
2047327
QPEPLRPRLCRLVRGEQGYGFHLHGEKGRRGQFIRRVE





PGSPAEAAALRAGDRLVEVNGVNVEGETHHQVVQRIKA





VEGQTRLLVVDQETDEELRRRNSS


 


322
SIP1 domain 2
2047327
PLRELRPRLCHLRKGPQGYGENLHSDKSRPGQYIRSVD





PGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKA





REDEARLLVVDPETDEHFKRNSS


 


323
SITAC 18 domain 1
8886071
PGVREIHLCKDERGKFGLRLRKVDQGLFVQLVQANTPA





SLVGLRFGDQLLQIDGRDCAGWSSHKAHQVVKKASGDK





IVVVVRDRPFQRTVTM


 


324
SITAC 18 domain 2
8886071
PFQRTVTMHKDSMGHVGFVIKKGKIVSLVKGSSAARNG





LLTNHYVCEVDGQNVIGLKDKKIMEILATAGNVVTLTI





IPSVIYEHIVEFIV


 


325
SNPC IIa domain 1
20809633
SLERPRFCLLSKEEGKSFGFHLQQELGRAGHVVCRVDP





GTSAQRQGLQEGDRILAVNNDVVEHEDYAVVVRRIRAS





SPRVLLTVLARHAHDVARAQ


 


326
SYNTENIN domain
2795862
LRDRPFERTITMHKDSTGHVGFIFKNGKITSIVKDSSA



2

ARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVV





TITIMPAFIFEHMNSS


 


327
SYNTENIN domain
2795862
LEIKQGIREVILCKDQDGKIGLRLKSIDNGIFVQLVQA



1

NSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQA





FGEKITMRIHRD


 


328
Syntrophin 1 alpha
1145727
QRRRVTVRKADAGGLGISIKGGRENKMPILISKIFKGL



domain 1

AADQTEALFVGDAILSVNGEDLSSATHDEAVQVLKKTG





KEVVLEVKYMKDVSPYFK


 


329
Syntrophin beta 2
476700
PVRRVRVVKQEAGGLGISIKGGRENRMPILISKIFPGL



domain 1

AADQSRALRLGDAILSVNGTDLRQATHDQAVQALKRAG





KEVLLEVKFIRE


 


330
Syntrophin gamma
9507162
EPFYSGERTVTIRRQTVGGFGLSIKGGAEHNIPVVVSK



1 domain 1

ISKEQRAELSGLLFIGDAILQINGINVRKCRHEEVVQV





LRNAGEEVTLTVSFLKRAPAFLKL


 


331
Syntrophin gamma
9507164
SHQGRNRRTVTLRRQPVGGLGLSIKGGSEHNVPVVISK



2 domain 1

IFEDQAADQTGMLFVGDAVLQVNGIHVENATHEEVVHL





LRNAGDEVTITVEYLREAPAFLK


 


332
TAX2-like protein
3253116
RGETKEVEVTKTEDALGLTITDNGAGYAFIKRIKEGSI



domain 1

INRIEAVCVGDSIEAINDHSIVGCRHYEVAKMLRELPK





SQPFTLRLVQPKRAF


 


333
TIAM1 domain 1
4507500
HSIHIEKSDTAADTYGFSLSSVEEDGIRRLYVNSVKET





GLASKKGLKAGDEILEINNRAADALNSSMLKDFLSQPS





LGLLVRTYPELE


 


334
TIAM2 domain 1
6912703
PLNVYDVQLTKTGSVCDFGFAVTAQVDERQHLSRIFIS





DVLPDGLAYGEGLRKGNEIMTLNGEAVSDLDLKQMEAL





FSEKSVGLTLIARPPDTKATL


 


335
TIP1 domain 1
2613001
QRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKT





DKGIYVTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMVT





HDQARKRLTKRSEEVVRLLVTRQSLQK


 


336
TIP2 domain 1
2613003
RKEVEVFKSEDALGLTITDNGAGYAFIKRIKEGSVIDH





IHLISVGDMIEAINGQSLLGCRHYEVARLLKELPRGRT





FTLKLTEPRK


 


337
TIP33 domain 1
2613007
HSHPRVVELPKTDEGLGFNVMGGKEQNSPIYISRIIPG





GVAERHGGLKRGDQLLSVNGVSVEGEHHEKAVELLKAA





KDSVKLVVRYTPKVL


 


338
TIP43 domain 1
2613011
LSNQKRGVKVLKQELGGLGISIKGGKENKMPILISKIF





KGLAADQTQALYVGDAILSVNGADLRDATHDEAVQALK





RAGKEVLLEVKYMREATPYVK


 


339
Unknown PDZ
22382223
IQRSSIKTVELIKGNLQSVGLTLRLVQSTDGYAGHVII



domain 1

ETVAPNSPAAIADLQRGDRLIAIGGVKITSTLQVLKLI





KQAGDRVLVYYERPVGQSNQGA


 


340
Vartul domain 1
1469875
ILTLTILRQTGGLGISIAGGKGSTPYKGDDEGIFISRV





SEEGPAARAGVRVGDKLLEVNGVALQGAEHHEAVEALR





GAGTAVQMRVWRERMVEPENAEFIVTD


 


341
Vartul domain 4
1469875
RELCIQKAPGERLGISIRGGARGHAGNPRDPTDEGIFI





SKVSPTGAAGRDGRLRVGLRLLEVNQQSLLGLTHGEAV





QLLRSVGDTLTVLVCDGFEASTDAALEVS


 


342
Vartul domain 3
1469875
LEGPYPVEEIRLPRAGGPLGLSIVGGSDHSSHPFGVQE





PGVFISKVLPRGLAARSGLRVGDRILAVNGQDVRDATH





QEAVSALLRPCLELSLLVRRDPAEFIVTD


 


343
Vartul domain 2
1469875
PLRQRHVACLARSERGLGFSIAGGKGSFPYRAGDAGIF





VSRIAEGGAAHRAGTLQVGDRVLSINGVDVTEARHDHA





VSLLTAASPTIALLLEREAGG


 


344
Vartul domains 1
1469875
TLTILRQTGGLGISIAGGKGSTPYKGDDEGIFISRVSE



and 2

EGPAARAGVRVGDKLLEGIFVSRIAEGGAAHRAGTLQV





GDRVLSINGVDVTEARHDHAVSLLTAASPTIALLLERE


 


345
X-11 beta domain 2
3005559
IPPVTTVLIKRPDLKYQLGESVQNGIICSLMRGGIAER





GGVRVGHRIIEINGQSVVATAHEKIVQALSNSVGEIHM





KTMPAAMFRLLTGQENSSL


 


346
X-11 beta domain 1
3005559
IHFSNSENCKELQLEKHKGEILGVVVVESGWGSILPTV





ILANMMNGGPAARSGKLSIGDQIMSINGTSLVGLPLAT





CQGIIKGLKNQTQVKLNIVSCPPVTTVLIKRNSS


 


347
ZO-1 domain 1
292937
IWEQHTVTLHRAPGEGFGIAISGGRDNPHFQSGETSIV





ISDVLKGGPAEGQLQENDRVAMVNGVSMDNVEHAFAVQ





QLRKSGKNAKITIRRKKKVQIPNSS


 


348
ZO-1 domain 2
292937
ISSQPAKPTKVTLVKSRKNEEYGLRLASHIFVKEISQD





SLAARDGNIQEGDVVLKINGTVTENMSLTDAKTLIERS





KGKLKMVVQRDRATLLNSS


 


349
ZO-1 domain 3
292937
IRMKLVKFRKGDSVGLRLAGGNDVGIFVAGVLEDSPAA





KEGLEEGDQILRVNNVDFTNIIREEAVLFLLDLPKGEE





VTILAQKKKDVFSN


 


350
ZO-2 domain 1
12734763
IQHTVTLHRAPGFGFGIAISGGRDNPHFQSGETSIVIS





DVLKGGPAEGQLQENDRVAMVNGVSMDNVEHAFAVQQL





RKSGKNAKITIRRKKKVQIPNSS


 


351
ZO-2 domain 3
12734763
HAPNTKMVRFKKGDSVGLRLAGGNDVGIFVAGIQEGTS





AEQEGLQEGDQILKVNTQDFRGLVREDAVLYLLEIPKG





EMVTILAQSRADVY


 


352
ZO-2 domain 2
12734763
RVLLMKSRANEEYGLRLGSQIFVKEMTRTGLATKDGNL





HEGDIILKINGTVTENMSLTDARKLIEKSRGKLQLVVL





RDS


 


353
ZO-3 domain 3
10092690
RGYSPDTRVVRFLKGKSIGLRLAGGNDVGIFVSGVQAG





SPADGQGIQEGDQILQVNDVPFQNLTREEAVQFLLGLP





PGEEMELVTQRKQDIFWKMVQSEFIVTD


 


354
ZO-3 domain 1
10092690
IPGNSTIWEQHTATLSKDPRRGFGIAISGGRDRPGGSM





VVSDVVPGGPAEGRLQTGDHIVMVNGVSMENATSAFAI





QILKTCTKMANITVKRPRRIHLPAEFIVTD


 


355
ZO-3 domain 2
10092690
QDVQMKPVKSVLVKRRDSEEFGVKLGSQIFIKHITDSG





LAARHRGLQEGDLILQINGVSSQNLSLNDTRRLIEKSE





GKLSLLVLRDRGQFLVNIPNSS





*: No GI number for this PDZ domain containing protein as it was computer cloned using rat Shank3 sequence against human genomic clone AC000036 and in silico spliced together nucleotides 6400-6496, 6985-7109, 7211-7400 to create hypothetical human Shank3.






Methods for Detecting the Presence of an Oncogenic HPV E6 Protein in a Sample
The invention provides a method of detecting the presence of an oncogenic HPV E6 protein in a sample. In general, the method involves contacting a biological sample containing or potentially containing an oncogenic HPV E6 protein with a PDZ domain polypeptide and detecting any binding of the oncogenic HPV E6 protein in said sample to the PDZ domain polypeptide using a subject antibody. In alternative embodiments, a sample may be contacted with a subject antibody, and the presence of the E6 protein may be detected using the PDZ domain polypeptide. In most embodiments, binding of an oncogenic HPV E6 protein to the PDZ domain polypeptide and a subject antibody indicates the presence of an oncogenic HPV E6 protein in the sample.
Biological samples to be analyzed using the methods of the invention may be obtained from any mammal, e.g., a human or a non-human animal model of HPV. In many embodiments, the biological sample is obtained from a living subject.
In some embodiments, the subject from whom the sample is obtained is apparently healthy, where the analysis is performed as a part of routine screening. In other embodiments, the subject is one who is susceptible to HPV, (e.g., as determined by family history; exposure to certain environmental factors; etc.). In other embodiments, the subject has symptoms of HPV (e.g., cervical warts, or the like). In other embodiments, the subject has been provisionally diagnosed as having HPV (e.g. as determined by other tests based on e.g., PCR).
The biological sample may be derived from any tissue, organ or group of cells of the subject. In some embodiments a cervical scrape, biopsy, or lavage is obtained from a subject. In other embodiments, the sample is a blood or urine sample.
In some embodiments, the biological sample is processed, e.g., to remove certain components that may interfere with an assay method of the invention, using methods that are standard in the art. In some embodiments, the biological sample is processed to enrich for proteins, e.g., by salt precipitation, and the like. In certain embodiments, the sample is processed in the presence proteasome inhibitor to inhibit degradation of the E6 protein.
In the assay methods of the invention, in some embodiments, the level of E6 protein in a sample may be quantified and/or compared to controls. Suitable control samples are from individuals known to be healthy, e.g., individuals known not to have HPV. Control samples can be from individuals genetically related to the subject being tested, but can also be from genetically unrelated individuals. A suitable control sample also includes a sample from an individual taken at a time point earlier than the time point at which the test sample is taken, e.g., a biological sample taken from the individual prior to exhibiting possible symptoms of HPV.
In certain embodiments, a sample is contacted to a solid support-bound PDZ domain polypeptide under conditions suitable for binding of the PDZ domain polypeptide to any PL proteins in the sample, and, after separation of unbound sample proteins from the bound proteins, the bound proteins are detected using the subject antibody using known methods.
Kits
The present invention also includes kits for carrying out the methods of the invention. A subject kit usually contains a subject antibody. In many embodiments, the kits contain a first and second binding partner, where the first binding partner is a PDZ domain polypeptide and the second binding partner is a subject antibody. In some embodiments, the second binding partner is labeled with a detectable label. In other embodiments, a secondary labeling component, such as a detectably labeled secondary antibody, is included. In some embodiments, a subject kit further comprises a means, such as a device or a system, for isolating oncogenic HPV E6 from the sample. The kit may optionally contain proteasome inhibitor.
A subject kit can further include, if desired, one or more of various conventional components, such as, for example, containers with one or more buffers, detection reagents or antibodies. Printed instructions, either as inserts or as labels, indicating quantities of the components to be used and guidelines for their use, can also be included in the kit. In the present disclosure it should be understood that the specified materials and conditions are important in practicing the invention but that unspecified materials and conditions are not excluded so long as they do not prevent the benefits of the invention from being realized. Exemplary embodiments of the diagnostic methods of the invention are described above in detail.
In a subject kit, the oncogenic E6 detection reaction may be performed using an aqueous or solid substrate, where the kit may comprise reagents for use with several separation and detection platforms such as test strips, sandwich assays, etc. In many embodiments of the test strip kit, the test strip has bound thereto a PDZ domain polypeptide that specifically binds the PL domain of an oncogenic E6 protein and captures oncogenic E6 protein on the solid support. The kit usually comprises a subject antibody for detection, which is either directly or indirectly detectable, and which binds to the oncogenic E6 protein to allow its detection. Kits may also include components for conducting western blots (e.g., pre-made gels, membranes, transfer systems, etc.); components for carrying out ELISAs (e.g., 96-well plates); components for carrying out immunoprecipitation (e.g. protein A); columns, especially spin columns, for affinity or size separation of oncogenic E6 protein from a sample (e.g. gel filtration columns, PDZ domain polypeptide columns, size exclusion columns, membrane cut-off spin columns etc.).
Subject kits may also contain control samples containing oncogenic or non-oncogenic E6, and/or a dilution series of oncogenic E6, where the dilution series represents a range of appropriate standards with which a user of the kit can compare their results and estimate the level of oncogenic E6 in their sample. Such a dilution series may provide an estimation of the progression of any cancer in a patient. Fluorescence, color, or autoradiological film development results may also be compared to a standard curves of fluorescence, color or film density provided by the kit.
In addition to above-mentioned components, the subject kits typically further include instructions for using the components of the kit to practice the subject methods. The instructions for practicing the subject methods are generally recorded on a suitable recording medium. For example, the instructions may be printed on a substrate, such as paper or plastic, etc. As such, the instructions may be present in the kits as a package insert, in the labeling of the container of the kit or components thereof (i.e., associated with the packaging or subpackaging) etc. In other embodiments, the instructions are present as an electronic storage data file present on a suitable computer readable storage medium, e.g. CD-ROM, diskette, etc. In yet other embodiments, the actual instructions are not present in the kit, but means for obtaining the instructions from a remote source, e.g. via the internet, are provided. An example of this embodiment is a kit that includes a web address where the instructions can be viewed and/or from which the instructions can be downloaded. As with the instructions, this means for obtaining the instructions is recorded on a suitable substrate.
Also provided by the subject invention are kits including at least a computer readable medium including programming as discussed above and instructions. The instructions may include installation or setup directions. The instructions may include directions for use of the invention with options or combinations of options as described above. In certain embodiments, the instructions include both types of information.
The instructions are generally recorded on a suitable recording medium. For example, the instructions may be printed on a substrate, such as paper or plastic, etc. As such, the instructions may be present in the kits as a package insert, in the labeling of the container of the kit or components thereof (i.e., associated with the packaging or subpackaging), etc. In other embodiments, the instructions are present as an electronic storage data file present on a suitable computer readable storage medium, e.g., CD-ROM, diskette, etc, including the same medium on which the program is presented.
Utility
The antibodies and methods of the instant invention are useful for a variety of diagnostic analyses. The instant antibodies and methods are useful for diagnosing infection by an oncogenic strain of HPV in an individual; for determining the likelihood of having cancer; for determining a patient's response to treatment for HPV; for determining the severity of HPV infection in an individual; and for monitoring the progression of HPV in an individual. The antibodies and the methods of the instant invention are useful in the diagnosis of infection with an oncogenic or a non-oncogenic strain of HPV associated with cancer, including cervical, ovarian, breast, anus, penis, prostate, larynx and the buccal cavity, tonsils, nasal passage, skin, bladder, head and neck squamous-cell, occasional periungal carcinomas, as well as benign anogenital warts. The antibodies and the methods of the instant invention are useful in the diagnosis of infection with an oncogenic or a non-oncogenic strain of HPV associated with Netherton's syndrome, epidermolysis verruciformis, endometriosis, and other disorders. The antibodies and the methods of the instant invention are useful in the diagnosis of infection with an oncogenic or a non-oncogenic strain of HPV in adult women, adult men, fetuses, infants, children, and immunocompromised individuals.
The subject methods may generally be performed on biological samples from living subjects. A particularly advantageous feature of the invention is that the methods can simultaneously detect, in one reaction, several known oncogenic strains of HPV.
In particular embodiments, the antibodies of the invention may be employed in immunohistological examination of a sample.
EXAMPLES
The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Centigrade, and pressure is at or near atmospheric.
Example 1
Sequence Analysis of HPV E6 Proteins to Determine Oncogenic Potential
PDZ proteins are known to bind certain carboxyl-terminal sequences of proteins (PLs). PL sequences that bind PDZ domains are predictable, and have been described in greater detail in U.S. patent application Ser. Nos. 09/710,059, 09/724,553 and 09/688,017. One of the major classes of PL motifs is the set of proteins terminating in the sequences -X-(S/T)-X-(V/I/L). We have examined the C-terminal sequences of E6 proteins from a number of HPV strains. All of the strains determined to be oncogenic by the National Cancer Institute exhibit a consensus PDZ binding sequence. Those E6 proteins from papillomavirus strains that are not cancerous lack a sequence that would be predicted to bind to PDZ domains, thus suggesting that interaction with PDZ proteins is a prerequisite for causing cancer in humans. This correlation between presence of a PL and ability to cause cancer is 100 % in the sequences examined (Table 3 A). In theory, with the disclosed PL consensus sequences from the patents listed supra, new variants of HPVs can be assessed for their ability to bind PDZ proteins and oncogenicity can be predicted on the basis of whether a PL is present. Earlier this year, five new oncogenic strains of Human papillomavirus were identified and their E6 proteins sequenced. As predicted, these proteins all contain a PL consensus sequence (Table 3 B).







TABLE 3A







Correlation of E6 PDZ-ligands and oncogenicity











HPV
E6 C-terminal
PL
Onco-
Seq


strain
sequence
yes/no
genic
ID No





HPV 4
GYCRNCIRKQ
No
No
 33


 


HPV 11
WTTCMEDLLP
No
No
 34


 


HPV 20
GICRLCKHFQ
No
No
 35


 


HPV 24 
KGLCRQCKQI
No
No
 36


 


HPV 28
WLRCTVRIPQ
No
No
 37


 


HPV 36
RQCKHFYNDW
No
No
 38


 


HPV 48
CRNCISHEGR
No
No
 39


 


HPV 50
CCRNCYEHEG
No
No
 40


 


HPV 16
SSRTRRETQL
Yes
Yes
 41


 


HPV 18
RLQRRRETQV
Yes
Yes
 42


 


HPV 31
WRRPRTETQV
Yes
Yes
 43


 


HPV 35
WKPTRRETEV
Yes
Yes
 44


 


HPV 30
RRTLRRETQV
Yes
Yes
 45


 


HPV 39
RRLTRRETQV
Yes
Yes
 46


 


HPV 45
RLRRRRETQV
Yes
Yes
 47


 


HPV 51
RLQRRNETQV
Yes
Yes
 48


 


HPV 52
RLQRRRVTQV
Yes
Yes
 49


 


HPV 56
TSREPRESTV
Yes
Yes
 50


 


HPV 59
QRQARSETLV
Yes
Yes
 51


 


HPV 58
RLQRRRQTQV
Yes
Yes
 52


 


HPV 33
RLQRRRETAL
Yes
Yes
 53


 


HPV 66
TSRQATESTV
Yes
 Yes*
 54


 


HPV 68
RRRTRQETQV
Yes
Yes
 55


 


HPV 69
RRREATETQV
Yes
Yes
 56


 


HPV 34
QCWRPSATVV
Yes
Yes
356


 


HPV 67
WRPQRTQTQV
Yes
Yes
357


 


HPV 70
RRRIRRETQV
Yes
Yes
358





Table 3A: E6 C-terminal sequences and oncogenicity.


HPV variants are listed at the left.


Sequences were identified from Genbank sequence records.


PL Yes/No was defined by a match or non-match to the consenses determined by the inventors and by Songyang et al. −X-(S/T)-X-(V/I/L).


Oncogenicity data collected from National Cancer Institute; Kawashima et al. (1986) J. Virol. 57:688-692; Kirii et al. (1998) Virus Genes 17:117-121; Forslund et al. (1996) J. Clin. Microbiol. 34:802-809.


*Only found in oncogenic strains co-transfected with other oncogenic proteins.













TABLE 3B







Correlation of recently 


identified oncogenic E6 proteins











HPV
E6 C-terminal
PL
onco-
Seq


strain
sequence
yes/no
genic
ID No





HPV 26
RPRRQTETQV
Yes
Yes
63


 


HPV 53
RHTTATESAV
Yes
Yes
64


 


HPV 66
TSRQATESTV
Yes
Yes
65


 


HPV 73
RCWRPSATVV
Yes
Yes
66


 


HPV 82
PPRQRSETQV
Yes
Yes
67





Table 3B: E6 C-terminal sequences and oncogenicity.


HPV variants are listed at the left.


Sequences were identified from Genbank sequence records.


PL Yes/No was defined by a match or non-match to the consensus sequence: −X-(S/T)-X-(V/I/L).


Oncogenicity data on new strains collected from N Engl J Med 2003; 348:518-527.






These tables provide a classification of the HPV strains based on the sequence of the C-terminal four amino acids of the E6 protein encoded by the HPV genome. The 21 oncogenic strains of HPV fall into one of 11 classes (based on the C-terminal four amino acids), and HPV strains not specifically listed above may also fall into these classes. As such, it is desirable to detect HPV strains from all 11 classes: the instant methods provide such detection.
A cross-reactive antibody of the invention may recognize E6 proteins from HPV strains of multiple (e.g., 2, 3, 4, 5, 6, or 7 or more different) classes.
Example 2
Identification of PDZ Domains that Interact with the C-Termini of Oncogenic E6 Proteins
In order to determine the PDZ domains that can be used to detect oncogenic E6 proteins in a diagnostic assay, the assay was used to identify interactions between E6 PLs and PDZ domains. Peptides were synthesized corresponding to the C-terminal amino acid sequences of E6 proteins from oncogenic strains of human papillomavirus. These peptides were assessed for the ability to bind PDZ domains using an assay and PDZ proteins synthesized from the expression constructs described in greater detail in U.S. patent application Ser. Nos. 09/710,059, 09/724,553 and 09/688,017. Results of these assays that show a high binding affinity are listed in Table 4 below.
As we can see below, there a large number of PDZ domains that bind some of the oncogenic E6 proteins and the second PDZ domain from MAGI-1 binds all of the oncogenic E6 PLs tested. The PDZ domain of TIP-1 binds all but one of the oncogenic E6 PLs tested, and may be useful in conjunction with MAGI-1 domain 2 for detecting the presence of oncogenic E6 proteins.
In a similar manner, peptides corresponding to the C-terminal ends of several non-oncogenic E6 proteins were tested with assay. None of the peptides showed any affinity for binding PDZ domains.







TABLE 4







higher affinity interactions between HPV E6 PLs and PDZ domains










HPV
PDZ binding partner
HPV
PDZ binding partner


strain
(signal 4 and 5 of 0-5)
strain
(signal 4 and 5 of 0-5)





HPV 35
Atrophin-1 interact. prot.
HPV 33
Magi1 (PDZ #2)


(T E V)
(PDZ # 1, 3, 5)
(T A L)
TIP1



Magi1 (PDZ # 2, 3, 4, 5)

DLG1



Lim-Ril

Vartul (PDZ #1)



FLJ 11215

KIAA 0807



MUPP-1 (PDZ #10)

KIAA 1095 (Semcap3) 



KIAA 1095 (PDZ #1)

(PDZ #1)



PTN-4

KIAA 1934 (PDZ #1)



INADL (PDZ #8)

NeDLG (PDZ #1, 2)



Vartul (PDZ # 1, 2, 3)

Rat outer membrane 



Syntrophin-1 alpha

(PDZ #1)



Syntrophin gamma-1

PSD 95 (PDZ #3 and 1-3)



TAX IP2





KIAA 0807





KIAA 1634 (PDZ #1)





DLG1 (PDZ1, 2)





NeDLG (1, 2, 3,)





Sim. Rat outer membrane





(PDZ #1)





MUPP-1 (PDZ #13)





PSD 95 (1, 2, 3)




HPV 58
Atrophin-1 interact. prot. 
HPV 66
DLG1 (PDZ #1, 2)


(T Q V)
(PDZ # 1)
(S T V)
NeDLG (PDZ #2)



Magi1 (PDZ #2)

PSD 95 (PDZ #1, 2, 3)



DLG1 (PDZ1, 2)

Magi1 (PDZ #2)



DLG2 (PDZ #2)

KIAA 0807



KIAA 0807

KIAA 1634 (PDZ #1)



KIAA 1634 (PDZ #1)

DLG2 (PDZ #2)



NeDLG (1, 2)

Rat outer membrane 



Sim. Rat outer membrane 

(PDZ #1)



(PDZ #1)

NeDLG (1, 2)



PSD 95 (1, 2, 3)

TIP-1



INADL (PDZ #8)





TIP-1




HPV 16*
TIP-1
HPV 52
Magi1 (PDZ #2)


(T Q L)
Magi1 (PDZ #2)
(T Q V)



HPV 18*
TIP1




(T Q V)
Magi1 (PDZ #2)





Table 4: Interactions between the E6 C-termini of several HPV variants and human PDZ domains. HPV strain denotes the strain from which the E6 C-terminal peptide sequence information was taken. Peptides used in the assay varied from 18 to 20 amino acids in length, and the terminal four residues are listed in parenthesis. Names to the right of each HPV E6 variant denote the human PDZ domain(s) (with domain number in parenthesis for proteins with multiple PDZ domains) that saturated binding with the E6 peptide in assay


*denotes that the PDZ domains of hDlg1 were not tested against these proteins yet due to limited material, although both have been shown to bind hDlg1 in the literature.






The subject antibodies may be used with these oncogenic HPV E6-binding PDZ proteins in methods of detecting oncogenic strains of HPV.
Materials and Methods for Examples 3-7
Immunization protocol: Five 8 week-old female BALB/c mice are immunized intraperitoneally, in the footpad, or subcutaneously on day zero with 20 μg of MBP-E6 fusion protein or 100 μg of E6 conjugated-peptide and 20 μg of polyI/polyC polymer or complete Freund's adjuvant. Animals are boosted with 20 μg of E6 protein and polyI/polyC or incomplete Freund's adjuvant. Test bleeds are performed 3 days after the last boostand screened by ELISA against the corresponding E6 protein. Immunoreactive mice have a final boost three days prior to fusion.
ELISA screening of serum antibody titer and B cell hybridoma supernatants: ELISA plates are coated with appropriate fusion protein, washed, and blocked with PBS containing 2% BSA (Sigma). Then the test sample (immune sera or hybridoma supernatant) is added, along with a pre-immune or irrelevant supernatant negative control. After incubation the plate is washed and anti-mouse IgG-HRP conjugate (Jackson Laboratories) in PBS/2 % BSA is added. After thorough washing, TMB substrate is added for 30 minutes, followed by termination of the reaction with 0.18 M H2 SO4 . The plate is then read at 450 nm using a Molecular Devices' THERMO Max microplate reader.
Fusion: On the day of fusion, the animals are sacrificed, blood collected, and the spleens excised and minced with scissors. The cells are then gently teased up and down with a pipette, filtered through a sterile 70 μm nylon filter and washed by centrifugation. Splenocytes and the FOX-NY myeloma partner (maintained prior to fusion in log growth) are resuspended in serum-free-RPMI medium, combined at a ratio of 4:1 and spun down together. The fusion is then performed by adding 1 ml of 50 % PEG (Sigma) drop-wise over one minute, followed by stirring the cells for one minute. Then 2 ml of RPMI/15 % FCS media is added drop-wise over two minutes, followed by 8 ml of RPMI/15 % FCS over 2 minutes with constant stirring. This mixture is centrifuged, and the cells are gently resuspended at 108 cells/ml in RPMI/15 % FCS+1 × HAT media (Sigma) and plated out in 96-well flat bottom plates at 200 μl/well. After 5 days  ̃100 μl old medium is replaced by aspirating out of wells, and adding 100 μl fresh RPMI/HAT medium. Hybridomas are kept in RPMI/HAT for  ̃7 days. Then are grown in RPMI/15 % FCS containing 1 × HT for  ̃1 week. Wells are assayed for antibody activity by ELISA when they are 10-30 % confluent.
Hybridoma cloning, antibody purification and isotyping: Wells whose supernatants give the desired activity were selected for cloning. Cells are cloned by limiting dilution in a 96-well flat bottom plate. Purification of antibodies from tissue culture supernatants is performed by protein G and A affinity chromatography (Amersham). The isotype of the antibodies is determined using Cytometric bead array.
Cell lines: Cervical cancer cell lines expressing listed strains of HPV E6 were purchased from ATCC, and are shown in the following table:















ATCC
Common


E6
GenBank


Name
Name
Organism
Tissue
type
Accession #







HTB-31
C-33A
human
cervix
None



HTB-32
HT-3
human
cervix
30



HTB-33
ME-180
human
cervix
68b
M73258


HTB-34
MS751
human
cervix
45
X74479


HTB-35
SiHa
human
cervix
16



CRL-1550
CaSki
human
cervix
16



CRL-1594
C-41
human
cervix
18



CRL-1595
C-4-II
human
cervix
18









Stably or transiently transfected cells were produced using the following methods:
The following stable cell lines were made: 3 A-HA-E6-26 (expresses HPV 26 E6); C33A-HA-E6-53 (expresses HPV 53 E6); C33 A-HA-E6-58 (expresses HPV 58 E6); C33 A-HA-E6-59 (expresses HPV 59 E6); C33 A-HA-E6-66 (expresses HPV 66 E6); C33 A-HA-E6-69 (expresses HPV 69 E6) and C33 A-HA-E6-73 (expresses HPV 73 E6).
Calcium Phosphate Transfection of Mammalian Cell Lines
Materials: Deionized water, 2 M CaCl2, 2 × HBS pH 7.1, 25 mM Chloroquine (1000 ×), DNA.
Day 0: Plate 0.8 million cells in each well of a 6-well plate the night before transfection. (2 wells for each construct, therefore, 3 constructs in a 6-well plate)
Day 1: a) Aliquot appropriate cell media and add Chloroquine (Add 12.5 μl for every 10 ml of media. The extra 2.5 μl is to account for the 500 ul of the calcium phosphate+DNA solution that will be added to the cells later). b) Aspirate media off the cells and add 2 mL of the media+Chloroquine solution. Return cells to incubator. c) In a 5 mL polypropylene tube, add the following in the order listed: i) deionized water, ii) DNA and iii) 2 M CaCl2 as follows:













DNA
Deionized water
2M CaCl2
2X HBS







10 μg
(DNA + 64 + dH20 = 500 μl
64 μl
500 μl









d) Add 500 μl of the DNA mix drop wise to the 2 × HBS while bubbling with automatic pipetman and Pasteur pipette; e) Add 500 μl DNA/calcium/phosphate solution to each well; and f) Incubate in incubator for 8 hours, then replace media with normal growth media.
Day 3: Start selection with G-418 (Gibco) at 1 mg/ml
Cells for transient expression of HPV 51 E6 were produced by standard methods.
Example 3
HPV-E6 Recombinant Protein Expression and Purification
Polynucleotides encoding E6 proteins of high-risk HPV types listed above were chemically synthesized (DNA 2.0, Menlo Park, Calif.) or cloned via RT-PCR from cervical cancer cell lines. Both maltose-binding-protein-E6 (MBP-E6) and glutathione-S-transferase-E6 (GST-E6) fusion protein types were used. Production of GST-E6 and MBP-E6 proteins were by standard protocols recommended by the suppliers (Amersham and New England Biolabs, respectively). Proteins were expressed in DH5α E. coli using IPTG driven induction. A 2 h induction at 37° C. yielded GST-E6 or MBP-E6 recombinant proteins at  ̃1 mg/L, whereas induction overnight at 20 ° C. and purification including rebinding of protein to the gel matrix resulted in final yield of 2-10 mg/L. Purity of MBP-E6 proteins was estimated to be >90 % based on PAGE analysis. Recombinant E6 fusion proteins were used as immunogens.
Example 4
Immunization, Fusion, Screening and Cloning of Hybridomas Secreting Monoclonal Antibodies Against E6 Protein
Mice were immunized with each of the HPV E6 proteins. A variety of immunization protocols including varying antigen doses (100 μg-10 μg), adjuvants (CFA/IFA, poly(I)-poly(C), CpG+Alum) and routes (subcutaneous, intraperitoneal) were tested. A service facility for animal care, handling of immunizations and sera collection was contracted (Josman, Napa, Calif.). Immunization projects were set up with 5-15 mice each. Sera of immunized mice were tested in ELISA against the recombinant E6 protein. Mice showing sufficiently high titers (OD above 1 at 1:1000 dilution) against E6 in their sera were selected for fusions.
To increase the frequency of hybridomas secreting of anti-E6 antibodies, the recombinant E6 protein used in the final boost contained a different tag from that used during the immunization (GST-E6 was used in the boost when immunizations occurred with MBP-E6, and vice versa)
Example 5
Spleen Cells of Selected Mice were Fused
Hybridoma supernatants were tested via direct antigen ELISA against the MBP-E6 used in the immunization and MBP protein as negative control. Supernatants that showed reactivity for MBP-E6 (immunogen) but not for MBP were selected for further analysis. Selected supernatants were tested further by slot western blot for reactivity against recombinant MBP-E6 and GST-E6, to reconfirm presence of anti-E6 mAb. At this stage, hybridomas were cloned by limiting dilution to isolate hybridoma clones secreting anti-E6 mAb.
To further characterize the reactivity of the hybridomas, selected supernatants were tested in an ELISA against the recombinant E6 proteins, as well as GST-INADL (PDZ) and GST-MAGI1-PDZ1 that served as negative controls. GST-INADL represents a class of proteins that, when purified in prokaryotic expression systems, tend to be associated with a bacterial contaminating that are also present in the MBP-/GST-E6 protein preparations used for immunizations. This control ensured that reactivity found in supernatants reflected a mAb binding to HPV-E6, and not against the associated contaminants.
Example 6
Cross-Reactivity Pattern of Anti-E6 Monoclonal Antibodies
The cross-reactivity pattern of anti-E6 mAbs against E6 proteins other than the one used as immunogen was tested. For this E6 panel test, a direct ELISA approach is used (recombinant E6 protein is coated on the plate).
Monoclonal antibodies against the E6 protein of high-risk HPV types that cause cervical cancer (e.g., HPV 16, 18, 26, 30, 31, 34, 45, 51, 52, 53, 58, 59, 66, 68b, 69, 70, 73, 82) were produced.
A summary of results showing cross-reactivity of the antibodies produced is shown In Table 5 below.












TABLE 5







HPV-E6







binding
Endogenous E6




mAb
HPV-E6 type binding
profile S2
detection S2
Immunogen and
Immunization route and


designation
profile - direct ELISA
ELISA
ELISA
boosts/last boost
adjuvant







F12-1B9
18, 45, 66
N.D.
N.D.
HPV18-[MBP]-E6/
subcutaneous/Adjuvant:


F12-1C9
18
N.D.
N.D.
HPV18-[GST]-E6
complete/incomplete


F12-1H12
18
N.D.
N.D.

Freund's (initial/follow up


F12-2D2
18, 45, 66
N.D.
N.D.

injections)


F12-3B2
18
N.D.
N.D.




F12-3D5
18, 45, 66, 82
18, 45
18, 45




F12-4A11
18
18
18




F12-4 E2
18
18, 45
N.D.




F12-5C2
18
N.D.
N.D.




F12-6D9
18, 45
N.D.
N.D.




F12-6F5
18
N.D.
N.D.




F12-6F6
18, 45
N.D.
N.D.




F12-6H2
18, 45, 66, 82
N.D.
N.D.




F12-7A10
18, 45
N.D.
N.D.




F12-7F10
18
N.D.
N.D.




F12-8A3
18, 45
N.D.
N.D.




F12-8B8
18
N.D.
N.D.




F16-4H12
16, 35
16
N.D.
HPV16-[MBP]-E6/
subcutaneous/Adjuvant:


F16-5D5
16, 35
16
does not
HPV16-[GST]-E6
complete/incomplete





recognize 16

Freund's (initial/follow up







injections)


F17-1 E11
26, 51, 52, 53, 58
N.D.
N.D.
HPV58-[MBP]-E6/
subctaneous/Adjuvant:


F17-6G9
33, 58
58
does not
HPV58-[GST]-E6
complete/incomplete





recognize 58

Freund's (initial/follow up







injections)


F18-3G11
16
16
does not
HPV16-[GST]-E6/
subcutaneous/Adjuvant:





recognize 16
HPV16-[MBP]-E6
complete/incomplete


F18-4C9
16
N.D.
N.D.

Freund's (initial/follow up


F18-5H3
16
N.D.
N.D.

injections)


F18-7H8
16
N.D.
N.D.




F18-8G11
16
N.D.
N.D.




F18-9B10
16, 73
N.D.
N.D.




F18-10 E6
16
16
16




F18-10 E10
16
N.D.
N.D.




F19-6D10
18, 68b
18, 68b
does not
DNA plasmid






recognize 18 or
immunization; boost






68b
with HPV18-E6 (MBP-



F19-6F9
18, 68b
18, 68b
N.D.
E6/GST-E6)



F19-7B12
18, 35, 68b
N.D.
N.D.




F19-7C7
18, 68b
N.D.
N.D.




F19-8E2
18, 35, 68b
N.D.
N.D.




F20-2H5
16, 18, 35, 45
18, 35, 45
does not
HPV45-[MBP]-E6/
subcutaneous/Adjuvant:





recognize 18 or
HPV45-[GST]-E6
complete/incomplete





45; 35 N.D.

Freund's (initial/follow up







injections)


F21-1D12
18, 30, 52, 58
30, 58
does not
HPV58-[MBP]-E6/
footpad injection/Adjuvant:





recognize 30 or
HPV58-[GST]-E6
CpG-ALUM





58




F21-3A3
18, 58
N.D.
N.D.




F21-3H2
18, 30, 52, 58
58
N.D.




F21-4 E10
18, 30, 52, 58
58
N.D.




F21-4F9
18, 33, 58
N.D.
N.D.




F21-4H1
18, 30, 33, 52, 58
33, 58
33, 58




F21-5B2
16, 18, 30, 52, 58, 59, 68b
N.D.
N.D.




F22-1C12
26, 51, 69
51
51
HPV51-[MBP]-E6/
subctaneous/Adjuvant:


F22-10D11
26, 30,
N.D.
N.D.
HPV51-[GST]-E6
complete/incomplete



31, 35, 51, 53, 66, 69, 82



Freund's (initial/follow up







injections)


F22-10F10
26, 51, 69
51
N.D.




F24-2D6
26, 51, 69, 82
26, 69
26, 69
HPV69-[MBP]-E6/
subcutaneous/Adjuvant:


F24-4B12
26, 51, 53, 69, 73, 82
N.D.
N.D.
HPV69-[GST]-E6
complete/incomplete







Freund's (initial/follow up


F24-4F2
26, 51, 69, 82
26, 69, 82
26, 69; 82 N.D.

injections)


F24-4G1
26, 51, 69, 82
N.D.
N.D.




F24-8H12
26, 51, 69, 82
26, 69, 82
N.D.




F24-9H12
26, 51, 69, 82
26, 69
N.D.




F25-2D11
73
N.D.
N.D.
HPV73-[MBP]-E6/
subcutaneous/Adjuvant:


F25-3D10
53, 73, 82
N.D.
N.D.
HPV73-[GST]-E6
complete/incomplete


F25-3 E5
16, 34, 59, 70, 73
N.D.
N.D.

Freund's (initial/follow up injections)


F25-4C11
16, 34, 59, 70, 73
34
does not







recognize 73, 34







N.D.




F26-1B10
51, 53
N.D.
N.D.
HPV53-[MBP]-E6/
subcutaneous/Adjuvant:


F26-1B11
53
N.D.
N.D.
HPV53-[GST]-E6
complete/incomplete


F26-1D9
53
N.D.
N.D.

Freund's (initial/follow up


F26-1D11
53
N.D.
N.D.

injections)


F26-2B12
53
N.D.
N.D.




F26-2G5
53
N.D.
N.D.




F26-3A8
30, 53, 66
N.D.
N.D.




F26-5H5
53
N.D.
N.D.




F26-6D10
53
N.D.
N.D.




F26-8B7
53
N.D.
N.D.




F26-8H9
53
N.D.
N.D.




F26-9C2
53
N.D.
N.D.




F26-9C7
53
N.D.
N.D.




F26-9D8
53
N.D.
N.D.




F26-9G5
53, 73, 82
N.D.
N.D.




F27-3A4
59
N.D.
N.D.
HPV59-[MBP]-E6/
subcutaneous/Adjuvant:






HPV59-[GST]-E6
complete/incomplete







Freund's (initial/follow up







injections)


6F4
16
16, 35, 69
recognizes 16
HPV16-
poly-I/poly-C adjuvant/three





and 69, 35 N.D.
[GST]E6/HPV16-
immunizations






[GST]E6



4C6
16
16
N.D.
HPV16-
poly-I/poly-C adjuvant/three






[GST]E6/HPV16-
immunizations






[GST]E6



3F8
16
16, 35, 51,
N.D.
HPV16-[MBP]E6-C-
poly-I/poly-C adjuvant/three




82, 31, 33

terminal
immunizations




and 58

portion/HPV16-







[MBP]E6-C-terminal







portion









FIG. 3 shows results obtained from a slot western blot of recombinant E6 protein, probed with hybridoma supernatants.
Example 7
Selection of Antibodies for HPV Diagnostic Test
Supernatants from hybridomas reacting with E6 proteins are tested together with the oncogenic PL detector in a sandwich ELISA with recombinant E6 fusion protein.
Monoclonal antibodies are tested in HPV diagnostic ELISA for their ability to detect E6 from cervical cancer cell lines or cells transfected with E6 (if cell lines are unavailable).
It is evident from the above results and discussion that the subject invention provides an important new means for detecting HPV E6 proteins. In particular, the subject invention provides a system for detecting oncogenic strains of HPV. It is superior to current methods because the PDZ protein isolates the oncogenic E6 protein from other analytes of a complex biological sample, and the protein is detected using an antibody that cross-reacts with more than one E6 protein. The specificity of detection lies in the PDZ protein and the antibody does not need to bind only oncogenic E6 proteins, as currently required in conventional methods. Accordingly, the subject methods and systems find use in a variety of different diagnostic applications. Accordingly, the present invention represents a significant contribution to the art.

## Claims

1. A monoclonal antibody that is non-human and that binds to a sub-sequence of a common sequence of an early gene protein from at least two oncogenic human papillomavirus (HPV) strains selected from the group consisting of HPV strains 16, 18, 31, 33, 52, and 58, wherein the common sequence is an amino acid sequence motif that is conserved within a same gene protein from the at least two oncogenic HPV strains, wherein the common sequence comprises at least 9 contiguous amino acids within a region of sequence similarity between the same early gene protein of the at least two oncogenic HPV strains, wherein the region of sequence similarity is located within amino acids 1-43 of the N-terminus of the same early gene protein or within 41 amino acids of the C-terminus of the same early gene protein, and wherein:
a) the early gene protein from the at least two oncogenic HPV strains is encoded by a nucleic acid sequence within the HPV early gene protein 6-HPV early gene protein 7 (E6-E7) region of an HPV genome; and
b) a dissociation constant of the monoclonal antibody for the early gene protein from the at least two oncogenic HPV strains is less than 10−5 M.

2. The monoclonal antibody of claim 1, wherein the antibody binds to SEQ ID NO: 7 or 8 with a dissociation constant of less than 10−5 M.

3. The monoclonal antibody of claim 1, wherein the antibody binds to an E6 peptide having SEQ ID NO: 11 or 12 with a dissociation constant of less than 10−5 M.

4. The monoclonal antibody of claim 1, wherein the antibody binds to an HPV E6 peptide having SEQ ID NO: 1, 2, 3, 4, 5, 6, 57, 58, or 59 with a dissociation constant of less than 10−5 M.

5. The monoclonal antibody of claim 1, wherein the antibody has a dissociation constant of less than 10−7 M for each of the at least two oncogenic strains.

6. The monoclonal antibody of claim 1, wherein the antibody has a dissociation constant of less than 10−8 M for each of the at least two oncogenic strains.

7. The monoclonal antibody of claim 1, wherein the antibody has a dissociation constant of less than 10−9 M for each of the at least two oncogenic strains.

8. An antibody composition comprising a mixture of monoclonal antibodies that bind to HPV early protein 6 (E6) proteins of oncogenic human papillomavirus (HPV) strains, wherein at least one of said monoclonal antibodies is the monoclonal antibody according to claim 1.

9. The antibody composition of claim 8, wherein at least said monoclonal antibody according to claim 1 binds to an E6 peptide having SEQ ID NO: 1, 2, 3, 4, 5, 6, 57, 58, or 59.

10. The antibody composition of claim 8, wherein said mixture of monoclonal antibodies binds to E6 proteins of HPV strains 16, 18, and 45.

11. The antibody composition of claim 8, wherein said mixture of monoclonal antibodies binds to E6 proteins of HPV strains 16, 18, 31, 33, 45, 52, 58, 35 and 59.

12. A diagnostic kit for the detection of a human papillomavirus (HPV) E6 polypeptide in a sample, comprising: the antibody composition of claim 8.

13. The diagnostic kit of claim 12, wherein said monoclonal antibodies are labeled.

14. The diagnostic kit of claim 12, further comprising a PDZ domain polypeptide that binds to an oncogenic HPV E6 polypeptide in a sample.

15. A method of detecting a human papillomavirus (HPV) E6 protein in a sample, comprising: contacting the antibody composition of claim 8 with said sample; and detecting any binding of said antibodies within said composition to said sample, wherein binding of said antibodies within said composition to said sample indicates the presence of an HPV E6 protein.

16. The method of claim 15, wherein said sample is suspected of containing an oncogenic strain of HPV.

17. A method of detecting the presence of an oncogenic human papillomavirus (HPV) early protein 6 (E6) protein in a sample, said method comprising: contacting a sample with a PDZ domain polypeptide; and detecting any binding of said oncogenic HPV E6 protein to said sample to said PDZ domain polypeptide using the antibody composition of claim 8; wherein binding of said oncogenic HPV E6 protein to said PDZ domain polypeptide indicates the presence of an oncogenic HPV E6 protein in said sample.

18. A system for detecting the presence of an oncogenic human papillomavirus (HPV) early protein 6 (E6) polypeptide in a sample, said system comprising: a first and a second binding partner for an oncogenic HPV E6 polypeptide, wherein said first binding partner is a PDZ domain protein and said second binding partner is the antibody of claim 1.

19. The system of claim 18, wherein at least one of said binding partners is attached to a solid support.

20. The monoclonal antibody of claim 1, wherein the at least two oncogenic HPV strains are selected from the group consisting of HPV strains: 16, 31, and 33.

21. The monoclonal antibody of claim 1, wherein the at least two oncogenic HPV strains are selected from the group consisting of HPV strains: 52, and 58.

22. The monoclonal antibody of claim 1, wherein the at least two oncogenic HPV strains are selected from the group consisting of HPV strains: 16 and 18.

23. The monoclonal antibody of claim 1, wherein the early gene protein is E6.

24. The monoclonal antibody of claim 1, wherein the antibody binds the oncogenic protein encoded by a nucleic acid sequence that encodes for a protein selected from the group consisting of SEQ ID NOs: 13, 14, 15, 16, 17, and 18 with a dissociation constant of less than 10−5 M.

25. The monoclonal antibody of claim 1, wherein the common sequence has a sequence corresponding to SEQ ID NO: 1.

26. The monoclonal antibody of claim 1, wherein the sub-sequence has a sequence corresponding to SEQ ID NO: 7.

27. The monoclonal antibody of claim 1, wherein the monoclonal antibody is a humanized antibody.

28. The monoclonal antibody of claim 1, wherein the monoclonal antibody is a chimeric antibody.

29. The monoclonal antibody of claim 1, wherein the dissociation constant of the monoclonal antibody for the early gene protein from the at least two oncogenic HPV strains is less than 10−5 M when measured by direct enzyme-linked immunosorbent assay (ELISA).

30. The monoclonal antibody of claim 1, wherein the dissociation constant of the monoclonal antibody for the early gene protein from the at least two oncogenic HPV strains is less than 10−8 M when measured by direct enzyme-linked immunosorbent assay (ELISA).

31. The monoclonal antibody of claim 1, wherein the monoclonal antibody is a mouse antibody.