CA2331769A1 - Prostate cancer-associated genes - Google Patents

Abstract

The invention provides novel prostate cancer-associated genes and polypeptides encoded by those genes. The invention also provides expression vectors, host cells, antibodies, agonists, and antagonists. The invention also provides methods for diagnosing, treating or preventing diseases.

Description

PROSTATE CANCER-ASSOCIATED GENES
A portion of the disclosure of this patent document contains material which is subject to copyright protection. The copyright owner has no objection to the facsimile reproduction by anyone of the patent document or the patent disclosure, as it appears in the Patent and Trademark Office patent file or records, but otherwise reserves all copyright rights whatsoever.
1 o TECHNICAL FIELD
The invention relates to a method for analyzing gene expression patterns. The invention also relates to eight prostate cancer-associated genes identified by the method and their corresponding polypeptides and to the use of these biomolecules in diagnosis, prognosis, treatment, prevention, and evaluation of therapies for diseases, particularly diseases associated with cell proliferation, such as cancer.
BACKGROUND OF THE INVENTION
2o The DNA sequences of many human genes have been determined, but for many of these genes, their biological function, and in particular their relationship to disease, is unknown or poorly understood. Current laboratory and computational methods to determine or predict the possible functions of newly-sequenced genes are slow and expensive. Thus, new methods that provide additional information on function are desirable.
Prostate cancer is a common malignancy in men over the age of 50, and the incidence increases with age. In the US, there are approximately 132,000 newly diagnosed cases of prostate cancer and more than 33,000 deaths from prostate cancer each year. The occurrences of prostate cancer vary among different regions in the world. For 3o example, there are 14 deaths per 100,000 men per year in the US, compared with 22 in Sweden and 2 in Japan.
Genes known to be involved in prostate cancer, such as prostate-specific antigen (PSA}, prostatic acid phosphatase (PAP), kallikrein, seminal plasma protein, and prostate-specific tranglutaminase, have been used or proposed as the basis for diagnostic and prognostic tests as well as therapeutic targets. In particular, prostate-specific antigen (PSA) is a protease used in diagnosis for prostate cancer (Morris, D. L. et al. (1998) J.
Clin. Lab. Anal. 12: 65-74). Prostatic acid phosphatase (PAP) is a phosphomonoesterase synthesized in the prostate and secreted into the seminal plasma under androgenic control (Ostrowski, W. S. and R. Kuciel (1994) CIin. Chim. Acta 226:121-129}, and has been used in diagnostic tests for prostate cancer and in prognostic tests for metastatic cancer (Presti, J. C., Jr. and P. R. Carroll (1996) Semin Urol Oncol 14(3): 134-138).
Kallikrein is a to protease expressed specifically in the prostate and has 80% sequence similarity with PSA
(Corey, E., K. R. et al. (1997) Urology 50: 567-572). Kallikrein is being evaluated for use in diagnostic tests for prostate cancer (Pannek, J. and Partin, A. W. (1997) Oncology 11:
1273-1282). Seminal plasma protein is a prostate-specific secreted protein with activity similar to inhibin, a member of the transforming growth factor superfamily implicated in prostate cancer (Mbikay, M., S. et al. (1987) DNA 6: 23-29; Thomas, T. Z. et al. (1998) Prostate 34: 34-43); deletion of the inhibin alpha gene in male rats results in development of primary gonadal granulosa/Sertoli cell tumors (Mellor, S. L.et al. (1998) J. Clin.
Endocrinol. Metab. 83: 969-975). Prostate-specific transglutaminase catalyzes post-translational protein cross-linking, and exhibits differential expression in prostate cancer cell lines (Dubbink, H. J. (1996) Biochem. J. 315: 901-908).
The diagnostic sensitivity and specificity and the prognostic accuracy of the tests based on the known genes are substantially less than 100 percent. For example, about 20 percent of the patients undergoing prostatectomy for prostate cancer have normal levels of PSA (Presti and Carroll, su ra . Therefore, identification of novel genes and polypeptides that are markers of and potential therapeutic targets for prostate cancer is desirable.
The present invention satisfies a need in the art by providing new compositions which are useful in diagnosis, prognosis, treatment, prevention, and evaluation of therapies for diseases, particularly diseases associated with cell proliferation, such as cancer. We have implemented a method for analyzing gene expression patterns and have identified eight human prostate cancer-associated genes by their coexpression with known prostate cancer-specific genes.

-2-SUMMARY OF THE INVENTION
In one aspect, the present invention provides a method for identifying biomolecules, such as polynucleotides or polypeptides, useful in the diagnosis, prognosis, treatment, preventiqn, and evaluation of therapies for diseases, particularly diseases associated with cell proliferation such as cancer, more particularly prostate cancer. The method can also be employed for elucidating genes involved in a common regulatory pathway.
The method comprises first characterizing expression patterns of polynucleotides 1o that are expressed in a plurality of cDNA libraries. The expressed polynucleotides comprise genes of known and unknown functions. Second, the expression patterns of one or more function-specific genes are compared with the expression patterns of one or more of the genes of unknown function to identify a subset of novel genes which have similar expression patterns to those of the function-specific genes.
The method compares the expression pattern of two genes by first generating an occurrence vector for each gene. The vector comprises entries for each gene wherein a gene's presence in a cDNA library is represented by a one and a gene's absence by a zero.
The vectors are then analyzed to determine whether the expression patterns of any of the genes are similar. Expression patterns are similar if a particular coexpression probability 2o threshold is met. Preferably, the coexpression probability threshold is less than 0.001, and more preferably less than 0.00001.
In a preferred embodiment, the function-specific genes are prostate cancer-specific gene sequences including prostate-specific antigen (PSA), prostatic acid phosphatase (PAP), kallikrein, seminal plasma protein, prostate-specific tranglutaminase, and the like.
These prostate cancer-specific genes are used to identify other polynucleotides of unidentified function that are predominantly coexpressed with the prostate cancer-specific genes. The polynucleotides analyzed by the present invention can be expressed sequence tags (ESTs), assembled sequences, full length gene coding sequences, introns, regulatory regions, 5' untranslated regions, 3' untranslated regions and the like.
3o In a second aspect, the invention entails a substantially purified polynucleotide identified by the method of the present invention as being associated with prostate cancer.
In particular, the polynucleotide comprises a sequence selected from the group consisting

-3-

4 PCT/US99/13524 of SEQ ID NOs: 1-8 or its complement or a variant having at least 70% sequence identity to SEQ ID NOs: 1-8 or a polynucleotide that hybridizes under stringent conditions to SEQ
ID NOs: 1-8 or a polynucleotide encoding SEQ ID NOs: 9 and 10. The present invention also entails a polynucleotide comprising at least 18 consecutive nucleotides of a sequence provided above. The polynucleotide is suitable for use in diagnosis, treatment, prognosis, or prevention of a cancer, and in particular, prostate cancer. The polynucleotide is also suitable for the evaluation of therapies for cancer.
In another aspect, the invention provides an expression vector comprising a polynucleotide described above, a host cell comprising the expression vectar, and a 1 o method for detecting a target polynucleotide in a sample.
In a further aspect, the invention provides a substantially purified polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID
N0:9 and SEQ ID NO:10. The invention also provides a substantially purified polypeptide having at least 85% identity to SEQ ID NOs:9-10. Additionally, the invention also provides a sequence with at least 6 sequential amino acids of SEQ ID NOs:9-10.
The invention also provides a method for producing a substantially purified polypeptide comprising the amino acid sequence referred to above, and antibodies, agonists, and antagonists which specifically bind to the polypeptide.
Pharmaceutical compositions comprising the polynucleotides or polypeptides of the invention are also contemplated. Methods for producing a polypeptide of the invention and methods for detecting a target polynucleotide complementary to a polynucleotide of the invention are also included.
In a general aspect, the invention entails a method for identifying biomolecules useful in the diagnosis or treatment of a disease or condition. The method comprises a) examining expression patterns of a plurality of biomolecules that are expressed in a plurality of cDNA libraries, said expressed biomolecules comprising one or more disease-specific biomolecules and one or more biomolecules of unknown function; and b) comparing the expression patterns of said disease-specific biomolecules with the expression patterns of the biomolecules of unknown function to identify a subset of the biomolecules of unknown function which have similar expression patterns to those of disease-specific biomolecules.

BRIEF DESCRIPTION OF THE SEQUENCE LISTING
The Sequence Listing provides exemplary prostate cancer-associated sequences including polynucleotide sequences, SEQ ID NOs: 1-8, and polypeptide sequences, SEQ
ID NOs: 9-10. Each sequence is identified by a sequence identification number (SEQ ID
NO) and by the Incyte Clone number from which the sequence was first identified.
DESCRIPTION OF THE INVENTION
It must be noted that as used herein and in the appended claims, the singular forms to "a," "an," and "the" include the plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to "a host cell" includes a plurality of such host cells, and a reference to "an antibody" is a reference to one or more antibodies and equivalents thereof known to those skilled in the art, and so forth.
DEFINITIONS
"NSEQ" refers generally to a polynucleotide sequence of the present invention, including SEQ ID NOs: 1-8. "PSEQ" refers generally to a polypeptide sequence of the present invention, including SEQ ID NOs: 9-10.
A " variant" refers to either a polynucleotide or a polypeptide whose sequence 2o diverges from SEQ ID NOs: 1-10 or SEQ ID NOs:9-10, respectively.
Polynucleotide sequence divergence may result from mutational changes such as deletions, additions, and substitutions of one or more nucleotides; it may also occur because of differences in codon usage. Each of these types of changes may occur alone, or in combination, one or more times in a given sequence. Polypeptide variants include sequences that possess at least one structural or functional characteristic of SEQ ID NOs: 9-10.
"Gene" or "gene sequence" refers to the partial or complete coding sequence of a gene. The term also refers to 5' or 3' untranslated regions. The gene may be in a sense or antisense (complementary) orientation.
"Prostate cancer-specific gene" refers to a gene sequence which has been 3o previously identified as useful in the diagnosis, treatment, prognosis, or prevention of prostate cancer. Typically, this means that the prostate cancer-specific gene is expressed at higher levels in prostate cancer tissue when compared with healthy tissue.

-5-"Prostate cancer-associated gene" refers to a gene sequence whose expression pattern is similar to that of the prostate cancer-specific genes and which are useful in the diagnosis,-treatment, prognosis, or.prevention of cancer. The gene sequences can also be used in the evaluation of therapies for cancer.
"Substantially purified" refers to a nucleic acid or an amino acid sequence that is removed from its natural environment and is isolated or separated, and is at least about 60% free, preferably about 75% free, and most preferably about 90% free from other components with which it is naturally present.
1o THE INVENTION
The present invention encompasses a method for identifying biomolecules that are associated with a specific disease, regulatory pathway, subcellular compartment, cell type, tissue type, or species. In particular, the method identifies gene sequences useful in diagnosis, prognosis, treatment, prevention, and evaluation of therapies for diseases 15 associated with cell proliferation, particularly cancer, and more particularly prostate cancer.
The method entails first identifying polynucleotides that are expressed in the cDNA libraries. The polynucleotides include genes of known function, genes known to be specifically expressed in a specific disease process, subcellular compartment, cell type, 20 tissue type, or species. Additionally, the polynucleotides include genes of unknown function. The expression patterns of the known genes are then compared with those of the genes of unknown function to determine whether a specified coexpression probability threshold is met. Through this comparison, a subset of the polynucleotides having a high coexpression probability with the known genes can be identified. The high coexpression 25 probability correlates with a particular coexpression probability threshold whihc is less than 0.001, and more preferably less than 0.00001.
The polynucleotides originate from cDNA libraries derived from a variety of sources including, but not limited to, eukaryotes such as human, mouse, rat, dog, monkey, plant, and yeast and prokaryotes such as bacteria and viruses. These polynucleotides can 3o also be selected from a variety of sequence types including, but not limited to, expressed sequence tags (ESTs), assembled polynucleotide sequences, full length gene coding regions, introns, regulatory sequences, 5' untranslated regions, and 3' untranslated regions.

-6-To have statistically significant analytical results, the polynucleotides need to be expressed in at least three cDNA libraries.
The cDNA libraries used in the coexpression analysis of the present invention can be obtained from blood vessels, heart, blood cells, cultured cells, connective tissue, epithelium, islets of Langerhans, neurons, phagocytes, biliary tract, esophagus, gastrointestinal system, liver, pancreas, fetus, placenta, chromaffin system, endocrine glands, ovary, uterus, penis, prostate, seminal vesicles, testis, bone marrow, immune system, cartilage, muscles, skeleton, central nervous system, ganglia, neuroglia, neurosecretory system, peripheral nervous system, bronchus, larynx, lung, nose, pleurus, l0 ear, eye, mouth, pharynx, exocrine glands, bladder, kidney, ureter, and the like. The number of cDNA libraries selected can range from as few as 20 to greater than 10,000.
Preferably, the number of the cDNA libraries is greater than 500.
In a preferred embodiment, gene sequences are assembled to reflect related sequences, such as assembled sequence fragments derived from a single transcript.
Assembly of the polynucleotide sequences can be performed using sequences of various types including, but not limited to, ESTs, extensions, or shotgun sequences.
In a most preferred embodiment, the polynucleotide sequences are derived from human sequences that have been assembled using the algorithm disclosed in "Database and System for Storing, Comparing and Displaying Related Biomolecular Sequence Information", Lincoln et al., Serial No:60/079,469, filed March 26, 1998, herein incorporated by reference.
Experimentally, differential expression of the polynucleoddes can be evaluated by methods including, but not limited to, differential display by spatial immobilization or by gel electrophoresis, genome mismatch scanning, representational difference analysis, and transcript imaging. Additionally, differential expression can be assessed by microarray technology. These methods may be used alone or in combination.
Genes known to be prostate cancer-specific can be selected based on the use of the genes as diagnostic or prognostic markers or as therapeutic targets for prostate cancer.
Preferably, the prostate cancer-specific genes include prostate-specific antigen (PSA), 3o prostatic acid phosphatase (PAP), kallikrein, seminal plasma protein, prostate-specific tranglutaminase, and the like.
The procedure for identifying novel genes that exhibit a statistically significant coexpression pattern with prostate cancer-specific genes is as follows. First, the presence or absence of a gene sequence in a cDNA library is defined: a gene is present in a cDNA
library when at least one cDNA fragment corresponding to that gene is detected in a cDNA sample taken from the library, and a gene is absent from a library when no corresponding cDNA fragment is detected in the sample.
Second, the significance of gene coexpression is evaluated using a probability method to measure a due-to-chance probability of the coexpression. The probability method can be the Fisher exact test, the chi-squared test, or the kappa test.
These tests and examples of their applications are well known in the art and can be found in standard to statistics texts (Agresti, A. (1990) Categorical Data Analysis. New York, NY, Wiley; Rice, J. A. (1988) Mathematical Statistics and Data Analysis. Pacific Grove, CA, Wadsworth &
Brooks/Cole). A Bonferroni correction (Rice, su ra, page 384) can also be applied in combination with one of the probability methods for correcting statistical results of one gene versus multiple other genes. In a preferred embodiment, the due-to-chance ~5 probability is measured by a Fisher exact test, and the threshold of the due-to-chance probability is set to less than 0.001, more preferably less than 0.00001.
To determine whether two genes, A and B, have similar coexpression patterns, occurrence data vectors can be generated as illustrated in Table 1, wherein a gene's presence is indicated by a one and its absence by a zero. A zero indicates that the gene 2o did not occur in the library, and a one indicates that it occurred at least once.
Table 1. Occurrence data for genes A and B
Library Library Library ... Library 25 gene 1 1 0 ... 0 A

gene 1 0 1 ... 0 B

For a given pair of genes, the occurrence data in Table 1 can be summarized in a 2x2 3o contingency table.
_g_ Table 2. Contingency table for co-occurrences of genes A and B
Gent A present Gene A absent Total Gene B present 8 2 10 Gene B absent 2 18 20 Total ( 10 I 20 I 30~

Table 2 presents co-occurrence data for gene A and gene B in a total of 30 libraries. Both gene A and gene B occur 10 times in the libraries. Table 2 summarizes and l0 presents 1 ) the number of times gene A and B are both present in a library, 2) the number of times gene A and B are both absent in a library, 3) the number of times gene A is present while gene B is absent, and 4) the number of times gene B is present while gene A
is absent. The upper left entry is the number of times the two genes co-occur in a library, and the middle right entry is the number of times neither gene occurs in a library. The off I S diagonal entries are the number of times one gene occurs while the other does not. Both A
and B are present eight times and absent 18 times, gene A is present while gene B is absent two times, and gene B is present while gene A is absent two times. The probability ("p-value") that the above association occurs due to chance as calculated using a Fisher exact test is 0.0003. Associations are generally considered significant if a p-value is less 2o than 0.01 (Agresti, supra; Rice, supra).
This method of estimating the probability for coexpression of two genes makes several assumptions. The method assumes that the libraries are independent and are identically sampled. However, in practical situations, the selected cDNA
libraries are not entirely independent because more than one library may be obtained from a single patient 25 or tissue, and they are not entirely identically sampled because different numbers of cDNA's may be sequenced from each library (typically ranging from 5,000 to 10,000 cDNA's per library). In addition, because a Fisher exact coexpression probability is calculated for each gene versus 41,419 other genes, a Bonferroni correction for multiple statistical tests is necessary.
3o Using the method of the present invention, we have identified eight novel genes that exhibit strong association, or coexpression, with known genes that are prostate cancer-specific. These prostate cancer-specific genes include glandular kallikrein, prostate seminal protein, protate-specific antigen, and prostatic acid phosphatase. The results presented in Tables 5 to 12 show that the expression of eight novel genes have direct or indirect association with the expression of cancer-specific genes, in particular prostate cancer-specific genes. Therefore, the novel genes can potentially be used in diagnosis, treatment, prognosis, or prevention of cancer, or in the evaluation of therapies for cancer.
Further, the gene products of the eight novel genes are potential therapeutic proteins and targets of anti-cancer therapeutics.
Therefore, in one embodiment, the present invention encompasses a polynucleotide to sequence comprising the sequence of SEQ ID NOs:I-8. These eight polynucleotides are shown by the method of the present invention to have strong coexpression association with prostate cancer-specific genes and with each other. The invention also encompasses a variant of the polynucleotide sequence, its complement, or 18 consecutive nucleotides of the sequences provided in the above described sequences. Variant polynucleotide t5 sequences typically have at least about 70%, more preferably at least about 85%, and most preferably at least about 95% polynucleotide sequence identity to NSEQ.
One preferred method for identifying variants entails using NSEQ and/or PSEQ
sequences to search against the GenBank primate (pri), rodent (rod), and mammalian (mam), vertebrate (vrtp), and eukaryote (eukp) databases, SwissProt, BLOCKS
(Bairoch, 20 A. et al. (1997) Nucleic Acids Res. 25:217-221), PFAM, and other databases that contain previously identified and annotated motifs, sequences, and gene functions.
Methods that search for primary sequence patterns with secondary structure gap penalties (Smith, T. et al. (1992) Protein Engineering 5:35-51) as well as algorithms such as BLAST
(Basic Local Alignment Search Tool; Altschul, S.F. (1993) J. Mol. Evol 36:290-300; and Altschul et al.
25 (1990) J. Mol. Biol. 215:403-410), BLOCKS (Henikoff S. and Henikoff G.J.
(1991) Nucleic Acids Research 19:6565-6572), Hidden Markov Models (HMM; Eddy, S.R.
(1996) Cur. Opin. Str. Biol. 6:361-365; and Sonnhammer, E.L.L. et al. (1997) Proteins 28:405-420), and the like, can be used to manipulate and analyze nucleotide and amino acid sequences. These databases, algorithms and other methods are well known in the art 3o and are described in Ausubel, F.M. et al. (1997; Short Protocols in Molecular Biolo~v, John Wiley & Sons, New York , NY )and in Meyers, R.A. ( 1995; Molecular Biology Biotechnolo~y, Wiley VCH, Inc, New York, NY, p 856-853).

Also encompassed by the invention are polynucleotide sequences that are capable of hybridizing to SEQ ID NOs: l-8, and fragments thereof under stringent conditions.
Stringent conditions can be defined by salt concentration, temperature, and other chemicals and conditions well known in the art. In particular, stringency can be increased S by reducing the concentration of salt, or raising the hybridization temperature.
For example, stringent salt concentration will ordinarily be less than about 7S0 mM
NaCI and 7S mM trisodium citrate, preferably less than about S00 mM NaCI and SO mM
trisodium citrate, and most preferably less than about 2S0 mM NaCI and 2S mM
trisodium citrate. Stringent temperature conditions will ordinarily include temperatures of at least about 30°C, more preferably of at least about 37°C, and most preferably of at least about 42°C. Varying additional parameters, such as hybridization time, the concentration of detergent (sodium dodecyl sulfate, SDS) or solvent (formamide), and the inclusion or exclusion of carrier DNA, are well known to those skilled in the art.
Additional variations on these conditions will be readily apparent to those skilled in the art (Wahl, G.M. and S.L. Berger (1987) Methods Enzymol. 152:399-407; Kimmel, A.R. (1987) Methods Enzymol. 1S2:S07-511; Ausubel, F.M. et al. (1997) Short Protocols in Molecular Biolo~v, John Wiley & Sons, New York, NY; and Sambrook, J. et al. (1989) Molecular Cloning Laborator~r Manual, Cold Spring Harbor Press, Plainview, NY).
NSEQ or the polynucleotide sequences encoding PSEQ can be extended utilizing a 2o partial nucleotide sequence and employing various PCR-based methods known in the art to detect upstream sequences, such as promoters and regulatory elements. (See, e.g., Dieffenbach, C.W. and G.S. Dveksler (1995; PCR Primerya Laboratory Manual, Cold Spring Harbor Press, Plainview, NY, pp.l-S; Sarkar, G. (1993; PCR Methods Applic.
2:318-322); Triglia, T. et al. (1988; Nucleic Acids Res. 16:8186); Lagerstrom, M. et al.
(1991; PCR Methods Applic. 1:111-119); and Parker, J.D. et al. (1991; Nucleic Acids Res.
19:30SS-306). Additionally, one may use PCR, nested primers, and PROMOTERFINDER libraries to walk genomic DNA (Clontech, Palo Alto, CA). This procedure avoids the need to screen libraries and is useful in finding intron/exon junctions.
For all PCR-based methods, primers may be designed using commercially available 3o software, such as OLIGO 4.06 Primer Analysis software (National Biosciences Inc., Plymouth MN) or another appropriate program, to be about 18 to 30 nucleotides in length, to have a GC content of about SO% or more, and to anneal to the template at temperatures -ll-of about 68°C to 72°C.
In another aspect of the invention, NSEQ or the polynucleotide sequences encoding PSEQ can be cloned in recombinant DNA molecules that direct expression of PSEQ or the polypeptides encoded by NSEQ, or structural or functional fragments thereof, in appropriate host cells. Due to the inherent degeneracy of the genetic code, other DNA
sequences which encode substantially the same or a functionally equivalent amino acid sequence may be produced and used to express the polypeptides of PSEQ or the polypeptides encoded by NSEQ. The nucleotide sequences of the present invention can be engineered using methods generally known in the art in order to alter the nucletide to sequences for a variety of purposes including, but not limited to, modification of the cloning, processing, and/or expression of the gene product. DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences. For example, oligonucleotide-mediated site-directed mutagenesis may be used to introduce mutations that create new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, and so forth.
In order to express a biologically active polypeptide encoded by NSEQ, NSEQ or the polynucleotide sequences encoding PSEQ, or derivatives thereof, may be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host.
These elements include regulatory sequences, such as enhancers, constitutive and inducible promoters, and 5' and 3' untranslated regions in the vector and in NSEQ or polynucleotide sequences encoding PSEQ. Methods which are well known to those skilled in the art may be used to construct expression vectors containing NSEQ
or polynucleotide sequences encoding PSEQ and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. (See, e.g., Sambrook (supra) and Ausubel, (supra).
A variety of expression vector/host cell systems may be utilized to contain and 3o express NSEQ or polynucleotide sequences encoding PSEQ. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with viral expression vectors (baculovirus); plant cell systems transformed with viral expression vectors, cauliflower mosaic virus (CaMV) or tobacco mosaic virus (TMV), or with bacterial expression vectors (Ti or pBR322 plasmids); or animal cell systems. The invention is not limited by the host cell employed.
For long term production of recombinant proteins in mammalian systems, stable expression of a polypeptide encoded by NSEQ in cell lines is preferred. For example, NSEQ or sequences encoding PSEQ can be transformed into cell lines using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector.
1o In general, host cells that contain NSEQ and that express PSEQ may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations, PCR amplification, and protein bioassay or immunoassay techniques which include membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein sequences. Immunological methods for detecting and measuring the expression of PSEQ
using either specific polyclonal or monoclonal antibodies are known in the art. Examples of such techniques include enzyme-linked immunosorbent assays (ELISAs), radioimmunoassays (RIAs), and fluorescence activated cell sorting (FACS).
Host cells transformed with NSEQ or polynucleotide sequences encoding PSEQ
2o may be cultured under conditions suitable for the expression and recovery of the protein from cell culture. The protein produced by a transformed cell may be secreted or retained intracellularly depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides of NSEQ or polynucleotides encoding PSEQ may be designed to contain signal sequences which direct secretion of PSEQ or polypeptides encoded by NSEQ through a prokaryotic or eukaryotic cell membrane.
In addition, a host cell strain may be chosen for its ability to modulate expression of the inserted sequences or to process the expressed protein in the desired fashion. Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, 3o glycosylation, phosphorylation, lipidation, and acylation. Post-translational processing which cleaves a "prepro" form of the protein may also be used to specify protein targeting, folding, and/or activity. Different host cells which have specific cellular machinery and _1;_ WO 99/673$4 PCT/US99/13524 characteristic mechanisms for post-translational activities (e.g., CHO, HeLa, MDCK, HEK293, and WI38), are available from the American Type Culture Collection (ATCC, Bethesda, MD) and may be chosen to ensure the correct modification and processing of the foreign protein.
In another embodiment of the invention, natural, modified, or recombinant NSEQ
or nucleic acid sequences encoding PSEQ are ligated to a heterologous sequence resulting in translation of a fusion protein containing heterologous protein moieties in any of the aforementioned host systems. Such heterologous protein moieties facilitate purification of fusion proteins using commercially available affinity matrices. Such moieties include, to but are not limited to, glutathione S-transferase (GST), maltose binding protein (MBP), thioredoxin (Trx), calmodulin binding peptide (CBP), 6-His, FLAG, c-myc, hemagglutinin (HA) and monoclonal antibody epitopes..
In another embodiment, NSEQ or sequences encoding PSEQ are synthesized, in whole or in part, using chemical methods well known in the art. (See, e.g., Caruthers, 15 M.H. et al. (1980) Nucl. Acids Res. Symp. Ser. 215-223; Hom, T. et aI.
(1980) Nucl.
Acids Res. Symp. Ser. 225-232; and Ausubel, supra). Alternatively, PSEQ or a polypeptide sequence encoded by NSEQ itself, or a fragment thereof, may be synthesized using chemical methods. For example, peptide synthesis can be performed using various solid-phase techniques (Roberge, J.Y. et al. (1995) Science 269:202-204).
Automated 2o synthesis may be achieved using the ABI 431 A Peptide Synthesizer (Perkin Elmer).
Additionally, PSEQ or the amino acid sequence encoded by NSEQ, or any part thereof, may be altered during direct synthesis and/or combined with sequences from other proteins, or any part thereof, to produce a polypeptide variant.
In another embodiment, the invention entails a substantially purified polypeptide 25 comprising the amino acid sequence selected from the group consisting of SEQ ID N0:9, SEQ ID NO:10, or fragments thereof. SEQ ID N0:9 is encoded by SEQ ID N0:4 and is a potential transmembrane protein which interacts with a cell surface receptor.
SEQ ID
NO:10 is encoded by SEQ ID N0:8 and has potential sequence homology with a family of GPI-linked cell-surface glycoproteins, Ly-6/u-PAR.
DIAGNOSTICS and THERAPEUTICS
The sequences of the these genes can be used in diagnosis, prognosis, treatment, prevention, and evaluation of therapies for diseases associated with cell proliferation, particularly cancer, and more particularly prostate cancer. Further, the amino acid sequences encoded by the novel genes are potential therapeutic proteins and targets of anti-cancer therapeutics.
In one preferred embodiment, the polynucleotide sequences of NSEQ or the polynucleotides encoding PSEQ are used for diagnostic purposes to determine the absence, presence, and excess expression of PSEQ, and to monitor regulation of the levels of mRNA or the polypeptides encoded by NSEQ during therapeutic intervention.
The polynucleotides may be at least 18 nucleotides long, complementary RNA and DNA
molecules, branched nucleic acids, and peptide nucleic acids (PNAs).
Alternatively, the polynucleotides are used to detect and quantitate gene expression in samples in which expression of PSEQ or the polypeptides encoded by NSEQ are correlated with disease.
Additionally, NSEQ or the polynucleotides encoding PSEQ can be used to detect genetic polymorphisms associated with a disease. These polymorphisms may be detected at the transcript cDNA or genomic level.
The specificity of the probe, whether it is made from a highly specific region, e.g., the 5' regulatory region, or from a less specific region, e.g., a conserved motif, and the stringency of the hybridization or amplification (maximal, high, intermediate, or low), will determine whether the probe identifies only naturally occurring sequences encoding 2o PSEQ, allelic variants, or related sequences.
Probes may also be used for the detection of related sequences, and should preferably have at least 50% sequence identity to any of the NSEQ or PSEQ-encoding sequences.
Means for producing specific hybridization probes for DNAs encoding PSEQ
include the cloning of NSEQ or polynucleotide sequences encoding PSEQ into vectors for the production of mRNA probes. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by means of the addition of the appropriate RNA polymerases and the appropriate labeled nucleotides.
Hybridization probes may be labeled by a variety of reporter groups, for example, by radionuclides such as 32P or 355, or by enzymatic labels, such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems, by fluorescent labels and the like. The polynucleotide sequences encoding PSEQ may be used in Southern or northern analysis, dot blot, or other membrane-based technologies; in PCR technologies;and in microarrays utilizing fluids or tissues from patients to detect altered PSEQ expression. Such qualitative or quantitative methods are well known in the art.
NSEQ or the nucleotide sequences encoding PSEQ can be labeled by standard methods and added to a fluid or tissue sample from a patient under conditions suitable for the formation of hybridization complexes. After a suitable incubation period, the sample is washed and the signal is quantitated and compared with a standard value. If the amount of signal in the patient sample is significantly altered in comparison to the standard value then the presence of altered levels of nucleotide sequences of NSEQ and those encoding PSEQ in the sample indicates the presence of the associated disease. Such assays may also be used to evaluate the efficacy of a particular therapeutic treatment regimen in animal studies, in clinical trials, or to monitor the treatment of an individual patient.
Once the presence of a disease is established and a treatment protocol is initiated, hybridization or amplification assays can be repeated on a regular basis to determine if the level of expression in the patient begins to approximate that which is observed in the normal subject. The results obtained from successive assays may be used to show the efficacy of treatment over a period ranging from several days to months.
The polynucleotides may be used for the diagnosis of a variety of diseases associated with cell proliferation including cancer such as adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus.
Alternatively, the polynucleotides may be used as targets in a microarray. The microarray can be used to monitor the expression level of large numbers of genes simultaneously and to identify splice variants, mutations, and polymorphisms.
This information may be used to determine gene function, to understand the genetic basis of a disease, to diagnose a disease, and to develop and monitor the activities of therapeutic agents.
3o In yet another alternative, polynucleotides may be used to generate hybridization probes useful in mapping the naturally occurring genomic sequence. Fluorescent in situ hybridization (FISH) may be correlated with other physical chromosome mapping techniques and genetic map data. (See, e.g., Heinz-Ulrich, et al. (1995) in Meyers, R.A.
(ed.) Molecular Biology and Biotechnology, VCH Publishers New York, NY, pp.

968).
In another embodiment, antibodies which specifically bind PSEQ may be used for the diagnosis of diseases characterized by the over-or-underexpression of PSEQ
or polypeptides encoded by NSEQ. Alternatively, one may use competitive drug screening assays in which neutralizing antibodies capable of binding PSEQ or the polypeptides encoded by NSEQ specifically compete with a test compound for binding the polypeptides. In this manner, antibodies can be used to detect the presence of any peptide to which shares one or more antigenic determinants with PSEQ or the polypeptides encoded by NSEQ. Diagnostic assays for PSEQ or the polypeptides encoded by NSEQ
include methods which utilize the antibody and a label to detect PSEQ or the polypeptided encoded by NSEQ in human body fluids or in extracts of cells or tissues. A
variety of protocols for measuring PSEQ or the polypeptides encoded by NSEQ, including ELISAs, RIAs, and FACS, are well known in the art and provide a basis for diagnosing altered or abnormal levels of the expression of PSEQ or the polypeptides encoded by NSEQ.
Normal or standard values for PSEQ expression are established by combining body fluids or cell extracts taken from normal subjects, preferably human, with antibody to PSEQ or a polypeptide encoded by NSEQ under conditions suitable for complex formation The 2o amount of standard complex formation may be quantitated by various methods, preferably by photometric means. Quantities of PSEQ or the polypeptides encoded by NSEQ
expressed in subject, control, and disease samples from biopsied tissues are compared with the standard values. Deviation between standard and subject values establishes the parameters for diagnosing or monitoring disease.
In another aspect, the polynucleotides and polypeptides of the present invention can be employed for treatment or the monitoring of therapeutic treatments for cancers.
The polynucleotides of NSEQ or those encoding PSEQ, or any fragment or complement thereof, may be used for therapeutic purposes. In one aspect, the complement of the polynucleotides of NSEQ or those encoding PSEQ may be used in situations in which it 3o would be desirable to block the transcription or translation of the mRNA.
Expression vectors derived from retroviruses, adenoviruses, or herpes or vaccinia viruses, or from various bacterial plasmids, may be used for delivery of nucleotide -t 7-sequences to the targeted organ, tissue, or cell population. Methods which are well known to those skilled in the art can be used to construct vectors to express nucleic acid sequences_complementary to the polynucleotides encoding PSEQ. (See, e.g., Sambrook, supra; and Ausubel, supra.) s Genes having polynucleotide sequences of NSEQ or those encoding PSEQ can be turned off by transforming a cell or tissue with expression vectors which express high levels of a polynucleotide, or fragment thereof, encoding PSEQ. Such constructs may be used to introduce untranslatable sense or antisense sequences into a cell.
Oligonucleotides derived from the transcription initiation site, e.g., between about positions -10 and +10 from the start site, are preferred. Similarly, inhibition can be achieved using triple helix base-pairing methodology. Triple helix pairing is useful because it causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or regulatory molecules. Recent therapeutic advances using triplex DNA have been described in the literature. (See, e.g., Gee, J.E. et al. (1994) in Huber, B.E. and B.I. Carr, Molecular and Immunoloy'c Approaches, Futura Publishing Co., Mt.
Kisco, NY, pp. 163-177.) Ribozymes, enzymatic RNA molecules, may also be used to catalyze the specific cleavage of RNA.
RNA molecules may be modified to increase intracellular stability and half life.
Possible modifications include, but are not limited to, the addition of flanking sequences at the 5' and/or 3' ends of the molecule, or the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages within the backbone of the molecule. This concept is inherent in the production of PNAs and can be extended in all of these molecules by the inclusion of nontraditional bases such as inosine, queosine, and wybutosine, as well as acetyl-, methyl-, thio-, and similarly modified forms of adenine, cytidine, guanine, thymine, and uridine which are not as easily recognized by endogenous endonucleases.
Many methods for introducing vectors into cells or tissues are available and equally suitable for use in vivo, in vitro, and ex vivo. For ex vivo therapy, vectors may be introduced into stem cells taken from the patient and clonally propagated for autologous transplant back into that same patient. Delivery by transfection, by liposome injections, or by polycationic amino polymers may be achieved using methods which are well known in the art. (See, e.g., Goldman, C.K. et al. (1997) Nature Biotechnology 15:462-466.) Further, an antagonist or antibody of a polypeptide of PSEQ or encoded by NSEQ
-t s-may be administered to a subject to treat or prevent a cancer associated with increased expression or activity of PSEQ. An antibody which specifically binds the polypeptide may be used directly as an antagonist or indirectly as a targeting or delivery mechanism for bringing a pharmaceutical agent to cells or tissue which express the the polypeptide.
Antibodies to PSEQ or polypeptides encoded by NSEQ may also be generated using methods that are well known in the art. Such antibodies may include, but are not limited to, polyclonal, monoclonal, chimeric, and single chain antibodies, Fab fragments, and fragments produced by a Fab expression library. Neutralizing antibodies (i.e., those which inhibit dimer formation) are especially preferred for therapeutic use.
Monoclonal to antibodies to PSEQ may be prepared using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique, the human B-cell hybridoma technique, and the EBV-hybridoma technique. In addition, techniques developed for the production of chimeric antibodies can be used. (See, for example, Molecular Biology and 15 Biotechnology, R.A. Myers, ed.,(1995)John Wiley & Sons, Inc., New York, NY).
Alternatively, techniques described for the production of single chain antibodies may be employed. Antibody fragments which contain specific binding sites for PSEQ or the polypeptide sequences encoded by NSEQ may also be generated.
Various immunoassays may be used for screening to identify antibodies having the 2o desired specificity. Numerous protocols for competitive binding or immunoradiometric assays using either polyclonal or monoclonal antibodies with established specificities are well known in the art.
Yet further, an agonist of a polypeptide of PSEQ or that encoded by NSEQ may be administered to a subject to treat or prevent a cancer associated with decreased expression 25 or activity of the polypeptide.
An additional aspect of the invention relates to the administration of a pharmaceutical or sterile composition, in conjunction with a pharmaceutically acceptable Garner, for any of the therapeutic effects discussed above. Such pharmaceutical compositions may consist of polypeptides of PSEQ or those encoded by NSEQ, antibodies 3o to the polypeptides, and mimetics, agonists, antagonists, or inhibitors of the polypeptides.
The compositions may be administered alone or in combination with at least one other agent, such as a stabilizing compound, which may be administered in any sterile, biocompatible pharmaceutical carrier including, but not limited to, saline, buffered saline, dextrose, and water. The compositions may be administered to a patient alone, or in combination with other agents, drugs, or hormones.
The pharmaceutical compositions utilized in this invention may be administered by s any number of routes including, but not limited to, oral, intravenous, intramuscular, infra-arterial, intramedullary, intrathecal, intraventricular, transdermal, subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, or rectal means.
In addition to the active ingredients, these pharmaceutical compositions may contain suitable pharmaceutically-acceptable carriers comprising excipients and auxiliaries l0 which facilitate processing of the active compounds into preparations which can be used pharmaceutically. Further details on techniques for formulation and administration may be found in the latest edition of Reminston's Pharmaceutical Sciences (Maack Publishing Co., Easton, PA).
For any compound, the therapeutically effective dose can be estimated initially 15 either in cell culture assays, e.g., of neoplastic cells or in animal models such as mice, rats, rabbits, dogs, or pigs. An animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.
A therapeutically effective dose refers to that amount of active ingredient, for 20 example, polypeptides of PSEQ or those encoded by NSEQ, or fragments thereof, antibodies of the polypeptides, and agonists, antagonists or inhibitors of the polypeptides, which ameliorates the symptoms or condition. Therapeutic efficacy and toxicity may be determined by standard pharmaceutical procedures in cell cultures or with experimental animals, such as by calculating the EDSO (the dose therapeutically effective in 50% of the 25 population) or LDso (the dose lethal to SO% of the population) statistics.
Any of the therapeutic methods described above may be applied to any subject in need of such therapy, including, for example, mammals such as dogs, cats, cows, horses, rabbits, monkeys, and most preferably, humans.
EXAMPLES

It is understood that this invention is not limited to the particular methodology, protocols, and reagents described, as these may vary. It is also understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims. The examples below are provide to illustrate the subject invention and are not included for the purpose of limiting the invention.
I. PROSTUT05 cDNA Library Construction For purposes of example, the preparation of the PROSTUTOS library is described.
to The PROSTUTOS cDNA library was constructed using polyA RNA isolated from prostate tumor tissue removed from a 69-year-old Caucasian male during a radical prostatectomy.
Pathology indicated adenocarcinoma (Gleason grade 3+4) involving the right side peripherally. The tumor invaded the capsule but did not extend beyond it;
perineural invasion was present. Adenofibromatous hyperplasia was also present. The right seminal vesicle was involved with tumor. The patient presented with elevated prostate specific antigen (PSA). Patient history included partial colectomy, and tobacco use.
Family history included congestive heart failure, multiple myeloma, hyperlipidemia, and rheumatoid arthritis.
The frozen tissue was homogenized and lysed using a Brinkmann Homogenizer Polytron PT-3000 (Brinkmann Instruments, Westbury, NJ) in guanidinium isothiocyanate solution. The lysate was centrifuged over a 5.7 M CsCI cushion using an Beckman SW28 rotor in a Beckman L8-70M Ultracentrifuge (Beckman Instruments) for 18 hours at 25,000 rpm at ambient temperature. The RNA was extracted -with acid phenol pH 4.7, precipitated using 0.3 M sodium acetate and 2.5 volumes of ethanol, resuspended in RNAse-free water, and treated with DNase at 37°C. mRNA extraction and precipitation were repeated as before. The mRNA was isolated with the Qiagen Oligotex kit (QIAGEN, Chatsworth, CA) and used to construct the cDNA library.
The mRNA was handled according to the recommended protocols in the Superscript Plasmid System for cDNA synthesis and plasmid cloning (GIBCOBRL).
The cDNAs were fractionated on a Sepharose CL4B column (Pharmacia), and those cDNAs exceeding 400 by were ligated into pSport I. The plasmid pSport I was subsequently transformed into DHSaTM competent cells (LifeTechnologies, Gaithersburg, MD).
II. Isolation and Sequencing of cDNA Clones Plasmid DNA was released from the cells and purified using the REAL Prep 96 plasmid kit (QIAGEN). This kit enabled the simultaneous purification of 96 samples in a 96-well block using multi-channel reagent dispensers. The recommended protocol was employed except for the following changes: 1 ) the bacteria were cultured in 1 ml of sterile Terrific Broth (LifeTechnologies) with carbenicillin at 25 mg/L and glycerol at 0.4%; 2) after inoculation, the cultures were incubated for 19 hours and at the end of incubation, the 1o cells were lysed with 0.3 ml of lysis buffer; and 3) following isopropanol precipitation, the plasmid DNA pellet was resuspended in 0.1 ml of distilled water. After the last step in the protocol, samples were transferred to a 96-well block for storage at 4°
C.
The cDNAs were prepared and sequenced by the method of Sanger et al. (1975, J.
Mol. Biol. 94:441f), using a Hamilton Micro Lab 2200 (Hamilton, Reno, NV) in combination with Peltier Thermal Cyclers (PTC200 from MJ Research, Watertown, MA) and Applied Biosystems 373 and 377 DNA Sequencing Systems.
III. Selection, Assembly, and Characterization of Sequences The sequences used for coexpression analysis were assembled from EST
2o sequences, 5' and 3' longread sequences, and full length coding sequences.
Selected assembled sequences were expressed in at least three cDNA libraries.
The assembly process is described as follows. EST sequence chromatograms were processed and verified. Quality scores were obtained using PHRED (Ewing, B. et al.
(1998) Genome Res. 8:175-185; Ewing, B. and P. Green (1998) Genome Res. 8:186-194).
Then the edited sequences were loaded into a relational database management system (RDBMS). The EST sequences were clustered into an initial set of bins using BLAST
with a product score of 50. All clusters of two or more sequences were created as bins.
The overlapping sequences represented in a bin correspond to the sequence of a transcribed gene.
3o Assembly of the component sequences within each bin was performed using a modification of Phrap, a publicly available program for assembling DNA
fragments (Green, P., University of Washington,,Seattle, WA). Bins that showed 82%
identity from a local pair-wise alignment between any of the consensus sequences were merged.
Bins were annotated by screening the consensus sequence in each bin against public databases, such as gbpri and genpept from NCBI. The annotation process involved a FASTn screen against the gbpri database in GenBank. Those hits with a percent identity of greater than or equal to 70% and an alignment length of greater than or equal to 100 base pairs were recorded as homolog hits. The residual unannotated sequences were screened by FASTx against genpept. Those hits with an E value of less than or equal to 10'g are recorded as homolog hits.
Sequences were then reclustered using BLASTn and Cross-Match, a program for 1o rapid protein and nucleic acid sequence comparison and database search (Green, P., University of Washington, Seattle, WA), sequentially. Any BLAST alignment between a sequence and a consensus sequence with a score greater than 150 was realigned using cross-match. The sequence was added to the bin whose consensus sequence gave the highest Smith-Waterman score amongst local alignments with at least 82%
identity. Non-matching sequences created new bins. The assembly and consensus generation processes were performed for the new bins.
IV. Co-expression Analyses of Known Prostate Cancer-Specific Genes Five known prostate cancer-specific genes were selected to test the validity of the 2o coexpression analysis method of the present invention in identifying genes that are closely associated with prostate cancer. The five known genes were prostate-specific antigen, glandular kallikrein, prostate seminal protein, prostatic acid phosphatase, and prostate transglutaminase. As shown, the method successfully identified the strong association of the known genes among themselves, indicating that the coexpression analysis method of the present invention was effective in identifying genes that are closely associated with prostate cancer.
Table 4 shows the top ten genes that were most closely associated with a known prostate cancer-specific gene. These genes are presented along with their p-values. The column headings have the following meanings:
P-value The probability that the observed number of co-occurrences is due to chance using the Fisher exact method.

Co-expressed Gene A gene that shows significant co-expressionthe with target.

No. Occur. The number of libraries in which the associatedgene occurs.

No. Co-occur The number of libraries in which both gene the target and the co-expressed gene occur.

No. Target Only The number of libraries in which gene only the target occurs.

1o No. Gene Only The number of libraries in which only the associated gene occurs.

No. Neither Occur The number of libraries in which target neither the gene nor the associated gene occur.

Table 4. Co-expression results for prostate-specific antigen P-value Co-expressed No. No. No. No. No.

Gene Occur Co-occur Target Gene Neither Only Only Occur 1.53E-31 Glandular 29 26 12 3 481 kallikrein 1.65E-26 1816556 24 22 16 2 482

7.48E-25 1864683 40 26 12 14 470

8.12E-25 1344875 29 23 15 6 478 3.38E-24 Prostate seminal30 23 15 7 477 protein 1.89E-23 Prostatic 35 24 14 11 473 acid phosphatase 2s 6.87E-18 1651189 28 19 19 9 475

9.OlE-18 Prostate 14 14 24 0 484 trans-glutaminase 4.61 E-141646118 93 27 11 66 418 1.58E-13 Human 27 16 22 11 473 neuropeptide Y

(NPY) mRNA

As a target, prostate-specific antigen occurred in 38 of 522 cDNA libraries studied, and showed strong coexpression with glandular kallikrein, prostate seminal protein, prostatic acid phosphatase, and prostate transglutaminase. The target also showed strong association with the human neuropeptide tyrosine (NPY) mRNA. In addition, four of the top ten genes that showed strong association with the target were novel Incyte assembled genes: 1816556, 1864683, 1344875, 1651189, and 1646118. These results are shown in Table 4 with association probability in the range of 1.58E-13 to 1.53E-31.
Similar results were observed when the other four known prostate cancer-specific genes, glandular kallikrein, prostate seminal protein, prostatic acid phosphatase, and prostate transglutaminase, were taken as target genes. These target genes were also found to be strongly associated with several known genes, many of which are cancer-related.
The cancer-related genes are human neuropeptide tyrosine (NPY), human serine protease encoded by TMPRSS2, sorbitol dehydrogenase isozyme, human Zn-alpha-2-glycoprotein, and MAT-8.
NPY was first isolated from a human pheochromocytoma tumor (Minth, C. D. et al. ( 1984) Proc Natl Acad Sci 81 ( 14): 4577-4581 ) and was reported to be involved in prostate cancer (Rogatnick, L. A. et al. (1990) Proc West Pharmacol Soc 33: 47-53; Mack, D., G. et al. (1997) Eur J Cancer 33:317-318). The TMPRSS2 gene was identified as a gene that encodes a serine protease domain specific for cleavage at Arg or Lys residues 2o (Paoloni-Giacobino, A. et al. (1997) Genomics 44:309-320). The protease activity of TMPRSS2 is similar to that of PSA and kallikrein, both human prostate cancer-specific genes. Sorbitol dehydrogenase isozyme has been used as a marker for male reproductive tissue, including the prostate (Holmes, R. S. et al. (1978) J Exp Zool 206:
279-88).
Significant activity of the enzyme accompanies damage to reproductive tissue.
Zn-alpha-2-glycoprotein is a secreted protein identified in hormone-responsive breast carcinomas (Freije, J. P. et al. (1993)Genomics 18:575-87) and was proposed as a marker for breast carcinomas (Lopez-Boado, Y. S. et al. (1994) Breast Cancer Res Treat 29:
247-58). It was shown to be prognostic for a 5-year breast cancer survival (Hurlimann, J.
and G. van Melle (1991) Am J Clin Pathol 95:835-43) and was reported to show differential expression in prostate carcinoma (Gagnon, S. et al. ( 1990) Am J
Pathol 136:
1147-52). MAT-8 was first identified in marine breast tumors and subsequently in primary human breast tumors and cell lines (Morrison, B. W. et al. (1995) J
Biol Chem 270: 2176-82). It was shown to be a marker for progression of breast cancer (Schiemann, S. et al. (1998) Clin Exp Metastasis 16:129-39). A relation to prostate cancer has not been previously_reported.
V. Identification of Novel Prostate Cancer-Associated Genes Using the coexpression analysis, we have identified eight novel genes that show strong association with prostate cancer from a total of 41,419 assembled gene sequences.
The degree of association was measured by probability values and has a cutoff of p value less than 0.00001. This was followed by annotation and literature searches to insure that 1o the genes that passed the probability test have strong association with known prostate cancer-specific genes. This process was reiterated so that the initial 41419 genes were reduced to the final eight prostate cancer-associated genes. Details of identification for the eight novel prostate cancer-associated genes are presented in Tables 5 to 12. These tables show the ten genes that were most closely associated for each target novel gene as measured by coexpression using the Fisher exact test. The column headings have the same meanings as in Example IV.
Table 5. Co-expression results for Incyte gene 842349 P-value Co-expressed No. No. N No. No.

Gene Occur Co-occur Target Gene Neither Only Only Occur 4.23E-11 Glandular 29 17 38 12 455 kallikrein 1.29E-09 Prostate 30 16 39 14 453 seminal protein 3.62E-09 1816556 24 14 41 10 457 8.56E-09 1344875 29 15 40 14 453 1.09E-08 TMPRSS2- 74 24 31 50 417 encoded serine protease 1.19E-08 Prostate- 38 17 38 21 446 specific antigen 2.45E-08 Prostatic 35 16 39 19 448 acid phosphatase 2.91 E-08 Human 27 14 41 13 454 neuropeptide Y

(NPY) mRNA

2.92E-08 1697453 96 27 28 69 398 3.14E-08 1864683 40 17 38 23 444 Incyte gene 842349 occurred in SS of 522 cDNA libraries studied and showed strong co-expression with several of the known prostate cancer-specific genes, including glandular kallikrein, prostate seminal protein, prostate-specific antigen, and prostatic acid phosphatase, as shown in Table 9. 842349 also showed strong association with a human 1o TMPRSS2-encoded serine protease. The serine protease was shown to be strongly associated with prostate cancer-specific prostatic acid phosphatase in Example IV.
Further, 842349 showed strong association with four novel Incyte genes, 1816556, 1344875, 1697453, and 1864683. These results are consistent with the notion that 842349 is associated with prostate cancer; and 842349 may be functionally or regulatorily 15 associated with at least four novel Incyte genes.
Table 6. Co-expression results for 1682557 P-value Co-expressed No. No. No. No. No.

Gene Occur Co-occur Target Gene Neither Only Only Occur 1.34E-07 1816556 24 5 0 19 498 20 3.40E-07 Human nicotinic10 4 1 6 511 acetylcholine receptor A

3.75E-07 Glandular 29 5 0 24 493 kallikrein 3.75E-07 1344875 29 5 0 24 493 1.02E-06 Prostatic 35 5 0 30 487 acid phosphatase 1.58E-06 Prostate- 38 5 0 33 484 specific antigen 2.08E-06 1864683 40 5 0 35 482 4.22E-06 1685804 S 3 2 2 515 9.53E-06 3096181 21 4 1 17 500 2.34E-OS 1794279 8 3 2 5 512 Incyte gene 1682557 occurred in 5 of 522 cDNA libraries studied and showed strong coexpression with several of the known prostate cancer-specific genes, such as glandular kallikrein, prostatic acid phosphatase, and prostate-specific antigen, as shown in 1o Table 10. 1682557 also exhibited strong coexpression with the human nicotinic acetylcholine receptor A, a neurotransmitter which is a ligand-gated canon channel and causes rapid depolarization in postsynaptic cells. Further, Table 10 shows that 842349 has strong association with five novel Incyte genes, 1816556, 1344875, 1697453, 1864683, and 1794279. These results are consistent with the notion that 1682557 is associated with prostate cancer; and 1682557 may be functionally or regulatorily associated with at least five novel Incyte genes.
Table 7. Co-expression results for 1816556 P-value Co-expressed No. No. No. No. No.

Gene Occur Co-Occur Target Gene Neither Only Only Occur 2o 1.20E-30 Glandular 29 22 2 7 491 kallikrein 1.11E-27 Prostatic 35 22 2 13 485 acid phosphatase 1.65E-26 Prostate- 38 22 2 16 482 specific antigen 1.SSE-25 1344875 29 20 4 9 489 1.SSE-23 1864683 40 21 3 19 479 8.19E-23 Prostate seminal30 19 5 11 487 protein 1.03E-16 Human gene 86 22 2 64 434 for alpha-2-glycopr otein 3.13E-16 Prostate 14 12 12 2 496 trans-glutaminase 1.08E-15 1651189 28 15 9 13 485 4.81E-15 2819055 44 17 7 27 471 Incyte gene 1816556 occurred in 24 of 522 cDNA libraries studied and showed strong co-expression with several of the known prostate cancer-specific genes, such as glandular kallikrein, prostatic acid phosphatase, and prostate-specific antigen, prostate seminal protein, and prostate transglutaminase, as shown in Table 11. 1816556 also l0 exhibited strong association with a human gene for ZN-alpha-2-glycoprotein which was shown in Example IV to be strongly associated with a prostate cancer-specific gene encoding prostatic transglutaminase. Further, 1816556 showed strong co-expression with four novel Incyte genes, 1344875, 1864683, 1651189, and 2819055. These results are consistent with the notion that I 816556 is associated with prostate cancer;
and 1816556 may be functionally or regulatorily associated with at least four novel Incyte genes.
Table 8. Co-expression results for 1864683 P-value Co-expressed No. No. No. No. No.

Gene Occur Co-Occur Target Gene Neither Only Only Occur 7.48E-25 Prostate- 38 26 14 12 470 specific antigen 4.SSE-24 1344875 29 23 17 6 476 4.SSE-24 Glandular 29 23 17 6 476 kallikrein I.SSE-23 1816556 24 21 19 3 479 1.43E-21 Prostate seminal30 22 18 8 474 protein 6.52E-21 Prostatic 35 23 17 12 470 acid phosphatase 5.43E-15 Prostate 14 13 27 1 481 trans-glutaminase 6.38E-15 TMPRSS2- 74 26 14 48 434 encoded serine protease 3.41E-14 1651189 28 17 23 11 471 1.47E-13 2819055 44 20 20 24 458 Incyte gene 1864683 occurred in 40 of 522 cDNA libraries studied and showed strong co-expression with several of the known prostate cancer-specific genes, such as prostate-specific antigen, glandular kallikrein, prostate seminal protein, prostatic acid phosphatase, and prostate transglutaminase, as shown in Table 8. 1864683 also exhibited strong association with a human TMPRSS2-encoded serine protease shown in Example IV
to be strongly associated with prostate cancer-specific gene encoding prostatic acid phosphatase. Further, 1864683 showed strong coexpression with four novel Incyte genes, 1344875, 1816556, 1651189, and 2819055. These results are consistent with the notion that 1864683 is associated with prostate cancer; and 1864683 may be functionally or regulatorily associated with at least four novel Incyte genes.
Table 9. Co-expression results for 2187866 P-value Co-expressed No. No. No. No. No.

Gene Occur Co-Occur Target Gene Neither Only Only Occur 9.11E-11 Prostatic 35 9 1 26 486 acid phosphatase 2.42E-10 1816556 24 8 2 16 496 1.38E-09 Glandular 29 8 2 21 491 kallikrein 1.38E-09 1344875 29 8 1 2 1 21 491 1.53E-08 Prostate- 38 8 2 30 482 specific antigen 2.38E-08 1864683 40 8 2 32 480 3.69E-08 Human LPAP 98 10 0 88 424 gene 5.41 E-08 2819055 44 8 2 36 476 1.32E-07 TMPRSS2- 74 9 1 65 447 encoded serine protease 2.34E-06 843197 7 4 6 3 509 Incyte gene 2187866 occurred in 10 of 522 cDNA libraries and showed strong 1 o association with several of the known prostate cancer-specific genes, such as prostatic acid phosphatase, glandular kallikrein, and prostate-specific antigen, as shown in Table 13.
2187866 also exhibited strong association with a human lymphocyte phosphatase-associated phosphoprotein (LPAP) gene and a human TMPRSS2-encoded serine protease.
LPAP is a 32 kDa protein that non-covalently binds tyrosine phosphatase CD45 (Bruyns, E., et al. (1998)Int Immunol 10: 185-94; Bruyns, E., A et al. (1996) Genomics 38: 79-83).
As specified in Example IV, TMPRSS2-encoded serine protease was associated with a prostate cancer-specific gene encoding prostatic acid phosphatase. Further, exhibited association with five novel Incyte genes, 1816556, 1344875, 1864683, 2819055, and 843197. These results are consistent with the notion that 2187866 is associated with 2o prostate cancer; and 2187866 may be functionally or regulatorily associated with at least five novel Incyte genes.
Table 10. Co-expression results for 3096181 P-value Co-expressedNo. No. No. No. No.

Gene Occur Co-Occur Target Gene Neither Only Only Occur 3.69E-13 1344875 29 13 8 16 485 4.96E-10 Glandular 29 11 10 18 483 kallikrein 6.84E-10 Prostate- 38 12 9 26 475 specific antigen 8.49E-10- Human gene 86 16 5 70 431 for ZN-alpha-2-glycoprotein 1.38E-09 1816556 24 10 11 14 487 5.35E-09 Prostatic 35 11 10 24 477 acid phosphatase 1.87E-08 Prostate 30 10 11 20 481 seminal protein 2.70E-08 1864683 40 11 10 29 472 1.26E-07 Human T-cell27 9 12 18 483 receptor gamma chain I .67E-07 Prostate 14 7 14 7 494 trans-glutaminase Incyte gene 3096181 occurred in 21 of 522 libraries studied and showed strong co-expression with several of the known prostate cancer-specific genes, such as glandular kallikrein, prostate-specific antigen, prostatic acid phosphatase, prostate seminal protein, and prostate transglutaminase, as shown in Table 14. 3096181 also exhibited strong coexpression with a human gene for ZN-alpha-2-glycoprotein and human T-cell receptor gamma chain. As specified in Example IV, the human gene for ZN-alpha-2-glycoprotein was associated with a prostate cancer-specific gene encoding prostatic transglutaminase.
ZN-alpha-2-glycoprotein itself was identified in hormone-responsive breast carcinomas (Freije et al., supra). Human T-cell receptor gamma/delta is expressed in tumor-infiltrating lymphocytes in breast carcinoma patients (Alam, S.M. et al. (1992) Immunol Lett 31:279-283) and in malignant lymphoma presenting with hepatosplenic disease (Farcet, J.
P. et al. (1990) Blood 75: 2213-2219). T-cell receptor gamma positive cells are over-expressed in cancer patients (Seki, S. et al. (1990) J Clin Invest 86:
409-15).
Further, 3096181 exhibited coexpression with three novel Incyte genes, 1344875, 1816556, and 1864683. These results are consistent with the notion that 3096181 is associated with prostate cancer; and 3096181 may be functionally or regulationally associated with at least three novel Incyte genes.
Table 11. Co-expression results for 3360806 ~,-, P-value Co-expressed No. No. No. No. No.

Gene Occur Co-Occur Target Gene Neither Only Only Occur 1.98E-11 Prostate- 38 16 18 22 466 specific antigen 6.S1E-10 1651189 28 13 21 15 473 8.24E-10 1864683 40 15 19 25 463 1.88E-08 1344875 29 12 22 17 471 101.88E-08 Glandular 29 12 22 17 471 kallikrein 3.OOE-08 Prostate seminal30 12 22 18 470 protein S.lOE-08 Human gene 86 19 15 67 421 for ZN-alpha-2-glycoprotein 3.19E-07 Prostate 14 8 26 6 482 trans-glutaminase 3.66E-07 1816556 24 10 24 14 474 is6.56E-07 1685861 133 22 12 111 377 Incyte gene 3360806 occurred in 34 of 522 cDNA libraries and showed strong co-expression with several of the known prostate cancer-specific genes, such as prostate-specific antigen, glandular kallikrein, prostate seminal protein, and prostate 20 transglutaminase, as shown in Table 1 S. 3360806 also exhibited strong co-expression with a human gene for ZN-alpha-2-glycoprotein shown in Example IV to be associated with a prostate cancer-specific gene encoding prostatic transglutaminase.
ZN-alpha-2-glycoprotein itself was also found in hormone-responsive breast carcinomas (Freije et al., supra). Further, 3360806 showed association with five novel Incyte genes, 25 1651189, 1864683, 1344875, 1816556, and 1685861. These results are consistent with the notion that 3360806 is associated with prostate cancer; and 3360806 may be functionally or regulationally associated with at least four novel Incyte genes.
Table 12. Co-expression results for 3458076 P-value Co-expressed No. No. No. No. No.

Gene Occur Co-Occur Target Gene Neither Only Only Occur 3.35E-08 1816556 24 6 1 18 497 1.17E-07 1344875 29 6 1 23 492 1.17E-07 Glandular 29 6 1 23 492 kallikrein 1.46E-07 Prostate seminal30 6 1 24 491 protein l0 3.96E-07 Prostatic 35 6 1 29 486 acid phosphatase 6.70E-07 Prostate- 38 6 1 32 483 specific antigen 9.29E-07 1864683 40 6 1 34 481 6.04E-06 1651189 28 5 2 23 492 1.09E-OS Prostate 14 4 3 10 505 trans-glutaminase 1.22E-OS Human 32 5 2 27 488 polymorphic CA dinucleotide repeat Incyte gene 3458076 occurred in 7 of 522 cDNA libraries and showed strong co-expression with several of the known prostate cancer-specific genes, such as glandular kallikrein, prostate seminal protein, prostatic acid phosphatase, prostate-specific antigen, 2o and prostate transglutaminase, as shown in Table 11. 3458076 also exhibited association with a human dinucleotide repeat flanking region, a region that flanks a polymorphic CA
micro satellite repeat from the long arm of chromosome 1 (Raymond, M. H., et al. (1987) GI 2182124, GenBank). Genes in this region have not been characterized.
Further, 3458076 showed coexpression with four novel Incyte genes, 1816556, 1344875, 1864683, and 1651189. These results are consistent with the notion that 3458076 is associated with prostate cancer; and 3458076 may be functionally or regulationally associated with at least four novel Incyte genes.
VI. Novel Prostate Cancer-Associated Genes Eight novel Incyte genes were identified from the data shown in Tables 5 to 12 to be associated with prostate cancer.
Nucleic acids comprising the consensus sequences of SEQ ID NOs: 1-10 of the 1o present invention were first identified from Incyte Clones 842349, 1682557, 1816556, 1864683, 2187866, 3096181, 3360806, and 3458076, respectively, and assembled according to Example III. BLAST and other motif searches were performed for SEQ ID
NOs: 1-8 according to Example VII. The sequences were translated and sequence identity was sought with known sequence. Of interest, the amino acid sequence encoded by SEQ
t5 ID NO: 1 from about nucleotide 195 to about nucleotide 446 showed 58%
sequence identity with a subunit of a mouse RNA polymerase I, PRA16 (GI 1778684); and the amino acid sequence encoded SEQ ID N0:3 from about 185 to about 825 showed about 76% sequence identity with a Sus scrofa enamel matrix serine protease (GI
2737921). The protease activity of the enamel matrix serine protease is consistent with that of PSA and 2o kallikrein, two of the known human prostate cancer-specific genes. SEQ ID
NO: 9 is an amino acid sequence coded by SEQ ID NO: 4. SEQ ID NO: 9 is 231 amino acids in length. Residue 188 to residue 209 encompass a potential transmembrane domain, and residue 1 to residue 47 is a potential signal peptide sequence. SEQ ID NO: 9 also has two potential casein kinase II phosphorylation sites at S 100 and S 142; one potential protein 25 kinase C phosphorylation site at S 147; and a potential cell attachment sequence encompassing residues R93GD which interacts with a cell surface receptor. SEQ
ID NO:
is an amino acid sequence coded by SEQ ID NO: 8. SEQ ID NO: 10 is 162 amino acids in length. The fragment from residue 83 to residue 99 resembles a potential BLOCK
signature of Ly-6/u-PAR, a family of GPI-linked cell-surface glycoproteins.
SEQ ID NO:
30 10 also has one potential N-glycosylation site at N4; one potential cAMP-and cGMP-dependent protein kinase phosphorylation site at T48; and three potential protein kinase C phosphorylation sites at T25, T34, and 544.

WO 99/67384 PCT/US99/13524 _ VII. Homology Searching for Prostate Cancer-Associated Genes and the Proteins Encoded by the Genes Polynucleotide sequences, SEQ ID NOs: 1-8, and polypeptide sequences, SEQ ID
s NOs: 9-10, were queried against databases derived from sources such as GenBank and SwissProt. These databases, which contain previously identified and annotated sequences, were searched for regions of similarity using Basic Local Alignment Search Tool (BLAST; Altschul, S.F. et al. (1990) J. Mol. Biol. 215: 403-410) and Smith-Waterman alignment (Smith, T. et al. (1992) Protein Engineering 5:35-51). BLAST
searched for to matches and reported only those that satisfied the probability thresholds of 10'zs or less for nucleotide sequences and 10'8 or less for polypeptide sequences.
The polypeptide sequences were also analyzed for known motif patterns using MOTIFS, SPSCAN, BLIMPS, and Hidden Markov Model (HMM)-based protocols.
MOTIFS (Genetics Computer Group, Madison, WI) searches polypeptide sequences for 15 patterns that match those defined in the Prosite Dictionary of Protein Sites and Patterns (Bairoch, A. et al. ( 1997) Nucleic Acids Res. 25:217-221 ), and displays the patterns found and their corresponding literature abstracts. SPSCAN (Genetics Computer Group, Madison, WI) searches for potential signal peptide sequences using a weighted matrix method (Nielsen, H. et al. (1997) Prot. Eng. 10: 1-6). Hits with a score of 5 or greater 2o were considered. BLIMPS uses a weighted matrix analysis algorithm to search for sequence similarity between the polypeptide sequences and those contained in BLOCKS, a database consisting of short amino acid segments, or blocks, of 3-60 amino acids in length, compiled from the PROSITE database (Henikoff, S. and G. J. Henikoff ( 1991 ) Nucleic Acids Res. 19:6565-6572; Bairoch et al., sera), and those in PRINTS, a protein 25 fingerprint database based on non-redundant sequences obtained from sources such as SwissProt, GenBank, PIR, and NRL-3D (Attwood, T. K. et al. (1997) J. Chem.
Inf.
Comput. Sci. 37:417-424). For the purposes of the present invention, the BLIMPS
searches reported matches with a cutoff score of 1000 or greater and a cutoff probability value of 1.0 x 10''. HMM-based protocols were based on a probabilistic approach and 3o searched for consensus primary structures of gene families in the protein sequences (Eddy, S.R. (1996) Cur. Opin. Str. Biol. 6:361-365; Sonnhammer, E.L.L. et al. (1997) Proteins 28:405-420). More than 500 known protein families with cutoff scores ranging from 10 to 50 bits were selected for use in this invention.
VIII. Extension of Polynucleotides The initial primers were designed from the cDNA using OLIGO 4.06 (National Biosciences, Plymouth, MN), or another appropriate program, to be about 22 to nucleotides in length, to have a GC content of about 50% or more, and to anneal to the target sequence at temperatures of about 68 °C to about 72°C.
Any stretch of nucleotides which would result in hairpin structures and primer-primer dimerizations were avoided.
Selected human cDNA libraries (GIBCOBRL) were used to extend the sequence. If more than one extension is necessary or desired, additional sets of primers are designed to further extend the known region.
High fidelity amplification was obtained by following the instructions for the XL-PCR kit (Perkin Elmer) and thoroughly mixing the enzyme and reaction mix. PCR
was performed using the Peltier Thermal Cycler (PTC200; M.J. Research, Watertown, MA), beginning with 40 pmol of each primer and the recommended concentrations of all other components of the kit.
A 5 ~cl to 10 ~l aliquot of the reaction mixture was analyzed by electrophoresis on a low concentration (about 0.6% to 0.8%) agarose mini-gel to determine which reactions were successful in extending the sequence. Bands thought to contain the largest products were excised from the gel, purified using QIAQuickTM (QIAGEN), and trimmed of overhangs using Klenow enzyme to facilitate religation and cloning.
After ethanol precipitation, the products were redissolved in 13 ~1 of ligation buffer, l,ul T4-DNA ligase (15 units) and 1/.cl T4 polynucleotide kinase were added, and the mixture was incubated at room temperature for 2 to 3 hours, or overnight at 16 ° C.
Competent E. coli cells (in 40 ,ul of appropriate media) were transformed with 3 ~1 of ligation mixture and cultured in 80 ~cl of SOC medium. After incubation for one hour at 37 ° C, the E. coli mixture was plated on Luria Bertani (LB) agar containing 2x Carb. The following day, several colonies were randomly picked from each plate and cultured in 1 SO
~cl of liquid LB/2x Carb medium placed in an individual well of an appropriate 3o commercially-available sterile 96-well microtiter plate.

IX. Labeling and Use of Individual Hybridization Probes Oligonucleotides are designed using state-of the-art software such as OLIGO
4.06 (National Biosciences) and labeled by combining 50 pmol of each oligomer, 250 ,uCi of [y-32p~ adenosine triphosphate (Amersham, Chicago, IL), and T4 polynucleotide kinase (DuPont NEN~, Boston, MA). The labeled oligonucleotides are substantially purified using a Sephadex G-25 superfine resin column (Pharmacia & Upjohn, Kalamazoo, MI).
An aliquot containing 10' counts per minute of the labeled probe is used in a typical membrane-based hybridization analysis of human genomic DNA digested with one of the following endonucleases: Ase I, Bgl II, Eco RI, Pst I, Xba l, or Pvu II
(DuPont NEN, to Boston, MA).
The DNA from each digest is fractionated on a 0.7 percent agarose gel and transferred to nylon membranes (Nytran Plus, Schleicher & Schuell, Durham, NH).
Hybridization is carried out for 16 hours at 40°C. To remove nonspecific signals, blots are sequentially washed at room temperature under increasingly stringent conditions up to is 0.1 x saline sodium citrate and 0.5% sodium dodecyl sulfate. After XOMAT
ARTM film (Kodak, Rochester, NY) is exposed to the blots to film for several hours, hybridization patterns are compared visually.

SEQUENCE LISTING
<110> INCYTE PHARMACEUTICALS, INC.
WALKER, Michael G.
VOLKMUTH, Wayne KLINGLER, Tod M.
SPRINZAK, Einat A.
<120> PROSTATE CANCER-ASSOCIATED GENES
<130> PB-0002 PCT
<140> To Be Assigned <141> Herewith <150> 09/102,615 <151> 1998-06-22 <160> 10 <170> PERL Program <210> 1 <211> 2215 <212> DNA
<213> Homo sapiens <220>
<221> misc_feature <223> Incyte clone 842349 <400> 1 angtcatnta ttatgaagat nacacaggtt cttgcagaga ttccaacagc tgcaaggggt 60 caacagctag aatcangcct ttctgaagga cagagtatgc tgtaaccaca aacttctaat 120 tctgggttct gcnccatcan gaanagaata tcctacagga cagttctcct tgtatactgc 180 ataaaggact anaatgtgga ttcatttctg cttgctttnt gatccttata gtcctttatg 240 ctggcctcaa acttgtcaag cacatgttgg cagacattna tgagctcatt caggcctctc 300 tganatggct caacagctgg aatggtacct cgngtctgaa tgcgtaaatn aagtttgctc 360 tcngaaggat gggntcggag tggaaccaca aaattncnct tncgggngtc gtcatgatct 420 attatcatgt actttctaac tgagccctct attttcttta ttttaataat atttctcccc 480 acttgagaat cacttgttag ttcttggtag gaattcagtt gggcaatgat aacttttatg 540 ggcaaaaaca ttctattata gtgaacaaat gaaaataaca gcgtattttc aatattttct 600 tattccttaa attccactct tttaacacta tgcttaacca cttaatgtga tgaaatattc 660 ctaaaagtta aatgactatt aaagcatata ttgttgcatg tatatattaa gtagccgata 720 ctctaaataa aaataccact gttacagata aatggggcct ttaaaaatat gaaaaacaaa 780 cttgtgaaaa tgtataaaag atgcatctgt tgtttcaaat ggcactatct tcttttcagt 840 actacaaaaa cagaataatt ttgaagtttt agaataaatg taatatattt actataattc 900 taaatgttta aatgcttttc taaaaatgca aaactatgat gtttagttgc tttattttac 960 ctctatgtga ttatttttct taattgttat tttttataat cattattttt ctgaaccatt 1020 cttctggcct cagaagtagg actgaattct actattgcta ggtgtgagaa agtggtggtg 1080 agaaccttag agcagtggag atttgctacc tggtctgtgt tttgagaagt gccccttaga 1140 aagttaaaag aatgtagaaa agatactcag tcttaatcct atgcaaaaaa aaaaaatcaa 1200 gtaattgttt tcctatgagg aaaataacca tgagctgtat catgctactt agcttttatg 1260 taaatatttc ttatgtctcc tctattaaga gtatttaaaa tcatatttaa atatgaatct 1320 attcatgcta acattatttt tcaaaacata catggaaatt tagcccagat tgtctacata 1380 taaggttttt atttgaattg taaaatattt aaaagtatga ataaaatata tttataggta 1440 tttatcagag atgattattt tgtgctacat acaggttggc taatgagctc tagtgttaaa 1500 ctacctgatt aatttcttat aaagcagcat aaccttggct tgattaagga attctacttt 1560 caaaaattaa tctgataata gtaacaaggt atattatact ttcattacaa tcaaattata 1620 gaaattactt gtgtaaaagg gcttcaagaa tatatccaat ttttaaatat tttaatatat 1680 ctcctatctg ataacttaat tcttctaaat taccacttgc cattaagcta tttcataata 1740 aattctgtac agtttccccc aaaaaaaaga gatttattta tgaaatattt aaagtttcta 1800 atgtggtatt taaataaagt aatcatnaat gnnataagtn aatatttatt taggaatact 1860 gtgaaacnct ganactaatt attnctcgtg tcagtcctat nnnantccct ggttttggga 1920 natnngnnaa nccagcctan aaatagnggt tgnnnaaatn anntttggtn aaannncatg 1980 nancctttaa annccntggg ttacnnttcn cntnggtatn tnaccanccc ccttccccac 2040 nnggtttaan aantttaatn aagtggttga aaatgggggc ctantcntna gcctttacaa 2100 cnttgtgtcc caatcanctg nggggtttna ancacaantt cccggatngg gtnnanttnc 2160 nnnggggnnc caactcgtgt nntgncccnc ncgacnnttg nacctcggnn aacna 2215 <210> 2 <211> 742 <212> DNA
<213> Homo Sapiens <220>
<221> misc_feature <223> Incyte clone 1682557 <400> 2 agcgtggggc tgctggactt ctgtgggcca ggtgtgcttc actccactgg aggccctgct 60 ctctgacctc ttccgggacc cggaccactg tcgccaggcc tactctgtct atgccttcat 120 gattagtctt gggggctgcc tgggctacct cctgcctgcc attgactggg acaccagtgc 180 cctggccccc tacctgggca cccaggagga gtgcctcttt ggcctgctca ccctcatctt 240 cctcacctgc gtagagccca cactgctggt ggctgaggag gcagcgctgg gccccaccga 300 gccagcagaa gggctgtcgg ccccctcctt gtcgccccac tgctgtccat gccgggcccg 360 cttggctttc cggaacctgg gcgccctgct tccccggctg caccagctgt gctgccgcat 420 gccccgcacc ctgcgccggc tcttcgtggc tgagctgtgc agctggatgg cactcatgac 480 ctnatngnat tcaattnaac tttcaaaggt ttnttttaaa aangggattt ttgntggggg 540 gnaanngggc tnttaacann gggncnttgc cccanaannc ntnaannccg gggaaannnn 600 ngggncccng aaananaatt ttngnatnan aaggcntttn gnaatnggnc aancttnggg 660 gttttttccc ngnaatnann gnantttccc cngntttttn ggttnttnnn ccaanngccc 720 ccgcntgggg gnaattantt tt 742 <210> 3 <211> 1040 <212> DNA
<213> Homo Sapiens <220>
<221> misc_feature <223> Incyte clone 1816556 <400> 3 ggggccctgg acggttttct ctatccactc agtgaatttg cagaggttgg tgtagacacc 60 tggcgcgcca acttggccac acggggcttt tccgaaagac acaaggccct gcaagtaccc 120 gttgcagatc aggggccccc cagagtcacc gttgcaggag tccttctggt cttgccctcc 180 gccgggcgag gactgcagcc cgcgctcgca gccctggcag gcggcactgg tcatggaaaa 240 cgaattgttc tgctcgccgc acactgtttc cagaagtgag tgcagagctc ctacaccatc 300 gggctgggcc tgcacagtct tgaggccgac caagagccag ggagccagat ggtggaggcc 360 agcctctccg tacggcaccc agagtacaac agacccttgc tcgctaacga cctcatgctc 420 atcaagttgg acgaatccgt gtccgagtct gacaccatcc ggagcatcag cattgcttcg 480 cagtgcccta ccgcggggaa ctcttgcctc gtttctggct ggggtctgct ggcgaacggc 540 agaatgccta ccgtgctgca gtgcgtgaac gtgtcggtgg tgtctgagga ggtctgcagt 600 aagctctatg acccgctgta ccaccccagc atgttctgcg ccggcggagg gcaagaccag 660 aaggactcct gcaacggtga ctctgggggg cccctgatct gcaacgggta cttgcagggc 720 cttgtgtctt tcggaaaagc cccgtgtggc caagttggcg tgccaggtgt ctacaccaac 780 ctctgcaaat tcactgagtg gatagagaaa accgtccagg ccagttaact ctggggactg 840 ggaacccatg aaattgaccc ccaaatacat cctgcggaag gaattcagga atatctgttc 900 ccagcccctc gtccctnagg cccaggagtc cacnncncaa aanantcnnt ncnctaaanc 960 nagggggtac anaatccccc aanaaaggan nntnncannn angacccang ggannnnnaa 1020 aaatttccnn naaaataggc 1040 <210> 4 <211> 2462 <212> DNA
<213> Homo Sapiens <220>
<221> misc_feature <223> Incyte clone 1864683 <400> 4 caacgacttt ccaaataatc tcaccagcgc cttccagctc aggcgtccta gaagcgtctt 60 gaagcctatg gccagctgtc tttgtgttcc ctctcacccg cctgtcctca cagctgagac 120 tcccaggaaa ccttcagact accttcctct gccttcagca aggggcgttg cccacattct 180 ctgagggtca gtggaagaac ctagactccc attgctagag gtagaaaggg gaagggtgct 240 ggggagcagg gctggtccac agcaggtctc gtgcagcagg tacctgtggt tccgccttct 300 catctccctg agactgctcc gacccttccc tcccaggctc tgtctgatgg cccctctccc 360 tctgcaggcg ttcggatggg cagcctgggg ctgttcctgc agtgcgccat ctccctggtc 420 ttctctctgg tcatggaccg gctggtgcag cgattcggca ctcgagcagt ctatttggcc 480 agtgtggcag ctttccctgt ggctgccggt gccacatgcc tgtcccacag tgtggccgtg 540 gtgacagctt cagccgccct caccgggttc accttctcag ccctgcagat cctgccctac 600 acactggcct ccctctacca ccgggagaag caggtgttcc tgcccaaata ccgaggggac 660 actggaggtg ctagcagtga ggacagcctg atgaccagct tcctgccagg ccctaagcct 720 ggagctccct tccctaatgg acacgtgggt gctggaggca gtggcctgct cccacctcca 780 cccgcgctct gcggggcctc tgcctgtgat gtctccgtac gtgtggtggt gggtgagccc 840 accgaggcca gggtggttcc gggccggggc atctgcctgg acctcgccat cctggatagt 900 gccttcctgc tgtcccaggt ggccccatcc ctgtttatgg gctccattgt ccagctcagc 960 cagtctgtca ctgcctatat ggtgtctgcc gcagcgctgg gtctggtcgc catttacttt 1020 gctacacagg tagtatttga caagagcgac ttggccaaat actcagcgta gaaaacttcc 1080 agcacattgg ggtggagggc ctgcctcact gggtcccagc tccctgctcc tgttagcccc 1140 atggggctgc cgggctggcc gccagtttct gttgctgcca aagtaatgtg gctctctgct 1200 gccaccctgt gctgctgagg tgcgtactgc acagctgggg gctggggcgt ccctctcctc 1260 tctccccagt ctctagggct gcctgactgg aggccttcca agggggtttc agtctggact 1320 tatacaggga ggccagaagg gctccatgca ctggaatgcg gggactctgc aggtggatta 1380 cccaggctca gggttaacag ctagcctcct agttgagaca cacctagaga agggtttttg 1440 ggagctgaat aaactcagtc acctggtttc ccatctctaa gccccttaac ctgcagcttc 1500 gtttaatgta gctcttgcat gggagtttct aggatgaaac actcctccat gggatttgaa 1560 catatgaaag ttatttgtag gggaagagtc ctgaggggca acacacaaga accaggtccc 1620 ctcagcccac agcactgtct ttttgctgat ccacccccct cttacctttt atcaggatgt 1680 ggcctgttgg tccttctgtt gccatcacag agacacaggc atttaaatat ttaacttatt 1740 tatttaacaa agtagaaggg aatccattgc tagcttttct gtgttggtgt ctaatatttg 1800 ggtagggtgg gggatcccca acaatcaggt cccctgagat agctggtcat tgggctgatc 1860 attgccagaa tcttcttctc ctggggtctg gccccccaaa atgcctaacc caggaccttg 1920 gaaattctac tcatcccaaa tgataattcc aaatgctgtt acccaaggtt agggtgttga 1980 aggaaggtag agggtggggc ttcaggtctc aacggcttcc ctaaccaccc ctcttctctt 2040 ggcccagcct ggttcccccc acttccactc ccctctactc tctctaggac tgggctgatg 2100 aaggcactgc ccaaaatttc ccctaccccc aactttcccc tacccccaac tttccccacc 2160 agctccacaa ccctgtttgg agctactgca ggaccagaag cacaaagtgc ggtttcccaa 2220 gcctttgtcc atctcagccc ccagagtata tctgtgcttg gggaatctca cacagaaact 2280 caggagcacc ccctgcctga gctaagggag gtcttatctc tcaggggggg tttaagtgcc 2340 gtttgcaata atgtcgtctt atttatttag cggggtgaat attttatact gtaagtgagc 2400 aatcagagta taatgtttat ggtgacaaaa ttaaaggctt tcttatatgt taaaaaaaaa 2460 as <210> 5 <211> 1567 <212> DNA
<213> Homo sapiens <220>
<221> misc_feature <223> Incyte clone 2187866 <400> 5 gcctcatccc tgggttgtgg tgtggacatt gtgggtgtct ccacaggagc cccagggcca 60 cgaaagctgg ggtggcctct gccccttctg gggttccttt tcctgcacag ctgctttctg 120 actccaccca cagctgggag caggtgccgg agccccggcc tgcatggccc tgtgaaggcc 180 actctgggcg tttgggtggg cgtgagtgcc ttcctctgct cccagcatgt ggttttctcc 240 gttggccgcc tcctggacct cctggtgcct gacatcccag agtctgtgga gatcaaagtg 300 aagcgggagt actacctggc taagcaggca ctggctgaga atgaggttct ttttggaacg 360 aacggaacaa aggatgagca gcccgagggc tcagagctca gctcccactg gacacccttc 420 acggttccca aggccagcca gctgcagcag tgacgcctgg aaggacatct ggtggtcctt 480 aggggagtgg cccctcctga gccctgcgag cagcgtcctt ttcctcttcc ctcaggcagc 540 ggctgtgtga accgctggct gctgttgtgc ctcatctctg ggcacattgc ctgcttcccc 600 ccagcgccgg cttctctcct cagagcgcct gtcactccat ccccggcagg gagggaccgt 660 cagctcacaa ggccctcttt gtttcctgct cccagacata agcccaaggg gcccctgcac 720 ccaagggacc ctgtccctcg gtggcctccc caggcccctg gacacgacag ttctcctcag 780 gcaggtgggc tttgtggtcc tcgccgcccc tggccacatc gccctctcct cttacacctg 840 gtgaccttcg aatgtttcag agcgcagggc cgttctccct cgtgtcctct ggacccaccc 900 gccccttcct gccctgtttg cgcagggaca tcacccacat gccccagctc tcggaccctg 960 cagctctgtg tcccaggcca cagcaaaggt ctgttgaacc cctccctcca ttcccagtta 1020 tctgggtcct ctggattctt ctgtttcttg aatcaggctc tgctttcccc ctagccacta 1080 caggcagcct ctgacagtgc cgctttactt gcattctgca gcaattacat gtgtcctttt 1140 gatccttgcc caacttccct ccctctccca gctcctggcc cctggcccag ggcccctctt 1200 gctgttttta cctctgttcc ttggggccta gtacccagca agcacccaaa tgggggaggt 1260 tttgggatga gaggaggaaa cgtgtatacc tgtaacatct ggtggctctt cccccagaag 1320 tttgtgttca tacataattg ttttccacgc tggatcataa tgtgacgtgc agttctgccc 1380 tgtgctgggg agccacatga agcttcccct ggctaacttg ctaccccgca gcaatcccag 1440 tgtggctgtc tgcttgctaa aaaatggatc tgtgctcatc tgtattgatg tccttggagt 1500 tctacaagtg gaacttaagt gtcaaaaaga atatgtggtt tttaggggga tcctctagag 1560 tcgacct 1567 <210> 6 <211> 1354 <212> DNA
<213> Homo sapiens <220>
<221> misc_feature <223> Incyte clone 3096181 <400> 6 taagaatgag tttcttactg aacaactttc taaaacgcaa attaaactca ataccttaaa 60 agataagttc cgtaagacaa gagatactct cagaaaaaag tcatcggctt tagaaactct 120 ccaaacgacc taagccaaac acagcagcaa ataaaggaaa tgaaagagat gtatgaaaat 180 gcagaagata aagtgaataa ttccactgga aagtggagct gtgtagaaga gaggatatgt 240 catctccaac atgaaaatcc gtgccttgaa cagcaactag atgatgttca tcagaaagag 300 gatcataaag agatagtaac taatatccaa agaggcttta ttgagagtag aaagaaagac 360 ctcatgctag aagagaaaag taagaagcta atgaatgaat gtgatcattt aaaagaaagt 420 ctctttcaat atgagagaga gaaagcagaa agagtagtgg ttgtgagaca acttcaacaa 480 gaagcggctg acagccctaa aaaaattaac tatgttagag tctccactgg aaggtatatc 540 acgttgtcat attaatttgg ttgagacaca ggtcccaaag aagaaattat ttcaagtgga 600 aagtcaattt gatgatctta tggcggagaa ggaagctgta tcttcaaaat gtgtcaattt 660 ggctaaagag aatcaagttt ttcaacagga gttattatct atgaaaaaag cacaacagga 720 atgtgaaaaa tttgaggagg ataaaagatg ttggaagaag aaatattaaa tcttaagaca 780 catatggaaa acagtatggt agaacttagt aaactacaag aatataaatc agagctagat 840 gaaaaggcaa tgcaggcagt agaaaaatta gaagaaatcc atttacagga acaagcacaa 900 tataaaaaac aattagagca gttaaacaag gatataatac agcttcacta aataagaagg 960 aactcacact taaagatgtg gaatgtaaat tctacaaaat gaaaactgct tatgaagagg 1020 ttacaactga gttagaagaa tataaggaag cctttgcagc agcattgana gctaacagtt 1080 ccatgtctaa nanattaact aaatcgaata aganaatagc aatgatcagt atcagctctt 1140 tatggngana gagcaggtga natattttct cagcactctt cctacnnggc gaggtcgaga 1200 gtcaccttgt gttgantatn cctacttngt ataggngctc agtcaganga tataatnctt 1260 ccaaatngcc cgtntggggt tcctancttt caggngcctn cagagnttcc ataattnaac 1320 ngnccnaggn gtanctttga nctgagggcc nntt 1354 <210> 7 <211> 2426 <212> DNA
<213> Homo sapiens <220>
<221> misc_feature <223> Incyte clone 3360806 <400> 7 ctcccttcct tctcaggggg tcccgagccc cgactagctt tgncctaact ccttcatcaa 60 aaganccccc gccagcttcc cacacctcat acgcagccac atctgcccta ttctccatgc 120 tttccagctt gcctgccctt cctcatctct ccctgcctgt gcagacctcc acccttcttt 180 cctccacccc tccatccccc aatgcttgta gaccttccat tcattccgtc tcatcgtgcg 240 tggtctctga tcgtccatca cctgaccttc tccaggactg tcttctcacc cttccccact 300 ccctggtccc cgggagcagc tccttctgcc cgactcactc acagtgcagg gaaaggaggc 360 agggaaaaga ccaggattct gtgagttctg aggttgccac, acacaaagaa gctgtggttt 420 ctctgcctcg gccactgatg agactaaaac tggcttcccc ttggagacgg cagatttcag 480 gctgatccct gcttaagccc tctcatcccc acgctggtcc tggtattgat acaagaccca 540 gctggtgaca aagcctccaa tcctgggggt ccacgagcct gggcctgaca ttcccagaac 600 taccgccagt ggcgccaggc ccccacagtc tgtggccgtg gtcttagccc ccagttccac 660 tctggatggg cctgtgacac cccaaagaga agaaggggac tctggatagg gtccccacat 720 ccagggcgtg gggagaccat tggcatttgg gaaccatttt ccttcgaacg gcttcccctt 780 gagctgagca ttctgcttgc tgcagtagac gggtcgcctt ttgcccatac cgaaattttc 840 tgaaattaaa tcgcacaccc ccaccatttc ctctccctgg ggatctggag gaacatcata 900 catagtaggt gaatcgtttt gtagagtgaa gaatgctaat gtaaagcaaa tagtcaccca 960 cgttccttgt aaatccaaat gtttctatat tgtagctttg cttaaaatgg gggtcggccc 1020 caactgcatc ctcctctttg gcgggctggg gagcggcccc cagccgggac gggagggcag 1080 cgaccccgag gcctcgtgga cgtgggagag agtgtggtgg gaagtcttga gcggaggagg 1140 ggatctgccc ttctccactc ctctcttgga tccgcctcgg tttcctgtnc ccccaccacc 1200 cgcctgcccc gcggaagacc gcccagtgag ccagccccca ccttccaggc gccttcgccc 1260 tggggatcca accaacttgt atcgagtggg cggggcaacg gctccccatt tttcccgagc 1320 cccgcccaca gagctcttag ccaatcctat gcagagagca tctcctggca ggggtctctt 1380 cccaaccaga ccccacccag gcacattagc gaccaggctt gggcttcccc agcgccccac 1440 caccaccacg tgcaggtgga gctctgggat gctatgttgg ggcggcaagc ggtgggccga 1500 gggccgggta ggctagcacg ggaggtaagg gtggtatggg atggggcggg ggcggtctag 1560 ggcaatagga gagcagagaa tgggggaact tgagggtggg gggagggcac cggagccttg 1620 ccaccatccc aggactttgg gcaagtcacc cgcactccct gggcctcggt ttccccatct 1680 gtaaaatgat ggtaataata cttcacctac ctcatagggg aggttgtgag gccaccatca 1740 cctgacctgg gggtcaaggc aggaggactc cgaaggtgct acccgtgagc aaagtgtaat 2800 taccgaatcc tgactgcaag gcccacctgc ccctccccca cagagcctcc agagctagct 1860 gaggccaacg caggcccatc cgtctcttca ctctgtcgca ggccctttca tgggcttcgt 1920 ctgccatctt tgtgggtgcc ctagacttag tccttatctt gtcctggttt cctttcttgt 1980 gaccatctcc ccatgaaagt gctgtacaaa ttccacccgc cccaggaccc ccgcacctgc 2040 cctctggcac cagatgccag ggaagggaca gaggaaaaca gccacaaaca agccaggggg 2100 gctccccgga gccccagggg tggggattgg tggccactgt ttgtatgttc ttgagtgcaa 2160 gtgttttata aaaaataaaa caaaaaccca ccatcacaaa aaaaaaaatt ttgcagcgaa 2220 gagaaatgaa gaaaaactga agaaaaaaaa aaaacnggaa ataagaacca tacaaaattt 2280 ttccaccaca cataccctct aagccagcaa gatttcctct ttgcaaaatc atatttttgt 2340 gggaatgggc cctgcttttt gtggcaaggc ctgttctgat taataaagga tcgtgaanan 2400 anaagttaaa nntgtgattt caanaa 2426 <210> 8 <211> 510 <212> DNA
<213> Homo Sapiens <220>
<221> misc_feature <223> Incyte clone 3458076 <400> 8 gatttaaaag ccgccggctg gcgcgcgtgg ggggcaagga agggggggcg gaaccagcct 60 gcncgcgctg gctccgggtg acagccgcgc gcctcggcca ggatctgagt gatgagacgt 120 gtccccactg aggtgcccca cagcagcagg tgttgagcat gggctgagaa gctggaccgg 180 caccaaaggg ctggcagaaa tgggcgcctg gctgattcct aggcagttgg cggcagcaag 240 gaggagaggc cgcagcttct ggagcagagc cgagacgaag cagttctgga gtgcctgaac 300 ggccccctga gccctacccg cctggcccac tatggtccag aggctgtggg tgagccgcct 360 gctgcggcac cggaaagccc agctcttgct ggtcaacctg ctaacctttg gcctggaggt 420 gtgtttggcc gcagattcac ctatgtgccg cctctgtgct ggaatggggg tagaggagaa 480 gttcatgacc atggtgctgg gatttggtcc 510 <210> 9 <211> 231 <212> PRT
<213> Homo Sapiens <220>
<221> misc_feature <223> Incyte cone 1864683 <400> 9 Met Gly Ser Leu Gly Leu Phe Leu Gln Cys Ala Ile Ser Leu Val Phe Ser Leu Val Met Asp Arg Leu Val Gln Arg Phe Gly Thr Arg Ala Val Tyr Leu Ala Ser Val Ala Ala Phe Pro Val Ala Ala Gly Ala Thr Cys Leu Ser His Ser Val Ala Val Val Thr Ala Ser Ala Ala Leu Thr~Gly Phe Thr Phe Ser Ala Leu Gln Ile Leu Pro Tyr Thr Leu Ala Ser Leu Tyr His Arg Glu Lys Gln Val Phe Leu Pro Lys Tyr Arg Gly Asp Thr Gly Gly Ala Ser Ser Glu Asp Ser Leu Met Thr Ser Phe Leu Pro Gly Pro Lys Pro Giy Ala Pro Phe Pro Asn Gly His Val Gly Ala Gly Gly Ser Gly Leu Leu Pro Pro Pro Pro Ala Leu Cys Gly Ala Ser Ala Cys Asp Val Ser Val Arg Val Val Val Gly Glu Pro Thr Glu Ala Arg Val Val Pro Gly Arg Gly Ile Cys Leu Asp Leu Ala Ile Leu Asp Ser Ala Phe Leu Leu Ser Gln Val Ala Pro Ser Leu Phe Met Gly Ser Ile Val Gln Leu Ser Gln Ser Val Thr Ala Tyr Met Val Ser Ala Ala Ala Leu Gly Leu Val Ala Ile Tyr Phe Ala Thr Gln Val Val Phe Asp Lys Ser Asp Leu Ala Lys Tyr Ser Ala <210> 10 <211> 162 <212> PRT
<213> Homo sapiens <220>
<221> misc_feature <223> Incyte clone 3458076 <400> 10 Met Val Met Asn Phe Ser Ser Thr Pro Ile Pro Ala Gln Arg Arg His Ile Gly Glu Ser Ala Ala Lys His Thr Ser Arg Pro Lys Val Ser Arg Leu Thr Ser Lys Ser Trp Ala Phe Arg Cys Arg Ser Arg Arg Leu Thr His Ser Leu Trp Thr Ile Val Gly Gln Ala Gly Arg Ala Gln Gly Ala Val Gln Ala Leu Gln Asn Cys Phe Val Ser Ala Leu Leu Gln Lys Leu Arg Pro Leu Leu Leu Ala Ala Ala Asn Cys Leu Gly Ile Ser Gln Ala Pro Ile Ser Ala Ser Pro Leu Val Pro Val Gln Leu Leu Ser Pro Cys Ser Thr Pro Ala Ala Val Gly His Leu Ser Gly Asp Thr Ser His His Ser Asp Pro Gly Arg Gly Ala Arg Leu Ser.Pro Gly Ala Ser Ala Xaa Arg Leu Val Pro Pro Pro Leu Pro Cys Pro Pro Arg Ala Pro Ala Gly Gly Phe g/g

Claims (20)

What is claimed is:

1. A method for identifying biomolecules useful in the diagnosis or treatment of a disease associated with cell proliferation, said method comprising:
a) examining expression patterns of polynucleotides that are expressed in a plurality of cDNA libraries, said expressed polynucleotides comprising one or more prostate cancer-specific genes and one or more genes of unknown function; and b) comparing the expression patterns of said prostate cancer-specific genes with the expression patterns of the genes of unknown function to identify a subset of the genes of unknown function which have similar expression patterns to those of prostate cancer-specific genes.

2 The method of claim 1, wherein said polynucleotides are selected from the group consisting of expressed sequence tags (ESTs), assembled sequences, full length gene coding sequences, 5' untranslated regions and 3' untranslated regions.

3. The method of claim 1, wherein said prostate cancer-specific genes are selected from the group consisting of prostate-specific antigen, prostatic acid phosphatase, kallikrein, seminal plasma protein and prostate-specific transglutaminase.

4. The method of claim 1, wherein said comparing comprises a) generating an occurrence data vector for each expressed polynucleotide;
b) analyzing vectors for two or more expressed polynucleotides to determine a coexpression probability; and c)determining whether the coexpression probability for said two or more expressed polynucleotides is less than a specified coexpression probability threshold.

The method of claim 1, further comprising the step of translating said subset of genes of unknown function to generate corresponding polypeptides.

6. A polynucleotide identified by the method of claim 1.

7. A polypeptide identified by the method of claim 5.

8. A substantially purified biomolecule for use in the diagnosis or treatment of a disease associated with cell proliferation, said biomolecule selected from the group consisting of:
(A) a polynucleotide selected from the group consisting of SEQ ID NOs: 1-8;
(B) a polynucleotide which encodes a polypeptide selected from the group consisting of SEQ ID NOs: 9-10;
(C) a polynucleotide having at least 70% identity to the polynucleotide of (A) or (B);
(D) a polynucleotide which is complementary to the polynucleotide of (A), (B), or (C);
(E) a polynucleotide comprising at least 18 sequential nucleotides of the polynucleotide of (A), (B), (C), or (D);
(F) a polypeptide selected from the group consisting of SEQ ID NOs: 9-10;
(G) a polypeptide having at least 85% identity to the polypeptide of (F); and (H) a polypeptide comprising at least 6 sequential amino acids of the polypeptide of (F)or (G).

9. The substantially purified biomolecule of claim 8, comprising a polynucleotide sequence selected from the group consisting of:
(A) a polynucleotide selected from the group consisting of SEQ ID NOs: 1-8;
(B) a polynucleotide which encodes a polypeptide selected from the group consisting of SEQ ID NOs: 9-10;
(C) a polynucleotide having at least 70% identity to the polynucleotide of (A) or (B);
(D) a polynucleotide which is complementary to the polynucleotide of (A), (B), or (C);
(E) a polynucleotide comprising at least 18 sequential nucleotides of the polynucleotide of (A), (B), (C), or (D); and (F) a polynucleotide which hybridizes under stringent conditions to the polynucleotide of (A), (B), (C), (D), or (E).

10. The substantially purified biomolecule of claim 8, comprising a polypeptide sequence selected from the group consisting of:
(A) a polypeptide selected from the group consisting of SEQ ID NOs:9-10;
(B) a polypeptide having at least 85% identity to the polypeptide of (A); and (C) a polypeptide comprising at least 6 sequential amino acids of the polypeptide of (A) or (B).

11. An expression vector comprising the polynucleotide of claim 9.

12. A host cell comprising the expression vector of claim 11.

13. A method for producing a polypeptide of claim 10, the method comprising the steps of:
a) culturing the host cell of claim 12 under conditions suitable for the expression of the polypeptide; and b) recovering the polypeptide from the host cell culture.

14. A pharmaceutical composition comprising the biomolecule of claim 8 in conjunction with a suitable pharmaceutical carrier.

15. An antibody which specifically binds to the polypeptide of claim 10.

16. A method for detecting a target polynucleotide in a biological sample, the method comprising the steps of:
(a) hybridizing the polynucleotide of claim 9 to the target polynucleotide to form a hybridization complex; and (b) detecting the hybridization complex, wherein the presence of the hybridization complex correlates with the presence of the target polynucleotide.

17. A method for identifying biomolecules useful in the diagnosis or treatment of a disease, said method comprising:
a) examining expression patterns of a plurality of biomolecules that are expressed in a plurality of cDNA libraries, said expressed biomolecules comprising one or more disease-specific biomolecules and one or more biomolecules of unknown function; and b)comparing the expression patterns of said disease-specific biomolecules with the expression patterns of the biomolecules of unknown function to identify a subset of the biomolecules of unknown function which have similar expression patterns to those of the disease-specific biomolecules.

18. The method of claim 17, wherein said comparing comprises a) generating an occurrence data vector for each expressed biomolecule;
b) analyzing vectors for two or more expressed biomolecules to determine a coexpression probability; and c)determining whether the coexpression probability for said two or more expressed biomolecules is less than a specified coexpression probability threshold.

19. A polynucleotide identified by the method of claim 17.

20. A polypeptide identified by the method of claim 17.