WO2002102985A3 - Pate, a gene expressed in prostate cancer, prostate and testis, and uses thereof - Google Patents

Abstract

An antibody is disclosed that specifically binds a PATE polypeptide. A nucleic acid sequence is disclosed that includes a PATE promoter or a conservative variant thereof. Methods are also disclosed for detecting prostate cancer in a subject. In one embodiment, a method is disclosed for producing an immune response against a cell expressing a PATE polypeptide in a subject. In another embodiment, a method is disclosed for inhibiting the growth of a malignant cell expressing a PATE polypeptide. A method is also disclosed for reducing the number of prostate cancer cells in a subject that includes administering to the subject a therapeutically effective amount of the PATE polypeptide or a polynucleotide encoding the PATE polypeptide. Kits for detecting PATE polypeptides and PATE polynucleotides are disclosed. In one embodiment, these kits are ofuse to detect prostate cancer. A method is also disclosed for increasing the proliferation of a prostate cell. The method includes contacting the prostate cell with a PATE polypeptide or transfecting the prostate cell with a nucleic acid encoding the P ATE polypeptide, thereby increasing the proliferation of the prostate cell.

Description

  PATE, A GENE EXPRESSED IN PROSTATE CANCER, PROSTATE AND
TESTIS, AND USES THEREOF
PRIORITY CLAIM This application claims priority to U.S. Provisional Patent Application No.
60/298,614, filed June 15, 2001, which is inco[phi]orated by reference in its entirety.
FIELD
This disclosure relates the prostate, specifically to polypeptides expressed specifically in the prostate and the testis, and to factors that stimulate the growth of prostate cells. The disclosure further relates to detection and treatment of prostate cancer.
BACKGROUND Cancer of the prostate is the most commonly diagnosed cancer in men and is the second most common cause of cancer death (Carter and Coffey, Prostate 16:3948, 1990; Armbruster, et al., Clinical Chemistry 39:181, 1993). If detected at an early stage, prostate cancer is potentially curable.

   However, a majority of cases are diagnosed at later stages when metastasis of the primary tumor has already occurred (Wang, et al., Meth. Cancer Res. 19:179, 1982). Even early diagnosis is problematic because not all individuals who test positive in these screens develop cancer.
Prostate specific antigen (PSA) is a 240 amino acid member of the glandular kallikrein gene family. (Wang, et al., 1982, supra; Wang, et al., Invest. Urology, 17:159, 1979; Bilhartz, et al., Urology, 38:95, 1991). PSA is a serine protease, produced by normal prostatic tissue, and secreted exclusively by the epithelial cells lining prostatic acini and ducts (Wang, et al., 1982, supra; Wang, et al., 1979, supra; Lilja, et al., World! Uroi, 11:188-191, 1993). Prostate specific antigen can be detected at low levels in the sera of healthy males without clinical evidence of prostate cancer.

   However, during neoplastic states, circulating levels of this antigen increase dramatically, correlating with the clinical stage of the disease
(Schellhammer, et al., Urologic Clinics of North America, 20:597, 1993; Huang, et al., Prostate 23:201, 1993). Prostate specific antigen is now the most widely used marker for prostate cancer. However, there clearly is a need to identify additional antigens to aid in the diagnosis of prostate cancer, and for use as therapeutic agents.
Present treatment for prostate cancer includes radical prostatectomy, radiation therapy, or hormonal therapy. With surgical intervention, complete eradication of the tumor is not always achieved and the observed re-occurrence of the cancer (12-68%) is dependent upon the initial clinical tumor stage (Zietman, et al., Cancer 71 :959, 1993).

   Thus, alternative methods of treatment including prophylaxis or prevention are desirable.
Immunotherapy is a potent new weapon against cancer. Immunotherapy involves evoking an immune response against cancer cells based on their production of target antigens. Immunotherapy based on cell-mediated immune responses involves generating a cell-mediated response to cells that produce particular antigenic determinants, while immunothrapy based on humoral immune responses involves generating specific antibodies to cells that produce particular antigenic determinants.
Cancer cells produce various proteins that can become the target of immunotherapy; antigenic determinants normally present on a specific cell type can also be immunogenic.

   For example, Rosenberg et al. have shown that tumor infiltrating lymphocytes target and recognize antigenic determinants of the protein MART- 1 , produced by both normal melanocytes and malignant melanoma cells.
Furthermore, active or passive immunotherapy directed against MART-1 or peptides of it that bind to MHC Class I molecules (epitopes of HLA A2, in particular) results in the destruction of melanoma cells as well as normal cells that produce MART-1 (Kawakami, et al, J. Immunol. 21:237, 1998). The tissue specificity of PSA has made it a potential target antigen for active specific immunotherapy (Armbruster, et al., Clin.

   Chemistry 39:181, 1993; Brawer, et al., Cancer Journal Clinic 39:361, 1989), especially in patients who have undergone a radical prostatectomy in which the only PSA expressing tissue in the body should be in metastatic deposits.
Recent studies using in- vitro immunization have shown the generation of CD4 and CD8 cells specific for PSA (Peace, et al., Cancer Vaccines: Structural Basis for Vaccine Development (Abstract), 1994; Correale, et al., 9th International Congress of Immunology (Abstract), 1995), and methods for inducing an immune response against PSA include the use of viral vectors incorporating DNA encoding PSA (e.g. see U.S. Patent No. 6,165,460; Hodge, et al., Cancer 63:231, 1995). Discovery of additional antigens expressed by the prostate gland can similarly be used to design immunotherapy methods for prostate cancer.

   Thus, it would be desirable to identify new differentiation antigens that are present in prostate cancer but which are not present in organs essential to survival.
SUMMARY
A new gene has been found that is specifically expressed in prostate cancer, prostate and testis. Due to its expression pattern, the gene has been denominated as "PATE," for Prostate And Testis Expressed gene. Antibodies have been produced that specifically bind to the PATE polypeptide. Moreover, the antibodies and nucleic acid and amino acid sequences are of use in detecting prostate cancer, and in treating prostate cancer.

   An antibody is disclosed herein that specifically binds a PATE polypeptide having an amino acid sequence selected from the group consisting of: (1) an amino acid sequence 80% homologous to SEQ ID NO:2; (2) a conservative variant of SEQ ID NO:2; (3) an immunogenic fragment comprising eight consecutive amino acids of SEQ ID NO:l that specifically binds to an antibody that specifically binds SEQ ID NO:2; and (4) SEQ ID NO:2. In one embodiment, a method is disclosed herein for detecting prostate cancer in a subject. The method includes contacting a sample obtained from the subject with an antibody that binds PATE for a sufficient amount of time to form an immune complex, and detecting the presence the immune complex. In one embodiment, a method is disclosed for producing an immune response against a cell expressing a PATE polypeptide in a subject.

   The method includes administering to the subject a therapeutically effective amount of the PATE polypeptide, thereby producing the immune response.
In another embodiment, a method is disclosed for inhibiting the growth of a malignant cell expressing a PATE polypeptide. The method includes culturing cytotoxic T lymphocytes (CTLs) or CTL precursor cells with the PATE polypeptide to produce activated CTLs or CTL precursors that recognize a PATE expressing cell, and contacting the malignant cell with the activated CTLs or CTLs matured from the CTL precursors.
In a further embodiment, a method is disclosed for inhibiting the growth of a malignant cell expressing a PATE polypeptide.

   The method includes contacting the malignant cell with an effective amount of a cell-growth inhibiting molecule that includes a ligand that specifically binds the PATE polypeptide.
A method is also disclosed for reducing the number of prostate cancer cells in a subject. The method includes administering to the subject a therapeutically effective amount of the PATE polypeptide or a polynucleotide encoding the PATE polypeptide, wherein the administration of the PATE polypeptide or the polynucleotide encoding the PATE polypeptide results in an immune response to the PATE polypeptide.
In one embodiment, kits for detecting PATE polypeptides and PATE polynucleotides are disclosed. In another embodiment, a method is disclosed for increasing the proliferation of a prostate cell.

   The method includes contacting the prostate cell with a PATE polypeptide or transfecting the prostate cell with a nucleic acid encoding the PATE polypeptide, thereby increasing the proliferation of the prostate cell.
In another embodiment, a nucleic acid sequence is disclosed that includes a PATE promoter or a conservative variant thereof. Vectors including these promoters, and host cells transformed with these vectors are also disclosed.
The foregoing and other features and advantages will become more apparent from the following detailed description of several embodiments, which proceeds with reference to the accompanying figures.
BRIEF DESCRIPTION OF THE FIGURES Fig. 1 is a set of schematic diagrams showing the ESTs of cluster GS-1 and the alignment of ESTs of PATE.

   Fig. 1A is a schematic diagram of GS-1; the cluster is 532 bp in length and contains five ESTs from prostate, one from testis and two from a pool of tissues. The positions of TATA box and potential AREs are shown. Locations of the PCR primer T339 and T340 are also shown. Fig. 2 is a digital image of RNA hybridization of a multiple tissue dot blot containing mRNA from 50 normal human cell types or tissues using a cDNA probe from the 3' end of the GS-1 transcript. The tissue distribution of GS-1 is shown. Strong expression is observed in Prostate (C7) and testis (Dl) samples. Fig. 3 is a digital image of a PCR analysis of cDNA from 24 different human tissues (Rapid Scan panel, Origene). The expected size of the GS-1 PCR product is indicated by an arrow (300 bp).

   Very strong signal of 300 bp PCR product is detected in testis (lane 14); with weak expression in prostate (lane 6) and adrenal gland (lane 10). Fig. 4 is a digital image of a Northern blot analysis showing expression and transcript sizes of PATE in different normal tissues. PCR probe generated from the GS-1 cluster was used for hybridization. The predominant transcript is about 1.5 kb in size and is highly expressed in prostate. The signal in testis lane is weak.
Fig. 5 is the nucleotide and deduced amino acid sequence of PATE cDNA. Putative polyadenylation signal is underlined. The PATE protein shown in this figure is encoded by the PATE gene (SEQ ID NO: 1) and has the amino acid sequence (SEQ ID NO:2) shown italicized in standard single letter code under the nucleotide sequence.

   The wild-type nucleotide sequence encoding the PATE protein (SEQ ID NO:3) is set forth in Fig. 5, commencing with the "A" over the first "M" of the amino acid sequence and ending with the second "T" over the "L" designating the amino acid at position 127 of the amino acid sequence.
Fig. 6 is a digital image of a Western blot analysis of anti-PATE antisera: A specific protein of molecular weight about 14 kDa is detected by anti-PATE IgG only in prostate and testis tissue extract. The tissue extract from brain was used as negative control.
Fig. 7 is the sequence of the promoter region of the PATE gene. About 2000 bp genomic DNA sequences from the upstream region of the PATE transcript were analyzed to identify the transcriptional regulatory elements (using MacVector program).

   There are three androgen responsive elements (ARE) and one consensus TATA box sequences were identified in the upstream DNA sequence of the PATE transcript. (Note: the promoter sequence ends with the last "A" before the letters "ATG" over the italicized capital "M" on the bottom line.) Fig. 8 is a digital image showing in situ localization of PATE rnRNA: Columns A and B represent two prostate cancer samples. Prostate tissue section stained with hematoxylin/eosin to show the general morphology and the types of cells (images marked 1 and 4). Prostate tissue section probed with plasmid Bluescript vector (without any cDNA insert) as a negative control (images marked 2 and 5). Note the absence of signal. Prostate tissue section probed with PATE (images 3 and 6).

   Note the strong signal in the tumor cells.
Fig. 9 is a set of digital images of an analysis of the protein product encoded by PATE. Fig. 9 A is a digital image of an analysis of the in vitro translated products of PATE cDNA: PATE cDNA was transcribed in vitro with T7 RNA polymerase and the RNA translated with wheat germ extract in presence of<35>S-methionine. The translated products were analyzed by SDS-PAGE and fluorography. Lane 1, PATE cDNA; lane 2, empty vector control; lane 3, luciferase cDNA as positive control. Fig. 9B is a digital image of a Western blot analysis of PATE transfected cell extract with anti-myc-tag antibody. A specific band of molecular weight about 16 kDa is detected by anti-myc-tag antibody in the membrane fraction of the transfected cell line.
Fig. 10 is a schematic diagram of an alignment of PATE with a three-finger toxin family member 1F94_A.

   Fig. 10A is an alignment that was performed manually by first aligning the 10 cysteines and then arranging the rest of the residues for the best alignment. The cysteine residues are serially numbered. Cysteines with same color are disulphide bonded to each other. Fig. 10B is a ribbon diagram (using Insight II, Biosym) of the X-ray structure of 1F94 A. The numbering of the cysteine residues correspond to that shown in Fig. 10A.
SEQUENCE LISTING The nucleic and amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, and three letter code for amino acids, as defined in 37 C.F.R. 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand.

   In the accompanying sequence listing: SEQ ID NO: 1 is a nucleic acid sequence of a gene encoding a PATE polypeptide.
SEQ ID NO:2 is the amino acid sequence of a PATE polypeptide. SEQ ID NO:3 is a nucleic acid encoding a PATE polypeptide. SEQ ID NO:4 is the nucleic acid sequence of the PATE promoter.
SEQ ID NOs: 5-8 are the nucleic acid sequences of primers. SEQ ID NO:9 is an amino acid sequence of a phospholipase A2 motif. SEQ ID NO: 10 and SEQ ID NO:l 1 are the amino acid sequences of PATE polypep tides.
DETAILED DESCRIPTION A novel gene product expressed in cells of the normal prostate and prostate cancer, termed PATE, is disclosed herein.
After defining some of the terms used herein, the discussion below sets forth the discovery of the nature and function of the PATE protein, nucleic acid sequences encoding PATE, and sequences that control the expression of this protein.

   As PATE is expressed in prostate cancer, it is of use in detecting prostate cancer cells. Diagnostic kits for PATE are thus disclosed.
Antibodies that specifically bind PATE are also disclosed herein. These antibodies are of use in detection assays, as well as in the production of immunoconjugates, such as immunotoxins, which can be used to target prostate cancer.
Nucleic acids encoding PATE, or a PATE polypeptide, can be used to produce an immune response against prostate cancer cells. Thus, pharmaceutical compositions including PATE, or a nucleic acid encoding PATE are also disclosed. As disclosed herein, PATE is a growth factor for prostate cells. Thus, methods of increasing the proliferation of cells using this polypeptide are also disclosed.
Terms
Unless otherwise noted, technical terms are used according to conventional usage.

   Definitions of common terms in molecular biology may be found in Benjamin Lewin, Genes V, published by Oxford University Press, 1994 (ISBN 0-19854287-9); Kendrew et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8).
In order to facilitate review of the various embodiments of the present disclosure, the following explanations of specific terms are provided:
Amplification: of a nucleic acid molecule (e.g., a DNA or RNA molecule) refers to use of a technique that increases the number of copies of a nucleic acid molecule in a specimen.

   An example of amplification is the polymerase chain reaction, in which a biological sample collected from a subject is contacted with a pair of oligonucleotide primers, under conditions that allow for the hybridization of the primers to a nucleic acid template in the sample. The primers are extended under suitable conditions, dissociated from the template, and then re-annealed, extended, and dissociated to amplify the number of copies of the nucleic acid. The product of amplification may be characterized by electrophoresis, restriction endonuclease cleavage patterns, oligonucleotide hybridization or ligation, and/or nucleic acid sequencing using standard techniques. Other examples of amplification include strand displacement amplification, as disclosed in U.S. Patent No.
5,744,311; transcription-free isothermal amplification, as disclosed in U.S.

   Patent No. 6,033,881; repair chain reaction amplification, as disclosed in WO 90/01069; ligase chain reaction amplification, as disclosed in EP-A-320 308; gap filling ligase chain reaction amplification, as disclosed in 5,427,930; and NASBA(TM) RNA transcription-free amplification, as disclosed in U.S. Patent No. 6,025,134.
Antibody: immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen binding site that specifically binds (immunoreacts with) an antigen. A naturally occurring antibody (e.g., IgG, IgM, IgD) includes four polypeptide chains, two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds. However, it has been shown that the antigen-binding function of an antibody can be performed by fragments of a naturally occurring antibody.

   Thus, these antigen-binding fragments are also intended to be designated by the term "antibody." Specific, non-limiting examples of binding fragments encompassed within the term antibody include (i) a Fab fragment consisting of the VL, VH, CL and CHI domains; (ii) an Fd fragment consisting of the VH and CHI domains; (iii) an Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (iv) a dAb fragment (Ward et al., Nature 341 :544-546, 1989) which consists of a VH domain; (v) an isolated complimentarity determining region (CDR); and (vi) a F(ab')2fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region. The phrase "single chain Fv" or "scFv" refers to an antibody in which the heavy chain and the light chain of a traditional two chain antibody have been joined to form one chain.

   Typically, a linker peptide is inserted between the two chains to allow for proper folding and creation of an active binding site.
Immunoglobulins and certain variants thereof are known and many have been prepared in recombinant cell culture (e.g., see U.S. Patent No. 4,745,055; U.S. Patent No. 4,444,487; WO 88/03565; EP 256,654; EP 120,694; EP 125, 023; Faoulkner, et al., Nature 298:286, 1982; Morrison, J. Immunol. 123:793, 1979; Morrison, et al., Ann Rev. Immunol 2:239, 1984). An antibody immunologically reactive with a particular antigen can also be generated by recombinant methods such as selection of libraries of recombinant antibodies in phage or similar vectors.

   See, e.g., Huse, et al., Science 246:1275-1281 (1989); Ward, et al., Nature 341:544546 (1989); and Vaughan, et al., Nature Biotech. \4:309-314 (1996).
Animal: Living multi-cellular vertebrate organisms, a category that includes, for example, mammals and birds. The term mammal includes both human and non-human mammals. Similarly, the term "subject" includes both human and veterinary subjects.
Conservative variants: "Conservative" amino acid substitutions are those substitutions that do not substantially affect or decrease an activity, such as a growth promoting activity, or antigenicity of PATE.

   Specific, non-limiting examples of a conservative substitution include the following examples: Original Residue Conservative Substitutions Ala Ser
Arg Lys
Asn Gin, His
Asp Glu
Cys Ser Gin Asn
Glu Asp
His Asn; Gin
He Leu, Val
Leu He; Val Lys Arg; Gin; Glu
Met Leu; He
Phe Met; Leu; Tyr
Ser Thr
Thr Ser Trp Tyr
Tyr Trp; Phe
Val He; Leu
The term conservative variation also includes the use of a substituted amino acid in place of an unsubstituted parent amino acid, provided that antibodies raised to the substituted polypeptide also immunoreact with the unsubstituted polypeptide.

   Non-conservative substitutions are those that reduce an activity or antigenicity. cDNA (complementary DNA): A piece of DNA lacking internal, noncoding segments (introns) and regulatory sequences that determine transcription. cDNA is synthesized in the laboratory by reverse transcription from messenger RNA extracted from cells.
Contacting: Placement in direct physical association. Includes both in solid, and liquid form. Degenerate variant: A polynucleotide encoding a PATE polypeptide that includes a sequence that is degenerate as a result of the genetic code. There are 20 natural amino acids, most of which are specified by more than one codon.

   Therefore, all degenerate nucleotide sequences are included as long as the amino acid sequence of the PATE polypeptide encoded by the nucleotide sequence is unchanged.
Effector molecule: The portion of a chimeric molecule that is intended to have a desired effect on a cell to which the chimeric molecule is targeted. Also known as an effector moiety (EM), therapeutic agent, or diagnostic agent," or similar terms.
Therapeutic agents include such compounds as nucleic acids, proteins, peptides, amino acids or derivatives, glycoproteins, radioisotopes, lipids, carbohydrates, or recombinant viruses. Nucleic acid therapeutic and diagnostic moieties include antisense nucleic acids, derivatized ohgonucleotides for covalent cross-linking with single or duplex DNA, and triplex forming ohgonucleotides.

   Alternatively, the molecule linked to a targeting moiety, such as an anti-PATE antibody, may be an encapsulation system, such as a liposome or micelle that contains a therapeutic composition such as a drug, a nucleic acid (e.g. an antisense nucleic acid), or another therapeutic moiety that is preferably shielded from direct exposure to the circulatory system. Means of preparing liposomes attached to antibodies are well known to those of skill in the art. See, for example, U.S. Patent No. 4,957,735; and Connor, et al., Pharm. Ther. 28:341-365 (1985). Diagnostic agents or moieties include radioisotopes and other detectable labels. Epitope: An antigenic determinant. These are particular chemical groups or peptide sequences on a molecule that are antigenic, i.e. that elicit a specific immune response.

   An antibody specifically binds a particular antigenic epitope on a polypeptide.
Expressed: Translation of a nucleic acid into a protein. Proteins may be expressed and remain intracellular, become a component of the cell surface membrane, or be secreted into the extracellular matrix or medium
Expression Control Sequences: Nucleic acid sequences that regulate the expression of a heterologous nucleic acid sequence to which it is operatively linked. Expression control sequences are operatively linked to a nucleic acid sequence when the expression control sequences control and regulate the transcription and, as appropriate, translation of the nucleic acid sequence.

   Thus expression control sequences can include appropriate promoters, enhancers, transcription terminators, a start codon (i.e., ATG) in front of a protein-encoding gene, splicing signal for introns, maintenance of the correct reading frame of that gene to permit proper translation of mRNA, and stop codons. The term "control sequences" is intended to include, at a minimum, components whose presence can influence expression, and can also include additional components whose presence is advantageous, for example, leader sequences and fusion partner sequences. Expression control sequences can include a promoter.
A promoter is a minimal sequence sufficient to direct transcription.

   Also included are those promoter elements which are sufficient to render promoterdependent gene expression controllable for cell-type specific, tissue-specific, or inducible by external signals or agents; such elements may be located in the 5' or 3' regions of the gene. Both constitutive and inducible promoters, are included (see e.g., Bitter, et al., Methods in Enzymology 153:516-544, 1987). For example, when cloning in bacterial systems, inducible promoters such as pL of bacteriophage lambda , plac, ptrp, ptac (ptrp-lac hybrid promoter) and the like may be used. In one embodiment, when cloning in mammalian cell systems, promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the retrovirus long terminal repeat; the adenovirus late promoter; the vaccinia virus 7.5K promoter) can be used.

   Promoters produced by recombinant DNA or synthetic techniques may also be used to provide for transcription of the nucleic acid sequences. A PATE promoter, which is a promoter operably linked to a PATE polypeptide in a naturally occurring system (e.g. a human cell) is disclosed herein. One specific, non-limiting example of a. PATE promoter is shown as SEQ ID NO:4, however, variants of this sequence are also disclosed herein. Growth Factor: A molecule that induces the proliferation of a cell.
Specific, non- limiting examples of a growth factor are epidermal growth factor (EGF), platelet derived growth factor (PDGF), and neural growth factor (NGF). In one embodiment, a growth factor is tissue specific as it induces the proliferation of a specific cell type.

   In one embodiment, a growth factor is specific for cells of the prostate or the testes.
Host cells: Cells in which a vector can be propagated and its DNA expressed. The cell may be prokaryotic or eukaryotic. The term also includes any progeny of the subject host cell. It is understood that all progeny may not be identical to the parental cell since there may be mutations that occur during replication. However, such progeny are included when the term "host cell" is used. Immune response: A response of a cell of the immune system, such as a B cell, T cell, or monocyte, to a stimulus. In one embodiment, the response is specific for a particular antigen (an "antigen-specific response"). In one embodiment, an immune response is a T cell response, such as a CD4+ response or a CD8+ response.

   In another embodiment, the response is a B cell response, and results in the production of specific antibodies. Immunoconjugate: A covalent linkage of an effector molecule to an antibody. The effector molecule can be an immunotoxin. Specific, non-limiting examples of toxins include, but are not limited to, abrin, ricin, Pseudomonas exotoxin (PE, such as PE35, PE37, PE38, and PE40), diphtheria toxin (DT), botulinum toxin, or modified toxins thereof, or other toxic agents that directly or indirectly inhibit cell growth or kill cells. For example, PE and DT are highly toxic compounds that typically bring about death through liver toxicity. PE and DT, however, can be modified into a form for use as an immunotoxin by removing the native targeting component of the toxin (e.g., domain la of PE and the B chain of DT) and replacing it with a different targeting moiety, such as an antibody.

   A "chimeric molecule" is a targeting moiety, such as a ligand or an antibody, conjugated (coupled) to an effector molecule. The term "conjugated" or "linked" refers to making two polypeptides into one contiguous polypeptide molecule. In one embodiment, an antibody is joined to an effector molecule (EM). In another embodiment, an antibody joined to an effector molecule is further joined to a lipid or other molecule to a protein or peptide to increase its half-life in the body. The linkage can be either by chemical or recombinant means. In one embodiment, the linkage is chemical, wherein a reaction between the antibody moiety and the effector molecule has produced a covalent bond formed between the two molecules to form one molecule. A peptide linker (short peptide sequence) can optionally be included between the antibody and the effector molecule.

   Because immunoconjugates were originally prepared from two molecules with separate functionalities, such as an antibody and an effector molecule, they are also sometimes refe[pi]ed to as "chimeric molecules." The term "chimeric molecule," as used herein, therefore refers to a targeting moiety, such as a ligand or an antibody, conjugated (coupled) to an effector molecule.
Immunogenic peptide: a peptide which comprises an allele-specific motif or other sequence such that the peptide will bind an MHC molecule and induce a cytotoxic T lymphocyte ("CTL") response, or a B cell response (e.g. antibody production) against the antigen from which the immunogenic peptide is derived. In one embodiment, immunogenic peptides are identified using sequence motifs or other methods, such as neural net or polynomial determinations, known in the art.

   Typically, algorithms are used to determine the "binding threshold" of peptides to select those with scores that give them a high probability of binding at a certain affinity and will be immunogenic. The algorithms are based either on the effects on MHC binding of a particular amino acid at a particular position, the effects on antibody binding of a particular amino acid at a particular position, or the effects on binding of a particular substitution in a motif-containing peptide. Within the context of an immunogenic peptide, a "conserved residue" is one which appears in a significantly higher frequency than would be expected by random distribution at a particular position in a peptide.

   In one embodiment, a conserved residue is one where the MHC structure may provide a contact point with the immunogenic peptide.
Immunogenic composition: A composition comprising a PATE polypeptide that induces a measurable CTL response against cells expressing PATE polypeptide, or induces a measurable B cell response (e.g. production of antibodies that specifically bind PATE) against a PATE polypeptide. It further refers to isolated nucleic acids encoding a PATE polypeptide that can be used to express the PATE polypeptide (and thus be used to elicit an immune response against this polypeptide). For in vitro use, the immunogenic composition may consist of the isolated protein or peptide. For in vivo use, the immunogenic composition will typically comprise the protein or peptide in pharmaceutically acceptable carriers, and/or other agents.

   Any particular peptide, PATE polypeptide, or nucleic acid encoding the polypeptide, can be readily tested for its ability to induce a CTL or B cell response by art-recognized assays. Immunogenic compositions can include adjuvants, which are well known to one of skill in the art.
Immunologically Reactive Conditions: Includes reference to conditions which allow an antibody raised against a particular epitope to bind to that epitope to a detectably greater degree than, and/or to the substantial exclusion of, binding to substantially all other epitopes. Immunologically reactive conditions are dependent upon the format of the antibody binding reaction and typically are those utilized in immunoassay protocols or those conditions encountered in vivo. See Harlow & Lane, supra, for a description of immunoassay formats and conditions.

   Preferably, the immunologically reactive conditions employed in the methods are "physiological conditions" which include reference to conditions (e.g., temperature, osmolarity, pH) that are typical inside a living mammal or a mammalian cell. While it is recognized that some organs are subject to extreme conditions, the intra-organismal and intracellular environment normally lies around pH 7 (i.e., from pH 6.0 to pH 8.0, more typically pH 6.5 to 7.5), contains water as the predominant solvent, and exists at a temperature above 0[deg.] C and below 50[deg.] C.

   Osmolarity is within the range that is supportive of cell viability and proliferation.
Isolated: An "isolated" biological component (such as a nucleic acid or protein or organelle) has been substantially separated or purified away from other biological components in the cell of the organism in which the component naturally occurs, i.e., other chromosomal and extra-chromosomal DNA and RNA, proteins and organelles. Nucleic acids and proteins that have been "isolated" include nucleic acids and proteins purified by standard purification methods. The term also embraces nucleic acids and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids.
Label: A detectable compound or composition that is conjugated directly or indirectly to another molecule to facilitate detection of that molecule.

   Specific, nonlimiting examples of labels include fluorescent tags, enzymatic linkages, and radioactive isotopes. Ligand: Any molecule which specifically binds a PATE protein and includes, inter alia, antibodies that specifically bind a PATE protein. In prefe[pi]ed embodiments, the ligand is a protein or a small molecule (one with a molecular weight less than 6 kiloDaltons).

   A ligand can inhibit an activity of PATE (antagonist) such as, but not limited to, the ability of PATE to increase proliferation of prostate cells.
Linker peptide: A peptide within an antibody binding fragment (e.g., Fv fragment) which serves to indirectly bond the variable heavy chain to the variable light chain. "Linker" can also refer to a peptide serving to link a targeting moiety, such as a scFv, to an effector molecule, such as a cytotoxin or a detectable label.
The terms "conjugating," "joining," "bonding" or "linking" refer to making two polypeptides into one contiguous polypeptide molecule, or to covalently attaching a radionuclide or other molecule to a polypeptide, such as an scFv. In the specific context, the terms include reference to joining a ligand, such as an antibody moiety, to an effector molecule ("EM").

   The linkage can be either by chemical or recombinant means. "Chemical means" refers to a reaction between the antibody moiety and the effector molecule such that there is a covalent bond formed between the two molecules to form one molecule.
Lymphocytes: A type of white blood cell that is involved in the immune defenses of the body. There are two main types of lymphocytes: B-cells and T-cells.
Mammal: This term includes both human and non-human mammals. Similarly, the term "subject" includes both human and veterinary subjects. Major Histocompatibility Complex or MHC: generic designation meant to encompass the histocompatibility antigen systems described in different species, including the human leukocyte antigens ("HLA").

   The term "motif refers to the pattern of residues in a peptide of defined length, usually about 8 to about 11 amino acids, which is recognized by a particular MHC allele. The peptide motifs are typically different for each MHC allele and differ in the pattern of the highly conserved residues and negative binding residues.
Oligonucleotide: A linear polynucleotide sequence of up to about 100 nucleotide bases in length.
Open reading frame (ORF): a series of nucleotide triplets (codons) coding for amino acids without any internal termination codons. These sequences are usually translatable into a peptide. Operably linked: A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence.

   For instance, a promoter, such as the PATE promoter, is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences are contiguous and, where necessary to join two protein-coding regions, in the same reading frame.
ORF (open reading frame): A series of nucleotide triplets (codons) coding for amino acids without any termination codons. These sequences are usually translatable into a peptide.
Peptide: A chain of amino acids of between 3 and 30 amino acids in length. In one embodiment, a peptide is from about 10 to about 25 amino acids in length. In yet another embodiment, a peptide is from about 11 to about 20 amino acids in length. In yet another embodiment, a peptide is about 12 amino acids in length.

   A "PATE peptide" is a series of contiguous amino acid residues from the
PATE protein, as discussed above. With respect to immunogenic compositions comprising a PATE peptide, the term further refers to variations of these peptides in which there are conservative substitutions of one or more amino acids, so long as the variations do not alter by more than 20% the ability of the peptide, to produce a B cell response, or, when bound to a Major Histocompatibility Complex Class I molecule, to activate cytotoxic T lymphocytes against cells expressing wild-type PATE protein, induction of CTLs using synthetic peptides and CTL cytotoxicity assays are taught in, e.g., U.S. Patent 5,662,907.
Peptide Modifications: PATE polypeptides include synthetic embodiments of peptides described herein.

   In addition, analogues (non-peptide organic molecules), derivatives (chemically functionalized peptide molecules obtained starting with the disclosed peptide sequences) and variants (homo logs) of these proteins can be utilized in the methods described herein. Each polypeptide is comprised of a sequence of amino acids, which may be either L- and/or D- amino acids, naturally occurring and otherwise.
Peptides may be modified by a variety of chemical techniques to produce derivatives having essentially the same activity as the unmodified peptides, and optionally having other desirable properties.

   For example, carboxylic acid groups of the protein, whether carboxyl-terminal or side chain, may be provided in the form of a salt of a pharmaceutically-acceptable cation or esterified to form a C[iota]-C16ester, or converted to an amide of formula NR[iota]R2wherein R] and R2are each independently H or Ci-Ci[omicron]alkyl, or combined to form a heterocyclic ring, such as a 5- or 6membered ring. Amino groups of the peptide, whether amino-terminal or side chain, may be in the form of a pharmaceutically-acceptable acid addition salt, such as the HC1, HBr, acetic, benzoic, toluene sulfonic, maleic, tartaric and other organic salts, or may be modified to Ci-Ci[beta] alkyl or dialkyl amino or further converted to an amide.
Hydroxyl groups of the peptide side chains may be converted to C[iota]-C16alkoxy or to a C[iota]-C[iota]6ester using well-recognized techniques.

   Phenyl and phenolic rings of the peptide side chains may be substituted with one or more halogen atoms, such as fluorine, chlorine, bromine or iodine, or with C[iota]-C16alkyl, C[iota]-C16alkoxy, carboxylic acids and esters thereof, or amides of such carboxylic acids. Methylene groups of the peptide side chains can be extended to homologous C2-C4alkylenes. Thiols can be protected with any one of a number of well-recognized protecting groups, such as acetamide groups. Those skilled in the art will also recognize methods for introducing cyclic structures into the PATE peptides to select and provide conformational constraints to the structure that result in enhanced stability.

   Peptidomimetic and organomimetic embodiments are envisioned, whereby the three-dimensional arrangement of the chemical constituents of such peptido- and organomimetics mimic the three-dimensional a[pi]angement of the peptide backbone and component amino acid side chains, resulting in such peptido- and organomimetics of a PATE polypeptide having measurable or enhanced ability to generate an immune response. For computer modeling applications, a pharmacophore is an idealized, three-dimensional definition of the structural requirements for biological activity. Peptido- and organomimetics can be designed to fit each pharmacophore with current computer modeling software (using computer assisted drug design or CADD).

   See Walters, "Computer-Assisted Modeling of Drugs", in Klegerman & Groves, eds., 1993, Pharmaceutical Biotechnology, Interpharm Press: Buffalo Grove, IL, pp. 165-174 and Principles of Pharmacology Munson (ed.) 1995, Ch. 102, for descriptions of techniques used in CADD. Also included are mimetics prepared using such techniques..
Pharmaceutically acceptable carriers: The pharmaceutically acceptable carriers of use are conventional. Remington 's Pharmaceutical Sciences, by E. W. Martin, Mack Publishing Co., Easton, PA, 15th Edition (1975), describes compositions and formulations suitable for pharmaceutical delivery of the fusion proteins herein disclosed.
In general, the nature of the carrier will depend on the particular mode of administration being employed.

   For instance, parenteral formulations usually comprise injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle. For solid compositions (e.g., powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate.

   In addition to biologicallyneutral carriers, pharmaceutical compositions to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.
Polynucleotide: The term polynucleotide or nucleic acid sequence refers to a polymeric form of nucleotide at least 10 bases in length. A recombinant polynucleotide includes a polynucleotide that is not immediately contiguous with both of the coding sequences with which it is immediately contiguous (one on the 5' end and one on the 3' end) in the naturally occurring genome of the organism from which it is derived.

   The term therefore includes, for example, a recombinant DNA which is inco[phi]orated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e.g., a cDNA) independent of other sequences. The nucleotides can be ribonucleotides, deoxyribonucleotides, or modified forms of either nucleotide. The term includes single -and double -stranded forms of DNA. A PATE polynucleotide is a nucleic acid encoding a PATE polypeptide.
Polypeptide: Any chain of amino acids, regardless of length or posttranslational modification (e.g., glycosylation or phosphorylation). In one embodiment, the polypeptide is PATE polypeptide.

   A "residue" refers to an amino acid or amino acid mimetic inco[phi]orated in a polypeptide by an amide bond or amide bond mimetic.
Probes and primers: A probe comprises an isolated nucleic acid attached to a detectable label or reporter molecule. Primers are short nucleic acids, preferably DNA ohgonucleotides 15 nucleotides or more in length. Primers may be annealed to a complementary target DNA strand by nucleic acid hybridization to form a hybrid between the primer and the target DNA strand, and then extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification of a nucleic acid sequence, e.g., by the polymerase chain reaction
(PCR) or other nucleic-acid amplification methods known in the art. One of skill in the art will appreciate that the specificity of a particular probe or primer increases with its length.

   Thus, for example, a primer comprising 20 consecutive nucleotides will anneal to a target with a higher specificity than a corresponding primer of only 15 nucleotides. Thus, in order to obtain greater specificity, probes and primers may be selected that comprise 20, 25, 30, 35, 40, 50 or more consecutive nucleotides. Promoter: A promoter is an a[pi]ay of nucleic acid control sequences that directs transcription of a nucleic acid. A promoter includes necessary nucleic acid sequences near the start site of transcription, such as, in the case of a polymerase II type promoter, a TATA element. A promoter also optionally includes distal enhancer or repressor elements which can be located as much as several thousand base pairs from the start site of transcription. Both constitutive and inducible promoters are included (see e.g., Bitter, et al., Methods in Enzymology 153:516-544, 1987).

   Specific, non-limiting examples of promoters include promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the retrovirus long terminal repeat; the adenovirus late promoter; the vaccinia virus 7.5K promoter) may be used. Promoters produced by recombinant DNA or synthetic techniques may also be used. A polynucleotide can be inserted into an expression vector that contains a promoter sequence which facilitates the efficient transcription of the inserted genetic sequence of the host. The expression vector typically contains an origin of replication, a promoter, as well as specific nucleic acid sequences that allow phenotypic selection of the transformed cells. A PATE promoter is disclosed herein. In one embodiment, the JPATE promoter directs expression of a heterologous gene in cells of the prostate or the testes.

   A conservative variant of a promoter is a nucleotide sequence that has one or more nucleotide substitutions, so long as the nucleotide sequence still retains the ability to direct transcription of a nucleic acid. In one embodiment, a conservative variant of a promoter that has one or more nucleotide substitutions, wherein the sequence retains the ability to direct transcription at the same level as the sequence without the nucleotide substitutions. One specific, non-limiting example of a conservative variant of a promoter is SEQ ID NO:4, wherein one nucleotide is substituted, and wherein the variant directs transcription of a heterologous nucleic sequence. Another specific, non-limiting example of a conservative variant of a promoter is SEQ ED NO:4, wherein at most five nucleotides are substituted, and wherein the variant directs transcription of a heterologous nucleic sequence.

   Thus, the conservative variant and SEQ ID NO:4 produce transcripts at of the heterologous nucleic acid sequences at the same rate or the same absolute level in a cell.
Protein Purification: The PATE polypeptides disclosed herein can be purified by any of the means known in the art. See, e.g., Guide to Protein Purification, ed. Deutscher, Meth. Enzymol. 185, Academic Press, San Diego, 1990; and Scopes, Protein Purification: Principles and Practice, Springer Verlag, New York, 1982. Substantial purification denotes purification from other proteins or cellular components. A substantially purified protein is at least 60%, 70%, 80%, 90%, 95% or 98% pure. Thus, in one specific, non-limiting example, a substantially purified protein is 90% free of other proteins or cellular components.
Purified: The term purified does not require absolute purity; rather, it is intended as a relative term.

   Thus, for example, a purified peptide preparation is one in which the peptide or protein is more enriched than the peptide or protein is in its natural environment within a cell. In one embodiment, a preparation is purified such that the protein or peptide represents at least 50% of the total peptide or protein content of the preparation. Recombinant: A recombinant nucleic acid is one that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence.

   This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques.
Selectively hybridize: Hybridization under moderately or highly stringent conditions that excludes non-related nucleotide sequences.
In nucleic acid hybridization reactions, the conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (e.g., GC v. AT content), and nucleic acid type (e.g., RNA v. DNA) of the hybridizing regions of the nucleic acids can be considered in selecting hybridization conditions.

   An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter.
A specific, non- limiting example of progressively higher stringency conditions is as follows: 2 x SSC/0.1% SDS at about room temperature (hybridization conditions); 0.2 x SSC/0.1% SDS at about room temperature (low stringency conditions); 0.2 x SSC/0.1% SDS at about 42[deg.]C (moderate stringency conditions); and 0.1 x SSC at about 68[deg.]C (high stringency conditions). One of skill in the art can readily determine variations on these conditions (e.g., Molecular Cloning: A Laboratory Manual, 2nd ed., Vol. 1-3, ed. Sambrook et al., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989).

   Washing can be carried out using only one of these conditions, e.g., high stringency conditions, or each of the conditions can be used, e.g., for 10-15 minutes each, in the order listed above, repeating any or all of the steps listed. However, as mentioned above, optimal conditions will vary, depending on the particular hybridization reaction involved, and can be determined empirically.
Sequence identity: The similarity between amino acid sequences is expressed in terms of the similarity between the sequences, otherwise referred to as sequence identity. Sequence identity is frequently measured in terms of percentage identity (or similarity or homology); the higher the percentage, the more similar the two sequences are.

   Homologues or variants of a PATE polypeptide will possess a relatively high degree of sequence identity when aligned using standard methods.
Methods of alignment of sequences for comparison are well known in the art. Various programs and alignment algorithms are described in: Smith and Waterman, Adv. Appl. Math. 2:482, 1981 ; Needleman and Wunsch, J. Mol. Biol. 48:443, 1970; Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85:2444, 1988; Higgins and Sha[phi], Gene 73:237, 1988; Higgins and Sha[phi], CABIOS 5:151, 1989; Co[phi]et, et al., Nucleic Acids Research 16: 10881, 1988; and Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85:2444, 1988. Altschul, et al., Nature Genet., 6:119, 1994 presents a detailed consideration of sequence alignment methods and homology calculations.
The NCBI Basic Local Alignment Search Tool (BLAST) (Altschul, et al., J. Mol.

   Biol. 215:403, 1990) is available from several sources, including the National Center for Biotechnology Information (NCBI, Bethesda, MD) and on the Internet, for use in connection with the sequence analysis programs blastp, blastn, blastx, tblastn and tblastx. A description of how to determine sequence identity using this program is available on the NCBI website on the internet.
Homologues and variants of a PATE polypeptide are typically characterized by possession of at least about 75%, for example at least about 80%, sequence identity counted over the full length alignment with the amino acid sequence of PATE using the NCBI Blast 2.0, gapped blastp set to default parameters.

   For comparisons of amino acid sequences of greater than about 30 amino acids, the Blast 2 sequences function is employed using the default BLOSUM62 matrix set to default parameters, (gap existence cost of 11 , and a per residue gap cost of 1). When aligning short peptides (fewer than around 30 amino acids), the alignment should be performed using the Blast 2 sequences function, employing the PAM30 matrix set to default parameters (open gap 9, extension gap 1 penalties). Proteins with even greater similarity to the reference sequences will show increasing percentage identities when assessed by this method, such as at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity.

   When less than the entire sequence is being compared for sequence identity, homologues and variants will typically possess at least 80% sequence identity over short windows of 10-20 amino acids, and may possess sequence identities of at least 85% or at least 90% or 95% depending on their similarity to the reference sequence. Methods for determining sequence identity over such short windows are available at the NCBI website on the internet. One of skill in the art will appreciate that these sequence identity ranges are provided for guidance only; it is entirely possible that strongly significant homologues could be obtained that fall outside of the ranges provided.
Specific binding agent: An agent that binds substantially only to a defined target. Thus a PATE specific binding agent is an agent that binds substantially to a PATE polypeptide.

   In one embodiment, the specific binding agent is a monoclonal or polyclonal antibody that specifically binds the PATE polypeptide. The term "specifically binds" refers with respect to an antigen, such as
PATE, to the preferential association of an antibody or other ligand, in whole or part, with a cell or tissue bearing that antigen and not to cells or tissues lacking that antigen. It is, of course, recognized that a certain degree of non-specific interaction may occur between a molecule and a non-target cell or tissue. Nevertheless, specific binding may be distinguished as mediated through specific recognition of the antigen. Although selectively reactive antibodies bind antigen, they may do so with low affinity.

   On the other hand, specific binding results in a much stronger association between the antibody (or other ligand) and cells bearing the antigen than between the bound antibody (or other ligand) and cells lacking the antigen. Specific binding typically results in greater than 2-fold, preferably greater than 5-fold, more preferably greater than 10-fold and most preferably greater than 100-fold increase in amount of bound antibody or other ligand (per unit time) to a cell or tissue bearing PATE as compared to a cell or tissue lacking PATE. Specific binding to a protein under such conditions requires an antibody that is selected for its specificity for a particular protein. A variety of immunoassay formats are appropriate for selecting antibodies or other ligands specifically immunoreactive with a particular protein.

   For example, solid-phase ELISA immunoassays are routinely used to select monoclonal antibodies specifically immunoreactive with a protein. See Harlow & Lane, ANTIBODIES, A LABORATORY MANUAL, Cold Spring Harbor Publications, New York (1988), for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity. Subject: Living multi-cellular vertebrate organisms, a category that includes both human veterinary subjects, including human and non-human mammals.
T Cell: A white blood cell critical to the immune response. T cells include, but are not limited to, CD4<+>T cells and CD8<+>T cells. A CD4<+>T lymphocyte is an immune cell that carries a marker on its surface known as "cluster of differentiation 4" (CD4).

   These cells, also known as helper T cells, help orchestrate the immune response, including antibody responses as well as killer T cell responses. CD8<+>T cells carry the "cluster of differentiation 8" (CD8) marker. In one embodiment, a CD8 T cells is a cytotoxic T lymphocytes. In another embodiment, a CD8 cell is a suppressor T cell. Targeting moiety: A portion of a chimeric molecule intended to provide the molecule with the ability to bind specifically to the PATE protein.

   A "ligand" is a targeting molecule specific for the PATE protein and is generally synonymous with "targeting moiety." An antibody is one version of a ligand.
Therapeutically active polypeptide: An agent, such as a PATE polypeptide that causes induction of an immune response, as measured by clinical response (for example increase in a population of immune cells, production of antibody that specifically binds PATE, or measurable reduction of tumor burden). Therapeutically active molecules can also be made from nucleic acids.

   Examples of a nucleic acid based therapeutically active molecule is a nucleic acid sequence that encodes a PATE polypeptide, wherein the nucleic acid sequence is operably linked to a control element such as a promoter.
Therapeutically active agents can also include organic or other chemical compounds that mimic the effects of PATE.
The terms "therapeutically effective fragment of PATE" or "therapeutically effective variant of PATE" includes any fragment of PATE, or variant of PATE, that retains a function of PATE, or retains an antigenic epitope of PATE.
In one embodiment, a therapeutically effective amount of a fragment of PATE is an amount used to generate an immune response, or to treat prostate cancer in a subject. Specific, non-limiting examples are the N-terminal half of PATE or the C-terminal half of PATE.

   Treatment refers to a therapeutic intervention that ameliorates a sign or symptom of prostate cancer, or a reduction in tumor burden.
Transduced: A transduced cell is a cell into which has been introduced a nucleic acid molecule by molecular biology techniques. As used herein, the term transduction encompasses all techniques by which a nucleic acid molecule might be introduced into such a cell, including transfection with viral vectors, transformation with plasmid vectors, and introduction of naked DNA by electroporation, lipofection, and particle gun acceleration. Vector: A nucleic acid molecule as introduced into a host cell, thereby producing a transformed host cell. A vector may include nucleic acid sequences that permit it to replicate in a host cell, such as an origin of replication.

   A vector may also include one or more selectable marker genes and other genetic elements known in the art.
Unless otherwise explained, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The singular terms "a," "an," and "the" include plural referents unless context clearly indicates otherwise. Similarly, the word "or" is intended to include "and" unless the context clearly indicates otherwise. It is further to be understood that all base sizes or amino acid sizes, and all molecular weight or molecular mass values, given for nucleic acids or polypeptides are approximate, and are provided for description. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing, suitable methods and materials are described below.

   The term "comprises" means "includes." All publications, patent applications, patents, and other references mentioned herein are inco[phi]orated by reference in their entirety. In case of conflict, the present specification, including explanations of terms, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.
PATE Polynucleotides and Polypeptides
Substantially purified Novel Gene Expressed in Prostate (PATE) polypeptides are disclosed herein. In one embodiment, a PATE polypeptide has a sequence 75%, 85%, 90%, 95%, or 99% homologous to the amino acid sequence set forth in SEQ ID NO:2 (see Fig. 5). In another embodiment, a PATE polypeptide has a sequence as set forth a SEQ ID NO:2 or is a conservative variant of SEQ ID NO:2.

   In a further embodiment, a PATE polypeptide is encoded by SEQ ID NO: 1 or SEQ ID NO:3, or has an amino acid sequence as set forth as SEQ ID NO:2. Fragments and variants of a PATE polypeptide can readily be prepared by one of skill in the art using molecular techniques. In one embodiment, a fragment of a PATE polypeptide includes at least 8, 10, 15, or 20 consecutive amino acids of a PATE polypeptide. In another embodiment, a fragment of a PATE polypeptide includes a specific antigenic epitope found on full-length PATE.
One skilled in the art, given the disclosure herein, can purify PATE polypeptide using standard techniques for protein purification. The substantially pure polypeptide will yield a single major band on a non-reducing polyacrylamide gel.

   The purity of the PATE polypeptide can also be determined by amino-terminal amino acid sequence analysis.
Minor modifications of the PATE polypeptide primary amino acid sequences may result in peptides which have substantially equivalent activity as compared to the unmodified counte[phi]art polypeptide described herein. Such modifications may be deliberate, as by site-directed mutagenesis, or may be spontaneous. All of the polypeptides produced by these modifications are included herein.
Polynucleotides encoding PATE polypeptide are also provided, and are termed PATE polynucleotides. These polynucleotides include DNA, cDNA and RNA sequences which encode PATE. Two specific, non-limiting examples of polynucleotides encoding a PATE polypeptide are SEQ ID NO:l and SEQ ID NO:3.

   It is understood that all polynucleotides encoding a PATE polypeptide are also included herein, as long as they encode a polypeptide with the recognized activity, such as the binding to an antibody that recognizes a PATE polypeptide. The PATE polynucleotides include sequences that are degenerate as a result of the genetic code. There are 20 natural amino acids, most of which are specified by more than one codon. Therefore, all degenerate nucleotide sequences are included as long as the amino acid sequence of the PATE polypeptide encoded by the nucleotide sequence is functionally unchanged.
Another specific non- limiting example of a polynucleotide encoding PATE is a polynucleotide having at least 75%, 85%, 90%, 95%, or 99% homologous to SEQ HD NO:l or SEQ ID NO:3 that encodes a polypeptide having an antigenic epitope or function of PATE.

   Yet another specific non-limiting example of a polynucleotide encoding PATE is a polynucleotide that encodes a polypeptide that is specifically bound by an antibody that specifically binds SEQ ID NO:2. The PATE polynucleotides include a recombinant DNA which is inco[phi]orated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e.g., a cDNA) independent of other sequences. The nucleotides can be ribonucleotides, deoxyribonucleotides, or modified forms of either nucleotide. The term includes single and double forms of DNA.

   Also included are fragments of the above-described nucleic acid sequences that are and are at least 15 bases in length, which is sufficient to permit the fragment to selectively hybridize to DNA that encodes the disclosed PATE polypeptide (e.g. a polynucleotide that encodes SEQ YD NO:2 or a variant thereof) under physiological conditions. The term "selectively hybridize" refers to hybridization under moderately or highly stringent conditions, which excludes non-related nucleotide sequences. The PATE polynucleotide sequence disclosed herein include, but are not limited to, SEQ ID NO:l or SEQ ID NO:3, degenerate variants of SEQ ED NO:l or SEQ JD NO:3, and sequences that encode conservative variations of a PATE polypeptide. DNA sequences encoding PATE polypeptide can be expressed in vitro by
DNA transfer into a suitable host cell. The cell may be prokaryotic or eukaryotic.

   The term also includes any progeny of the subject host cell. It is understood that all progeny may not be identical to the parental cell since there may be mutations that occur during replication. Methods of stable transfer, meaning that the foreign DNA is continuously maintained in the host, are known in the art.
PATE polynucleotide sequences can be operatively linked to expression control sequences. An expression control sequence operatively linked to a coding sequence is ligated such that expression of the coding sequence is achieved under conditions compatible with the expression control sequences.

   The expression control sequences include, but are not limited to appropriate promoters, enhancers, transcription terminators, a start codon (i.e., ATG) in front of a protein-encoding gene, splicing signal for introns, maintenance of the correct reading frame of that gene to permit proper translation of mRNA, and stop codons.
The polynucleotide sequences encoding PATE may be inserted into an expression vector including, but not limited to a plasmid, virus or other vehicle that can be manipulated to allow insertion or inco[phi]oration of sequences and can be expressed in either prokaryotes or eukaryotes. Hosts can include microbial, yeast, insect and mammalian organisms. Methods of expressing DNA sequences having eukaryotic or viral sequences in prokaryotes are well known in the art.

   Biologically functional viral and plasmid DNA vectors capable of expression and replication in a host are known in the art.
Transformation of a host cell with recombinant DNA may be carried out by conventional techniques as are well known to those skilled in the art. Where the host is prokaryotic, such as E. coli, competent cells which are capable of DNA uptake can be prepared from cells harvested after exponential growth phase and subsequently treated by the CaCl2method using procedures well known in the art. Alternatively, MgCl2or RbCl can be used.

   Transformation can also be performed after forming a protoplast of the host cell if desired, or by electroporation.
When the host is a eukaryote, such methods of transfection of DNA as calcium phosphate coprecipitates, conventional mechanical procedures such as microinjection, electroporation, insertion of a plasmid encased in liposomes, or virus vectors may be used. Eukaryotic cells can also be cotransformed with PATE polynucleotide sequences, and a second foreign DNA molecule encoding a selectable phenotype, such as the he[phi]es simplex fhymidine kinase gene. Another method is to use a eukaryotic viral vector, such as simian virus 40 (SV40) or bovine papilloma virus, to transiently infect or transform eukaryotic cells and express the protein (see for example, Eukaryotic Viral Vectors.

   Cold Spring Harbor Laboratory, Gluzman ed., 1982).
Isolation and purification of recombinantly expressed polypeptide may be carried out by conventional means including preparative chromatography and immunological separations. Promoter Sequences
Specifically disclosed herein is a polynucleotide sequence of a PATE promoter. In one specific, non- limiting example, the PATE promoter nucleotide sequence is SEQ ID NO:4 or a conservative variant thereof. An "isolated polynucleotide" is a polynucleotide that is not immediately contiguous with both of the coding sequences with which it is immediately contiguous (one on the 5' end and one on the 3' end) in the naturally occurring genome of the organism from which it is derived. Thus, in one embodiment, an isolated PATE promoter from a specific species is not adjacent to the PATE coding sequences from the same species.

   The term therefore includes, for example, a recombinant DNA which is inco[phi]orated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e.g., a cDNA) independent of other sequences.
DNA sequences encoding a polypeptide can be expressed in vitro by DNA transfer into a suitable host cell. The host cell can be any cell in which a vector can be propagated and its DNA expressed. The cell may be prokaryotic or eukaryotic. Specific, non-limiting examples of a host cell of use a cell from a cell line or a primary cell in culture. In one embodiment, the cell is a cell of a prostate cell line or a primary prostate cell in culture. The term also includes any progeny of the subject host cell.

   It is understood that all progeny may not be identical to the parental cell since there may be mutations that occur during replication. Methods of stable transfer, meaning that the foreign DNA is continuously maintained in the host, are known in the art. DNA sequences encoding a polypeptide can be also expressed in vivo. The T TE promoter sequences may be inco[phi]orated into an expression vector. In one embodiment, the expression vector is a plasmid, virus or other vehicle known in the art that has been manipulated by insertion or inco[phi]oration of the PATE promoter sequences. A polynucleotide sequence which encodes any polypeptide of interest can be operatively linked to the PATE promoter sequence.

   In one embodiment, the PATE promoter sequence is operatively linked to a coding sequence; the PATE promoter is ligated such that expression of the coding sequence is achieved under appropriate conditions. Thus the PATE promoter sequence regulates the transcription of the nucleic acid sequence. Other expression control sequences such as, enhancers, transcription terminators, a start codon (i.e., ATG) in front of a protein-encoding gene, splicing signal for introns, maintenance of the co[pi]ect reading frame of that gene to permit proper translation of mRNA, and stop codons, can also be utilized in conjunction with the PATE promoter sequence.
In one specific non-limiting example, an expression vector contains an origin of replication, a PATE promoter, as well as a specific protein coding sequence of interest, and a sequence which allows phenotypic selection of the transformed cells.

   Protein coding sequences of interest include, but are not limited to, enzymes, receptors, antigenic epitopes, and markers. Vectors suitable for use include, but are not limited to the T7-based expression vector for expression in bacteria (Rosenberg, et al., Gene 56:125, 1987), the pMSXND expression vector for expression in mammalian cells (Lee and Nathans, J. Biol. Chem. 263:3521, 1988) and baculovirus-derived vectors for expression in insect cells. The PATE promoter can be utilized in eukaryotic cells. Hosts can include any mammalian cell. Methods of expressing DNA sequences having eukaryotic or viral sequences are well known in the art. Biologically functional viral and plasmid DNA vectors capable of expression and replication in a host are known in the art, and can be utilized with a PATE promoter sequence.

   Any host cell can be transformed with a vector including a PATE promoter sequence. The genetic change is generally achieved by introduction of the DNA into the genome of the cell (i.e., stable). Transformation of a host cell with recombinant DNA may be carried out by conventional techniques as are well known to those skilled in the art. When the host is a eukaryote, such methods of transfection of DNA as calcium phosphate co-precipitates, conventional mechanical procedures such as microinjection, electroporation, insertion of a plasmid encased in liposomes, or virus vectors may be used. Eukaryotic cells can also be cotransformed with DNA sequences including the PATE promoter operably linked to a heterologous nucleic acid of interest, and a second foreign DNA molecule encoding a selectable phenotype, such as the he[phi]es simplex thymidine kinase gene.

   Another method is to use a eukaryotic viral vector, such as simian virus 40 (SV40) or bovine papilloma virus, to transiently infect or transform eukaryotic cells and express the protein (see for example, Eukaryotic Viral Vectors, Cold Spring Harbor Laboratory, Gluzman ed., 1982) from the UGRP1 promoter.
In another embodiment, a PATE promoter is used to express an antisense molecule or a ribozyme. The natural mechanism for producing proteins in living cells starts with the DNA being transcribed into RNA. The resulting RNA molecule is then translated into a protein. This chain of events (DNA-^RNA-> Protein) allows for the regulation of the protein at three different levels. At the first level of regulation the DNA can be targeted. This is done such that the process of making the RNA is inhibited.

   For example, a small circular oligonucleotide molecule can be placed in contact with the DNA thus inhibiting and/or altering transcription (Wolf, Nature Biotechnology 16:341-344, 1998). At the next level the transcription of the RNA can be inhibited. This can be done through the use of complementary polynucleotide sequences that bind to the target RNA molecule. In some instances these polynucleotide molecules can be designed so that they are catalytic (for example, a ribozyme). In other words, they can be designed so that they can bind to a first target RNA, cleave it, and then move on to cleave a second RNA. Finally, at the third level, the protein itself can be regulated through the use of antibodies and other therapeutic molecules, as already discussed.
The use of complementary polynucleotide sequences is referred to as antisense technology.

   Therefore, these polynucleotide molecules are commonly called antisense molecules. One of ordinary skill in the art will appreciate that antisense molecules can be designed, and produced in many different ways. These antisense molecules can be produced in a cell, such as a prostate or a testes cell, using a PATE promoter.
Antibodies
A PATE polypeptide or a fragment or conservative variant thereof can be used to produce antibodies which are immunoreactive or bind to an epitope of PATE. Polyclonal antibodies, antibodies which consist essentially of pooled monoclonal antibodies with different epitopic specificities, as well as distinct monoclonal antibody preparations are included. The preparation of polyclonal antibodies is well-known to those skilled in the art.

   See, for example, Green, et al., "Production of Polyclonal Antisera," in: Immunochemical Protocols pages 1-5, Manson, ed., Humana Press 1992; Coligan, et al., "Production of Polyclonal Antisera in Rabbits, Rats, Mice and Hamsters," in: Current Protocols in Immunology, section 2.4.1, 1992.
The preparation of monoclonal antibodies likewise is conventional. See, for example, Kohler & Milstein, Nature 256:495, 1975; Coligan, et al., sections 2.5.12.6.7; and Harlow, et al., in: Antibodies: a Laboratory Manual, page 726, Cold Spring Harbor Pub., 1988.

   Briefly, monoclonal antibodies can be obtained by injecting mice with a composition comprising an antigen, verifying the presence of antibody production by removing a serum sample, removing the spleen to obtain B lymphocytes, fusing the B lymphocytes with myeloma cells to produce hybridomas, cloning the hybridomas, selecting positive clones that produce antibodies to the antigen, and isolating the antibodies from the hybridoma cultures. Monoclonal antibodies can be isolated and purified from hybridoma cultures by a variety of wellestablished techniques. Such isolation techniques include affinity chromatography with Protein-A Sepharose, size-exclusion chromatography, and ion-exchange chromatography. See, e.g., Coligan, et al., sections 2.7.1-2.7.12 and sections 2.9.12.9.3; Barnes, et al., Purification of Immunoglobulin G (IgG), in: Methods in Molecular Biology.

   Vol. 10, pages 79-104, Humana Press, 1992.
Methods of in vitro and in vivo multiplication of monoclonal antibodies are well known to those skilled in the art. Multiplication in vitro may be carried out in suitable culture media such as Dulbecco's Modified Eagle Medium or RPMI 1640 medium, optionally supplemented by a mammalian serum such as fetal calf serum or trace elements and growth-sustaining supplements such as normal mouse peritoneal exudate cells, spleen cells, fhymocytes or bone ma[pi]ow macrophages. Production in vitro provides relatively pure antibody preparations and allows scale-up to yield large amounts of the desired antibodies. Large-scale hybridoma cultivation can be carried out by homogenous suspension culture in an airlift reactor, in a continuous stirrer reactor, or in immobilized or entrapped cell culture.

   Multiplication in vivo may be carried out by injecting cell clones into mammals histocompatible with the parent cells, e.g., syngeneic mice, to cause growth of antibody-producing tumors. Optionally, the animals are primed with a hydrocarbon, especially oils such as pristane (tetramethylpentadecane) prior to injection. After one to three weeks, the desired monoclonal antibody is recovered from the body fluid of the animal.
Antibodies can also be derived from subhuman primate antibody. General techniques for raising therapeutically useful antibodies in baboons can be found, for example, in WO 91/11465, 1991, and Losman, et al., Int. J. Cancer 46:310, 1990.
Alternatively, an antibody that specifically binds a PATE polypeptide can be derived from a humanized monoclonal antibody.

   Humanized monoclonal antibodies are produced by transferring mouse complementarity determining regions from heavy and light variable chains of the mouse immunoglobulin into a human variable domain, and then substituting human residues in the framework regions of the murine counte[phi]arts. The use of antibody components derived from humanized monoclonal antibodies obviates potential problems associated with the irnmunogenicity of murine constant regions. General techniques for cloning murine immunoglobulin variable domains are described, for example, by Orlandi, et al., Proc. Nat'lAcad. Sci. U.S.A. 86:3833, 1989. Techniques for producing humanized monoclonal antibodies are described, for example, by Jones, et al., Nature 321:522, 1986; Riechmann, et al., Nature 332:323, 1988; Verhoeyen, et al., Science 239:1534, 1988; Carter, et al., Proc. Nat'lAcad. Sci.

   U.S.A. 89:4285, 1992; Sandhu, Crit. Rev. Biotech.12:437, 1992; and Singer, et al., J. Immunol[Lambda]50:2S44, 1993.
Antibodies can be derived from human antibody fragments isolated from a combinatorial immunoglobulin library. See, for example, Barbas, et al., in: Methods: a Companion to Methods in Enzymology. Vol. 2, page 119, 1991; Winter, et al., Ann. Rev. Immunol.12:433, 1994. Cloning and expression vectors that are useful for producing a human immunoglobulin phage library can be obtained, for example, from STRATAGENE Cloning Systems (La Jolla, CA).
In addition, antibodies can be derived from a human monoclonal antibody. Such antibodies are obtained from transgenic mice that have been "engineered" to produce specific human antibodies in response to antigenic challenge.

   In this technique, elements of the human heavy and light chain loci are introduced into strains of mice derived from embryonic stem cell lines that contain targeted disruptions of the endogenous heavy and light chain loci. The transgenic mice can synthesize human antibodies specific for human antigens, and the mice can be used to produce human antibody-secreting hybridomas. Methods for obtaining human antibodies from transgenic mice are described by Green, et al., Nature Genet. 7:13, 1994; Lonberg, et al., Nature 368:856, 1994; and Taylor, et al., Int. Immunol.6:579, 1994.
Antibodies include intact molecules as well as fragments thereof, such as Fab, F(ab')2, and Fv which are capable of binding the epitopic determinant.

   These antibody fragments retain some ability to selectively bind with their antigen or receptor and are defined as follows: (1) Fab, the fragment which contains a monovalent antigen-binding fragment of an antibody molecule, can be produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain;
(2) Fab', the fragment of an antibody molecule can be obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain; two Fab' fragments are obtained per antibody molecule;
(3) (Fab')2, the fragment of the antibody that can be obtained by treating whole antibody with the enzyme pepsin without subsequent reduction;

   F(ab')2is a dimer of two Fab' fragments held together by two disulfide bonds;
(4) Fv, defined as a genetically engineered fragment containing the variable region of the light chain and the variable region of the heavy chain expressed as two chains; and
(5) Single chain antibody (SCA), defined as a genetically engineered molecule containing the variable region of the light chain, the variable region of the heavy chain, linked by a suitable polypeptide linker as a genetically fused single chain molecule.
Methods of making these fragments are known in the art. (See for example, Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York, 1988). An epitope is any antigenic determinant on an antigen to which the paratope of an antibody binds.

   Epitopic determinants usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains and usually have specific three dimensional structural characteristics, as well as specific charge characteristics.
Antibody fragments can be prepared by proteolytic hydrolysis of the antibody or by expression in E. coli of DNA encoding the fragment. Antibody fragments can be obtained by pepsin or papain digestion of whole antibodies by conventional methods. For example, antibody fragments can be produced by enzymatic cleavage of antibodies with pepsin to provide a 5S fragment denoted F(ab')2. This fragment can be further cleaved using a thiol reducing agent, and optionally a blocking group for the sulfhydryl groups resulting from cleavage of disulfide linkages, to produce 3.5S Fab' monovalent fragments.

   Alternatively, an enzymatic cleavage using pepsin produces two monovalent Fab' fragments and an Fc fragment directly (see U.S. Patents No. 4,036,945 and No. 4,331,647, and references contained therein; Nisonhoff, et al., Arch. Biochem. Biophys.89:23 , 1960; Porter, Biochem. J. 73:119, 1959; Edelman, et al., Methods in Enzymology. Vol. 1, page 422, Academic Press, 1967; and Coligan, et al. at sections 2.8.1-2.8.10 and 2.10.1-2.10.4).
Other methods of cleaving antibodies, such as separation of heavy chains to form monovalent light-heavy chain fragments, further cleavage of fragments, or other enzymatic, chemical, or genetic techniques may also be used, so long as the fragments bind to the antigen that is recognized by the intact antibody.
For example, Fv fragments comprise an association of VHand VLchains. This association may be noncovalent (Inbar, et al., Proc. Nat'l Acad. Sci.

   U.S.A. 69:2659, 1972). Alternatively, the variable chains can be linked by an intermolecular disulfide bond or cross-linked by chemicals such as glutaraldehyde. See, e.g., Sandhu, supra. Preferably, the Fv fragments comprise VHand VLchains connected by a peptide linker. These single-chain antigen binding proteins (sFv) are prepared by constructing a structural gene comprising DNA sequences encoding the VHand VLdomains connected by an oligonucleotide. The structural gene is inserted into an expression vector, which is subsequently introduced into a host cell such as E. coli. The recombinant host cells synthesize a single polypeptide chain with a linker peptide bridging the two V domains. Methods for producing sFvs are known in the art (see Whitlow, et al., Methods: a Companion to Methods in Enzymology, Vol. 2, page 97, 1991; Bird, et al., Science 242:423, 1988; U.S.

   Patent No. 4,946,778; Pack, et al., Bio/Technology 11 :1271, 1993; and Sandhu, supra). Another form of an antibody fragment is a peptide coding for a single complementarity-determining region (CDR). CDR peptides ("minimal recognition units") can be obtained by constructing genes encoding the CDR of an antibody of interest. Such genes are prepared, for example, by using the polymerase chain reaction to synthesize the variable region from RNA of antibody-producing cells (Larrick, et al., Methods: a Companion to Methods in Enzymology, Vol. 2, page 106, 1991). Antibodies can be prepared using an intact polypeptide or fragments containing small peptides of interest as the immunizing antigen.

   The polypeptide or a peptide used to immunize an animal can be derived from substantially purified polypeptide produced in host cells, in vitro translated cDNA, or chemical synthesis which can be conjugated to a carrier protein, if desired. Such commonly used carriers which are chemically coupled to the peptide include keyhole limpet hemocyanin (KLH), thyro globulin, bovine serum albumin (BSA), and tetanus toxoid. The coupled peptide is then used to immunize the animal (e.g., a mouse, a rat, or a rabbit).
Polyclonal or monoclonal antibodies can be further purified, for example, by binding to and elution from a matrix to which the polypeptide or a peptide to which the antibodies were raised is bound.

   Those of skill in the art will know of various techniques common in the immunology arts for purification and/or concentration of polyclonal antibodies, as well as monoclonal antibodies (See for example, Coligan, et al., Unit 9, Current Protocols in Immunology, Wiley Interscience, 1991). It is also possible to use the anti-idiotype technology to produce monoclonal antibodies which mimic an epitope. For example, an anti-idiotypic monoclonal antibody made to a first monoclonal antibody will have a binding domain in the hypervariable region that is the "image" of the epitope bound by the first monoclonal antibody. Effector molecules, e.g., therapeutic, diagnostic, or detection moieties, can be linked to an antibody that specifically binds PATE, using any number of means known to those of skill in the art. Both covalent and noncovalent attachment means may be used.

   The procedure for attaching an effector molecule to an antibody varies according to the chemical structure of the effector. Polypeptides typically contain variety of functional groups; e.g., carboxylic acid (COOH), free amine (-NH2) or sulfhydryl (-SH) groups, which are available for reaction with a suitable functional group on an antibody to result in the binding of the effector molecule. Alternatively, the antibody is derivatized to expose or attach additional reactive functional groups. The derivatization may involve attachment of any of a number of linker molecules such as those available from Pierce Chemical Company, Rockford Illinois. The linker can be any molecule used to join the antibody to the effector molecule. The linker is capable of forming covalent bonds to both the antibody and to the effector molecule.

   Suitable linkers are well known to those of skill in the art and include, but are not limited to, straight or branched-chain carbon linkers, heterocyclic carbon linkers, or peptide linkers. Where the antibody and the effector molecule are polypeptides, the linkers may be joined to the constituent amino acids through their side groups (e.g., through a disulfide linkage to cysteine) or to the alpha carbon amino and carboxyl groups of the terminal amino acids.
In some circumstances, it is desirable to free the effector molecule from the antibody when the immunoconjugate has reached its target site. Therefore, in these circumstances, immunoconjugates will comprise linkages that are cleavable in the vicinity of the target site.

   Cleavage of the linker to release the effector molecule from the antibody may be prompted by enzymatic activity or conditions to which the immunoconjugate is subjected either inside the target cell or in the vicinity of the target site. When the target site is a tumor, a linker which is cleavable under conditions present at the tumor site (e.g. when exposed to tumor-associated enzymes or acidic pH) may be used.
In view of the large number of methods that have been reported for attaching a variety of radiodiagnostic compounds, radiotherapeutic compounds, label (e.g. enzymes or fluorescent molecules) drugs, toxins, and other agents to antibodies one skilled in the art will be able to determine a suitable method for attaching a given agent to an antibody or other polypeptide.
The immunoconjugates can be prepared by cloning techniques.

   Examples of appropriate cloning and sequencing techniques, and instructions sufficient to directpersons of skill through many cloning exercises are found in Sambrook, et al., Molecular Cloning: A Laboratory Manual (2ND ED.), Vols. 1-3, Cold Spring Harbor Laboratory (1989)), Berger and Kimmel (eds.), Guide to Molecular Cloning Techniques, Academic Press, Inc., San Diego CA (1987)), or Ausubel, et al. (eds.), CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Greene Publishing and WileyInterscience, NY (1987). Product information from manufacturers of biological reagents and experimental equipment also provide useful information. Such manufacturers include the SIGMA chemical company (Saint Louis, MO), R&D systems (Minneapolis, MN), Pharmacia LKB Biotechnology (Piscataway, NJ), CLONTECH Laboratories, Inc.

   (Palo Alto, CA), Chem Genes Co[phi]., Aldrich Chemical Company (Milwaukee, WI), Glen Research, Inc., GEBCO BRL Life Technologies, Inc. (Gaithersburg, MD), Fluka Chemica-Biochemika Analytika (Fluka Chemie AG, Buchs, Switzerland), Invitrogen, San Diego, CA, and Applied Biosystems (Foster City, CA), as well as many other commercial sources known to one of skill.
Nucleic acids encoding native effector molecules or anti-PATE antibodies can be modified to form the effector molecule, antibodies, or immunoconjugates. Modification by site-directed mutagenesis is well known in the art. Nucleic acids encoding effector molecule or anti-PATE antibodies can be amplified by in vitro methods. Amplification methods include the polymerase chain reaction (PCR), the ligase chain reaction (LCR), the transcription-based amplification system (TAS), the self-sustained sequence replication system (3SR).

   A wide variety of cloning methods, host cells, and in vitro amplification methodologies are well known in the art. In one embodiment, immunoconjugates are prepared by inserting a cDNA which encodes an anti-PATE scFv antibody into a vector which comprises the cDNA encoding the effector molecule. The insertion is made so that the scFv and the EM are read in frame, that is in one continuous polypeptide which contains a functional Fv region and a functional EM region. In a particularly preferred embodiment, cDNA encoding a Pseudomonas toxin fragment is ligated to a scFv so that the toxin is located at the carboxyl terminus of the scFv. t addition to recombinant methods, the immunoconjugates, effector molecules, and antibodies can also be constructed in whole or in part using standard peptide synthesis.

   Solid phase synthesis of the polypeptides of less than about 50 amino acids in length may be accomplished by attaching the C-terminal amino acid of the sequence to an insoluble support followed by sequential addition of the remaining amino acids in the sequence. Techniques for solid phase synthesis are described by Barany & Merrifield, The Peptides: Analysis, Synthesis, Biology. VOL. 2: Special Methods in Peptide Synthesis, Part A. pp. 3-284; Merrifield, et al. J. Am.Chem.Soc. 85:2149-2156 (1963), and Stewart, et al., Solid Phase Peptide Synthesis, 2nd ed., Pierce Chem. Co., Rockford, 111. (1984). Proteins of greater length may be synthesized by condensation of the amino and carboxyl termini of shorter fragments.

   Methods of forming peptide bonds by activation of a carboxyl terminal end (e.g., by the use of the coupling reagent N, N'dicycylohexylcarbodiimide) are known to those of skill. Once the nucleic acids encoding an EM, anti-PATE antibody, or an immunoconjugate, are isolated and cloned, one may express the desired protein in a recombinantly engineered cell such as bacteria, plant, yeast, insect and mammalian cells. It is expected that those of skill in the art are knowledgeable in the numerous expression systems available for expression of proteins including E. coli, other bacterial hosts, yeast, and various higher eukaryotic cells such as the COS, CHO, HeLa and myeloma cell lines.
Antibodies can be covalently or non-covalently linked to a detectable label.

   Detectable labels suitable for such use include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Useful labels in the present invention include magnetic beads (e.g. DYNABEADS), fluorescent dyes (e.g., fluorescein isothiocyanate, Texas red, rhodamine, green fluorescent protein, and the like), radiolabels (e.g.,<3>H,<125>1,<35>S,<14>C, or<32>P), enzymes (e.g., horse radish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic (e.g. polystyrene, polypropylene, latex, etc.) beads.
Means of detecting such labels are well known to those of skill in the art.

   Thus, for example, radiolabels may be detected using photographic film or scintillation counters, fluorescent markers may be detected using a photodetector to detect emitted illumination. Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate, and colorimetric labels are detected by simply visualizing the colored label.
Therapeutic Methods and Pharmaceutical Compositions
A PATE polypeptide can be administered to a subject in order to generate an immune response.

   In one embodiment, a therapeutically effective amount of a PATE polypeptide is administered to a subject to treat prostate cancer.
The PATE polypeptide can be administered by any means known to one of skill in the art (see Banga, A., Parenteral Controlled Delivery of Therapeutic Peptides and Proteins, in Therapeutic Peptides and Proteins, Technomic Publishing Co., Inc., Lancaster, PA, 1995) such as by intramuscluar, subcutaneous, or intravenous injection, but even oral, nasal, or anal administration is contemplated. In one embodiment, administration is by subcutaneous or intramuscular injection. To extend the time during which the peptide or protein is available to stimulate a response, the peptide or protein can be provided as an implant, an oily injection, or as a particulate system.

   The particulate system can be a microparticle, a microcapsule, a microsphere, a nanocapsule, or similar particle, (see, e.g., Banga, supra). A particulate carrier based on a synthetic polymer has been shown to act as an adjuvant to enhance the immune response, in addition to providing a controlled release. Aluminum salts may also be used as adjuvants to produce a humoral immune response. Thus, in one embodiment, a PATE polypeptide is administered in a manner to induce a humoral response.
In another embodiment, a PATE polypeptide is administered in a manner to direct the immune response to a cellular response (that is, a CTL response), rather than a humoral (antibody) response. For peptide based vaccines, it is preferable if the peptides comprise motifs recognized by alleles having a wide distribution in the human population.

   Since the MHC alleles occur at different frequencies within different ethnic groups and races, the choice of target MHC may depend upon the target population. For example, the majority of the Caucasoid population can be covered by peptides which bind to four HLA allele subtypes, HLA-A2.1, Al, A3.2, and A24.1, while adding peptides binding to a first allele, HLA-AI 1.2, encompasses the majority of the Asian population. See, e.g., International Publication No.

   WO 94/20127; Sidney, J., et al., "Broadly Reactive HLA Restricted T Cell Epitopes and their Implications for Vaccine Design," in Kaufmann, ed., Concepts in Vaccine Design (Walter de Gruyter, Berlin, 1996).
Analysis of numerous alleles has also permitted characterization of the alleles by "supertypes," which recognize antigen presented for recognition by the presence of certain amino acids or types of amino acids in certain positions. For example, the B7-like supertype recognizes proline in position 2 and hydrophobic or aliphatic amino acids at the C-terminus, whereas the A3 -like supertype is defined by a shared preference for peptides bearing (in single letter code) A, L, I, V, M, S, or T at position 2 and a positively charged residue at the C-terminus. See, Sidney, supra.

   Binding motifs for alleles HLA-AI, A2.1, A3.2, Al 1.2, and A24, for example, are well characterized (see, e.g., Rammensee, et &\., Ann. Rev. Immun. 11:213-244
(1993); Ruppert, et al., Cell, 74:929-937 (1993); Kubo, et al., J. Immun., 152:39133924 (1994)); these alleles are expressed in 90% of the Caucasian population. In fact, the "sequence motifs" and "anchor residues of the various MHC alleles have been analyzed in detail and hundreds of peptide ligands for the more important class I molecules have been reported (reviewed in Rammensee, et al., Immunogenetics, 41 :178-228 (1995) ("Rammensee, 1995")).

   Rammensee, 1995 sets forth for each allele the "anchor" residues at positions 2 and 9, any auxiliary anchor positions for the particular allele, and prefe[pi]ed residues at other positions.
The selection and screening of peptide epitopes for their MHC binding capacity and in vitro and in vivo activation of CTLs has also been closely studied and is taught in the literature. See, e.g., Celis, E., et al., Cancer Biol, 6:329-336 (1995); Chesnut, R., et al., "Design and Testing of Peptide-Based Cytotoxic T-Cell Mediated Immunotherapeutics to Treat Infectious Diseases and Cancer," in Powell, M. and Newman, M., eds., Vaccine Design: The Subunit and Adjuvant Approach (Plenum Press, New York, 1995); Celis, E., et al., Mol.

   Immunol, 31:1423-1430 (1994) (hereafter, "Celis, 1994"); Lanzavecchia, A., Science, 260:937-943 (1993); Celis, E., et al., Proc Natl Acad Sci U.S.A. 91 :2105-2109 (1994); Sinigaglia, F., and Hammer, J., J. Exp. Med.181 :449-451 (1995).
For example, Celis, et al., Mol. Immun.3\:\423-\430 (1994) ("Celis, 1994"), describes the identification of potential CTL epitopes of MAGE-1. They screened the 309 amino acid sequence of the MAGE-1 protein for the presence of peptides 910 residues in length, containing binding motifs for HLA-AI, -A2.1, -A3.2, -Al 1, and A24, and synthesized 170 such peptides. The peptides were tested for their binding to purified MHC molecules by standard assays and those with high or intermediate affinity to the purified MHC molecules selected as potential epitopes for melanoma-specific CTL.

   Peptides so selected are then candidates for testing for their ability to activate CTLs. A variety of assays for this pu[phi]ose are known in the art, and include immunization of transgenic mice, in vitro CTL studies using PBMC or tumor infiltrating lymphocytes isolated from patients with cancers of the relevant type, and in vitro inductions using PBMC from normal HLA-typed individuals. See, e.g., Celis, 1994; Vitiello, et al., J. Exp. Med, 173:1007-1015 (1991); Traversari, et al., J. Exp. Med, 176:1453-1457 (1992); Celis, et al., Proc Natl Acad Sci U.S.A., 91 :2105-2109 (1994). The tumor associated antigens MAGE-2 and MAGE-3 have also been used as the basis for the development of 9-mer and 10-mer synthetic peptides which bind to a chosen HLA allele and which stimulate CTLs against those antigens. See, U.S.

   Patent 5,662,907.
Recent studies and advances in combinatorial peptide chemistry have improved the ability to describe and to predict the specificities of HLA molecules. See, e.g., Buus, S., Curr. Opin. Immunol, 11:209-213 (1999); Schafer, j., et al., Vaccine, 16:1880-1884 (1998). Additional methods for predicting whether a particular peptide will bind to a MHC molecule have been developed and have been asserted to be more accurate than the use of sequence motifs. For example, Gulukota, K., et al., J. Mol. Biol, 267:1258-1267 (1997), teach what they style as neural net and polynomial methods for predicting whether a particular peptide will bind to a MHC molecule. The methods are complementary, with one eliminating false positives and the other better at eliminating false negatives.
A number of means for inducing cellular responses, both in vitro and in vivo, are known .

   Lipids have been identified as agents capable of assisting in priming CTL in vivo against various antigens. For example, as described in U.S. Patent No. 5,662,907, palmitic acid residues can be attached to the alpha and epsilon amino groups of a lysine residue and then linked (e.g., via one or more linking residues, such as glycine, glycine-glycine, serine, serine-serine, or the like) to an immunogenic peptide. The lipidated peptide can then be injected directly in a micellar form, inco[phi]orated in a liposome, or emulsified in an adjuvant. As another example, E. coli lipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine can be used to prime tumor specific CTL when covalently attached to an appropriate peptide (see, Deres, et al., Nature 342:561, 1989).

   Further, as the induction of neutralizing antibodies can also be primed with the same molecule conjugated to a peptide which displays an appropriate epitope, the two compositions can be combined to elicit both humoral and cell-mediated responses where that is deemed desirable.
In yet another embodiment, to induce a CTL response to an immunogenic PATE polypeptide or fragment thereof, a MHC class Il-restricted T-helper epitope is added to the CTL antigenic peptide to induce T-helper cells to secrete cytokines in the microenvironment to activate CTL precursor cells.

   The technique further involves adding short lipid molecules to retain the construct at the site of the injection for several days to localize the antigen at the site of the injection and enhance its proximity to dendritic cells or other "professional" antigen presenting cells over a period of time (see Chesnut et al., "Design and Testing of Peptide-Based Cytotoxic T-Cell-Mediated Immunotherapeutics to Treat Infectious Diseases and Cancer," in Powell, et al., eds., Vaccine Design, the Subunit and Adjuvant Approach, Plenum Press, New York, 1995). A pharmaceutical composition including a PATE polypeptide is thus provided. In one embodiment, the PATE polypeptide, or fragment thereof, is mixed with an adjuvant containing two or more of a stabilizing detergent, a micelleforming agent, and an oil. Suitable stabilizing detergents, micelle-forming agents, and oils are detailed in U.S.

   Patent Nos. 5, 585,103; 5,709,860; 5,270,202; and 5,695,770, all of which are inco[phi]orated by reference. A stabilizing detergent is any detergent that allows the components of the emulsion to remain as a stable emulsion. Such detergents include polysorbate, 80 (TWEEN) (Sorbitan-mono-9 octadecenoate-poly(oxy-l,2-ethanediyl; manufactured by ICI Americas, Wilmington, Del.), TWEEN 40(TM), TWEEN 20(TM), TWEEN 60(TM), Zwittergent(TM) 312, TEEPOL HB7(TM), and SPAN 85(TM). These detergents are usually provided in an amount of approximately 0.05 to 0.5%, preferably at about 0.2%. A micelle forming agent is an agent which is able to stabilize the emulsion formed with the other components such that a micelle-like structure is formed. Such agents generally cause some irritation at the site of injection in order to recruit macrophages to enhance the cellular response.

   Examples of such agents include polymer surfactants described by BASF Wyandotte publications, e.g., Schmolka, J. Am. Oil. Chem. Soc. 54:110 (1977), and Hunter, et al., J. Immunol 129:1244 (1981), PLURONIC(TM)
L62LF, L101, and L64, PEG1000, and TETRONIC(TM) 1501, 150R1, 701, 901, 1301, and 130R1. The chemical structures of such agents are well known in the art. In one embodiment, the agent is chosen to have a hydrophile-lipophile balance (HLB) of between 0 and 2, as defined by Hunter and Bennett, J. Immun. 133:3167 (1984).

   The agent can be provided in an effective amount, for example between 0.5 and 10%, most preferably in an amount between 1.25 and 5%.
The oil included in the composition is chosen to promote the retention of the antigen in oil-in- water emulsion, i.e., to provide a vehicle for the desired antigen, and preferably has a melting temperature of less than 65[deg.] C. such that emulsion is formed either at room temperature (about 20[deg.] C. to 25[deg.] C), or once the temperature of the emulsion is brought down to room temperature. Examples of such oils include squalene, Squalane, EICOSANE(TM), tetratetracontane, glycerol, and peanut oil or other vegetable oils. In one specific, non-limiting_example, the oil is provided in an amount between 1 and 10%, most preferably between 2.5 and 5%.

   The oil should be both biodegradable and biocompatible so that the body can break down the oil over time, and so that no adverse affects, such as granulomas, are evident upon use of the oil.
An adjuvant can be included in the composition. In one embodiment, the adjuvant is a mixture of stabilizing detergents, micelle-forming agent, and oil available under the name Provax(R) (IDEC Pharmaceuticals, San Diego, CA).
In another embodiment, a pharmaceutical composition includes a nucleic acid encoding a PATE polypeptide or immunogenic fragment thereof. A therapeutically effective amount of the PATE polynucleotide can be administered to a subject in order to generate an immune response. In one specific, non- limiting example a therapeutically effective amount of the PATE polynucleotide is administered to a subject to treat prostate cancer.

   One approach to administration of nucleic acids is direct immunization with plasmid DNA, such as with a mammalian expression plasmid. As described above, the nucleotide sequence encoding PATE, or an immunogenic peptide thereof, can be placed under the control of a promoter to increase expression of the molecule.
Immunization by nucleic acid constructs is well known in the art and taught, for example, in U.S. Patent No. 5,643,578 (which describes methods of immunizing vertebrates by introducing DNA encoding a desired antigen to elicit a cell-mediated or a humoral response) and U.S. Patent Nos. 5,593,972 and 5,817,637 (which describe operably linking a nucleic acid sequence encoding an antigen to regulatory sequences enabling expression). U.S. Patent No. 5,880,103 describes several methods of delivery of nucleic acids encoding immunogenic peptides or other antigens to an organism.

   The methods include liposomal delivery of the nucleic acids (or of the synthetic peptides themselves), and immune-stimulating constructs, or ISCOMS(TM), negatively charged cage-like structures of 30-40 nm in size formed spontaneously on mixing cholesterol and Quil A(TM) (saponin). Protective immunity has been generated in a variety of experimental models of infection, including toxoplasmosis and Epstein-Barr virus-induced tumors, using ISCOMS(TM) as the delivery vehicle for antigens (Mowat and Donachie, Immunol. Today 12:383, 1991). Doses of antigen as low as 1 [mu]g encapsulated in ISCOMS(TM) have been found to produce class I mediated CTL responses (Takahashi, et al., Nature 344:873, 1990).

   In another approach to using nucleic acids for immunization, a PATE polypeptide or an immunogenic peptide thereof can also be expressed by attenuated viral hosts or vectors or bacterial vectors. Recombinant vaccinia virus, adenoassociated virus (AAV), he[phi]esvirus, retrovirus, or other viral vectors can be used to express the peptide or protein, thereby eliciting a CTL response. For example, vaccinia vectors and methods useful in immunization protocols are described in U.S. Patent No. 4,722,848. BCG (Bacillus Calmette Guerin) provides another vector for expression of the peptides (see Stover, Nature 351:456-460, 1991). En one embodiment, a nucleic acid encoding a PATE polypeptide or an immunogenic fragment thereof is introduced directly into cells.

   For example, the nucleic acid may be loaded onto gold microspheres by standard methods and introduced into the skin by a device such as Bio-Rad's Helios(TM) Gene Gun. The nucleic acids can be "naked," consisting of plasmids under control of a strong promoter. Typically, the DNA is injected into muscle, although it can also be injected directly into other sites, including tissues in proximity to metastases. Dosages for injection are usually around 0.5 [mu]g/kg to about 50 mg/kg, and typically are about 0.005 mg/kg to about 5 mg/kg (see, e.g., U.S. Patent No. 5,589,466). In addition, the cell growth inhibiting chimeric molecules including an antibody that specifically binds PATE linked to a toxin (i.e., PE linked to an antiPATE antibody), can be prepared in pharmaceutical compositions.
Toxins can be employed with antibodies that specifically bind PATE to yield immunotoxins.

   Exemplary toxins include ricin, abrin, diphtheria toxin and subunits thereof, as well as botulinum toxins A through F. These toxins are readily available from commercial sources (e.g., Sigma Chemical Company, St. Louis, MO). Diphtheria toxin is isolated from Corynebacterium diphtheriae. Ricin is the lectin RCA60 from Ricinus communis (Castor bean). The term also references toxic variants thereof. For example, see, U.S. Patent Nos. 5,079,163 and 4,689,401. Ricinus communis agglutinin (RCA) occurs in two forms designated RCA60and RCA120according to their molecular weights of approximately 65 and 120 kD respectively (Nicholson & Blaustein, J. Biochim. Biophys. Ada 266:543 (1972)). The A chain is responsible for inactivating protein synthesis and killing cells.

   The B chain binds ricin to cell-surface galactose residues and facilitates transport of the A chain into the cytosol (Olsnes, et al, Nature 249:627-631 (1974) and U.S. Patent No. 3,060,165).
Abrin includes toxic lectins from Abrus precatorius. The toxic principles, abrin a, b, c, and d, have a molecular weight of from about 63 and 67 kD and are composed of two disulfide-linked polypeptide chains A and B. The A chain inhibits protein synthesis; the B-chain (abrin-b) binds to D-galactose residues (see, Funatsu, et al., Agr. Biol. Chem.52[Lambda]095 (1988); and Olsnes, Methods Enzymol.50:330-335 (1978)). In several embodiments, the toxin is Pseudomonas exotoxin (PE). The term "Pseudomonas exotoxin" as used herein refers to a full-length native (naturally occurring) PE or a PE that has been modified.

   Such modifications may include, but are not limited to, elimination of domain la, various amino acid deletions in domains lb, II and III, single amino acid substitutions and the addition of one or more sequences at the carboxyl terminus such as KDEL and REDL. See Siegall, et al., J. Biol. Chem.264:l4256 (1989). In a preferred embodiment, the cytotoxic fragment of PE retains at least 50%, preferably 75%, more preferably at least 90%, and most preferably 95% of the cytotoxicity of native PE. In a most preferred embodiment, the cytotoxic fragment is more toxic than native PE.
Native Pseudomonas exotoxin A (PE) is an extremely active monomeric protein (molecular weight 66 kD), secreted by Pseudomonas aeruginosa, which inhibits protein synthesis in eukaryotic cells. The native PE sequence is provided as SEQ ED NO:l of commonly assigned U.S.

   Patent No. 5,602,095, inco[phi]orated herein by reference. The method of action is inactivation of the ADP-ribosylation of elongation factor 2 (EF-2). The exotoxin contains three structural domains that act in concert to cause cytotoxicity. Domain la (amino acids 1-252) mediates cell binding. Domain II (amino acids 253-364) is responsible for translocation into the cytosol and domain III (amino acids 400-613) mediates ADP ribosylation of elongation factor 2. The function of domain lb (amino acids 365-399) remains undefined, although a large part of it, amino acids 365-380, can be deleted without loss of cytotoxicity. See Siegall, et al., J. Biol. Chem. 264: 14256-14261 (1989), inco[phi]orated by reference herein.
PE employed includes the native sequence, cytotoxic fragments of the native sequence, and conservatively modified variants of native PE and its cytotoxic fragments.

   Cytotoxic fragments of PE include those which are cytotoxic with or without subsequent proteolytic or other processing in the target cell (e.g., as a protein or pre-protein). Cytotoxic fragments of PE include PE40, PE38, PE37, and PE35. PE40 is a truncated derivative of PE as previously described in the art. See, Pai, et al., Proc. Nat'lAcad. Sci. U.S.A. 88:3358-62 (1991); and Kondo, et al., J.
Biol. Chem. 263:9470-9475 (1988). PE35 is a 35 kD carboxyl-terminal fragment of PE composed of a met at position 280 followed by amino acids 281-364 and 381 613 of native PE. PE37, another truncated derivative of PE, is described in U.S. Patent No. 5,821,238. PE38 is a truncated PE pro-protein composed of amino acids 253-364 and 381-613 which is activated to its cytotoxic form upon processing within a cell (see U.S. Patent No. 5,608,039, inco[phi]orated herein by reference).

   In a particularly preferred embodiment, PE38 is the toxic moiety of the immunotoxin, however, other cytotoxic fragments, such as PE35, PE37, and PE40, are contemplated and are disclosed in U.S. Patents 5,602,095; 5,821,238; and 4,892,827, each of which is inco[phi]orated herein by reference.
These cell growth inhibiting molecules can be administered by any method known to one of skill in the art. For example, to treat prostate cancer, the pharmaceutical compositions can be administered directly into the prostate gland. Metastases of prostate cancer may be treated by intravenous administration or by localized delivery to the tissue surrounding the tumor.
The compositions for administration will commonly comprise a solution of the cell growth inhibiting chimeric molecules dissolved in a pharmaceutically acceptable carrier, preferably an aqueous carrier.

   A variety of aqueous carriers can be used, e.g., buffered saline and the like. These solutions are sterile and generally free of undesirable matter. These compositions may be sterilized by conventional, well known sterilization techniques. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents and the like, for example, sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate and the like.

   The concentration of cell growth inhibiting molecules in these formulations can vary widely, and will be selected primarily based on fluid volumes, viscosities, body weight and the like in accordance with the particular mode of administration selected and the patient's needs.
In one specific, non-limiting example, a pharmaceutical composition for intravenous administration, such as an immunotoxin, would be about 0.1 to 10 mg per patient per day. Dosages from 0.1 up to about 100 mg per patient per day may be used, particularly if the agent is administered to a secluded site and not into the circulatory or lymph system, such as into a body cavity or into a lumen of an organ.

   Actual methods for preparing administrable compositions will be known or apparent to those skilled in the art and are described in more detail in such publications as Remingtons Pharmaceutical Sciences, 19<th>Ed., Mack Publishing Company, Easton, Pennsylvania (1995). The compositions can be administered for therapeutic treatments. In therapeutic applications, compositions are administered to a patient suffering from a disease, such as prostate cancer, in a therapeutically effective amount, which is an amount sufficient to cure or at least partially arrest the disease or a sign or symptom of the disease. Amounts effective for this use will depend upon the severity of the disease and the general state of the patient's health.

   An effective amount of the compound is that which provides either subjective relief of a symptom(s) or an objectively identifiable improvement as noted by the clinician or other qualified observer.
Single or multiple administrations of the compositions are administered depending on the dosage and frequency as required and tolerated by the patient. In one embodiment, the dosage is administered once as a bolus, but in another embodiment can be applied periodically until either a therapeutic result is achieved. Generally, the dose is sufficient to treat or ameliorate symptoms or signs of disease without producing unacceptable toxicity to the patient. Controlled release parenteral formulations of cell growth inhibiting chimeric molecules can be made as implants, oily injections, or as particulate systems.

   For a broad overview of protein delivery systems (see Banga, A.J., Therapeutic Peptides and Proteins: Formulation, Processing, and Delivery Systems, Technomic Publishing Company, Inc., Lancaster, PA, 1995). Particulate systems include microspheres, microparticles, microcapsules, nanocapsules, nanospheres, and nanoparticles. Microcapsules contain the therapeutic protein as a central core. In microspheres the therapeutic is dispersed throughout the particle. Particles, microspheres, and microcapsules smaller than about 1 [mu]m are generally referred to as nanoparticles, nanospheres, and nanocapsules, respectively. Capillaries have a diameter of approximately 5 [mu]m so that only nanoparticles are administered intravenously.

   Microparticles are typically around 100 [mu]m in diameter and are administered subcutaneously or intramuscularly (see Kreuter, J., Colloidal Drug Delivery Systems, J. Kreuter, ed., Marcel Dekker, Inc., New York, NY, pp. 219-342, 1994; Tice & Tabibi, Treatise on Controlled Drug Delivery, A. Kydonieus, ed., Marcel Dekker, Inc. New York, NY, pp. 315-339, 1992).
Polymers can be used for ion-controlled release. Various degradable and nondegradable polymeric matrices for use in controlled drug delivery are known in the art (Langer, R., Accounts Chem. Res. 26:537, 1993). For example, the block copolymer, polaxamer 407 exists as a viscous yet mobile liquid at low temperatures but forms a semisolid gel at body temperature. It has shown to be an effective vehicle for formulation and sustained delivery of recombinant interleukin-2 and urease (Johnston, et al., Pharm.

   Res. 9:425, 1992); and Pec, et al, J. Parent. Sci.
Tech. 44(2):58, 1990). Alternatively, hydroxyapatite has been used as a microcarrier for controlled release of proteins (Ijntema, et al., Int. J. Pharm.112:215, 1994). In yet another aspect, liposomes are used for controlled release as well as drug targeting of the lipid-capsulated drug (Betageri, et al., Liposome Drug Delivery Systems, Technomic Publishing Co., Inc., Lancaster, PA, 1993). Numerous additional systems for controlled delivery of therapeutic proteins are known ( e.g., U.S. Pat. No. 5,055,303, 5,188,837, 4,235,871, 4,501,728, 4,837,028 4,957,735 and 5,019,369, 5,055,303; 5,514,670; 5,413,797; 5,268,164; 5,004,697; 4,902,505; 5,506,206, 5,271,961; 5,254,342 and 5,534,496).
Ex vivo Uses of the PATE Polypeptides
The compositions and methods can be used ex vivo to augment an organism's immune response.

   In this regard, a portion of the organism's lymphocytes are removed and cultured in vitro with high doses of the immunogenic peptides or the PATE protein, providing a stimulatory concentration of peptide in the cell medium in excess of that which could be achieved in the body. Following treatment to stimulate the CTLs, the cells are returned to the host, allowing the activated CTLs to attack PATE-expressing cells in the organism.
In one method, CTL responses to PATE-expressing cells are induced by incubating in tissue culture a patient's CTL precursor cells together with a source of antigen presenting cells and the appropriate immunogenic peptide or the PATE protein. After an appropriate incubation period (which may be 1-4 weeks), the CTL precursors are activated and mature and expand into CTLs.

   To optimize in vitro conditions, the culture of stimulator cells is typically maintained in an appropriate serum-free medium. Peripheral blood lymphocytes are conveniently isolated following simple venipuncture or leukopheresis of normal donors or patients and used as the responder cell sources of CTL precursors. In one embodiment, the appropriate APC are incubated with about 10-100 [mu]M of peptide in serum-free media for 4 hours under appropriate culture conditions. The peptide-loaded APC are then incubated with the responder cell populations in vitro for 5 to 10 days under optimized culture conditions.

   Positive CTL activation can be determined by assaying the cultures for the presence of CTLs that kill radiolabeled target cells, both specific peptide-pulsed targets as well as target cells expressing endogenously processed form of the PATE protein from which the peptide sequence was derived. Specificity and MHC restriction of the CTL of a patient can be determined by a number of methods known in the art. For instance, CTL restriction can be determined by testing against different peptide target cells expressing appropriate or inappropriate human MHC class I. The peptides that test positive in the MHC binding assays and give rise to specific CTL responses are identified as immunogenic peptides. More details about the selection of CTLs and their separation from antigen presenting cells are set forth in, e.g., U.S. Patent No. 5,932,224.

   See also; WO 95/25122.
Antigen presenting cells may also be exposed to vectors carrying nucleic acid sequences encoding the immunogenic peptides or the PATE protein, or "naked" DNA encoding the peptides or proteins can be introduced by the Helios(TM) Gene Gun or other methods. Feigner, U.S. Patent No. 6,214,804, for example, teaches methods for introducing isolated polynucleotides to the interior of cells for expression. Once dosed or transfected, the cells may be propagated in vitro or returned to the patient. Conveniently, the cells are propagated in vitro until they reach a predetermined cell density, after which they are reintroduced into the host.
Return of cells to the host may be by any of several methods well known in the art, and include procedures such as those exemplified in U.S. Patent No.
4,844,893 to Honsik and U.S. Patent No. 4,690,915 to Rosenberg.

   Conveniently, the cells may be reintroduced by intravenous infusion. Diagnostic Methods and Kits
A method is provided herein for the detection of PATE-expressing prostate cells or prostate tissue in a biological sample. The sample can be any sample that includes PATE polypeptide or a nucleic acid encoding PATE polypeptide. Such samples include, but are not limited to, tissue from biopsies, autopsies, and pathology specimens. Biological samples also include sections of tissues, such as frozen sections taken for histological pu[phi]oses. Biological samples further include body fluids, such as blood, serum, or urine. A biological sample is typically obtained from a mammal, such as a rat, mouse, cow, dog, guinea pig, rabbit, or primate. In one embodiment the primate is macaque, chimpanzee, or a human.

   In a further embodiment the subject has prostate cancer, or is suspected of having prostate cancer.
In one embodiment, a method is provided for detecting a PATE polypeptide. Kits for detecting a PATE polypeptide of fragment thereof will typically comprise an antibody that specifically binds PATE. In some embodiments, an antibody fragment, such as an Fv fragment is included in the kit. For in vivo uses, the antibody is preferably an scFv fragment. In a further embodiment the antibody is labeled (e.g. fluorescent, radioactive, or an enzymatic label). In one embodiment, a kit includes instructional materials disclosing means of use of an antibody that specifically binds a PATE polypeptide or fragment thereof (e.g. for detection of PATE expressing cells in a sample).

   The instructional materials may be written, in an electronic form (e.g. computer diskette or compact disk) or may be visual (e.g. video files). The kits may also include additional components to facilitate the particular application for which the kit is designed.
Thus, for example, the kit may additionally contain means of detecting a label (e.g. enzyme substrates for enzymatic labels, filter sets to detect fluorescent labels, appropriate secondary labels such as a secondary antibody, or the like). The kits may additionally include buffers and other reagents routinely used for the practice of a particular method. Such kits and appropriate contents are well known to those of skill in the art. In one embodiment, the diagnostic kit comprises an immunoassay.

   Although the details of the immunoassays may vary with the particular format employed, the method of detecting a PATE polypeptide or fragment thereof in a biological sample generally comprises the steps of contacting the biological sample with an antibody which specifically reacts, under immunologically reactive conditions, to PATE. The antibody is allowed to specifically bind under immunologically reactive conditions to form an immune complex, and the presence of the immune complex (bound antibody) is detected directly or indirectly.
In an alternative set of embodiments, kits can be provided for detecting nucleic acids encoding PATE or a fragment thereof in a biological sample. For example, sample from a subject can be tested to determine whether nucleic acids encoding PATE protein are present.

   In one embodiment, an amplification procedure is utilized to detect nucleic acids encoding PATE. In another embodiment, a blotting procedure (e.g. Northern Blot or Dot Blot) is used to detect the presence of nucleic acids encoding PATE. Thus, a kit can include probes cr primers that specifically hybridize to nucleic acids encoding PATE.
In one embodiment, a kit provides a primer that amplifies nucleic acid encoding PATE. Conveniently, the amplification is performed by polymerase chain reaction (PCR). A number of other techniques are, however, known in the art and are contemplated for use. For example, Marshall, U.S. Patent No. 5,686,272, discloses the amplification of RNA sequences using ligase chain reaction, or "LCR," (Landegren, et al., Science 241:1077, 1988); Wu et al., Genomics 4:569 ,1989; Barany, in PCR Methods and Applications 1:5, 1991); and Barany, Proc. Natl. Acad.

   Sci.U.S.A.S$ \89, 1991). Or, the RNA can be reverse transcribed into DNA and then amplified by LCR, PCR, or other methods. An exemplar protocol for conducting reverse transcription of RNA is taught in U.S. Patent No. 5,705,365. Selection of appropriate primers and PCR protocols are taught, for example, in Innis, M., et al., eds., PCR Protocols 1990 (Academic Press, San Diego CA).
In one embodiment, the kit includes instructional materials disclosing means of use for the primer or probe. The kits may also include additional components to facilitate the particular application for which the kit is designed. The kits may additionally include buffers and other reagents routinely used for the practice of a particular method.

   Such kits and appropriate contents are well known to those of skill in the art.
The invention is illustrated by the following non-limiting Examples.
EXAMPLES
Example 1 Material and Methods Primers: The nucleotide sequence of the primers used in the experiments disclosed herein are as follows:
T339; 5'GTG CTC CAGAGG AAG AGGAAT ATG CAC A3' (SEQ ID NO:5)
T340; 5'CAT TGT GAA GAG GCT GAG GCAACA ACC T3' (SEQ ID NO:6)
T364; 5'GGG GAC AAG TTT GTA CAAAAAAGC AGG CTC GGA GAA CCT GTA CTT CCA GTC CAT GTG CCA CCT CCA GTT CCC A3' (SEQ JD NO:7)
T365; GGG GAC CAC TTT GTA CAA GAAAGC TGG GTT ATT ACT AAA GGT CTT CAT TGC ACA GG3' (SEQ IDNO:8).
Dot Blot and Northern Blot Hybridizations: The human multiple tissue RNA dot blot (RNA Masterblot, Clontech, Palo Alto, CA) and northern blot (Multiple Tissue Northern blot, Clontech) hybridizations were carried out as described previously (7).

   Briefly, the RNA membranes were prehybridized for more than 2 h in hybridization solution (Hybrisol I, Oncor, Gaithersburg, MD) at 45[deg.] C. The probe labeled with<32>P by random primer extension (Lofstrand Labs Ltd, Gaithersburg, MD), was added to the blots and hybridized for another 16 h. The blots were then washed 2 x 15 minutes each in 2xSSC, 0.1% SDS, at room temperature and then washed 2 x 15 minutes in 0.2xSSC, 0.1% SDS, at 60[deg.] C. Finally, the membranes were exposed on x-ray film for 1 - 2 days.
RT-PCR Analysis: PCR was performed on cDNA from 24 different human tissues using the Rapid-Scan gene expression panel (OriGene Technologies, Inc., Rockville, MD).

   The thermocycling protocol was: initial denaturation at 94[deg.] C for 3 minutes, 35 cycles of denaturation at 94[deg.] C for 1 minute, annealing at 65[deg.] C for 1 minute, and elongation at 72[deg.] C for 2 minutes. The PCR primers used were T339 and T340. The PCR reactions were analyzed on 1.5% agarose gels. In Situ Hybridization: In situ hybridization of PATE mRNA on prostate cancer tissues was performed as described earlier (6, 8). Biotinylated probes were prepared using PATE (1500 bp) and U6 (250 bp) cDNA cloned in pBluescript II (+) plasmid using the BioNick Labeling System kit (Life Technologies) according to the manufacturer' s instructions. Biotinylated pBluescript II (+) without any insert was used as a negative control. Slides were hybridized using the in situ Hybridization and Detection System (Life Technologies) according to the manufacturer' s instructions.

   The slides were counter stained using 0.2% Light Green stain, rinsed through a series of alcohol grades and mounted in Cytoseal. Microscopic evaluation was performed using a Nikon Eclipse 800 microscope. RA CE PCR: Rapid amplification of cDNA ends (RACE) was performed on
Marathon Ready normal prostate and testis cDNA (Clontech). The gene specific primer used for the 5'RACE was T340. The 5'RACE PCR product was gel purified (QIAquick gel extraction, Qiagen, Santa Clarita, CA) and cloned into the pCR2.1 TOPO vector (Invitrogen). Clones were analyzed by restriction digestion using the EcoRI restriction enzyme.

   The longest clones were sequenced using Perkin-Elmer's dRhodamine terminator sequencing kit (Perkin-Elmer Applied System, Warrington, UK).
In Vitro Translation: The in vitro transcription and translation of the PATE cDNA was carried out using T7 RNA polymerase and wheat germ extract (TNT, Promega, Madison, WI) following manufacturer's instructions.<35>S-Met (ICN, Costa Mesa, CA) was inco[phi]orated in the reaction for visualization of translated products. The reaction mixture was heated at 95[deg.]C in reducing sample buffer and then analyzed under reducing conditions on a polyacrylamide gel (18% PAGE, Tris/Glycine, Bio-Rad, Hercules, CA) together with a pre-stained protein molecular weight marker (Bio-Rad). The gel was dried and subjected to autoradiography. Preparation of Cell Extracts and Western Blot Analysis.

   NTH 3T3 cells were transiently transfected with a eukaryotic expression plasmid (pcDNA3.1-myc His) expressing PATE with a myc epitope tag at the carboxy terminus. Forty-eight h after transfection cells were harvested and analyzed. Whole cell, cytoplasmic, membrane, and nuclear protein extracts were prepared as described previously (4). Twenty-five [mu]g of protein extracts (5 [mu]g for subcellular fractions) were run on a 18% Tris-Glycine gel (Bio-Rad) and transferred to a 0.2 [mu]m PVDF membrane (BioRad) in transfer buffer (25 mM Tris, 192 mM glycine, 20% (v/v) methanol, pH 8.3) at 4[deg.]C for 3 h at 30 V.

   Filters were probed with 10 [mu]g/ml anti-myc-tag monoclonal (9E10) antibody (Santa Cruz Biotechnology, CA,) and their respective signals were detected using a chemiluminescence western blotting kit according to the manufacturer's instructions (Roche Molecular Biochemicals, Indianapolis, IN).
Antibody Production: The construct PATE-MBP, containing the PATE open reading frame fused in frame to maltose binding protein (MBP), was expressed under control of the T7 promoter in E. coli. Inclusion bodies were prepared, then the protein was purified by using amylose column and prepared for rabbit immunization as described before (Liu, et al., The Prostate, 47: 125-131 (2001)). White New Zealand rabbits were used for immunization. For each injection, 1 mg of the purified fusion protein was injected at days 1, 21 and 42. Serum was collected once every week beginning on day 49.

   The IgG fraction of the antiserum was purified using an ImmunoPure IgG (protein A) purification kit (Pierce).
Example 2 Computer Analysis and Specificity of GS1 Cluster The GS-1 cluster (Unigene clusters Hs.126189 and Hs.148565) was identified by computer analysis as partially prostate and testis specific (Fig. 1). There are a total of 11 ESTs: 6 are from prostate, 3 are from testis and 2 are from RNA prepared from a pool of tissues containing testis, fetal lung and B cells. All ESTs are localized to chromosome 1 lq24.2 on the human genome.
To determine experimentally the tissue specificity of the GS-1 cluster, a multi-tissue dot blot analysis was performed using a PCR generated DNA fragment from the cluster as a probe.

   As shown in Fig. 2, among the 50 different samples of normal and fetal tissue examined, GS-1 is only detected in prostate (C7) and testis (Dl) but not in essential tissues such as brain (Al), heart (CI), kidney (El), liver (E2), lung (F2) and adrenal gland (D5). Because GS-1 is expressed in prostate and testis, the gene was named PATE. To confirm the dot blot result a more sensitive PCR based analysis was used to validate tissue specific expression of PATE. In this analysis a panel of cDNAs isolated from 24 different normal tissues was used. PCR reactions were performed with a primer pair (T339 and T340) designed from the DNA sequence of GS-1 cluster. As shown in Fig. 3, a strong specific band of 300 bp was detected in testis (lane 14). There was also a signal detected in prostate (lane 6) and a weak signal in adrenal gland (lane 10).

   No expression was detected in essential tissues such as lung (lane 18), liver (lane 20), brain (lane 24), kidney (lane 22) and heart (lane 23). This data validates the computer analysis and indicates the cluster is specific for testis and prostate with some expression in adrenal gland.
Example 3 Full-Length cDNA Cloning of PATE To determine the transcript size of PATE, a Northern blot analysis was performed using a blot containing mRNAs from different tissues including prostate and testis. The PCR generated probe that was used for dot blot analysis was also used in this experiment. As shown in Fig. 3, a band of about 1.5 kb in size is detected in both the prostate (lane 6) and in testis (lane 3). The intensity of the band detected in the prostate sample is much higher than the intensity observed in testis.

   To isolate the full-length cDNA for PATE the 5' and 3' RACE PCR method was employed and a clone of 1.5 kb in size was isolated. Complete nucleotide sequence (deposited in the GenBank with an accession number AF462605) of the cDNA reveals that it has an open reading frame of 127 amino acids (Fig. 3). The estimated molecular weight of the protein encoded by the PATE cDNA is about 14.3 kDa. The amino acid sequence analysis of the predicted ORF shows that PATE is a cysteine rich protein with a phospholipase A2 motif (FRCCRSHDLC, SEQ JD NO:9) at the carboxy terminus (see Fig. 5). Example 4 Antibodies
To identify the protein expressed in prostate tissue, rabbit polyclonal antibodies were produced against the putative open reading frame of the gene fused with maltose binding protein. The IgG fraction of the antisera was purified using a protein A column.

   As shown in Fig. 6, a band at a molecular weight of about 14.0 kD was detected in lanes containing protein extract from prostate and testis. Shown also is a tissue extract from a brain sample as a negative control. No specific bands were detected using IgG prepared from preimmune serum. These results show that the protein product produced from the PATE transcript is about 14 kDa in size. However, it was not clear that these antibodies were specific.
Thus, anti-PATE antibodies were also produced using partial synthesized peptides of PATE as the immunogen. Two peptides were made that correspond to regions of PATE. Specifically, an N-terminal polypeptide (NT, RNDAVNEIVAVKNNFPVC, a.a. 26-42 plus one additional Cys at the C-terminus, SEQ JD NO: 10) and a second loop polypeptide
(2L,MVGRMFKRDGNPWLTFMGC, a.a. 76-94, SEQ ED NO: 11) regions of PATE, were synthesized.

   These peptides were conjugated to keyhole-limpet hemocyanin (KLH) using the cystein residues by maleimide chemistry. The conjugates were injected to rabbits and mice 2-4 times with or without Freund's adjuvant.
All anti-sera from all immunized animals showed high titer (<10000 fold) in an ELISA, in which the peptide-bovine serum albumin conjugate was used as the antigen. Also, all anti-sera detected recombinant PATE protein produced in E. coli. in a Western blot analysis.
Example 5 Genomic Organization and Analysis of the Promoter Region of PATE BLAST analysis of the PATE cDNA against the human genome sequence demonstrates that PATE is localized at chromosome 1 lq24 (see Fig. 1). It is comprised of 5 exons and 4 introns and spread across only about a 3.5 kb region.

   The genomic sequence of this region of the chromosome is complete and thus an analsis of the promoter region of the PATE gene was possible (see Fig. 7). Examination of the sequence upstream of the PATE transcript reveals a perfect TATA-box at -48 bp region from the start of the transcript. There are also 3 potential androgen response elements (ARE), upstream of the transcription start site indicating that PATE expression may be regulated by androgen (Fig. 1).
Example 6 PATE mRNA is Expressed in Epithelial Cells of Normal Prostate and Prostate
Cancer To determine the cell types in normal prostate and prostate cancer that express PATE mRNA, in situ hybridization was performed with a biotin labeled PATE cDNA as a probe as described in Example 1. As shown in Fig.8, PATE mRNA is highly expressed in prostatic epithelial cells of two prostate cancer specimens.

   There is no signal with a probe that does not contain the PATE insert indicating the specificity of the hybridization reaction; also there is no detectable signal in cells in the stromal compartment of the tissue indicating that PATE is specifically expressed in the epithelial cells of the prostate.
Example 7 The PATE Transcript Encodes a 14 kDa Membrane Associated Protein Analysis of the sequence of the PATE cDNA indicates that it has a predicted
ORF of 127 amino acids with an estimated molecular weight of 14.3 kDa. To determine the size of the protein encoded by the PATE cDNA, in vitro transcription and couple translation was performed utilizing the T7 polymerase and wheat germ extract system. As shown in Fig. 9A, PATE cDNA produced a specific band of about 14 kDa in size, whereas the empty vector produced no specific protein product.

   A plasmid containing luciferase cDNA was used as a positive control and gave rise to an expected 62 kDa product.
To determine the subcellular localization of PATE, a eukaryotic expression plasmid (pcDNA3.1/PT-myc-His) was constructed that expresses PATE with a Myc-His epitope tag at the carboxy terminus. Nuclear, cytoplasmic and membrane fractions were prepared from NEH 3T3 cells transiently transfected with the expression plasmid pcDNA3.1/PT-myc-His. As shown in Fig. 9B, a strong specific band at a molecular weight of about 16.0 kD (14 kDa PATE with 2 kDa from the tag) was detected in the lane containing protein extracts from the membrane fraction when anti-myc-tag monoclonal antibody was used. There was a very weak band of similar size in the cytoplasmic fraction. There was no detectable signal from the extract of the cells transfected with empty vector.

   This result indicates that the PATE gene encodes a 14 kDa protein and the protein is associated with the membrane fraction of the cell.
Thus, a new gene, PATE, which is highly expressed in prostate cancer and testis has been identified. The name PATE is selected to indicate its expression pattern (Expressed in Prostate And TEstis). PATE is a small protein with a molecular weight of 14 kDa. When PATE protein sequences were analyzed using the ExPASy site (available on the internet) for signal peptide prediction, the SignalP program predicted a 21 amino acid signal peptide with a likely cleavage site between G21 and S22. This suggests that PATE is processed and is then either secreted or remains bound to the cell membrane. Transfection experiments reveal that PATE is associated with the membrane fraction.

   A BLASTP run against the NCBI's nr database (using the NCBI BLAST program available on the internet) using the PATE putative protein sequence resulted in hits to the acrosomal vesicle proteins, SP-10, with e-scores between 0.003 and 0.07. The acrosomal vesical protein SP-10 may be involved in sperm-zona binding and penetration. The aligned part of the SP10 protein belongs to a snake toxin family of proteins according to the sequencebased protein classification database, pfam.
When fold recognition programs were run for the PATE amino acid sequence, three different programs, 3D-PSSM (Kelley et al., J. Mol. Biol. 299, 499520, 2000), GenTHREADER (Jones, J. Mol. Biol. 287, 797-815, 1999), and
Bioinbgu (Fischer, Pac. Symp.

   Biocomput. 119-130, 2000), predicted a protein in the same snake toxin family (PDB file names lf94 or lcdt) as the highest scoring hit with high to medium prediction confidence.
According to the manually procured protein structure classification database, SCOP (Murzin, et al., J. Mol. Biol.247 -.536-540, 1995), the superfamily of protein structures, that contains the snake venom toxin also includes many neurotoxins and cardiotoxins. It also contains CD59 (Fletcher, et al., Structure 2:185-199, 1994; Kieffer, et al., Biochemistry 33:4471-4482, 1994) and an extracellular domain of the activin receptor (Greenwald, et al., Nat. Struct. Biol. 6:18-22, 1999). The recently described bone mo[phi]hogenic protein (BMP) receptor contains a domain of similar structure (Kirsch, et al., Nat. Struct. Biol. 7:492-496, 2000).

   These structures contain 5 or 6 strands that extend like the fingers of a hand, which are tied together in the "palm" region of the molecule by 4 or 5 disulfide bonds (Fig. 10). PATE contains 12 cysteines, two of which are in the putative signal sequence. The receptor proteins are homologous to the extracellular domain of the TGF-[beta] receptor and urokinasetype plasminogen activator (Jokiranata, et al., FEBSLett. 376:31-36, 1995). These are transmembrane proteins that bind the TGF-[beta] family of cytokines and relay their signal through phosphorylation of other proteins. CD59 is a member of the ly6 superfamily. It is a cell-surface glycoprotein anchored to the membrane by means of glycosylphosphatidylinositol (GPI). It is believed to interfere with the full assembly of the membrane attack complex of the complement system (Davies & Lachmann, Immunol. Res. 12:258-275, 1993).

   The prostate stem cell antigen (Reiter, et al.,
Proc. Natl. Acad. Sci. U.S.A. 95:1735-1740, 1998) is also belong to this family of 10 cysteine proteins.
The number and the pattern of cysteine residues in the PATE sequence, as well as partial sequence homology and the results of several protein fold prediction programs, suggest that PATE protein may have a structure similar to these proteins. The PATE sequence does not appear to have a transmembrane segment nor the motif for the GPI anchor that CD59 and PSCA proteins have; therefore it may be anchored to the membrane by interaction with another protein or means of some other lipid molecule.

   In fact, the common characteristic of all the proteins with this structure is that they interact with other proteins, PATE can also be expected to be involved in protein-protein interactions.
The PATE promoter region has three putative androgen response elements, suggesting that its expression is probably regulated by androgen. The TARP promoter, like that of PATE, also has andogen response element and is induced by testosterone treatment of LnCAP cells (Tsavaler, et al., Cancer Res. 61 :3760-3769, 2001). Example 8 PATE is a Secreted Protein
Four hundred thousand 293T parental cells or 293T/Pate-myc-his cells were grown to confluence in T-75 flasks (5 days). The media from each cell-line was removed and clarified by centrifugation at 13,000 [phi]m for 10 minutes.

   Two ml of media per sample was used to immunoprecipitate either Pate-myc-his using a monoclonal anti-myc antibody (1 ug/sample) or anti-actin polyclonal antisera (1 ug/sample) and Protein G-agarose. Media from parental 293T cells were used as a negative control. Cell lysates were prepared and equal amounts of cell lysates and immunoprecrpitated proteins were separated by SDS-PAGE. Following transfer on to PVDF membrane, the blots were sequentially probed either with the anti-myc monoclonal antibody ( lug/ml) or with a monoclonal anti-actin antibody (1 ug/ml) as indicated, followed by HRP-conjugated anti-mouse IgGl monoclonal antibody. Membranes were washed three times with TBST (0.1 % Tween 20) between each incubation period. Detection was performed using ECL.

   A band of the expected molecular weight for PATE-myc-his was detected only in the medium from the cells transfected with PATE-myc-his plasmid. No actin was detected in the medium indicating release of PATE was not due to cell lysis.
These experiments demonstrate that PATE is a secreted protein.
Example 9 PATE Induces Proliferation of Prostate Cells In order to determine if PATE acts as a growth factor for prostate cells, a vector was constructed including an Rous Sarcoma Virus (RSV) promoter operably linked to a nucleic acid encoding PATE. This vector was transfected into a prostate cancer cells line PC3, and proliferation of the cells was measured.

   Proliferation of the cells transfected with the vector including PATE was significantly increased, indicating that PATE acts as a growth factor for prostate cells.
As PATE is a secreted protein (see Example 7), it is likely that PATE is a growth factor for prostate cells that works as an autocrine factor. It is hypothesized that increased production of PATE by prostate cancer cells leads to increased proliferation of these cells. Thus, it is likely that inhibition of PATE, either using an antibody or a small molecule or polypeptide that binds PATE and inhibits its activity, will dramatically decrease the proliferation of prostate cancer cells.

   In addition, it is likely that increased expression of PATE serves as a marker of prostate cancer cells that are likely to undergo rapid proliferation.
It will be apparent that the precise details of the methods or compositions described may be varied or modified without departing from the spirit of the described invention. We claim all such modifications and variations that fall within the scope and spirit of the claims below.

Claims

We claim:

1. An antibody that specifically binds a polypeptide having an amino acid sequence selected from the group consisting of:

(1) an amino acid sequence 80% homologous to SEQ JD NO:2;

(2) a conservative variant of SEQ JD NO:2;

(3) an immunogenic fragment comprising eight consecutive amino acids of SEQ ED NO: 1 that specifically binds to an antibody that specifically binds

SEQ ED NO:2; and

(4) SEQ ED NO:2.

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

3. The antibody of claim 1, comprising a detectable label.

4. The antibody of claim 3, wherein the label is a fluorescent, enzymatic or radioactive label.

5. The antibody of claim 1, conjugated to a toxin.

6. A method for detecting prostate cancer in a subject, comprising contacting a sample obtained from the subject with the antibody of claim 1 for a sufficient amount of time to form an immune complex; detecting the presence the immune complex, wherein the presence of an immune complex demonstrates the presence of prostate cancer in the subject.

7. The method of claim 6, wherein the sample is a biopsy, blood, serum, or urine sample.

8. The method of claim 7, wherein the sample is a biopsy sample of nonprostate origin.

9. The method of claim 6, wherein the antibody is labeled.

10. A method for detecting a prostate cancer in a subject, comprising detecting the expression of the a PATE polypeptide in a sample from the subject, wherein the PATE polypeptide has an amino acid sequence selected from the group consisting of: (1) an amino acid sequence 80% homologous to SEQ ED NO: 1 ;

(2) a conservative variant of SEQ JD NO: 1 ;

(3) an immunogenic fragment comprising eight consecutive amino acids of SEQ ID NO:l that specifically binds to an antibody that specifically binds SEQ ED NO: 1; and (4) SEQ ED NO: 1 wherein an increase in the expression of the PATE polyeptide as compared to a control indicates the presence of the prostate cancer.

11. The method of claim 10, wherein detecting the expression of PATE polypeptide comprises detecting PATE polypeptide in the sample.

12. The method of claim 22, wherein detecting the expression of the PATE polypeptide comprises contacting the sample with an antibody that specifically binds the PATE polypeptide for a sufficient amount of time to form an immune complex; and detecting the presence of the immune complex.

13. The method of claim 10, wherein detecting the expression of the PATE polypeptide comprises detecting the presence of mRNA encoding the PATE polypeptide.

14. The method of claim 13, wherein detecting the presence of mRNA encoding the PATE polypeptide comprises a Northern Blot analysis, an RNA dot blot analysis, or a reverse transcriptase polypermase chain reaction (RT-PCR) assay.

15. A method for producing an immune response against a cell expressing a

PATE polypeptide in a subject, comprising administering to the subject a therapeutically effective amount of the a PATE polypeptide having an amino acid sequence selected from the group consisting of: (1) an amino acid sequence 80% homologous to SEQ JD NO:l; (2) a conservative variant of SEQ ED NO: 1 ;

(3) an immunogenic fragment comprising eight consecutive amino acids of SEQ JD NO:l that specifically binds to an antibody that specifically binds SEQ ED NO: 1; and

(4) SEQ ED NO:l, or a polynucleotide encoding the PATE polypeptide, thereby producing the immune response.

16. The method of claim 15, wherein the immune response is a T cell response.

17. The method of claim 15, wherein the immune response is a B cell response.

18. The method of claim 15, wherein the subject has prostate cancer or testicular cancer.

19. The method of claim 15, wherein the subject has prostate cancer.

20. The method of claim 19, wherein the immune response decreases the growth of the prostate cancer.

21. A method for inhibiting the growth of a malignant cell expressing a PATE polypeptide, wherein the PATE polypeptide has an amino acid sequence selected from the group consisting of:

(1) an amino acid sequence 80% homologous to SEQ JD NO:l; (2) a conservative variant of SEQ JD NO: 1 ;

(3) an immunogenic fragment comprising eight consecutive amino acids of SEQ ED NO:l that specifically binds to an antibody that specifically binds SEQ ED NO: 1; and

(4) SEQ ID NO: 1

the method comprising,

(i) culturing cytotoxic T lymphocytes (CTLs) or CTL precursor cells with the PATE polypeptideto produce activated CTLs or CTL precursors that recognize a PATE expressing cell, and

(ii) contacting the malignant cell with the activated CTLs or CTLs matured from the CTL precursors, thereby inhibiting the growth of the malignant cell.

22. A method for inhibiting the growth of a malignant cell expressing a PATE polypeptide having an amino acid sequence selected from the group consisting of:

(1) an amino acid sequence 80% homologous to SEQ JD NO:l;

(2) a conservative variant of SEQ ID NO:l;

(3) an immunogenic fragment comprising eight consecutive amino acids of SEQ ED NO:l that specifically binds to an antibody that specifically binds SEQ ED NO: 1; and

(4) SEQ ED NO: 1, the method comprising: contacting the malignant cell with an effective amount of a cell-growth inhibiting molecule, wherein the cell growth inhibiting molecule comprises a ligand that specifically binds the PATE polypeptide, thereby inhibiting the growth of the cell expressing PATE.

23. The method of claim 22, wherein the ligand is an antibody which specifically binds the PATE polypeptide covalently linked to an effector molecule which inhibits the growth of cells,

24. The method of claim 23, wherein said antibody is a monoclonal antibody.

25. The method of claim 23, wherein the effector molecule is a chemotherapeutic agent.

26. The method of claim 23, wherein the effector molecule comprises a toxic moiety.

27. The method of claim 26, wherein the toxic moiety is selected from the group consisting of ricin A, abrin, diphtheria toxin or a subunit thereof, Pseudomonas exotoxin or a portion thereof, and botulinum toxins A through F.

28. The method of claim 27, wherein the Pseudomonas exotoxin is selected from the group consisting of PE35, PE37, PE38, and PE40.

29. A method for reducing the number of prostate cancer cells in a subject, comprising administering to the subject a therapeutically effective amount of the PATE polypeptide or a polynucleotide encoding the PATE polypeptide, wherein the PATE polypeptide has an amino acid sequence selected from the group consisting of:

(1) an amino acid sequence 80% homologous to SEQ ID NO:l;

(2) a conservative variant of SEQ ED NO:l;

(3) an immunogenic fragment comprising eight consecutive amino acids of SEQ JD NO:l that specifically binds to an antibody that specifically binds SEQ ED NO: 1; and (4) SEQ ED NO: 1, wherein the administration of the PATE polypeptide or the polynucleotide encoding the PATE polypeptide results in an immune response to the PATE polypeptide, thereby reducing the number of prostate cancer cells in the subject.

30. A method for reducing the number of prostate cancer cells in a subject, comprising administering to the subject a therapeutically effective amount of the antibody of claim 1 , thereby reducing the number of prostate cancer cells in the subject.

31. A kit for detecting an polynucleotide encoding PATE polypeptide in a sample, comprising an isolated nucleic acid sequence of at least ten nucleotides in length that specifically binds to SEQ JD NO:l or SEQ ED NO:3 under highly stringent hybridization conditions; and instructions for the use of the isolated nucleic acid sequence.

32. A kit for detecting a PATE polypeptide in a sample, comprising a container comprising the antibody of claim 1 ; and instructions for the use of the antibody.

33. A method for increasing the proliferation of a prostate cell, comprising contacting the prostate cell with a PATE polypeptide having an amino acid sequence selected from the group consisting of:

(1) an amino acid sequence 80% homologous to SEQ JD NO:2;

(2) a conservative variant of SEQ ID NO:2;

(3) an immunogenic fragment comprising eight consecutive amino acids of SEQ ID NO:2 that specifically binds to an antibody that specifically binds

SEQ ED NO:2; and

(4) SEQ ED NO:2, or transfecting the prostate cell with a nucleic acid encoding the PATE polypeptide, thereby increasing the proliferation of the prostate cell.

34. The method of claim 33, wherein the PATE polypeptide has an amino acid sequence 80% homologous to SEQ JD NO:2.

35. The method of claim 33, wherein the PATE polypeptide has an amino acid sequence that is a conservative variant of SEQ JD NO:2.

36. The method of claim 33, wherein the PATE polypeptide an immunogenic fragment of SEQ JD NO:2 that specifically binds an antibody that specifically binds SEQ ED NO: 1.

37. The method of claim 33, wherein the PATE polypeptide has an amino acid sequence as set forth as SEQ JD NO:2.

38. A nucleic acid sequence comprising SEQ ED NO:4, or a conservative variant thereof.

39. A vector comprising the nucleic acid sequence of claim 38.

40. The vector of claim 39, wherein the vector is a viral vector.

41. A host cell transfected with the vector of claim 39.

42. The host cell of claim 41, wherein the host cell is a mammalian cell.

43. The host cell of claim 42, wherein the host cell is a human cell.

44. The nucleic acid sequence of claim 38, operably linked to a heterologous nucleic acid.

45. The nucleic acid of claim 44, wherein the heterologous nucleic acid encodes a polypeptide.

46. The nucleic acid of claim 44, wherein the heterologous nucleic acid is an antisense molecule or a ribozyme.

47. A nucleic acid sequence consisting essentially of SEQ JD NO:4.