Nucleic acids and corresponding proteins entitled 83P2H3 and CaTrF2E11 useful in treatment and detection of cancer

FIELD OF THE INVENTION

[0002] The invention described herein relates to a novel gene and its encoded protein, termed 83P2H3, and to diagnostic and therapeutic methods and compositions useful in the management of various cancers that express 83P2H3.

BACKGROUND OF THE INVENTION

[0003] Cancer is the second leading cause of human death next to coronary disease. Worldwide, millions of people die from cancer every year. In the United States alone, as reported by the American Cancer Society, cancer causes the death of well over a half-million people annually, with over 1.2 million new cases diagnosed per year. While deaths from heart disease have been declining significantly, those resulting from cancer generally are on the rise. In the early part of the next century, cancer is predicted to become the leading cause of death.

[0004] Worldwide, several cancers stand out as the leading killers. In particular, carcinomas of the lung, prostate, breast, colon, pancreas, and ovary represent the primary causes of cancer death. These and virtually all other carcinomas share a common lethal feature. With very few exceptions, metastatic disease from a carcinoma is fatal. Moreover, even for those cancer patients who initially survive their primary cancers, common experience has shown that their lives are dramatically altered. Many cancer patients experience strong anxieties driven by the awareness of the potential for recurrence or treatment failure. Many cancer patients experience physical debilitations following treatment. Furthermore, many cancer patients experience a recurrence.

[0005] Worldwide, prostate cancer is the fourth most prevalent cancer in men. In North America and Northern Europe, it is by far the most common cancer in males and is the second leading cause of cancer death in men. In the United States alone, well over 30,000 men die annually of this disease—second only to lung cancer. Despite the magnitude of these figures, there is still no effective treatment for metastatic prostate cancer. Surgical prostatectomy, radiation therapy, hormone ablation therapy, surgical castration and chemotherapy continue to be the main treatment modalities. Unfortunately, these treatments are ineffective for many and are often associated with undesirable consequences.

[0006] On the diagnostic front, the lack of a prostate tumor marker that can accurately detect early-stage, localized tumors remains a significant limitation in the diagnosis and management of this disease. Although the serum prostate specific antigen (PSA) assay has been a very useful tool, however its specificity and general utility is widely regarded as lacking in several important respects.

[0007] Progress in identifying additional specific markers for prostate cancer has been improved by the generation of prostate cancer xenografts that can recapitulate different stages of the disease in mice. The LAPC (Los Angeles Prostate Cancer) xenografts are prostate cancer xenografts that have survived passage in severe combined immune deficient (SCID) mice and have exhibited the capacity to mimic the transition from androgen dependence to androgen independence (Klein et al., 1997, Nat. Med. 3:402). More recently identified prostate cancer markers include PCTA-1 (Su et al., 1996, Proc. Natl. Acad. Sci. USA 93: 7252), prostate-specific membrane (PSM) antigen (Pinto et al., Clin Cancer Res Sep. 2, 1996 (9): 1445-51), STEAP (Hubert, et al., Proc Natl Acad Sci U.S.A. Dec. 7, 1999; 96(25): 14523-8) and prostate stem cell antigen (PSCA) (Reiter et al., 1998, Proc. Natl. Acad. Sci. USA 95: 1735).

[0008] While previously identified markers such as PSA, PSM, PCTA and PSCA have facilitated efforts to diagnose and treat prostate cancer, there is need for the identification of additional markers and therapeutic targets for prostate and related cancers in order to further improve diagnosis and therapy.

[0009] Renal cell carcinoma (RCC) accounts for approximately 3 percent of adult malignancies. Once adenomas reach a diameter of 2 to 3 cm, malignant potential exists. In the adult, the two principal malignant renal tumors are renal cell adenocarcinoma and transitional cell carcinoma of the renal pelvis or ureter. The incidence of renal cell adenocarcinoma is estimated at more than 29,000 cases in the United States, and more than 11,600 patients died of this disease in 1998. Transitional cell carcinoma is less frequent, with an incidence of approximately 500 cases per year in the United States.

[0010] Surgery has been the primary therapy for renal cell adenocarcinoma for many decades. Until recently, metastatic disease has been refractory to any systemic therapy. With recent developments in systemic therapies, particularly immunotherapies, metastatic renal cell carcinoma may be approached aggressively in appropriate patients with a possibility of durable responses. Nevertheless, there is a remaining need for effective therapies for these patients.

[0011] Of all new cases of cancer in the United States, bladder cancer represents approximately 5 percent in men (fifth most common neoplasm) and 3 percent in women (eighth most common neoplasm). The incidence is increasing slowly, concurrent with an increasing older population. In 1998, there was an estimated 54,500 cases, including 39,500 in men and 15,000 in women. The age-adjusted incidence in the United States is 32 per 100,000 for men and 8 per 100,000 in women. The historic male/female ratio of 3:1 may be decreasing related to smoking patterns in women. There were an estimated 11,000 deaths from bladder cancer in 1998 (7,800 in men and 3,900 in women). Bladder cancer incidence and mortality strongly increase with age and will be an increasing problem as the population becomes more elderly.

[0012] Most bladder cancers recur in the bladder. Bladder cancer is managed with a combination of transurethral resection of the bladder (TUR) and intravesical chemotherapy or immunotherapy. The multifocal and recurrent nature of bladder cancer points out the limitations of TUR. Most muscle-invasive cancers are not cured by TUR alone. Radical cystectomy and urinary diversion is the most effective means to eliminate the cancer but carry an undeniable impact on urinary and sexual function. There continues to be a significant need for treatment modalities that are beneficial for bladder cancer patients.

[0013] An estimated 130,200 cases of colorectal cancer occurred in 2000 in the United States, including 93,800 cases of colon cancer and 36,400 of rectal cancer. Colorectal cancers are the third most common cancers in men and women. Incidence rates declined significantly during 1992-1996 (−2.1% per year). Research suggests that these declines have been due to increased screening and polyp removal, preventing progression of polyps to invasive cancers. There were an estimated 56,300 deaths (47,700 from colon cancer, 8,600 from rectal cancer) in 2000, accounting for about 11% of all U.S. cancer deaths.

[0014] At present, surgery is the most common form of therapy for colorectal cancer, and for cancers that have not spread, it is frequently curative. Chemotherapy, or chemotherapy plus radiation is given before or after surgery to most patients whose cancer has deeply perforated the bowel wall or has spread to the lymph nodes. A permanent colostomy (creation of an abdominal opening for elimination of body wastes) is occasionally needed for colon cancer and is infrequently required for rectal cancer. There continues to be a need for effective diagnostic and treatment modalities for colorectal cancer.

[0015] There were an estimated 164,100 new cases of lung and bronchial cancer in 2000, accounting for 14% of all U.S. cancer diagnoses. The incidence rate of lung and bronchial cancer is declining significantly in men, from a high of 86.5 per 100,000 in 1984 to 70.0 in 1996. In the 1990s, the rate of increase among women began to slow. In 1996, the incidence rate in women was 42.3 per 100,000.

[0016] Lung and bronchial cancer caused an estimated 156,900 deaths in 2000, accounting for 28% of all cancer deaths. During 1992-1996, mortality from lung cancer declined significantly among men (−1.7% per year) while rates for women were still significantly increasing (0.9% per year). Since 1987, more women have died each year of lung cancer than breast cancer, which, for over 40 years, was the major cause of cancer death in women. Decreasing lung cancer incidence and mortality rates most likely resulted from decreased smoking rates over the previous 30 years; however, decreasing smoking patterns among women lag behind those of men. Of concern, although the declines in adult tobacco use have slowed, tobacco use in youth is increasing again.

[0017] Treatment options for lung and bronchial cancer are determined by the type and stage of the cancer and include surgery, radiation therapy, and chemotherapy. For many localized cancers, surgery is usually the treatment of choice. Because the disease has usually spread by the time it is discovered, radiation therapy and chemotherapy are often needed in combination with surgery. Chemotherapy alone or combined with radiation is the treatment of choice for small cell lung cancer; on this regimen, a large percentage of patients experience remission, which in some cases is long lasting. There is however, an ongoing need for effective treatment and diagnostic approaches for lunch and bronchial cancers.

[0018] An estimated 182,800 new invasive cases of breast cancer were expected to occur among women in the United States during 2000. Additionally, about 1,400 new cases of breast cancer were expected to be diagnosed in men in 2000. After increasing about 4% per year in the 1980s, breast cancer incidence rates in women have leveled off in the 1990s to about 110.6 cases per 100,000.

[0019] In the U.S. alone, there were an estimated 41,200 deaths (40,800 women, 400 men) in 2000 due to breast cancer. Breast cancer ranks second among cancer deaths in women. According to the most recent data, mortality rates declined significantly during 1992-1996 with the largest decreases in younger women, both white and black. These decreases were probably the result of earlier detection and improved treatment.

[0020] Taking into account the medical circumstances and the patient's preferences, treatment of breast cancer may involve lumpectomy (local removal of the tumor) and removal of the lymph nodes under the arm; mastectomy (surgical removal of the breast) and removal of the lymph nodes under the arm; radiation therapy; chemotherapy; or hormone therapy. Often, two or more methods are used in combination. Numerous studies have shown that, for early stage disease, long-term survival rates after lumpectomy plus radiotherapy are similar to survival rates after modified radical mastectomy. Significant advances in reconstruction techniques provide several options for breast reconstruction after mastectomy. Recently, such reconstruction has been done at the same time as the mastectomy.

[0021] Local excision of ductal carcinoma in situ (DCIS) with adequate amounts of surrounding normal breast tissue may prevent the local recurrence of the DCIS. Radiation to the breast and/or tamoxifen may reduce the chance of DCIS occurring in the remaining breast tissue. This is important because DCIS, if left untreated, may develop into invasive breast cancer. Nevertheless, there are serious side effects or sequelae to these treatments. There is, therefore, a need for efficacious breast cancer treatments.

[0022] There were an estimated 23,100 new cases of ovarian cancer in the United States in 2000. It accounts for 4% of all cancers among women and ranks second among gynecologic cancers. During 1992-1996, ovarian cancer incidence rates were significantly declining. Consequent to ovarian cancer, there were an estimated 14,000 deaths in 2000. Ovarian cancer causes more deaths than any other cancer of the female reproductive system.

[0023] Surgery, radiation therapy, and chemotherapy are treatment options for ovarian cancer. Surgery usually includes the removal of one or both ovaries, the fallopian tubes (salpingo-oophorectomy), and the uterus (hysterectomy). In some very early tumors, only the involved ovary will be removed, especially in young women who wish to have children. In advanced disease, an attempt is made to remove all intra-abdominal disease to enhance the effect of chemotherapy. There continues to be an important need for effective treatment options for ovarian cancer.

[0024] There were an estimated 28,300 new cases of pancreatic cancer in the United States in 2000. Over the past 20 years, rates of pancreatic cancer have declined in men. Rates among women have remained approximately constant but may be beginning to decline. Pancreatic cancer caused an estimated 28,200 deaths in 2000 in the United States. Over the past 20 years, there has been a slight but significant decrease in mortality rates among men (about −0.9% per year) while rates have increased slightly among women.

[0025] Surgery, radiation therapy, and chemotherapy are treatment options for pancreatic cancer. These treatment options can extend survival and/or relieve symptoms in many patients but are not likely to produce a cure for most. There is a significant need for additional therapeutic and diagnostic options for pancreatic cancer.

SUMMARY OF THE INVENTION

[0026] The present invention relates to a novel gene, designated 83P2H3, that is over-expressed in multiple cancers listed in Table I. Northern blot expression analysis of 83P2H3 gene expression in normal tissues shows a restricted expression pattern in adult tissues. The nucleotide (FIG. 2) and amino acid (FIG. 2, and FIG. 3) sequences of 83P2H3 are provided. The tissue-related profile of 83P2H3 in normal adult tissues, combined with the over-expression observed in prostate and other tumors, shows that 83P2H3 is aberrantly over-expressed in at least some cancers, and thus serves as a useful diagnostic and/or therapeutic target for cancers of tissues such as prostate.

[0027] The invention provides polynucleotides corresponding or complementary to all or part of the 83P2H3 genes, mRNAs, and/or coding sequences, preferably in isolated form, including polynucleotides encoding 83P2H3-related proteins and fragments of 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more than 25 contiguous amino acids; at least 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 85, 90, 95, 100 or more than 100 contiguous amino acids of a 83P2H3-related protein, as well as the peptides/proteins themselves; DNA, RNA, DNA/RNA hybrids, and related molecules, polynucleotides or oligonucleotides complementary or having at least a 90% homology to the 83P2H3 genes or mRNA sequences or parts thereof, and polynucleotides or oligonucleotides that hybridize to the 83P2H3 genes, mRNAs, or to 83P2H3-encoding polynucleotides. Also provided are means for isolating cDNAs and the genes encoding 83P2H3. Recombinant DNA molecules containing 83P2H3 polynucleotides, cells transformed or transduced with such molecules, and host-vector systems for the expression of 83P2H3 gene products are also provided. The invention further provides antibodies that bind to 83P2H3 proteins and polypeptide fragments thereof, including polyclonal and monoclonal antibodies, murine and other mammalian antibodies, chimeric antibodies, humanized and fully human antibodies, and antibodies labeled with a detectable marker.

[0028] The invention further provides methods for detecting the presence and status of 83P2H3 polynucleotides, and proteins in various biological samples, as well as methods for identifying cells that express 83P2H.3. A typical embodiment of this invention provides methods for monitoring 83P2H3 gene products in a tissue or hematology sample having or suspected of having some form of growth dysregulation such as cancer.

[0029] The invention further provides various immunogenic or therapeutic compositions and strategies for treating cancers that express 83P2H3 such as prostate cancers, including therapies aimed at inhibiting the transcription, translation, processing or function of 83P2H3 as well as cancer vaccines.

BRIEF DESCRIPTION OF THE FIGURES

[0030]
FIG. 1A. 83P2H3 SSH sequence. The 83P2H3 SSH sequence contains 405 bp (SEQ ID NO: 701).

[0031]
FIG. 1B. CaTrF2E11 nucleic acid sequence (SEQ ID NO: 704) and amino acid sequence (SEQ ID NO: 705).

[0032]
FIG. 2A-B. The cDNA (SEQ ID NO:702) and amino acid sequence (SEQ ID NO:703) of 83P2H3.

[0033]
FIG. 2C-D. The cDNA (SEQ ID NO:706) and amino acid sequence (SEQ ID NO:707) of CaTrF2E11.

[0034]
FIG. 3A. Amino acid sequence of 83P2H3 (SEQ ID NO:703). The 83P2H3 protein has 725 amino acids with calculated molecular weight of 83.2 kDa, and pI of 7.56. 83P2H3 is predicted to be a cell surface protein that functions as an ion transporter.

[0035]
FIG. 3B. Amino acid sequence of CaTrF2E11 (SEQ ID NO:707).

[0036]
FIG. 4A-E. 83P2H3 BLAST alignment with Homo sapiens gene for CaT-like B protein, Genbank accession HSA243501. The sequences are 99% identical.

[0037]
FIG. 5A-B. Northern blot analysis of 83P2H3 expression in various normal human tissues. Two multiple tissue northern blots (Clontech) were probed with the 83P2H3 SSH fragment. Size standards in kilobases (kb) are indicated on the side. Each lane contains 2 μg of mRNA. The results show the expression of 83P2H3 in prostate, and, to a lesser extent, in placenta and pancreas. Lanes in FIG. 5A represent the following tissues: 1) heart; 2) brain; 3) placenta; 4) lung; 5) liver; 6) skeletal muscle; 7) kidney; 8) pancreas. Lanes in FIG. 5B represent the following tissues: 1) spleen; 2) thymus; 3) prostate; 4) testis; 5) ovary; 6) small intestine; 7) colon; 8) leukocytes.

[0038]
FIG. 6. Northern blot analysis of 83P2H3 expression in prostate cancer cell lines and xenografts. RNA was extracted from the LAPC xenografts and prostate cancer cell lines. Northern blots with 10 μg of total RNA per lane were probed with the 83P2H3 SSH fragment. Size standards in kilobases (kb,) are indicated on the side. Lanes represent: 1) PrEC; 2) LAPC-4 AD; 3) LAPC-4 AI; 4) LAPC-9 AD; 5) LAPC-9 AI; 6) LNCaP; 7) PC-3; 8) DU145; 9) TsuPr1; 10) LAPC-4 CL.

[0039]
FIG. 7. Expression of 83P2H3 in prostate cancer patient samples. RNA was extracted from prostate tumors and normal adjacent tissue derived from prostate cancer patients. Northern blots with 10 μg of total RNA per lane were probed with the 83P2H3 SSH fragment. Size standards in kilobases (kb) are indicated on the side. Lanes represent: 1) Patient 1, normal adjacent tissue; 2) Patient 1, Gleason 9 tumor; 3) Patient 2, normal adjacent tissue; 4) Patient 2, Gleason 7 tumor.

[0040]
FIG. 8A-C. RT-PCR Expression of CaTrF2E11 in Normal Tissues and in Bladder and Kidney Cancer. First strand cDNA was prepared from normal tissues, and from bladder cancer pool and kidney cancer pool. Normalization was performed by PCR using primers to actin and GAPDH. Semi-quantitative PCR, using primers to CaTrF2E11, was performed at 30 cycles of amplification. Expression of CaTrF2E11 is observed in normal kidney and prostate, and in bladder cancer pool and kidney cancer pool. Lanes represent: 1) Colon; 2) Ovaries; 3) Leukocytes; 4) Prostate; 5) Small Intestine; 6) Spleen; 7) Testis; 8) Thymus; 9) Brain; 10) Heart; 11) Kidney; 12) Liver; 13) Lung; 14) Pancreas; 15) Placenta; 16) Skeletal muscle; 17) Prostate; 18) Bladder Cancer Pool; 19) Kidney Cancer Pool.

[0041]
FIG. 9. Expression of CaTrF2E11 by RT-PCR. First strand cDNA was prepared from vital pool 1 (VP1: liver, lung and kidney), vital pool 2 (VP2, pancreas, colon and stomach), bladder cancer pool, kidney cancer pool, and lung cancer pool. Normalization was performed by PCR using primers to actin and GAPDH. Semi-quantitative PCR, using primers to CaTrF2E11, was performed at 30 cycles of amplification. Expression of CaTrF2E11 is observed in bladder cancer pool, kidney cancer pool, lung cancer pool and VP1. Lower level expression is also detected in ovarian cancer pool and VP2. Lane 1, Vital Pool 1; Lane 2, Vital Pool 2; Lane 3, Bladder Cancer Pool; Lane 4, Kidney Cancer Pool; Lane 5, Lung Cancer Pool; Lane 6, Ovarian Cancer Pool.

[0042]
FIG. 10A-B. Expression of CaTrF2E11 in normal human tissues. Two multiple tissue northern blots, with 2 μg of mRNA/lane, were probed with the CaTrF2E11 fragment. Size standards in kilobases (kb) are indicated on the side. The results show expression of CaTrF2E11 in kidney and to lower levels in placenta and prostate. Lanes in FIG. 10A represent: 1) Heart; 2) Brain; 3) Placenta; 4) Lung; 5) Liver; 6) Skeletal Muscle; 7) Kidney; 8) Pancreas. Lanes in FIG. 10B represent: 1) Spleen; 2) Thymus; 3) Prostate; 4) Testis; 5) Ovary; 6) Small Intestine; 7) Colon; 8) Leukocytes.

[0043]
FIG. 11. Expression of CaTrF2E11 in lung cancer patient specimens. RNA was extracted from lung cancer cell lines (CL), lung tumors (T), and their normal adjacent tissues (NAT) isolated from lung cancer patients. Northern blots with 10 μg of total RNA/lane were probed with the CaTrF2E11 fragment. Size standards in kilobases (kb) are indicated on the side. The results show expression of CaTrF2E11 in 1 of 3 lung cancer cell lines and in 2 lung tumors. The expression detected in one NAT(isolated from diseased tissues) but not in normal tissue, isolated from healthy donors, may indicate that this tissue is not fully normal and that CaTrF2E11 may be expressed in early stage tumors. Pt.1, Squamous carcinoma, stage IB; Pt.2, Squamous carcinoma, stage IIB. Cell lines listed in order: CALU-1, A427, NCI-H82.

[0044]
FIG. 12. Expression of 83P2H3 in human tumors by RT-PCR. First strand cDNA was prepared from a vital pool 1 (VP1: liver, lung and kidney), a vital pool 2 (VP2: pancreas, colon and stomach), a LAPC xenograft pool (LAPC-4AD, LAPC-4AI, LAPC-9AD and LAPC-9AI), a prostate cancer pool, and a metastatic cancer pool. The metastatic cancer pool consisted of metastatic tissues from cancers of the following organs: breast, ovarian, pancreas, colon, prostate and bladder. Normalization was performed by PCR using primers to actin and GAPDH. Semi-quantitative PCR, using primers to 83p2H3, was performed at 30 cycles of amplification. Results show expression of 83P2H3 in VP2, xenograft pool, prostate cancer pool and metastatic cancer pool. Lane 1 is VP1; lane 2 is VP2; lane 3 is xenograft pool; lane 4 is prostate cancer pool; lane 5 is metastasis pool; lane 6 is water.

[0045]
FIG. 13A-B. Two Projected Models for 83P2H3 PCaT. 83P2H3 may be expressed at the cell surface in either of two configurations, namely containing five or six transmembrane domains. Both configurations show the amino terminal end to be intracellular. The six transmembrane model predicts the C-terminus to be intracellular, while the five transmembrane model predicts the C-terminus to be extracellular. The models exhibit an ion channel signature, predicted pore structure and ankyrin repeats (ANK).

[0046]
FIG. 14A. Hydrophilicity amino acid profile of 83P2H3 determined by computer algorithm sequence analysis using the method of Hopp and Woods (Hopp T. P., Woods K. R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828) accessed on the Protscale website (www.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

[0047]
FIG. 14B. Hydrophilicity amino acid profile of CaTrF2E11 determined by computer algorithm sequence analysis using the method of Hopp and Woods (Hopp T. P., Woods K. R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828) accessed on the Protscale website (www.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

[0048]
FIG. 15A. Hydropathicity amino acid profile of 83P2H3 determined by computer algorithm sequence analysis using the method of Kyte and Doolittle (Kyte J., Doolittle R. F., 1982. J. Mol. Biol. 157:105-132) accessed on the ProtScale website (www.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

[0049]
FIG. 15B. Hydropathicity amino acid profile of CaTrF2E11 determined by computer algorithm sequence analysis using the method of Kyte and Doolittle (Kyte J., Doolittle R. F., 1982. J. Mol. Biol. 157:105-132) accessed on the ProtScale website (www.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

[0050]
FIG. 16A. Percent accessible residues amino acid profile of 83P2H3 determined by computer algorithm sequence analysis using the method of Janin (Janin J., 1979 Nature 277:491-492) accessed on the ProtScale website (www.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

[0051]
FIG. 16B. Percent accessible residues amino acid profile of CaTrF2E11 determined by computer algorithm sequence analysis using the method of Janin (Janin J., 1979 Nature 277:491-492) accessed on the ProtScale website (www.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

[0052]
FIG. 17A. Average flexibility amino acid profile of 83P2H3 determined by computer algorithm sequence analysis using the method of Bhaskaran and Ponnuswamy (Bhaskaran R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res. 32:242-255) accessed on the ProtScale website (www.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

[0053]
FIG. 17B. Average flexibility amino acid profile of CaTrF2E11 determined by computer algorithm sequence analysis using the method of Bhaskaran and Ponnuswamy (Bhaskaran R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res. 32:242-255) accessed on the ProtScale website (www.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

[0054]
FIG. 18A. Beta-turn amino acid profile of 83P2H3 determined by computer algorithm sequence analysis using the method of Deleage and Roux (Deleage, G., Roux B. 1987 Protein Engineering 1:289-294) accessed on the ProtScale website (www.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

[0055]
FIG. 18B. Beta-turn amino acid profile of CaTrF2E11 determined by computer algorithm sequence analysis using the method of Deleage and Roux (Deleage, G., Roux B. 1987 Protein Engineering 1:289-294) accessed on the ProtScale website (www.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server.

[0056]
FIG. 19A-F. Plasma membrane staining of 83P2H3 by C-terminal-directed antibodies. Panels A-C: Rabbit and mouse polyclonal antibodies specific for C-terminal amino acids 615-725 of 83P2H3 protein and an anti-HIS tag polyclonal antibody (Santa Cruz Biotechnology, Inc., Santa Cruz, Calif.) were used to stain 293T cells transfected with either empty vector, or with a pcDNA 3.1 83P2H3 expression vector that contains a terminal HIS tag. Staining was detected by incubation with species specific FITC-conjugated secondary antibodies and analysis on a Coulter Epics XL flow cytometer. The respective fluorescent profiles of the two populations are indicated with arrows. Panels D-E: 293T-83P2H3 HIS tagged cells were stained with anti-HIS polyclonal antibody and FITC-conjugated secondary antibody and examined by bright field and fluorescent microscopy. A representative stained cell is shown. Panel F: Immunohistochemical analysis of 83P2H3 expression in 293T cells. Parrafin embedded 293T-83P2H3 cells were sectioned, mounted and stained with anti-83P2H3 rabbit polyclonal antibody (5 μg/ml). Staining was visualized by incubation with biotinylated anti-rabbit IgG secondary antibody, followed by avidin-conjugated HRP then developed with diaminobenzidine substrate. Arrows mark areas indicative of plasma membrane staining.

[0057]
FIG. 20A-F. Recognition of 83P2H3 in 293T cells by anti-83P2H3 mouse polyclonal antibodies and hybridoma supernatants. Panels A-C: 293T cells transfected with either empty vector or with a pCDNA 3.1 83P2H3 expression vector that contains a carboxyl-terminal HIS tag. Cells were stained with a mouse polyclonal antibody from mice immunized with a GST-83P2H3 cleavage product that encodes amino acids 615-725 (20A) and with supernatants of two hybridomas (#4 (20B) and #8A (20C)) that were generated by fusion of myeloma cells with spleen cells of similarly immunized mice. Staining was detected by incubation with anti-mouse FITC-conjugated secondary antibody and analysis on a Coulter Epics XL flow cytometer. The respective fluorescent profiles of the two populations are indicated with arrows. Panels D-F: The mouse polyclonal antibody (20D) and anti-83P2H3 hybridoma supernatants (20E-F) were also analyzed by Western blotting on 83P2H3 and vector transfected 293T cells. Cell lysates were separated by SDS-PAGE, transferred to nitrocellulose, blocked, and incubated with a 1:200 dilution of the mouse polyclonal antibody and hybridoma supernatants. Anti-83P2H3 immunoreactive bands were detected by incubation with anti-mouse IgG HRP-conjugated secondary antibody and visualized by enhanced chemiluninescence and exposure to autoradiography film. Indicated with an arrow is a band representing full length 83P2H3 and with brackets aggregates and degradation products 83P2H3.

[0058]
FIG. 21A-B. Expression of hCaT in prostate cancer cells and fibroblasts induces the phosphorylation of ERK MAPK in these cell lines. Several mitogenic stimuli associated with cell growth and proliferation, have been shown to induce ERK activation (Price D T et al. J Urol. 1999, 162:1537-42.). Control and 83P2H3/hCaT-expressing PC3 (FIG. 21A) and NIH 3T3 (FIG. 21B) cell lines were compared for their ability to induce ERK phosphorylation. Cells were grown in low (0.1-0.5%) concentrations of FBS and either left untreated or stimulated with 10% FBS for 5 min. Whole cell lysates were separated by SDS-PAGE and analyzed by Western blotting using an anti-phospho-ERK monoclonal antibody (New England Nuclear, Bedford, Mass.). Anti-ERK overlays were used to evaluate protein loading. The data showed that expression of hCaT alone is sufficient to induce ERK phosphorylation in PC3 and NIH 3T3 cells. ERK phosphorylation was further enhanced by FBS. These results indicate that hCaT mediates ERK activation and mitogenic signaling in PC3 and NIH 3T3 cells.

[0059]
FIG. 22. Mediation of ERK phosphorylation by hCaT via a variety of ion channel activators. Control and 83P2H3/hCaT-expressing PC3 cell were compared for their ability to induce ERK phosphorylation in response to ion channel activators known to regulate intracellular calcium levels in several cell types. PC3 cells, stably transduced with pSR alpha neo or 83P2H3/hCaT were grown in 0.1% FBS and treated with 10% FBS, cAMP, forskolin, PMA, ionomycin or LPA for 5 min. Whole cell lysates were separated by SDS-PAGE and analyzed by Western blotting using an anti-phospho-ERK monoclonal antibody (New England Nuclear, Bedford, Mass.). Anti-ERK overlays were used to evaluate protein loading. Treatment with each of 10% FBS, cAMP, ionomycin, PMA and LPA induced ERK phosphorylation in hCaT-expressing PC3 cells. In contrast, only PMA induced ERK phosphorylation in PC3-neo cells.

[0060]
FIG. 23. Alteration of tyrosine phosphorylation by hCaT in NIH 3T3 cells. Control and 83P2H3/hCaT-expressing NIH 3T3 cell lines were compared for their ability to alter the phosphorylation state of tyrosine-phosphorylated proteins. Cells were grown in 0.1% FBS and either left untreated or stimulated with 10% FBS for 5 min. Whole cell lysates were separated by SDS-PAGE and analyzed by Western blotting using an anti-phosphotyrosine monoclonal antibody. The data showed that expression of hCaT alone is sufficient to induce phosphorylation of p180 and p132 in NIH 3T3 cells. In addition, expression of hCaT induced the loss of tyrosine phosphorylation of p75-p82 in the same cell type. These results indicate that hCaT regulates the tyrosine phosphorylation state of several proteins in NIH 3T3 cells, and thereby controls downstream signaling pathways that may be critical for tumor growth and survival.

[0061]
FIG. 24. Expression of hCaT induces the proliferation of NIH 3T3 cells. Due to the importance of calcium transporters in cell growth, we investigated the effect of 83P2H3/hCaT on proliferation. Control and 83P2H3/hCaT-expressing NIH 3T3 cell lines were grown in 0.1% FBS and either left untreated or stimulated with 10% FBS for 24 hours. Proliferation was measured in triplicate. NIH 3T3 cells expressing constitutively active Ras were used as a positive control. The data show that expression of hCaT induced a 3-fold increase in the proliferation of NIH 3T3 grown in the presence of FBS. This increase in cell growth was comparable to the effect of the strong oncogene Ras.

[0062]
FIG. 25A-C. Induction of calcium flux in prostate cancer cells by hCaT. The prostate cancer cell line PC3 was transduced with pSRalpha retrovirus carrying either the neo cassette alone or 83P2H3/hCaT. Stable PC3-neo and PC3-hCaT cells were examined for their ability to respond to extracellular stimuli by inducing calcium flux. PC3 cells were loaded with two calcium indicators, namely fura red and fluo4 (Molecular Probes, Eugene, Oreg.) and analyzed by flow cytometry in the absence and presence of exogenous calcium. The data indicated that, while PC3-neo showed little responsiveness to calcium, exogenous calcium induced a calcium flux in PC3-CaT cells. Similar results were obtained in two separate experiments. These data indicates that 83P2H3/hCaT functions as a calcium transporter in PC3 cells.

[0063]
FIG. 26. Expression of hCaT induces the phosphorylation of calmodulin kinase. The transport of ions across membranes is regulated by calmodulin and calmodulin kinases (CaMK). Since the phosphorylation of CamK reflects its activation, the effect of hCaT on the phosphorylation of CaMK was investigated. Control and 83P2H3-expressing PC3 cell lines were compared for their ability to alter the phosphorylation state of CaMKII. Cells were grown in 0.1% FBS and either left untreated or stimulated with 10% FBS, ionomycin or calcium. Whole cell lysates were separated by SDS-PAGE and analyzed by Western blotting using an anti-phospho-CaMKII antibody. The results indicate that expression of hCaT was sufficient to enhance the phosphorylation and activation of CaMKII in PC3 cells.

[0064]
FIG. 27A-F. Cell surface expression of hCaT by C-terminal-specific antibodies. 293T cells were transfected with an expression vector encoding 83P2H3 HIS-tagged (PCDNA 3.1 MYC/HIS, Invitrogen), and the cell surface localization was determined by immunofluorescence. FIG. 27A shows detection of 293T cells carrying empty vector or hCaT using a GST-fusion polyclonal antibody. FIG. 27B shows detection of 293T cells carrying empty vector or hCaT using an antibody directed against His to identify the C-terminus. FIG. 27C-D show a PC3-CaT cell detected by immunofluorescence using a GST-fusion polyclonal antibody, or phase contrast microscopy, respectively. FIG. 27E-F show a 293T cell detected by phase contrast microscopy, or immunofluorescence using an antibody directed against His to identify the C-terminus, respectively.

[0065]
FIG. 28. Expression of CaTrF2E11 in human patient cancer specimens. RNA was extracted from a pool of 3 bladder cancer tumors, kidney cancer tumors and lung cancer tumors derived from cancer patients, and from normal prostate (NP), bladder (NB), kidney (NK) and colon (NC). Northern blots with 10 μg of total RNA/lane were probed with the CaTrF2E11 fragment. Size standards in kilobases (kb) are indicated on the side. The results show expression of CaTrF2E11 in bladder cancer pool, kidney cancer pool, lung cancer pool, but not in the normal tissues. Bladder Cancer Pool=grade 2, 3; Kidney Cancer Pool=grade 2, 2, 3; Lung Cancer Pool=SQ.IA, SQ.IIIA, LCC; NP=Normal Prostate; NB=Normal Bladder; NK=Normal Kidney; NC=Normal Colon.

[0066]
FIG. 29. Expression of CaTrF2E11 in bladder cancer patient specimens. RNA was extracted from the bladder cancer cell line SCaBER (CL), normal bladder (Nb), bladder tumors (T) and their matched normal adjacent tissue (N) isolated from bladder cancer patients. Northern blots with 10 μg of total RNA/lane were probed with the CaTrF2E11 fragment. Size standards in kilobases (kb) are indicated on the side. The results show expression of CaTrF2E11 in the bladder cancer cell line, and in the bladder cancer tissues. The expression detected in normal adjacent tissue (isolated from diseased tissues) but not in normal tissue, isolated from healthy donors, may indicate that this tissue is not fully normal and that CaTrF2E11 may be expressed in early stage tumors. P1—Transitional, grade 2; P2—Transitional, grade 2; P3—Transitional, grade 2; P4—Transitional; CL=Bladder cancer cell line SCABER; P=Patient; Nb=Normal Bladder; N=Normal adjacent tissue; T=Tumor.

[0067]
FIG. 30. Expression of CaTrF2E11 in kidney cancer patient specimens. RNA was extracted from kidney cancer cell lines (CL), kidney tumors (T) and their matched normal adjacent tissue (N) isolated from kidney cancer patients. Northern blots with 10 μg of total RNA/lane were probed with the CaTrF2E11 fragment. Size standards in kilobases (kb) are indicated on the side. The results show expression of CaTrF2E11 in 2 of 3 kidney cancer cell lines, and in both normal and kidney tumor tissues. CL=cell lines listed in order: 769-P, A498, Caki-1; NAT=Normal adjacent tissue; T=Tumor Pt. 1, Papillary carcinoma, grade 2; Pt.2, Clear cell type, grade 2; Pt.3, Clear cell type, grade 2; Pt.4, Clear cell type, grade 2; Pt.5, Clear cell type, grade 3; Pt.6, Clear cell type, grade

[0068]
FIG. 31A-C. Overexpression of 83P2H3 in an engineered cell line. PC3 human prostate cancer cells were engineered to overexpress 83P2H3 by retroviral transduction of the 83P2H3 cDNA. Panel A: Northern blot analysis of 83P2H3 expression in PC3 or PC3-83P2H3 stably transduced cells. Arrow indicates the retroviral transcript encoding the 83P2H3 cDNA. Panel B: Immunofluorescent analysis of 83P2H3 expression in PC3-83P2H3 cells using a rabbit polyclonal antibody directed to amino acids 615-725. Anti-83P2H3 staining of cells was detected following incubation with an FITC-conjugated anti-rabbit IgG secondary antibody. A representative stained cell is shown. Panel C: Phase contrast image of the cell depicted in Panel B.

DETAILED DESCRIPTION OF THE INVENTION

Outline of Sections

[0069] I.) Definitions

[0070] II.) 83P2H3 Polynucleotides

[0071] II.A.) Uses of 83P2H3 Polynucleotides

[0072] II.A.1.) Monitoring of Genetic Abnormalities

[0073] II.A.2.) Antisense Embodiments

[0074] II.A.3.) Primers and Primer Pairs

[0075] II.A.4.) Isolation of 83P2H3-Encoding Nucleic Acid Molecules

[0076] II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector Systems

[0077] III.) 83P2H3-related Proteins

[0078] III.A.) Motif-bearing Protein Embodiments

[0079] III.B.) Expression of 83P2H3-related Proteins

[0080] III.C.) Modifications of 83P2H3-related Proteins

[0081] III.D.) Uses of 83P2H3-related Proteins

[0082] IV.) 83P2H3 Antibodies

[0083] V.) 83P2H3 Cellular Immune Responses

[0084] VI.) 83P2H3 Transgenic Animals

[0085] VII.) Methods for the Detection of 83P2H3

[0086] VIII.) Methods for Monitoring the Status of 83P2H3-related Genes and Their Products

[0087] IX.) Identification of Molecules That Interact With 83P2H3

[0088] X.) Therapeutic Methods and Compositions

[0089] X.A.) Anti-Cancer Vaccines

[0090] X.B.) 83P2H3 as a Target for Antibody-Based Therapy

[0091] X.C.) 83P2H3 as a Target for Cellular Immune Responses

[0092] X.C.1. Minigene Vaccines

[0093] X.C.2. Combinations of CTL Peptides with Helper Peptides

[0094] X.C.3. Combinations of CTL Peptides with T Cell Priming Agents

[0095] X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL and/or HTL Peptides

[0096] X.D.) Adoptive Immunotherapy

[0097] X.E.) Administration of Vaccines for Therapeutic or Prophylactic Purposes

[0098] XI.) Diagnostic and Prognostic Embodiments of 83P2H3.

[0099] XII.) Inhibition of 83P2H3 Protein Function

[0100] XII.A.) Inhibition of 83P2H3 With Intracellular Antibodies

[0101] XII.B.) Inhibition of 83P2H3 with Recombinant Proteins

[0102] XII.C.) Inhibition of 83P2H3 Transcription or Translation

[0103] XII.D.) General Considerations for Therapeutic Strategies

[0104] XIII.) KITS

[0105] I.) Definitions

[0106] Unless otherwise defined, all terms of art, notations and other scientific terms or terminology used herein are intended to have the meanings commonly understood by those of skill in the art to which this invention pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art. Many of the techniques and procedures described or referenced herein are well understood and commonly employed using conventional methodology by those skilled in the art, such as, for example, the widely utilized molecular cloning methodologies described in Sambrook et al., Molecular Cloning: A Laboratory Manual 2nd. edition (1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. As appropriate, procedures involving the use of commercially available kits and reagents are generally carried out in accordance with manufacturer defined protocols and/or parameters unless otherwise noted.

[0107] As used herein “83P2H3” and “PCaT” are synonyms. Moreover any reference to “83P2H3” or “PCaT also refer to the family member CaTrF2E11, unless the context clearly indicates otherwise to one of ordinary skill in the art.

[0108] The terms “advanced prostate cancer”, “locally advanced prostate cancer”, “advanced disease” and “locally advanced disease” mean prostate cancers that have extended through the prostate capsule, and are meant to include stage C disease under the American Urological Association (AUA) system, stage C1-C2 disease under the Whitmore-Jewett system, and stage T3-T4 and N+ disease under the TNM (tumor, node, metastasis) system. In general, surgery is not recommended for patients with locally advanced disease, and these patients have substantially less favorable outcomes compared to patients having clinically localized (organ-confined) prostate cancer. Locally advanced disease is clinically identified by palpable evidence of induration beyond the lateral border of the prostate, or asymmetry or induration above the prostate base. Locally advanced prostate cancer is presently diagnosed pathologically following radical prostatectomy if the tumor invades or penetrates the prostatic capsule, extends into the surgical margin, or invades the seminal vesicles.

[0109] “Altering the native glycosylation pattern” is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence 83P2H3 (either by removing the underlying glycosylation site or by deleting the glycosylation by chemical and/or enzymatic means), and/or adding one or more glycosylation sites that are not present in the native sequence 83P2H3. In addition, the phrase includes qualitative changes in the glycosylation of the native proteins, involving a change in the nature and proportions of the various carbohydrate moieties present.

[0110] The term “analog” refers to a molecule which is structurally similar or shares similar or corresponding attributes with another molecule (e.g. a 83P2H3-related protein). For example an analog of the 83P2H3 protein can be specifically bound by an antibody or T cell that specifically binds to 83P2H3.

[0111] The term “antibody” is used in the broadest sense. Therefore an “antibody” can be naturally occurring or man-made such as monoclonal antibodies produced by conventional hybridoma technology. Anti-83P2H3 antibodies comprise monoclonal and polyclonal antibodies as well as fragments containing the antigen-binding domain and/or one or more complementarity determining regions of these antibodies.

[0112] An “antibody fragment” is defined as at least a portion of the variable region of the immunoglobulin molecule that binds to its target, i.e., the antigen-binding region. In one embodiment it specifically covers single anti-83P2H3 antibodies and clones thereof (including agonist, antagonist and neutralizing antibodies) and anti-83P2H3 antibody compositions with polyepitopic specificity.

[0113] The term “codon optimized sequences” refers to nucleotide sequences that have been optimized for a particular host species by replacing any codons having a usage frequency of less than about 20%. Nucleotide sequences that have been optimized for expression in a given host species by elimination of spurious polyadenylation sequences, elimination of exon/intron splicing signals, elimination of transposon-like repeats and/or optimization of GC content in addition to codon optimization are referred to herein as an “expression enhanced sequences.”

[0114] The term “cytotoxic agent” refers to a substance that inhibits or prevents the function of cells and/or causes destruction of cells. The term is intended to include radioactive isotopes chemotherapeutic agents, and toxins such as small molecule toxins or enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof. Examples of cytotoxic agents include, but are not limited to maytansinoids, yttrium, bismuth, ricin, ricin A-chain, doxorubicin, daunorubicin, taxol, ethidium bromide, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, dihydroxy anthracin dione, actinomycin, diphtheria toxin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A chain, modeccin A chain, alpha-sarcin, gelonin, mitogellin, retstrictocin, phenomycin, enomycin, curicin, crotin, calicheamicin, sapaonaria officinalis inhibitor, and glucocorticoid and other chemotherapeutic agents, as well as radioisotopes such as At211, I131, I125, Y90, Re186, Re188, Sm153, Bi212, P32 and radioactive isotopes of Lu. Antibodies may also be conjugated to an anti-cancer pro-drug activating enzyme capable of converting the pro-drug to its active form.

[0115] The term “homolog” refers to a molecule which exhibits homology to another molecule, by for example, having sequences of chemical residues that are the same or similar at corresponding positions.

[0116] “Human Leukocyte Antigen” or “HLA” is a human class I or class II Major Histocompatibility Complex (MHC) protein (see, e.g., Stites, et al., IMMUNOLOGY, 8TH ED., Lange Publishing, Los Altos, Calif. (1994).

[0117] The terms “hybridize”, “hybridizing”, “hybridizes” and the like, used in the context of polynucleotides, are meant to refer to conventional hybridization conditions, preferably such as hybridization in 50% formamide/6×SSC/0.1% SDS/100 μg/ml ssDNA, in which temperatures for hybridization are above 37 degrees C. and temperatures for washing in 0.1×SSC/0.1% SDS are above 55 degrees C.

[0118] The phrases “isolated” or “biologically pure” refer to material which is substantially or essentially free from components which normally accompany the material as it is found in its native state. Thus, isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment. For example, a polynucleotide is said to be “isolated” when it is substantially separated from contaminant polynucleotides that correspond or are complementary to genes other than the 83P2H3 gene or that encode polypeptides other than 83P2H3 gene product or fragments thereof. A skilled artisan can readily employ nucleic acid isolation procedures to obtain an isolated 83P2H3 polynucleotide. A protein is said to be “isolated,” for example, when physical, mechanical or chemical methods are employed to remove the 83P2H3 protein from cellular constituents that are normally associated with the protein. A skilled artisan can readily employ standard purification methods to obtain an isolated 83P2H3 protein. Alternatively, an isolated protein can be prepared by chemical means.

[0119] The term “mammal” refers to any organism classified as a mammal, including mice, rats, rabbits, dogs, cats, cows, horses and humans. In one embodiment of the invention, the mammal is a mouse. In another embodiment of the invention, the mammal is a human.

[0120] The terms “metastatic prostate cancer” and “metastatic disease” mean prostate cancers that have spread to regional lymph nodes or to distant sites, and are meant to include stage D disease under the AUA system and stage T×N×M+ under the TNM system. As is the case with locally advanced prostate cancer, surgery is generally not indicated for patients with metastatic disease, and hormonal (androgen ablation) therapy is a preferred treatment modality. Patients with metastatic prostate cancer eventually develop an androgen-refractory state within 12 to 18 months of treatment initiation. Approximately half of these androgen-refractory patients die within 6 months after developing that status. The most common site for prostate cancer metastasis is bone. Prostate cancer bone metastases are often osteoblastic rather than osteolytic (i.e., resulting in net bone formation). Bone metastases are found most frequently in the spine, followed by the femur, pelvis, rib cage, skull and humerus. Other common sites for metastasis include lymph nodes, lung, liver and brain. Metastatic prostate cancer is typically diagnosed by open or laparoscopic pelvic lymphadenectomy, whole body radionuclide scans, skeletal radiography, and/or bone lesion biopsy.

[0121] The term “monoclonal antibody” refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the antibodies comprising the population are identical except for possible naturally occurring mutations that are present in minor amounts.

[0122] A “motif”, as in biological motif of an 83P2H3-related protein, refers to any pattern of amino acids forming part of the primary sequence of a protein, that is associated with a particular function (e.g. protein-protein interaction, protein-DNA interaction, etc) or modification (e.g. that is phosphorylated, glycosylated or amidated), or localization (e.g. secretory sequence, nuclear localization sequence, etc.) or a sequence that is correlated with being immunogenic, either humorally or cellularly. A motif can be either contiguous or capable of being aligned to certain positions that are generally correlated with a certain function or property. In the context of HLA motifs, “motif” refers to the pattern of residues in a peptide of defined length, usually a peptide of from about 8 to about 13 amino acids for a class I HLA motif and from about 6 to about 25 amino acids for a class II HLA motif, which is recognized by a particular HLA molecule. Peptide motifs for HLA binding are typically different for each protein encoded by each human HLA allele and differ in the pattern of the primary and secondary anchor residues.

[0123] A “pharmaceutical excipient” comprises a material such as an adjuvant, a carrier, pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservative, and the like.

[0124] “Pharmaceutically acceptable” refers to a non-toxic, inert, and/or composition that is physiologically compatible with humans or other mammals.

[0125] The term “polynucleotide” means a polymeric form of nucleotides of at least 10 bases or base pairs in length, either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide, and is meant to include single and double stranded forms of DNA and/or RNA. In the art, this term if often used interchangeably with “oligonucleotide”. A polynucleotide can comprise a nucleotide sequence disclosed herein wherein thymidine (T) (as shown for example in SEQ ID NO: 702) can also be uracil (U); this definition pertains to the differences between the chemical structures of DNA and RNA, in particular the observation that one of the four major bases in RNA is uracil (U) instead of thymidine (T).

[0126] The term “polypeptide” means a polymer of at least about 4, 5, 6, 7, or 8 amino acids. Throughout the specification, standard three letter or single letter designations for amino acids are used. In the art, this term is often used interchangeably with “peptide” or “protein”.

[0127] The term “prevent” or “protect against” a condition or disease means to hinder, reduce or delay the onset or progression of the condition or disease.

[0128] An HLA “primary anchor residue” is an amino acid at a specific position along a peptide sequence which is understood to provide a contact point between the immunogenic peptide and the HLA molecule. One to three, usually two, primary anchor residues within a peptide of defined length generally defines a “motif” for an immunogenic peptide. These residues are understood to fit in close contact with peptide binding groove of an HLA molecule, with their side chains buried in specific pockets of the binding groove. In one embodiment, for example, the primary anchor residues for an HLA class I molecule are located at position 2 (from the amino terminal position) and at the carboxyl terminal position of a 8, 9, 10, 11, or 12 residue peptide epitope in accordance with the invention. In another embodiment, for example, the primary anchor residues of a peptide that will bind an HLA class II molecule are spaced relative to each other, rather than to the termini of a peptide, where the peptide is generally of at least 9 amino acids in length. The primary anchor positions for each motif and supermotif are set forth in Table IV. For example, analog peptides can be created by altering the presence or absence of particular residues in the primary and/or secondary anchor positions shown in Table IV. Such analogs are used to modulate the binding affinity and/or population coverage of a peptide comprising a particular HLA motif or supermotif.

[0129] A “recombinant” DNA or RNA molecule is a DNA or RNA molecule that has been subjected to molecular manipulation in vitro.

[0130] “Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured nucleic acid sequences to reanneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature that can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology, Wiley Interscience Publishers, (1995).

[0131] “Stringent conditions” or “high stringency conditions”, as defined herein, are identified by, but not limited to, those that: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50° C.; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42° C.; or (3) employ 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 MM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5×Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2×SSC (sodium chloride/sodium, citrate) and 50% formamide at 55° C., followed by a high-stringency wash consisting of 0.1×SSC containing EDTA at 55° C. “Moderately stringent conditions” are described by, but not limited to, those in Sambrook et al., Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Press, 1989, and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and % SDS) less stringent than those described above. An example of moderately stringent conditions is overnight incubation at 37° C. in a solution comprising: 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 mg/mL denatured sheared salmon sperm DNA, followed by washing the filters in 1×SSC at about 37-50° C. The skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.

[0132] An HLA “supermotif” is a peptide binding specificity shared by HLA molecules encoded by two or more HLA alleles.

[0133] A “transgenic animal” (e.g., a mouse or rat) is an animal having cells that contain a transgene, which transgene was introduced into the animal or an ancestor of the animal at a prenatal, e.g., an embryonic stage. A “transgene” is a DNA that is integrated into the genome of a cell from which a transgenic animal develops.

[0134] As used herein, an HLA or cellular immune response “vaccine” is a composition that contains or encodes one or more peptides of the invention. There are numerous embodiments of such vaccines, such as a cocktail of one or more individual peptides; one or more peptides of the invention comprised by a polyepitopic peptide; or nucleic acids that encode such individual peptides or polypeptides, e.g., a minigene that encodes a polyepitopic peptide. The “one or more peptides” can include any whole unit integer from 1-150 or more, e.g., at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, or 150 or more peptides of the invention. The peptides or polypeptides can optionally be modified, such as by lipidation, addition of targeting or other sequences. HLA class I peptides of the invention can be admixed with, or linked to, HLA class II peptides, to facilitate activation of both cytotoxic T lymphocytes and helper T lymphocytes. HLA vaccines can also comprise peptide-pulsed antigen presenting cells, e.g., dendritic cells.

[0135] The term “variant” refers to a molecule that exhibits a variation from a described type or norm, such as a protein that has one or more different amino acid residues in the corresponding position(s) of a specifically described protein (e.g. the 83P2H3 protein shown in FIG. 2 or FIG. 3). An analog is an example of a variant protein.

[0136] The 83P2H3-related proteins of the invention include those specifically identified herein, as well as allelic variants, conservative substitution variants, analogs and homologs that can be isolated/generated and characterized without undue experimentation following the methods outlined herein or readily available in the art. Unless the context clearly indicates otherwise, “83P2H3” also refers to family members, such as the CaTrF2E11 identified herein, and any of the alternative splice variants disclosed herein. Fusion proteins that combine parts of different 83P2H3 proteins or fragments thereof, as well as fusion proteins of a 83P2H3 protein and a heterologous polypeptide are also included. Such 83P2H3 proteins are collectively referred to as the 83P2H3-related proteins, the proteins of the invention, or 83P2H3. The term “83P2H3-related protein” refers to a polypeptide fragment or an 83P2H3 protein sequence of 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more than 25 amino acids; or, at least 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 85, 90, 95, 100 or more than 100 amino acids.

[0137] II.) 83P2H3 Polynucleotides

[0138] One aspect of the invention provides polynucleotides corresponding or complementary to all or part of an 83P2H3 gene, mRNA, and/or coding sequence, preferably in isolated form, including polynucleotides encoding an 83P2H3-related protein and fragments thereof, DNA, RNA, DNA/RNA hybrid, and related molecules, polynucleotides or oligonucleotides complementary to an 83P2H3 gene or mRNA sequence or a part thereof, and polynucleotides or oligonucleotides that hybridize to an 83P2H3 gene, mRNA, or to an 83P2H3 encoding polynucleotide (collectively, “83P2H3 polynucleotides”). In all instances when referred to in this section, T can also be U in FIG. 2.

[0139] Embodiments of a 83P2H3 polynucleotide include: a 83P2H3 polynucleotide having the sequence shown in FIG. 2, the nucleotide sequence of 83P2H3 as shown in FIG. 2, wherein T is U; at least 10 contiguous nucleotides of a polynucleotide having the sequence as shown in FIG. 2; or, at least 10 contiguous nucleotides of a polynucleotide having the sequence as shown in FIG. 2 where T is U. For example, embodiments of 83P2H3 nucleotides comprise, without limitation:

[0140] (a) a polynucleotide comprising or consisting of the sequence as shown in FIG. 2 (SEQ ID NO.: 702), wherein T can also be U;

[0141] (b) a polynucleotide comprising or consisting of the sequence as shown in FIG. 2 (SEQ ID NO.: 702), from nucleotide residue number 201 through nucleotide residue number 2378, wherein T can also be U;

[0142] (c) a polynucleotide that encodes a 83P2H3-related protein whose sequence is encoded by the cDNAs contained in the plasmid designated p83P2H3-C deposited with American Type Culture Collection as Accession No. PTA-1893;

[0143] (d) a polynucleotide that encodes an 83P2H3-related protein that is at least 90% homologous to the entire amino acid sequence shown in SEQ ID NO.: 702;

[0144] (e) a polynucleotide that encodes an 83P2H3-related protein that is at least 90% identical to the entire amino acid sequence shown in SEQ ID NO: 702;

[0145] (f) a polynucleotide that encodes at least one peptide set forth in Tables V-XVIII;

[0146] (g) a polynucleotide that encodes a peptide region of at least 5 amino acids of FIG. 3 in any whole number increment up to 725 that includes an amino acid position having a value greater than 0.5 in the Hydrophilicity profile of FIG. 14;

[0147] (h) a polynucleotide that encodes a peptide region of at least 5 amino acids of FIG. 3 in any whole number increment up to 725 that includes an amino acid position having a value less than 0.5 in the Hydropathicity profile of FIG. 15;

[0148] (i) a polynucleotide that encodes a peptide region of at least 5 amino acids of FIG. 3 in any whole number increment up to 725 that includes an amino acid position having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 16;

[0149] (j) a polynucleotide that encodes a peptide region of at least 5 amino acids of FIG. 3 in any whole number increment up to 725 that includes an amino acid position having a value greater than 0.5 in the Average Flexibility profile on FIG. 17;

[0150] (k) a polynucleotide that encodes a peptide region of at least 5 amino acids of FIG. 3 in any whole number increment up to 725 that includes an amino acid position having a value greater than 0.5 in the Beta-turn profile of FIG. 18;

[0151] (l) a polynucleotide that is fully complementary to a polynucleotide of any one of (a)-(k);

[0152] (m) a polynucleotide that selectively hybridizes under stringent conditions to a polynucleotide of (a)-(l); and

[0153] (n) a peptide that is encoded by any of (a)-(k).

[0154] (o) a polynucleotide of any of (a)-(m) or peptide of (o) together with a pharmaceutical excipient and/or in a human unit dose form.

[0155] As used herein, a range is understood to specifically disclose all whole unit positions thereof.

[0156] Typical embodiments of the invention disclosed herein include 83P2H3 polynucleotides that encode specific portions of the 83P2H3 mRNA sequence (and those which are complementary to such sequences) such as those that encode the protein and fragments thereof, for example of 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700 or 725 contiguous amino acids.

[0157] For example, representative embodiments of the invention disclosed herein include: polynucleotides and their encoded peptides themselves encoding about amino acid 1 to about amino acid 10 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 10 to about amino acid 20 of the 83P2H3 protein shown in FIG. 2, or FIG. 3, polynucleotides encoding about amino acid 20 to about amino acid 30 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 30 to about amino acid 40 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 40 to about amino acid 50 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 50 to about amino acid 60 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 60 to about amino acid 70 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 70 to about amino acid 80 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 80 to about amino acid 90 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 90 to about amino acid 100 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, in increments of about 10 amino acids, ending at the carboxyl terminal amino acid set forth in FIG. 2 or FIG. 3. Accordingly polynucleotides encoding portions of the amino acid sequence (of about 10 amino acids), of amino acids 100 through the carboxyl terminal amino acid of the 83P2H3 protein are embodiments of the invention. Wherein it is understood that each particular amino acid position discloses that position plus or minus five amino acid residues.

[0158] Polynucleotides encoding relatively long portions of the 83P2H3 protein are also within the scope of the invention. For example, polynucleotides encoding from about amino acid 1 (or 20 or 30 or 40 etc.) to about amino acid 20, (or 30, or 40 or 50 etc.) of the 83P2H3 protein shown in FIG. 2 or FIG. 3 can be generated by a variety of techniques well known in the art. These polynucleotide fragments can include any portion of the 83P2H3 sequence as shown in FIG. 2 or FIG. 3.

[0159] Additional illustrative embodiments of the invention disclosed herein include 83P2H3 polynucleotide fragments encoding one or more of the biological motifs contained within the 83P2H3 protein sequence, including one or more of the motif-bearing subsequences of the 83P2H3 protein set forth in Tables V-XVIII. In another embodiment, typical polynucleotide fragments of the invention encode one or more of the regions of 83P2H3 that exhibit homology to a known molecule. In another embodiment of the invention, typical polynucleotide fragments can encode one or more of the 83P2H3 N-glycosylation sites, cAMP and cGMP-dependent protein kinase phosphorylation sites, casein kinase II phosphorylation sites or N-myristoylation site and amidation sites.

[0160] With respect to 83P2H3 family members, such as CaTrF2E11 described in FIG. 1, FIG. 2 and FIG. 3, polynucleotides encoding all or a portion of the protein are within the scope of the invention. In some embodiments, the fragment or variant of the CaTrF2E11 protein having the amino acid sequence set forth in FIG. 3 comprises the portion of CaTrF2E11 described in FIG. 1B or one or more of the motifs or domains of CaTrF2E11 described in Table XIX(B) or Table XX.

[0161] II.A.) Uses of 83P2H3 Polynucleotides

[0162] II.A.1.) Monitoring of Genetic Abnormalities

[0163] The polynucleotides of the preceding paragraphs have a number of different specific uses. The human 83P2H3 gene maps to the chromosomal location set forth in Example 3. For example, because the 83P2H3 gene maps to this chromosome, polynucleotides that encode different regions of the 83P2H3 protein are used to characterize cytogenetic abnormalities of this chromosomal locale, such as abnormalities that are identified as being associated with various cancers. In certain genes, a variety of chromosomal abnormalities including rearrangements have been identified as frequent cytogenetic abnormalities in a number of different cancers (see e.g. Krajinovic et al., Mutat. Res. 382(3-4): 81-83 (1998); Johansson et al., Blood 86(10): 3905-3914 (1995) and Finger et al., P.N.A.S. 85(23): 9158-9162 (1988)). Thus, polynucleotides encoding specific regions of the 83P2H3 protein provide new tools that can be used to delineate, with greater precision than previously possible, cytogenetic abnormalities in the chromosomal region that encodes 83P2H3 that may contribute to the malignant phenotype. In this context, these polynucleotides satisfy a need in the art for expanding the sensitivity of chromosomal screening in order to identify more subtle and less common chromosomal abnormalities (see e.g. Evans et al., Am. J. Obstet. Gynecol 171(4): 1055-1057 (1994)).

[0164] Furthermore, as 83P2H3 was shown to be highly expressed in prostate and other cancers, 83P2H3 polynucleotides are used in methods assessing the status of 83P2H3 gene products in normal versus cancerous tissues. Typically, polynucleotides that encode specific regions of the 83P2H3 protein are used to assess the presence of perturbations (such as deletions, insertions, point mutations, or alterations resulting in a loss of an antigen etc.) in specific regions of the 83P2H3 gene, such as such regions containing one or more motifs. Exemplary assays include both RT-PCR assays as well as single-strand conformation polymorphism (SSCP) analysis (see, e.g., Marrogi et al., J. Cutan. Pathol. 26(8): 369-378 (1999), both of which utilize polynucleotides encoding specific regions of a protein to examine these regions within the protein.

[0165] II.A.2.) Antisense Embodiments

[0166] Other specifically contemplated nucleic acid related embodiments of the invention disclosed herein are genomic DNA, cDNAs, ribozymes, and antisense molecules, as well as nucleic acid molecules based on an alternative backbone, or including alternative bases, whether derived from natural sources or synthesized, and include molecules capable of inhibiting the RNA or protein expression of 83P2H3. For example, antisense molecules can be RNAs or other molecules, including peptide nucleic acids (PNAs) or non-nucleic acid molecules such as phosphorothioate derivatives, that specifically bind DNA or RNA in a base pair-dependent manner. A skilled artisan can readily obtain these classes of nucleic acid molecules using the 83P2H3 polynucleotides and polynucleotide sequences disclosed herein.

[0167] Antisense technology entails the administration of exogenous oligonucleotides that bind to a target polynucleotide located within the cells. The term “antisense” refers to the fact that such oligonucleotides are complementary to their intracellular targets, e.g., 83P2H3. See for example, Jack Cohen, Oligodeoxynucleotides, Antisense Inhibitors of Gene Expression, CRC Press, 1989; and Synthesis 1:1-5 (1988). The 83P2H3 antisense oligonucleotides of the present invention include derivatives such as S-oligonucleotides (phosphorothioate derivatives or S-oligos, see, Jack Cohen, supra), which exhibit enhanced cancer cell growth inhibitory action. S-oligos (nucleoside phosphorothioates) are isoelectronic analogs of an oligonucleotide (O-oligo) in which a nonbridging oxygen atom of the phosphate group is replaced by a sulfur atom. The S-oligos of the present invention can be prepared by treatment of the corresponding O-oligos with 3H-1,2-benzodithiol-3-one-1,1-dioxide, which is a sulfur transfer reagent. See Iyer, R. P. et al, J. Org. Chem. 55:4693-4698 (1990); and Iyer, R. P. et al., J. Am. Chem. Soc. 112:1253-1254 (1990). Additional 83P2H3 antisense oligonucleotides of the present invention include morpholino antisense oligonucleotides known in the art (see, e.g., Partridge et al., 1996, Antisense & Nucleic Acid Drug Development 6: 169-175).

[0168] The 83P2H3 antisense oligonucleotides of the present invention typically can be RNA or DNA that is complementary to and stably hybridizes with the first 100 5′ codons or last 100 3′ codons of the 83P2H3 genomic sequence or the corresponding mRNA. Absolute complementarity is not required, although high degrees of complementarity are preferred. Use of an oligonucleotide complementary to this region allows for the selective hybridization to 83P2H3 mRNA and not to mRNA specifying other regulatory subunits of protein kinase. In one embodiment, 83P2H3 antisense oligonucleotides of the present invention are 15 to 30-mer fragments of the antisense DNA molecule that have a sequence that hybridizes to 83P2H3 mRNA. Optionally, 83P2H3 antisense oligonucleotide is a 30-mer oligonucleotide that is complementary to a region in the first 10 5′ codons or last 10 3′ codons of 83P2H3. Alternatively, the antisense molecules are modified to employ ribozymes in the inhibition of 83P2H3 expression, see, e.g., L. A. Couture & D. T. Stinchcomb; Trends Genet 12: 510-515 (1996).

[0169] II.A.3.) Primers and Primer Pairs

[0170] Further specific embodiments of this nucleotides of the invention include primers and primer pairs, which allow the specific amplification of polynucleotides of the invention or of any specific parts thereof, and probes that selectively or specifically hybridize to nucleic acid molecules of the invention or to any part thereof. Probes can be labeled with a detectable marker, such as, for example, a radioisotope, fluorescent compound, bioluminescent compound, a chemiluminescent compound, metal chelator or enzyme. Such probes and primers are used to detect the presence of a 83P2H3 polynucleotide in a sample and as a means for detecting a cell expressing a 83P2H3 protein.

[0171] Examples of such probes include polypeptides comprising all or part of the human 83P2H3 cDNA sequence shown in FIG. 2. Examples of primer pairs capable of specifically amplifying 83P2H3 mRNAs are also described in the Examples. As will be understood by the skilled artisan, a great many different primers and probes can be prepared based on the sequences provided herein and used effectively to amplify and/or detect a 83P2H3 mRNA.

[0172] The 83P2H3 polynucleotides of the invention are useful for a variety of purposes, including but not limited to their use as probes and primers for the amplification and/or detection of the 83P2H3 gene(s), mRNA(s), or fragments thereof; as reagents for the diagnosis and/or prognosis of prostate cancer and other cancers; as coding sequences capable of directing the expression of 83P2H3 polypeptides; as tools for modulating or inhibiting the expression of the 83P2H3 gene(s) and/or translation of the 83P2H3 transcript(s); and as therapeutic agents.

[0173] II.A.4.) Isolation of 83P2H3-Encoding Nucleic Acid Molecules

[0174] The 83P2H3 cDNA sequences described herein enable the isolation of other polynucleotides encoding 83P2H3 gene product(s), as well as the isolation of polynucleotides encoding 83P2H3 gene product homologs, alternatively spliced isoforms, allelic variants, and mutant forms of the 83P2H3 gene product as well as polynucleotides that encode analogs of 83P2H3-related proteins. Various molecular cloning methods that can be employed to isolate full length cDNAs encoding an 83P2H3 gene are well known (see, for example, Sambrook, J. et al., Molecular Cloning: A Laboratory Manual, 2d edition, Cold Spring Harbor Press, New York, 1989; Current Protocols in Molecular Biology. Ausubel et al., Eds., Wiley and Sons, 1995). For example, lambda phage cloning methodologies can be conveniently employed, using commercially available cloning systems (e.g., Lambda ZAP Express, Stratagene). Phage clones containing 83P2H3 gene cDNAs can be identified by probing with a labeled 83P2H3 cDNA or a fragment thereof. For example, in one embodiment, the 83P2H3 cDNA (FIG. 2) or a portion thereof can be synthesized and used as a probe to retrieve overlapping and full-length cDNAs corresponding to a 83P2H3 gene. The 83P2H3 gene itself can be isolated by screening genomic DNA libraries, bacterial artificial chromosome libraries (BACs), yeast artificial chromosome libraries (YACs), and the like, with 83P2H3 DNA probes or primers.

[0175] II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector Systems

[0176] The invention also provides recombinant DNA or RNA molecules containing an 83P2H3 polynucleotide, a fragment, analog or homologue thereof, including but not limited to phages, plasmids, phagemids, cosmids, YACs, BACs, as well as various viral and non-viral vectors well known in the art, and cells transformed or transfected with such recombinant DNA or RNA molecules. Methods for generating such molecules are well known (see, for example, Sambrook et al, 1989, supra).

[0177] The invention further provides a host-vector system comprising a recombinant DNA molecule containing a 83P2H3 polynucleotide, fragment, analog or homologue thereof within a suitable prokaryotic or eukaryotic host cell. Examples of suitable eukaryotic host cells include a yeast cell, a plant cell, or an animal cell, such as a mammalian cell or an insect cell (e.g., a baculovirus-infectible cell such as an Sf9 or HighFive cell). Examples of suitable mammalian cells include various prostate cancer cell lines such as DU145 and TsuPr1, other transfectable or transducible prostate cancer cell lines, primary cells (PrEC), as well as a number of mammalian cells routinely used for the expression of recombinant proteins (e.g., COS, CHO, 293, 293T cells). More particularly, a polynucleotide comprising the coding sequence of 83P2H3 or a fragment, analog or homolog thereof can be used to generate 83P2H3 proteins or fragments thereof using any number of host-vector systems routinely used and widely known in the art.

[0178] A wide range of host-vector systems suitable for the expression of 83P2H3 proteins or fragments thereof are available, see for example, Sambrook et al., 1989, supra; Current Protocols in Molecular Biology, 1995, supra). Preferred vectors for mammalian expression include but are not limited to pcDNA 3.1 myc-His-tag (Invitrogen) and the retroviral vector pSRαtkneo (Muller et al., 1991, MCB 11: 1785). Using these expression vectors, 83P2H3 can be expressed in several prostate cancer and non-prostate cell lines, including for example 293, 293T, rat-1, NIH 3T3 and TsuPr1. The host-vector systems of the invention are useful for the production of a 83P2H3 protein or fragment thereof. Such host-vector systems can be employed to study the functional properties of 83P2H3 and 83P2H3 mutations or analogs.

[0179] Recombinant human 83P2H3 protein or an analog or homolog or fragment thereof can be produced by mammalian cells transfected with a construct encoding a 83P2H3-related nucleotide. For example, 293T cells can be transfected with an expression plasmid encoding 83P2H3 or fragment, analog or homolog thereof, the 83P2H3 or related protein is expressed in the 293T cells, and the recombinant 83P2H3 protein is isolated using standard purification methods (e.g., affinity purification using anti-83P2H3 antibodies). In another embodiment, a 83P2H3 coding sequence is subcloned into the retroviral vector pSRαMSVtkneo and used to infect various mammalian cell lines, such as NIH 3T3, TsuPr1, 293 and rat-1 in order to establish 83P2H3 expressing cell lines. Various other expression systems well known in the art can also be employed. Expression constructs encoding a leader peptide joined in frame to the 83P2H3 coding sequence can be used for the generation of a secreted form of recombinant 83P2H3 protein.

[0180] As discussed herein, redundancy in the genetic code permits variation in 83P2H3 gene sequences. In particular, it is known in the art that specific host species often have specific codon preferences, and thus one can adapt the disclosed sequence as preferred for a desired host. For example, preferred analog codon sequences typically have rare codons (i.e., codons having a usage frequency of less than about 20% in known sequences of the desired host) replaced with higher frequency codons. Codon preferences for a specific species are calculated, for example, by utilizing codon usage tables available on the INTERNET such as at URLwww.dna.affrc.go.jp/˜nakamura/codon.html.

[0181] Additional sequence modifications are known to enhance protein expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon/intron splice site signals, transposon-like repeats, and/or other such well-characterized sequences that are deleterious to gene expression. The GC content of the sequence is adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. Where possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures. Other useful modifications include the addition of a translational initiation consensus sequence at the start of the open reading frame, as described in Kozak, Mol. Cell Biol., 9:5073-5080 (1989). Skilled artisans understand that the general rule that eukaryotic ribosomes initiate translation exclusively at the 5′ proximal AUG codon is abrogated only under rare conditions (see, e.g., Kozak PNAS 92(7): 2662-2666, (1995) and Kozak NAR 15(20): 8125-8148 (1987)).

[0182] III.) 83P2H3-related Proteins Another aspect of the present invention provides 83P2H3-related proteins. Specific embodiments of 83P2H3 proteins comprise a polypeptide having all or part of the amino acid sequence of human 83P2H3 as shown in FIG. 2 or FIG. 3. Alternatively, embodiments of 83P2H3 proteins comprise variant, homolog or analog polypeptides that have alterations in the amino acid sequence of 83P2H3 shown in FIG. 2 or FIG. 3.

[0183] In general, naturally occurring allelic variants of human 83P2H3 share a high degree of structural identity and homology (e.g., 90% or more homology). Typically, allelic variants of the 83P2H3 protein contain conservative amino acid substitutions within the 83P2H3 sequences described herein or contain a substitution of an amino acid from a corresponding position in a homologue of 83P2H3. One class of 83P2H3 allelic variants are proteins that share a high degree of homology with at least a small region of a particular 83P2H3 amino acid sequence, but further contain a radical departure from the sequence, such as a non-conservative substitution, truncation, insertion or frame shift. In comparisons of protein sequences, the terms, similarity, identity, and homology each have a distinct meaning as appreciated in the field of genetics. Moreover, orthology and paralogy can be important concepts describing the relationship of members of a given protein family in one organism to the members of the same family in other organisms.

[0184] Amino acid abbreviations are provided in Table II. Conservative amino acid substitutions can frequently be made in a protein without altering either the conformation or the function of the protein. Proteins of the invention can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 conservative substitutions. Such changes include substituting any of isoleucine (I), valine (V), and leucine (L) for any other of these hydrophobic amino acids; aspartic acid (D) for glutamic acid (E) and vice versa; glutamine (Q) for asparagine (N) and vice versa; and serine (S) for threonine (T) and vice versa. Other substitutions can also be considered conservative, depending on the environment of the particular amino acid and its role in the three-dimensional structure of the protein. For example, glycine (G) and alanine (A) can frequently be interchangeable, as can alanine (A) and valine (V). Methionine (M), which is relatively hydrophobic, can frequently be interchanged with leucine and isoleucine, and sometimes with valine. Lysine (K) and arginine (R) are frequently interchangeable in locations in which the significant feature of the amino acid residue is its charge and the differing pK's of these two amino acid residues are not significant. Still other changes can be considered “conservative” in particular environments (see, e.g. Table III herein; pages 13-15 “Biochemistry” 2nd ED. Lubert Stryer ed (Stanford University); Henikoff et al., PNAS 1992 Vol 89 10915-10919; Lei et al., J Biol Chem May 19, 1995; 270(20):11882-6).

[0185] Embodiments of the invention disclosed herein include a wide variety of art-accepted variants or analogs of 83P2H3 proteins such as polypeptides having amino acid insertions, deletions and substitutions. 83P2H3 variants can be made using methods known in the art such as site-directed mutagenesis, alanine scanning, and PCR mutagenesis. Site-directed mutagenesis (Carter et al., Nucl. Acids Res., 13:4331 (1986); Zoller et al., Nucl. Acids Res., 10:6487 (1987)), cassette mutagenesis (Wells et al., Gene, 34:315 (1985)), restriction selection mutagenesis (Wells et al., Philos. Trans. R. Soc. London SerA, 317:415 (1986)) or other known techniques can be performed on the cloned DNA to produce the 83P2H3 variant DNA.

[0186] Scanning amino acid analysis can also be employed to identify one or more amino acids along a contiguous sequence that is involved in a specific biological activity such as a protein-protein interaction. Among the preferred scanning amino acids are relatively small, neutral amino acids. Such amino acids include alanine, glycine, serine, and cysteine. Alanine is typically a preferred scanning amino acid among this group because it eliminates the side-chain beyond the beta-carbon and is less likely to alter the main-chain conformation of the variant. Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found in both buried and exposed positions (Creighton, The Proteins, (W. H. Freeman & Co., N.Y.); Chothia, J. Mol. Biol., 150:1 (1976)). If alanine substitution does not yield adequate amounts of variant, an isosteric amino acid can be used.

[0187] As defined herein, 83P2H3 variants, analogs or homologs, have the distinguishing attribute of having at least one epitope that is “cross reactive” with a 83P2H3 protein having the amino acid sequence of SEQ ID NO: 703. As used in this sentence, “cross reactive” means that an antibody or T cell that specifically binds to an 83P2H3 variant also specifically binds to the 83P2H3 protein having the amino acid sequence of SEQ ID NO: 703. A polypeptide ceases to be a variant of the protein shown in SEQ ID NO: 703 when it no longer contains any epitope capable of being recognized by an antibody or T cell that specifically binds to the 83P2H3 protein. Those skilled in the art understand that antibodies that recognize proteins bind to epitopes of varying size, and a grouping of the order of about four or five amino acids, contiguous or not, is regarded as a typical number of amino acids in a minimal epitope. See, e.g., Nair et al., J. Immunol 2000 165(12): 6949-6955; Hebbes et al., Mol Immunol (1989) 26(9):865-73; Schwartz et al., J Immunol (1985) 135(4):2598-608.

[0188] Another class of 83P2H3-related protein variants share 70%, 75%, 80%, 85% or 90% or more similarity with the amino acid sequence of SEQ ID NO: 703 or a fragment thereof. Another specific class of 83P2H3 protein variants or analogs comprise one or more of the 83P2H3 biological motifs described herein or presently known in the art. Thus, encompassed by the present invention are analogs of 83P2H3 fragments (nucleic or amino acid) that have altered functional (e.g. immunogenic) properties relative to the starting fragment. It is to be appreciated that motifs now or which become part of the art are to be applied to the nucleic or amino acid sequences of FIG. 2 or FIG. 3.

[0189] As discussed herein, embodiments of the claimed invention include polypeptides containing less than the full amino acid sequence of the 83P2H3 protein shown in FIG. 2 or FIG. 3. For example, representative embodiments of the invention comprise peptides/proteins having any 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more contiguous amino acids of the 83P2H3 protein shown in FIG. 2 or FIG. 3.

[0190] Moreover, representative embodiments of the invention disclosed herein include polypeptides consisting of about amino acid 1 to about amino acid 10 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 10 to about amino acid 20 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 20 to about amino acid 30 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 30 to about amino acid 40 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 40 to about amino acid 50 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 50 to about amino acid 60 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 60 to about amino acid 70 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 70 to about amino acid 80 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 80 to about amino acid 90 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 90 to about amino acid 100 of the 83P2H3 protein shown in FIG. 2 or FIG. 3, etc. throughout the entirety of the 83P2H3 amino acid sequence. Moreover, polypeptides consisting of about amino acid 1 (or 20 or 30 or 40 etc.) to about amino acid 20, (or 130, or 140 or 150 etc.) of the 83P2H3 protein shown in FIG. 2 or FIG. 3 are embodiments of the invention. It is to be appreciated that the starting and stopping positions in this paragraph refer to the specified position as well as that position plus or minus 5 residues. 83P2H3-related proteins are generated using standard peptide synthesis technology or using chemical cleavage methods well known in the art. Alternatively, recombinant methods can be used to generate nucleic acid molecules that encode a 83P2H3-related protein. In one embodiment, nucleic acid molecules provide a means to generate defined fragments of the 83P2H3 protein (or variants, homologs or analogs thereof).

[0191] III.A.) Motif-bearing Protein Embodiments

[0192] Additional illustrative embodiments of the invention disclosed herein include 83P2H3 polypeptides comprising the amino acid residues of one or more of the biological motifs contained within the 83P2H3 polypeptide sequence set forth in FIG. 2 or FIG. 3. Various motifs are known in the art, and a protein can be evaluated for the presence of such motifs by a number of publicly available Internet sites (see, e.g., URL addresses: pfam.wustl.edu/; searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html psort.ims.u-tokyo.ac.jp/; www.cbs.dtu.dk/; www.ebi.ac.uk/interpro/scan.html; www.expasy.ch/tools/scnpsitl.html; Epimatrix™ and Epimer™, Brown University, www.brown.edu/Research/TB-HIV_Lab/epimatrix.html; and BIMAS, bimas.dcrt.nih.gov/.).

[0193] Motif bearing subsequences of the 83P2H3 protein are set forth and identified in Table XIX.

[0194] Table XX sets forth several frequently occurring motifs based on pfam searches (see URL address pfam.wustl.edu/). The columns of Table XX list (1) motif name abbreviation, (2) percent identity found amongst the different member of the motif family, (3) motif name or description and (4) most common function; location information is included if the motif is relevant for location.

[0195] Polypeptides comprising one or more of the 83P2H3 motifs discussed above are useful in elucidating the specific characteristics of a malignant phenotype in view of the observation that the 83P2H3 motifs discussed above are associated with growth dysregulation and because 83P2H3 is overexpressed in certain cancers (See, e.g., Table I). Casein kinase II, cAMP and camp-dependent protein kinase, and Protein Kinase C, for example, are enzymes known to be associated with the development of the malignant phenotype (see e.g. Chen et al., Lab Invest., 78(2): 165-174 (1998); Gaiddon et al., Endocrinology 136(10): 4331-4338 (1995); Hall et al., Nucleic Acids Research 24(6): 1119-1126 (1996); Peterziel et al., Oncogene 18(46): 6322-6329 (1999) and O'Brian, Oncol. Rep. 5(2): 305-309 (1998)). Moreover, both glycosylation and myristoylation are protein modifications also associated with cancer and cancer progression (see e.g. Dennis et al., Biochem. Biophys. Acta 1473(1):21-34 (1999); Raju et al., Exp. Cell Res. 235(1): 145-154 (1997)). Amidation is another protein modification also associated with cancer and cancer progression (see e.g. Treston et al., J. Natl. Cancer Inst. Monogr. (13): 169-175 (1992)).

[0196] In another embodiment, proteins of the invention comprise one or more of the immunoreactive epitopes identified in accordance with art-accepted methods, such as the peptides set forth in Tables V-XVIII. CTL epitopes can be determined using specific algorithms to identify peptides within an 83P2H3 protein that are capable of optimally binding to specified HLA alleles (e.g., Table IV; Epimatrix™ and Epimer™, Brown University, URL www.brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html; and BIMAS, URL bimas.dcrt.nih.gov/.) Moreover, processes for identifying peptides that have sufficient binding affinity for HLA molecules and which are correlated with being immunogenic epitopes, are well known in the art, and are carried out without undue experimentation. In addition, processes for identifying peptides that are immunogenic epitopes, are well known in the art, and are carried out without undue experimentation either in vitro or in vivo.

[0197] Also known in the art are principles for creating analogs of such epitopes in order to modulate immunogenicity. For example, one begins with an epitope that bears a CTL or HTL motif (see, e.g., the HLA Class I and HLA Class II motifs/supermotifs of Table IV). The epitope is analoged by substituting out an amino acid at one of the specified positions, and replacing it with another amino acid specified for that position. For example, one can substitute out a deleterious residue in favor of any other residue, such as a preferred residue as defined in Table IV; substitute a less-preferred residue with a preferred residue as defined in Table IV; or substitute an originally-occurring preferred residue with another preferred residue as defined in Table IV. Substitutions can occur at primary anchor positions or at other positions in a peptide; see, e.g., Table IV.

[0198] A variety of references reflect the art regarding the identification and generation of epitopes in a protein of interest as well as analogs thereof. See, for example, WO 9733602 to Chesnut et al.; Sette, Immunogenetics 1999 50(3-4): 201-212; Sette et al., J. Immunol. 2001166(2): 1389-1397; Sidney et al., Hum. Immunol. 1997 58(1): 12-20; Kondo et al., Immunogenetics 1997 45(4): 249-258; Sidney et al., J. Immunol. 1996 157(8): 3480-90; and Falk et al., Nature 351: 290-6 (1991); Hunt et al., Science 255:1261-3 (1992); Parker et al., J. Immunol. 149:3580-7 (1992); Parker et al., J. Immunol. 152:163-75 (1994)); Kast et al., 1994 152(8): 3904-12; Borras-Cuesta et al., Hum. Immunol. 2000 61(3): 266-278; Alexander et al., J. Immunol. 2000 164(3); 164(3): 1625-1633; Alexander et al., PMID: 7895164, UI: 95202582; O'Sullivan et al., J. Immunol. 1991 147(8): 2663-2669; Alexander et al., Immunity 1994 1(9): 751-761 and Alexander et al., Immunol. Res. 1998 18(2): 79-92.

[0199] Related embodiments of the inventions include polypeptides comprising combinations of the different motifs set forth in Table XIX, and/or, one or more of the predicted CTL epitopes of Table V through Table XVIII, and/or, one or more of the T cell binding motifs known in the art. Preferred embodiments contain no insertions, deletions or substitutions either within the motifs or the intervening sequences of the polypeptides. In addition, embodiments which include a number of either N-terminal and/or C-terminal amino acid residues on either side of these motifs may be desirable (to, for example, include a greater portion of the polypeptide architecture in which the motif is located). Typically the number of N-terminal and/or C-terminal amino acid residues on either side of a motif is between about 1 to about 100 amino acid residues, preferably 5 to about 50 amino acid residues. 83P2H3-related proteins are embodied in many forms, preferably in isolated form. A purified 83P2H3 protein molecule will be substantially free of other proteins or molecules that impair the binding of 83P2H3 to antibody, T cell or other ligand. The nature and degree of isolation and purification will depend on the intended use. Embodiments of a 83P2H3-related proteins include purified 83P2H3-related proteins and functional, soluble 83P2H3-related proteins. In one embodiment, a functional, soluble 83P2H3 protein or fragment thereof retains the ability to be bound by antibody, T cell or other ligand.

[0200] The invention also provides 83P2H3 proteins comprising biologically active fragments of the 83P2H3 amino acid sequence shown in FIG. 2 or FIG. 3. Such proteins exhibit properties of the 83P2H3 protein, such as the ability to elicit the generation of antibodies that specifically bind an epitope associated with the 83P2H3 protein; to be bound by such antibodies; to elicit the activation of HTL or CTL; and/or, to be recognized by HTL or CTL. 83P2H3-related polypeptides that contain particularly interesting structures can be predicted and/or identified using various analytical techniques well known in the art, including, for example, the methods of Chou-Fasman, Garnier-Robson, Kyte-Doolittle, Eisenberg, Karplus-Schultz or Jameson-Wolf analysis, or on the basis of immunogenicity. Fragments that contain such structures are particularly useful in generating subunit-specific anti-83P2H3 antibodies, or T cells or in identifying cellular factors that bind to 83P2H3.

[0201] CTL epitopes can be determined using specific algorithms to identify peptides within an 83P2H3 protein that are capable of optimally binding to specified HLA alleles (e.g., by using the SYFPEITHI site at World Wide Web URL syfpeithi.bmi-heidelberg.com/; the listings in Table IV(A)-(E); Epimatrix™ and Epimer™, Brown University, URL (www.brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html); and BIMAS, URL bimas.dcrt.nih.gov/). Illustrating this, peptide epitopes from 83P2H3 that are presented in the context of human MHC class I molecules HLA-A1, A2, A3, A11, A24, B7 and B35 were predicted (Tables V-XVIII). Specifically, the complete amino acid sequence of the 83P2H3 protein was entered into the HLA Peptide Motif Search algorithm found in the Bioinformatics and Molecular Analysis Section (BIMAS) web site listed above. The HLA peptide motif search algorithm was developed by Dr. Ken Parker based on binding of specific peptide sequences in the groove of HLA Class I molecules, in particular HLA-A2 (see, e.g., Falk et al., Nature 351: 290-6 (1991); Hunt et al., Science 255:1261-3 (1992); Parker et al., J. Immunol. 149:3580-7 (1992); Parker et al., J. Immunol. 152:163-75 (1994)). This algorithm allows location and ranking of 8-mer, 9-mer, and 10-mer peptides from a complete protein sequence for predicted binding to HLA-A2 as well as numerous other HLA Class I molecules. Many HLA class I binding peptides are 8-, 9-, 10 or 11-mers. For example, for class I HLA-A2, the epitopes preferably contain a leucine (L) or methionine (M) at position 2 and a valine (V) or leucine (L) at the C-terminus (see, e.g., Parker et al., J. Immunol. 149:3580-7 (1992)). Selected results of 83P2H3 predicted binding peptides are shown in Tables V-XVIII herein. In Tables V-XVIII, the top 50 ranking candidates, 9-mers and 10-mers, for each family member are shown along with their location, the amino acid sequence of each specific peptide, and an estimated binding score. The binding score corresponds to the estimated half time of dissociation of complexes containing the peptide at 37° C. at pH 6.5. Peptides with the highest binding score are predicted to be the most tightly bound to HLA Class I on the cell surface for the greatest period of time and thus represent the best immunogenic targets for T-cell recognition.

[0202] Actual binding of peptides to an HLA allele can be evaluated by stabilization of HLA expression on the antigen-processing defective cell line T2 (see, e.g., Xue et al., Prostate 30:73-8 (1997) and Peshwa et al., Prostate 36:129-38 (1998)). Immunogenicity of specific peptides can be evaluated in vitro by stimulation of CD8+ cytotoxic T lymphocytes (CTL) in the presence of antigen presenting cells such as dendritic cells.

[0203] It is to be appreciated that every epitope predicted by the BIMAS site, Epimer™ and Epimatrix™ sites, or specified by the HLA class I or class II motifs available in the art or which become part of the art such as set forth in Table IV (or determined using World Wide Web site URL syfpeithi.bmi-heidelberg.com/) are to be “applied” to the 83P2H3 protein. As used in this context “applied” means that the 83P2H3 protein is evaluated, e.g., visually or by computer-based patterns finding methods, as appreciated by those of skill in the relevant art. Every subsequence of the 83P2H3 of 8, 9, 10, or 11 amino acid residues that bears an HLA Class I motif, or a subsequence of 9 or more amino acid residues that bear an HLA Class II motif are within the scope of the invention.

[0204] III.B.) Expression of 83P2H3-related Proteins

[0205] In an embodiment described in the examples that follow, 83P2H3 can be conveniently expressed in cells (such as 293T cells) transfected with a commercially available expression vector such as a CMV-driven expression vector encoding 83P2H3 with a C-terminal 6XHis and MYC tag (pcDNA3.1/mycHIS, Invitrogen or Tag5, GenHunter Corporation, Nashville Tenn.). The Tag5 vector provides an IgGK secretion signal that can be used to facilitate the production of a secreted 83P2H3 protein in transfected cells. The secreted HIS-tagged 83P2H3 in the culture media can be purified, e.g., using a nickel column using standard techniques.

[0206] III.C.) Modifications of 83P2H3-related Proteins

[0207] Modifications of 83P2H3-related proteins such as covalent modifications are included within the scope of this invention. One type of covalent modification includes reacting targeted amino acid residues of a 83P2H3 polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C-terminal residues of the 83P2H3. Another type of covalent modification of the 83P2H3 polypeptide included within the scope of this invention comprises altering the native glycosylation pattern of a protein of the invention. Another type of covalent modification of 83P2H3 comprises linking the 83P2H3 polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol (PEG), polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Pat. Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337.

[0208] The 83P2H3-related proteins of the present invention can also be modified to form a chimeric molecule comprising 83P2H3 fused to another, heterologous polypeptide or amino acid sequence. Such a chimeric molecule can be synthesized chemically or recombinantly. A chimeric molecule can have a protein of the invention fused to another tumor-associated antigen or fragment thereof. Alternatively, a protein in accordance with the invention can comprise a fusion of fragments of the 83P2H3 sequence (amino or nucleic acid) such that a molecule is created that is not, through its length, directly homologous to the amino or nucleic acid sequences shown in FIG. 2 or FIG. 3. Such a chimeric molecule can comprise multiples of the same subsequence of 83P2H3. A chimeric molecule can comprise a fusion of a 83P2H3-related protein with a polyhistidine epitope tag, which provides an epitope to which immobilized nickel can selectively bind, with cytokines or with growth factors. The epitope tag is generally placed at the amino- or carboxyl-terminus of the 83P2H3. In an alternative embodiment, the chimeric molecule can comprise a fusion of a 83P2H3-related protein with an immunoglobulin or a particular region of an immunoglobulin. For a bivalent form of the chimeric molecule (also referred to as an “immunoadhesin”), such a fusion could be to the Fc region of an IgG molecule. The Ig fusions preferably include the substitution of a soluble (transmembrane domain deleted or inactivated) form of a 83P2H3 polypeptide in place of at least one variable region within an Ig molecule. In a preferred embodiment, the immunoglobulin fusion includes the hinge, CH2 and CH3, or the hinge, CHI, CH2 and CH3 regions of an IgGI molecule. For the production of immunoglobulin fusions see, e.g., U.S. Pat. No. 5,428,130 issued Jun. 27, 1995.

[0209] III.D.) Uses of 83P2H3-related Proteins

[0210] The proteins of the invention have a number of different specific uses. As 83P2H3 is highly expressed in prostate and other cancers, 83P2H3-related proteins are used in methods that assess the status of 83P2H3 gene products in normal versus cancerous tissues, thereby elucidating the malignant phenotype. Typically, polypeptides from specific regions of the 83P2H3 protein are used to assess the presence of perturbations (such as deletions, insertions, point mutations etc.) in those regions (such as regions containing one or more motifs). Exemplary assays utilize antibodies or T cells targeting 83P2H3-related proteins comprising the amino acid residues of one or more of the biological motifs contained within the 83P2H3 polypeptide sequence in order to evaluate the characteristics of this region in normal versus cancerous tissues or to elicit an immune response to the epitope. Alternatively, 83P2H3-related proteins that contain the amino acid residues of one or more of the biological motifs in the 83P2H3 protein are used to screen for factors that interact with that region of 83P2H3.

[0211]

83
P2H3 protein fragments/subsequences are particularly useful in generating and characterizing domain-specific antibodies (e.g., antibodies recognizing an extracellular or intracellular epitope of an 83P2H3 protein), for identifying agents or cellular factors that bind to 83P2H3 or a particular structural domain thereof, and in various therapeutic and diagnostic contexts, including but not limited to diagnostic assays, cancer vaccines and methods of preparing such vaccines.

[0212] Proteins encoded by the 83P2H3 genes, or by analogs, homologs or fragments thereof, have a variety of uses, including but not limited to generating antibodies and in methods for identifying ligands and other agents and cellular constituents that bind to an 83P2H3 gene product. Antibodies raised against an 83P2H3 protein or fragment thereof are useful in diagnostic and prognostic assays, and imaging methodologies in the management of human cancers characterized by expression of 83P2H3 protein, such as those listed in Table I. Such antibodies can be expressed intracellularly and used in methods of treating patients with such cancers. 83P2H3-related nucleic acids or proteins are also used in generating HTL or CTL responses.

[0213] Various immunological assays useful for the detection of 83P2H3 proteins are used, including but not limited to various types of radioimmunoassays, enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunofluorescent assays (ELIFA), immunocytochemical methods, and the like. Antibodies can be labeled and used as immunological imaging reagents capable of detecting 83P2H3-expressing cells (e.g., in radioscintigraphic imaging methods). 83P2H3 proteins are also particularly useful in generating cancer vaccines, as further described herein.

[0214] IV.) 83P2H3 Antibodies

[0215] Another aspect of the invention provides antibodies that bind to 83P2H3-related proteins. Preferred antibodies specifically bind to a 83P2H3-related protein and do not bind (or bind weakly) to peptides or proteins that are not 83P2H3-related proteins. For example, antibodies bind 83P2H3 can bind 83P2H3-related proteins such as the homologs or analogs thereof

[0216] 83P2H3 antibodies of the invention are particularly useful in prostate cancer diagnostic and prognostic assays, and imaging methodologies. Similarly, such antibodies are useful in the treatment, diagnosis, and/or prognosis of other cancers, to the extent 83P2H3 is also expressed or overexpressed in these other cancers. Moreover, intracellularly expressed antibodies (e.g., single chain antibodies) are therapeutically useful in treating cancers in which the expression of 83P2H3 is involved, such as advanced or metastatic prostate cancers.

[0217] The invention also provides various immunological assays useful for the detection and quantification of 83P2H3 and mutant 83P2H3-related proteins. Such assays can comprise one or more 83P2H3 antibodies capable of recognizing and binding a 83P2H3-related protein, as appropriate. These assays are performed within various immunological assay formats well known in the art, including but not limited to various types of radioimmunoassays, enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunofluorescent assays (ELIFA), and the like.

[0218] Immunological non-antibody assays of the invention also comprise T cell immunogenicity assays (inhibitory or stimulatory) as well as major histocompatibility complex (MHC) binding assays.

[0219] In addition, immunological imaging methods capable of detecting prostate cancer and other cancers expressing 83P2H3 are also provided by the invention, including but not limited to radioscintigraphic imaging methods using labeled 83P2H3 antibodies. Such assays are clinically useful in the detection, monitoring, and prognosis of 83P2H3 expressing cancers such as prostate cancer.

[0220] 83P2H3 antibodies are also used in methods for purifying a 83P2H3-related protein and for isolating 83P2H3 homologues and related molecules. For example, a method of purifying a 83P2H3-related protein comprises incubating an 83P2H3 antibody, which has been coupled to a solid matrix, with a lysate or other solution containing a 83P2H3-related protein under conditions that permit the 83P2H3 antibody to bind to the 83P2H3-related protein; washing the solid matrix to eliminate impurities; and eluting the 83P2H3-related protein from the coupled antibody. Other uses of the 83P2H3 antibodies of the invention include generating anti-idiotypic antibodies that minic the 83P2H3 protein.

[0221] Various methods for the preparation of antibodies are well known in the art. For example, antibodies can be prepared by immunizing a suitable mammalian host using a 83P2H3-related protein, peptide, or fragment, in isolated or immunoconjugated form (Antibodies: A Laboratory Manual, CSH Press, Eds., Harlow, and Lane (1988); Harlow, Antibodies, Cold Spring Harbor Press, NY (1989)). In addition, fusion proteins of 83P2H3 can also be used, such as a 83P2H3 GST-fusion protein. In a particular embodiment, a GST fusion protein comprising all or most of the amino acid sequence of FIG. 2 or FIG. 3 is produced, then used as an immunogen to generate appropriate antibodies. In another embodiment, a 83P2H3-related protein is synthesized and used as an immunogen.

[0222] In addition, naked DNA immunization techniques known in the art are used (with or without purified 83P2H3-related protein or 83P2H3 expressing cells) to generate an immune response to the encoded immunogen (for review, see Donnelly et al., 1997, Ann. Rev. Immunol. 15: 617-648).

[0223] The amino acid sequence of 83P2H3 as shown in FIG. 2 or FIG. 3 can be analyzed to select specific regions of the 83P2H3 protein for generating antibodies. For example, hydrophobicity and hydrophilicity analyses of the 83P2H3 amino acid sequence are used to identify hydrophilic regions in the 83P2H3 structure. Regions of the 83P2H3 protein that show immunogenic structure, as well as other regions and domains, can readily be identified using various other methods known in the art, such as Chou-Fasman, Garnier-Robson, Kyte-Doolittle, Eisenberg, Karplus-Schultz or Jameson-Wolf analysis. Thus, each region identified by any of these programs or methods is within the scope of the present invention. Methods for the generation of 83P2H3 antibodies are further illustrated by way of the examples provided herein. Methods for preparing a protein or polypeptide for use as an immunogen are well known in the art. Also well known in the art are methods for preparing immunogenic conjugates of a protein with a carrier, such as BSA, KLH or other carrier protein. In some circumstances, direct conjugation using, for example, carbodiimide reagents are used; in other instances linking reagents such as those supplied by Pierce Chemical Co., Rockford, Ill., are effective. Administration of a 83P2H3 immunogen is often conducted by injection over a suitable time period and with use of a suitable adjuvant, as is understood in the art. During the immunization schedule, titers of antibodies can be taken to determine adequacy of antibody formation.

[0224] 83P2H3 monoclonal antibodies can be produced by various means well known in the art. For example, immortalized cell lines that secrete a desired monoclonal antibody are prepared using the standard hybridoma technology of Kohler and Milstein or modifications that immortalize antibody-producing B cells, as is generally known. Immortalized cell lines that secrete the desired antibodies are screened by immunoassay in which the antigen is a 83P2H3-related protein. When the appropriate immortalized cell culture is identified, the cells can be expanded and antibodies produced either from in vitro cultures or from ascites fluid.

[0225] The antibodies or fragments of the invention can also be produced, by recombinant means. Regions that bind specifically to the desired regions of the 83P2H3 protein can also be produced in the context of chimeric or complementarity determining region (CDR) grafted antibodies of multiple species origin. Humanized or human 83P2H3 antibodies can also be produced, and are preferred for use in therapeutic contexts. Methods for humanizing murine and other non-human antibodies, by substituting one or more of the non-human antibody CDRs for corresponding human antibody sequences, are well known (see for example, Jones et al., 1986, Nature 321: 522-525; Riechmann et al., 1988, Nature 332: 323-327; Verhoeyen et al., 1988, Science 239: 1534-1536). See also, Carter et al., 1993, Proc. Natl. Acad. Sci. USA 89: 4285 and Sims et al., 1993, J. Immunol. 151: 2296.

[0226] Methods for producing fully human monoclonal antibodies include phage display and transgenic methods (for review, see Vaughan et al., 1998, Nature Biotechnology 16: 535-539). Fully human 83P2H3 monoclonal antibodies can be generated using cloning technologies employing large human Ig gene combinatorial libraries (i.e., phage display) (Griffiths and Hoogenboom, Building an in vitro immune system: human antibodies from phage display libraries. In: Protein Engineering of Antibody Molecules for Prophylactic and Therapeutic Applications in Man, Clark, M. (Ed.), Nottingham Academic, pp 45-64 (1993); Burton and Barbas, Human Antibodies from combinatorial libraries. Id., pp 65-82). Fully human 83P2H3 monoclonal antibodies can also be produced using transgenic mice engineered to contain human immunoglobulin gene loci as described in PCT Patent Application WO98/24893, Kucherlapati and Jakobovits et al., published Dec. 3, 1997 (see also, Jakobovits, 1998, Exp. Opin. Invest. Drugs 7(4): 607-614; U.S. Pat. No. 6,162,963 issued Dec. 19, 2000; U.S. Pat. No. 6,150,584 issued Nov. 12, 2000; and, U.S. Pat. No. 6,114,598 issued Sep. 5, 2000). This method avoids the in vitro manipulation required with phage display technology and efficiently produces high affinity authentic human antibodies.

[0227] Reactivity of 83P2H3 antibodies with an 83P2H3-related protein can be established by a number of well known means, including Western blot, immunoprecipitation, ELISA, and FACS analyses using, as appropriate, 83P2H3-related proteins, 83P2H3-expressing cells or extracts thereof. A 83P2H3 antibody or fragment thereof can be labeled with a detectable marker or conjugated to a second molecule. Suitable detectable markers include, but are not limited to, a radioisotope, a fluorescent compound, a bioluminescent compound, chemiluminescent compound, a metal chelator or an enzyme. Further, bi-specific antibodies specific for two or more 83P2H3 epitopes are generated using methods generally known in the art. Homodimeric antibodies can also be generated by cross-linking techniques known in the art (e.g., Wolff et al., Cancer Res. 53: 2560-2565).

[0228] V.) 83P2H3 Cellular Immune Responses

[0229] The mechanism by which T cells recognize antigens has been delineated. Efficacious peptide epitope vaccine compositions of the invention induce a therapeutic or prophylactic immune responses in very broad segments of the world-wide population. For an understanding of the value and efficacy of compositions of the invention that induce cellular immune responses, a brief review of immunology-related technology is provided.

[0230] A complex of an HLA molecule and a peptidic antigen acts as the ligand recognized by HLA-restricted T cells (Buus, S. et al., Cell 47:1071, 1986; Babbitt, B. P. et al., Nature 317:359, 1985; Townsend, A. and Bodmer, H., Annu. Rev. Immunol. 7:601, 1989; Germain, R. N., Annu. Rev. Immunol. 11:403, 1993). Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues that correspond to motifs required for specific binding to HLA antigen molecules have been identified and are set forth in Table IV (see also, e.g., Southwood, et al., J. Immunol. 160:3363, 1998; Rammensee, et al., Immunogenetics 41:178, 1995; Rammensee et al., SYFPEITHI, access via World Wide Web at URL syfpeithi.bmi-heidelberg.com/; Sette, A. and Sidney, J. Curr. Opin. Immunol. 10:478, 1998; Engelhard, V. H., Curr. Opin. Immunol. 6:13, 1994; Sette, A. and Grey, H. M., Curr. Opin. Immunol. 4:79, 1992; Sinigaglia, F. and Hammer, J. Curr. Biol. 6:52, 1994; Ruppert et al., Cell 74:929-937, 1993; Kondo et al., J. Immunol. 155:4307-4312, 1995; Sidney et al., J. Immunol. 157:3480-3490, 1996; Sidney et al., Human Immunol. 45:79-93, 1996; Sette, A. and Sidney, J. Immunogenetics 1999 November; 50(3-4):201-12, Review).

[0231] Furthermore, x-ray crystallographic analyses of HLA-peptide complexes have revealed pockets within the peptide binding cleft/groove of HLA molecules which accommodate, in an allele-specific mode, residues borne by peptide ligands; these residues in turn determine the HLA binding capacity of the peptides in which they are present. (See, e.g., Madden, D. R. Annu. Rev. Immunol. 13:587, 1995; Smith, et al., Immunity 4:203, 1996; Fremont et al., Immunity 8:305, 1998; Stern et al., Structure 2:245, 1994; Jones, E. Y. Curr. Opin. Immunol 9:75, 1997; Brown, J. H. et al., Nature 364:33, 1993; Guo, H. C. et al., Proc. Natl. Acad. Sci. USA 90:8053, 1993; Guo, H. C. et al., Nature 360:364, 1992; Silver, M. L. et al., Nature 360:367, 1992; Matsumura, M. et al., Science 257:927, 1992; Madden et al., Cell 70:1035, 1992; Fremont, D. H. et al., Science 257:919, 1992; Saper, M. A., Bjorkman, P. J. and Wiley, D. C., J. Mol. Biol. 219:277, 1991.)

[0232] Accordingly, the definition of class I and class II allele-specific HLA binding motifs, or class I or class II supermotifs allows identification of regions within a protein that are correlated with binding to particular HLA antigen(s).

[0233] Thus, by a process of HLA motif identification, candidates for epitope-based vaccines have been identified; such candidates can be further evaluated by HLA-peptide binding assays to determine binding affinity and/or the time period of association of the epitope and its corresponding HLA molecule. Additional confirmatory work can be performed to select, amongst these vaccine candidates, epitopes with preferred characteristics in terms of population coverage, and/or immunogenicity.

[0234] Various strategies can be utilized to evaluate cellular immunogenicity, including:

[0235] 1) Evaluation of primary T cell cultures from normal individuals (see, e.g., Wentworth, P. A. et al., Mol. Immunol. 32:603, 1995; Celis, E. et al., Proc. Natl. Acad. Sci. USA 91:2105, 1994; Tsai, V. et al., J. Immunol. 158:1796, 1997; Kawashima, I. et al., Human Immunol. 59:1, 1998). This procedure involves the stimulation of peripheral blood lymphocytes (PBL) from normal subjects with a test peptide in the presence of antigen presenting cells in vitro over a period of several weeks. T cells specific for the peptide become activated during this time and are detected using, e.g., a lymphokine- or 51Cr-release assay involving peptide sensitized target cells.

[0236] 2) Immunization of HLA transgenic nice (see, e.g., Wentworth, P. A. et al., J. Immunol. 26:97, 1996; Wentworth, P. A. et al., Int. Immunol. 8:651, 1996; Alexander, J. et al., J. Immunol. 159:4753, 1997). For example, in such methods peptides in incomplete Freund's adjuvant are administered subcutaneously to HLA transgenic mice. Several weeks following immunization, splenocytes are removed and cultured in vitro in the presence of test peptide for approximately one week. Peptide-specific T cells are detected using, e.g., a 51Cr-release assay involving peptide sensitized target cells and target cells expressing endogenously generated antigen.

[0237] 3) Demonstration of recall T cell responses from immune individuals who have been either effectively vaccinated and/or from chronically ill patients (see, e.g., Rehermann, B. et al., J. Exp. Med. 181:1047, 1995; Doolan, D. L. et al., Immunity 7:97, 1997; Bertoni, R. et al., J. Clin. Invest. 100:503, 1997; Threlkeld, S. C. et al., J. Immunol. 159:1648, 1997; Diepolder, H. M. et al., J. Virol. 71:6011, 1997). Accordingly, recall responses are detected by culturing PBL from subjects that have been exposed to the antigen due to disease and thus have generated an immune response “naturally”, or from patients who were vaccinated against the antigen. PBL from subjects are cultured in vitro for 1-2 weeks in the presence of test peptide plus antigen presenting cells (APC) to allow activation of “memory” T cells, as compared to “naive” T cells. At the end of the culture period, T cell activity is detected using assays including 51Cr release involving peptide-sensitized targets, T cell proliferation, or lymphokine release.

[0238] VI.) 83P2H3 Transgenic Animals

[0239] Nucleic acids that encode a 83P2H3-related protein can also be used to generate either transgenic animals or “knock out” animals which, in turn, are useful in the development and screening of therapeutically useful reagents. In accordance with established techniques, cDNA encoding 83P2H3 can be used to clone genomic DNA that encodes 83P2H3. The cloned genomic sequences can then be used to generate transgenic animals containing cells that express DNA that encode 83P2H3. Methods for generating transgenic animals, particularly animals such as mice or rats, have become conventional in the art and are described, for example, in U.S. Pat. No. 4,736,866 issued Apr. 12, 1988, and U.S. Pat. No. 4,870,009 issued Sep. 26, 1989. Typically, particular cells would be targeted for 83P2H3 transgene incorporation with tissue-specific enhancers.

[0240] Transgenic animals that include a copy of a transgene encoding 83P2H3 can be used to examine the effect of increased expression of DNA that encodes 83P2H3. Such animals can be used as tester animals for reagents thought to confer protection from, for example, pathological conditions associated with its overexpression. In accordance with this aspect of the invention, an animal is treated with a reagent and a reduced incidence of a pathological condition, compared to untreated animals that bear the transgene, would indicate a potential therapeutic intervention for the pathological condition.

[0241] Alternatively, non-human homologues of 83P2H3 can be used to construct a 83P2H3 “knock out” animal that has a defective or altered gene encoding 83P2H3 as a result of homologous recombination between the endogenous gene encoding 83P2H3 and altered genomic DNA encoding 83P2H3 introduced into an embryonic cell of the animal. For example, cDNA that encodes 83P2H3 can be used to clone genomic DNA encoding 83P2H3 in accordance with established techniques. A portion of the genomic DNA encoding 83P2H3 can be deleted or replaced with another gene, such as a gene encoding a selectable marker that can be used to monitor integration. Typically, several kilobases of unaltered flanking DNA (both at the 5′ and 3′ ends) are included in the vector (see, e.g., Thomas and Capecchi, Cell, 51:503 (1987) for a description of homologous recombination vectors). The vector is introduced into an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced DNA has homologously recombined with the endogenous DNA are selected (see, e.g., Li et al., Cell, 69:915 (1992)). The selected cells are then injected into a blastocyst of an animal (e.g., a mouse or rat) to form aggregation chimeras (see, e.g.,, Bradley, in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, E. J. Robertson, ed. (IRL, Oxford, 1987), pp. 113-152). A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal, and the embryo brought to term to create a “knock out” animal. Progeny harboring the homologously recombined DNA in their germ cells can be identified by standard techniques and used to breed animals in which all cells of the animal contain the homologously recombined DNA. Knock out animals can be characterized, for example, for their ability to defend against certain pathological conditions or for their development of pathological conditions due to absence of the 83P2H3 polypeptide.

[0242] VII.) Methods for the Detection of 83P2H3

[0243] Another aspect of the present invention relates to methods for detecting 83P2H3 polynucleotides and 83P2H3-related proteins, as well as methods for identifying a cell that expresses 83P2H3. The expression profile of 83P2H3 makes it a diagnostic marker for metastasized disease. Accordingly, the status of 83P2H3 gene products provides information useful for predicting a variety of factors including susceptibility to advanced stage disease, rate of progression, and/or tumor aggressiveness. As discussed in detail herein, the status of 83P2H3 gene products in patient samples can be analyzed by a variety protocols that are well known in the art including immunohistochemical analysis, the variety of Northern blotting techniques including in situ hybridization, RT-PCR analysis (for example on laser capture micro-dissected samples), Western blot analysis and tissue array analysis.

[0244] More particularly, the invention provides assays for the detection of 83P2H3 polynucleotides in a biological sample, such as serum, bone, prostate, and other tissues, urine, semen, cell preparations, and the like. Detectable 83P2H3 polynucleotides include, for example, a 83P2H3 gene or fragment thereof, 83P2H3 mRNA, alternative splice variant 83P2H3 mRNAs, and recombinant DNA or RNA molecules that contain a 83P2H3 polynucleotide. A number of methods for amplifying and/or detecting the presence of 83P2H3 polynucleotides are well known in the art and can be employed in the practice of this aspect of the invention.

[0245] In one embodiment, a method for detecting an 83P2H3 mRNA in a biological sample comprises producing cDNA from the sample by reverse transcription using at least one primer; amplifying the cDNA so produced using an 83P2H3 polynucleotides as sense and antisense primers to amplify 83P2H3 cDNAs therein; and detecting the presence of the amplified 83P2H3 cDNA. Optionally, the sequence of the amplified 83P2H3 cDNA can be determined.

[0246] In another embodiment, a method of detecting a 83P2H3 gene in a biological sample comprises first isolating genomic DNA from the sample; amplifying the isolated genomic DNA using 83P2H3 polynucleotides as sense and antisense primers; and detecting the presence of the amplified 83P2H3 gene. Any number of appropriate sense and antisense probe combinations can be designed from the nucleotide sequence provided for the 83P2H3 (FIG. 2) and used for this purpose.

[0247] The invention also provides assays for detecting the presence of an 83P2H3 protein in a tissue or other biological sample such as serum, semen, bone, prostate, urine, cell preparations, and the like. Methods for detecting a 83P2H3-related protein are also well known and include, for example, immunoprecipitation, immunohistochemical analysis, Western blot analysis, molecular binding assays, ELISA, ELIFA and the like. For example, a method of detecting the presence of a 83P2H3-related protein in a biological sample comprises first contacting the sample with a 83P2H3 antibody, a 83P2H3-reactive fragment thereof, or a recombinant protein containing an antigen binding region of a 83P2H3 antibody; and then detecting the binding of 83P2H3-related protein in the sample.

[0248] Methods for identifying a cell that expresses 83P2H3 are also within the scope of the invention. In one embodiment, an assay for identifying a cell that expresses a 83P2H3 gene comprises detecting the presence of 83P2H3 mRNA in the cell. Methods for the detection of particular mRNAs in cells are well known and include, for example, hybridization assays using complementary DNA probes (such as in situ hybridization using labeled 83P2H3 riboprobes, Northern blot and related techniques) and various nucleic acid amplification assays (such as RT-PCR using complementary primers specific for 83P2H3, and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like). Alternatively, an assay for identifying a cell that expresses a 83P2H3 gene comprises detecting the presence of 83P2H3-related protein in the cell or secreted by the cell. Various methods for the detection of proteins are well known in the art and are employed for the detection of 83P2H3-related proteins and cells that express 83P2H3-related proteins.

[0249] 83P2H3 expression analysis is also useful as a tool for identifying and evaluating agents that modulate 83P2H3 gene expression. For example, 83P2H3 expression is significantly upregulated in prostate cancer, and is expressed in cancers of the tissues listed in Table I. Identification of a molecule or biological agent that inhibits 83P2H3 expression or over-expression in cancer cells is of therapeutic value. For example, such an agent can be identified by using a screen that quantifies 83P2H3 expression by RT-PCR, nucleic acid hybridization or antibody binding.

[0250] VIII.) Methods for Monitoring the Status of 83P2H3-related Genes and Their Products

[0251] Oncogenesis is known to be a multistep process where cellular growth becomes progressively dysregulated and cells progress from a normal physiological state to precancerous and then cancerous states (see, e.g., Alers et al., Lab Invest. 77(5): 437-438 (1997) and Isaacs et al., Cancer Surv. 23: 19-32 (1995)). In this context, examining a biological sample for evidence of dysregulated cell growth (such as aberrant 83P2H3 expression in cancers) allows for early detection of such aberrant physiology, before a pathologic state such as cancer has progressed to a stage that therapeutic options are more limited and or the prognosis is worse. In such examinations, the status of 83P2H3 in a biological sample of interest can be compared, for example, to the status of 83P2H3 in a corresponding normal sample (e.g. a sample from that individual or alternatively another individual that is not affected by a pathology). An alteration in the status of 83P2H3 in the biological sample (as compared to the normal sample) provides evidence of dysregulated cellular growth. In addition to using a biological sample that is not affected by a pathology as a normal sample, one can also use a predetermined normative value such as a predetermined normal level of mRNA expression (see, e.g., Grever et al., J. Comp. Neurol. Dec 9, 1996; 376(2):306-14 and U.S. Pat. No. 5,837,501) to compare 83P2H3 status sample.

[0252] The term “status” in this context is used according to its art accepted meaning and refers to the condition or state of a gene and its products. Typically, skilled artisans use a number of parameters to evaluate the condition or state of a gene and its products. These include, but are not limited to the location of expressed gene products (including the location of 83P2H3 expressing cells) as well as the level, and biological activity of expressed gene products (such as 83P2H3 mRNA, polynucleotides and polypeptides). Typically, an alteration in the status of 83P2H3 comprises a change in the location of 83P2H3 and/or 83P2H3 expressing cells and/or an increase in 83P2H3 mRNA and/or protein expression.

[0253] 83P2H3 status in a sample can be analyzed by a number of means well known in the art, including without limitation, immunohistochemical analysis, in situ hybridization, RT-PCR analysis on laser capture micro-dissected samples, Western blot analysis, and tissue array analysis. Typical protocols for evaluating the status of the 83P2H3 gene and gene products are found, for example in Ausubel et al. eds., 1995, Current Protocols In Molecular Biology, Units 2 (Northern Blotting), 4 (Southern Blotting), 15 (Immunoblotting) and 18 (PCR Analysis). Thus, the status of 83P2H3 in a biological sample is evaluated by various methods utilized by skilled artisans including, but not limited to genomic Southern analysis (to examine, for example perturbations in the 83P2H3 gene), Northern analysis and/or PCR analysis of 83P2H3 mRNA (to examine, for example alterations in the polynucleotide sequences or expression levels of 83P2H3 mRNAs), and, Western and/or immunohistochemical analysis (to examine, for example alterations in polypeptide sequences, alterations in polypeptide localization within a sample, alterations in expression levels of 83P2H3 proteins and/or associations of 83P2H3 proteins with polypeptide binding partners). Detectable 83P2H3 polynucleotides include, for example, a 83P2H3 gene or fragment thereof, 83P2H3 mRNA, alternative splice variants, 83P2H3 mRNAs, and recombinant DNA or RNA molecules containing a 83P2H3 polynucleotide.

[0254] The expression profile of 83P2H3 makes it a diagnostic marker for local and/or metastasized disease, and provides information on the growth or oncogenic potential of a biological sample. In particular, the status of 83P2H3 provides information useful for predicting susceptibility to particular disease stages, progression, and/or tumor aggressiveness. The invention provides methods and assays for determining 83P2H3 status and diagnosing cancers that express 83P2H3, such as cancers of the tissues listed in Table I. For example, because 83P2H3 mRNA is so highly expressed in prostate and other cancers relative to normal prostate tissue, assays that evaluate the levels of 83P2H3 mRNA transcripts or proteins in a biological sample can be used to diagnose a disease associated with 83P2H3 dysregulation, and can provide prognostic information useful in defining appropriate therapeutic options.

[0255] The expression status of 83P2H3 provides information including the presence, stage and location of dysplastic, precancerous and cancerous cells, predicting susceptibility to various stages of disease, and/or for gauging tumor aggressiveness. Moreover, the expression profile makes it useful as an imaging reagent for metastasized disease. Consequently, an aspect of the invention is directed to the various molecular prognostic and diagnostic methods for examining the status of 83P2H3 in biological samples such as those from individuals suffering from, or suspected of suffering from a pathology characterized by dysregulated cellular growth, such as cancer.

[0256] As described above, the status of 83P2H3 in a biological sample can be examined by a number of well-known procedures in the art. For example, the status of 83P2H3 in a biological sample taken from a specific location in the body can be examined by evaluating the sample for the presence or absence of 83P2H3 expressing cells (e.g. those that express 83P2H3 mRNAs or proteins). This examination can provide evidence of dysregulated cellular growth, for example, when 83P2H3-expressing cells are found in a biological sample that does not normally contain such cells (such as a lymph node), because such alterations in the status of 83P2H3 in a biological sample are often associated with dysregulated cellular growth. Specifically, one indicator of dysregulated cellular growth is the metastases of cancer cells from an organ of origin (such as the prostate) to a different area of the body (such as a lymph node). In this context, evidence of dysregulated cellular growth is important for example because occult lymph node metastases can be detected in a substantial proportion of patients with prostate cancer, and such metastases are associated with known predictors of disease progression (see, e.g., Murphy et al., Prostate 42(4): 315-317 (2000);Su et al., Semin. Surg. Oncol. 18(1): 17-28 (2000) and Freeman et al., J Urol 1995 August 154(2 Pt 1):474-8).

[0257] In one aspect, the invention provides methods for monitoring 83P2H3 gene products by determining the status of 83P2H3 gene products expressed by cells from an individual suspected of having a disease associated with dysregulated cell growth (such as hyperplasia or cancer) and then comparing the status so determined to the status of 83P2H3 gene products in a corresponding normal sample. The presence of aberrant 83P2H3 gene products in the test sample relative to the normal sample provides an indication of the presence of dysregulated cell growth within the cells of the individual.

[0258] In another aspect, the invention provides assays useful in determining the presence of cancer in an individual, comprising detecting a significant increase in 83P2H3 mRNA or protein expression in a test cell or tissue sample relative to expression levels in the corresponding normal cell or tissue. The presence of 83P2H3 mRNA can, for example, be evaluated in tissue samples including but not limited to those listed in Table I. The presence of significant 83P2H3 expression in any of these tissues is useful to indicate the emergence, presence and/or severity of a cancer, since the corresponding normal tissues do not express 83P2H3 mRNA or express it at lower levels.

[0259] In a related embodiment, 83P2H3 status is determined at the protein level rather than at the nucleic acid level. For example, such a method comprises determining the level of 83P2H3 protein expressed by cells in a test tissue sample and comparing the level so determined to the level of 83P2H3 expressed in a corresponding normal sample. In one embodiment, the presence of 83P2H3 protein is evaluated, for example, using immunohistochemical methods. 83P2H3 antibodies or binding partners capable of detecting 83P2H3 protein expression are used in a variety of assay formats well known in the art for this purpose.

[0260] In a further embodiment, one can evaluate the status of 83P2H3 nucleotide and amino acid sequences in a biological sample in order to identify perturbations in the structure of these molecules. These perturbations can include insertions, deletions, substitutions and the like. Such evaluations are useful because perturbations in the nucleotide and amino acid sequences are observed in a large number of proteins associated with a growth dysregulated phenotype (see, e.g., Marrogi et al., 1999, J. Cutan. Pathol. 26(8):369-378). For example, a mutation in the sequence of 83P2H3 may be indicative of the presence or promotion of a tumor. Such assays therefore have diagnostic and predictive value where a mutation in 83P2H3 indicates a potential loss of function or increase in tumor growth.

[0261] A wide variety of assays for observing perturbations in nucleotide and amino acid sequences are well known in the art. For example, the size and structure of nucleic acid or amino acid sequences of 83P2H3 gene products are observed by the Northern, Southern, Western, PCR and DNA sequencing protocols discussed herein. In addition, other methods for observing perturbations in nucleotide and amino acid sequences such as single strand conformation polymorphism analysis are well known in the art (see, e.g., U.S. Pat. No. 5,382,510 issued Sep. 7, 1999, and U.S. Pat. No. 5,952,170 issued Jan. 17, 1995).

[0262] Additionally, one can examine the methylation status of the 83P2H3 gene in a biological sample. Aberrant demethylation and/or hypermethylation of CpG islands in gene 5′ regulatory regions frequently occurs in immortalized and transformed cells, and can result in altered expression of various genes. For example, promoter hypermethylation of the pi-class glutathione S-transferase (a protein expressed in normal prostate but not expressed in >90% of prostate carcinomas) appears to permanently silence transcription of this gene and is the most frequently detected genomic alteration in prostate carcinomas (De Marzo et al., Am. J. Pathol. 155(6): 1985-1992 (1999)). In addition, this alteration is present in at least 70% of cases of high-grade prostatic intraepithelial neoplasia (PIN) (Brooks et al, Cancer Epidemiol. Biomarkers Prev., 1998, 7:531-536). In another example, expression of the LAGE-I tumor specific gene (which is not expressed in normal prostate but is expressed in 25-50% of prostate cancers) is induced by deoxy-azacytidine in lymphoblastoid cells, suggesting that tumoral expression is due to demethylation (Lethe et al., Int. J. Cancer 76(6): 903-908 (1998)). A variety of assays for examining methylation status of a gene are well known in the art. For example, one can utilize, in Southern hybridization approaches, methylation-sensitive restriction enzymes which cannot cleave sequences that contain methylated CpG sites to assess the methylation status of CpG islands. In addition, MSP (methylation specific PCR) can rapidly profile the methylation status of all the CpG sites present in a CpG island of a given gene. This procedure involves initial modification of DNA by sodium bisulfite (which will convert all unmethylated cytosines to uracil) followed by amplification using primers specific for methylated versus unmethylated DNA. Protocols involving methylation interference can also be found for example in Current Protocols In Molecular Biology, Unit 12, Frederick M. Ausubel et al. eds., 1995.

[0263] Gene amplification is an additional method for assessing the status of 83P2H3. Gene amplification is measured in a sample directly, for example, by conventional Southern blotting or Northern blotting to quantitate the transcription of mRNA (Thomas, 1980, Proc. Natl. Acad. Sci. USA, 77:5201-5205), dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein. Alternatively, antibodies are employed that recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn are labeled and the assay carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected.

[0264] Biopsied tissue or peripheral blood can be conveniently assayed for the presence of cancer cells using for example, Northern, dot blot or RT-PCR analysis to detect 83P2H3 expression. The presence of RT-PCR amplifiable 83P2H3 mRNA provides an indication of the presence of cancer. RT-PCR assays are well known in the art. RT-PCR detection assays for tumor cells in peripheral blood are currently being evaluated for use in the diagnosis and management of a number of human solid tumors. In the prostate cancer field, these include RT-PCR assays for the detection of cells expressing PSA and PSM (Verkaik et al., 1997, Urol. Res. 25:373-384; Ghossein et al., 1995, J. Clin. Oncol. 13:1195-2000; Heston et al., 1995, Clin. Chem 41:1687-1688).

[0265] A further aspect of the invention is an assessment of the susceptibility that an individual has for developing cancer. In one embodiment, a method for predicting susceptibility to cancer comprises detecting 83P2H3 mRNA or 83P2H3 protein in a tissue sample, its presence indicating susceptibility to cancer, wherein the degree of 83P2H3 mRNA expression correlates to the degree of susceptibility. In a specific embodiment, the presence of 83P2H3 in prostate or other tissue is examined, with the presence of 83P2H3 in the sample providing an indication of prostate cancer susceptibility (or the emergence or existence of a prostate tumor). Similarly, one can evaluate the integrity 83P2H3 nucleotide and amino acid sequences in a biological sample, in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like. The presence of one or more perturbations in 83P2H3 gene products in the sample is an indication of cancer susceptibility (or the emergence or existence of a tumor).

[0266] The invention also comprises methods for gauging tumor aggressiveness. In one embodiment, a method for gauging aggressiveness of a tumor comprises determining the level of 83P2H3 mRNA or 83P2H3 protein expressed by tumor cells, comparing the level so determined to the level of 83P2H3 mRNA or 83P2H3 protein expressed in a corresponding normal tissue taken from the same individual or a normal tissue reference sample, wherein the degree of 83P2H3 mRNA or 83P2H3 protein expression in the tumor sample relative to the normal sample indicates the degree of aggressiveness. In a specific embodiment, aggressiveness of a tumor is evaluated by determining the extent to which 83P2H3 is expressed in the tumor cells, with higher expression levels indicating more aggressive tumors. Another embodiment is the evaluation of the integrity of 83P2H3 nucleotide and amino acid sequences in a biological sample, in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like. The presence of one or more perturbations indicates more aggressive tumors.

[0267] Another embodiment of the invention is directed to methods for observing the progression of a malignancy in an individual over time. In one embodiment, methods for observing the progression of a malignancy in an individual over time comprise determining the level of 83P2H3 mRNA or 83P2H3 protein expressed by cells in a sample of the tumor, comparing the level so determined to the level of 83P2H3 mRNA or 83P2H3 protein expressed in an equivalent tissue sample taken from the same individual at a different time, wherein the degree of 83P2H3 mRNA or 83P2H3 protein expression in the tumor sample over time provides information on the progression of the cancer. In a specific embodiment, the progression of a cancer is evaluated by determining 83P2H3 expression in the tumor cells over time, where increased expression over time indicates a progression of the cancer. Also, one can evaluate the integrity 83P2H3 nucleotide and amino acid sequences in a biological sample in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like, where the presence of one or more perturbations indicates a progression of the cancer.

[0268] The above diagnostic approaches can be combined with any one of a wide variety of prognostic and diagnostic protocols known in the art. For example, another embodiment of the invention is directed to methods for observing a coincidence between the expression of 83P2H3 gene and 83P2H3 gene products (or perturbations in 83P2H3 gene and 83P2H3 gene products) and a factor that is associated with malignancy, as a means for diagnosing and prognosticating the status of a tissue sample. A wide variety of factors associated with malignancy can be utilized, such as the expression of genes associated with malignancy (e.g. PSA, PSCA and PSM expression for prostate cancer etc.) as well as gross cytological observations (see, e.g., Bocking et al., 1984, Anal. Quant. Cytol. 6(2):74-88; Epstein, 1995, Hum. Pathol. 26(2):223-9; Thorson et al., 1998, Mod. Pathol. 11(6):543-51; Baisden et al., 1999, Am. J. Surg. Pathol. 23(8):918-24). Methods for observing a coincidence between the expression of 83P2H3 gene and 83P2H3 gene products (or perturbations in 83P2H3 gene and 83P2H3 gene products) and another factor that is associated with malignancy are useful, for example, because the presence of a set of specific factors that coincide with disease provides information crucial for diagnosing and prognosticating the status of a tissue sample.

[0269] In one embodiment, methods for observing a coincidence between the expression of 83P2H3 gene and 83P2H3 gene products (or perturbations in 83P2H3 gene and 83P2H3 gene products) and another factor associated with malignancy entails detecting the overexpression of 83P2H3 mRNA or protein in a tissue sample, detecting the overexpression of PSA mRNA or protein in a tissue sample (or PSCA or PSM expression), and observing a coincidence of 83P2H3 mRNA or protein and PSA mRNA or protein overexpression (or PSCA or PSM expression). In a specific embodiment, the expression of 83P2H3 and PSA mRNA in prostate tissue is examined, where the coincidence of 83P2H3 and PSA mRNA overexpression in the sample indicates the existence of prostate cancer, prostate cancer susceptibility or the emergence or status of a prostate tumor.

[0270] Methods for detecting and quantifying the expression of 83P2H3 mRNA or protein are described herein, and standard nucleic acid and protein detection and quantification technologies are well known in the art Standard methods for the detection and quantification of 83P2H3 mRNA include in situ hybridization using labeled 83P2H3 riboprobes, Northern blot and related techniques using 83P2H3 polynucleotide probes, RT-PCR analysis using primers specific for 83P2H3, and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like. In a specific embodiment, semi-quantitative RT-PCR is used to detect and quantify 83P2H3 mRNA expression. Any number of primers capable of amplifying 83P2H3 can be used for this purpose, including but not limited to the various primer sets specifically described herein. In a specific embodiment, polyclonal or monoclonal antibodies specifically reactive with the wild-type 83P2H3 protein can be used in an immunohistochemical assay of biopsied tissue.

[0271] IX.) Identification of Molecules That Interact With 83P2H3

[0272] The 83P2H3 protein and nucleic acid sequences disclosed herein allow a skilled artisan to identify proteins, small molecules and other agents that interact with 83P2H3, as well as pathways activated by 83P2H3 via any one of a variety of art accepted protocols. For example, one can utilize one of the so-called interaction trap systems (also referred to as the “two-hybrid assay”). In such systems, molecules interact and reconstitute a transcription factor which directs expression of a reporter gene, whereupon the expression of the reporter gene is assayed. Other systems identify protein-protein interactions in vivo through reconstitution of a eukaryotic transcriptional activator, see, e.g., U.S. Pat. No. 5,955,280 issued Sep. 21, 1999, U.S. Pat. No. 5,925,523 issued Jul. 20, 1999, U.S. Pat. No. 5,846,722 issued Dec. 8, 1998 and U.S. Pat. No. 6,004,746 issued Dec. 21, 1999. Algorithms are also available in the art for genome-based predictions of protein function (see, e.g., Marcotte, et al., Nature 402: Nov. 4, 1999, 83-86).

[0273] Alternatively one can screen peptide libraries to identify molecules that interact with 83P2H3 protein sequences. In such methods, peptides that bind to a molecule such as 83P2H3 are identified by screening libraries that encode a random or controlled collection of amino acids. Peptides encoded by the libraries are expressed as fusion proteins of bacteriophage coat proteins, the bacteriophage particles are then screened against the protein of interest.

[0274] Accordingly, peptides having a wide variety of uses, such as therapeutic, prognostic or diagnostic reagents, are thus identified without any prior information on the structure of the expected ligand or receptor molecule. Typical peptide libraries and screening methods that can be used to identify molecules that interact with 83P2H3 protein sequences are disclosed for example in U.S. Pat. No. 5,723,286 issued Mar. 3, 1998 and U.S. Pat. No. 5,733,731 issued Mar. 31, 1998.

[0275] Alternatively, cell lines that express 83P2H3 are used to identify protein-protein interactions mediated by 83P2H3. Such interactions can be examined using immunoprecipitation techniques (see, e.g., Hamilton B J, et al. Biochem. Biophys. Res. Commun. 1999, 261:646-51). 83P2H3 protein can be immunoprecipitated from 83P2H3-expressing cell lines using anti-83P2H3 antibodies. Alternatively, antibodies against His-tag can be used in a cell line engineered to express 83P2H3 (vectors mentioned above). The immunoprecipitated complex can be examined for protein association by procedures such as Western blotting, 35S-methionine labeling of proteins, protein microsequencing, silver staining and two-dimensional gel electrophoresis.

[0276] Small molecules and ligands that interact with 83P2H3 can be identified through related embodiments of such screening assays. For example, small molecules can be identified that interfere with protein function, including molecules that interfere with 83P2H3's ability to mediate phosphorylation and de-phosphorylation, interaction with DNA or RNA molecules as an indication of regulation of cell cycles, second messenger signaling or tumorigenesis. Similarly, small molecules that modulate ion channel, protein pump, or cell communication function of 83P2H3 are identified and used to treat patients that have a cancer that expresses the 83P2H3 antigen (see, e.g., Hille, B., Ionic Channels of Excitable Membranes 2nd Ed., Sinauer Assoc., Sunderland, Mass., 1992). Moreover, ligands that regulate 83P2H3 function can be identified based on their ability to bind 83P2H3 and activate a reporter construct. Typical methods are discussed for example in U.S. Pat. No. 5,928,868 issued Jul. 27, 1999, and include methods for forming hybrid ligands in which at least one ligand is a small molecule. In an illustrative embodiment, cells engineered to express a fusion protein of 83P2H3 and a DNA-binding protein are used to co-express a fusion protein of a hybrid ligand/small molecule and a cDNA library transcriptional activator protein. The cells further contain a reporter gene, the expression of which is conditioned on the proximity of the first and second fusion proteins to each other, an event that occurs only if the hybrid ligand binds to target sites on both hybrid proteins. Those cells that express the reporter gene are selected and the unknown small molecule or the unknown ligand is identified. This method provides a means of identifying both activators and inhibitors of 83P2H3.

[0277] An embodiment of this invention comprises a method of screening for a molecule that interacts with an 83P2H3 amino acid sequence shown in FIG. 2 or FIG. 3, comprising the steps of contacting a population of molecules with the 83P2H3 amino acid sequence, allowing the population of molecules and the 83P2H3 amino acid sequence to interact under conditions that facilitate an interaction, determining the presence of a molecule that interacts with the 83P2H3 amino acid sequence, and then separating molecules that do not interact with the 83P2H3 amino acid sequence from molecules that do. In a specific embodiment, the method further comprises purifying a molecule that interacts with the 83P2H3 amino acid sequence. The identified molecule can be used to modulate a function performed by 83P2H3. In a preferred embodiment, the 83P2H3 amino acid sequence is contacted with a library of peptides.

[0278] X.) Therapeutic Methods and Compositions

[0279] The identification of 83P2H3 as a protein that is normally expressed in a restricted set of tissues, but which is also expressed in prostate and other cancers, opens a number of therapeutic approaches to the treatment of such cancers. As discussed herein, it is possible that 83P2H3 functions as a transcription factor involved in activating tumor-promoting genes or repressing genes that block tumorigenesis.

[0280] Accordingly, therapeutic approaches that inhibit the activity of the 83P2H3 protein are useful for patients suffering from a cancer that expresses 83P2H3. These therapeutic approaches generally fall into two classes. One class comprises various methods for inhibiting the binding or association of the 83P2H3 protein with its binding partner or with other proteins. Another class comprises a variety of methods for inhibiting the transcription of the 83P2H3 gene or translation of 83P2H3 mRNA.

[0281] X.A.) Anti-Cancer Vaccines

[0282] The invention further provides cancer vaccines comprising a 83P2H3-related protein or 83P2H3-related nucleic acid. In view of the expression of 83P2H3, cancer vaccines prevent and/or treat 83P2H3-expressing cancers with minimal or no effects on non-target tissues. The use of a tumor antigen in a vaccine that generates humoral and/or cell-mediated immune responses as anti-cancer therapy is well known in the art and has been employed in prostate cancer using human PSMA and rodent PAP immunogens (Hodge et al., 1995, Int. J. Cancer 63:231-237; Fong et al., 1997,J. Immunol. 159:3113-3117).

[0283] Such methods can be readily practiced by employing a 83P2H3-related protein, or an 83P2H3-encoding nucleic acid molecule and recombinant vectors capable of expressing and presenting the 83P2H3 immunogen (which typically comprises a number of antibody or T cell epitopes). Skilled artisans understand that a wide variety of vaccine systems for delivery of immunoreactive epitopes are known in the art (see, e.g., Heryln et al., Ann Med 1999 February 31(1):66-78; Maruyama et al., Cancer Immunol Immunother 2000 Jun 49(3): 123-32) Briefly, such methods of generating an immune response (e.g. humoral and/or cell-mediated) in a mammal, comprise the steps of: exposing the mammal's immune system to an immunoreactive epitope (e.g. an epitope present in the 83P2H3 protein shown in SEQ ID NO: 703 or analog or homolog thereof) so that the mammal generates an immune response that is specific for that epitope (e.g. generates antibodies that specifically recognize that epitope). In a preferred method, the 83P2H3 immunogen contains a biological motif, see e.g., Tables V-XVIII, or a peptide of a size range from 83P2H3 indicated in FIG. 14, FIG. 15, FIG. 16, FIG. 17, and FIG. 18.

[0284] The entire 83P2H3 protein, immunogenic regions or epitopes thereof can be combined and delivered by various means. Such vaccine compositions can include, for example, lipopeptides (e.g., Vitiello, A. et al., J. Clin. Invest. 95:341, 1995), peptide compositions encapsulated in poly(DL-lactide-co-glycolide) (“PLG”) microspheres (see, e.g., Eldridge, et al., Molec. Immunol. 28:287-294, 1991: Alonso et al., Vaccine 12:299-306, 1994; Jones et al., Vaccine 13:675-681, 1995), peptide compositions contained in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi et al., Nature 344:873-875, 1990; Hu et al., Clin Exp Immunol. 113:235-243, 1998), multiple antigen peptide systems (MAPs) (see e.g., Tam, J. P., Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413, 1988; Tam, J. P., J. Immunol. Methods 196:17-32, 1996), peptides formulated as multivalent peptides; peptides for use in ballistic delivery systems, typically crystallized peptides, viral delivery vectors (Perkus, M. E. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 379, 1996; Chakrabarti, S. et al., Nature 320:535, 1986; Hu, S. L. et al., Nature 320:537, 1986; Kieny, M.-P. et al., AIDS Bio/Technology 4:790, 1986; Top, F. H. et al., J. Infect. Dis. 124:148, 1971; Chanda, P. K. et al., Virology 175:535, 1990), particles of viral or synthetic origin (e.g., Kofler, N. et al., J. Immunol. Methods. 192:25, 1996; Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993; Falo, L. D., Jr. et al., Nature Med. 7:649, 1995), adjuvants (Warren, H. S., Vogel, F. R., and Chedid, L. A. Annu. Rev. Immunol. 4:369, 1986; Gupta, R. K. et al., Vaccine 11:293, 1993), liposomes (Reddy, R. et al., J. Immunol. 148:1585, 1992; Rock, K. L., Immunol. Today 17:131, 1996), or, naked or particle absorbed cDNA (Ulmer, J. B. et al., Science 259:1745, 1993; Robinson, H. L., Hunt, L. A., and Webster, R. G., Vaccine 11:957, 1993; Shiver, J. W. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 423, 1996; Cease, K. B., and Berzofsky, J. A., Annu. Rev. Immunol. 12:923, 1994 and Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993). Toxin-targeted delivery technologies, also known as receptor mediated targeting, such as those of Avant Immunotherapeutics, Inc. (Needham, Mass.) may also be used.

[0285] In patients with 83P2H3-associated cancer, the vaccine compositions of the invention can also be used in conjunction with other treatments used for cancer, e.g., surgery, chemotherapy, drug therapies, radiation therapies, etc. including use in combination with immune adjuvants such as IL-2, IL-12, GM-CSF, and the like.

[0286] Cellular Vaccines

[0287] CTL epitopes can be determined using specific algorithms to identify peptides within 83P2H3 protein that bind corresponding HLA alleles (see e.g., Table IV; Epimer™ and Epimatrix™, Brown University (URL www.brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html); and, BIMAS, (URL bimas.dcrt.nih.gov/; SYFPEITHI at URL syfpeithi.bmi-heidelberg.com/). In a preferred embodiment, the 83P2H3 immunogen contains one or more amino acid sequences identified using techniques well known in the art, such as the sequences shown in Tables V-XVIII or a peptide of 8, 9, 10 or 11 amino acids specified by an HLA Class I motif/supermotif (e.g., Table IV (A), Table IV (D), or Table IV (E)) and/or a peptide of at least 9 amino acids that comprises an HLA Class II motif/supermotif (e.g., Table IV (B) or Table IV (C)). As is appreciated in the art, the HLA Class I binding groove is essentially closed ended so that peptides of only a particular size range can fit into the groove and be bound, generally HLA Class I epitopes are 8, 9, 10, or 11 amino acids long. In contrast, the HLA Class II binding groove is essentially open ended; therefore a peptide of about 9 or more amino acids can be bound by an HLA Class II molecule. Due to the binding groove differences between HLA Class I and II, HLA Class I motifs are length specific, i.e., position two of a Class I motif is the second amino acid in an amino to carboxyl direction of the peptide. The amino acid positions in a Class II motif are relative only to each other, not the overall peptide, i.e., additional amino acids can be attached to the amino and/or carboxyl termini of a motif-bearing sequence. HLA Class II epitopes are often 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 amino acids long, or longer than 25 amino acids.

[0288] Antibody-based Vaccines

[0289] A wide variety of methods for generating an immune response in a mammal are known in the art (for example as the first step in the generation of hybridomas). Methods of generating an immune response in a mammal comprise exposing the mammal's immune system to an immunogenic epitope on a protein (e.g. the 83P2H3 protein) so that an immune response is generated. A typical embodiment consists of a method for generating an immune response to 83P2H3 in a host, by contacting the host with a sufficient amount of at least one 83P2H3 B cell or cytotoxic T-cell epitope or analog thereof; and at least one periodic interval thereafter re-contacting the host with the 83P2H3 B cell or cytotoxic T-cell epitope or analog thereof. A specific embodiment consists of a method of generating an immune response against a 83P2H3-related protein or a man-made multiepitopic peptide comprising: administering 83P2H3 immunogen (e.g. the 83P2H3 protein or a peptide fragment thereof, an 83P2H fusion protein or analog etc.) in a vaccine preparation to a human or another mammal. Typically, such vaccine preparations further contain a suitable adjuvant (see, e.g., U.S. Pat. No. 6,146,635) or a universal helper epitope such as a PADRE™ peptide (Epimmune Inc., San Diego, Calif.; see, e.g., Alexander et al., J. Immunol. 2000 164(3); 164(3): 1625-1633; Alexander et al., Immunity 1994 1(9); 751-761 and Alexander et al., Immunol. Res. 1998 18(2): 79-92). An alternative method comprises generating an immune response in an individual against a 83P2H3 immunogen by: administering in vivo to muscle or skin of the individual's body a DNA molecule that comprises a DNA sequence that encodes an 83P2H3 immunogen, the DNA sequence operatively linked to regulatory sequences which control the expression of the DNA sequence; wherein the DNA molecule is taken up by cells, the DNA sequence is expressed in the cells and an immune response is generated against the immunogen (see, e.g., U.S. Pat. No. 5,962,428). Optionally a genetic vaccine facilitator such as anionic lipids; saponins; lectins; estrogenic compounds; hydroxylated lower alkyls; dimethyl sulfoxide; and urea is also administered.

[0290] Nucleic Acid Vaccines

[0291] Vaccine compositions of the invention include nucleic acid-mediated modalities. DNA or RNA that encode protein(s) of the invention can be administered to a patient. Genetic immunization methods can be employed to generate prophylactic or therapeutic humoral and cellular immune responses directed against cancer cells expressing 83P2H3. Constructs comprising DNA encoding a 83P2H3-related protein/immunogen and appropriate regulatory sequences can be injected directly into muscle or skin of an individual, such that the cells of the muscle or skin take-up the construct and express the encoded 83P2H3 protein/immunogen. Alternatively, a vaccine comprises a 83P2H3-related protein. Expression of the 83P2H3-related protein immunogen results in the generation of prophylactic or therapeutic humoral and cellular immunity against cells that bear 83P2H3 protein. Various prophylactic and therapeutic genetic immunization techniques known in the art can be used (for review, see information and references published at Internet address www.genweb.com). Nucleic acid-based delivery is described, for instance, in Wolff et. al., Science 247:1465 (1990) as well as U.S. Pat. Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524; 5,679,647; WO 98/04720. Examples of DNA-based delivery technologies include “naked DNA”, facilitated (bupivicaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated (“gene gun”) or pressure-mediated delivery (see, e.g., U.S. Pat. No. 5,922,687).

[0292] For therapeutic or prophylactic immunization purposes, proteins of the invention can be expressed by viral or bacterial vectors. Various viral gene delivery systems that can be used in the practice of the invention include, but are not limited to, vaccinia, fowlpox, canarypox, adenovirus, influenza, poliovirus, adeno-associated virus, lentivirus, and sindbis virus (see, e.g., Restifo, 1996, Curr. Opin. Immunol. 8:658-663; Tsang et al. J. Natl. Cancer Inst. 87:982-990 (1995)). Non-viral delivery systems can also be employed by introducing naked DNA encoding a 83P2H3-related protein into the patient (e.g., intramuscularly or intradermally) to induce an anti-tumor response.

[0293] Vaccinia virus is used, for example, as a vector to express nucleotide sequences that encode the peptides of the invention. Upon introduction into a host, the recombinant vaccinia virus expresses the protein immunogenic peptide, and thereby elicit a host immune response. Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover et al., Nature 351:456-460 (1991). A wide variety of other vectors useful for therapeutic administration or immunization of the peptides of the invention, e.g. adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like, will be apparent to those skilled in the art from the description herein.

[0294] Thus, gene delivery systems are used to deliver a 83P2H3-related nucleic acid molecule. In one embodiment, the full-length human 83P2H3 cDNA is employed. In another embodiment, 83P2H3 nucleic acid molecules encoding specific cytotoxic T lymphocyte (CTL) and/or antibody epitopes are employed.

[0295] Ex Vivo Vaccines

[0296] Various ex vivo strategies can also be employed to generate an immune response. One approach involves the use of antigen presenting cells (APCs) such as dendritic cells (DC) to present 83P2H3 antigen to a patient's immune system. Dendritic cells express MHC class I and II molecules, B7 co-stimulator, and IL-12, and are thus highly specialized antigen presenting cells. In prostate cancer, autologous dendritic cells pulsed with peptides of the prostate-specific membrane antigen (PSMA) are being used in a Phase I clinical trial to stimulate prostate cancer patients' immune systems (Tjoa et al., 1996, Prostate 28:65-69; Murphy et al., 1996, Prostate 29:371-380). Thus, dendritic cells can be used to present 83P2H3 peptides to T cells in the context of MHC class I or II molecules. In one embodiment, autologous dendritic cells are pulsed with 83P2H3 peptides capable of binding to MHC class I and/or class II molecules. In another embodiment, dendritic cells are pulsed with the complete 83P2H3 protein. Yet another embodiment involves engineering the overexpression of the 83P2H3 gene in dendritic cells using various implementing vectors known in the art, such as adenovirus (Arthur et al., 1997, Cancer Gene Ther. 4:17-25), retrovirus (Henderson et al., 1996, Cancer Res. 56:3763-3770), lentivirus, adeno-associated virus, DNA transfection (Ribas et al., 1997, Cancer Res. 57:2865-2869), or tumor-derived RNA transfection (Ashley et al., 1997, J. Exp. Med. 186:1177-1182). Cells that express 83P2H3 can also be engineered to express immune modulators, such as GM-CSF, and used as immunizing agents.

[0297] X.B.) 83P2H3 as a Target for Antibody-based Therapy

[0298] 83P2H3 is an attractive target for antibody-based therapeutic strategies. A number of antibody strategies are known in the art for targeting both extracellular and intracellular molecules (see, e.g., complement and ADCC mediated killing as well as the use of intrabodies). Because 83P2H3 is expressed by cancer cells of various lineages relative to corresponding normal cells, systemic administration of 83P2H3-immunoreactive compositions are prepared that exhibit excellent sensitivity without toxic, non-specific and/or non-target effects caused by binding of the immunoreactive composition to non-target organs and tissues. Antibodies specifically reactive with domains of 83P2H3 are useful to treat 83P2H3-expressing cancers systemically, either as conjugates with a toxin or therapeutic agent, or as naked antibodies capable of inhibiting cell proliferation or function.

[0299] 83P2H3 antibodies can be introduced into a patient such that the antibody binds to 83P2H3 and modulates a function, such as an interaction with a binding partner, and consequently mediates destruction of the tumor cells and/or inhibits the growth of the tumor cells. Mechanisms by which such antibodies exert a therapeutic effect can include complement-mediated cytolysis, antibody-dependent cellular cytotoxicity, modulation of the physiological function of 83P2H3, inhibition of ligand binding or signal transduction pathways, modulation of tumor cell differentiation, alteration of tumor angiogenesis factor profiles, and/or apoptosis.

[0300] Those skilled in the art understand that antibodies can be used to specifically target and bind immunogenic molecules such as an immunogenic region of the 83P2H3 sequence shown in FIG. 2 or FIG. 3. In addition, skilled artisans understand that it is routine to conjugate antibodies to cytotoxic agents (see, e.g., Slevers et al. Blood 93:11 3678-3684 (Jun. 1, 1999)). When cytotoxic and/or therapeutic agents are delivered directly to cells, such as by conjugating them to antibodies specific for a molecule expressed by that cell (e.g. 83P2H3), the cytotoxic agent will exert its known biological effect (i.e. cytotoxicity) on those cells.

[0301] A wide variety of compositions and methods for using antibody-cytotoxic agent conjugates to kill cells are known in the art. In the context of cancers, typical methods entail administering to an animal having a tumor a biologically effective amount of a conjugate comprising a selected cytotoxic and/or therapeutic agent linked to a targeting agent (e.g. an anti-83P2H3 antibody) that binds to a marker (e.g. 83P2H3) expressed, accessible to binding or localized on the cell surfaces. A typical embodiment is a method of delivering a cytotoxic and/or therapeutic agent to a cell expressing 83P2H3, comprising conjugating the cytotoxic agent to an antibody that immunospecifically binds to a 83P2H3 epitope, and, exposing the cell to the antibody-agent conjugate. Another illustrative embodiment is a method of treating an individual suspected of suffering from metastasized cancer, comprising a step of administering parenterally to said individual a pharmaceutical composition comprising a therapeutically effective amount of an antibody conjugated to a cytotoxic and/or therapeutic agent.

[0302] Cancer immunotherapy using anti-83P2H3 antibodies can be done in accordance with various approaches that have been successfully employed in the treatment of other types of cancer, including but not limited to colon cancer (Arlen et al., 1998, Crit. Rev. Immunol. 18:133-138), multiple myeloma (Ozaki et al., 1997, Blood 90:3179-3186, Tsunenari et al., 1997, Blood 90:2437-2444), gastric cancer (Kasprzyk et al., 1992, Cancer Res. 52:2771-2776), B-cell lymphoma (Funakoshi et al., 1996, J. Immunother. Emphasis Tumor Immunol. 19:93-101), leukemia (Zhong et al., 1996, Leuk. Res. 20:581-589), colorectal cancer (Moun et al., 1994, Cancer Res. 54:6160-6166; Velders et al., 1995, Cancer Res. 55:4398-4403), and breast cancer (Shepard et al., 1991, J. Clin. Immunol. 11:117-127). Some therapeutic approaches involve conjugation of naked antibody to a toxin, such as the conjugation of y91 or I131 to anti-CD20 antibodies (e.g., Zevalin™, IDEC Pharmaceuticals Corp. or Bexxar™, Coulter Pharmaceuticals), while others involve co-administration of antibodies and other therapeutic agents, such as Herceptin™ (trastuzumab) with paclitaxel (Genentech, Inc.). To treat prostate cancer, for example, 83P2H3 antibodies can be administered in conjunction with radiation, chemotherapy or hormone ablation.

[0303] Although 83P2H3 antibody therapy is useful for all stages of cancer, antibody therapy can be particularly appropriate in advanced or metastatic cancers. Treatment with the antibody therapy of the invention is indicated for patients who have received one or more rounds of chemotherapy. Alternatively, antibody therapy of the invention is combined with a chemotherapeutic or radiation regimen for patients who have not received chemotherapeutic treatment. Additionally, antibody therapy can enable the use of reduced dosages of concomitant chemotherapy, particularly for patients who do not tolerate the toxicity of the chemotherapeutic agent very well.

[0304] Cancer patients can be evaluated for the presence and level of 83P2H3 expression, preferably using immunohistochemical assessments of tumor tissue, quantitative 83P2H3 imaging, or other techniques that reliably indicate the presence and degree of 83P2H3 expression. Immunohistochemical analysis of tumor biopsies or surgical specimens is preferred for this purpose. Methods for immunohistochemical analysis of tumor tissues are well known in the art.

[0305] Anti-83P2H3 monoclonal antibodies that treat prostate and other cancers include those that initiate a potent immune response against the tumor or those that are directly cytotoxic. In this regard, anti-83P2H3 monoclonal antibodies (mAbs) can elicit tumor cell lysis by either complement-mediated or antibody-dependent cell cytotoxicity (ADCC) mechanisms, both of which require an intact Fc portion of the immunoglobulin molecule for interaction with effector cell Fc receptor sites on complement proteins. In addition, anti-83P2H3 mAbs that exert a direct biological effect on tumor growth are useful to treat cancers that express 83P2H3. Mechanisms by which directly cytotoxic mAbs act include: inhibition of cell growth, modulation of cellular differentiation, modulation of tumor angiogenesis factor profiles, and the induction of apoptosis. The mechanism(s) by which a particular anti-83P2H3 mAb exerts an anti-tumor effect is evaluated using any number of in vitro assays that evaluate cell death such as ADCC, ADMMC, complement-mediated cell lysis, and so forth, as is generally known in the art.

[0306] In some patients, the use of murine or other non-human monoclonal antibodies, or human/mouse chimeric mAbs can induce moderate to strong immune responses against the non-human antibody. This can result in clearance of the antibody from circulation and reduced efficacy. In the most severe cases, such an immune response can lead to the extensive formation of immune complexes which, potentially, can cause renal failure. Accordingly, preferred monoclonal antibodies used in the therapeutic methods of the invention are those that are either fully human or humanized and that bind specifically to the target 83P2H3 antigen with high affinity but exhibit low or no antigenicity in the patient.

[0307] Therapeutic methods of the invention contemplate the administration of single anti-83P2H3 mAbs as well as combinations, or cocktails, of different mAbs. Such mAb cocktails can have certain advantages inasmuch as they contain mAbs that target different epitopes, exploit different effector mechanisms or combine directly cytotoxic mAbs with mAbs that rely on immune effector functionality. Such mAbs in combination can exhibit synergistic therapeutic effects. In addition, anti-83P2H3 mAbs can be administered concomitantly with other therapeutic modalities, including but not limited to various chemotherapeutic agents, androgen-blockers, immune modulators (e.g., IL-2, GM-CSF), surgery or radiation. The anti-83P2H3 mAbs are administered in their “naked” or unconjugated form, or can have a therapeutic agent(s) conjugated to them.

[0308] Anti-83P2H3 antibody formulations are administered via any route capable of delivering the antibodies to a tumor cell. Routes of administration include, but are not limited to, intravenous, intraperitoneal, intramuscular, intratumor, intradermal, and the like. Treatment generally involves repeated administration of the anti-83P2H3 antibody preparation, via an acceptable route of administration such as intravenous injection (IV), typically at a dose in the range of about 0.1 to about 10 mg/kg body weight. In general, doses in the range of 10-500 mg mAb per week are effective and well tolerated.

[0309] Based on clinical experience with the Herceptin mAb in the treatment of metastatic breast cancer, an initial loading dose of approximately 4 mg/kg patient body weight IV, followed by weekly doses of about 2 mg/kg IV of the anti-83P2H3 mAb preparation represents an acceptable dosing regimen. Preferably, the initial loading dose is administered as a 90 minute or longer infusion. The periodic maintenance dose is administered as a 30 minute or longer infusion, provided the initial dose was well tolerated. As appreciated by those of skill in the art, various factors can influence the ideal dose regimen in a particular case. Such factors include, for example, the binding affinity and half life of the Ab or mAbs used, the degree of 83P2H3 expression in the patient, the extent of circulating shed 83P2H3 antigen, the desired steady-state antibody concentration level, frequency of treatment, and the influence of chemotherapeutic or other agents used in combination with the treatment method of the invention, as well as the health status of a particular patient.

[0310] Optionally, patients should be evaluated for the levels of 83P2H3 in a given sample (e.g. the levels of circulating 83P2H3 antigen and/or 83P2H3 expressing cells) in order to assist in the determination of the most effective dosing regimen, etc. Such evaluations are also used for monitoring purposes throughout therapy, and are useful to gauge therapeutic success in combination with the evaluation of other parameters (such as serum PSA levels in prostate cancer therapy).

[0311] Anti-idiotypic anti-83P2H3 antibodies can also be used in anti-cancer therapy as a vaccine for inducing an immune response to cells expressing a 83P2H3-related protein. In particular, the generation of anti-idiotypic antibodies is well known in the art; this methodology can readily be adapted to generate anti-idiotypic anti-83P2H3 antibodies that mimic an epitope on a 83P2H3-related protein (see, for example, Wagner et al., 1997, Hybridoma 16: 33-40; Foon et al., 1995, J. Clin. Invest. 96:334-342; Herlyn et al., 1996, Cancer Immunol. Immunother. 43:65-76). Such an anti-idiotypic antibody can be used in cancer vaccine strategies.

[0312] X.C.) 83P2H3 as a Target for Cellular Immune Responses

[0313] Vaccines and methods of preparing vaccines that contain an immunogenically effective amount of one or more HLA-binding peptides as described herein are further embodiments of the invention. Furthermore, vaccines in accordance with the invention encompass compositions of one or more of the claimed peptides. A peptide can be present in a vaccine individually. Alternatively, the peptide can exist as a homopolymer comprising multiple copies of the same peptide, or as a heteropolymer of various peptides. Polymers have the advantage of increased immunological reaction and, where different peptide epitopes are used to make up the polymer, the additional ability to induce antibodies and/or CTLs that react with different antigenic determinants of the pathogenic organism or tumor-related peptide targeted for an immune response. The composition can be a naturally occurring region of an antigen or can be prepared, e.g., recombinantly or by chemical synthesis.

[0314] Carriers that can be used with vaccines of the invention are well known in the art, and include, e.g., thyroglobulin, albumins such as human serum albumin, tetanus toxoid, polyamino acids such as poly L-lysine, poly L-glutamic acid, influenza, hepatitis B virus core protein, and the like. The vaccines can contain a physiologically tolerable (i.e., acceptable) diluent such as water, or saline, preferably phosphate buffered saline. The vaccines also typically include an adjuvant. Adjuvants such as incomplete Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum are examples of materials well known in the art. Additionally, as disclosed herein, CTL responses can be primed by conjugating peptides of the invention to lipids, such as tripalnitoyl-S-glycerylcysteinlyseryl-serine (P3CSS). Moreover, an adjuvant such as a synthetic cytosine-phosphorothiolated-guanine-containing (CpG) oligonucleotides has been found to increase CTL responses 10- to 100-fold. (see, e.g. Davila and Celis J. Immunol. 165:539-547 (2000)).

[0315] Upon immunization with a peptide composition in accordance with the invention, via injection, aerosol, oral, transdermal, transmucosal, intrapleural, intrathecal, or other suitable routes, the immune system of the host responds to the vaccine by producing large amounts of CTLs and/or HTLs specific for the desired antigen. Consequently, the host becomes at least partially immune to later development of cells that express or overexpress 83P2H3 antigen, or derives at least some therapeutic benefit when the antigen was tumor-associated.

[0316] In some embodiments, it may be desirable to combine the class I peptide components with components that induce or facilitate neutralizing antibody and or helper T cell responses directed to the target antigen. A preferred embodiment of such a composition comprises class I and class II epitopes in accordance with the invention. An alternative embodiment of such a composition comprises a class I and/or class II epitope in accordance with the invention, along with a cross reactive HTL epitope such as PADRE™ (Epimmune, San Diego, Calif.) molecule (described e.g., in U.S. Pat. No. 5,736,142).

[0317] A vaccine of the invention can also include antigen-presenting cells (APC), such as dendritic cells (DC), as a vehicle to present peptides of the invention. Vaccine compositions can be created in vitro, following dendritic cell mobilization and harvesting, whereby loading of dendritic cells occurs in vitro. For example, dendritic cells are transfected, e.g., with a minigene in accordance with the invention, or are pulsed with peptides. The dendritic cell can then be administered to a patient to elicit immune responses in vivo. Vaccine compositions, either DNA- or peptide-based, can also be administered in vivo in combination with dendritic cell mobilization whereby loading of dendritic cells occurs in vivo.

[0318] Preferably, the following principles are utilized when selecting an array of epitopes for inclusion in a polyepitopic composition for use in a vaccine, or for selecting discrete epitopes to be included in a vaccine and/or to be encoded by nucleic acids such as a minigene. It is preferred that each of the following principles be balanced in order to make the selection. The multiple epitopes to be incorporated in a given vaccine composition may be, but need not be, contiguous in sequence in the native antigen from which the epitopes are derived.

[0319] 1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with tumor clearance. For HLA Class I this includes 3-4 epitopes that come from at least one tumor associated antigen (TAA). For HLA Class II a similar rationale is employed; again 3-4 epitopes are selected from at least one TAA (see, e.g., Rosenberg et al., Science 278:1447-1450). Epitopes from one TAA may be used in combination with epitopes from one or more additional TAAs to produce a vaccine that targets tumors with varying expression patterns of frequently-expressed TAAs.

[0320] 2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC50 of 500 nM or less, often 200 nM or less; and for Class II an IC50 of 1000 nM or less.

[0321] 3.) Sufficient supermotif bearing-peptides, or a sufficient array of allele-specific motif-bearing peptides, are selected to give broad population coverage. For example, it is preferable to have at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess the breadth, or redundancy of, population coverage.

[0322] 4.) When selecting epitopes from cancer-related antigens it is often useful to select analogs because the patient may have developed tolerance to the native epitope.

[0323] 5.) Of particular relevance are epitopes referred to as “nested epitopes.” Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A nested peptide sequence can comprise B cell, HLA class I and/or HLA class II epitopes. When providing nested epitopes, a general objective is to provide the greatest number of epitopes per sequence. Thus, an aspect is to avoid providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a multi-epitopic sequence, such as a sequence comprising nested epitopes, it is generally important to screen the sequence in order to insure that it does not have pathological or other deleterious biological properties.

[0324] 6.) If a polyepitopic protein is created, or when creating a minigene, an objective is to generate the smallest peptide that encompasses the epitopes of interest. This principle is similar, if not the same as that employed when selecting a peptide comprising nested epitopes. However, with an artificial polyepitopic peptide, the size minimization objective is balanced against the need to integrate any spacer sequences between epitopes in the polyepitopic protein. Spacer amino acid residues can, for example, be introduced to avoid junctional epitopes (an epitope recognized by the immune system, not present in the target antigen, and only created by the man-made juxtaposition of epitopes), or to facilitate cleavage between epitopes and thereby enhance epitope presentation. Junctional epitopes are generally to be avoided because the recipient may generate an immune response to that non-native epitope. Of particular concern is a junctional epitope that is a “dominant epitope.” A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed.

[0325] 7.) In cases where the sequences of multiple variants of the same target protein are available, potential peptide epitopes can also be selected on the basis of their conservancy. For example, a criterion for conservancy may define that the entire sequence of an HLA class I binding peptide or the entire 9-mer core of a class II binding peptide be conserved in a designated percentage of the sequences evaluated for a specific protein antigen.

[0326] X.C.1. Minigene Vaccines

[0327] A number of different approaches are available which allow simultaneous delivery of multiple epitopes. Nucleic acids encoding the peptides of the invention are a particularly useful embodiment of the invention. Epitopes for inclusion in a minigene are preferably selected according to the guidelines set forth in the previous section. A preferred means of administering nucleic acids encoding the peptides of the invention uses minigene constructs encoding a peptide comprising one or multiple epitopes of the invention.

[0328] The use of multi-epitope minigenes is described below and in, Ishioka et al., J. Immunol. 162:3915-3925, 1999; An, L. and Whitton, J. L., J. Virol. 71:2292, 1997; Thomson, S. A. et al., J. Immunol. 157:822, 1996; Whitton, J. L. et al., J. Virol. 67:348, 1993; Hanke, R. et al., Vaccine 16:426, 1998. For example, a multi-epitope DNA plasmid encoding supermotif- and/or motif-bearing epitopes derived 83P2H3, the PADRE® universal helper T cell epitope (or multiple HTL epitopes from 83P2H3), and an endoplasmic reticulum-translocating signal sequence can be engineered. A vaccine may also comprise epitopes that are derived from other TAAs.

[0329] The immunogenicity of a multi-epitopic minigene can be tested in transgenic mice to evaluate the magnitude of CTL induction responses against the epitopes tested. Further, the immunogenicity of DNA-encoded epitopes in vivo can be correlated with the in vitro responses of specific CTL lines against target cells transfected with the DNA plasmid. Thus, these experiments can show that the minigene serves to both: 1.) generate a CTL response and 2.) that the induced CTLs recognized cells expressing the encoded epitopes.

[0330] For example, to create a DNA sequence encoding the selected epitopes (minigene) for expression in human cells, the amino acid sequences of the epitopes may be reverse translated. A human codon usage table can be used to guide the codon choice for each amino acid. These epitope-encoding DNA sequences may be directly adjoined, so that when translated, a continuous polypeptide sequence is created. To optimize expression and/or immunogenicity, additional elements can be incorporated into the minigene design. Examples of amino acid sequences that can be reverse translated and included in the minigene sequence include: HLA class I epitopes, HLA class II epitopes, antibody epitopes, a ubiquitination signal sequence, and/or an endoplasmic reticulum targeting signal. In addition, HLA presentation of CTL and HTL epitopes may be improved by including synthetic (e.g. poly-alanine) or naturally-occurring flanking sequences adjacent to the CTL or HTL epitopes; these larger peptides comprising the epitope(s) are within the scope of the invention.

[0331] The minigene sequence may be converted to DNA by assembling oligonucleotides that encode the plus and minus strands of the minigene. Overlapping oligonucleotides (30-100 bases long) may be synthesized, phosphorylated, purified and annealed under appropriate conditions using well known techniques. The ends of the oligonucleotides can be joined, for example, using T4 DNA ligase. This synthetic minigene, encoding the epitope polypeptide, can then be cloned into a desired expression vector.

[0332] Standard regulatory sequences well known to those of skill in the art are preferably included in the vector to ensure expression in the target cells. Several vector elements are desirable: a promoter with a down-stream cloning site for minigene insertion; a polyadenylation signal for efficient transcription termination; an E. coli origin of replication; and an E. coli selectable marker (e.g. ampicillin or kanamycin resistance). Numerous promoters can be used for this purpose, e.g., the human cytomegalovirus (hCMV) promoter. See, e.g., U.S. Pat. Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.

[0333] Additional vector modifications may be desired to optimize minigene expression and immunogenicity. In some cases, introns are required for efficient gene expression, and one or more synthetic or naturally-occurring introns could be incorporated into the transcribed region of the minigene. The inclusion of mRNA stabilization sequences and sequences for replication in mammalian cells may also be considered for increasing minigene expression.

[0334] Once an expression vector is selected, the minigene is cloned into the polylinker region downstream of the promoter. This plasmid is transformed into an appropriate E. coli strain, and DNA is prepared using standard techniques. The orientation and DNA sequence of the minigene, as well as all other elements included in the vector, are confirmed using restriction mapping and DNA sequence analysis. Bacterial cells harboring the correct plasmid can be stored as a master cell bank and a working cell bank.

[0335] In addition, immunostimulatory sequences (ISSs or CpGs) appear to play a role in the immunogenicity of DNA vaccines. These sequences may be included in the vector, outside the minigene coding sequence, if desired to enhance immunogenicity.

[0336] In some embodiments, a bi-cistronic expression vector which allows production of both the minigene-encoded epitopes and a second protein (included to enhance or decrease immunogenicity) can be used. Examples of proteins or polypeptides that could beneficially enhance the immune response if co-expressed include cytokines (e.g., IL-2, IL-12, GM-CSF), cytokine-inducing molecules (e.g., LeIF), costimulatory molecules, or for HTL responses, pan-DR binding proteins (PADRE™, Epimmune, San Diego, Calif.). Helper (HTL) epitopes can be joined to intracellular targeting signals and expressed separately from expressed CTL epitopes; this allows direction of the HTL epitopes to a cell compartment different than that of the CTL epitopes. If required, this could facilitate more efficient entry of HTL epitopes into the HLA class II pathway, thereby improving HTL induction. In contrast to HTL or CTL induction, specifically decreasing the immune response by co-expression of immunosuppressive molecules (e.g. TGF-β) may be beneficial in certain diseases.

[0337] Therapeutic quantities of plasmid DNA can be produced for example, by fermentation in E. coli, followed by purification. Aliquots from the working cell bank are used to inoculate growth medium, and grown to saturation in shaker flasks or a bioreactor according to well-known techniques. Plasmid DNA can be purified using standard bioseparation technologies such as solid phase anion-exchange resins supplied by QIAGEN, Inc. (Valencia, Calif.). If required, supercoiled DNA can be isolated from the open circular and linear forms using gel electrophoresis or other methods.

[0338] Purified plasmid DNA can be prepared for injection using a variety of formulations. The simplest of these is reconstitution of lyophilized DNA in sterile phosphate-buffer saline (PBS). This approach, known as “naked DNA,” is currently being used for intramuscular (IM) administration in clinical trials. To maximize the immunotherapeutic effects of minigene DNA vaccines, an alternative method for formulating purified plasmid DNA may be desirable. A variety of methods have been described, and new techniques may become available. Cationic lipids, glycolipids, and fusogenic liposomes can also be used in the formulation (see, e.g., as described by WO 93/24640; Mannino & Gould-Fogerite, Bio Techniques 6(7): 682 (1988); U.S. Pat No. 5,279,833; WO 91/06309; and Felgner, et al., Proc. Nat'l Acad. Sci. USA 84:7413 (1987). In addition, peptides and compounds referred to collectively as protective, interactive, non-condensing compounds (PINC) could also be complexed to purified plasmid DNA to influence variables such as stability, intramuscular dispersion, or trafficking to specific organs or cell types.

[0339] Target cell sensitization can be used as a functional assay for expression and HLA class I presentation of minigene-encoded CTL epitopes. For example, the plasmid DNA is introduced into a mammalian cell line that is suitable as a target for standard CTL chromium release assays. The transfection method used will be dependent on the final formulation. Electroporation can be used for “naked” DNA, whereas cationic lipids allow direct in vitro transfection. A plasmid expressing green fluorescent protein (GFP) can be co-transfected to allow enrichment of transfected cells using fluorescence activated cell sorting (FACS). These cells are then chromium-51 (51Cr) labeled and used as target cells for epitope-specific CTL lines; cytolysis, detected by 51Cr release, indicates both production of, and HLA presentation of, minigene-encoded CTL epitopes. Expression of HTL epitopes may be evaluated in an analogous manner using assays to assess HTL activity.

[0340] In vivo immunogenicity is a second approach for functional testing of minigene DNA formulations. Transgenic mice expressing appropriate human HLA proteins are immunized with the DNA product. The dose and route of administration are formulation dependent (e.g., IM for DNA in PBS, intraperitoneal (i.p.) for lipid-complexed DNA). Twenty-one days after immunization, splenocytes are harvested and restimulated for one week in the presence of peptides encoding each epitope being tested. Thereafter, for CTL effector cells, assays are conducted for cytolysis of peptide-loaded, 51Cr-labeled target cells using standard techniques. Lysis of target cells that were sensitized by HLA loaded with peptide epitopes, corresponding to minigene-encoded epitopes, demonstrates DNA vaccine function for in vivo induction of CTLs. Immunogenicity of HTL epitopes is evaluated in transgenic mice in an analogous manner.

[0341] Alternatively, the nucleic acids can be administered using ballistic delivery as described, for instance, in U.S. Pat. No. 5,204,253. Using this technique, particles comprised solely of DNA are administered. In a further alternative embodiment, DNA can be adhered to particles, such as gold particles.

[0342] Minigenes can also be delivered using other bacterial or viral delivery systems well known in the art, e.g., an expression construct encoding epitopes of the invention can be incorporated into a viral vector such as vaccinia.

[0343] X.C.2. Combinations of CTL Peptides with Helper Peptides

[0344] Vaccine compositions comprising CTL peptides of the invention can be modified, e.g., analoged, to provide desired attributes, such as improved serum half life, broadened population coverage or enhanced immunogenicity.

[0345] For instance, the ability of a peptide to induce CTL activity can be enhanced by linking the peptide to a sequence which contains at least one epitope that is capable of inducing a T helper cell response. Although a CTL peptide can be directly linked to a T helper peptide, often CTL epitope/HTL epitope conjugates are linked by a spacer molecule. The spacer is typically comprised of relatively small, neutral molecules, such as amino acids or amino acid mimetics, which are substantially uncharged under physiological conditions. The spacers are typically selected from, e.g., Ala, Gly, or other neutral spacers of nonpolar amino acids or neutral polar amino acids. It will be understood that the optionally present spacer need not be comprised of the same residues and thus may be a hetero- or homo-oligomer. When present, the spacer will usually be at least one or two residues, more usually three to six residues and sometimes 10 or more residues. The CTL peptide epitope can be linked to the T helper peptide epitope either directly or via a spacer either at the amino or carboxy terminus of the CTL peptide. The amino terminus of either the immunogenic peptide or the T helper peptide may be acylated.

[0346] In certain embodiments, the T helper peptide is one that is recognized by T helper cells present in a majority of a genetically diverse population. This can be accomplished by selecting peptides that bind to many, most, or all of the HLA class II molecules. Examples of such amino acid bind many HLA Class II molecules include sequences from antigens such as tetanus toxoid at positions 830-843 (QYIKANSKFIGITE; SEQ ID NO: 710), Plasmodium falciparum circumsporozoite (CS) protein at positions 378-398 (DIEKKIAKMEKASSVFNVVNS; SEQ ID NO: 711), and Streptococcus 18 kD protein at positions 116-131 (GAVDSILGGVATYGAA; SEQ ID NO: 712). Other examples include peptides bearing a DR 1-4-7 supermotif, or either of the DR3 motifs.

[0347] Alternatively, it is possible to prepare synthetic peptides capable of stimulating T helper lymphocytes, in a loosely HLA-restricted fashion, using amino acid sequences not found in nature (see, e.g., PCT publication WO 95/07707). These synthetic compounds called Pan-DR-binding epitopes (e.g., PADRE™, Epimmune, Inc., San Diego, Calif.) are designed to most preferably bind most HLA-DR (human HLA class II) molecules. For instance, a pan-DR-binding epitope peptide having the formula: aKXVAAWTLKAAa (SEQ ID NO: 713), where “X” is either cyclohexylalanine, phenylalanine, or tyrosine, and a is either D-alanine or L-alanine, has been found to bind to most HLA-DR alleles, and to stimulate the response of T helper lymphocytes from most individuals, regardless of their HLA type. An alternative of a pan-DR binding epitope comprises all “L” natural amino acids and can be provided in the form of nucleic acids that encode the epitope.

[0348] HTL peptide epitopes can also be modified to alter their biological properties. For example, they can be modified to include D-amino acids to increase their resistance to proteases and thus extend their serum half life, or they can be conjugated to other molecules such as lipids, proteins, carbohydrates, and the like to increase their biological activity. For example, a T helper peptide can be conjugated to one or more palmitic acid chains at either the amino or carboxyl termini.

[0349] X.C.3. Combinations of CTL Peptides with T Cell Priming Agents

[0350] In some embodiments it may be desirable to include in the pharmaceutical compositions of the invention at least one component which primes B lymphocytes or T lymphocytes. Lipids have been identified as agents capable of priming CTL in vivo. For example, palmitic acid residues can be attached to the ε- and α-amino groups of a lysine residue and then linked, e.g., via one or more linking residues such as Gly, Gly-Gly-, Ser, Ser-Ser, or the like, to an immunogenic peptide. The lipidated peptide can then be administered either directly in a micelle or particle, incorporated into a liposome, or emulsified in an adjuvant, e.g., incomplete Freund's adjuvant. In a preferred embodiment, a particularly effective immunogenic composition comprises palmitic acid attached to ε- and α-amino groups of Lys, which is attached via linkage, e.g., Ser-Ser, to the amino terminus of the immunogenic peptide.

[0351] As another example of lipid priming of CTL responses, E. coli lipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P3CSS) can be used to prime virus specific CTL when covalently attached to an appropriate peptide (see, e.g., Deres, et al., Nature 342:561, 1989). Peptides of the invention can be coupled to P3CSS, for example, and the lipopeptide administered to an individual to specifically prime an immune response to the target antigen. Moreover, because the induction of neutralizing antibodies can also be primed with P3CSS-conjugated epitopes, two such compositions can be combined to more effectively elicit both humoral and cell-mediated responses.

[0352] X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL and/or HTL Peptides

[0353] An embodiment of a vaccine composition in accordance with the invention comprises ex vivo administration of a cocktail of epitope-bearing peptides to PBMC, or isolated DC therefrom, from the patient's blood. A pharmaceutical to facilitate harvesting of DC can be used, such as Progenipoietin™ (Pharmacia-Monsanto, St. Louis, Mo.) or GM-CSF/IL-4. After pulsing the DC with peptides and prior to reinfusion into patients, the DC are washed to remove unbound peptides. In this embodiment, a vaccine comprises peptide-pulsed DCs which present the pulsed peptide epitopes complexed with HLA molecules on their surfaces.

[0354] The DC can be pulsed ex vivo with a cocktail of peptides, some of which stimulate CTL responses to 83P2H3. Optionally, a helper T cell (HTL) peptide, such as a natural or artificial loosely restricted HLA Class II peptide, can be included to facilitate the CTL response. Thus, a vaccine in accordance with the invention is used to treat a cancer which expresses or overexpresses 83P2H3.

[0355] X.D. Adoptive Immunotherapy

[0356] Antigenic 83P2H3-related peptides are used to elicit a CTL and/or HTL response ex vivo, as well. The resulting CTL or HTL cells, can be used to treat tumors in patients that do not respond to other conventional forms of therapy, or will not respond to a therapeutic vaccine peptide or nucleic acid in accordance with the invention. Ex vivo CTL or HTL responses to a particular antigen are induced by incubating in tissue culture the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of antigen-presenting cells (APC), such as dendritic cells, and the appropriate immunogenic peptide. After an appropriate incubation time (typically about 7-28 days), in which the precursor cells are activated and expanded into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cell (e.g., a tumor cell). Transfected dendritic cells may also be used as antigen presenting cells.

[0357] X.E. Administration of Vaccines for Therapeutic or Prophylactic Purposes

[0358] Pharmaceutical and vaccine compositions of the invention are typically used to treat and/or prevent a cancer that expresses or overexpresses 83P2H3. In therapeutic applications, peptide and/or nucleic acid compositions are administered to a patient in an amount sufficient to elicit an effective B cell, CTL and/or HTL response to the antigen and to cure or at least partially arrest or slow symptoms and/or complications. An amount adequate to accomplish this is defined as “therapeutically effective dose.” Amounts effective for this use will depend on, e.g., the particular composition administered, the manner of administration, the stage and severity of the disease being treated, the weight and general state of health of the patient, and the judgment of the prescribing physician.

[0359] For pharmaceutical compositions, the immunogenic peptides of the invention, or DNA encoding them, are generally administered to an individual already bearing a tumor that expresses 83P2H3. The peptides or DNA encoding them can be administered individually or as fusions of one or more peptide sequences. Patients can be treated with the immunogenic peptides separately or in conjunction with other treatments, such as surgery, as appropriate.

[0360] For therapeutic use, administration should generally begin at the first diagnosis of 83P2H3-associated cancer. This is followed by boosting doses until at least symptoms are substantially abated and for a period thereafter. The embodiment of the vaccine composition (i.e., including, but not limited to embodiments such as peptide cocktails, polyepitopic polypeptides, minigenes, or TAA-specific CTLs or pulsed dendritic cells) delivered to the patient may vary according to the stage of the disease or the patient's health status. For example, in a patient with a tumor that expresses 83P2H3, a vaccine comprising 83P2H3-specific CTL may be more efficacious in killing tumor cells in patient with advanced disease than alternative embodiments.

[0361] It is generally important to provide an amount of the peptide epitope delivered by a mode of administration sufficient to effectively stimulate a cytotoxic T cell response; compositions which stimulate helper T cell responses can also be given in accordance with this embodiment of the invention.

[0362] The dosage for an initial therapeutic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1,000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. Boosting dosages of between about 1.0 μg to about 50,000 μg of peptide pursuant to a boosting regimen over weeks to months may be administered depending upon the patient's response and condition as determined by measuring the specific activity of CTL and HTL obtained from the patient's blood. Administration should continue until at least clinical symptoms or laboratory tests indicate that the neoplasia, has been eliminated or reduced and for a period thereafter. The dosages, routes of administration, and dose schedules are adjusted in accordance with methodologies known in the art.

[0363] In certain embodiments, the peptides and compositions of the present invention are employed in serious disease states, that is, life-threatening or potentially life threatening situations. In such cases, as a result of the minimal amounts of extraneous substances and the relative nontoxic nature of the peptides in preferred compositions of the invention, it is possible and may be felt desirable by the treating physician to administer substantial excesses of these peptide compositions relative to these stated dosage amounts.

[0364] The vaccine compositions of the invention can also be used purely as prophylactic agents. Generally the dosage for an initial prophylactic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. This is followed by boosting dosages of between about 1.0 μg to about 50,000 μg of peptide administered at defined intervals from about four weeks to six months after the initial administration of vaccine. The immunogenicity of the vaccine can be assessed by measuring the specific activity of CTL and HTL obtained from a sample of the patient's blood.

[0365] The pharmaceutical compositions for therapeutic treatment are intended for parenteral, topical, oral, nasal, intrathecal, or local (e.g. as a cream or topical ointment) administration. Preferably, the pharmaceutical compositions are administered parentally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly. Thus, the invention provides compositions for parenteral administration which comprise a solution of the immunogenic peptides dissolved or suspended in an acceptable carrier, preferably an aqueous carrier.

[0366] A variety of aqueous carriers may be used, e.g., water, buffered water, 0.8% saline, 0.3% glycine, hyaluronic acid and the like. These compositions may be sterilized by conventional, well-known sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration.

[0367] The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservatives, and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.

[0368] The concentration of peptides of the invention in the pharmaceutical formulations can vary widely, i.e., from less than about 0.1%, usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected.

[0369] A human unit dose form of the peptide composition is typically included in a pharmaceutical composition that comprises a human unit dose of an acceptable carrier, preferably an aqueous carrier, and is administered in a volume of fluid that is known by those of skill in the art to be used for administration of such compositions to humans (see, e.g., Remington's Pharmaceutical Sciences, 17th Edition, A. Gennaro, Editor, Mack Publishing Co., Easton, Pa., 1985).

[0370] Proteins(s) of the invention, and/or nucleic acids encoding the protein(s), can also be administered via liposomes, which may also serve to: 1) target the proteins(s) to a particular tissue, such as lymphoid tissue; 2) to target selectively to diseases cells; or, 3) to increase the half-life of the peptide composition. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations, the peptide to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to a receptor prevalent among lymphoid cells, such as monoclonal antibodies which bind to the CD45 antigen, or with other therapeutic or immunogenic compositions. Thus, liposomes either filled or decorated with a desired peptide of the invention can be directed to the site of lymphoid cells, where the liposomes then deliver the peptide compositions. Liposomes for use in accordance with the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka, et al., Ann. Rev. Biophys. Bioeng. 9:467 (1980), and U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.

[0371] For targeting cells of the immune system, a ligand to be incorporated into the liposome can include, e.g., antibodies or fragments thereof specific for cell surface determinants of the desired immune system cells. A liposome suspension containing a peptide may be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the peptide being delivered, and the stage of the disease being treated.

[0372] For solid compositions, conventional nontoxic solid carriers may be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any of the normally employed excipients, such as those carriers previously listed, and generally 10-95% of active ingredient, that is, one or more peptides of the invention, and more preferably at a concentration of 25%-75%.

[0373] For aerosol administration, immunogenic peptides are preferably supplied in finely divided form along with a surfactant and propellant. Typical percentages of peptides are 0.01%-20% by weight, preferably 1%-10%. The surfactant must, of course, be nontoxic, and preferably soluble in the propellant. Representative of such agents are the esters or partial esters of fatty acids containing from 6 to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides may be employed. The surfactant may constitute 0.1%-20% by weight of the composition, preferably 0.25-5%. The balance of the composition is ordinarily propellant. A carrier can also be included, as desired, as with, e.g., lecithin for intranasal delivery.

[0374] XI.) Diagnostic and Prognostic Embodiments of 83P2H3

[0375] As disclosed herein, 83P2H3 polynucleotides, polypeptides, reactive cytotoxic T cells (CTL), reactive helper T cells (HTL) and anti-polypeptide antibodies are used in well known diagnostic, prognostic and therapeutic assays that examine conditions associated with dysregulated cell growth such as cancer, in particular the cancers listed in Table I (see, e.g., both its specific pattern of tissue expression as well as its overexpression in certain cancers as described for example in Example 4).

[0376] 83P2H3 can be analogized to a prostate associated antigen PSA, the archetypal marker that has been used by medical practitioners for years to identify and monitor the presence of prostate cancer (see, e.g., Merrill et al., J. Urol. 163(2): 503-5120 (2000); Polascik et al., J. Urol. Aug; 162(2):293-306 (1999) and Fortier et al., J. Nat. Cancer Inst. 91(19): 1635-1640(1999)). A variety of other diagnostic markers are also used in similar contexts including p53 and K-ras (see, e.g., Tulchinsky et al., Int J Mol Med Jul. 4, 1999(1):99-102 and Minimoto et al., Cancer Detect Prev 2000;24(1):1-12). Therefore, disclosure of the 83P2H3 polynucleotides and polypeptides (as well as the 83P2H3 polynucleotide probes and anti-83P2H3 antibodies used to identify the presence of these molecules) and their properties allows skilled artisans to utilize these molecules in methods that are analogous to those used, for example, in a variety of diagnostic assays directed to examining conditions associated with cancer.

[0377] Typical embodiments of diagnostic methods which utilize the 83P2H3 polynucleotides, polypeptides, reactive T cells and antibodies are analogous to those methods from well-established diagnostic assays which employ, e.g., PSA polynucleotides, polypeptides, reactive T cells and antibodies. For example, just as PSA polynucleotides are used as probes (for example in Northern analysis, see, e.g., Sharief et al., Biochem. Mol. Biol. Int. 33(3):567-74(1994)) and primers (for example in PCR analysis, see, e.g., Okegawa et al., J. Urol. 163(4): 1189-1190 (2000)) to observe the presence and/or the level of PSA mRNAs in methods of monitoring PSA overexpression or the metastasis of prostate cancers, the 83P2H3 polynucleotides described herein can be utilized in the same way to detect 83P2H3 overexpression or the metastasis of prostate and other cancers expressing this gene. Alternatively, just as PSA polypeptides are used to generate antibodies specific for PSA which can then be used to observe the presence and/or the level of PSA proteins in methods to monitor PSA protein overexpression (see, e.g., Stephan et al., Urology 55(4):560-3 (2000)) or the metastasis of prostate cells (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3):233-7 (1996)), the 83P2H3 polypeptides described herein can be utilized to generate antibodies for use in detecting 83P2H3 overexpression or the metastasis of prostate cells and cells of other cancers expressing this gene.

[0378] Specifically, because metastases involves the movement of cancer cells from an organ of origin (such as the lung or prostate gland etc.) to a different area of the body (such as a lymph node), assays which examine a biological sample for the presence of cells expressing 83P2H3 polynucleotides and/or polypeptides can be used to provide evidence of metastasis. For example, when a biological sample from tissue that does not normally contain 83P2H3-expressing cells (lymph node) is found to contain 83P2H3-expressing cells such as the 83P2H3 expression seen in LAPC4 and LAPC9, xenografts isolated from lymph node and bone metastasis, respectively, this finding is indicative of metastasis.

[0379] Alternatively 83P2H3 polynucleotides and/or polypeptides can be used to provide evidence of cancer, for example, when cells in a biological sample that do not normally express 83P2H3 or express 83P2H3 at a different level are found to express 83P2H3 or have an increased expression of 83P2H3 (see, e.g., the 83P2H3 expression in the cancers listed in Table I and in patient samples etc. shown in the accompanying Figures). In such assays, artisans may further wish to generate supplementary evidence of metastasis by testing the biological sample for the presence of a second tissue restricted marker (in addition to 83P2H3) such as PSA, PSCA etc. (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3): 233-237 (1996)).

[0380] Just as PSA polynucleotide fragments and polynucleotide variants are employed by skilled artisans for use in methods of monitoring PSA, 83P2H3 polynucleotide fragments and polynucleotide variants are used in an analogous manner. In particular, typical PSA polynucleotides used in methods of monitoring PSA are probes or primers which consist of fragments of the PSA cDNA sequence. Illustrating this, primers used to PCR amplify a PSA polynucleotide must include less than the whole PSA sequence to function in the polymerase chain reaction. In the context of such PCR reactions, skilled artisans generally create a variety of different polynucleotide fragments that can be used as primers in order to amplify different portions of a polynucleotide of interest or to optimize amplification reactions (see, e.g., Caetano-Anolles, G. Biotechniques 25(3): 472-476, 478-480 (1998); Robertson et al., Methods Mol. Biol. 98:121-154 (1998)). An additional illustration of the use of such fragments is provided in Example 4, where a 83P2H3 polynucleotide fragment is used as a probe to show the expression of 83P2H3 RNAs in cancer cells. In addition, variant polynucleotide sequences are typically used as primers and probes for the corresponding mRNAs in PCR and Northern analyses (see, e.g., Sawai et al., Fetal Diagn. Ther. Nov.-Dec. 11, 1996(6):407-13 and Current Protocols In Molecular Biology, Volume 2, Unit 2, Frederick M. Ausubel et al. eds., 1995)). Polynucleotide fragments and variants are useful in this context where they are capable of binding to a target polynucleotide sequence (e.g. the 83P2H3 polynucleotide shown in SEQ ID NO: 701) under conditions of high stringency.

[0381] Furthermore, PSA polypeptides which contain an epitope that can be recognized by an antibody or T cell that specifically binds to that epitope are used in methods of monitoring PSA. 83P2H3 polypeptide fragments and polypeptide analogs or variants can also be used in an analogous manner. This practice of using polypeptide fragments or polypeptide variants to generate antibodies (such as anti-PSA antibodies or T cells) is typical in the art with a wide variety of systems such as fusion proteins being used by practitioners (see, e.g., Current Protocols In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubel et al. eds., 1995). In this context, each epitope(s) functions to provide the architecture with which an antibody or T cell is reactive. Typically, skilled artisans create a variety of different polypeptide fragments that can be used in order to generate immune responses specific for different portions of a polypeptide of interest (see, e.g., U.S. Pat. No. 5,840,501 and U.S. Pat. No. 5,939,533). For example it may be preferable to utilize a polypeptide comprising one of the 83P2H3 biological motifs discussed herein or a motif-bearing subsequence which is readily identified by one of skill in the art based on motifs available in the art. Polypeptide fragments, variants or analogs are typically useful in this context as long as they comprise an epitope capable of generating an antibody or T cell specific for a target polypeptide sequence (e.g. the 83P2H3 polypeptide shown in SEQ ID NO: 703).

[0382] As shown herein, the 83P2H3 polynucleotides and polypeptides (as well as the 83P2H3 polynucleotide probes and anti-83P2H3 antibodies or T cells used to identify the presence of these molecules) exhibit specific properties that make them useful in diagnosing cancers such as those listed in Table I. Diagnostic assays that measure the presence of 83P2H3 gene products, in order to evaluate the presence or onset of a disease condition described herein, such as prostate cancer, are used to identify patients for preventive measures or further monitoring, as has been done so successfully with PSA. Moreover, these materials satisfy a need in the art for molecules having similar or complementary characteristics to PSA in situations where, for example, a definite diagnosis of metastasis of prostatic origin cannot be made on the basis of a test for PSA alone (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3): 233-237 (1996)), and consequently, materials such as 83P2H3 polynucleotides and polypeptides (as well as the 83P2H3 polynucleotide probes and anti-83P2H3 antibodies used to identify the presence of these molecules) must be employed to confirm metastases of prostatic origin.

[0383] Finally, in addition to their use in diagnostic assays, the 83P2H3 polynucleotides disclosed herein have a number of other specific utilities such as their use in the identification of oncogenetic associated chromosomal abnormalities in the chromosomal region to which the 83P2H3 gene maps (see Example 3 below). Moreover, in addition to their use in diagnostic assays, the 83P2H3-related proteins and polynucleotides disclosed herein have other utilities such as their use in the forensic analysis of tissues of unknown origin (see, e.g., Takahama K Forensic Sci Int Jun 28, 1996; 80(1-2): 63-9).

[0384] Additionally, 83P2H3-related proteins or polynucleotides of the invention can be used to treat a pathologic condition characterized by the over-expression of 83P2H3. For example, the amino acid or nucleic acid sequence of FIG. 2 or FIG. 3, or fragments of either, can be used to generate an immune response to the 83P2H3 antigen. Antibodies or other molecules that react with 83P2H3 can be used to modulate the function of this molecule, and thereby provide a therapeutic benefit.

[0385] XII.) Inhibition of 83P2H3 Protein Function

[0386] The invention includes various methods and compositions for inhibiting the binding of 83P2H3 to its binding partner or its association with other protein(s) as well as methods for inhibiting 83P2H3 function.

[0387] XII.A.) Inhibition of 83P2H3 With Intracellular Antibodies

[0388] In one approach, a recombinant vector that encodes single chain antibodies that specifically bind to 83P2H3 are introduced into 83P2H3 expressing cells via gene transfer technologies. Accordingly, the encoded single chain anti-83P2H3 antibody is expressed intracellularly, binds to 83P2H3 protein, and thereby inhibits its function. Methods for engineering such intracellular single chain antibodies are well known. Such intracellular antibodies, also known as “intrabodies”, are specifically targeted to a particular compartment within the cell, providing control over where the inhibitory activity of the treatment is focused. This technology has been successfully applied in the art (for review, see Richardson and Marasco, 1995, TIBTECH vol. 13). Intrabodies have been shown to virtually eliminate the expression of otherwise abundant cell surface receptors (see, e.g., Richardson et al., 1995, Proc. Natl. Acad. Sci. USA 92: 3137-3141; Beerli et al., 1994, J. Biol. Chem. 289: 23931-23936; Deshane et al., 1994, Gene Ther. 1: 332-337).

[0389] Single chain antibodies comprise the variable domains of the heavy and light chain joined by a flexible linker polypeptide, and are expressed as a single polypeptide. Optionally, single chain antibodies are expressed as a single chain variable region fragment joined to the light chain constant region. Well-known intracellular trafficking signals are engineered into recombinant polynucleotide vectors encoding such single chain antibodies in order to precisely target the intrabody to the desired intracellular compartment. For example, intrabodies targeted to the endoplasmic reticulum (ER) are engineered to incorporate a leader peptide and, optionally, a C-terminal ER retention signal, such as the KDEL amino acid motif. Intrabodies intended to exert activity in the nucleus are engineered to include a nuclear localization signal. Lipid moieties are joined to intrabodies in order to tether the intrabody to the cytosolic side of the plasma membrane. Intrabodies can also be targeted to exert function in the cytosol. For example, cytosolic intrabodies are used to sequester factors within the cytosol, thereby preventing them from being transported to their natural cellular destination.

[0390] In one embodiment, intrabodies are used to capture 83P2H3 in the nucleus, thereby preventing its activity within the nucleus. Nuclear targeting signals are engineered into such 83P2H3 intrabodies in order to achieve the desired targeting. Such 83P2H3 intrabodies are designed to bind specifically to a particular 83P2H3 domain. In another embodiment, cytosolic intrabodies that specifically bind to the 83P2H3 protein are used to prevent 83P2H3 from gaining access to the nucleus, thereby preventing it from exerting any biological activity within the nucleus (e.g., preventing 83P2H3 from forming transcription complexes with other factors).

[0391] In order to specifically direct the expression of such intrabodies to particular cells, the transcription of the intrabody is placed under the regulatory control of an appropriate tumor-specific promoter and/or enhancer. In order to target intrabody expression specifically to prostate, for example, the PSA promoter and/or promoter/enhancer can be utilized (See, for example, U.S. Pat. No. 5,919,652 issued Jul. 6, 1999).

[0392] XII.B.) Inhibition of 83P2H3 with Recombinant Proteins

[0393] In another approach, recombinant molecules bind to 83P2H3 and thereby inhibit 83P2H3 function. For example, these recombinant molecules prevent or inhibit 83P2H3 from accessing/binding to its binding partner(s) or associating with other protein(s). Such recombinant molecules can, for example, contain the reactive part(s) of a 83P2H3 specific antibody molecule. In a particular embodiment, the 83P2H3 binding domain of a 83P2H3 binding partner is engineered into a dimeric fusion protein, whereby the fusion protein comprises two 83P2H3 ligand binding domains linked to the Fc portion of a human IgG, such as human IgG1. Such IgG portion can contain, for example, the CH2 and CH3 domains and the hinge region, but not the CH1 domain. Such dimeric fusion proteins are administered in soluble form to patients suffering from a cancer associated with the expression of 83P2H3, whereby the dimeric fusion protein specifically binds to 83P2H3 and blocks 83P2H3 interaction with a binding partner. Such dimeric fusion proteins are further combined into multimeric proteins using known antibody linking technologies.

[0394] XII.C.) Inhibition of 83P2H3 Transcription or Translation

[0395] The present invention also comprises various methods and compositions for inhibiting the transcription of the 83P2H3 gene. Similarly, the invention also provides methods and compositions for inhibiting the translation of 83P2H3 mRNA into protein.

[0396] In one approach, a method of inhibiting the transcription of the 83P2H3 gene comprises contacting the 83P2H3 gene with a 83P2H3 antisense polynucleotide. In another approach, a method of inhibiting 83P2H3 mRNA translation comprises contacting the 83P2H3 mRNA with an antisense polynucleotide. In another approach, a 83P2H3 specific ribozyme is used to cleave the 83P2H3 message, thereby inhibiting translation. Such antisense and ribozyme based methods can also be directed to the regulatory regions of the 83P2H3 gene, such as the 83P2H3 promoter and/or enhancer elements. Similarly, proteins capable of inhibiting a 83P2H3 gene transcription factor are used to inhibit 83P2H3 mRNA transcription. The various polynucleotides and compositions useful in the aforementioned methods have been described above. The use of antisense and ribozyme molecules to inhibit transcription and translation is well known in the art.

[0397] Other factors that inhibit the transcription of 83P2H3 by interfering with 83P2H3 transcriptional activation are also useful to treat cancers expressing 83P2H3. Similarly, factors that interfere with 83P2H3 processing are useful to treat cancers that express 83P2H3. Cancer treatment methods utilizing such factors are also within the scope of the invention.

[0398] XH.D.) General Considerations for Therapeutic Strategies

[0399] Gene transfer and gene therapy technologies can be used to deliver therapeutic polynucleotide molecules to tumor cells synthesizing 83P2H3 (i.e., antisense, ribozyme, polynucleotides encoding intrabodies and other 83P2H3 inhibitory molecules). A number of gene therapy approaches are known in the art. Recombinant vectors encoding 83P2H3 antisense polynucleotides, ribozymes, factors capable of interfering with 83P2H3 transcription, and so forth, can be delivered to target tumor cells using such gene therapy approaches.

[0400] The above therapeutic approaches can be combined with any one of a wide variety of surgical, chemotherapy or radiation therapy regimens. The therapeutic approaches of the invention can enable the use of reduced dosages of chemotherapy (or other therapies) and/or less frequent administration, an advantage for all patients and particularly for those that do not tolerate the toxicity of the chemotherapeutic agent well.

[0401] The anti-tumor activity of a particular composition (e.g., antisense, ribozyme, intrabody), or a combination of such compositions, can be evaluated using various in vitro and in vivo assay systems. In vitro assays that evaluate therapeutic activity include cell growth assays, soft agar assays and other assays indicative of tumor promoting activity, binding assays capable of determining the extent to which a therapeutic composition will inhibit the binding of 83P2H3 to a binding partner, etc.

[0402] In vivo, the effect of a 83P2H3 therapeutic composition can be evaluated in a suitable animal model. For example, xenogenic prostate cancer models can be used, wherein human prostate cancer explants or passaged xenograft tissues are introduced into immune compromised animals, such as nude or SCID mice (Klein et al., 1997, Nature Medicine 3: 402-408). For example, PCT Patent Application WO98/16628, Sawyers et al., published Apr. 23, 1998, describes various xenograft models of human prostate cancer capable of recapitulating the development of primary tumors, micrometastasis, and the formation of osteoblastic metastases characteristic of late stage disease. Efficacy can be predicted using assays that measure inhibition of tumor formation, tumor regression or metastasis, and the like.

[0403] In vivo assays that evaluate the promotion of apoptosis are useful in evaluating therapeutic compositions. In one embodiment, xenografts from tumor bearing mice treated with the therapeutic composition can be examined for the presence of apoptotic foci and compared to untreated control xenograft-bearing mice. The extent to which apoptotic foci are found in the tumors of the treated mice provides an indication of the therapeutic efficacy of the composition.

[0404] The therapeutic compositions used in the practice of the foregoing methods can be formulated into pharmaceutical compositions comprising a carrier suitable for the desired delivery method. Suitable carriers include any material that when combined with the therapeutic composition retains the anti-tumor function of the therapeutic composition and is generally non-reactive with the patient's immune system. Examples include, but are not limited to, any of a number of standard pharmaceutical carriers such as sterile phosphate buffered saline solutions, bacteriostatic water, and the like (see, generally, Remington's Pharmaceutical Sciences 16th Edition, A. Osal., Ed., 1980).

[0405] Therapeutic formulations can be solubilized and administered via any route capable of delivering the therapeutic composition to the tumor site. Potentially effective routes of administration include, but are not limited to, intravenous, parenteral, intraperitoneal, intramuscular, intratumor, intradermal, intraorgan, orthotopic, and the like. A preferred formulation for intravenous injection comprises the therapeutic composition in a solution of preserved bacteriostatic water, sterile unpreserved water, and/or diluted in polyvinylchloride or polyethylene bags containing 0.9% sterile Sodium Chloride for Injection, USP. Therapeutic protein preparations can be lyophilized and stored as sterile powders, preferably under vacuum, and then reconstituted in bacteriostatic water (containing for example, benzyl alcohol preservative) or in sterile water prior to injection.

[0406] Dosages and administration protocols for the treatment of cancers using the foregoing methods will vary with the method and the target cancer, and will generally depend on a number of other factors appreciated in the art.

[0407] XIII.) Kits

[0408] For use in the diagnostic and therapeutic applications described herein, kits are also within the scope of the invention. Such kits can comprise a carrier, package or container that is compartmentalized to receive one or more containers such as vials, tubes, and the like, each of the container(s) comprising one of the separate elements to be used in the method. For example, the container(s) can comprise a probe that is or can be detectably labeled. Such probe can be an antibody or polynucleotide specific for a 83P2H3-related protein or a 83P2H3 gene or message, respectively. Where the method utilizes nucleic acid hybridization to detect the target nucleic acid, the kit can also have containers containing nucleotide(s) for amplification of the target nucleic acid sequence and/or a container comprising a reporter-means, such as a biotin-binding protein, such as avidin or streptavidin, bound to a reporter molecule, such as an enzymatic, florescent, or radioisotope label. The kit can include all or part of the amino acid sequence of FIG. 2 or FIG. 3 or analogs thereof, or a nucleic acid molecules that encodes such amino acid sequences.

[0409] The kit of the invention will typically comprise the container described above and one or more other containers comprising materials desirable from a commercial and user standpoint including buffers, diluents, filters, needles, syringes, and package inserts with instructions for use.

[0410] A label can be present on the container to indicate that the composition is used for a specific therapy or non-therapeutic application, and can also indicate directions for either in vivo or in vitro use, such as those described above. Directions and or other information can also be included on an insert which is included with the kit.

EXAMPLES

[0411] Various aspects of the invention are further described and illustrated by way of the several examples that follow, none of which are intended to limit the scope of the invention.

Example 1

SSH-Generated Isolation of a cDNA Fragment of the 83P2H3 Gene

[0412] To isolate genes that are involved in the progression of androgen dependent (AD) prostate cancer to androgen independent (AI) cancer, an experiment was conducted with the LAPC-4 AD xenograft in male SCID mice. Mice that harbored LAPC-4 AD xenografts were castrated when the tumors reached a size of 1 cm in diameter. The tumors regressed in size and temporarily stopped producing the androgen dependent protein PSA. Seven to fourteen days post-castration, PSA levels were detectable again in the blood of the mice. Eventually the tumors develop an AI phenotype and start growing again in the castrated males. Tumors were harvested at different time points after castration to identify genes that are turned on or off during the transition to androgen independence.

[0413] Two SSH experiments led to the isolation of numerous candidate gene fragment clones (SSH clones). All candidate clones were sequenced and subjected to homology analysis against all sequences in the major public gene and EST databases in order to provide information on the identity of the corresponding gene and to help guide the decision to analyze a particular gene for differential expression. In general, gene fragments that had no homology to any known sequence in any of the searched databases, and thus considered to represent novel genes, as well as gene fragments showing homology to previously sequenced expressed sequence tags (ESTs), were subjected to differential expression analysis by RT-PCR and/or northern analysis.

[0414] The gene 83P2H3 was derived from an LAPC-4 AD minus LAPC-4 AD (3 days post-castration) subtraction. The SSH DNA sequence of 405 bp (FIG. 1A) is 99% (399/400 bp) identical to Homo sapiens calcium transport protein CaT1 gene (GenBank accession AF304463). A 83P2H3 cDNA (clone C) of 2,899 bp was isolated from a human placental library (pEAK8 vector, Pangene) revealing an ORF of 725 amino acids (FIGS. 2A and 3A). The nucleotide and protein sequences of 83P2H3 shows homology to human mRNA for CaT-like B protein (FIGS. 4A-E).

[0415] Materials and Methods

[0416] LAPC Xenografts and Human Tissues

[0417] LAPC xenografts were obtained from Dr. Charles Sawyers (UCLA) and generated as described (Klein et al, 1997, Nature Med. 3: 402-408; Craft et al., 1999, Cancer Res. 59: 5030-5036). Androgen dependent and independent LAPC-4 AD and AI xenografts were grown in male SCID mice and were passaged as small tissue chunks in recipient males. LAPC-4 AI xenografts were derived from LAPC-4 AD tumors, respectively. To generate the AI xenografts, male mice bearing AD tumors were castrated and maintained for 2-3 months. After the tumors re-grew, the tumors were harvested and passaged in castrated males or in female SCID mice.

[0418] Cell Lines

[0419] Human cell lines (e.g., HeLa) were obtained from the ATCC and were maintained in DMEM with 5% fetal calf serum.

[0420] RNA Isolation

[0421] Tumor tissue and cell lines were homogenized in Trizol reagent (Life Technologies, Gibco BRL) using 10 ml/g tissue or 10 ml/108 cells to isolate total RNA. Poly A RNA was purified from total RNA using Qiagen's Oligotex mRNA Mini and Midi kits. Total and mRNA were quantified by spectrophotometric analysis (O.D. 260/280 nm) and analyzed by gel electrophoresis.

[0422] Oligonucleotides

[0423] The following HPLC purified oligonucleotides were used.

1DPNCDN (cDNA synthesis primer):(SEQ ID NO: 714)5′TTTTGATCAAGCTT303′Adaptor 1:(SEQ ID NO: 715)5′CTAATACGACTCACTATAGGGCTCGAGCGGCCGCCCGGGCAG3′(SEQ ID NO: 716)3′GGCCCGTCCTAG5′Adaptor 2:(SEQ ID NO: 717)5′GTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAG3′(SEQ ID NO: 718)3′CGGCTCCTAG5′PCR primer 1:(SEQ ID NO: 719)5′CTAATACGACTCACTATAGGGC3′Nested primer (NP) 1:(SEQ ID NO: 720)5′TCGAGCGGCCGCCCGGGCAGGA3′Nested primer (NP)2:(SEQ ID NO: 721)5′AGCGTGGTCGCGGCCGAGGA3′

[0424] Suppression Subtractive Hybridization

[0425] Suppression Subtractive Hybridization (SSH) was used to identify cDNAs corresponding to genes that may be differentially expressed in prostate cancer. The SSH reaction utilized cDNA from two LAPC-4 AD xenografts. Specifically, to isolate genes that are involved in the progression of androgen dependent (AD) prostate cancer to androgen independent (AI) cancer, an experiment was conducted with the LAPC-4 AD xenograft in male SCID mice. Mice that harbored LAPC-4 AD xenografts were castrated when the tumors reached a size of 1 cm in diameter. The tumors regressed in size and temporarily stopped producing the androgen dependent protein PSA. Seven to fourteen days post-castration, PSA levels were detectable again in the blood of the mice. Eventually the tumors develop an AI phenotype and start growing again in the castrated males. Tumors were harvested at different time points after castration to identify genes that are turned on or off during the transition to androgen independence.

[0426] The gene 83P2H3 was derived from an LAPC-4 AD tumor (grown in intact male mouse) minus an LAPC-4 AD tumor (3 days post-castration) subtraction. The SSH DNA sequence (FIG. 1) was identified.

[0427] The cDNA derived from an LAPC-4 AD tumor (3 days post-castration) was used as the source of the “driver” cDNA, while the cDNA from the LAPC-9 AD tumor (grown in intact male mouse) was used as the source of the “tester” cDNA. Double stranded cDNAs corresponding to tester and driver cDNAs were synthesized from 2 μg of poly(A)+ RNA isolated from the relevant xenograft tissue, as described above, using CLONTECH's PCR-Select cDNA Subtraction Kit and 1 ng of oligonucleotide DPNCDN as primer. First- and second-strand synthesis were carried out as described in the Kit's user manual protocol (CLONTECH Protocol No. PT1117-1, Catalog No. K1804-1). The resulting cDNA was digested with Dpn II for 3 hrs at 37° C. Digested cDNA was extracted with phenol/chloroform (1:1) and ethanol precipitated.

[0428] Driver cDNA was generated by combining in a 1:1 ratio Dpn II digested cDNA from the relevant xenograft source (see above) with a mix of digested cDNAs derived from the human cell lines HeLa, 293, A431, Colo205, and mouse liver.

[0429] Tester cDNA was generated by diluting 1 μl of Dpn II digested cDNA from the relevant xenograft source (see above) (400 ng) in 5 μl of water. The diluted cDNA (2 μl, 160 ng) was then ligated to 2 μl of Adaptor 1 and Adaptor 2 (10 μM), in separate ligation reactions, in a total volume of 10 μl at 16° C. overnight, using 400 u of T4 DNA ligase (CLONTECH). Ligation was terminated with 1 μl of 0.2 M EDTA and heating at 72° C. for 5 min.

[0430] The first hybridization was performed by adding 1.5 μl (600 ng) of driver cDNA to each of two tubes containing 1.5 μl (20 ng) Adaptor 1- and Adaptor 2-ligated tester cDNA. In a final volume of 4 μl, the samples were overlaid with mineral oil, denatured in an MJ Research thermal cycler at 98° C. for 1.5 minutes, and then were allowed to hybridize for 8 hrs at 68° C. The two hybridizations were then mixed together with an additional 1 μl of fresh denatured driver cDNA and were allowed to hybridize overnight at 68° C. The second hybridization was then diluted in 200 μl of 20 mM Hepes, pH 8.3, 50 mM NaCl, 0.2 mM EDTA, heated at 70° C. for 7 min. and stored at −20° C.

[0431] PCR Amplification Cloning and Sequencing of Gene Fragments Generated from SSH

[0432] To amplify gene fragments resulting from SSH reactions, two PCR amplifications were performed. In the primary PCR reaction 1 μl of the diluted final hybridization mix was added to 1 μl of PCR primer 1 (10 μM), 0.5 μl dNTP mix (10 μM), 2.5 μl 10×reaction buffer (CLONTECH) and 0.5 μl 50×Advantage cDNA polymerase Mix (CLONTECH) in a final volume of 25 μl. PCR 1 was conducted using the following conditions: 75° C. for 5 min., 94° C. for 25 sec., then 27 cycles of 94° C. for 10 sec, 66° C. for 30 sec, 72° C. for 1.5 min. Five separate primary PCR reactions were performed for each experiment. The products were pooled and diluted 1:10 with water. For the secondary PCR reaction, 1 μl from the pooled and diluted primary PCR reaction was added to the same reaction mix as used for PCR 1, except that primers NP1 and NP2 (10 μM) were used instead of PCR primer 1. PCR 2 was performed using 10-12 cycles of 94° C. for 10 sec, 68° C. for 30 sec, and 72° C. for 1.5 minutes. The PCR products were analyzed using 2% agarose gel electrophoresis.

[0433] The PCR products were inserted into pCR2.1 using the T/A vector cloning kit (Invitrogen). Transformed E. coli were subjected to blue/white and ampicillin selection. White colonies were picked and arrayed into 96 well plates and were grown in liquid culture overnight. To identify inserts, PCR amplification was performed on 1 ml of bacterial culture using the conditions of PCR1 and NP1 and NP2 as primers. PCR products were analyzed using 2% agarose gel electrophoresis.

[0434] Bacterial clones were stored in 20% glycerol in a 96 well format. Plasmid DNA was prepared, sequenced, and subjected to nucleic acid homology searches of the GenBank, dBest, and NCI-CGAP databases.

[0435] RT-PCR Expression Analysis

[0436] First strand cDNAs can be generated from 1 μg of mRNA with oligo (dT) 12-18 priming using the Gibco-BRL Superscript Preamplification system. The manufacturer's protocol was used which included an incubation for 50 min at 42° C. with reverse transcriptase followed by RNAse H treatment at 37° C. for 20 min. After completing the reaction, the volume can be increased to 200 μl with water prior to normalization. First strand cDNAs from 16 different normal human tissues can be obtained from Clontech.

[0437] Normalization of the first strand cDNAs from multiple tissues was performed by using the primers 5′atatcgccgcgctcgtcgtcgacaa3′ (SEQ ID NO: 722) and 5′agccacacgcagctcattgtagaagg3′ (SEQ ID NO: 723) to amplify β-actin. First strand cDNA (5 μl) were amplified in a total volume of 50 μl containing 0.4 μM primers, 0.2 μM each dNTPs, 1×PCR buffer (Clontech, 10 mM Tris-HCL, 1.5 mM MgCl2, 50 mM KCl, pH8.3) and 1×Klentaq DNA polymerase (Clontech). Five μl of the PCR reaction can be removed at 18, 20, and 22 cycles and used for agarose gel electrophoresis. PCR was performed using an MJ Research thermal cycler under the following conditions: Initial denaturation can be at 94° C. for 15 sec, followed by a 18, 20, and 22 cycles of 94° C. for 15, 65° C. for 2 min, 72° C. for 5 sec. A final extension at 72° C. was carried out for 2 min. After agarose gel electrophoresis, the band intensities of the 283 b.p. β-actin bands from multiple tissues were compared by visual inspection. Dilution factors for the first strand cDNAs were calculated to result in equal β-actin band intensities in all tissues after 22 cycles of PCR. Three rounds of normalization can be required to achieve equal band intensities in all tissues after 22 cycles of PCR.

[0438] To determine expression levels of the 83P2H3 gene, 5 μl of normalized first strand cDNA were analyzed by PCR using 26, and 30 cycles of amplification. Semi-quantitative expression analysis can be achieved by comparing the PCR products at cycle numbers that give light band intensities.

[0439] A typical RT-PCR expression analysis is shown in FIG. 12. RT-PCR expression analysis was performed on first strand cDNAs generated using pools of tissues from multiple samples. The cDNAs were shown to be normalized using beta-actin PCR. Expression of 83P2H3 was observed in prostate cancer xenografts, prostate cancer tissue pools, and metastatic cancer tissue pools.

Example 1B

83P2H3 Family Member Identification

[0440] A degenerate oligo PCR strategy was utilized to identify family members of the calcium transporter, 83P2H3. The family member CaTrF2E11 was identified (FIG. 1B).

[0441] Materials and Methods

[0442] A protein alignment between 83P2H3, AJ133128 (rabbit Calcium transporter), and AAD26363.1 (human vanilloid receptor-like protein) revealed at least two conserved regions. The conserved protein sequences listed below were used to design degenerate oligos where (a) represents adenine, (c) cytosine, (g) guanine, (t) thymine, (R) adenine or guanine, (Y) cytosine or thymine, (M) adenine and cytosine and (I) inosine.

2Conserved AminoAcid SequenceDegenerate OligoG(Q/H)(T/S)ALHIA83P2H3.FM1a:5′ggIcaIWSIgcIYtIcaYatHgc 3′Y(F/Y)GE(H/L)PLS(F/L)AA83P2H3.FM2.1: 5′aRIgaIaRIggIWgYtcIccRWaRta 3′83P2H3.FM2.2: 5′aRRctIaRIggYaaYtcIccRWaRta 3′

[0443] PCR optimization was performed using the Master Amp™ PCR Optimization Kit from Epicentre Technologies, Madison Wis. (catalogue no. M07201). The kit provides 12 PCR optimization buffers, A through L, that differ in composition. RT-PCR utilized 83P2H3.FM1a and an equimolar mix of 83P2H3.FM2.1 and 83P2H3.FM2.2 to amplify CaTrF2E11 from prostate cancer (1 patient), kidney cancer pool (2 kidney cancers), and bladder cancer pool (3 bladder cancers) first strand cDNAs. The first strand cDNAs were generated from polyA mRNA using Superscript reverse transcriptase (catalogue no. 18089-011 ; Life Technologies, Rockville Md.). The first strand cDNAs were diluted to 150 μl for each μg of polyA mRNA used in the reverse transcriptase reaction and 5 μl was used in the RT-PCR reaction. Master Amp™ buffer G was the most optimal buffer for RT-PCR amplification. The sense (83P2H3.FM1a) and anti-sense degenerate oligos (83P2H3.FM2.1/FM2.2) were at 1.2 μM and the reaction volume was 50 μl. Thermal cycling conditions consisted of a single denaturation step at 92° C. for 1 min followed by 35 cycles of 96° C. for 30 sec, 50° C. for 2 min and 72° C. for 1 min. A 10 min, 72° C. final extension completed the thermal cycling.

[0444] To remove primer-dimer and to prepare the PCR products for cloning, the Qiagen PCR Purification Kit was used (catalogue no. 28104, Valencia Calif.). The purified RT-PCR product was cloned into pCR2.1 using the Invitrogen TA Cloning Kit (catalogue no. K2000-J10, Carlsbad Calif.). White colonies from the transformation were picked into 96-well microtiter plates, grown overnight, and stored at −70° C. in 20% glycerol. Clones were sequenced, assembled into contigs, and family members were identified.

[0445] Results

[0446] The CaTrF2E11 sequences was identified in multiple clones from prostate cancer (3/17), bladder cancer (11/17), and kidney cancer (3/17). The presence of CaTrF2E11 in all three cancers suggests a role in cancer while the high incidence of CaTrF2E11 in bladder cancer is indicative of a greater significance. In addition, expression analysis by RT-PCR and Northern blot analysis show expression in bladder, prostate, kidney, and lung cancer (FIG. 8, FIG. 9, FIG. 28, FIG. 29, FIG. 30).

[0447] The nucleic and amino acid sequences and ORFs for CaTrF2E11 are provided in FIG. 1A. The CaTrF2E11 sequence is 161 bp in length and codes for a 53 amino acid polypeptide. The highest homology at the DNA and protein level is with the calcium transporter described in the published PCT appliction number WO200032766-A1 (FIG. 3B). Other DNA and protein homologies were found with mouse and human vanilloid receptor-related osmotically activated channel (OTRPC4; GenBank Accessions NP—071300 and XP—027181 respectively). CaTrF2E11 maps to 12q24.1 (Liedtke et al., Cell 103: 525-535, 2000).

Example 2

Full Length Cloning of 83P2H3 & Protein Topology

[0448] A full length 83P2H3 cDNA clone (clone C) of 2899 bp was isolated from a human placenta library, revealing an ORF of 725 amino acids (FIG. 2A-B and 3A). The human prostate CaT (PCaT)/83P2H3 ORF encodes a transporter protein with 6 predicted transmembrane domains, and is predicted to be a type IIIa plasma membrane protein using the PSORT program (available at the PSORT WWW Server at URL psort.nibb.acjp:8800/form.html). The protein includes intracellular N-and C-terminal sequences. The hCaT/83P2H3 cDNA sequence is 99% identical to CaT-like B protein (FIG. 4A-E).

[0449] The 83P2H3 cDNA clone C was deposited on May 19, 2000, with the American Type Culture Collection (ATCC; 10801 University Blvd, Manassas, Va. 20110) as plasmid p83P2H3-C, and has been assigned Accession No. PTA-1893.

[0450] Protein Topology

[0451] Bioinformatic analysis and homology to ion transporters indicate that 83P2H3 may be expressed at the cell surface in one of two configurations. 83P2H3 may contain either 5 or 6 transmembrane domains that span the cytoplasmic membrane (FIG. 13). Both configurations show the amino terminal end to be intracellular, and share the first 3 transmembrane domains (TM). The six TM (TM Pred: http://www.ch.embnet.org/) model predicts TM1 to span aa 331-349, TM2 aa 390-408, TM3 aa 427-445, TM4 aa 451-469, TM5 aa 490-508, and TM6 aa 554-576, with the C-terminus being intracellular. The five TM model (Sosui: http://www.tuat.ac.jp/˜mitaku/adv_sosui) predicts TM1 to span aa 329-351, TM2 aa 384-406, TM3 aa 433-455, TM4 aa 489-506 and TM5 aa 559-576, suggesting that the ion transporter pore is located at the 29 aa long second extracellular loop, and that the C-terminus is extracellular.

Example 3

Chromosomal Mapping of the 83P2H3 Gene

[0452] Chromosomal localization can implicate genes in disease pathogenesis. Several chromosome mapping approaches are available including fluorescent in situ hybridization (FISH), human/hamster radiation hybrid (RH) panels (Walter et al., 1994; Nature Genetics 7:22; Research Genetics, Huntsville Ala.), human-rodent somatic cell hybrid panels such as is available from the Coriell Institute (Camden, N.J.), and genomic viewers utilizing BLAST homologies to sequenced and mapped genomic clones (NCBI, Bethesda, Md.).

[0453] The chromosomal localization of 83P2H3 was determined using the GeneBridge4 Human/Hamster radiation hybrid (RH) panel (Walter et al., 1994; Nature Genetics 7:22)(Research Genetics, Huntsville Ala.).

[0454] The following PCR primers were used:

383P2H3.15′ACCAGGTTCATGTTCTGGTTCACA 3′83P2H3.25′GCTCAAGTATGAGGATTGCAAGGT 3′

[0455] The resulting 83P2H3 mapping vector for the 93 radiation hybrid panel DNAs (0000000110000010001000100100110000000111000000100110101100100000012000002100000011 01100000100), and the mapping program available at the internet address http:/www-genome.wi.mit.edu/cgi-bin/contig/rhmapper.pl, localizes the 83P2H3 gene to chromosome 7q34, a region frequently amplified or rearranged in cancer (Arranz E, et al., Cancer Genet Cytogenet 2000 February;117(1):41-4; Ong S T, Le Beau M M. Semin Oncol 1998 August;25(4):447-60; Johnson E, Cotter F E. Blood Rev 1997 March;11(l):46-55).

[0456] The 83P2H3 family member, CaTrF2E11, maps to 12q24.1 (Liedtke et al., Cell 103: 525-535, 2000).

Example 4A

Expression Analysis of 83P2H3 in Normal Tissues, Cancer Cell Lines and Patient Samples

[0457] 83P2H3 mRNA expression in normal human tissues was analyzed by northern blotting of multiple tissue blots (Clontech; Palo Alto, Calif.), comprising a total of 16 different normal human tissues, using labeled 83P2H3 SSH fragment (Example 1A) as a probe. RNA samples were quantitatively normalized with a β-actin probe. Northern blot analysis using an 83P2H3 SSH fragment probe performed on 16 normal tissues showed predominant expression of a 2.5-3 kb transcript in prostate, placenta, and pancreas (FIG. 5).

[0458] To analyze 83P2H3 expression in cancer tissues, northern blotting was performed on RNA derived from the LAPC xenografts, and several prostate cancer cell lines. The results show high expression levels in LAPC-4 AD, LAPC-9 AD, LAPC-9 AI, LNCaP and LAPC-4 CL (cell line) (FIG. 6). Lower expression was observed in LAPC-4 AI.

[0459] Northern analysis also shows that 83P2H3 is expressed in prostate tumor tissues and the normal adjacent prostate tissue derived from prostate cancer patients (FIG. 7).

[0460] RT-PCR is used to analyze expression of 83P2H3 in various tissues, including patient-derived cancers. First strand cDNAs are generated from 1 μg of mRNA with oligo (dT) 12-18 priming using the Gibco-BRL Superscript Preamplification System. The manufacturer's protocol is preferably followed, and includes an incubation for 50 min at 42° C. with reverse transcriptase followed by RNAse H treatment at 37° C. for 20 min. After completing the reaction, the volume is increased to 200 μl with water prior to normalization. First strand cDNAs are prepared from various tissues of interest. Normalization can be performed by PCR using primers to actin and GAPDH. Semi-quantitative PCR is performed using primers to 83P2H3.

[0461] In the present example, first strand cDNA was prepared from a vital pool 1 (VP1: liver, lung and kidney), a vital pool 2 (VP2: pancreas, colon and stomach), a LAPC xenograft pool (LAPC-4AD, LAPC-4AI, LAPC-9AD and LAPC-9AI), a prostate cancer pool, and a metastatic cancer pool. The metastatic cancer pool consisted of metastatic tissues from cancers of the following organs: breast, ovarian, pancreas, colon, prostate and bladder. Normalization was performed by PCR using primers to actin and GAPDH. Semi-quantitative PCR, using primers to 83p2H3, was performed at 30 cycles of amplification. Results show expression of 83P2H3 in VP2, xenograft pool, prostate cancer pool and metastatic cancer pool (FIG. 12).

[0462] These data indicate that 83P2H3 represents a suitable cancer target for diagnosis and therapy.

Example 4B

Expression Analysis of CaTrF2E11 in Normal Tissues and Patient Specimens

[0463] Analysis of CaTrF2E11 by RT-PCR is shown in FIG. 8 and FIG. 9. Normal tissue expression is restricted to kidney and prostate. Analysis of human patient cancer RNA pools shows expression in bladder and kidney cancer pools (FIG. 8 and FIG. 9), and in lung and ovarian cancer pools (FIG. 9).

[0464] Extensive northern blot analysis of CaTrF2E11 in 16 human normal tissues confirms the expression observed by RT-PCR (FIG. 10). An approximately 4 kb transcript is detected in kidney, placenta, and to lower levels in prostate.

[0465] Northern blot analysis of CaTrF2E11 on patient tumor specimens shows expression in bladder tumor tissues, kidney tumor tissues and lung tumor tissues derived from cancer patients (FIG. 28). Northern blot analysis of individual bladder cancer patient specimens shows expression of CaTrF2E11 in all 4 bladder tumors tested and in one bladder cancer cell line SCaBER (FIG. 29). The expression detected in normal adjacent tissue (isolated from a patient) but not in normal tissue (isolated from a healthy donor) may indicate that this tissue is not fully normal and that CaTrF2E11 may be expressed in early stage tumors.

[0466] Expression of CaTrF2E11 is also detected in 2 of 3 kidney cancer cell lines, and in all normal and kidney cancer tissues tested (FIG. 30). In lung cancer samples, CaTrF2E11 expression is observed in the CALU-1 cancer cell line and in 2 lung tumor tissues isolated from lung cancer patients (FIG. 11). The expression detected in normal adjacent tissues (isolated from a patient) but not in normal tissues (isolated from a healthy donor) may indicate that these tissues are not fully normal and that CaTrF2E11 may be expressed in early stage tumors.

[0467] The restricted expression of CaTrF2E11 in normal tissues and the expression detected in bladder cancer, lung cancer, ovarian cancer, and kidney cancer suggest that CaTrF2E11 is a potential therapeutic target and a diagnostic marker for human cancers.

Example 5A

Production of Recombinant 83P2H3 in Prokaryotic Systems

[0468] A. In vitro Transcription and Translation Constructs

[0469] PCRII: To generate 83P2H3 sense and anti-sense RNA probes for RNA in situ investigations, pCRII constructs (Invitrogen, Carlsbad Calif.) are generated encoding either all or fragments of the 83P2H3 cDNA. The pCRII vector has Sp6 and T7 promoters flanking the insert to drive the transcription of 83P2H3 RNA for use as probes in RNA in situ hybridization experiments. These probes are used to analyze the cell and tissue expression of 83P2H3 at the RNA level. Transcribed 83P2H3 RNA representing the cDNA amino acid coding region of the 83P2H3 gene is used in in vitro translation systems such as the TnT™ Coupled Reticulolysate System (Promega, Corp., Madison, Wis.) to synthesize 83P2H3 protein.

[0470] B. Bacterial Constructs

[0471] pGEX Constructs: To generate recombinant 83P2H3 proteins in bacteria that are fused to the Glutathione S-transferase (GST) protein, all or parts of the 83P2H3 cDNA protein coding sequence are fused to the GST gene by cloning into pGEX-6P-1 or any other GST-fusion vector of the pGEX family (Amersham Pharmacia Biotech, Piscataway, N.J.). The constructs allow controlled expression of recombinant 83P2H3 protein sequences with GST fused at the amino-terminus and a six histidine epitope (6×His) at the carboxyl-terminus. The GST and 6×His tags permit purification of the recombinant fusion protein from induced bacteria with the appropriate affinity matrix and allow recognition of the fusion protein with anti-GST and His antibodies. The six histidine epitope tag is generated by adding 6 histidine codons to the cloning primer at the 3′ end of the open reading frame (ORF). A proteolytic cleavage site, such as the PreScission™ recognition site in pGEX-6P-1, may be employed such that it permits cleavage of the GST tag from 83P2H3-related protein. The ampicillin resistance gene and pBR322 origin permits selection and maintenance of the pGEX plasmids in E. coli. For example, constructs are made utilizing pGEX-6P-1 such that the following regions of 158P1D7 are expressed as an amino-terminal fusions to GST: amino acids 1 to 725; or any 8, 9, 10, 11, 12,13, 14,15, or more contiguous amino acids from 83P2H3 or analogs thereof.

[0472] In one embodiment, amino acids 615-725 of 83P2H3 was cloned into pGEX-6P-1 vector and the fusion protein was purified from induced bacteria. The fusion protein was subjected to proteolytic digestion with PreScission™ protease and the cleavage product free of GST sequences were used as an immunogen to generate polyclonal and monoclonal antibodies (see sections entitled “Generation of Polyclonal Antibodies” and “Generation of Monoclonal Antibodies”, examples 6 and 7 respectively).

[0473] pMAL Constructs: To generate recombinant 83P2H3 proteins that are fused to maltose-binding protein (MBP) in bacterial cells, all or parts of the 83P2H3 cDNA protein coding sequence are fused to the MBP gene by cloning into the pMAL-c2X and pMAL-p2X vectors (New England Biolabs, Beverly, Mass.). The constructs allow controlled expression of recombinant 83P2H3 protein sequences with MBP fused at the amino-terminus and a 6×His epitope at the carboxyl-terminus. The MBP and 6×His tags permit purification of the recombinant protein from induced bacteria with the appropriate affinity matrix and allow recognition of the fusion protein with anti-MBP and anti-His antibodies. The 6×His is generated by adding the histidine codons to the 3′ cloning primer. A Factor Xa recognition site permits cleavage of the pMAL tag from 83P2H3. The pMAL-c2X and pMAL-p2X vectors are optimized to express the recombinant protein in the cytoplasm or periplasm respectively. Periplasm expression enhances folding of proteins with disulfide bonds. For example, constructs are made utilizing pMAL-c2X and pMAL-p2X such that the following regions of the 83P2H3 protein are expressed as amino-terminal fusions to MBP: amino acids 1 to 725; or any 8, 9, 10, 11, 12,13, 14, 15, or more contiguous amino acids from 83P2H3 or analogs thereof.

[0474] pET Constructs: To express 83P2H3 in bacterial cells, all or parts of the 83P2H3 cDNA protein coding sequence is cloned into the pET family of vectors (Novagen, Madison, Wis.). These vectors allow tightly controlled expression of recombinant 83P2H3 protein in bacteria with and without fusion to proteins that enhance solubility, such as NusA and thioredoxin (Trx), and epitope tags, such as 6×His and S-Tag™ that aid purification and detection of the recombinant protein. For example, constructs are made utilizing pET NusA fusion system 43.1 such that the following regions of the 83P2H3 protein are expressed as an amino-terminal fusions to NusA: amino acids 1 to 725; or any 8, 9, 10, 11, 12,13, 14, 15, or more contiguous amino acids from 83P2H3 or analogs thereof.

[0475] C. Yeast Constructs

[0476] pESC Constructs: To express 83P2H3 in the yeast species Saccharomyces cerevisiae for generation of recombinant protein and functional studies, all or parts of the 83P2H3 cDNA protein coding sequence are cloned into the pESC family of vectors each of which contain 1 of 4 selectable markers, HIS3, TRP1, LEU2, and URA3 (Stratagene, La Jolla, Calif.). These vectors allow controlled expression from the same plasmid of up to 2 different genes or cloned sequences containing either Flag™ or Myc epitope tags in the same yeast cell. This system is useful to confirm protein-protein interactions of 83P2H3. In addition, expression in yeast yields similar post-translational modifications, such as glycosylations and phosphorylations, that are found when expressed in eukaryotic cells. For example, constructs are made utilizing pESC-HIS such that the following regions of the 83P2H3 protein are expressed: amino acids 1 to 725; or any 8, 9, 10, 11, 12,13, 14, 15, or more contiguous amino acids from 83P2H3 or analogs thereof.

[0477] pESP Constructs: To express 83P2H3 in the yeast species Saccharomyces pombe, all or parts of the 83P2H3 cDNA protein coding sequence are cloned into the pESP family of vectors. These vectors allow controlled high level of expression of a 83P2H3 protein sequence that is fused at either the amino terminus or at the carboxyl terminus to GST which aids purification of the recombinant protein. A Flag™ epitope tag allows detection of the recombinant protein with anti-Flag™ antibody. For example, constructs are made utilizing pESP-1 vector such that the following regions of the 83P2H3 protein are expressed as amino-terminal fusions to GST: amino acids 1 to 725; or any 8, 9, 10, 11, 12,13, 14, 15, or more contiguous amino acids from 83P2H3 or analogs thereof.

Example 5B

Production of Recombinant CaTrF2E11 in Prokaryotic Systems

[0478] A. Bacterial Constructs

[0479] pGEX Constructs: To generate recombinant CaTrF2E11 proteins in bacteria that are fused to the Glutathione S-transferase (GST) protein, all or parts of the CaTrF2E11 nucleic acid sequence are fused to the GST gene by cloning into pGEX-6P-1 or any other GST-fusion vector of the pGEX family (Amersham Pharmacia Biotech, Piscataway, N.J.). The constructs allow controlled expression of recombinant CaTrF2E11 protein sequences with GST fused at the N-terminus and a six histidine epitope at the C-terminus. The GST and HIS tags permit purification of the recombinant fusion protein from induced bacteria with the appropriate affinity matrix and allow recognition of the fusion protein with anti-GST and HIS antibodies. The six histidine epitope tag is generated by adding the histidine codons to the cloning primer at the 3′ end of the open reading frame (ORF). A proteolytic cleavage site, such as the PreScission™ recognition site in pGEX-6P-1, may be employed such that it permits cleavage of the GST tag from CaTrF2E11-related protein. The ampicillin resistance gene and pBR322 origin permits selection and maintenance of the pGEX plasmids in E. coli. For example, constructs are made utilizing pGEX-6P-1 such that the following regions of 158P1D7 are expressed as an amino-terminal fusions to GST: amino acids 1 to 963; or any 8, 9, 10, 11, 12,13, 14,15, or more contiguous amino acids from CaTrF2E11 or analogs thereof

[0480] PMAL Constructs: To generate recombinant CaTrF2E11 proteins that are fused to maltose-binding protein (MBP) in bacterial cells, all or parts of the CaTrF2E11 nucleic acid sequence are fused to the MBP gene by cloning into the pMAL-c2X and pMAL-p2X vectors (New England Biolabs, Beverly, Mass.). The constructs allow controlled expression of recombinant CaTrF2E11 protein sequences with MBP fused at the N-terminus and a six histidine epitope at the C-terminus. The MBP and HIS tags permit purification of the recombinant protein from induced bacteria with the appropriate affinity matrix and allow recognition of the fusion protein with anti-MBP and anti-HIS antibodies. The six histidine epitope tag is generated by adding the histidine codons to the 3′ cloning primer. A Factor Xa recognition site permits cleavage of the pMAL tag from CaTrF2E11. The pMAL-c2X and pMAL-p2X vectors are optimized to express the recombinant protein in the cytoplasm or periplasm respectively. Periplasm expression enhances folding of proteins with disulfide bonds. For example, constructs are made utilizing pMAL-c2X and pMAL-p2X such that the following regions of the CaTrF2E11 protein are expressed as amino-terminal fusions to MBP: amino acids 1 to 963; or any 8, 9, 10, 11, 12, 13, 14, 15, or more contiguous amino acids from CaTrF2E11 or analogs thereof

[0481] pET Constructs: To express CaTrF2E11 in bacterial cells, all or parts of the CaTrF2E11 sequence is cloned into the pET family of vectors (Novagen, Madison, Wis.). These vectors allow tightly controlled expression of recombinant CaTrF2E11 protein in bacteria with and without fusion to proteins that enhance solubility, such as NusA and thioredoxin (Trx), and epitope tags, such as 6×His and S-Tag™ that aid purification and detection of the recombinant protein. For example, constructs are made utilizing pET NusA fusion system 43.1 such that the following regions of the CaTrF2E11 protein are expressed as an amino-terminal fusions to NusA : amino acids 1 to 963; or any 8, 9, 10, 11, 12, 13, 14, 15, or more contiguous amino acids from CaTrF2E11 or analogs thereof.

[0482] B. Yeast Constructs

[0483] pESC: To express CaTrF2E11 in the yeast species Saccharomyces cerevisiae for generation of recombinant protein and functional studies, all or parts of the CaTrF2E11 sequence is cloned into the pESC family of vectors each of which contain 1 of 4 selectable markers, HIS3, TRP1, LEU2, and URA3 (Stratagene, La Jolla, Calif.). These vectors allow controlled expression from the same plasmid of up to 2 different genes or cloned sequences containing either Flag™ or Myc epitope tags in the same yeast cell. This system is useful to study protein-protein interactions of CaTrF2E11. In addition, expression in yeast yields similar post-translational modifications, such as glycosylations and phosphorylations, that are found when expressed in eukaryotic cells. For example, constructs are made utilizing pESC-HIS such that the following regions of the CaTrF2E11 protein are expressed: amino acids 1 to 963; or any 8, 9, 10, 11, 12, 13, 14, 15, or more contiguous amino acids from CaTrF2E11 or analogs thereof.

[0484] pESP: To express CaTrF2E11 in the yeast species Saccharomyces pombe, all or parts of the CaTrF2E11 sequence is cloned into the pESP family of vectors. These vectors allow controlled high level of expression of a CaTrF2E11 protein sequence that is fused at either the amino terminus or at the carboxyl terminus to GST which aids purification of the recombinant protein. A Flag™ epitope tag allows detection of the recombinant protein with anti-Flag™ antibody. For example, constructs are made utilizing pESP-1 vector such that the following regions of the CaTrF2E11 protein are expressed as amino-terminal fusions to GST: amino acids 1 to 963; or any 8, 9, 10, 11, 12, 13, 14, 15, or more contiguous amino acids from CaTrF2E11 or analogs thereof.

[0485] PCRII: To generate CaTrF2E11 sense and anti-sense riboprobes for RNA in situ investigations, pCRII constructs (Invitrogen, Carlsbad Calif.) are generated using cDNA sequence encoding all or fragments of the cDNA. The pCRII vector has Sp6 and T7 promoters flanking the insert to drive the production of CaTrF2E11 RNA riboprobes for use in RNA in situ hybridization experiments.

Example 6A

Production of Recombinant 83P2H3 in Eukaryotic Systems

[0486] A. Mammalian Constructs

[0487] To express recombinant 83P2H3 in eukaryotic cells, the fall or partial length 83P2H3 cDNA sequences can be cloned into any one of a variety of expression vectors known in the art. The constructs can be transfected into any one of a wide variety of mammalian cells such as 293T cells. Transfected 293T cell lysates can be probed with the anti-83P2H3 polyclonal serum, described above.

[0488] pcDNA4/HisMax Constructs: To express 83P2H3 in mammalian cells, the 83P2H3 ORF is cloned into pCDNA4/HisMax Version A (Invitrogen, Carlsbad, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter and the SP 163 translational enhancer. The recombinant protein has XpressTM and six histidine epitopes fused to the N-terminus. The pCDNA4/HisMax vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Zeocin resistance gene allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coli. The following regions of 83P2H3 are expressed in this construct, amino acids 1 to 725; or any 8, 9, 10, 11, 12, 13, 14, 15, or more contiguous amino acids from 83P2H3, variants, or analogs thereof.

[0489] pcDNA3.1/MycHis Constructs: To express 83P2H3 in mammalian cells, the ORFs with consensus Kozak translation initiation site arecloned into pCDNA3. 1/MycHis Version A (Invitrogen, Carlsbad, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter. The recombinant proteins have the myc epitope and six histidines fused to the C-terminus. The pCDNA3.1/MycHis vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability, along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Neomycin resistance gene can be used, as it allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coli. The following regions of 83P2H3 are expressed in this construct, amino acids 1 to 725; or any 8, 9, 10, 11, 12, 13, 14, 15, or more contiguous amino acids from 83P2H3, variants, or analogs thereof.

[0490] pcDNA3.1 Construct: To express 83P2H3 in mammalian cells the ORF with consensus Kozak translation initiation site was cloned into pCDNA3.1 (Invitrogen, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter. The pCDNA3.1 vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Neomycin resistance gene allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coli. The following regions of 83P2H3 are expressed in this construct, amino acids 1 to 725; or any 8, 9, 10, 11, 12, 13, 14, 15, or more contiguous amino acids from 83P2H3, variants, or analogs thereof.

[0491] pcDNA3.1/CT-GFP-TOPO Construct: To express 83P2H3 in mammalian cells and to allow detection of the recombinant proteins using fluorescence, the ORFs with consensus Kozak translation initiation site are cloned into pCDNA3.1 CT-GFP-TOPO (Invitrogen, Calif.). Protein expression is driven from the cytomegaloviras (CMV) promoter. The recombinant proteins have the Green Fluorescent Protein (GFP) fused to the C-terminus facilitating non-invasive, in vivo detection and cell biology studies. The pCDNA3.1 CT-GFP-TOPO vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Neomycin resistance gene allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE I origin permits selection and maintenance of the plasmid in E. coli. An additional construct with a N-terminal GFP fusion is made in pCDNA3.1/NT-GFP-TOPO spanning the entire length of the 83P2H3 protein. The following regions of 83P2H3 are expressed in this construct, amino acids 1 to 725; or any 8, 9, 10, 11, 12, 13, 14, 15, or more contiguous amino acids from 83P2H3, variants, or analogs thereof.

[0492] PAPtag: The 83P2H3 ORFs are cloned into pAPtag-5 (GenHunter Corp. Nashville, Tenn.). This construct generates an alkaline phosphatase fusion at the C-terminus of the 83P2H3 proteins while fusing the IgGK signal sequence to N-terminus. The resulting recombinant 83P2H3 proteins are optimized for secretion into the media of transfected mammalian cells and can be used to identify proteins such as ligands or receptors that interact with the 83P2H3 proteins. Protein expression is driven from the CMV promoter and the recombinant proteins also contain myc and six histidines fused to the C-terminus of alkaline phosphatase. The Zeocin resistance gene allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene permits selection of the plasmid in E. coli. The following regions of 83P2H3 are expressed in this construct, amino acids 1 to 725; or any 8, 9, 10, 11, 12, 13, 14, 15, or more contiguous amino acids from 83P2H3, variants, or analogs thereof.

[0493] ptag5: The 83P2H3 ORFs are also cloned into pTag-5. This vector is similar to pAPtag but without the alkaline phosphatase fusion. This construct generates an immunoglobulin G1 Fc fusion at the C-terminus of the 83P2H3 protein while fusing the IgGK signal sequence to the N-terminus. The resulting recombinant 83P2H3 proteins are optimized for secretion into the media of transfected mammalian cells, and can be used to identify proteins such as ligands or receptors that interact with the 83P2H3 proteins. Protein expression is driven from the CMV promoter and the recombinant protein also contains myc and six histidines fused to the C-terminus of alkaline phosphatase. The Zeocin resistance gene allows for selection of mammalian cells expressing the protein, and the ampicillin resistance gene permits selection of the plasmid in E. coli. The following regions of 83P2H3 are expressed in this construct, amino acids 1 to 725; or any 8, 9, 10, 11, 12,13, 14,15, or more contiguous amino acids from 83P2H3, variants, or analogs thereof.

[0494] PsecFc: The 83P2H3 ORFs are also cloned into psecFc. The psecFc vector was assembled by cloning immunoglobulin G1 Fc (hinge, CH2, CH3 regions) into pSecTag2 (Invitrogen, Calif.). This construct generates an immunoglobulin G1 Fc fusion at the C-terminus of the 83P2H3 proteins, while fusing the IgG-kappa signal sequence to N-terminus. The resulting recombinant 83P2H3 protein is optimized for secretion into the media of transfected mammalian cells, and can be used to identify proteins such as ligands or receptors that interact with the 83P2H3 protein. Protein expression is driven from the CMV promoter and the recombinant protein also contain myc and six histidines fused to the C-terminus of alkaline phosphatase. The Zeocin resistance gene allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene permits selection of the plasmid in E. coli. The following regions of 83P2H3 are expressed in this construct, amino acids 1 to 725; or any 8, 9, 10, 11, 12, 13, 14, 15, or more contiguous amino acids from 83P2H3, variants, or analogs thereof.

[0495] pSRα Constructs: To generate mammalian cell lines that express 83P2H3 constitutively, the 83P2H3 ORF was cloned into pSRα construct. Amphotropic and ecotropic retroviruses were generated by transfection of pSRα constructs into the 293T-10A1 packaging line or co-transfection of pSRα and a helper plasmid (containing deleted packaging sequences) into the 293 cells, respectively. The retrovirus was used to infect a variety of mammalian cell lines, resulting in the integration of the cloned gene, 83P2H3, into the host cell-lines. Protein expression is driven from a long terminal repeat (LTR). The Neomycin resistance gene allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE1 origin permit selection and maintenance of the plasmid in E. coli. The retroviral vectors can thereafter be used for infection and generation of various cell lines using, for example, SCaBER, NIH 3T3, TsuPr1, 293 or rat-1 cells.

[0496] Additional pSRα constructs are made that fuse an epitope tag such as the FLAG tag to the C-terminus of 83P2H3 sequences to allow detection using anti-epitope tag antibodies. For example, the FLAG sequence 5′ gat tac aag gat gac gac gat aag 3′ is added to cloning primer at the 3′ end of the ORF. Additional pSRα constructs are made to produce both N-terminal and C-terminal GFP and myc/6 HIS fusion proteins of the full-length 83P2H3 proteins. The following regions of 83P2H3 are expressed in such constructs, amino acids 1 to 725; or any 8, 9, 10, 11, 12, 13, 14, 15, or more contiguous amino acids from 83P2H3, variants, or analogs thereof.

[0497] Additional Viral Vectors: Additional constructs are made for viral-mediated delivery and expression of 83P2H3. High virus titer leading to high level expression of 83P2H3 is achieved in viral delivery systems such as adenoviral vectors and herpes amplicon vectors. The 83P2H3 coding sequences or fragments thereof are amplified by PCR and subcloned into the AdEasy shuffle vector (Stratagene). Recombination and virus packaging are performed according to the manufacturer's instructions to generate adenoviral vectors. Alternatively, 83P2H3 coding sequences or fragments thereof are cloned into the HSV-1 vector (Imgenex) to generate herpes viral vectors. The viral vectors are thereafter used for infection of various cell lines such as SCaBER, NIH 3T3, 293 or rat-1 cells. The following regions of 83P2H3 are expressed in this construct, amino acids 1 to 725; or any 8, 9, 10, 11, 12, 13, 14, 15, or more contiguous amino acids from 83P2H3, variants, or analogs thereof.

[0498] Regulated Expression Systems: To control expression of 83P2H3 in mammalian cells, coding sequences of 83P2H3 are cloned into regulated mammalian expression systems such as the T-Rex System (Invitrogen), the GeneSwitch System (Invitrogen) and the tightly-regulated Ecdysone System (Sratagene). These systems allow the study of the temporal and concentration dependent effects of recombinant 83P2H3. These vectors are thereafter used to control expression of 83P2H3 in various cell lines such as SCaBER, NIH 3T3, 293 or rat-1 cells. The following regions of 83P2H3 are expressed in these constructs, amino acids 1 to 725; or any 8, 9, 10, 11, 12, 13, 14, 15, or more contiguous amino acids from 83P2H3, variants, or analogs thereof.

[0499] B. Baculovirus Expression Systems

[0500] To generate recombinant 83P2H3 proteins in a baculovirus expression system, 83P2H3 ORFs are cloned into the baculovirus transfer vector pBlueBac 4.5 (Invitrogen), which provides a His-tag at the N-terminus. Specifically, pBlueBac-83P2H3 is co-transfected with helper plasmid pBac-N-Blue (Invitrogen) into SF9 (Spodoptera frugiperda) insect cells to generate recombinant baculovirus (see Invitrogen instruction manual for details). Baculovirus is then collected from cell supernatant and purified by plaque assay.

[0501] Recombinant 83P2H3 protein is then generated by infection of HighFive insect cells (Invitrogen) with purified baculovirus. Recombinant 83P2H3 protein can be detected using anti-83P2H3 or anti-His-tag antibody. 83P2H3 protein can be purified and used in various cell-based assays or as immunogen to generate polyclonal and monoclonal antibodies specific for 83P2H3.

[0502] The following regions of 83P2H3 are expressed in this construct, amino acids 1 to 725; or any 8, 9, 10, 11, 12, 13, 14, 15, or more contiguous amino acids from 83P2H3, variants, or analogs thereof.

Example 6B

Production of Recombinant CaTrF2E11 in Eukaryotic Systems

[0503] A. Mammalian Constructs

[0504] To express recombinant CaTrF2E11 in eukaryotic cells, the full or partial length CaTrF2E11 cDNA sequences can be cloned into any one of a variety of expression vectors known in the art. The constructs can be transfected into any one of a wide variety of mammalian cells such as 293T cells. Transfected 293T cells can be screened for recombinant CaTrF2E11 as described above.

[0505] pCDNA4/HisMax Constructs: To express CaTrF2E11 in mammalian cells, the CaTrF2E11 ORF is cloned into pCDNA4/HisMax Version A (Invitrogen, Carlsbad, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter and the SP163 translational enhancer. The recombinant protein has XpressTM and six histidine epitopes fused to the N-terminus. The pCDNA4/HisMax vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Zeocin resistance gene allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coli.

[0506] pCDNA3.1/MycHis Constructs: To express CaTrF2E11 in mammalian cells, the ORFs with consensus Kozak translation initiation site are cloned into pCDNA3.1/MycHis Version A (Invitrogen, Carlsbad, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter. The recombinant proteins have the myc epitope and six histidines fused to the C-terminus. The pCDNA3.1/MycHis vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability, along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Neomycin resistance gene can be used, as it allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coli.

[0507] pCDNA3.1/CT-GFP-TOPO Construct: To express CaTrF2E11 in mammalian cells and to allow detection of the recombinant proteins using fluorescence, the ORFs with consensus Kozak translation initiation site are cloned into pCDNA3.1CT-GFP-TOPO (Invitrogen, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter. The recombinant proteins have the Green Fluorescent Protein (GFP) fused to the C-terminus facilitating non-invasive, in vivo detection and cell biology studies. The pCDNA3.1CT-GFP-TOPO vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Neomycin resistance gene allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coli. An additional construct with a N-terminal GFP fusion is made in pCDNA3.1/NT-GFP-TOPO spanning the entire length of the CaTrF2E11 protein.

[0508] PAPtag: The CaTrF2E11 sequences are cloned into pAPtag-5 (GenHunter Corp. Nashville, Tenn.). This construct generates an alkaline phosphatase fusion at the C-terminus of the CaTrF2E11 proteins while fusing the IgGK signal sequence to N-terminus. The resulting recombinant CaTrF2E11 proteins are optimized for secretion into the media of transfected mammalian cells and can be used to identify proteins such as ligands or receptors that interact with the CaTrF2E11 proteins. Protein expression is driven from the CMV promoter and the recombinant proteins also contain myc and six histidines fused to the C-terminus of alkaline phosphatase. The Zeocin resistance gene allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene permits selection of the plasmid in E. coli.

[0509] ptag5: The CaTrF2E11 sequences are also cloned into pTag-5. This vector is similar to pAPtag but without the alkaline phosphatase fusion. This construct generates an immunoglobulin G1 Fc fusion at the C-terminus of the CaTrF2E11 protein while fusing the IgGK signal sequence to the N-terminus. The resulting recombinant CaTrF2E11 proteins are optimized for secretion into the media of transfected mammalian cells, and can be used to identify proteins such as ligands or receptors that interact with the CaTrF2E11 proteins. Protein expression is driven from the CMV promoter and the recombinant protein also contains myc and six histidines fused to the C-terminus of alkaline phosphatase. The Zeocin resistance gene allows for selection of mammalian cells expressing the protein, and the ampicillin resistance gene permits selection of the plasmid in E. coli.

[0510] PsecFc: The CaTrF2E11 sequences are also cloned into psecFc. The psecFc vector was assembled by cloning immunoglobulin G1 Fc (hinge, CH2, CH3 regions) into pSecTag2 (Invitrogen, Calif.). This construct generates an immunoglobulin G1 Fc fusion at the C-terminus of the CaTrF2E11 proteins, while fusing the IgGK signal sequence to N-terminus. The resulting recombinant CaTrF2E11 protein is optimized for secretion into the media of transfected mammalian cells, and can be used to identify proteins such as ligands or receptors that interact with the CaTrF2E11 protein. Protein expression is driven from the CMV promoter and the recombinant proteins also contain myc and six histidines fused to the C-terminus of alkaline phosphatase. The Zeocin resistance gene allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene permits selection of the plasmid in E. coli.

[0511] pSRα Constructs: To generate mammalian cell lines that express CaTrF2E11 constitutively, the sequences are cloned into pSRα constructs. Amphotropic and ecotropic retroviruses are generated by transfection of pSRα constructs into the 293T-10A1 packaging line or co-transfection of pSRα and a helper plasmid (containing deleted packaging sequences) into the 293 cells, respectively. The retrovirus can be used to infect a variety of mammalian cell lines, resulting in the integration of the cloned gene, CaTrF2E11, into the host cell-lines. Protein expression is driven from a long terminal repeat (LTR). The Neomycin resistance gene allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE1 origin permit selection and maintenance of the plasmid in E. coli. The retroviral vectors can thereafter be used for infection and generation of various cell lines using, for example, SCaBER, NIH 3T3, TsuPr1, 293 or rat-1 cells.

[0512] Additional pSRα constructs are made that fuse an epitope tag such as the FLAG tag to the C-terminus of CaTrF2E11 sequences to allow detection using anti-epitope tag antibodies. For example, the FLAG sequence 5′ gat tac aag gat gac gac gat aag 3′ is added to cloning primer at the 3′ end of the ORF. Additional pSRα constructs are made to produce both N-terminal and C-terminal GFP and myc/6 HIS fusion proteins of the full-length CaTrF2E11 proteins.

[0513] Additional Viral Vectors: Additional constructs are made for viral-mediated delivery and expression of CaTrF2E11. High virus titer leading to high level expression of CaTrF2E11 is achieved in viral delivery systems such as adenoviral vectors and herpes amplicon vectors. The CaTrF2E11 coding sequences or fragments thereof are amplified by PCR and subcloned into the AdEasy shuttle vector (Stratagene). Recombination and virus packaging are performed according to the manufacturer's instructions to generate adenoviral vectors. Alternatively, CaTrF2E11 coding sequences or fragments thereof are cloned into the HSV-1 vector (Imgenex) to generate herpes viral vectors. The viral vectors are thereafter used for infection of various cell lines such as SCaBER, NIH 3T3, 293 or rat-1 cells.

[0514] Regulated Expression Systems: To control expression of CaTrF2E11 in mammalian cells, coding sequences of CaTrF2E11 are cloned into regulated mammalian expression systems such as the T-Rex System (Invitrogen), the GeneSwitch System (Invitrogen) and the tightly-regulated Ecdysone System (Sratagene). These systems allow the study of the temporal and concentration dependent effects of recombinant CaTrF2E11. These vectors are thereafter used to control expression of CaTrF2E11 in various cell lines such as SCABER, NIH 3T3, 293 or rat-1 cells.

[0515] B. Baculovirus Expression Systems

[0516] To generate recombinant CaTrF2E11 proteins in a baculovirus expression system, CaTrF2E11 ORFs are cloned into the baculovirus transfer vector pBlueBac 4.5 (Invitrogen), which provides a His-tag at the N-terminus. Specifically, pBlueBac-CaTrF2E11 is co-transfected with helper plasmid pBac-N-Blue (Invitrogen) into SF9 (Spodoptera frugiperda) insect cells to generate recombinant baculovirus (see Invitrogen instruction manual for details). Baculovirus is then collected from cell supernatant and purified by plaque assay. Recombinant CaTrF2E11 protein is then generated by infection of HighFive insect cells (Invitrogen) with purified baculovirus. Recombinant CaTrF2E11 protein can be detected using anti-CaTrF2E11 or anti-His-tag antibody. CaTrF2E11 protein can be purified and used in various cell-based assays or as immunogen to generate polyclonal and monoclonal antibodies specific for CaTrF2E11.

Example 7A

Antigenicity Profiles of 83P2H3

[0517]
FIG. 14A, FIG. 15A, FIG. 16A, FIG. 17A, and FIG. 18A depict graphically five amino acid profiles of the 83P2H3 amino acid sequence, each assessment available by accessing the ProtScale website (URL www.expasy.ch/cgi-bin/protscale.pl) on the ExPasy molecular biology server.

[0518] These profiles: FIG. 14A, Hydrophilicity, (Hopp T. P., Woods K. R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828); FIG. 15A, Hydropathicity, (Kyte J., Doolittle R. F., 1982. J. Mol. Biol. 157:105-132); FIG. 16A, Percentage Accessible Residues (Janin J., 1979 Nature 277:491-492); FIG. 17A, Average Flexibility, (Bhaskaran R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res. 32:242-255); FIG. 18A, Beta-turn (Deleage, G., Roux B. 1987 Protein Engineering 1:289-294); and optionally others available in the art, such as on the ProtScale website, were used to identify antigenic regions of the 83P2H3 protein. Each of the above amino acid profiles of 83P2H3 were generated using the following ProtScale parameters for analysis: 1) A window size of 9; 2) 100% weight of the window edges compared to the window center; and, 3) amino acid profile values normalized to lie between 0 and 1.

[0519] Hydrophilicity (FIG. 14A), Hydropathicity (FIG. 15A) and Percentage Accessible Residues (FIG. 16A) profiles were used to determine stretches of hydrophilic amino acids (i.e., values greater than 0.5 on the Hydrophilicity and Percentage Accessible Residues profile, and values less than 0.5 on the Hydropathicity profile). Such regions are likely to be exposed to the aqueous environment, be present on the surface of the protein, and thus available for immune recognition, such as by antibodies.

[0520] Average Flexibility (FIG. 17A) and Beta-turn (FIG. 18A) profiles determine stretches of amino acids (i.e., values greater than 0.5 on the Beta-turn profile and the Average Flexibility profile) that are not constrained in secondary structures such as beta sheets and alpha helices. Such regions are also more likely to be exposed on the protein and thus accessible to immune recognition, such as by antibodies.

[0521] Antigenic sequences of the 83P2H3 protein indicated, e.g., by the profiles set forth in FIG. 14A, FIG. 15A, FIG. 16A, FIG. 17A, or FIG. 18A are used to prepare immunogens, either peptides or nucleic acids that encode them, to generate therapeutic and diagnostic anti-83P2H3 antibodies. The immunogen can be any 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 25, 30, 35, 40, 45, 50 or more than 50 contiguous amino acids, or the corresponding nucleic acids that encode them, from the 83P2H3 protein. In particular, peptide immunogens of the invention can comprise, a peptide region of at least 5 amino acids of FIG. 2A-B in any whole number increment up to 725 that includes an amino acid position having a value greater than 0.5 in the Hydrophilicity profile of FIG. 14A; a peptide region of at least 5 amino acids of FIG. 2A-B in any whole number increment up to 725 that includes an amino acid position having a value less than 0.5 in the Hydropathicity profile of FIG. 15A; a peptide region of at least 5 amino acids of FIG. 2A-B in any whole number increment up to 725 that includes an amino acid position having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 16A; a peptide region of at least 5 amino acids of FIG. 2A-B in any whole number increment up to 725 that includes an amino acid position having a value greater than 0.5 in the Average Flexibility profile on FIG. 17A; and, a peptide region of at least 5 amino acids of FIG. 2A-B in any whole number increment up to 725 that includes an amino acid position having a value greater than 0.5 in the Beta-turn profile of FIG. 18A. Peptide immunogens of the invention can also comprise nucleic acids that encode any of the forgoing. All immunogens of the invention, peptide or nucleic acid, can be embodied in human unit dose form, or comprised by a composition that includes a pharmaceutical excipient compatible with human physiology.

Example 7B

Antigenicity Profiles of CaTrF2E11

[0522]
FIG. 14B, FIG. 15B, FIG. 16B, FIG. 17B, and FIG. 18B depict graphically five amino acid profiles of the CaTrF2E11 amino acid sequence, each assessment available by accessing the ProtScale website (URL www.expasy.ch/cgi-bin/protscale.pl) on the ExPasy molecular biology server.

[0523] These profiles: FIG. 14B, Hydrophilicity, (Hopp T. P., Woods K. R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828); FIG. 15B, Hydropathicity, (Kyte J., Doolittle R. F., 1982. J. Mol. Biol. 157:105-132); FIG. 16B, Percentage Accessible Residues (Janin J., 1979 Nature 277:491-492); FIG. 17B, Average Flexibility, (Bhaskaran R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res. 32:242-255); FIG. 18B, Beta-turn (Deleage, G., Roux B. 1987 Protein Engineering 1:289-294); and optionally others available in the art, such as on the ProtScale website, were used to identify antigenic regions of the CaTrF2E11 protein. Each of the above amino acid profiles of CaTrF2E11 were generated using the following ProtScale parameters for analysis: 1) A window size of 9; 2) 100% weight of the window edges compared to the window center; and, 3) amino acid profile values normalized to lie between 0 and 1.

[0524] Hydrophilicity (FIG. 14B), Hydropathicity (FIG. 15B) and Percentage Accessible Residues (FIG. 16B) profiles were used to determine stretches of hydrophilic amino acids (i.e., values greater than 0.5 on the Hydrophilicity and Percentage Accessible Residues profile, and values less than 0.5 on the Hydropathicity profile). Such regions are likely to be exposed to the aqueous environment, be present on the surface of the protein, and thus available for immune recognition, such as by antibodies.

[0525] Average Flexibility (FIG. 17B) and Beta-turn (FIG. 18B) profiles determine stretches of amino acids (i.e., values greater than 0.5 on the Beta-turn profile and the Average Flexibility profile) that are not constrained in secondary structures such as beta sheets and alpha helices. Such regions are also more likely to be exposed on the protein and thus accessible to immune recognition, such as by antibodies.

[0526] Antigenic sequences of the CaTrF2E11 protein indicated, e.g., by the profiles set forth in FIG. 14B, FIG. 15B, FIG. 16B, FIG. 17B, or FIG. 18B are used to prepare immunogens, either peptides or nucleic acids that encode them, to generate therapeutic and diagnostic anti-CaTrF2E11 antibodies. The immunogen can be any 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 25, 30, 35, 40, 45, 50 or more than 50 contiguous amino acids, or the corresponding nucleic acids that encode them, from the CaTrF2E11 protein. In particular, peptide immunogens of the invention can comprise, a peptide region of at least 5 amino acids of FIG. 2C-D in any whole number increment up to 963 that includes an amino acid position having a value greater than 0.5 in the Hydrophilicity profile of FIG. 14B; a peptide region of at least 5 amino acids of FIG. 2C-D in any whole number increment up to 963 that includes an amino acid position having a value less than 0.5 in the Hydropathicity profile of FIG. 15B; a peptide region of at least 5 amino acids of FIG. 2C-D in any whole number increment up to 963 that includes an amino acid position having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 16B; a peptide region of at least 5 amino acids of FIG. 2C-D in any whole number increment up to 963 that includes an amino acid position having a value greater than 0.5 in the Average Flexibility profile on FIG. 17B; and, a peptide region of at least 5 amino acids of FIG. 2C-D in any whole number increment up to 963 that includes an amino acid position having a value greater than 0.5 in the Beta-turn profile of FIG. 18B. Peptide immunogens of the invention can also comprise nucleic acids that encode any of the forgoing. All immunogens of the invention, peptide or nucleic acid, can be embodied in human unit dose form, or comprised by a composition that includes a pharmaceutical excipient compatible with human physiology.

Example 8A

Generation of 83P2H3 Polyclonal Antibodies

[0527] Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. In addition to immunizing with the full length 83P2H3 protein, computer algorithms are employed in design of immunogens that, based on amino acid sequence analysis contain characteristics of being antigenic and available for recognition by the immune system of the immunized host (see the Example entitled “Antigenicity Profiles”). Such regions would be predicted to be hydrophilic, flexible, in beta-turn conformations, and be exposed on the surface of the protein (see, e.g., FIG. 14A, FIG. 15A, FIG. 16A, FIG. 17A, or FIG. 18A for amino acid profiles that indicate such regions of 83P2H3).

[0528] For example, 83P2H3 recombinant bacterial fusion proteins or peptides encoding hydrophilic, flexible, beta-turn regions of the 83P2H3 sequence, such as amino acids 350-389 are used, and amino acids 615-725 of 83P2H3 were used as antigens to generate polyclonal antibodies in New Zealand White rabbits. It is useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include, but are not limited to, keyhole limpet hemocyanin (KLH), serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. In one embodiment, a peptide encoding amino acids 367-385 of 83P2H3 is conjugated to KLH and used to immunize the rabbit. Alternatively the immunizing agent may include all or portions of the 83P2H3 protein, analogs or fusion proteins thereof. For example, the 83P2H3 amino acid sequence can be fused using recombinant DNA techniques to any one of a variety of fusion protein partners that are well known in the art such as glutathione-S-transferase (GST) and HIS tagged fusion proteins. Such fusion proteins are purified from induced bacteria using the appropriate affinity matrix. Other recombinant bacterial fusion proteins that may be employed include maltose binding protein, LacZ, thioredoxin, NusA, or an immunoglobulin constant region (see e.g. the section entitled “Expression of PHOR1F5D6 in Prokaryotic Systems” Current and Protocols In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubul et al. eds., 1995; Linsley, P. S., Brady, W., Urnes, M., Grosmaire, L., Damle, N., and Ledbetter, L. (1991) J.Exp.Med. 174, 561-566).

[0529] During the immunization protocol, it is useful to mix or emulsify the antigen in adjuvants that enhance the immune response of the host animal. Examples of adjuvants include, but are not limited to, complete Freund's adjuvant (CFA) and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).

[0530] In a typical protocol, rabbits are initially immunized subcutaneously with up to 200 μg, typically 100-200 μg, of fusion protein or peptide conjugated to KLH mixed in complete Freund's adjuvant (CFA). Rabbits are then injected subcutaneously every two weeks with up to 200 μg, typically 100-200 μg, of the immunogen in incomplete Freund's adjuvant (IFA). Test bleeds are taken approximately 7-10 days following each immunization and used to monitor the titer of the antiserum by ELISA.

[0531] To test serum, such as rabbit serum, for reactivity with 83P2H3 proteins, the full-length 83P2H3 cDNA can be cloned into an expression vector such as one that provides a 6 His tag at the carboxyl-terminus (pCDNA 3.1 myc-his, Invitrogen, see the Example herein entitled “Production of Recombinant 83P2H3 in Eukaryotic Systems”). After transfection of the constructs into 293T cells, cell lysates are probed with the anti-83P2H3 serum and with anti-His antibody (Santa Cruz Biotechnologies, Santa Cruz, Calif.) to determine specific reactivity to denatured 83P2H3 protein using the Western blot technique. In addition, recognition of native protein by the antiserum can be determined by flow cytometric analysis of 293T or other recombinant 83P2H3-expressing cells. Alternatively, specificity of the antiserum is tested by Western blot, immunoprecipitation, and flow cytometric techniques using lysates of cells that endogenously express 83P2H3.

[0532] Sera from rabbits immunized with fusion proteins, such as GST and MBP fusion proteins, are purified by depletion of antibodies reactive to GST, MBP, or other fusion partner sequence by passage over an affinity column containing the fusion partner either alone or in the context of an irrelevant fusion protein. Sera from His-tagged protein and peptide immunized rabbits as well as fusion partner depleted sera are further purified by passage over an affinity column composed of the original protein immunogen or free peptide coupled to Affigel matrix (BioRad).

[0533] In one embodiment, a GST-fusion protein encoding amino acids 615-725 of 83P2H3 was produced and purified and a cleavage product was generated in which GST sequences were removed by proteolytic cleavage. This cleavage protein was used to generate a polyclonal antibody by immunization of a rabbit. The rabbit immune serum was partially purified by removal of anti-bacterial and anti-GST reactive antibodies by passage over an irrelevant GST-fusion protein column and then further purified by protein G column chromatography. This polyclonal antibody specifically recognized 83P2H3 protein on 293T cells by Western blotting and immunohistochemistry, and stained the surface of 293T-83P2H3 and PC3-83P2H3 cells demonstrating that the 83P2H3 protein residues in the plasma membrane (FIG. 19 and FIG. 31).

Example 8B

Generation of CaTrF2E11 Polyclonal Antibodies

[0534] Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. In addition to immunizing with the full length CaTrF2E11 protein, computer algorithms are employed in design of immunogens that, based on amino acid sequence analysis contain characteristics of being antigenic and available for recognition by the immune system of the immunized host (see the Example entitled “Antigenicity Profiles”). Such regions would be predicted to be hydrophilic, flexible, in beta-turn conformations, and be exposed on the surface of the protein (see, e.g., FIG. 14B, FIG. 15B, FIG. 16B, FIG. 17B, or FIG. 18B for amino acid profiles that indicate such regions of CaTrF2E11).

[0535] For example, CaTrF2E11 recombinant bacterial fusion proteins or peptides encoding hydrophilic, flexible, beta-turn regions of the CaTrF2E11 sequence, such as amino acids 586-606, 733-758, and amino acids 812-963 of CaTrF2E11 are used as antigens to generate polyclonal antibodies in New Zealand White rabbits. It is useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include, but are not limited to, keyhole limpet hemocyanin (KLH), serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. In one embodiment, a peptide encoding amino acids 586-606 of CaTrF2E11 is conjugated to KLH and used to immunize the rabbit. Alternatively the immunizing agent may include all or portions of the CaTrF2E11 protein, analogs or fusion proteins thereof. For example, the CaTrF2E11 amino acid sequence can be fused using recombinant DNA techniques to any one of a variety of fusion protein partners that are well known in the art such as glutathione-S-transferase (GST) and HIS tagged fusion proteins. Such fusion proteins are purified from induced bacteria using the appropriate affinity matrix. Other recombinant bacterial fusion proteins that may be employed include maltose binding protein, LacZ, thioredoxin, NusA, or an immunoglobulin constant region (see e.g. the section entitled “Expression of PHOR1F5D6 in Prokaryotic Systems” and Current Protocols In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubul et al. eds., 1995; Linsley, P. S., Brady, W., Urnes, M., Grosmaire, L., Damle, N., and Ledbetter, L. (1991) J.Exp.Med. 174, 561-566; Novagen, Madison, Wis.). In one embodiment, a GST-fusion protein encoding amino acids 816-963 of CaTrF2E11 is produced and purified and a cleavage product is generated in which GST sequences are removed by proteolytic cleavage. This cleavage protein is used to generate a polyclonal antibody by immunization of a rabbit.

[0536] During the immunization protocol, it is useful to mix or emulsify the antigen in adjuvants that enhance the immune response of the host animal. Examples of adjuvants include, but are not limited to, complete Freund's adjuvant (CFA) and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).

[0537] In a typical protocol, rabbits are initially immunized subcutaneously with up to 200 μg, typically 100-200 μg, of fusion protein or peptide conjugated to KLH mixed in complete Freund's adjuvant (CFA). Rabbits are then injected subcutaneously every two weeks with up to 200 μg, typically 100-200 μg, of the immunogen in incomplete Freund's adjuvant (IFA). Test bleeds are taken approximately 7-10 days following each immunization and used to monitor the titer of the antiserum by ELISA.

[0538] To test serum, such as rabbit serum, for reactivity with CaTrF2E11 proteins, the full-length CaTrF2E11 cDNA can be cloned into an expression vector such as one that provides a 6 His tag at the carboxyl-terminus (pCDNA 3.1 myc-his, Invitrogen, see the Example entitled “Production of Recombinant CaTrF2E11 in Eukaryotic Systems”). After transfection of the constructs into 293T cells, cell lysates are probed with the anti-CaTrF2E11 serum and with anti-His antibody (Santa Cruz Biotechnologies, Santa Cruz, Calif.) to determine specific reactivity to denatured CaTrF2E11 protein using the Western blot technique. In addition, recognition of native protein by the antiserum can be determined by flow cytometric analysis of 293T or other recombinant CaTrF2E11-expressing cells. Alternatively, specificity of the antiserum is tested by Western blot, immunoprecipitation, and flow cytometric techniques using lysates of cells that endogenously express CaTrF2E11.

[0539] Sera from rabbits immunized with fusion proteins, such as GST and MBP fusion proteins, are purified by depletion of antibodies reactive to GST, MBP, or other fusion partner sequence by passage over an affinity column containing the fusion partner either alone or in the context of an irrelevant fusion protein. Sera from His-tagged protein and peptide immunized rabbits as well as fusion partner depleted sera are further purified by passage over an affinity column composed of the original protein immunogen or free peptide coupled to Affigel matrix (BioRad).

Example 9A

Generation of 83P2H3 Monoclonal Antibodies (mAbs)

[0540] In one embodiment, therapeutic mAbs to 83P2H3 comprise those that react with epitopes of the protein that would disrupt or modulate the biological function of 83P2H3, for example those that disrupt the Ca2+ transport function of 83P2H3. Therapeutic mAbs also comprise those which specifically bind epitopes of 83P2H3 exposed on the cell surface and thus are useful in targeting mAb-toxin conjugates. Immunogens for generation of such mAbs include those designed to encode or contain the entire 83P2H3 protein or regions of the 83P2H3 protein predicted to be antigenic from computer analysis of the amino acid sequence (see, e.g., FIG. 14A, FIG. 15A, FIG. 16A, FIG. 17A, or FIG. 18A, and the Example entitled “Antigenicity Profiles”).

[0541] Immunogens include peptides, recombinant bacterial proteins, and mammalian expressed Tag 5 proteins and human and murine IgG Fc fusion proteins. In addition, cells expressing high levels of 83P2H3, such as 293T-83P2H3 cells, are used to immunize mice. To generate mAbs to 83P2H3, mice are first immunized intraperitoneally (IP) with, typically, 10-50 μg of protein immunogen or 107 83P2H3-expressing cells mixed in complete Freund's adjuvant. Mice are then subsequently immunized IP every 2-4 weeks with, typically, 10-50 μg of protein immunogen or 107 cells mixed in incomplete Freund's adjuvant. Alternatively, MPL-TDM adjuvant is used in immunizations.

[0542] Alternatively, a DNA-based immunization protocol is employed in which a mammalian expression vector encoding 83P2H3 sequence is used to immunize mice by direct injection of the plasmid DNA. For example, either pCDNA 3.1 encoding the full length 83P2H3 cDNA, or amino acids 615-725 of 83P2H3 (predicted to contain ntigenic sequences from analysis, see, e.g., FIG. 14A, FIG. 15A, FIG. 16A, FIG. 17A, or FIG. 18A) fused at the N-terminus to an IgK leader sequence and at the C-terminus to the coding sequence of the murine or human IgG Fc region, is used. This protocol is used alone or in combination with protein or cell-based immunogens. Test bleeds are taken 7-10 days following immunization to monitor titer and specificity of the immune response. Once appropriate reactivity and specificity is obtained as determined by ELISA, Western blotting, immunoprecipitation, and flow cytometric analyses, fusion and hybridoma generation is then carried out with established procedures well known in the art (see, e.g., Harlow and Lane, 1988).

[0543] In one embodiment for generating 83P2H3 monoclonal antibodies, a glutathione-S-transferase (GST) fusion protein encoding amino acids 615-725 of 83P2H3 protein was expressed and purified. An 83P2H3 amino acid-specific cleavage fragment of the immunogen in which GST was removed by site-specific proteolysis was then used as immunogen. Balb C mice were initially immunized intraperitoneally with 25 μg of the 83P2H3 cleavage protein mixed in complete Freund's adjuvant. Mice were subsequently immunized every two weeks with 25 μg of 83P2H3 cleavage protein mixed in incomplete Freund's adjuvant for a total of three immunizations. The titer of serun from immunized mice was determined by ELISA using the full length GST-fusion protein and the cleaved immunogen. Reactivity and specificity of serum to full length 83P2H3 protein was monitored by Western blotting and flow cytometry using 293T cells transfected with an expression vector encoding the 83P2H3 cDNA (see e.g., the Example entitled “Production of Recombinant 83P2H3 in Eukaryotic Systems”). As can be seen in FIG. 19A-F, serum from a representative immunized mouse specifically recognized 83P2H3 on the surface of 293T cells as determined by flow cytometry and in 293T cell lysates by Western blotting. Two mice showing the strongest reactivity were rested and given a final injection of GST-83P2H3 fusion protein in PBS and then sacrificed four days later. The spleens of the sacrificed mice were then harvested and fused to SPO/2 myeloma cells using standard procedures (Harlow and Lane, 1988). Supernatants from growth wells following HAT selection were screened by ELISA, Western blot, and flow cytometry to identify 83P2H3 specific antibody-producing clones. As shown in FIG. 20A-F, two hybridoma supernatants, #4 and #8A, specifically recognized 83P2H3 protein by Western blotting and stained the surface of 293T-83P2H3 cells.

[0544] The binding affinity of a 83P2H3 monoclonal antibody is determined using standard technologies. Affinity measurements quantify the strength of antibody to epitope binding and are used to help define which 83P2H3 monoclonal antibodies preferred for diagnostic or therapeutic use, as appreciated by one of skill in the art. The BIAcore system (Uppsala, Sweden) is a preferred method for determining binding affinity. The BIAcore system uses surface plasmon resonance (SPR, Welford K. 1991, Opt. Quant. Elect. 23:1; Morton and Myszka, 1998, Methods in Enzymology 295: 268) to monitor biomolecular interactions in real time. BIAcore analysis conveniently generates association rate constants, dissociation rate constants, equilibrium dissociation constants, and affinity constants.

Example 9B

Generation of CaTrF2E11 Monoclonal Antibodies (mAbs)

[0545] In one embodiment, therapeutic mAbs to CaTrF2E11 comprise those that react with epitopes of the protein that would disrupt or modulate the biological function of CaTrF2E11, for example those that disrupt the ion transport function of CaTrF2E11. Therapeutic mAbs also comprise those which specifically bind epitopes of CaTrF2E11 exposed on the cell surface and thus are useful in targeting mAb-toxin conjugates. Immunogens for generation of such mAbs include those designed to encode or contain the entire CaTrF2E11 protein or regions of the CaTrF2E11 protein predicted to be antigenic from computer analysis of the amino acid sequence (see, e.g., FIG. 14B, FIG. 15B, FIG. 16B, FIG. 17B, or FIG. 18B, and the Example entitled “Antigenicity Profiles”).

[0546] Immunogens include peptides, recombinant bacterial proteins, and mammalian expressed Tag 5 proteins and human and murine IgG Fc fusion proteins. In addition, cells expressing high levels of 83P2H3, such as 293T-83P2H3 cells, are used to immunize mice. To generate mAbs to 83P2H3, mice are first immunized intraperitoneally (IP) with, typically, 10-50 μg of protein immunogen or 107 83P2H3-expressing cells mixed in complete Freund's adjuvant. Mice are then subsequently immunized IP every 2-4 weeks with, typically, 10-50 μg of protein immunogen or 107 cells mixed in incomplete Freund's adjuvant. Alternatively, MPL-TDM adjuvant is used in immunizations. Alternatively, a DNA-based immunization protocol is employed in which a mammalian expression vector encoding CaTrF2E11 sequence is used to immunize mice by direct injection of the plasmid DNA. For example, either pCDNA 3.1 encoding the full length CaTrF2E11 cDNA, or amino acids 816-963 of CaTrF2E11 (predicted to be antigenic from sequence analysis, see, e.g., FIG. 14B, FIG. 15B, FIG. 16B, FIG. 17B, or FIG. 18B) fused at the N-terminus to an IgK leader sequence and at the C-terminus to the coding sequence of the murine or human IgG Fc region, is used. This protocol is used alone or in combination with protein or cell-based immunogens. Test bleeds are taken 7-10 days following immunization to monitor titer and specificity of the immune response. Once appropriate reactivity and specificity is obtained as determined by ELISA, Western blotting, immunoprecipitation, and flow cytometric analyses, fusion and hybridoma generation is then carried out with established procedures well known in the art (see, e.g., Harlow and Lane, 1988).

[0547] In one embodiment for generating CaTrF2E11 monoclonal antibodies, a peptide is synthesized encoding amino acids 733-758 and is coupled to KLH. Balb C mice are initially immunized intraperitoneally with 25 μg of the peptide conjugate mixed in complete Freund's adjuvant. Mice are subsequently immunized every two weeks with 25 μg of peptide conjugate mixed in incomplete Freund's adjuvant for a total of three immunizations. The titer of serum from immunized mice is determined by ELISA using non-conjugated free peptide. Reactivity and specificity of serum to full length CaTrF2E11 protein is monitored by Western blotting and flow cytometry using 293T cells transfected with an expression vector encoding the CaTrF2E11 cDNA (see e.g., the Example entitled “Production of Recombinant CaTrF2E11 in Eukaryotic Systems”). Mice showing the strongest reactivity are rested and given a final injection of peptide conjugate in PBS and then sacrificed four days later. The spleens of the sacrificed mice are then harvested and fused to SPO/2 myeloma cells using standard procedures (Harlow and Lane, 1988). Supernatants from growth wells following HAT selection are screened by ELISA, Western blot, and flow cytometry to identify CaTrF2E11 specific antibody-producing clones.

[0548] The binding affinity of a CaTrF2E11 monoclonal antibody is determined using standard technologies. Affinity measurements quantify the strength of antibody to epitope binding and are used to help define which CaTrF2E11 monoclonal antibodies preferred for diagnostic or therapeutic use, as appreciated by one of skill in the art. The BIAcore system (Uppsala, Sweden) is a preferred method for determining binding affinity. The BIAcore system uses surface plasmon resonance (SPR, Welford K. 1991, Opt. Quant. Elect. 23:1; Morton and Myszka, 1998, Methods in Enzymology 295: 268) to monitor biomolecular interactions in real time. BIAcore analysis conveniently generates association rate constants, dissociation rate constants, equilibrium dissociation constants, and affinity constants.

Example 10

HLA Class I and Class II Binding Assays

[0549] HLA class I and class II binding assays using purified HLA molecules are performed in accordance with disclosed protocols (e.g., PCT publications WO 94/20127 and WO 94/03205; Sidney et al., Current Protocols in Immunology 18.3.1 (1998); Sidney, et al., J. Immunol. 154:247 (1995); Sette, et al., Mol. Immunol. 31:813 (1994)). Briefly, purified MHC molecules (5 to 500 nM) are incubated with various unlabeled peptide inhibitors and 1-10 nM 125I-radiolabeled probe peptides as described. Following incubation, MHC-peptide complexes are separated from free peptide by gel filtration and the fraction of peptide bound is determined. Typically, in preliminary experiments, each MHC preparation is titered in the presence of fixed amounts of radiolabeled peptides to determine the concentration of HLA molecules necessary to bind 10-20% of the total radioactivity. All subsequent inhibition and direct binding assays are performed using these HLA concentrations.

[0550] Since under these conditions [label]<[HLA] and IC50≧[HLA], the measured IC50 values are reasonable approximations of the true KD values. Peptide inhibitors are typically tested at concentrations ranging from 120 μg/ml to 1.2 ng/ml, and are tested in two to four completely independent experiments. To allow comparison of the data obtained in different experiments, a relative binding figure is calculated for each peptide by dividing the IC50 of a positive control for inhibition by the IC50 for each tested peptide (typically unlabeled versions of the radiolabeled probe peptide). For database purposes, and inter-experiment comparisons, relative binding values are compiled. These values can subsequently be converted back into IC50 nM values by dividing the IC50 nM of the positive controls for inhibition by the relative binding of the peptide of interest. This method of data compilation is accurate and consistent for comparing peptides that have been tested on different days, or with different lots of purified MHC.

[0551] Binding assays as outlined above may be used to analyze HLA supermotif and/or HLA motif-bearing peptides.

Example 11

Identification of HLA Supermotif- and Motif-Bearing CTL Candidate Epitopes

[0552] HLA vaccine compositions of the invention can include multiple epitopes. The multiple epitopes can comprise multiple HLA supermotifs or motifs to achieve broad population coverage. This example illustrates the identification of supermotif- and motif-bearing epitopes for the inclusion in such a vaccine composition. Calculation of population coverage is performed using the strategy described below.

[0553] Computer Searches and Algorithms for Identification of Supermotif and/or Motif-bearing Epitopes

[0554] The searches performed to identify the motif-bearing peptide sequences in the Example entitled “Antigenicity Profiles” and Tables V-XVIII employ the protein sequence data from the gene product of 83P2H3 set forth in FIG. 2 and FIG. 3.

[0555] Computer searches for epitopes bearing HLA Class I or Class II supermotifs or motifs are performed as follows. All translated 83P2H3 protein sequences are analyzed using a text string search software program to identify potential peptide sequences containing appropriate HLA binding motifs; such programs are readily produced in accordance with information in the art in view of known motif/supermotif disclosures. Furthermore, such calculations can be made mentally.

[0556] Identified A2-, A3-, and DR-supermotif sequences are scored using polynomial algorithms to predict their capacity to bind to specific HLA-Class I or Class II molecules. These polynomial algorithms account for the impact of different amino acids at different positions, and are essentially based on the premise that the overall affinity (or ΔG) of peptide-HLA molecule interactions can be approximated as a linear polynomial function of the type:

[0557] “ΔG”=a1i×a2i×a3i . . . ×ani

[0558] where aji is a coefficient which represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. The crucial assumption of this method is that the effects at each position are essentially independent of each other (i.e., independent binding of individual side-chains). When residue j occurs at position i in the peptide, it is assumed to contribute a constant amount ji to the free energy of binding of the peptide irrespective of the sequence of the rest of the peptide.

[0559] The method of derivation of specific algorithm coefficients has been described in Gulukota et al., J. Mol. Biol. 267:1258-126, 1997; (see also Sidney et al., Human Immunol. 45:79-93, 1996; and Southwood et al., J. Immunol. 160:3363-3373, 1998). Briefly, for all i positions, anchor and non-anchor alike, the geometric mean of the average relative binding (ARB) of all peptides carrying j is calculated relative to the remainder of the group, and used as the estimate of ji. For Class II peptides, if multiple alignments are possible, only the highest scoring alignment is utilized, following an iterative procedure. To calculate an algorithm score of a given peptide in a test set, the ARB values corresponding to the sequence of the peptide are multiplied. If this product exceeds a chosen threshold, the peptide is predicted to bind. Appropriate thresholds are chosen as a function of the degree of stringency of prediction desired.

[0560] Selection of HLA-A2 Supertype Cross-reactive Peptides

[0561] Complete protein sequences from 83P2H3 are scanned utilizing motif identification software, to identify 8-, 9-10- and 11-mer sequences containing the HLA-A2-supermotif main anchor specificity. Typically, these sequences are then scored using the protocol described above and the peptides corresponding to the positive-scoring sequences are synthesized and tested for their capacity to bind purified HLA-A*0201 molecules in vitro (HLA-A*0201 is considered a prototype A2 supertype molecule).

[0562] These peptides are then tested for the capacity to bind to additional A2-supertype molecules (A*0202, A*0203, A*0206, and A*6802). Peptides that bind to at least three of the five A2-supertype alleles tested are typically deemed A2-supertype cross-reactive binders. Preferred peptides bind at an affinity equal to or less than 500 nM to three or more HLA-A2 supertype molecules.

[0563] Selection of HLA-A3 Supermotif-bearing Epitopes

[0564] The 83P2H3 protein sequence scanned above is also examined for the presence of peptides with the HLA-A3-supermotif primary anchors. Peptides corresponding to the HLA A3 supermotif-bearing sequences are then synthesized and tested for binding to HLA-A*0301 and HLA-A*1101 molecules, the molecules encoded by the two most prevalent A3-supertype alleles. The peptides that bind at least one of the two alleles with binding affinities of ≦500 nM, often ≦200 nM, are then tested for binding cross-reactivity to the other common A3-supertype alleles (e.g., A*3101, A*3301, and A*6801) to identify those that can bind at least three of the five HLA-A3-supertype molecules tested.

[0565] Selection of HLA-B7 Supermotif Bearing Epitopes

[0566] The 83P2H3 protein is also analyzed for the presence of 8-, 9-10-, or 11-mer peptides with the HLA-B7-supermotif. Corresponding peptides are synthesized and tested for binding to HLA-B*0702, the molecule encoded by the most common B7-supertype allele (i.e., the prototype B7 supertype allele). Peptides binding B*0702 with IC50 of <500 nM are identified using standard methods. These peptides are then tested for binding to other common B7-supertype molecules (e.g., B*3501, B*5101, B*5301, and B*5401). Peptides capable of binding to three or more of the five B7-supertype alleles tested are thereby identified.

[0567] Selection of A1 and A24 Motif-bearing Epitopes

[0568] To further increase population coverage, HLA-A1 and -A24 epitopes can also be incorporated into vaccine compositions. An analysis of the 83P2H3 protein can also be performed to identify HLA-A1- and A24-motif-containing sequences.

[0569] High affinity and/or cross-reactive binding epitopes that bear other motif and/or supermotifs are identified using analogous methodology.

Example 12

Confirmation of Immunogenicity

[0570] Cross-reactive candidate CTL A2-supermotif-bearing peptides that are identified as described herein are selected for in vitro immunogenicity testing. Testing is performed using the following methodology:

[0571] Target Cell Lines for Cellular Screening

[0572] The .221A2.1 cell line, produced by transferring the HLA-A2.1 gene into the HLA-A, -B, -C null mutant human B-lymphoblastoid cell line 721.221, is used as the peptide-loaded target to measure activity of HLA-A2.1-restricted CTL. This cell line is grown in RPMI-1640 medium supplemented with antibiotics, sodium pyruvate, nonessential amino acids and 10% (v/v) heat inactivated FCS. Cells that express an antigen of interest, or transfectants comprising the gene encoding the antigen of interest, can be used as target cells to test the ability of peptide-specific CTLs to recognize endogenous antigen.

[0573] Primary CTL Induction Cultures

[0574] Generation of Dendritic Cells (DC): PBMCs are thawed in RPMI with 30 μg/ml DNAse, washed twice and resuspended in complete medium (RPMI-1640 plus 5% AB human serum, non-essential amino acids, sodium pyruvate, L-glutamine and penicillin/streptomycin). The monocytes are purified by plating 10×106 PBMC/well in a 6-well plate. After 2 hours at 37° C., the non-adherent cells are removed by gently shaking the plates and aspirating the supernatants. The wells are washed a total of three times with 3 ml RPMI to remove most of the non-adherent and loosely adherent cells. Three ml of complete medium containing 50 ng/ml of GM-CSF and 1,000 U/ml of IL-4 are then added to each well. TNFα is added to the DCs on day 6 at 75 ng/ml and the cells are used for CTL induction cultures on day 7.

[0575] Induction of CTL with DC and Peptide: CD8+ T-cells are isolated by positive selection with Dynal immunomagnetic beads (Dynabeads® M-450) and the detacha-bead® reagent. Typically about 200-250×106 PBMC are processed to obtain 24×106 CD8+ T-cells (enough for a 48-well plate culture). Briefly, the PBMCs are thawed in RPMI with 30 μg/ml DNAse, washed once with PBS containing 1% human AB serum and resuspended in PBS/1% AB serum at a concentration of 20×106 cells/ml. The magnetic beads are washed 3 times with PBS/AB serum, added to the cells (140 μl beads/20×106 cells) and incubated for 1 hour at 4° C. with continuous mixing. The beads and cells are washed 4× with PBS/AB serum to remove the nonadherent cells and resuspended at 100×106 cells/ml (based on the original cell number) in PBS/AB serum containing 100 μl/ml detacha-bead® reagent and 30 μgl/ml DNAse. The mixture is incubated for 1 hour at room temperature with continuous mixing. The beads are washed again with PBS/AB/DNAse to collect the CD8+ T-cells. The DC are collected and centrifuged at 1300 rpm for 5-7 minutes, washed once with PBS with 1% BSA, counted and pulsed with 40 μg/ml of peptide at a cell concentration of 1-2×106/ml in the presence of 3 μg/ml β2-microglobulin for 4 hours at 20° C. The DC are then irradiated (4,200 rads), washed 1 time with medium and counted again.

[0576] Setting up induction cultures: 0.25 ml cytokine-generated DC (at 1×105 cells/mil) are co-cultured with 0.25 ml of CD8+ T-cells (at 2×106 cell/ml) in each well of a 48-well plate in the presence of 10 ng/ml of IL-7. Recombinant human IL-10 is added the next day at a final concentration of 10 ng/ml and rhuman IL-2 is added 48 hours later at 10 IU/ml.

[0577] Restimulation of the induction cultures with peptide-pulsed adherent cells: Seven and fourteen days after the primary induction, the cells are restimulated with peptide-pulsed adherent cells. The PBMCs are thawed and washed twice with RPMI and DNAse. The cells are resuspended at 5×106 cells/ml and irradiated at ˜4200 rads. The PBMCs are plated at 2×106 in 0.5 ml complete medium per well and incubated for 2 hours at 37° C. The plates are washed twice with RPMI by tapping the plate gently to remove the nonadherent cells and the adherent cells pulsed with 10 μg/ml of peptide in the presence of 3 μg/ml 622 microglobulin in 0.25 ml RPMI/5% AB per well for 2 hours at 37° C. Peptide solution from each well is aspirated and the wells are washed once with RPMI. Most of the media is aspirated from the induction cultures (CD8+ cells) and brought to 0.5 ml with fresh media. The cells are then transferred to the wells containing the peptide-pulsed adherent cells. Twenty four hours later recombinant human IL-10 is added at a final concentration of 10 ng/ml and recombinant human IL2 is added the next day and again 2-3 days later at 50 IU/ml (Tsai et al., Critical Reviews in Immunology 18(1-2):65-75, 1998). Seven days later, the cultures are assayed for CTL activity in a 51Cr release assay. In some experiments the cultures are assayed for peptide-specific recognition in the in situ IFNγ ELISA at the time of the second restimulation followed by assay of endogenous recognition 7 days later. After expansion, activity is measured in both assays for a side-by-side comparison.

[0578] Measurement of CTL Lytic Activity by 51Cr Release

[0579] Seven days after the second restimulation, cytotoxicity is determined in a standard (5 hr) 51Cr release assay by assaying individual wells at a single E:T. Peptide-pulsed targets are prepared by incubating the cells with 10 μg/ml peptide overnight at 37° C.

[0580] Adherent target cells are removed from culture flasks with trypsin-EDTA. Target cells are labeled with 200 μCi of 51Cr sodium chromate (Dupont, Wilmington, Del.) for 1 hour at 37° C. Labeled target cells are resuspended at 106 per ml and diluted 1:10 with K562 cells at a concentration of 3.3×106/ml (an NK-sensitive erythroblastoma cell line used to reduce non-specific lysis). Target cells (100 μl) and effectors (100 μl) are plated in 96 well round-bottom plates and incubated for 5 hours at 37° C. At that time, 100 μl of supernatant are collected from each well and percent lysis is determined according to the formula: [(cpm of the test sample-cpm of the spontaneous 51Cr release sample)/(cpm of the maximal 51Cr release sample-cpm of the spontaneous 51Cr release sample)]×100.

[0581] Maximum and spontaneous release are determined by incubating the labeled targets with 1% Triton X-100 and media alone, respectively. A positive culture is defined as one in which the specific lysis (sample-background) is 10% or higher in the case of individual wells and is 15% or more at the two highest E:T ratios when expanded cultures are assayed.

[0582] In situ Measurement of Human IFNγ Production as an Indicator of Peptide-specific and Endogenous Recognition

[0583] Immulon 2 plates are coated with mouse anti-human IFNγ monoclonal antibody (4 μg/ml 0.1M NaHCO3, pH8.2) overnight at 4° C. The plates are washed with Ca2+, Mg2+-free PBS/0.05% Tween 20 and blocked with PBS/10% FCS for two hours, after which the CTLs (100 μl/well) and targets (100 μl/well) are added to each well, leaving empty wells for the standards and blanks (which received media only). The target cells, either peptide-pulsed or endogenous targets, are used at a concentration of 1×106 cells/ml. The plates are incubated for 48 hours at 37° C. with 5% CO2.

[0584] Recombinant human IFN-gamma is added to the standard wells starting at 400 pg or 1200 pg/100 microliter/well and the plate incubated for two hours at 37° C. The plates are washed and 100 μl of biotinylated mouse anti-human IFN-gamma monoclonal antibody (2 microgram/ml in PBS/3% FCS/0.05% Tween 20) are added and incubated for 2 hours at room temperature. After washing again, 100 microliter HRP-streptavidin (1:4000) are added and the plates incubated for one hour at room temperature. The plates are then washed 6× with wash buffer, 100 microliter/well developing solution (TMB 1:1) are added, and the plates allowed to develop for 5-15 minutes. The reaction is stopped with 50 microliter/well 1M H3PO4 and read at OD450. A culture is considered positive if it measured at least 50 pg of IFN-gamma/well above background and is twice the background level of expression.

[0585] CTL Expansion

[0586] Those cultures that demonstrate specific lytic activity against peptide-pulsed targets and/or tumor targets are expanded over a two week period with anti-CD3. Briefly, 5×104 CD8+ cells are added to a T25 flask containing the following: 1×106 irradiated (4,200 rad) PBMC (autologous or allogeneic) per ml, 2×105 irradiated (8,000 rad) EBV-transformed cells per ml, and OKT3 (anti-CD3) at 30 ng per ml in RPMI-1640 containing 10% (v/v) human AB serum, non-essential amino acids, sodium pyruvate, 25 μM 2-mercaptoethanol, L-glutamine and penicillin/streptomycin. Recombinant human IL2 is added 24 hours later at a final concentration of 200 IU/ml and every three days thereafter with fresh media at 50 IU/ml. The cells are split if the cell concentration exceeds 1×106/ml and the cultures are assayed between days 13 and 15 at E:T ratios of 30, 10, 3 and 1:1 in the 51Cr release assay or at 1×106/ml in the in situ IFNγ assay using the same targets as before the expansion.

[0587] Cultures are expanded in the absence of anti-CD3+ as follows. Those cultures that demonstrate specific lytic activity against peptide and endogenous targets are selected and 5×104 CD8+ cells are added to a T25 flask containing the following: 1×106 autologous PBMC per ml which have been peptide-pulsed with 10 μg/ml peptide for two hours at 37° C. and irradiated (4,200 rad); 2×105 irradiated (8,000 rad) EBV-transformed cells per ml RPMI-1640 containing 10% (v/v) human AB serum, non-essential AA, sodium pyruvate, 25 mM 2-ME, L-glutamine and gentamicin.

[0588] Immunogenicity of A2 Supermotif-bearing Peptides A2-supermotif cross-reactive binding peptides are tested in the cellular assay for the ability to induce peptide-specific CTL in normal individuals. In this analysis, a peptide is typically considered to be an epitope if it induces peptide-specific CTLs in at least individuals, and preferably, also recognizes the endogenously expressed peptide.

[0589] Immunogenicity can also be confirmed using PBMCs isolated from patients bearing a tumor that expresses 83P2H3. Briefly, PBMCs are isolated from patients, re-stimulated with peptide-pulsed monocytes and assayed for the ability to recognize peptide-pulsed target cells as well as transfected cells endogenously expressing the antigen.

[0590] Evaluation of A*03/A11 Immunogenicity

[0591] HLA-A3 supermotif-bearing cross-reactive binding peptides are also evaluated for immunogenicity using methodology analogous for that used to evaluate the immunogenicity of the HLA-A2 supermotif peptides.

[0592] Evaluation of B7 Immunogenicity

[0593] Immunogenicity screening of the B7-supertype cross-reactive binding peptides identified as set forth herein are evaluated in a manner analogous to the evaluation of A2-and A3-supermotif-bearing peptides.

[0594] Peptides bearing other supermotifs/motifs, e.g., HLA-A1, HLA-A24 etc. are also evaluated using similar methodology.

Example 13

Implementation of the Extended Supermotif to Improve the Binding Capacity of Native Epitopes by Creating Analogs

[0595] HLA motifs and supermotifs (comprising primary and/or secondary residues) are useful in the identification and preparation of highly cross-reactive native peptides, as demonstrated herein. Moreover, the definition of HLA motifs and supermotifs also allows one to engineer highly cross-reactive epitopes by identifying residues within a native peptide sequence which can be analoged to confer upon the peptide certain characteristics, e.g. greater cross-reactivity within the group of HLA molecules that comprise a supertype, and/or greater binding affinity for some or all of those HLA molecules. Examples of analoging peptides to exhibit modulated binding affinity are set forth in this example.

[0596] Analoging at Primary Anchor Residues

[0597] Peptide engineering strategies are implemented to further increase the cross-reactivity of the epitopes. For example, the main anchors of A2-supermotif-bearing peptides are altered, for example, to introduce a preferred L, I, V, or M at position 2, and I or V at the C-terminus.

[0598] To analyze the cross-reactivity of the analog peptides, each engineered analog is initially tested for binding to the prototype A2 supertype allele A*0201, then, if A*0201 binding capacity is maintained, for A2-supertype cross-reactivity.

[0599] Alternatively, a peptide is tested for binding to one or all supertype members and then analoged to modulate binding affinity to any one (or more) of the supertype members to add population coverage.

[0600] The selection of analogs for immunogenicity in a cellular screening analysis is typically further restricted by the capacity of the parent wild type (WT) peptide to bind at least weakly, i.e., bind at an IC50 of 5000 nM or less, to three of more A2 supertype alleles. The rationale for this requirement is that the WT peptides must be present endogenously in sufficient quantity to be biologically relevant. Analoged peptides have been shown to have increased immunogenicity and cross-reactivity by T cells specific for the parent epitope (see, e.g., Parkhurst et al., J. Immunol. 157:2539, 1996; and Pogue et al., Proc. Natl. Acad. Sci. USA 92:8166, 1995).

[0601] In the cellular screening of these peptide analogs, it is important to demonstrate that analog-specific CTLs are also able to recognize the wild-type peptide and, when possible, target cells that endogenously express the epitope.

[0602] Analoging of HLA-A3 and B7-Supermotif-bearing Peptides

[0603] Analogs of HLA-A3 supermotif-bearing epitopes are generated using strategies similar to those employed in analoging HLA-A2 supermotif-bearing peptides. For example, peptides binding to 3/5 of the A3-supertype molecules are engineered at primary anchor residues to possess a preferred residue (V, S, M, or A) at position 2.

[0604] The analog peptides are then tested for the ability to bind A*03 and A* 11 (prototype A3 supertype alleles). Those peptides that demonstrate <500 nM binding capacity are then tested for A3-supertype cross-reactivity.

[0605] Similarly to the A2- and A3-motif bearing peptides, peptides binding 3 or more B7-supertype alleles can be improved, where possible, to achieve increased cross-reactive binding or greater binding affinity or binding half life. B7 supermotif-bearing peptides are, for example, engineered to possess a preferred residue (V, I, L, or F) at the C-terminal primary anchor position, as demonstrated by Sidney et al. (J. Immunol. 157:3480-3490, 1996).

[0606] Analoging at primary anchor residues of other motif and/or supermotif-bearing epitopes is performed in a like manner.

[0607] The analog peptides are then be tested for immunogenicity, typically in a cellular screening assay. Again, it is generally important to demonstrate that analog-specific CTLs are also able to recognize the wild-type peptide and, when possible, targets that endogenously express the epitope.

[0608] Analoging at Secondary Anchor Residues

[0609] Moreover, HLA supermotifs are of value in engineering highly cross-reactive peptides and/or peptides that bind HLA molecules with increased affinity by identifying particular residues at secondary anchor positions that are associated with such properties. For example, the binding capacity of a B7 supermotif-bearing peptide with an F residue at position 1 is analyzed. The peptide is then analoged to, for example, substitute L for F at position 1. The analoged peptide is evaluated for increased binding affinity, binding half life and/or increased cross-reactivity. Such a procedure identifies analoged peptides with enhanced properties.

[0610] Engineered analogs with sufficiently improved binding capacity or cross-reactivity can also be tested for immunogenicity in HLA-B7-transgenic mice, following for example, IFA immunization or lipopeptide immunization. Analoged peptides are additionally tested for the ability to stimulate a recall response using PBMC from patients with 83P2H3-expressing tumors.

[0611] Other Analoging Strategies

[0612] Another form of peptide analogizing, unrelated to anchor positions, involves the substitution of a cysteine with α-amino butyric acid. Due to its chemical nature, cysteine has the propensity to form disulfide bridges and sufficiently alter the peptide structurally so as to reduce binding capacity. Substitution of α-amino butyric acid for cysteine not only alleviates this problem, but has been shown to improve binding and crossbinding capabilities in some instances (see, e.g., the review by Sette et al., In: Persistent Viral Infections, Eds. R. Ahmed and I. Chen, John Wiley & Sons, England, 1999).

[0613] Thus, by the use of single amino acid substitutions, the binding properties and/or cross-reactivity of peptide ligands for HLA supertype molecules can be modulated.

Example 14

Identification of 83P2H3/CaTrF2E11-Derived Sequences with HLA-DR Binding Motifs

[0614] Peptide epitopes bearing an HLA class II supermotif or motif are identified as outlined below using methodology similar to that described for HLA Class I peptides.

[0615] Selection of HLA-DR-supermotif-bearing Epitopes

[0616] To identify 83P2H3-derived, HLA class II HTL epitopes, the 83P2H3 antigen is analyzed for the presence of sequences bearing an HLA-DR-motif or supermotif. Specifically, 15-mer sequences are selected comprising a DR-supermotif, comprising a 9-mer core, and three-residue N- and C-terminal flanking regions (15 amino acids total).

[0617] Protocols for predicting peptide binding to DR molecules have been developed (Southwood et al., J. Immunol. 160:3363-3373, 1998). These protocols, specific for individual DR molecules, allow the scoring, and ranking, of 9-mer core regions. Each protocol not only scores peptide sequences for the presence of DR-supermotif primary anchors (i.e., at position 1 and position 6) within a 9-mer core, but additionally evaluates sequences for the presence of secondary anchors. Using allele-specific selection tables (see, e.g., Southwood et al., ibid.), it has been found that these protocols efficiently select peptide sequences with a high probability of binding a particular DR molecule. Additionally, it has been found that performing these protocols in tandem, specifically those for DR1, DR4w4, and DR7, can efficiently select DR cross-reactive peptides.

[0618] The 83P2H3-derived peptides identified above are tested for their binding capacity for various common HLA-DR molecules. All peptides are initially tested for binding to the DR molecules in the primary panel: DR1, DR4w4, and DR7. Peptides binding at least two of these three DR molecules are then tested for binding to DR2w2 β1, DR2w2 β2, DR6w19, and DR9 molecules in secondary assays. Finally, peptides binding at least two of the four secondary panel DR molecules, and thus cumulatively at least four of seven different DR molecules, are screened for binding to DR4w15, DR5w11, and DR8w2 molecules in tertiary assays. Peptides binding at least seven of the ten DR molecules comprising the primary, secondary, and tertiary screening assays are considered cross-reactive DR binders. 83P2H3-derived peptides found to bind common HLA-DR alleles are of particular interest.

[0619] Selection of DR3 Motif Peptides

[0620] Because HLA-DR3 is an allele that is prevalent in Caucasian, Black, and Hispanic populations, DR3 binding capacity is a relevant criterion in the selection of HTL epitopes. Thus, peptides shown to be candidates may also be assayed for their DR3 binding capacity. However, in view of the binding specificity of the DR3 motif, peptides binding only to DR3 can also be considered as candidates for inclusion in a vaccine formulation.

[0621] To efficiently identify peptides that bind DR3, target 83P2H3 antigens are analyzed for sequences carrying one of the two DR3-specific binding motifs reported by Geluk et al. (J. Immunol. 152:5742-5748, 1994). The corresponding peptides are then synthesized and tested for the ability to bind DR3 with an affinity of 1 μM or better, i.e., less than 1 μM. Peptides are found that meet this binding criterion and qualify as HLA class II high affinity binders.

[0622] DR3 binding epitopes identified in this manner are included in vaccine compositions with DR supermotif-bearing peptide epitopes.

[0623] Similarly to the case of HLA class I motif-bearing peptides, the class II motif-bearing peptides are analoged to improve affinity or cross-reactivity. For example, aspartic acid at position 4 of the 9-mer core sequence is an optimal residue for DR3 binding, and substitution for that residue often improves DR 3 binding.

Example 15

Immunogenicity of 83P2H3/CaTrF2E11-derived HTL Epitopes

[0624] This example determines immunogenic DR supermotif- and DR3 motif-bearing epitopes among those identified using the methodology set forth herein.

[0625] Immunogenicity of HTL epitopes are evaluated in a manner analogous to the determination of immunogenicity of CTL epitopes, by assessing the ability to stimulate HTL responses and/or by using appropriate transgenic mouse models. Immunogenicity is determined by screening for: 1.) in vitro primary induction using normal PBMC or 2.) recall responses from patients who have 83P2H3-expressing tumors.

Example 16

Calculation of Phenotypic Frequencies of HLA-supertypes in Various Ethnic Backgrounds to Determine Breadth of Population Coverage

[0626] This example illustrates the assessment of the breadth of population coverage of a vaccine composition comprised of multiple epitopes comprising multiple supermotifs and/or motifs.

[0627] In order to analyze population coverage, gene frequencies of HLA alleles are determined. Gene frequencies for each HLA allele are calculated from antigen or allele frequencies utilizing the binomial distribution formulae gf-1-(SQRT(1-af)) (see, e.g., Sidney et al., Human Immunol. 45:79-93, 1996). To obtain overall phenotypic frequencies, cumulative gene frequencies are calculated, and the cumulative antigen frequencies derived by the use of the inverse formula [af=1(1-Cgf)2].

[0628] Where frequency data is not available at the level of DNA typing, correspondence to the serologically defined antigen frequencies is assumed. To obtain total potential supertype population coverage no linkage disequilibrium is assumed, and only alleles confirmed to belong to each of the supertypes are included (minimal estimates). Estimates of total potential coverage achieved by inter-loci combinations are made by adding to the A coverage the proportion of the non-A covered population that could be expected to be covered by the B alleles considered (e.g., total=A+B*(1−A)). Confirmed members of the A3-like supertype are A3, A11, A31, A*3301, and A*6801. Although the A3-like supertype may also include A34, A66, and A*7401, these alleles were not included in overall frequency calculations. Likewise, confirmed members of the A2-like supertype family are A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*6802, and A*6901. Finally, the B7-like supertype-confirmed alleles are: B7, B*3501-03, B51, B*5301, B*5401, B*5501-2, B*5601, B*6701, and B*7801 (potentially also B*1401, B*3504-06, B*4201, and B*5602).

[0629] Population coverage achieved by combining the A2-, A3- and B7-supertypes is approximately 86% in five major ethnic groups. Coverage may be extended by including peptides bearing the A1 and A24 motifs. On average, A1 is present in 12% and A24 in 29% of the population across five different major ethnic groups (Caucasian, North American Black, Chinese, Japanese, and Hispanic). Together, these alleles are represented with an average frequency of 39% in these same ethnic populations. The total coverage across the major ethnicities when A1 and A24 are combined with the coverage of the A2-, A3- and B7-supertype alleles is >95%. An analogous approach can be used to estimate population coverage achieved with combinations of class II motif-bearing epitopes.

[0630] Immunogenicity studies in humans (e.g., Bertoni et al., J. Clin. Invest. 100:503, 1997; Doolan et al., Immunity 7:97, 1997; and Threlkeld et al., J. Immunol. 159:1648, 1997) have shown that highly cross-reactive binding peptides are almost always recognized as epitopes. The use of highly cross-reactive binding peptides is an important selection criterion in identifying candidate epitopes for inclusion in a vaccine that is immunogenic in a diverse population.

[0631] With a sufficient number of epitopes (as disclosed herein and from the art), an average population coverage is predicted to be greater than 95% in each of five major ethnic populations. The game theory Monte Carlo simulation analysis, which is known in the art (see e.g., Osborne, M. J. and Rubinstein, A. “A course in game theory” MIT Press, 1994), can be used to estimate what percentage of the individuals in a population comprised of the Caucasian, North American Black, Japanese, Chinese, and Hispanic ethnic groups would recognize the vaccine epitopes described herein. A preferred percentage is 90%. A more preferred percentage is 95%.

Example 17

CTL Recognition of Endogenously Processed Antigens After Priming

[0632] This example determines that CTL induced by native or analoged peptide epitopes identified and selected as described herein recognize endogenously synthesized, i.e., native antigens.

[0633] Effector cells isolated from transgenic mice that are immunized with peptide epitopes, for example HLA-A2 supermotif-bearing epitopes, are re-stimulated in vitro using peptide-coated stimulator cells. Six days later, effector cells are assayed for cytotoxicity and the cell lines that contain peptide-specific cytotoxic activity are further re-stimulated. An additional six days later, these cell lines are tested for cytotoxic activity on 51Cr labeled Jurkat-A2.1/Kb target cells in the absence or presence of peptide, and also tested on 51Cr labeled target cells bearing the endogenously synthesized antigen, i.e. cells that are stably transfected with 83P2H3 expression vectors.

[0634] The results demonstrate that CTL lines obtained from animals primed with peptide epitope recognize endogenously synthesized 83P2H3 antigen. The choice of transgenic mouse model to be used for such an analysis depends upon the epitope(s) that are being evaluated. In addition to HLA-A*0201/Kb transgenic mice, several other transgenic mouse models including mice with human A11, which may also be used to evaluate A3 epitopes, and B7 alleles have been characterized and others (e.g., transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed, which may be used to evaluate HTL epitopes.

Example 18

Activity of CTL-HTL Conjugated Epitopes In Transgenic Mice

[0635] This example illustrates the induction of CTLs and HTLs in transgenic mice, by use of a 83P2H3-derived CTL and HTL peptide vaccine compositions. The vaccine composition used herein comprise peptides to be administered to a patient with a 83P2H3-expressing tumor. The peptide composition can comprise multiple CTL and/or HTL epitopes. The epitopes are identified using methodology as described herein. This example also illustrates that enhanced immunogenicity can be achieved by inclusion of one or more HTL epitopes in a CTL vaccine composition; such a peptide composition can comprise an HTL epitope conjugated to a CTL epitope. The CTL epitope can be one that binds to multiple HLA family members at an affinity of 500 nM or less, or analogs of that epitope. The peptides may be lipidated, if desired.

[0636] Immunization procedures: Immunization of transgenic mice is performed as described (Alexander et al., J. Immunol. 159:4753-4761, 1997). For example, A2/Kb mice, which are transgenic for the human HLA A2.1 allele and are used to assess the immunogenicity of HLA-A*0201 motif- or HLA-A2 supermotif-bearing epitopes, and are primed subcutaneously (base of the tail) with a 0.1 ml of peptide in Incomplete Freund's Adjuvant, or if the peptide composition is a lipidated CTL/HTL conjugate, in DMSO/saline, or if the peptide composition is a polypeptide, in PBS or Incomplete Freund's Adjuvant. Seven days after priming, splenocytes obtained from these animals are restimulated with syngeneic irradiated LPS-activated lymphoblasts coated with peptide.

[0637] Cell lines: Target cells for peptide-specific cytotoxicity assays are Jurkat cells transfected with the HLA-A2.1/Kb chimeric gene (e.g., Vitiello et al., J. Exp. Med. 173:1007, 1991).

[0638] In vitro CTL activation: One week after priming, spleen cells (30×106 cells/flask) are co-cultured at 37° C. with syngeneic, irradiated (3000 rads), peptide coated lymphoblasts (10×106 cells/flask) in 10 ml of culture medium/T25 flask. After six days, effector cells are harvested and assayed for cytotoxic activity.

[0639] Assay for cytotoxic activity: Target cells (1.0 to 1.5×106) are incubated at 37° C. in the presence of 200 μl of 51Cr. After 60 minutes, cells are washed three times and resuspended in R10 medium. Peptide is added where required at a concentration of 1 μg/ml. For the assay, 104 51Cr-labeled target cells are added to different concentrations of effector cells (final volume of 200 μl) in U-bottom 96-well plates. After a six hour incubation period at 37° C., a 0.1 ml aliquot of supernatant is removed from each well and radioactivity is determined in a Micromedic automatic gamma counter. The percent specific lysis is determined by the formula: percent specific release=100×(experimental release-spontaneous release)/(maximum release-spontaneous release). To facilitate comparison between separate CTL assays run under the same conditions, % 51Cr release data is expressed as lytic units/106 cells. One lytic unit is arbitrarily defined as the number of effector cells required to achieve 30% lysis of 10,000 target cells in a six hour 51Cr release assay. To obtain specific lytic units/106, the lytic units/106 obtained in the absence of peptide is subtracted from the lytic units/106 obtained in the presence of peptide. For example, if 30% 51Cr release is obtained at the effector (E): target (T) ratio of 50:1 (i.e., 5×105 effector cells for 10,000 targets) in the absence of peptide and 5:1 (i.e., 5×104 effector cells for 10,000 targets) in the presence of peptide, the specific lytic units would be: [({fraction (1/50,000)})-({fraction (1/500,000)})]×106=18 LU.

[0640] The results are analyzed to assess the magnitude of the CTL responses of animals injected with the immunogenic CTL/HTL conjugate vaccine preparation and are compared to the magnitude of the CTL response achieved using, for example, CTL epitopes as outlined above in the Example entitled “Confirmation of Immunogenicity”. Analyses similar to this may be performed to evaluate the immunogenicity of peptide conjugates containing multiple CTL epitopes and/or multiple HTL epitopes. In accordance with these procedures, it is found that a CTL response is induced, and concomitantly that an HTL response is induced upon administration of such compositions.

Example 19

Selection of CTL and HTL Epitopes for Inclusion in an 83P2H3/CaTrF2E11-specific Vaccine

[0641] This example illustrates a procedure for selecting peptide epitopes for vaccine compositions of the invention. The peptides in the composition can be in the form of a nucleic acid sequence, either single or one or more sequences (i.e., minigene) that encodes peptide(s), or can be single and/or polyepitopic peptides.

[0642] The following principles are utilized when selecting a plurality of epitopes for inclusion in a vaccine composition. Each of the following principles is balanced in order to make the selection.

[0643] Epitopes are selected which, upon administration, mimic immune responses that are correlated with 83P2H3 clearance. The number of epitopes used depends on observations of patients who spontaneously clear 83P2H3. For example, if it has been observed that patients who spontaneously clear 83P2H3 generate an immune response to at least three (3) from 83P2H3 antigen, then three or four (3-4) epitopes should be included for HLA class I. A similar rationale is used to determine HLA class II epitopes.

[0644] Epitopes are often selected that have a binding affinity of an IC50 of 500 nM or less for an HLA class I molecule, or for class II, an IC50 of 1000 nM or less; or HLA Class I peptides with high binding scores form the BIMAS web site, at URL bimas.dcrt.nih.gov/.

[0645] In order to achieve broad coverage of the vaccine through out a diverse population, sufficient supermotif bearing peptides, or a sufficient array of allele-specific motif bearing peptides, are selected to give broad population coverage. In one embodiment, epitopes are selected to provide at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess breadth, or redundancy, of population coverage.

[0646] When creating polyepitopic compositions, or a minigene that encodes same, it is typically desirable to generate the smallest peptide possible that encompasses the epitopes of interest. The principles employed are similar, if not the same, as those employed when selecting a peptide comprising nested epitopes. For example, a protein sequence for the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. Epitopes may be nested or overlapping (i.e., frame shifted relative to one another). For example, with overlapping epitopes, two 9-mer epitopes and one 10-mer epitope can be present in a 10 amino acid peptide. Each epitope can be exposed and bound by an HLA molecule upon administration of such a peptide. A multi-epitopic, peptide can be generated synthetically, recombinantly, or via cleavage from the native source. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes. This embodiment provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup that is presently unknown. Furthermore, this embodiment (absent the creating of any analogs) directs the immune response to multiple peptide sequences that are actually present in 83P2H3, thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing nucleic acid vaccine compositions. Related to this embodiment, computer programs can be derived in accordance with principles in the art, which identify in a target sequence, the greatest number of epitopes per sequence length.

[0647] A vaccine composition comprised of selected peptides, when administered, is safe, efficacious, and elicits an immune response similar in magnitude to an immune response that controls or clears cells that bear or overexpress 83P2H3.

Example 20

Construction of “Minigene” Multi-Epitope DNA Plasmids

[0648] This example discusses the construction of a minigene expression plasmid. Minigene plasmids may, of course, contain various configurations of B cell, CTL and/or HTL epitopes or epitope analogs as described herein.

[0649] A minigene expression plasmid typically includes multiple CTL and HTL peptide epitopes. In the present example, HLA-A2,-A3,-B7 supermotif-bearing peptide epitopes and HLA-A1 and -A24 motif-bearing peptide epitopes are used in conjunction with DR supermotif-bearing epitopes and/or DR3 epitopes. HLA class I supermotif or motif-bearing peptide epitopes derived 83P2H3, are selected such that multiple supermotifs/motifs are represented to ensure broad population coverage. Similarly, HLA class II epitopes are selected from 83P2H3 to provide broad population coverage, i.e. both HLA DR-1-4-7 supermotif-bearing epitopes and HLA DR-3 motif-bearing epitopes are selected for inclusion in the minigene construct. The selected CTL and HTL epitopes are then incorporated into a minigene for expression in an expression vector.

[0650] Such a construct may additionally include sequences that direct the HTL epitopes to the endoplasmic reticulum. For example, the Ii protein may be fused to one or more HTL epitopes as described in the art, wherein the CLIP sequence of the Ii protein is removed and replaced with an HLA class II epitope sequence so that HLA class II epitope is directed to the endoplasmic reticulum, where the epitope binds to an HLA class II molecules.

[0651] This example illustrates the methods to be used for construction of a minigene-bearing expression plasmid. Other expression vectors that may be used for minigene compositions are available and known to those of skill in the art.

[0652] The minigene DNA plasmid of this example contains a consensus Kozak sequence and a consensus murine kappa Ig-light chain signal sequence followed by CTL and/or HTL epitopes selected in accordance with principles disclosed herein. The sequence encodes an open reading frame fused to the Myc and His antibody epitope tag coded for by the pCDNA 3.1 Myc-His vector.

[0653] Overlapping oligonucleotides that can, for example, average about 70 nucleotides in length with 15 nucleotide overlaps, are synthesized and HPLC-purified. The oligonucleotides encode the selected peptide epitopes as well as appropriate linker nucleotides, Kozak sequence, and signal sequence. The final multiepitope minigene is assembled by extending the overlapping oligonucleotides in three sets of reactions using PCR. A Perkin/Elmer 9600 PCR machine is used and a total of 30 cycles are performed using the following conditions: 95° C. for 15 sec, annealing temperature (5° below the lowest calculated Tm of each primer pair) for 30 sec, and 72° C. for 1 min.

[0654] For example, a minigene is prepared as follows. For a first PCR reaction, 5 μg of each of two oligonucleotides are annealed and extended: In an example using eight oligonucleotides, i.e., four pairs of primers, oligonucleotides 1+2, 3+4, 5+6, and 7+8 are combined in 100 μl reactions containing Pfu polymerase buffer (1×=10 mM KCL, 10 mM (NH4)2SO4, 20 mM Tris-chloride, pH 8.75, 2 mM MgSO4, 0.1% Triton X-100, 100 μg/ml BSA), 0.25 mM each dNTP, and 2.5 U of Pfu polymerase. The full-length dimer products are gel-purified, and two reactions containing the product of 1+2 and 3+4, and the product of 5+6 and 7+8 are mixed, annealed, and extended for 10 cycles. Half of the two reactions are then mixed, and 5 cycles of annealing and extension carried out before flanking primers are added to amplify the full length product. The full-length product is gel-purified and cloned into pCR-blunt (Invitrogen) and individual clones are screened by sequencing.

Example 21

The Plasmid Construct and the Degree to Which It Induces Immunogenicity

[0655] The degree to which a plasmid construct, for example a plasmid constructed in accordance with the previous Example, is able to induce immunogenicity is evaluated in vitro by testing for epitope presentation by APC following transduction or transfection of the APC with an epitope-expressing nucleic acid construct. Such a study determines “antigenicity” and allows the use of human APC. The assay determines the ability of the epitope to be presented by the APC in a context that is recognized by a T cell by quantifying the density of epitope-HLA class I complexes on the cell surface. Quantitation can be performed by directly measuring the amount of peptide eluted from the APC (see, e.g. Sijts et al., J. Immunol. 156:683-692, 1996; Demotz et al., Nature 342:682-684, 1989); or the number of peptide-HLA class I complexes can be estimated by measuring the amount of lysis or lymphokine release induced by diseased or transfected target cells, and then determining the concentration of peptide necessary to obtain equivalent levels of lysis or lymphokine release (see, e.g., Kageyama et al., J. Immunol. 154:567-576, 1995).

[0656] Alternatively, immunogenicity is evaluated through in vivo injections into mice and subsequent in vitro assessment of CTL and HTL activity, which are analyzed using cytotoxicity and proliferation assays, respectively, as detailed e.g., in Alexander et al., Immunity 1:751-761, 1994.

[0657] For example, to assess the capacity of a DNA minigene construct containing at least one HLA-A2 supermotif peptide to induce CTLs in vivo, HLA-A2.1/Kb transgenic mice, for example, are immunized intramuscularly with 100 μg of naked cDNA. As a means of comparing the level of CTLs induced by cDNA immunization, a control group of animals is also immunized with an actual peptide composition that comprises multiple epitopes synthesized as a single polypeptide as they would be encoded by the minigene.

[0658] Splenocytes from immunized animals are stimulated twice with each of the respective compositions (peptide epitopes encoded in the minigene or the polyepitopic peptide), then assayed for peptide-specific cytotoxic activity in a 51Cr release assay. The results indicate the magnitude of the CTL response directed against the A2-restricted epitope, thus indicating the in vivo immunogenicity of the minigene vaccine and polyepitopic vaccine.

[0659] It is, therefore, found that the minigene elicits immune responses directed toward the HLA-A2 supermotif peptide epitopes as does the polyepitopic peptide vaccine. A similar analysis is also performed using other HLA-A3 and HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 and HLA-B7 motif or supermotif epitopes, whereby it is also found that the minigene elicits appropriate immune responses directed toward the provided epitopes.

[0660] To assess the capacity of a class II epitope-encoding minigene to induce HTLs in vivo, DR transgenic mice, or for those epitopes that cross react with the appropriate mouse MHC molecule, I-Ab-restricted mice, for example, are immunized intramuscularly with 100 μg of plasmid DNA. As a means of comparing the level of HTLs induced by DNA immunization, a group of control animals is also immunized with an actual peptide composition emulsified in complete Freund's adjuvant. CD4+ T cells, i.e. HTLs, are purified from splenocytes of immunized animals and stimulated with each of the respective compositions (peptides encoded in the minigene). The HTL response is measured using a 3H-thymidine incorporation proliferation assay, (see, e.g., Alexander et al. Immunity 1:751-761, 1994). The results indicate the magnitude of the HTL response, thus demonstrating the in vivo immunogenicity of the minigene.

[0661] DNA minigenes, constructed as described in the previous Example, can also be evaluated as a vaccine in combination with a boosting agent using a prime boost protocol. The boosting agent can consist of recombinant protein (e.g., Barnett et al., Aids Res. and Human Retroviruses 14, Supplement 3:S299-S309, 1998) or recombinant vaccinia, for example, expressing a minigene or DNA encoding the complete protein of interest (see, e.g., Hanke et al., Vaccine 16:439-445, 1998; Sedegah et al., Proc. Natl. Acad. Sci USA 95:7648-53, 1998; Hanke and McMichael, Immunol. Letters 66:177-181, 1999; and Robinson et al., Nature Med. 5:526-34, 1999).

[0662] For example, the efficacy of the DNA minigene used in a prime boost protocol is initially evaluated in transgenic mice. In this example, A2.1/Kb transgenic mice are immunized IM with 100 μg of a DNA minigene encoding the immunogenic peptides including at least one HLA-A2 supermotif-bearing peptide. After an incubation period (ranging from 3-9 weeks), the mice are boosted IP with 107 pfu/mouse of a recombinant vaccinia virus expressing the same sequence encoded by the DNA minigene. Control mice are immunized with 100 μg of DNA or recombinant vaccinia without the minigene sequence, or with DNA encoding the minigene, but without the vaccinia boost. After an additional incubation period of two weeks, splenocytes from the mice are immediately assayed for peptide-specific activity in an ELISPOT assay. Additionally, splenocytes are stimulated in vitro with the A2-restricted peptide epitopes encoded in the minigene and recombinant vaccinia, then assayed for peptide-specific activity in an alpha, beta and/or gamma IFN ELISA.

[0663] It is found that the minigene utilized in a prime-boost protocol elicits greater immune responses toward the HLA-A2 supermotif peptides than with DNA alone. Such an analysis can also be performed using HLA-A11 or HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 or HLA-B7 motif or supermotif epitopes. The use of prime boost protocols in humans is described below in the Example entitled “Induction of CTL Responses Using a Prime Boost Protocol.”

Example 22

Peptide Composition for Prophylactic Uses

[0664] Vaccine compositions of the present invention can be used to prevent 83P2H3 expression in persons who are at risk for tumors that bear this antigen. For example, a polyepitopic peptide epitope composition (or a nucleic acid comprising the same) containing multiple CTL and HTL epitopes such as those selected in the above Examples, which are also selected to target greater than 80% of the population, is administered to individuals at risk for a 83P2H3-associated tumor.

[0665] For example, a peptide-based composition is provided as a single polypeptide that encompasses multiple epitopes. The vaccine is typically administered in a physiological solution that comprises an adjuvant, such as Incomplete Freund's Adjuvant. The dose of peptide for the initial immunization is from about 1 to about 50,000 μg, generally 100-5,000 μg, for a 70 kg patient. The initial administration of vaccine is followed by booster dosages at 4 weeks followed by evaluation of the magnitude of the immune response in the patient, by techniques that determine the presence of epitope-specific CTL populations in a PBMC sample. Additional booster doses are administered as required. The composition is found to be both safe and efficacious as a prophylaxis against 83P2H3-associated disease.

[0666] Alternatively, a composition typically comprising transfecting agents is used for the administration of a nucleic acid-based vaccine in accordance with methodologies known in the art and disclosed herein.

Example 23

Polyepitopic Vaccine Compositions Derived from Native 83P2H3/CaTrF2E11 Sequences

[0667] A native 83P2H3 polyprotein sequence is screened, preferably using computer algorithms defined for each class I and/or class II supermotif or motif, to identify “relatively short” regions of the polyprotein that comprise multiple epitopes. The “relatively short” regions are preferably less in length than an entire native antigen. This relatively short sequence that contains multiple distinct or overlapping, “nested” epitopes is selected; it can be used to generate a minigene construct. The construct is engineered to express the peptide, which corresponds to the native protein sequence. The “relatively short” peptide is generally less than 250 amino acids in length, often less than 100 amino acids in length, preferably less than 75 amino acids in length, and more preferably less than 50 amino acids in length. The protein sequence of the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. As noted herein, epitope motifs may be nested or overlapping (i.e., frame shifted relative to one another). For example, with overlapping epitopes, two 9-mer epitopes and one 10-mer epitope can be present in a 10 amino acid peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes.

[0668] The vaccine composition will include, for example, multiple CTL epitopes from 83P2H3 antigen and at least one HTL epitope. This polyepitopic native sequence is administered either as a peptide or as a nucleic acid sequence which encodes the peptide. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide.

[0669] The embodiment of this example provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup that is presently unknown. Furthermore, this embodiment (excluding an analoged embodiment) directs the immune response to multiple peptide sequences that are actually present in native 83P2H3, thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing peptide or nucleic acid vaccine compositions.

[0670] Related to this embodiment, computer programs are available in the art which can be used to identify in a target sequence, the greatest number of epitopes per sequence length.

Example 24

Polyepitopic Vaccine Compositions From Multiple Antigens

[0671] The 83P2H3 peptide epitopes of the present invention are used in conjunction with epitopes from other target tumor-associated antigens, to create a vaccine composition that is useful for the prevention or treatment of cancer that expresses 83P2H3 and such other antigens. For example, a vaccine composition can be provided as a single polypeptide that incorporates multiple epitopes from 83P2H3 as well as tumor-associated antigens that are often expressed with a target cancer associated with 83P2H3 expression, or can be administered as a composition comprising a cocktail of one or more discrete epitopes. Alternatively, the vaccine can be administered as a minigene construct or as dendritic cells which have been loaded with the peptide epitopes in vitro.

Example 25

Use of Peptides to Evaluate an Immune Response

[0672] Peptides of the invention may be used to analyze an immune response for the presence of specific antibodies, CTL or HTL directed to 83P2H3. Such an analysis can be performed in a manner described by Ogg et al., Science 279:2103-2106, 1998. In this Example, peptides in accordance with the invention are used as a reagent for diagnostic or prognostic purposes, not as an immunogen.

[0673] In this example highly sensitive human leukocyte antigen tetrameric complexes (“tetramers”) are used for a cross-sectional analysis of, for example, 83P2H3 HLA-A*0201-specific CTL frequencies from HLA A*0201-positive individuals at different stages of disease or following immunization comprising an 83P2H3 peptide containing an A*0201 motif. Tetrameric complexes are synthesized as described (Musey et al., N. Engl. J. Med. 337:1267, 1997). Briefly, purified HLA heavy chain (A*0201 in this example) and β2-microglobulin are synthesized by means of a prokaryotic expression system. The heavy chain is modified by deletion of the transmembrane-cytosolic tail and COOH-terminal addition of a sequence containing a BirA enzymatic biotinylation site. The heavy chain, β2-microglobulin, and peptide are refolded by dilution. The 45-kD refolded product is isolated by fast protein liquid chromatography and then biotinylated by BirA in the presence of biotin (Sigma, St. Louis, Mo.), adenosine 5′ triphosphate and magnesium. Streptavidin-phycoerythrin conjugate is added in a 1:4 molar ratio, and the tetrameric product is concentrated to 1 mg/ml. The resulting product is referred to as tetramer-phycoerythrin.

[0674] For the analysis of patient blood samples, approximately one million PBMCs are centrifuged at 300 g for 5 minutes and resuspended in 50 μl of cold phosphate-buffered saline. Tri-color analysis is performed with the tetramer-phycoerythrin, along with anti-CD8-Tricolor, and anti-CD38. The PBMCs are incubated with tetramer and antibodies on ice for 30 to 60 min and then washed twice before formaldehyde fixation. Gates are applied to contain >99.98% of control samples. Controls for the tetramers include both A*0201-negative individuals and A*0201-positive non-diseased donors. The percentage of cells stained with the tetramer is then determined by flow cytometry. The results indicate the number of cells in the PBMC sample that contain epitope-restricted CTLs, thereby readily indicating the extent of immune response to the 83P2H3 epitope, and thus the status of exposure to 83P2H3, or exposure to a vaccine that elicits a protective or therapeutic response.

Example 26

Use of Peptide Epitopes to Evaluate Recall Responses

[0675] The peptide epitopes of the invention are used as reagents to evaluate T cell responses, such as acute or recall responses, in patients. Such an analysis may be performed on patients who have recovered from 83P2H3-associated disease or who have been vaccinated with an 83P2H3 vaccine.

[0676] For example, the class I restricted CTL response of persons who have been vaccinated may be analyzed. The vaccine may be any 83P2H3 vaccine. PBMC are collected from vaccinated individuals and HLA typed. Appropriate peptide epitopes of the invention that, optimally, bear supermotifs to provide cross-reactivity with multiple HLA supertype family members, are then used for analysis of samples derived from individuals who bear that HLA type.

[0677] PBMC from vaccinated individuals are separated on Ficoll-Histopaque density gradients (Sigma Chemical Co., St. Louis, Mo.), washed three times in HBSS (GIBCO Laboratories), resuspended in RPMI-1640 (GIBCO Laboratories) supplemented with L-glutamine (2 mM), penicillin (50 U/ml), streptomycin (50 μg/ml), and Hepes (10 mM) containing 10% heat-inactivated human AB serum (complete RPMI) and plated using microculture formats. A synthetic peptide comprising an epitope of the invention is added at 10 μg/ml to each well and HBV core 128-140 epitope is added at 1 μg/ml to each well as a source of T cell help during the first week of stimulation.

[0678] In the microculture format, 4×105 PBMC are stimulated with peptide in 8 replicate cultures in 96-well round bottom plate in 100 μl/well of complete RPMI. On days 3 and 10, 100 UL of complete RPMI and 20 U/ml final concentration of rIL-2 are added to each well. On day 7 the cultures are transferred into a 96-well flat-bottom plate and restimulated with peptide, rIL-2 and 105 irradiated (3,000 rad) autologous feeder cells. The cultures are tested for cytotoxic activity on day 14. A positive CTL response requires two or more of the eight replicate cultures to display greater than 10% specific 51Cr release, based on comparison with non-diseased control subjects as previously described (Rehermann, et al., Nature Med. 2:1104,1108, 1996; Rehermann et al., J. Clin. Invest. 97:1655-1665, 1996; and Rehermann et al. J. Clin. Invest. 98:1432-1440, 1996).

[0679] Target cell lines are autologous and allogeneic EBV-transformed B-LCL that are either purchased from the American Society for Histoconipatibility and Immunogenetics (ASHI, Boston, Mass.) or established from the pool of patients as described (Guilhot, et al. J. Virol. 66:2670-2678, 1992).

[0680] Cytotoxicity assays are performed in the following manner. Target cells consist of either allogeneic HLA-matched or autologous EBV-transformed B lymphoblastoid cell line that are incubated overnight with the synthetic peptide epitope of the invention at 10 μM, and labeled with 100 μCi of 51Cr (Amersham Corp., Arlington Heights, Ill.) for 1 hour after which they are washed four times with HBSS.

[0681] Cytolytic activity is determined in a standard 4-h, split well 51Cr release assay using U-bottomed 96 well plates containing 3,000 targets/well. Stimulated PBMC are tested at effector/target (E/T) ratios of 20-50:1 on day 14. Percent cytotoxicity is determined from the formula: 100×[(experimental release-spontaneous release)/maximum release-spontaneous release)]. Maximum release is determined by lysis of targets by detergent (2% Triton X-100; Sigma Chemical Co., St. Louis, Mo.). Spontaneous release is <25% of maximum release for all experiments.

[0682] The results of such an analysis indicate the extent to which HLA-restricted CTL populations have been stimulated by previous exposure to 83P2H3 or an 83P2H3 vaccine.

[0683] Similarly, Class II restricted HTL responses may also be analyzed. Purified PBMC are cultured in a 96-well flat bottom plate at a density of 1.5×105 cells/well and are stimulated with 10 μg/ml synthetic peptide of the invention, whole 83P2H3 antigen, or PHA. Cells are routinely plated in replicates of 4-6 wells for each condition. After seven days of culture, the medium is removed and replaced with fresh medium containing 10 U/ml IL-2. Two days later, 1 μCi 3H-thymidine is added to each well and incubation is continued for an additional 18 hours. Cellular DNA is then harvested on glass fiber mats and analyzed for 3H-thymidine incorporation. Antigen-specific T cell proliferation is calculated as the ratio of 3H-thymidine incorporation in the presence of antigen divided by the 3H-thymidine incorporation in the absence of antigen.

Example 27

Induction Of Specific CTL Response In Humans

[0684] A human clinical trial for an immunogenic composition comprising CTL and HTL epitopes of the invention is set up as an IND Phase I, dose escalation study and carried out as a randomized, double-blind, placebo-controlled trial. Such a trial is designed, for example, as follows:

[0685] A total of about 27 individuals are enrolled and divided into 3 groups:

[0686] Group I: 3 subjects are injected with placebo and 6 subjects are injected with 5 μg of peptide composition;

[0687] Group II: 3 subjects are injected with placebo and 6 subjects are injected with 50 μg peptide composition;

[0688] Group III: 3 subjects are injected with placebo and 6 subjects are injected with 500 μg of peptide composition.

[0689] After 4 weeks following the first injection, all subjects receive a booster inoculation at the same dosage.

[0690] The endpoints measured in this study relate to the safety and tolerability of the peptide composition as well as its immunogenicity. Cellular immune responses to the peptide composition are an index of the intrinsic activity of this the peptide composition, and can therefore be viewed as a measure of biological efficacy. The following summarize the clinical and laboratory data that relate to safety and efficacy endpoints.

[0691] Safety: The incidence of adverse events is monitored in the placebo and drug treatment group and assessed in terms of degree and reversibility.

[0692] Evaluation of Vaccine Efficacy: For evaluation of vaccine efficacy, subjects are bled before and after injection. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.

[0693] The vaccine is found to be both safe and efficacious.

Example 28

Phase II Trials In Patients Expressing 83P2H3

[0694] Phase II trials are performed to study the effect of administering the CTL-HTL peptide compositions to patients having cancer that expresses 83P2H3. The main objectives of the trial are to determine an effective dose and regimen for inducing CTLs in cancer patients that express 83P2H3, to establish the safety of inducing a CTL and HTL response in these patients, and to see to what extent activation of CTLs improves the clinical picture of these patients, as manifested, e.g., by the reduction and/or shrinking of lesions. Such a study is designed, for example, as follows:

[0695] The studies are performed in multiple centers. The trial design is an open-label, uncontrolled, dose escalation protocol wherein the peptide composition is administered as a single dose followed six weeks later by a single booster shot of the same dose. The dosages are 50, 500 and 5,000 micrograms per injection. Drug-associated adverse effects (severity and reversibility) are recorded.

[0696] There are three patient groupings. The first group is injected with 50 micrograms of the peptide composition and the second and third groups with 500 and 5,000 micrograms of peptide composition, respectively. The patients within each group range in age from 21-65 and represent diverse ethnic backgrounds. All of them have a tumor that expresses 83P2H3.

[0697] Clinical manifestations or antigen-specific T-cell responses are monitored to assess the effects of administering the peptide compositions. The vaccine composition is found to be both safe and efficacious in the treatment of 83P2H3-associated disease.

Example 29

Induction of CTL Responses Using a Prime Boost Protocol

[0698] A prime boost protocol similar in its underlying principle to that used to evaluate the efficacy of a DNA vaccine in transgenic mice, such as described above in the Example entitled “The Plasmid Construct and the Degree to Which It Induces Immunogenicity,” can also be used for the administration of the vaccine to humans. Such a vaccine regimen can include an initial administration of, for example, naked DNA followed by a boost using recombinant virus encoding the vaccine, or recombinant protein/polypeptide or a peptide mixture administered in an adjuvant.

[0699] For example, the initial immunization may be performed using an expression vector, such as that constructed in the Example entitled “Construction of ‘Minigene’ Multi-Epitope DNA Plasmids” in the form of naked nucleic acid administered IM (or SC or ID) in the amounts of 0.5-5 mg at multiple sites. The nucleic acid (0.1 to 1000 μg) can also be administered using a gene gun. Following an incubation period of 3-4 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5-107 to 5×109 pfu. An alternative recombinant virus, such as an MVA, canarypox, adenovirus, or adeno-associated virus, can also be used for the booster, or the polyepitopic protein or a mixture of the peptides can be administered. For evaluation of vaccine efficacy, patient blood samples are obtained before immunization as well as at intervals following administration of the initial vaccine and booster doses of the vaccine. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.

[0700] Analysis of the results indicates that a magnitude of response sufficient to achieve a therapeutic or protective immunity against 83P2H3 is generated.

Example 30

Administration of Vaccine Compositions Using Dendritic Cells (DC)

[0701] Vaccines comprising peptide epitopes of the invention can be administered using APCs, or “professional” APCs such as DC. In this example, peptide-pulsed DC are administered to a patient to stimulate a CTL response in vivo. In this method, dendritic cells are isolated, expanded, and pulsed with a vaccine comprising peptide CTL and HTL epitopes of the invention. The dendritic cells are infused back into the patient to elicit CTL and HTL responses in vivo. The induced CTL and HTL then destroy or facilitate destruction, respectively, of the target cells that bear the 83P2H3 protein from which the epitopes in the vaccine are derived.

[0702] For example, a cocktail of epitope-comprising peptides is administered ex vivo to PBMC, or isolated DC therefrom. A pharmaceutical to facilitate harvesting of DC can be used, such as Progenipoietin™ (Monsanto, St. Louis, Mo.) or GM-CSF/IL-4. After pulsing the DC with peptides, and prior to reinfusion into patients, the DC are washed to remove unbound peptides.

[0703] As appreciated clinically, and readily determined by one of skill based on clinical outcomes, the number of DC reinfused into the patient can vary (see, e.g., Nature Med. 4:328, 1998; Nature Med. 2:52, 1996 and Prostate 32:272, 1997). Although 2-50×106 DC per patient are typically administered, larger number of DC, such as 107 or 108 can also be provided. Such cell populations typically contain between 50-90% DC.

[0704] In some embodiments, peptide-loaded PBMC are injected into patients without purification of the DC. For example, PBMC generated after treatment with an agent such as Progenipoietin™ are injected into patients without purification of the DC. The total number of PBMC that are administered often ranges from 108 to 1010. Generally, the cell doses injected into patients is based on the percentage of DC in the blood of each patient, as determined, for example, by immunofluorescence analysis with specific anti-DC antibodies. Thus, for example, if Progenipoietin™ mobilizes 2% DC in the peripheral blood of a given patient, and that patient is to receive 5×106 DC, then the patient will be injected with a total of 2.5×108 peptide-loaded PBMC. The percent DC mobilized by an agent such as Progenipoietin™ is typically estimated to be between 2-10%, but can vary as appreciated by one of skill in the art.

[0705] Ex vivo Activation of CTL/HTL Responses

[0706] Alternatively, ex vivo CTL or HTL responses to 83P2H3 antigens can be induced by incubating, in tissue culture, the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of APC, such as DC, and immunogenic peptides. After an appropriate incubation time (typically about 7-28 days), in which the precursor cells are activated and expanded into effector cells, the cells are infused into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cells, i.e., tumor cells.

Example 31

An Alternative Method of Identifying Motif-Bearing Peptides

[0707] Another method of identifying motif-bearing peptides is to elute them from cells bearing defined MHC molecules. For example, EBV transformed B cell lines used for tissue typing have been extensively characterized to determine which HLA molecules they express. In certain cases these cells express only a single type of HLA molecule. These cells can be transfected with nucleic acids that express the antigen of interest, e.g. 83P2H3. Peptides produced by endogenous antigen processing of peptides produced as a result of transfection will then bind to HLA molecules within the cell and be transported and displayed on the cell's surface. Peptides are then eluted from the HLA molecules by exposure to mild acid conditions and their amino acid sequence determined, e.g., by mass spectral analysis (e.g., Kubo et al., J. Immunol. 152:3913, 1994). Because the majority of peptides that bind a particular HLA molecule are motif-bearing, this is an alternative modality for obtaining the motif-bearing peptides correlated with the particular HLA molecule expressed on the cell.

[0708] Alternatively, cell lines that do not express endogenous HLA molecules can be transfected with an expression construct encoding a single HLA allele. These cells can then be used as described, i.e., they can then be transfected with nucleic acids that encode 83P2H3 to isolate peptides corresponding to 83P2H3 that have been presented on the cell surface. Peptides obtained from such an analysis will bear motif(s) that correspond to binding to the single HLA allele that is expressed in the cell.

[0709] As appreciated by one in the art, one can perform a similar analysis on a cell bearing more than one HLA allele and subsequently determine peptides specific for each HLA allele expressed. Moreover, one of skill would also recognize that means other than transfection, such as loading with a protein antigen, can be used to provide a source of antigen to the cell.

Example 32

Complementary Polynucleotides

[0710] Sequences complementary to the 83P2H3-encoding sequences, or any parts thereof, are used to detect, decrease, or inhibit expression of naturally occurring 83P2H3. Although use of oligonucleotides comprising from about 15 to 30 base pairs is described, essentially the same procedure is used with smaller or with larger sequence fragments. Appropriate oligonucleotides are designed using, e.g., OLIGO 4.06 software (National Biosciences) and the coding sequence of 83P2H3. To inhibit transcription, a complementary oligonucleotide is designed from the most unique 5′ sequence and used to prevent promoter binding to the coding sequence. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding to the 83P2H3-encoding transcript.

Example 33

Purification of Naturally-occurring or Recombinant 83P2H3/CaTrF2E11 Using 83P2H3/CaTrF2E11 Specific Antibodies

[0711] Naturally occurring or recombinant 83P2H3 is substantially purified by immunoaffinity chromatography using antibodies specific for 83P2H3. An immunoaffinity column is constructed by covalently coupling anti-83P2H3 antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech). After the coupling, the resin is blocked and washed according to the manufacturer's instructions.

[0712] Media containing 83P2H3 are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of 83P2H3 (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/83P2H3 binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and GCR.P is collected.

Example 34

Identification of Molecules Which Interact with 83P2H3/CaTrF2E11

[0713] 83P2H3, or biologically active fragments thereof, are labeled with 1211 Bolton-Hunter reagent. (See, e.g., Bolton et al. (1973) Biochem. J. 133:529.) Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled 83P2H3, washed, and any wells with labeled 83P2H3 complex are assayed. Data obtained using different concentrations of 83P2H3 are used to calculate values for the number, affinity, and association of 83P2H3 with the candidate molecules.

Example 35A

In Vivo Assay for 83P2H3 Tumor Growth Promotion

[0714] The effect of the 83P2H3 protein on tumor cell growth is evaluated in vivo by gene overexpression in tumor-bearing mice. For example, SCID mice are injected subcutaneously on each flank with 1×106 of either PC3, TSUPR1, or DU145 cells containing tkNeo empty vector or 83P2H3. At least two strategies may be used: (1) Constitutive 83P2H3 expression under regulation of a promoter such as a constitutive promoter obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,211,504 published Jul. 5, 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), or from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, provided such promoters are compatible with the host cell systems, and (2) Regulated expression under control of an inducible vector system, such as ecdysone, tet, etc., provided such promoters are compatible with the host cell systems. Tumor volume is then monitored at the appearance of palpable tumors and followed over time to determine if 83P2H3-expressing cells grow at a faster rate and whether tumors produced by 83P2H3-expressing cells demonstrate characteristics of altered aggressiveness (e.g. enhanced metastasis, vascularization, reduced responsiveness to chemotherapeutic drugs).

[0715] Additionally, mice can be implanted with 1×105 of the same cells orthotopically to determine if 83P2H3 has an effect on local growth in the prostate or on the ability of the cells to metastasize, specifically to lungs, lymph nodes, and bone marrow.

[0716] The assay is also useful to determine the 83P2H3 inhibitory effect of candidate therapeutic compositions, such as for example, 83P2H3 intrabodies, 83P2H3 antisense molecules and ribozymes.

Example 35B

In Vivo Assay for CaTr F2E11 Tumor Growth Promotion

[0717] The effect of the CaTr F2E11 protein on tumor cell growth is evaluated in vivo by gene overexpression in tumor-bearing mice. For example, SCID mice are injected subcutaneously on each flank with 1×106 of cells containing tkNeo empty vector or CaTr F2E11. At least two strategies may be used: (1) Constitutive CaTr F2E11 expression under regulation constitutive promoter such as those obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,211,504 published Jul 5, 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), or from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, provided such promoters are compatible with the host cell systems, and (2) Regulated expression under control of an inducible vector system, such as ecdysone, tet, etc., provided such promoters are compatible with the host cell systems. Tumor volume is then monitored at the appearance of palpable tumors and followed over time to determine if CaTr F2E11-expressing cells grow at a faster rate and whether tumors produced by CaTr F2E11-expressing cells demonstrate characteristics of altered aggressiveness (e.g. enhanced metastasis, vascularization, reduced responsiveness to chemotherapeutic drugs).

[0718] Additionally, mice can be implanted with 1×105 of the same cells orthotopically to determine if CaTr F2E11 has an effect on local growth in the prostate or on the ability of the cells to metastasize, specifically to lungs, lymph nodes, and bone marrow.

[0719] The assay is also useful to determine the CaTr F2E11 inhibitory effect of candidate therapeutic compositions, such as for example, CaTr F2E11 intrabodies, CaTr F2E11 antisense molecules and ribozymes.

Example 36A

83
P2H3 Monoclonal Antibody-mediated Inhibition of Prostate Tumors In Vivo

[0720] The significant expression of 83P2H3, in cancer tissues, together with its restrictive expression in normal tissues along with its expected cell surface expression makes 83P2H3 an excellent target for antibody therapy. Similarly, 83P2H3 is a target for T cell-based immunotherapy. Thus, the therapeutic efficacy of anti-83P2H3 mAbs in human prostate cancer xenograft mouse models is evaluated by using androgen-independent LAPC-4 and LAPC-9 xenografts (Craft, N., et al.,. Cancer Res, 1999. 59(19): p. 5030-6) and the androgen independent recombinant cell line PC3-83P2H3 (see, e.g., Kaighn, M. E., et al., Invest Urol, 1979. 17(1): p. 16-23).

[0721] Antibody efficacy on tumor growth and metastasis formation is studied, e.g., in a mouse orthotopic prostate cancer xenograft model. The antibodies can be unconjugated, as discussed in this Example, or can be conjugated to a therapeutic modality, as appreciated in the art. Anti-83P2H3 mAbs inhibit formation of both the androgen-dependent LAPC-9 and androgen-independent PC3-83P2H3 tumor xenografts. Anti-83P2H3 mAbs also retard the growth of established orthotopic tumors and prolonged survival of tumor-bearing mice. These results indicate the utility of anti-83P2H3 mAbs in the treatment of local and advanced stages of prostate cancer. (See, e.g., (Saffran, D., et al., PNAS 10:1073-1078 or www.pnas.org/cgi/doi/10.1073/pnas.051624698)

[0722] Administration of the anti-83P2H3 mAbs led to retardation of established orthotopic tumor growth and inhibition of metastasis to distant sites, resulting in a significant prolongation in the survival of tumor-bearing mice. These studies indicate that 83P2H3 as an attractive target for immunotherapy and demonstrate the therapeutic potential of anti-83P2H3 mAbs for the treatment of local and metastatic prostate cancer. This example demonstrates that unconjugated 83P2H3 monoclonal antibodies are effective to inhibit the growth of human prostate tumor xenografts grown in SCID mice; accordingly a combination of such efficacious monoclonal antibodies is also effective.

[0723] Tumor Inhibition Using Multiple Unconjugated 83P2H3 mAbs

[0724] Materials and Methods

[0725] 83P2H3 Monoclonal Antibodies

[0726] Monoclonal antibodies are raised against 83P2H3 as described in the Example entitled “Generation of 83P2H3 Monoclonal Antibodies (mAbs).” The antibodies are characterized by ELISA, Western blot, FACS, and immunoprecipitation for their capacity to bind 83P2H3. Epitope mapping data for the anti-83P2H3 mAbs, as determined by ELISA and Western analysis, recognize epitopes on the 83P2H3 protein. Immunohistochemical analysis of prostate cancer tissues and cells with these antibodies is performed.

[0727] The monoclonal antibodies are purified from ascites or hybridoma tissue culture supernatants by Protein-G Sepharose chromatography, dialyzed against PBS, filter sterilized, and stored at −20° C. Protein determinations are performed by a Bradford assay (Bio-Rad, Hercules, Calif.). A therapeutic monoclonal antibody or a cocktail comprising a mixture of individual monoclonal antibodies is prepared and used for the treatment of mice receiving subcutaneous or orthotopic injections of LAPC-9 prostate tumor xenografts.

[0728] Prostate Cancer Xenografts and Cell Lines

[0729] The LAPC-9 xenograft, which expresses a wild-type androgen receptor and produces prostate-specific antigen (PSA), is passaged in 6- to 8-week-old male ICR-severe combined immunodeficient (SCID) mice (Taconic Farms) by s.c. trocar implant (Craft, N., et al., supra). Single-cell suspensions of LAPC-9 tumor cells are prepared as described in Craft, et al. The prostate carcinoma cell line PC3 (American Type Culture Collection) is maintained in DMEM supplemented with L-glutamine and 10% (vol/vol) FBS.

[0730] A PC3-83P2H3 cell population is generated by retroviral gene transfer as described in Hubert, R. S., et al., STEAP: a prostate-specific cell-surface antigen highly expressed in human prostate tumors. Proc Natl Acad Sci U S A, 1999. 96(25): p. 14523-8. Anti-83P2H3 staining is detected by using an FITC-conjugated goat anti-mouse antibody (Southern Biotechnology Associates) followed by analysis on a Coulter Epics-XL flow cytometer.

[0731] Xenograft Mouse Models

[0732] Subcutaneous (s.c.) tumors are generated by injection of 1×106 LAPC-9, PC3, or PC3-83P2H3 cells mixed at a 1:1 dilution with Matrigel (Collaborative Research) in the right flank of male SCID mice. To test antibody efficacy on tumor formation, i.p. antibody injections are started on the same day as tumor-cell injections. As a control, mice are injected with either purified mouse IgG (ICN) or PBS; or a purified monoclonal antibody that recognizes an irrelevant antigen not expressed in human cells. In preliminary studies, no difference is found between mouse IgG or PBS on tumor growth. Tumor sizes are determined by vernier caliper measurements, and the tumor volume is calculated as length×width×height. Mice with s.c. tumors greater than 1.5 cm in diameter are sacrificed. PSA levels are determined by using a PSA ELISA kit (Anogen, Mississauga, Ontario). Circulating levels of anti-83P2H3 mAbs are determined by a capture ELISA kit (Bethyl Laboratories, Montgomery, Tex.). (See, e.g., (Saffran, D., et al., PNAS 10: 1073-1078 or www.pnas.org/cgi/doi/10.1073/pnas.051624698).

[0733] Orthotopic injections are performed under anesthesia by using ketamine/xylazine. An incision is made through the abdominal muscles to expose the bladder and seminal vesicles, which then are delivered through the incision to expose the dorsal prostate. LAPC-9 cells (5×105) mixed with Matrigel are injected into each dorsal lobe in a 10-μl volume. To monitor tumor growth, mice are bled on a weekly basis for determination of PSA levels. Based on the PSA levels, the mice are segregated into groups for the appropriate treatments. To test the effect of anti-83P2H3 mAbs on established orthotopic tumors, i.p. antibody injections are started when PSA levels reach 2-80 ng/ml.

[0734] Anti-83P2H3 mAbs Inhibit Growth of 83P2H3-Expressing Prostate-Cancer Tumors

[0735] The effect of anti-83P2H3 mAbs on tumor formation is tested by using the LAPC-9 orthotopic model. As compared with the s.c. tumor model, the orthotopic model, which requires injection of tumor cells directly in the mouse prostate, results in a local tumor growth, development of metastasis in distal sites, deterioration of mouse health, and subsequent death (Saffran, D., et al., PNAS supra; Fu, X., et al., Int J Cancer, 1992. 52(6): p. 987-90; Kubota, T., J Cell Biochem, 1994. 56(1): p. 4-8). The features make the orthotopic model more representative of human disease progression and allowed us to follow the therapeutic effect of mAbs on clinically relevant end points.

[0736] Accordingly, LAPC-9 tumor cells are injected into the mouse prostate, and 2 days later, the mice are segregated into two groups and treated with either: a) 50-2000 μg, usually 200-500 μg, of anti-83P2H3 Ab, or b) PBS three times per week for two to five weeks. Mice are monitored weekly for circulating PSA levels as an indicator of tumor growth.

[0737] A major advantage of the orthotopic prostate-cancer model is the ability to study the development of metastases. Formation of metastasis in mice bearing established orthotopic tumors is studies by IHC analysis on lung sections using an antibody against a prostate-specific cell-surface protein STEAP expressed at high levels in LAPC-9 xenografts (Hubert, R. S., et al., Proc Natl Acad Sci U S A, 1999. 96(25): p. 14523-8).

[0738] Mice bearing established orthotopic LAPC-9 tumors are administered 1000 μg injections of either anti-83P2H3 mAb or PBS over a 4-week period. Mice in both groups are allowed to establish a high tumor burden (PSA levels greater than 300 ng/ml), to ensure a high frequency of metastasis formation in mouse lungs. Mice then are killed and their prostate and lungs are analyzed for the presence of LAPC-9 cells by anti-STEAP IHC analysis.

[0739] These studies demonstrate a broad anti-tumor efficacy of anti-83P2H3 antibodies on initiation and progression of prostate cancer in xenograft mouse models. Anti-83P2H3 antibodies inhibit tumor formation of both androgen-dependent and androgen-independent tumors as well as retarding the growth of already established tumors and prolong the survival of treated mice. Moreover, anti-83P2H3 mAbs demonstrate a dramatic inhibitory effect on the spread of local prostate tumor to distal sites, even in the presence of a large tumor burden. Thus, anti-83P2H3 mAbs are efficacious on major clinically relevant end points/PSA levels (tumor growth), prolongation of survival, and health.

Example 36B

CaTr F2E11 Monoclonal Antibody-mediated Inhibition of Prostate Tumors In Vivo

[0740] The significant expression of CaTr F2E11, in cancer tissues along with its expected cell surface expression makes CaTr F2E11 an excellent target for antibody therapy. Similarly, CaTr F2E11 is a target for T cell-based immunotherapy. Thus, the therapeutic efficacy of anti-CaTr F2E11 mabs in human prostate cancer xenograft mouse models is evaluated by using androgen-independent LAPC-4 and LAPC-9 xenografts (Craft, N., et al., Cancer Res, 1999. 59(19): p. 5030-6) and the androgen independent recombinant cell line PC3-CaTr F2E11 (see, e.g., Kaighn, M. E., et al., Invest Urol, 1979. 17(1): p. 16-23). Similarly the therapeutic effect of anti-CaTr F2E11 Ab in human bladder and lung cancer will be evaluated using xenograft animal models of bladder (UM-UC3, Scaber, etc) and lung (A427, SK-Lu, etc) cancer that lack or express CaTr F2E11.

[0741] Antibody efficacy on tumor growth and metastasis formation is studied, e.g., in a mouse orthotopic prostate cancer xenograft model. The antibodies can be unconjugated, as discussed in this Example, or can be conjugated to a therapeutic modality, as appreciated in the art. Anti-CaTr F2E11 mAbs can inhibit formation of tumors in xenografts. Anti-CaTr F2E11 can retard the growth of established orthotopic tumors and prolonged survival of tumor-bearing mice. These results indicate the utility of anti-CaTr F2E11 mAbs in the treatment of local and advanced stages of prostate cancer. (Saffran, D., et al., PNAS 10:1073-1078 or www.pnas.org/cgi/doi/10.1073/pnas.051624698)

[0742] Tumor Inhibition Using Multiple Unconjugated CaTr F2E11 mAbs

[0743] Materials and Methods

[0744] CaTr F2E11 Monoclonal Antibodies

[0745] Monoclonal antibodies are raised against CaTr F2E11 as described in the Example entitled “Generation of CaTr F2E11 Monoclonal Antibodies (mAbs).” The antibodies are characterized by ELISA, Western blot, FACS, and immunoprecipitation for their capacity to bind CaTr F2E11. Epitope mapping data for the anti-CaTr F2E11 mAbs, as determined by ELISA and Western analysis, recognize epitopes on the CaTr F2E11 protein. Immunohistochemical analysis of prostate cancer tissues and cells with these antibodies is performed.

[0746] The monoclonal antibodies are purified from ascites or hybridoma tissue culture supernatants by Protein-G Sepharose chromatography, dialyzed against PBS, filter sterilized, and stored at −20° C. Protein determinations are performed by a Bradford assay (Bio-Rad, Hercules, Calif.). A therapeutic monoclonal antibody or a cocktail comprising a mixture of individual monoclonal antibodies is prepared and used for the treatment of mice receiving subcutaneous or orthotopic injections of LAPC-9 prostate tumor xenografts.

[0747] Prostate Cancer Xenografts and Cell Lines

[0748] The LAPC-9 xenograft, which expresses a wild-type androgen receptor and produces prostate-specific antigen (PSA), is passaged in 6- to 8-week-old male ICR-severe combined immunodeficient (SCID) mice (Taconic Farms) by s.c. trocar implant (Craft, N., et al., supra). Single-cell suspensions of LAPC-9 tumor cells are prepared as described in Craft, et al. The prostate carcinoma cell line PC3 (American Type Culture Collection) is maintained in DMEM supplemented with L-glutamine and 10% (vol/vol) FBS.

[0749] A PC3-CaTr F2E11 cell population is generated by retroviral gene transfer as described in Hubert, R. S., et al., STEAP: a prostate-specific cell-surface antigen highly expressed in human prostate tumors. Proc Natl Acad Sci U S A, 1999. 96(25): p. 14523-8. Anti-CaTr F2E11 staining is detected by using an FITC-conjugated goat anti-mouse antibody (Southern Biotechnology Associates) followed by analysis on a Coulter Epics-XL flow cytometer.

[0750] Xenograft Mouse Models

[0751] Subcutaneous (s.c.) tumors are generated by injection of 1×106 LAPC-9, PC3, or PC3-CaTr F2E11 cells mixed at a 1:1 dilution with Matrigel (Collaborative Research) in the right flank of male SCID mice. To test antibody efficacy on tumor formation, i.p. antibody injections are started on the same day as tumor-cell injections. As a control, mice are injected with either purified mouse IgG (ICN) or PBS; or a purified monoclonal antibody that recognizes an irrelevant antigen not expressed in human cells. In preliminary studies, no difference is found between mouse IgG or PBS on tumor growth. Tumor sizes are determined by vernier caliper measurements, and the tumor volume is calculated as length×width×height. Mice with s.c. tumors greater than 1.5 cm in diameter are sacrificed. PSA levels are determined by using a PSA ELISA kit (Anogen, Mississauga, Ontario). Circulating levels of anti-CaTr F2E11 mAbs are determined by a capture ELISA kit (Bethyl Laboratories, Montgomery, Tex.). (See, e.g., (Saffran, D., et al., PNAS 10:1073-1078 or www.pnas.org/cgi/doi/10.1073/pnas.051624698)

[0752] Orthotopic injections are performed under anesthesia by using ketamine/xylazine. An incision is made through the abdominal muscles to expose the bladder and seminal vesicles, which then are delivered through the incision to expose the dorsal prostate. LAPC-9 cells (5×105 ) mixed with Matrigel are injected into each dorsal lobe in a 10-μl volume. To monitor tumor growth, mice are bled on a weekly basis for determination of PSA levels. Based on the PSA levels, the mice are segregated into groups for the appropriate treatments. To test the effect of anti-CaTr F2E11 mAbs on established orthotopic tumors, i.p. antibody injections are started when PSA levels reach 2-80 ng/ml.

[0753] Anti-CaTr F2E11 mAbs Inhibit Growth of CaTr F2E11-Expressing Prostate-Cancer Tumors

[0754] The effect of anti-CaTr F2E11 mAbs on tumor formation is tested by using the LAPC-9 orthotopic model. As compared with the s.c. tumor model, the orthotopic model, which requires injection of tumor cells directly in the mouse prostate, results in a local tumor growth, development of metastasis in distal sites, deterioration of mouse health, and subsequent death (Saffran, D., et al., PNAS supra; Fu, X., et al., Int J Cancer, 1992. 52(6): p. 987-90; Kubota, T., J Cell Biochem, 1994. 56(1): p. 4-8). The features make the orthotopic model more representative of human disease progression and allowed us to follow the therapeutic effect of mAbs on clinically relevant end points.

[0755] Accordingly, LAPC-9 tumor cells are injected into the mouse prostate, and 2 days later, the mice are segregated into two groups and treated with either: a) 50-2000 μg, usually 200-500 μg, of anti-CaTr F2E11 Ab, or b) PBS three times per week for two to five weeks. Mice are monitored weekly for circulating PSA levels as an indicator of tumor growth.

[0756] A major advantage of the orthotopic prostate-cancer model is the ability to study the development of metastases. Formation of metastasis in mice bearing established orthotopic tumors is studies by IHC analysis on lung sections using an antibody against a prostate-specific cell-surface protein STEAP expressed at high levels in LAPC-9 xenografts (Hubert, R. S., et al., Proc Natl Acad Sci U S A, 1999. 96(25): p. 14523-8).

[0757] Mice bearing established orthotopic LAPC-9 tumors are administered 1000 μg injections of either anti-CaTr F2E11 mAb or PBS over a 4-week period. Mice in both groups are allowed to establish a high tumor burden (PSA levels greater than 300 ng/ml), to ensure a high frequency of metastasis formation in mouse lungs. Mice then are killed and their prostate and lungs are analyzed for the presence of LAPC-9 cells by anti-STEAP IHC analysis.

[0758] These studies demonstrate a broad anti-tumor efficacy of anti-CaTr F2E1 antibodies on initiation and progression of prostate cancer in xenograft mouse models. Anti-CaTr F2E11 antibodies inhibit tumor formation of both androgen-dependent and androgen-independent tumors as well as retarding the growth of already established tumors and prolong the survival of treated mice. Moreover, anti-CaTr F2E11 mabs demonstrate a dramatic inhibitory effect on the spread of local prostate tumor to distal sites, even in the presence of a large tumor burden. Thus, anti-CaTr F2E11 mAbs are efficacious on major clinically relevant end points/PSA levels (tumor growth), prolongation of survival, and health.

Example 37A

Comparison of 83P2H3 to Known Genes

[0759] 83P2H3 hCaT is a 725 amino acid protein with a calculated MW of 83.2kDa, and PI of 7.56. 83P2H3 is predicted to be a cell surface protein that functions as an ion transporter. 83P2H3 shows 84% identity and 90% homology to a mouse calcium transporter (gi 9081801). 83P2H3 show 99% identity to the recently cloned human calcium transporter CaT1 (gp:AF304463).

[0760] As disclosed in the priority application (U.S. Ser. No. 60/226,329, filed Aug. 17, 2000), 83P2H3 PcaT (also referred to as hCaT) participates in calcium signaling as well as tumor initiation and progression, can be expressed in 293T cells, and functions as a calcium transporter. Recent studies published in a peer-reviewed journal have validated these disclosures. These studies have shown that the human CaT1 functions as a calcium transporter when expressed in Xenopus laevis and 293T human kidney cells (J. Biol Chem 2001, 276:29461). In addition, the study confirms, by in situ hybridization, that CaT1 is highly expressed in prostate cancer.

[0761] The following show the alignment of PcaT/83P2H3 with these similar human and mouse calcium transporters:

4Alignment with hCaT JBC 2001,276:19461>gp:AF304463_1 calcium transport protein CaT1 [Homo sap (725 aa)initn: 4862 init1: 4862 opt: 4862 Z-score: 5671.1 bits: 1059.9 E( ): 0Smith-Waterman score: 4862; 99.724|identity (99.724|ungapped)in 725 aa overlap (1-725:1-725) 10 20 30 40 50 60queryMGLSLPKEKGLILCLWSKFCRWFQRRESWAQSRDEQNLLQQKRIWESPLLLAAKDNDVQAgp:AF3MGLSLPKEKGLILCLWSKFCRWFQRRESWAQSRDEQDLLQQKRIWESPLLLAAKDNDVQA 10 20 30 40 50 60 70 80 90 100 110 120queryLNKLLKYEDCKVHQRGAMGETALHIAALYDNLEAAMVLMEAAPELVFEPMTSELYEGQTAgp:AF3LNKLLKYEDCKVHHRGAMGETALHIAALYDNLEAAMVLMEAAPELVFEPMTSELYEGQTA 70 80 90 100 110 120 130 140 150 160 170 180queryLHIAVVNQNMNLVRALLARRASVSARATGTAFRRSPCNLIYFGEHPLSFAACVNSEEIVRgp:AF3LHIAVVNQNMNLVRALLARRASVSARATGTAFRRSPCNLIYFGEHPLSFAACVNSEEIVR 130 140 150 160 170 180 190 200 210 220 230 240queryLLIEHGADIRAQDSLGNTVLHILILQPNKTFACQMYNLLLSYDRHGDHLQPLDLVPNHQGgp:AF3LLIEHGADIRAQDSLGNTVLHILILQPNKTFACQMYNLLLSYDRHGDHLQPLDLVPNHQG 190 200 210 220 230 240 250 260 270 280 290 300queryLTPFKLAGVEGNTVMFQHLMQKRKHTQWTYGPLTSTLYDLTEIDSSGDEQSLLELIITTKgp:AF3LTPFKLAGVEGNTVMFQHLMQKRKHTQWTYGPLTSTLYDLTEIDSSGDEQSLLELIITTK 250 260 270 280 290 300 310 320 330 340 350 360queryKREARQILDQTPVKELVSLKWKRYGRPYFCMLGAIYLLYIICFTMCCIYRPLKPRTNNRTgp:AF3KREARQILDQTPVKELVSLKWKRYGRPYFCMLGAIYLLYIICFTMCCIYRPLKPRTNNRT 310 320 330 340 350 360 370 380 390 400 410 420querySPRDNTLLQQKLLQEAYMTPKDDIRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTIgp:AF3SPRDNTLLQQKLLQEAYMTPKDDIRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTI 370 380 390 400 410 420 430 440 450 460 470 480queryLGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIgp:AF3LGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTI 430 440 450 460 470 480 490 500 510 520 530 540queryMIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTIgp:AF3MIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTI 490 500 510 520 530 540 550 560 570 580 590 600queryIDGPANYNVDLFFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATgp:AF3IDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVAT 550 560 570 580 590 600 610 620 630 640 650 660queryTVMLERKLPRCLWPRSGICGREYGLGDRWFLRVEDRQDLNRQRIQRYAQAFHTRGSEDLDgp:AF3TVMLERKLPRCLWPRSGICGREYGLGDRWFLRVEDRQDLNRQRIQRYAQAFHTRGSEDLD 610 620 630 640 650 660 670 680 690 700 710 720queryKDSVEKLELGCPFSPHLSLPMPSVSRSTSRSSANWERLRQGTLRRDLRGIINRGLEDGESgp:AF3KDSVEKLELGCPFSPHLSLPMPSVSRSTSRSSANWERLRQGTLRRDLRGIINRGLEDGES 670 680 690 700 710 720queryWEYQIgp:AF3WEYQI

[0762]

5

Mouse Cat1

>gi 9081801 calcium transporting protein homolog [Mus musculus]

Score=1189 bits (3077), Expect 0.0

Identifies=622/732 (84|), Positives=668/732 (90|), Gaps 10/732 (1|)

Query:
1
MGLSLPKEKGLILCLWSKFCRWFQRRESWAQSRDEQNLLQQKRIWESPLLLAAKDNDVQA
60

MG SLPKEKGLILCLW+KFCRWF R+ESWAQSRDEQNLLQQKRIWESPLLLAAK+NDVQA

Sbjct:
1
MGWSLPKEKGLILCLWNKFCRWFHRQESWAQSRDEQNLLQQKRIWESPLLLAAKENDVQA
60

Query:
61
LNKLLKYEDCKVHQRGAMGETALHIAALYDNLEAAMVLMEAAPELVFEPMTSELYEGQTA
120

L+KLLK+E C+VHQRGAMGETALHIAALYDNLEAAMVLMEAAPELVFEPMTSELYEGQTA

Sbjct:
61
LSKLLKFEGCEVHQRGAMGETALHIAALYDNLEAAMVLMEAAPELVFEPMTSELYEGQTA
120

Query:
121
LHIAVVNQNMNLVRALLARRASVSARATGTAFRRSPCNIYFGEHPLSFAACVNSEEIVR
180

LH+AV+NQN+N TG+F P Y+GEHPLSFAACV SE R

Sbjct:
121
LHMAVINQNVNLVRALLARRASVSARATGSVFTTGPYKPHYYGEHPLSFAACVGSEGDGR
180

Query:
181
LLIEHGADIRAQDSLGN-TVLHILILQPNKTFACQMYNLLLSYDRHGDHLQPLDLVPNHQ
239

LLIEHGADIPAQ G +ILILQPNKTFACQMYNLLLSYD GDHL+L+LVPN+Q

Sbjct:
181
LLIEHGADIRAQGLSGKYEYYNILILQPNKTFACQMYNLLLSYDG-GDHLKSLELVPNNQ
239

Query:
240
GLTPFKLAGVEGNTVMFQHLMQKRKHTQWTYGPLTSTLYDLTEIDSSGDEQSLLBLIITT
299

GLTPFKLAGVEGN VMFQHLMQKRKH QWTYGPLTSTLYDLTEIDSSGD+QSLLELI+TT

Sbjct:
240
GLTPFKLAGVEGNIVMFQHLMQKRKHIQWTYGPLTSTLYDLTEIDSSGDDQSLLELIVTT
299

Query:
300
KKREARQILDQTPVKELVSLKWKRYGRPYFCMLGAIYLLYIICFTMCCIYRPLKPRTNNR
359

KKREARQILDQTPVKELVSLKWKRYGRPYFC+LGAIY+LYIICFTMCC+YRPLKPR NR

Sbjct:
300
KKREARQILDQTPVKELVSLKWKRYGRPYFCVLGAIYVLYIICFTMCCVYRPLKPRITNR
359

Query:
360
TSPRDNTLLQQKLLQEAYMTPKDDIRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQT
419

T+PRDNTL+QQKLLQEAY+TPKDD+RLVGELV+++GA+IILLVE+PDIFR+GVTRFFGQT

Sbjct:
360
TNPRDNTLMQQKLLQEAYVTPKDDLRLVGELVSIVGAVIILLVEIPDIFRLGVTRFFGQT
419

Query:
420
ILGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALV-LGWCNVMYFARGFQMLGPF
478

ILGGPFHV+IITYAFMVLVTMVMRL + GEVVPMSFA L C+ FARGFQMLGPF

Sbjct:
420
ILGGPFHVIIITYAFMVLVTMVMRLTNVDGEVVPMSFARCWLVQCH--DFARGFQMLGPF
477

Query:
479
TIM-IQKMIFGDLMR-FCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFEL
536

T+ +++IFGDL FCWLMAVVTILGFASAFYIIFQTEDP+ELGHFYDYPMALFSTFEL

Sbjct:
478
TLHDSRRLIFGDLNAIFCWLMAVVILGFASAFYIIFQTEDPDELGHFYDYPMALFSTFEL
537

Query:
537
FLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQ
596

FLTIIDGPANY+VDLPFMYS+TYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQ

Sbjct:
538
FLTIIDGPANYDVDLPFMYSVTYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQ
597

Query:
597
IVATTVMLERKLPRCLWPRSGICGREYGLGDRWFLRVEDRQDLNRQRIQRYAQAFHTRG-
655

+VATTVMLERKLPRCLWPRSGICGREYGLGDRWFLRVEDRQDLNRQRI+RYAQAF +

Sbjct:
598
VVATTVMLERKLPRCLWPRSGICGREYGLGDRWFLRVEDRQDLNRQRIRRYAQAFQQQDG
657

Query:
656
--SEDLDKDSVEKLELGCPFSPHLSLPMPSVSRSTSRSSANWERLRQGTLRRDLRGIINR
713

SEDL+KDS EKLE
PF +LS P P NWERLRQG LR+DLRGIINR

Sbjct:
658
LYSEDLEKDSGEKLETARPFGAYLSFPTPSVSRSTSRSSTNWERLRQGALRKDLRGIINR
717

Query:
714
GLEDGESWEYQI 725

GLEDGE WEYQI

Sbjct:
718
GLEDGEGWEYQI
729

Example 37B

Comparison of CaTr F2E11 to Known Genes

[0763] CaTr F2E11 is a 963 amino acid protein with a calculated MW of 107.7 kDa, and PI of 8.23. CaTr F2E11 is predicted to be a cell surface protein that functions as an ion transporter. CaTr F2E11 shows 91% identity and 93% homology to a mouse osmosensitive receptor potential channel (PubMed cite: gi 11528502) (http://www.ncbi.nlm.nih.gov/). CaTr F2E11 show 96% identity to human vanilloid receptor-related osmotically activated channel (PubMed cite:gi 14767872).

[0764] The following shows the alignment of CaTr F2E11 with human vallinoid receptor-related channel.

6Alignment with of CaTr F2E11 with human Vanilloid receptorQuery=CaTr F2E11Subject=gi+5114767872 vanilloid receptor-related osmotically activatedchannelQuery:276EFREPSTGKTCLPKALLNLSNGRNDTIPVLLDIAERTGNMREFINSPFRDIYYRGQTALH335E EPSTGKTCLPKALLNLSNGRNDTIPVLLDIAERTGNNREFINSPFRDIYYRGQTALHSbjct:5EVLEPSTGKTCLPKALLNLSNGRNDTIPVLLDIAERTGNMREFINSPFRDIYYRGQTALH64Query:336IAIERRCKHYVELLVAQGADVHAQARGRFFQPKDEGGYFYFGELPLSLAACTNQPHIVNY395IAIERRCKHYVELLVAQGADVHAQARGRFFQPKDEGGYFYFGELPLSLAACTNQPHIVNYSbjct:65IAIERRCKHYVELLVAQGADVHAQARGRFFQPKDEGGYFYFGELPLSLAACTNQPHIVNY124Query:396LTENPHKKADMRRQDSRGNTVLHALVAIADNTRENTKFVTKMYDLLLLKCARLFPDSNLE455LTENPHKKADMRRQDSRGNTVLHALVAIADNTRENTKFVTKMYDLLLLKCARLFPDSNLESbjct:125LTENPHKKADMRRQDSRGNTVLHALVAIADNTRENTKFVTKMYDLLLLKCARLFPDSNLE184Query:456AVLNNDGLSPLMMAAKTGKIGIFQHIIRREVTDEDTRHLSRKSKDWAYGPVXXXXXXXXX515AVLNNDGLSPLMMAAKTGKIG+FQHIIRREVTDEDTRHLSRK KDWAYGPVSbjct:185AVLNNDGLSPLMMAAKTGKIGVFQHIIRREVTDEDTRHLSRKKDWAYGPVYSSLYDLSS244Query:516XXTCGEEASVLEILVYNSKIENRHEMLAVEPINELLRDKWRKFGAVSFYINVVSYLCAMV575TCGEEASVLEILVYNSKIENRHEMLAVEPINELLRDKWRKFGAVSFYINVVSYLCAMVSbjct:245LDTCGEEASVLEILVYNSKIENRHEMLAVEPINELLRDKWRKFGAVSFYINVVSYLCAMV304Query:576IFTLTAYYQPLEGTPPYPYRTTVDYLRLAGEVITLFTGVLFFFTNIKDLFMKKCPGVNSL635IFTLTAYYQPLEGTPPYPYRTTVDYLRLAGEVITLFTGVLFFFTNIKDLFMKKCPGVNSLSbjct:305IFTLTAYYQPLEGTPPYPYRTTVDYLRLAGEVITLFTGVLFFFTNIKDLFMKKCPGVNSL364Query:636FIDGSFQLLYFIYSVLVIVSAALYLAGIEAYLAMMVFALVLGWMNALYFTRGLKLTGTYS695FIDGSFQLLYFIYSVLVIVSAALYLAGIEAYLA+MVFALVLGWMNALYFTRGLKLTGTYSSbjCt:365FIDGSFQLLYFIYSVLVIVSAALYLAGIEAYLAVMVFALVLGWMNALYFTRGLKLTGTYS424Query:696IMIQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCANMKVCNEDQTNCTVPTYPSCRDS755IMIQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCANMKVCNEDQTNCTVPTYPSCRDSSbjct:425IMIQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCANMKVCNEDQTNCTVPTYPSCRDS484Query:756ETFSTFLLDLFKLTIGMGDLEMLSSTKYPVVFIILLVTYIILTSVLLLNMLIALMGETVG815ETFSTFLLDLFKLTIGMGDLEMLSSTKYPVVFIILLVTYIILT VLLLNMLIALMGETVGSbjCt:485ETFSTFLLDLFKLTIGMGDLEMLSSTKYPVVFIILLVTYIILTFVLLLNMLIALMGETVG544Query:816QVSKESKHIWKLQWATTILDIERSFPVFLRKAFRSGEMVTVGKSSDGTPDRRWCFRVDEV875QVSKESKHIWKLQWATTILDIERSFPVFLRKAFRSGEMVTVGKSSDGTPDRRWCFRV+EVSbjCt:545QVSKESKHIWKLQWATTILDIERSFPVFLRKAFRSGEMVTVGKSSDGTPDRRWCFRVNEV604Query:876NWSHWNQNLGIINEDPGKNETYQYY 900NWSHWNQNLGIINEDPGKNE +QYYSbjct:605NWSHWNQNLGIINEDPGKNEXHQYY 629

[0765] Vallinoid receptors are mostly ligand-gated ion channels that can be activated by a variety of stimuli including capsaicin, vanilloids, protons and heat. A well-studied vallinoid receptor is VR1 which transmits pain sensations and induces muscle contraction in a variety of tissues (Szallasi A, Di Marzo V. Trends Neurosci. 2000, 23:491; Yiangou Y. BJU Int. 2001, 87:774). VR1 mediates calcium responsiveness in ganglia, terminals of neurons and muscles (Caterina M J. Annu Rev Neurosci. 2001;24:487; ). The ion channel activity of VR1 is regulated by ligands as well as post-translational modification including phosphorylation (Vellani V et al. J Physiol. 2001, 534:813). VR1 is proposed to play a role in increasing cell proliferation and blood flow in the stomach and gut (Nozawa Y et al. Neurosci Lett. 2001, 309:33).

[0766] Based on its significant homology to vallinoid receptors, CaTr F2E11 also participates in calcium signaling, cation transport, as well as tumor initiation and progression and angiogenesis.

[0767] Moreover, CaTr F2E11 contains several protein motifs with known functional significance, including an ion channel motif at aa 608-810 and two ankyrin motifs starting at aa 329 and aa 376 (http://www.sanger.ac.uk).

Example 38A

Identification of Potential Signal Transduction Pathways

[0768] Many mammalian proteins have been reported to interact with signaling molecules and to participate in regulating signaling pathways (J Neurochem. 2001; 76:217-223). Using immunoprecipitation and Western blotting techniques, proteins are identified that associate with 83P2H3 and mediate signaling events. Several pathways known to play a role in cancer biology can be regulated by several of these genes, including phospholipid pathways such as P13K, AKT, etc, adhesion and migration pathways, including FAK, Rho, Rac-1, etc, as well as mitogenic/survival cascades such as ERK, p38, etc (Cell Growth Differ. 2000,11:279; J Biol Chem. 1999, 274:801; Oncogene 2000, 19:3003, J. Cell Biol. 1997, 138:913.). Using Western blotting techniques, the ability of 83P2H3 to regulate these pathways is examined. Cells expressing 83P2H3 and cells lacking these genes are either left untreated or stimulated with ions, channel activators, or antibodies. Cell lysates are analyzed using anti-phospho-specific antibodies (Cell Signaling, Santa Cruz Biotechnology) in order to detect phosphorylation and regulation of ERK, p38, AKT, P13K, PLC and other signaling molecules.

[0769]
FIG. 21, FIG. 22, and FIG. 23 show that expression of 83P2H3 regulates the phosphorylation of several proteins in NIH 3T3 cells, and induces the activation of the ERK pathway in prostate cancer cells. FIG. 26 shows that expression of hCaT induces the phosphorylation of calmodulin kinase. The transport of ions across membranes is regulated by calmodulin and calmodulin kinases (CaMK). Since the phosphorylation of CamK reflects its activation, the effect of hCaT on the phosphorylation of CaMK was investigated. Control and 83P2H3-expressing PC3 cell lines were compared for their ability to alter the phosphorylation state of CaMKII. Cells were grown in 0.1% FBS and either left untreated or stimulated with 10% FBS, ionomycin or calcium. Whole cell lysates were separated by SDS-PAGE and analyzed by Western blotting using an anti-phospho-CaMKII antibody. The results indicate that expression of hCaT was sufficient to enhance the phosphorylation and activation of CaMKII in PC3 cells. When 83P2H3 play a role in the regulation of signaling pathways, whether individually or communally, it is used as a target for diagnostic, preventative and therapeutic purposes.

[0770] To determine whether 83P2H3 directly or indirectly activates known signal transduction pathways in cells, luciferase (luc) based transcriptional reporter assays are carried out in cells expressing individual genes. These transcriptional reporters contain consensus-binding sites for known transcription factors that lie downstream of well-characterized signal transduction pathways. The reporters and examples of these associated transcription factors, signal transduction pathways, and activation stimuli are listed below.

[0771] 1. NFkB-luc, NFkB/Rel; Ik-kinase/SAPK; growth/apoptosis/stress

[0772] 2. SRE-luc, SRF/TCF/ELK1; MAPK/SAPK; growth/differentiation

[0773] 3. AP-1-luc, FOS/JUN; MAPK/SAPK/PKC; growth/apoptosis/stress

[0774] 4. ARE-luc, androgen receptor; steroids/MAPK; growth/differentiation/apoptosis

[0775] 5. p53-luc, p53; SAPK; growth/differentiation/apoptosis

[0776] 6. CRE-luc, CREB/ATF2; PKA/p38; growth/apoptosis/stress

[0777] Gene-mediated effects are assayed in cells showing mRNA expression. Luciferase reporter plasmids can be introduced by lipid-mediated transfection (TFX-50, Promega). Luciferase activity, an indicator of relative transcriptional activity, is measured by incubation of cell extracts with luciferin substrate and luminescence of the reaction is monitored in a luminometer. Signaling pathways activated by 83P2H3 are mapped and used for the identification and validation of therapeutic targets. When these genes are involved in cell signaling, they are used as targets for diagnostic, preventative and therapeutic purposes.

Example 38B

Identification of Potential Signal Transduction Pathways

[0778] Many mammalian proteins have been reported to interact with signaling molecules and to participate in regulating signaling pathways (J Neurochem 2001; 76:217-223). Vanilloid receptors have been documented to activate calcium-mediated signaling as well as protein kinases (Vellani V et al. J Physiol. 2001, 534:813; Szallasi A et al. Mol Pharmacol. 1999, 56:581). Using immunoprecipitation and Western blotting techniques, proteins are identified that associate with CaTr F2E11 and mediate signaling events. Several pathways known to play a role in cancer biology can be regulated by several of these genes, including phospholipid pathways such as PI3K, AKT, etc, adhesion and migration pathways, including FAK, Rho, Rac-1, etc, as well as mitogenic/survival cascades such as ERK, p38, etc (Cell Growth Differ. 2000,11:279; J Biol Chem. 1999, 274:801; Oncogene 2000, 19:3003, J. Cell Biol. 1997, 138:913.). Using Western blotting techniques, CaTr F2E11's regulation of these pathways is determined. Cells expressing CaTr F2E11 and cells lacking these genes are either left untreated or stimulated with ions, channel activators, or antibodies. Cell lysates are analyzed using anti-phospho-specific antibodies (Cell Signaling, Santa Cruz Biotechnology) in order to detect phosphorylation and regulation of ERK, p38, AKT, PI3K, PLC and other signaling molecules.

[0779] It is found that CaTr F2E11 plays a role in the regulation of signaling pathways, individually or communally, it is used as a target for diagnostic, preventative and therapeutic purposes.

[0780] To determine that CaTr F2E11 directly or indirectly activates known signal transduction pathways in cells, luciferase (luc) based transcriptional reporter assays are carried out in cells expressing individual genes. These transcriptional reporters contain consensus-binding sites for known transcription factors that lie downstream of well-characterized signal transduction pathways. The reporters and examples of these associated transcription factors, signal transduction pathways, and activation stimuli are listed below.

[0781] 7. NFkB-luc, NFkB/Rel; Ik-kinase/SAPK; growth/apoptosis/stress

[0782] 8. SRE-luc, SRF/TCF/ELK1; MAPK/SAPK; growth/differentiation

[0783] 9. AP-1-luc, FOS/JUN; MAPK/SAPK/PKC; growth/apoptosis/stress

[0784] 10. ARE-luc, androgen receptor; steroids/MAPK; growth/differentiation/apoptosis

[0785] 11. p53-luc, p53; SAPK; growth/differentiation/apoptosis

[0786] 12. CRE-luc, CREB/ATF2; PKA/p38; growth/apoptosis/stress

[0787] Gene-mediated effects are assayed in cells showing mRNA expression. Luciferase reporter plasmids can be introduced by lipid-mediated transfection (TFX-50, Promega). Luciferase activity, an indicator of relative transcriptional activity, is measured by incubation of cell extracts with luciferin substrate and luminescence of the reaction is monitored in a luminometer. Signaling pathways activated by CaTr F2E11 are mapped and used for the identification and validation of therapeutic targets. Thus, this gene is used as targets for diagnostic, prognistic, preventative and therapeutic purposes.

Example 39A

Involvement in Tumor Progression

[0788] 83P2H3 can contribute to the growth of cancer cells. The role of 83P2H3 in tumor growth is investigated in a variety of primary and transfected cell lines including prostate, colon, bladder and kidney cell lines as well as NIH 3T3 cells engineered to stably express 83P2H3. Parental cells lacking our 83P2H3 and cells expressing the gene are evaluated for cell growth using a well-documented proliferation assay (Fraser S P, Grimes J A, Djamgoz M B. Prostate. 2000;44:61, Johnson D E, Ochieng J, Evans S L. Anticancer Drugs. 1996, 7:288). FIG. 24 shows that expression of 83P2H3 in NIH-3T3 enhances the proliferation of these cells relative to control 83P2H3 negative cells. These results indicate that 83P2H3 plays a critical role in tumor cell growth.

[0789] To determine the role of 83P2H3/hCaT in the transformation process, the effect of 83P2H3 in colony forming assays is evaluated. Parental NIH3T3 cells lacking 83P2H3 are compared to NHI-3T3 cells expressing 83P2H3, using a soft agar assay under stringent and more permissive conditions (Song Z. et al. Cancer Res. 2000; 60:6730).

[0790] To determine the role of 83P2H3 in invasion and metastasis of cancer cells, a well-established Transwell Insert System assay (Becton Dickinson) (Cancer Res. 1999; 59:6010) is used. Control cells, including prostate, colon, bladder and kidney cell lines lacking 83P2H3 are compared to cells expressing 83P2H3. Cells are loaded with the fluorescent dye, calcein, and plated in the top well of the Transwell insert coated with a basement membrane analog. Invasion is determined by fluorescence of cells in the lower chamber relative to the fluorescence of the entire cell population. 83P2H3 can also play a role in cell cycle and apoptosis. Parental cells and cells expressing 83P2H3 are compared for differences in cell cycle regulation using a well-established BrdU assay (Abdel-Malek Z A. J Cell Physiol. 1988, 136:247). In short, cells are grown under both optimal (full serum) and limiting (low serum) conditions are labeled with BrdU and stained with anti-BrdU Ab and propidium iodide. Cells are analyzed for entry into the GI, S, and G2M phases of the cell cycle. Alternatively, the effect of stress on apoptosis is evaluated in control parental cells and cells expressing genes under consideration, including normal and tumor prostate, colon and lung cells. Engineered and parental cells are treated with various chemotherapeutic agents, such as etoposide, flutamide, etc, and protein synthesis inhibitors, such as cycloheximide. Cells are stained with annexin V-FITC and cell death is measured by FACS analysis.

[0791] The function of 83P2H3 is evaluated using anti-sense RNA technology coupled to the various functional assays described above, e.g. growth, invasion and migration. Anti-sense RNA oligonucleotides can be introduced into 83P2H3 expressing cells, thereby preventing the expression of 83P2H3. Control and anti-sense containing cells are analyzed for proliferation, invasion, migration, apoptotic and transcriptional potential. The local as well as systemic effect of the loss of 83P2H3 expression is evaluated.

[0792] When 83P2H3 plays a role in cell growth, transformation, invasion or apoptosis, it is used as a target for diagnostic, preventative and therapeutic purposes.

Example 39B

Involvement in Tumor Progression

[0793] Based on its homology to vallinoid receptors and transient receptor potential (Trp) family of ion channels (Wissenbach U et al. FEBS Lett. 2000 485:127), CaTr F2E11 contributes to the growth of cancer cells. The role of CaTr F2E11 in tumor growth is investigated in a variety of primary and transfected cell lines including prostate, colon, bladder and kidney cell lines as well as NIH 3T3 cells engineered to stably express CaTr F2E11. Parental cells lacking our CaTr F2E11 and cells expressing the gene are evaluated for cell growth using a well-documented proliferation assay (Fraser S P, Grimes J A, Djamgoz M B. Prostate. 2000;44:61, Johnson D E, Ochieng J, Evans S L. Anticancer Drugs. 1996, 7:288). FIG. 24 shows that expression of CaTr F2E11 in NIH-3T3 enhances the proliferation of these cells relative to control CaTr F2E11 negative cells. These results indicate that CaTr F2E11 plays a critical role in tumor cell growth.

[0794] To determine CaTr F2E I's role in transformation, the effect of CaTr F2E11 in colony forming assays is evaluated. Parental NIH3T3 cells lacking CaTr F2E11 are compared to NHI-3T3 cells expressing CaTr F2E11, using a soft agar assay under stringent and more permissive conditions (Song Z. et al. Cancer Res. 2000; 60:6730).

[0795] To determine the role of CaTr F2E11 in invasion and metastasis of cancer cells, a well-established Transwell Insert System assay (Becton Dickinson) (Cancer Res. 1999; 59:6010) is used. Control cells, including prostate, colon, bladder and kidney cell lines lacking CaTr F2E11 are compared to cells expressing CaTr F2E11. Cells are loaded with the fluorescent dye, calcein, and plated in the top well of the Transwell insert coated with a basement membrane analog. Invasion is determined by fluorescence of cells in the lower chamber relative to the fluorescence of the entire cell population.

[0796] CaTr F2E11 also plays a role in cell cycle and apoptosis. Parental cells and cells expressing CaTr F2E11 are compared for differences in cell cycle regulation using a well-established BrdU assay (Abdel-Malek Z A. J Cell Physiol. 1988, 136:247). In short, cells grown under both optimal (full serum) and limiting (low serum) conditions are labeled with BrdU and stained with anti-BrdU Ab and propidium iodide. Cells are analyzed for entry into the G1, S, and G2M phases of the cell cycle. Alternatively, the effect of stress on apoptosis is evaluated in control parental cells and cells expressing genes under consideration, including normal and tumor prostate, colon and lung cells. Engineered and parental cells are treated with various chemotherapeutic agents, such as etoposide, flutamide, etc, and protein synthesis inhibitors, such as cycloheximide. Cells are stained with annexin V-FITC and cell death is measured by FACS analysis.

[0797] The function of CaTr F2E11 is evaluated using anti-sense RNA technology coupled to the various functional assays described above, e.g. growth, invasion and migration. Anti-sense RNA oligonucleotides can be introduced into CaTr F2E11 expressing cells, thereby preventing the expression of CaTr F2E11. Control and anti-sense containing cells are analyzed for proliferation, invasion, migration, apoptotic and transcriptional potential. The local as well as systemic effect of the loss of CaTr F2E11 expression is evaluated.

[0798] Thus, CaTr F2E11 plays a role in cell growth, transformation, invasion and/or apoptosis, and is a target for diagnostic, prognostic preventative and therapeutic purposes.

Example 40A

Regulation of Transcription

[0799] Several ion transporters have been shown to play a role in transcriptional regulation of eukaryotic genes. Regulation of gene expression can be evaluated by studying gene expression in cells expressing or lacking 83P2H3. For this purpose, two types of experiments are performed. In the first set of experiments, RNA from parental and gene-expressing cells are extracted and hybridized to commercially available gene arrays (Clontech) (Smid-Koopman, E, et al. Br. J. Cancer 2000 83:246). Resting cells as well as cells treated with ions, FBS or androgen are compared. Differentially expressed genes are identified in accordance with procedures known in the art. The differentially expressed genes are then mapped to biological pathways (see, e.g., Chen K et al. Thyroid. 2001. 11:41.).

[0800] In the second set of experiments, specific transcriptional pathway activation is evaluated using commercially available (Stratagene) luciferase reporter constructs including: NFkB-luc, SRE-luc, ELK1-luc, ARE-luc, p53-luc, and CRE-luc. These transcriptional reporters contain consensus binding sites for known transcription factors that lie downstream of well-characterized signal transduction pathways, and represent a good tool to ascertain pathway activation and screen for positive and negative modulators of pathway activation.

[0801] When 83P2H3 plays a role in gene regulation, it is used as a target for diagnostic, prognostic, preventative and therapeutic purposes.

Example 40B

Regulation of Transcription

[0802] Several ion transporters, including vanilloid receptors, have been shown to play a role in transcriptional regulation of eukaryotic genes (Int Immunopharmacol. 2001, 1:777). Regulation of gene expression can be evaluated by studying gene expression in cells expressing or lacking CaTr F2E11. For this purpose, two types of experiments are performed.

[0803] In the first set of experiments, RNA from parental and gene-expressing cells are extracted and hybridized to commercially available gene arrays (Clontech) (Smid-Koopman, E, et al. Br. J. Cancer 2000 83:246). Resting cells as well as cells treated with ions, FBS or androgen are compared. Differentially expressed genes are identified in accordance with procedures known in the art. The differentially expressed genes are then mapped to biological pathways (see, e.g., Chen K et al. Thyroid. 2001. 11:41.).

[0804] In the second set of experiments, specific transcriptional pathway activation is evaluated using commercially available (Stratagene) luciferase reporter constructs including: NFkB-luc, SRE-luc, ELK1-luc, ARE-luc, p53-luc, and CRE-luc. These transcriptional reporters contain consensus binding sites for known transcription factors that lie downstream of well-characterized signal transduction pathways, and represent a good tool to ascertain pathway activation and screen for positive and negative modulators of pathway activation.

[0805] Thus, CaTr F2E11 plays a role in gene regulation, and it is used as a target for diagnostic, prognostic, preventative and therapeutic purposes.

Example 41A

Subcellular Localization and Cell Binding

[0806] Based on bioinformatic analysis and hypothesized function, 83P2H3 is proposed to be located at the cell surface. The cellular location of 83P2H3 is assessed using subcellular fractionation techniques widely used in cellular biology (Storrie B, et al. Methods Enzymol. 1990; 182:203-25). A variety of cell lines, including prostate, kidney and bladder cell lines can be separated into nuclear, cytosolic and membrane fractions. Gene expression and location in nuclei, heavy membranes (lysosomes, peroxisomes, and mitochondria), light membranes (plasma membrane and endoplasmic reticulum), and soluble protein fractions can be tested using Western blotting techniques.

[0807] Alternatively, 293T cells can be transfected with an expression vector encoding 83P2H3 HIS-tagged (PCDNA 3.1 MYC/HIS, Invitrogen) as shown in FIG. 27A-F, and the subcellular localization of 83P2H3 is determined by immunofluorescence. Alternatively, the location of the HIS-tagged 83P2H3 is followed by Western blotting.

[0808] When 83P2H3 is localized to specific subcellular locale, such as the cell surface, it is used as a target for diagnostic, preventative and therapeutic purposes as appreciated by one of ordinary skill in the art.

Example 41B

Subcellular Localization and Cell Binding

[0809] Based on bioinformatic analysis and disclosed function, CaTr F2E11 is located at the cell surface. The cellular location of CaTr F2E11 is assessed using subcellular fractionation techniques widely used in cellular biology (Storrie B, et al. Methods Enzymol. 1990;182:203-25). A variety of cell lines, including prostate, kidney and bladder cell lines can be separated into nuclear, cytosolic and membrane fractions. Gene expression and location in nuclei, heavy membranes (lysosomes, peroxisomes, and mitochondria), light membranes (plasma membrane and endoplasmic reticulum), and soluble protein fractions can be tested using Western blotting techniques.

[0810] Alternatively, 293T cells can be transfected with an expression vector encoding CaTr F2E11 HIS-tagged (PcDNA 3.1 MYC/HIS, Invitrogen), and the subcellular localization of CaTr F2E11 determined by immunofluorescence. Alternatively, the location of the HIS-tagged CaTr F2E11 is followed by Western blotting.

[0811] Thus, CaTr F2E11 is localized to specific subcellular locale, namely the cell surface, and it is used as a target for diagnostic, preventative and therapeutic purposes as appreciated by one of ordinary skill in the art.

Example 42A

Protein and Ion Transporter Function

[0812] Based on bioinformatic analysis, 83P2H3 is likely to function as a transporter. To determine whether 83P2H3 functions as an ion channel, FACS analysis and electrophysiology techniques are used (Gergely L, Cook L, Agnello V. Clin Diagn Lab Immunol. 1997;4:70; Skryma R, et al. J Physiol. 2000, 527: 71). Using FACS analysis and commercially available indicators (Molecular Probes), parental cells and cells expressing 83P2H3 are compared for their ability to transport calcium, sodium and potassium. Prostate, colon, bladder and kidney normal and tumor cell lines are used in these studies. For example cells loaded with calcium responsive indicators such as Fluo4 and Fura red are incubated in the presence or absence of ions and analyzed by flow cytometry.

[0813] Information derived from these experiments provides a data regarding important mechanisms by which cancer cells are regulated. This is particularly true in the case of calcium, as calcium channel inhibitors have been reported to induce the death of certain cancer cells, including prostate cancer cell lines (Batra S, Popper L D, Hartley-Asp B. Prostate. 1991,19: 299). FIG. 25 shows that 83P2H3 mediates calcium transport in the prostate cancer cell line PC3, and as such, may regulate prostate cancer growth by regulating intracellular levels of calcium.

[0814] Using a modified rhodamine retention assay (Davies J et al. Science 2000, 290:2295; Leith C et al. Blood 1995, 86:2329) it is determined whether 83P2H3 functions as a protein transporter. Cell lines, such as prostate, colon, bladder and kidney cancer and normal cells, expressing or lacking 83P2H3 are loaded with Calcein AM (Molecular Probes). Cells are examined over time for dye transport using a fluorescent microscope or fluorometer. Quantitation is performed using a fluorometer (Hollo Z. et al., Biochim. Biophys. Acta. 1994. 1191:384). Information obtained from such experiments is used to determine whether 83P2H3 serves to extrude chemotherapeutic drugs, such as doxorubicin, paclitaxel, etoposide, etc, from tumor cells, thereby lowering drug content and reducing tumor responsiveness to treatment. Such a system is also used to determine whether 83P2H3 functions in transporting small molecules.

[0815] When 83P2H3 functions as a transporter, it is used as a target for preventative and therapeutic purposes as well as drug sensitivity/resistance.

[0816] Using electrophysiology, uninjected oocytes and oocytes injected with gene-specific cRNA are compared for ion channel activity. Patch/voltage clamp assays are performed on oocytes in the presence or absence of selected ions, including calcium, potassium, sodium, etc. Ion channel activators (such as cAMP/GMP, forskolin, TPA, etc) and inhibitors (such as calcicludine, conotoxin, TEA, tetrodotoxin, etc) are used to evaluate the function of 83P2H3 as an ion channel (Schweitz H. et al. Proc. Natl. Acad. Sci. 1994.91:878; Skryma R. et al. Prostate. 1997.33:112). Using similar techniques, it was recently demonstrated that hCaT induces calcium flux in 293T cells (Wissenbach, U., et al. J. Biol. Chem. 2001, 276: 19461). The magnitude of the flux shown in this paper was similar to the one observed in figure A, where hCaT was expressed in prostate cancer cells.

[0817] When 83P2H3 functions as an ion channel, it is used as a target for diagnostic, preventative and therapeutic purposes.

Example 42

Protein and Ion Transporter Function

[0818] CaTr F2E11 is disclosed herein to function as a transporter. To conform that CaTr F2E11 functions as an ion channel, FACS analysis and electrophysiology techniques are used (Gergely L, Cook L, Agnello V. Clin Diagn Lab Immunol. 1997;4:70; Skryma R, et al. J Physiol. 2000, 527: 71). Using FACS analysis and commercially available indicators (Molecular Probes), parental cells and cells expressing CaTr F2E11 are compared for their ability to transport calcium, sodium and potassium. Prostate, colon, bladder and kidney normal and tumor cell lines are used in these studies. For example cells loaded with calcium responsive indicators such as Fluo4 and Fura red are incubated in the presence or absence of ions and analyzed by flow cytometry.

[0819] Information derived from these experiments provides a data regarding important mechanisms by which cancer cells are regulated. This is particularly true in the case of calcium, as calcium channel inhibitors have been reported to induce the death of certain cancer cells, including prostate cancer cell lines (Batra S, Popper L D, Hartley-Asp B. Prostate. 1991,19: 299). FIG. 25 shows that CaTr F2E11 mediates calcium transport in the prostate cancer cell line PC3, and as such, can regulate prostate cancer growth by regulating intracellular levels of calcium.

[0820] Using a modified rhodamine retention assay (Davies J et al. Science 2000, 290:2295; Leith C et al. Blood 1995, 86:2329) it is determined that CaTr F2E11 functions as a protein transporter. Cell lines, such as prostate, colon, bladder and kidney cancer and normal cells, expressing or lacking CaTr F2E11 are loaded with Calcein AM (Molecular Probes). Cells are examined over time for dye transport using a fluorescent microscope or fluorometer. Quantitation is performed using a fluorometer (Hollo Z. et al., Biochim. Biophys. Acta. 1994. 1191:384). Information obtained from such experiments is used to determine that CaTr F2E11 serves to extrude chemotherapeutic drugs, such as doxorubicin, paclitaxel, etoposide, etc, from tumor cells, thereby lowering drug content and reducing tumor responsiveness to treatment. Such a system is also used to determine that CaTr F2E11 functions in transporting small molecules.

[0821] Thus, CaTr F2E11's function as a transporter, and it is a target for preventative, prognostic, diagnostic and therapeutic purposes as well as drug sensitivity/resistance.

[0822] Using electrophysiology, uninjected oocytes and oocytes injected with gene-specific cRNA are compared for ion channel activity. Patch/voltage clamp assays are performed on oocytes in the presence or absence of selected ions, including calcium, potassium, sodium, etc. Ion channel activators (such as cAMP/GMP, forskolin, TPA, etc) and inhibitors (such as calcicludine, conotoxin, TEA, tetrodotoxin, etc) are used to evaluate the function of CaTr F2E11 as an ion channel (Schweitz H. et al. Proc. Natl. Acad. Sci. 1994. 91:878; Skryma R. et al. Prostate. 1997. 33:112). Using similar techniques, it was recently demonstrated that hCaT induces calcium flux in 293T cells (Wissenbach, U., et al. J. Biol. Chem. 2001, 276: 19461). The magnitude of the flux shown in this paper was similar to the one observed in FIG. 25A-C, where hCaT was expressed in prostate cancer cells.

Example 43A

Involvement in Cell-Cell Communication

[0823] Cell-cell communication is essential in maintaining organ integrity and homeostasis, both of which become dysregulated during tumor formation and progression. Intercellular communications can be measured using two types of assays (J. Biol. Chem. 2000, 275:25207). In the first assay, cells loaded with a fluorescent dye are incubated in the presence of unlabeled recipient cells and the cell populations are examined under fluorescent microscopy. This qualitative assay measures the exchange of dye between adjacent cells. In the second assay system, donor and recipient cell populations are treated as above and quantitative measurements of the recipient cell population are performed by FACS analysis. Using these two assay systems, cells expressing or lacking 83P2H3 are compared and it is determines whether 83P2H3 enhances or suppresses cell communications. This assay is used to identify small molecules and/or specific antibodies that modulate cell-cell communication.

[0824] When 83P2H3 functions in cell-cell communication, it is used as a target for diagnostic, preventative and therapeutic purposes

Example 43B

Involvement in Cell-Cell Communication

[0825] Cell-cell communication is essential in maintaining organ integrity and homeostasis, both of which become dysregulated during tumor formation and progression. Intercellular communications can be measured using two types of assays (J. Biol. Chem. 2000, 275:25207). In the first assay, cells loaded with a fluorescent dye are incubated in the presence of unlabeled recipient cells and the cell populations are examined under fluorescent microscopy. This qualitative assay measures the exchange of dye between adjacent cells. In the second assay system, donor and recipient cell populations are treated as above and quantitative measurements of the recipient cell population are performed by FACS analysis. Using these two assay systems, cells expressing or lacking CaTr F2E11 are compared and it is determined that CaTr F2E11 enhances or suppresses cell communications. This assay is used to identify small molecules and/or specific antibodies that modulate cell-cell communication.

[0826] Thus, as CaTr F2E11 functions in cell-cell communication, it is used as a target for diagnostic, preventative and therapeutic purposes

Example 44A

Protein-Protein Interaction

[0827] Several ion transporters have been shown to interact with other proteins, thereby forming a protein complex that can regulate ion transport, cell division, gene transcription, and cell transformation (Biochem Biophys Res Commun. 2000, 277: 611; J Biol Chem. 1999; 274: 20812). Using immunoprecipitation techniques as well as two yeast hybrid systems, we can identify proteins that associate with 83P2H3. Immunoprecipitates from cells expressing 83P2H3 and cells lacking 83P2H3 are compared for specific protein-protein associations. 83P2H3 may also associate with, for example, effector molecules, such as adaptor proteins, SNARE proteins, signaling molecules, syntaxins, ATPase subunits, etc (J Biol Chem. 1999; 274: 20812; Proc Natl Acad Sci U S A 1998, 95:14523). Studies comparing 83P2H3 positive and 83P2H3 negative cells as well as studies comparing unstimulated/resting cells and cells treated with epithelial cell activators, such as cytokines, growth factors, androgen and anti-integrin Ab reveal unique interactions.

[0828] In addition, protein-protein interactions are studied using two yeast hybrid methodologies (see, e.g., Curr Opin Chem Biol. 1999, 3:64). A vector carrying a library of proteins fused to the activation domain of a transcription factor is introduced into yeast expressing a 83P2H3-DNA-binding domain fusion protein and a reporter construct. Protein-protein interaction is detected by colorinetric reporter activity. Specific association with effector molecules and transcription factors directs one of skill to the mode of action of 83P2H3, and thus identifies therapeutic, preventative and/or diagnostic targets for cancer. This and similar assays are also used to identify and screen for small molecules that interact with 83P2H3.

[0829] When 83P2H3 associates with proteins or small molecules is used as a target for diagnostic, prognostic, preventative and therapeutic purposes.

Example 44B

Protein-Protein Interaction

[0830] Several ion transporters have been shown to interact with other proteins, thereby forming a protein complex that can regulate ion transport, cell division, gene transcription, and cell transformation (Biochem Biophys Res Commun. 2000, 277: 611; J Biol Chem. 1999; 274: 20812). In addition to forming multimers of VR1 molecules, VR1 has been shown to associate with other ion channels including (Kedei N et al J Biol Chem. 2001, 276:28613;: Premkumar L S Proc Natl Acad Sci U S A. 2001, 98:6537.) Using immunoprecipitation techniques as well as two yeast hybrid systems, proteins that associate with CaTr F2E11 are identified. Immunoprecipitates from cells expressing CaTr F2E11 and cells lacking CaTr F2E11 are compared for specific protein-protein associations. CaTr F2E11 associates with, for example, effector molecules, such as adaptor proteins, SNARE proteins, signaling molecules, syntaxins, ATPase subunits, etc (J Biol Chem. 1999; 274: 20812; Proc Natl Acad Sci U S A 1998, 95:14523). Studies comparing CaTr F2E11 positive and CaTr F2E11 negative cells as well as studies comparing unstimulated/resting cells and cells treated with epithelial cell activators, such as cytokines, growth factors, androgen and anti-integrin Ab reveal unique interactions.

[0831] In addition, protein-protein interactions are studied using two yeast hybrid methodologies (see, e.g., Curr Opin Chem Biol. 1999, 3:64). A vector carrying a library of proteins fused to the activation domain of a transcription factor is introduced into yeast expressing a CaTr F2E11-DNA-binding domain fusion protein and a reporter construct. Protein-protein interaction is detected by colorimetric reporter activity. Specific association with effector molecules and transcription factors directs one of skill to the mode of action of CaTr F2E11, and thus identifies therapeutic, preventative and/or diagnostic targets for cancer. This and similar assays are also used to identify and screen for small molecules that interact with CaTr F2E11.

[0832] Thus, CaTr F2E11 associates with proteins or small molecules and is used as a target for diagnostic, prognostic, preventative and therapeutic purposes.

Example 45

Splice Variants

[0833] Splice variants are also called alternative transcripts. When a gene is transcribed from genomic DNA, the initial RNA is generally spliced to produce functional mRNA, which has only exons and is used for translation into an amino acid sequence. Accordingly, a given gene can have zero to many alternatively spliced mRNA products. Alternative transcripts each have a unique exon makeup, and can have different coding and/or non-coding (5′ or 3′ end) portions, from the original transcript. Alternative transcripts can code for similar proteins with same or similar function or may encode proteins with different functions, and may be expressed in the same tissue at the same time, or at different tissue at different times, proteins encoded by alternative transcripts can have similar or different cellular or extracellular localizations, e.g., be secreted.

[0834] Splice variants are identified by a variety of art-accepted methods. For example, splice variants are identified by use of EST data. First, all human ESTs were grouped into clusters which show direct or indirect identity with each other. Second, ESTs in the same cluster were further grouped into sub-clusters and assembled into a consensus sequence. The starting gene is compared to the consensus sequence(s). Each consensus sequence is a potential splice variant for that gene. Even when a variant is identified that is not a full-length clone, that portion of the variant is very useful for antigen generation and for further cloning of the full-length splice variant, using techniques known in the art. Computer programs that predicted genes based on genomic sequence, such as Grail (http://compbio.ornl.gov/Grail-bin/EmptyGrailForm) and GenScan (http://genes.mit.edu/GENSCAN.html), also predict transcripts that can be splice variants (also see., e.g., Southan C., “A genomic perspective on human proteases,” FEBS Lett. Jun. 8, 2001;498(2-3):214-8; de Souza S J, et al., “Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags,” Proc. Natl Acad Sci U S A. Nov. 7, 2000;97(23): 12690-3; Jia H P, et al., Discovery of new human beta-defensins using a genomics-based approach,” Gene. Jan. 24, 2001;263(1-2):211-8.)

[0835] Using the EST assembly method, we identified three splice variants (designated as A, B and C), as shown below. Table XXI shows the nucleotide sequences of the splice variants. Table XXII shows the alignment of the splice variants with the PCaT nucleic acid sequence. Table XXIII displays the single longest alignment of an amino acid sequence encoded by a splice variant, out of all six potential reading frames with PCaT. Thus, for each splice variant, a variant's reading frame that encodes the longest single contiguous peptide homology between PCaT and the variant is the proper reading frame orientation for the variant. Due to the possibility of sequencing errors in EST or genomic data, other peptides in the relevant reading frame orientation (5′ to 3′ or 3′ to 5′) can also be encoded by the variant. Table XXIV lays out all amino acid translations of the splice variants for their respective reading frame orientations in each of the three reading frames. Tables XXI through XXIV are set forth herein on a variant-by-variant basis.

[0836] To further conform the parameters of the splice variants a variety of techniques are available in the art, such as proteomic validation, PCR-based validation, and 5′ RACE validation, etc. (see e.g., Proteomic Validation: Brennan S O, Fellowes A P, George P M.; “Albumin banks peninsula: a new termination variant characterised by electrospray mass spectrometry.” Biochim Biophys Acta. Aug. 17, 1999;1433(1-2):321-6; Ferranti P, et al., “Differential splicing of pre-messenger RNA produces multiple forms of mature caprine alpha(s1)-casein.” Eur J Biochem. Oct. 1, 1997;249(1):1-7; PCR-based Validation: Wellmann S, et al., “Specific reverse transcription-PCR quantification of vascular endothelial growth factor (VEGF) splice variants by LightCycler technology.” Clin Chem. 2001 April;47(4):654-60; Jia H P, et al., Discovery of new human beta-defensins using a genomics-based approach,” Gene. Jan. 24, 2001;263(1-2):211-8; PCR-based and 5′ RACE Validation: Brigle K E, et al., “Organization of the murine reduced folate carrier gene and identification of variant splice forms,” Biochin Biophys Acta. Aug. 7, 1997; 1353(2): 191-8.

[0837] It is known in the art that genomic regions are upregulated in cancers. When the genomic region to which PCaT maps is upregulated in a particular cancer, the splice variants of PCaT are upregulated as well. Disclosed herein is that PCaT has a particular expression profile. Splice variants of PCaT that are structurally and/or functionally similar to PCaT share this expression pattern, thus serving as tumor-associated markers/antigens.

[0838] Throughout this application, various website data content, publications, applications and patents are referenced. (Websites are referenced by their Uniform Resource Locator, or URL, addresses on the World Wide Web.) The disclosures of each of these references are hereby incorporated by reference herein in their entireties.

[0839] The present invention is not to be limited in scope by the embodiments disclosed herein, which are intended as single illustrations of individual aspects of the invention, and any that are functionally equivalent are within the scope of the invention. Various modifications to the models and methods of the invention, in addition to those described herein, will become apparent to those skilled in the art from the foregoing description and teachings, and are similarly intended to fall within the scope of the invention. Such modifications or other embodiments can be practiced without departing from the true scope and spirit of the invention.

[0840] TABLES

7TABLE IATissues that Express 83P2H3 When MalignantProstate

[0841]

8

TABLE IB

Tissues that Express CaTrF2E11 When Malignant

Prostate

Bladder

Kidney

Lung

Ovary

[0842]

9

TABLE II

AMINO ACID ABBREVIATIONS

SINGLE LETTER
THREE LETTER
FULL NAME

F
Phe
phenylalanine

L
Leu
leucine

S
Ser
serine

Y
Tyr
tyrosine

C
Cys
cysteine

W
Trp
tryptophan

P
Pro
proline

H
His
histidine

Q
Gln
glutamine

R
Arg
arginine

I
Ile
isoleucine

M
Met
methionine

T
Thr
threonine

N
Asn
asparagine

K
Lys
lysine

V
Val
valine

A
Ala
alanine

D
Asp
aspartic acid

E
Glu
glutamic acid

G
Gly
glycine

[0843]

10

TABLE III

AMINO ACID SUBSTITUTION MATRIX

Adapted from the GCG Software 9.0 BLOSUM62 amino acid substitution matrix (block substitution

matrix). The higher the value, the more likely a substitution is found in related, natural

proteins. (See web site for Molecular Biology Laboratory, Dept. of Clinical Pharmacology,

University of Berne, Switzerland, at URL www.ikp.unibe.ch/manual/blosum62.html)

A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y

4
0
−2
−1
−2
0
−2
−1
−1
−1
−1
−2
−1
−1
−1
1
0
0
−3
−2
A

9
−3
−4
−2
−3
−3
−1
−3
−1
−1
−3
−3
−3
−3
−1
−1
−1
−2
−2
C

6
2
−3
−1
−1
−3
−1
−4
−3
1
−1
0
−2
0
−1
−3
−4
−3
D

5
−3
−2
0
−3
1
−3
−2
0
−1
2
0
0
−1
−2
−3
−2
E

6
−3
−1
0
−3
0
0
−3
−4
−3
−3
−2
−2
−1
1
3
F

6
−2
−4
−2
−4
−3
0
−2
−2
−2
0
−2
−3
−2
−3
G

8
−3
−1
−3
−2
1
−2
0
0
−1
−2
−3
−2
2
H

4
−3
2
1
−3
−3
−3
−3
−2
−1
3
−3
−1
I

5
−2
−1
0
−1
1
2
0
−1
−2
−3
−2
K

4
2
−3
−3
−2
−2
−2
−1
1
−2
−1
L

5
−2
−2
0
−1
−1
−1
1
−1
−1
M

6
−2
0
0
1
0
−3
−4
−2
N

7
−1
−2
−1
−1
−2
−4
−3
P

5
1
0
−1
−2
−2
−1
Q

5
−1
−1
−3
−3
−2
R

4
1
−2
−3
−2
S

5
0
−2
−2
T

4
−3
−1
V

11
2
W

7
Y

[0844]

11

TABLE IV (A)

POSITION
POSITION
POSITION

2 (Primary
3 (Primary
C Terminus (Primary

Anchor)
Anchor)
Anchor)

SUPERMOTIFS

A1
TILVMS

FWY

A2
LIVMATQ

IVMATL

A3
VSMATLI

RK

A24
YFWIVLMT

FIYWLM

B7
P

VILFMWYA

B27
RHK

FYLWMIVA

B44
ED

FWYLIMVA

B58
ATS

FWYLIVMA

B62
QLIVMP

FWYMIVLA

MOTIFS

A1
TSM

Y

A1

DEAS
Y

A2.1
LMVQIAT

VLIMAT

A3
LMVISATF-

KYRHFA

CGD

A11
VTMLI-

KRYH

SAGNCDF

A24
YFWM

FLIW

A*3101
MVTALIS

RK

A*3301
MVALFIST

RK

A*6801
AVTMSLI

RK

B*0702
P

LMFWYAIV

B*3501
P

LMFWYIVA

B51
P

LIVFWYAM

B*5301
P

IMFWVALV

B*5401
P

ATIVLMFWY

[0845] Bolded residues are preferred, italicized residues are less preferred: A peptide is considered motif-bearing if it has primary anchors at each primary anchor position for a motif or supermotif as specified in the above table.

12TABLE IV (B)HLA CLASS II SUPERMOTIF169W, F, Y, V, .I, LA, V, I, L, P, C, S, TA, V, I, L, C, S, T, M, Y

[0846]

13

TABLE IV C

MOTIFS

1° anchor 1
2
3
4
5
1° anchor 6
7
8
9

DR4
preferred
FMYLIVW
M
T

I
VSTCPALIM
MH

MH

deleterious

W

R

WDE

DR1
preferred
MFLIVWY

PAMQ

VMATSPLIC
M

AVM

deleterious

C
CH
FD
CWD

GDE
D

DR7
preferred
MFLIVWY
M
W
A

IVMSACTPL
M

IV

deleterious

C

G

GRD
N
G

DR3
MOTIFS
1° anchor 1
2
3
1° anchor 4
5
1° anchor 6

motif a

LIVMFY

D

preferred

motif b

LIVMFAY

DNQEST

KRH

preferred

DR Supermotif

MFLIVWY

VMSTACPLI

Italicized residues indicate less preferred or “tolerated” residues.

[0847]

14

TABLE IV D

POSITION

SUPERMOTIFS

1
2
3
4
5
6
7
8
C-terminus

A1

1° Anchor

1° Anchor

TILVMS

FWY

A2

1° Anchor

1° Anchor

{overscore (LIVMATQ)}

LIVMAT

A3
preferred

1° Anchor
YFW (4/5)

YFW (3/5)
YFW (4/5)
P

1° Anchor

{overscore (VSMATLI)}

(4/5)
RK

deleterious
DE (3/5);

DE (4/5)

P (5/5)

A24

1° Anchor

1° Anchor

{overscore (YFWIVLMT)}

FIYWLM

B7
preferred
FWY (5/5)

1° Anchor

FWY (4/5)

FWY
1° Anchor

LIVM (3/5)
P

(3/5)
{overscore (VILFMWYA)}

deleterious
DE (3/5);

DE (3/5)
G (4/5)
QN (4/5)
DE

P (5/5);

(4/5)

G (4/5);

A (3/5);

QN (3/5)

B27

1° Anchor

1° Anchor

RHK

{overscore (FYLWMIVA)}

B44

1° Anchor

1° Anchor

ED

{overscore (FWYLIMVA)}

B58

1° Anchor

1° Anchor

ATS

{overscore (FWYLIVMA)}

B62

1° Anchor

1° Anchor

QLIVMP

{overscore (FWYMIVLA)}

[0848]

15

TABLE IV E

POSITION

1
2
3
4
5

A1
preferred
GFYW

1° Anchor

DEA
YFW

9-mer

STM

deleterious
DE

RHKLIVMP
A
G

A1
preferred
GRHK
ASTCLIVM

1° Anchor

GSTC

9-mer

DEAS

deleterious
A
RHKDEPYFW

DE
PQN

A1
preferred
YFW

1° Anchor

DEAQN
A
YFWQN

10-mer

STM

deleterious
GP

RHKGLIVM
DE
RHK

A1
preferred
YFW
STCLIVM

1° Anchor

A
YFW

10-mer

DEAS

deleterious
RHK
RHKDEPY

P

FW

A2.1
preferred
YFW
1° Anchor
YFW
STC
YFW

9-mer

{overscore (LMIVQAT)}

deleterious
DEP

DERKH

A2.1 10-
preferred
AYFW
1° Anchor
LVIM
G

mer

{overscore (LMIVQAT)}

deleterious
DEP

DE
RKHA
P

A3
preferred
RHK
1° Anchor
YFW
PRHKYFW
A

{overscore (LMVISATFCG)}

D

deleterious
DEP

DE

A11
preferred
A
1° Anchor
YFW
YFW
A

{overscore (VTLMISAGN)}

CDF

deleterious
DEP

A24
preferred
YFWRHK

1° Anchor

STC

9-mer

YFWM

deleterious
DEG

DE
G
QNP

A24
preferred

1° Anchor

P
YFWP

10-mer

YFWM

deleterious

GDE
QN
RHK

A3101
preferred
RHK
1° Anchor
YFW
P

{overscore (MVTALIS)}

deleterious
DEP

DE

ADE

A3301
preferred

1° Anchor
YFW

{overscore (MVALFIST)}

deleterious
GP

DE

A6801
preferred
YFWSTC

1° Anchor

YFWLIVM

AVTMSLI

deleterious
GP

DEG

RHK

B0702
preferred
RHKFWY

1° Anchor

RHK

RHK

P

deleterious
DEQNP

DEP
DE
DE

B3501
preferred
FWYLIVM

1° Anchor

FWY

P

deleterious
AGP

G

B51
preferred
LIVMFWY

1° Anchor

FWY
STC
FWY

P

deleterious
AGPDERHKS

DE

TC

B5301
preferred
LIVMFWY

1° Anchor

FWY
STC
FWY

P

deleterious
AGPQN

B5401
preferred
FWY

1° Anchor

FWYLIVM

LIVM

P

deleterious
GPQNDE

GDESTC

RHKDE

C-ter-

6
7
8
9
minus

or

C-terminus

A1
preferred
P
DEQN
YFW

1° Anchor

9-mer

Y

deleterious
A

A1
preferred
ASTC
LIVM
DE

1° Anchor

9-mer

Y

deleterious
RHK
PG
GP

A1
preferred

PASTC
GDE
P

1° Anchor

10-mer

Y

deleterious
QNA
RHKYFW
RHK
A

A1
preferred

PG
G
YFW

1° Anchor

10-mer

Y

deleterious
G

PRHK
QN

A2.1
preferred

A
P

1° Anchor

9-mer

VLIMAT

deleterious
RKH
DERKH

A2.1 10-
preferred
G

FYWL

1° Anchor

mer

VIM

VLIMAT

deleterious

RKH
DERKH
RKH

A3
preferred
YFW

P

1° Anchor

KYRHFA

deleterious

A11
preferred
YFW
YFW
P

1° Anchor

KRYH

deleterious

A
G

A24
preferred

YFW
YFW

1° Anchor

9-mer

FLIW

deleterious
DERHK
G
AQN

A24
preferred

P

1° Anchor

10-mer

FLIW

deleterious
DE
A
QN
DEA

A3101
preferred
YFW
YFW
AP

1° Anchor

RK

deleterious
DE
DE
DE

A3301
preferred

AYFW

1° Anchor

RK

deleterious

A6801
preferred

YFW
P

1° Anchor

RK

deleterious

A

B0702
preferred
RHK
RHK
PA
1° Anchor

{overscore (LMFWYAIV)}

deleterious
GDE
QN
DE

B3501
preferred

FWY

1° Anchor

{overscore (LMFWYIVA)}

deleterious
G

B51
preferred

G
FWY
1° Anchor

{overscore (LIVFWYAM)}

deleterious
G
DEQN
GDE

B5301
preferred

LIVMFWY
FWY
1° Anchor

{overscore (IMFWYALV)}

deleterious
G
RHKQN
DE

B5401
preferred

ALIVM
FWYAP
1° Anchor

{overscore (ATIVLMFWY)}

deleterious
DE
QNDGE
DE

Italicized residues indicate less preferred or “tolerated” residures.

The information in this Table is specific for 9-mers unless otherwise specified.

[0849]

16

TABLE V(A)

HLA Peptide Scoring Results-83P2H3-A1,9-mers

Score (Estimate of Half time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
401
LVEVPDIFR
45.000
1.

2
292
LLELIITTK
18.000
2.

3
248
GVEGNTVMF
18.000
3.

4
55
DNDVQALNK
12.500
4.

5
516
DPEELGHFY
11.250
5.

6
448
SGEVVPMSF
11.250
6.

7
182
LIEHGADIR
9.000
7.

8
373
LQEAYMTPK
2.700
8.

9
59
QALNKLLKY
2.500
9.

10
331
MLGAIYLLY
2.500
10.

11
548
NVDLPFMYS
2.500
11.

12
513
QTEDPEELG
2.250
12.

13
658
DLDKDSVEK
2.000
13.

14
666
KLELGCPFS
1.800
14.

15
91
NLEAAMVLM
1.800
15.

16
174
NSEEIVRLL
1.350
16.

17
111
TSELYEGQT
1.350
17.

18
655
GSEDLDKDS
1.350
18.

19
514
TEDPEELGH
1.250
19.

20
715
LEDGESWEY
1.250
20.

21
214
QMYNLLLSY
1.250
21.

22
153
RRSPCNLIY
1.250
22.

23
81
TALHIAALY
1.000
23.

24
459
VLGWCNVMY
1.000
24.

25
501
ILGFASAFY
1.000
25.

26
539
TIIDGPANY
1.000
26.

27
632
RVEDRQDLN
0.900
27.

28
154
RSPCNLIYF
0.750
28.

29
615
RSGICGREY
0.750
29.

30
404
VPDIFRMGV
0.625
30.

31
547
YNVDLPFMY
0.625
31.

32
551
LPFMYSITY
0.625
32.

33
487
FGDLMRFCW
0.625
33.

34
46
ESPLLLAAK
0.600
34.

35
341
ICFTMCCIY
0.500
35.

36
254
VMFQHLMQK
0.500
36.

37
523
FYDYPMALF
0.500
37.

38
485
MIFGDLMRF
0.500
38.

39
316
LVSLKWKRY
0.500
39.

40
504
FASAFYIIF
0.500
40.

41
146
RATGTAFRR
0.500
41.

42
598
VATTVMLER
0.500
42.

43
474
MLGPFTIMI
0.500
43.

44
624
GLGDRWFLR
0.500
44.

45
240
GLTPFKLAG
0.500
45.

46
377
YMTPKDDIR
0.500
46.

47
450
EVVPMSFAL
0.500
47.

48
599
ATTVMLERK
0.500
48.

49
479
TIMIQKMIF
0.500
49.

50
462
WCNVMYFAR
0.500
50.

[0850]

17

TABLE V(B)

HLA Peptide Scoring Results-CaTrF2E11-A1,9-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule Containing

Rank
Position
Listing
This Subsequence)
SEQ ID NO:

1
63
FLEPPPLAG
45.000
51.

2
944
RCDGHQQGY
25.000
52.

3
774
DLEMLSSTK
18.000
53.

4
209
SSDNKRWRK
15.000
54.

5
838
RSFPVFLRK
15.000
55.

6
850
SGEMVTVGK
9.000
56.

7
543
AVEPINELL
9.000
57.

8
859
SSDGTPDRR
7.500
58.

9
353
GADVHAQAR
5.000
59.

10
93
MADSSEGPR
5.000
60.

11
337
AIERRCKHY
4.500
61.

12
818
SKESKHIWK
4.500
62.

13
320
NSPFRDIYY
3.750
63.

14
523
ASVLEILVY
3.750
64.

15
597
TVDYLRLAG
2.500
65.

16
231
APQPPPILK
2.500
66.

17
762
LLDLFKLTI
2.500
67.

18
387
TNQPHIVNY
2.500
68.

19
692
GTYSIMIQK
2.500
69.

20
741
QTNCTVPTY
2.500
70.

21
759
STFLLDLFK
2.500
71.

22
368
KDEGGYFYF
2.250
72.

23
396
LTENPHKKA
2.250
73.

24
727
LLNPCANMK
2.000
74.

25
345
YVELLVAQG
1.800
75.

26
525
VLEILVYNS
1.800
76.

27
177
LLESTLYES
1.800
77.

28
662
GIEAYLAMM
1.800
78.

29
835
DIERSFPVF
1.800
79.

30
754
DSETFSTFL
1.350
80.

31
319
INSPFRDIY
1.250
81.

32
488
DEDTRHLSR
1.250
82.

33
300
DTIPVLLDI
1.250
83.

34
486
VTDEDTRHL
1.250
84.

35
830
ATTILDIER
1.250
85.

36
119
GGEAFPLSS
1.125
86.

37
604
AGEVITLFT
1.125
87.

38
575
VIFTLTAYY
1.000
88.

39
675
VLGWMNALY
1.000
89.

40
651
LVIVSAALY
1.000
90.

41
257
DLDGLLPFL
1.000
91.

42
85
SADGPGAGM
1.000
92.

43
534
KIENRHEML
0.900
93.

44
308
IAERTGNMR
0.900
94.

45
921
VVELNKNSN
0.900
95.

46
107
VAELPGDES
0.900
96.

47
197
DSLFDYGTY
0.750
97.

48
77
LSFPCRLSS
0.750
98.

49
194
APMDSLFDY
0.625
99.

50
772
MGDLEMLSS
0.625
100.

[0851]

18

TABLE VI(A)

HLA Peptide Scoring Results-83P2H3-A1,10-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
632
RVEDRQDLNR
45.000
101.

2
714
GLEDGESWEY
45.000
102.

3
106
VFEPMTSELY
22.500
103.

4
98
LMEAAPELVF
22.500
104.

5
292
LLELIITTKK
18.000
105.

6
513
QTEDPEELGH
11.250
106.

7
174
NSEEIVRLLI
6.750
107.

8
248
GVEGNTVMFQ
4.500
108.

9
401
LVEVPDIFRM
4.500
109.

10
182
LIEHGADIRA
4.500
110.

11
677
LSLPMPSVSR
3.000
111

12
514
TEDPEELGHF
2.500
112.

13
538
LTIIDGPANY
2.500
113.

14
550
DLPFMYSITY
2.500
114.

15
80
ETALHIAALY
2.500
115.

16
655
GSEDLDKDSV
1.350
116.

17
111
TSELYEGQTA
1.350
117.

18
478
FTIMIQKMIF
1.250
118.

19
330
CMLGAIYLLY
1.250
119.

20
704
RRDLRGIINR
1.250
120.

21
78
MGETALHIAA
1.125
121.

22
387
VGELVTVIGA
1.125
122.

23
162
FGEHPLSFAA
1.125
123.

24
253
TVMFQHLMQK
1.000
124.

25
458
LVLGWCNVMY
1.000
125.

26
57
DVQALNKLLK
1.000
126.

27
540
IIDGPANYNV
1.000
127.

28
548
NVDLPFMYSI
1.000
128.

29
500
VILGFASAFY
1.000
129.

30
33
RDEQNLLQQK
0.900
130.

31
313
VKELVSLKWK
0.900
131.

32
447
ASGEVVPMSF
0.750
132.

33
286
SGDEQSLLEL
0.625
133.

34
225
HGDHLQPLDL
0.625
134.

35
423
GPFHVLIITY
0.625
135.

36
585
VAHERDELWR
0.500
136.

37
495
WLMAVVILGF
0.500
137.

38
400
LLVEVPDIFR
0.500
138.

39
597
IVATTVMLER
0.500
139.

40
186
GADIRAQDSL
0.500
140.

41
171
ACVNSEEIVR
0.500
141.

42
282
EIDSSGDEQS
0.500
142.

43
341
ICFTMCCIYR
0.500
143.

44
204
ILQPNKTFAC
0.500
144.

45
601
TVMLERKLPR
0.500
145.

46
307
ILDQTPVKEL
0.500
146.

47
12
ILCLWSKFCR
0.500
147.

48
340
IICFTMCCIY
0.500
148.

49
315
ELVSLKWKRY
0.500
149.

50
334
AIYLLYIICF
0.500
150.

[0852]

19

TABLE V1(B)

HLA Peptide Scoring Results-CaTrF2E11-A1,10-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule Containing

Rank
Position
Listing
This Subsequence)
SEQ ID NO:

1
543
AVEPLNELLR
450.000
151.

2
63
FLEPPPLAGF
180.000
152.

3
636
FIDGSFQLLY
125.000
153.

4
774
DLEMLSSTKY
45.000
154.

5
255
TADLDGLLPF
25.000
155.

6
525
VLEILVYNSK
18.000
156.

7
209
SSDNKRWRKK
15.000
157.

8
888
NEDPGKNETY
12.500
158.

9
423
IADNTRENTK
10.000
159.

10
585
PLEGTPPYPY
9.000
160.

11
810
MGETVGQVSK
9.000
161.

12
754
DSETFSTFLL
6.750
162.

13
319
INSPFRDIYY
6.250
163.

14
4
VVGPGANLCF
5.000
164.

15
403
KADMRRQDSR
5.000
165.

16
662
GIEAYLAMMV
4.500
166.

17
893
KNETYQYYGF
4.500
167.

18
534
KIENRHEMLA
4.500
168.

19
462
GLSPLMMAAK
4.000
169.

20
639
GSFQLLYFIY
3.750
170.

21
744
CTVPTYPSCR
2.500
171.

22
498
SKDWAYGPVY
2.500
172.

23
193
KAPMDSLFDY
2.500
173.

24
174
PIDLLESTLY
2.500
174.

25
833
ILDIERSFPV
2.500
175.

26
618
FTNIKDLFMK
2.500
176.

27
386
CTNQPHIVNY
2.500
177.

28
711
LVYLLFMIGY
2.500
178.

29
257
DLDGLLPFLL
2.500
179.

30
522
EASVLEILVY
2.500
180.

31
487
TDEDTRHLSR
2.250
181.

32
547
INELLRDKWR
2.250
182.

33
260
GLLPFLLTHK
2.000
183.

34
73
CLTPLSFPCR
2.000
184.

35
219
IIEKQPQSPK
1.800
185.

36
427
TRENTKFVTK
1.800
186.

37
758
FSTFLLDLFK
1.500
187.

38
561
VSFYINVVSY
1.500
188.

39
96
SSEGPRAGPG
1.350
189.

40
486
VTDEDTRHLS
1.250
190.

41
272
LTDEEFREPS
1.250
191.

42
331
QTALHIAIER
1.250
192.

43
608
ITLFTGVLFF
1.250
193.

44
376
FGELPLSLAA
1.125
194.

45
604
AGEVITLFTG
1.125
195.

46
519
CGEEASVLEI
1.125
196.

47
353
GADVHAQARG
1.000
197.

48
695
SIMIQKILFK
1.000
198.

49
785
VVFIILLVTY
1.000
199.

50
93
MADSSEGPRA
1.000
200.

[0853]

20

TABLE VII(A)

HLA Peptide Scoring Results-83P2H3-A2, 9-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
577
MMGDTHWRV
2625.878
201.

2
336
YLLYIICFT
1604.438
202.

3
97
VLMEAAPEL
550.915
203.

4
291
SLLELIITT
260.008
204.

5
135
ALLARRASV
257.342
205.

6
419
TILGGPFHV
205.231
206.

7
385
RLVGELVTV
159.970
207.

8
337
LLYIICFTM
156.750
208.

9
399
ILLVEVPDI
150.931
209.

10
330
CMLGAIYLL
131.296
210.

11
457
ALVLGWCNV
118.238
211.

12
50
LLAAKDNDV
118.238
212.

13
472
FQMLGPFTI
104.419
213.

14
43
RIWESPLLL
99.957
214.

15
623
YGLGDRWFL
97.904
215.

16
371
KLLQEAYMT
96.503
216.

17
428
LIITYAFMV
94.295
217.

18
436
VLVTMVMRL
83.527
218.

19
87
ALYDNLEAA
73.458
219.

20
181
LLIEHGADI
72.717
220.

21
427
VLIITYAFM
69.676
221.

22
474
MLGPFTIMI
67.396
222.

23
553
FMYSITYAA
52.815
223.

24
569
LMLNLLIAM
51.908
224.

25
12
ILCLWSKFC
46.451
225.

26
204
ILQPNKTFA
46.451
226.

27
430
ITYAFMVLV
45.929
227.

28
489
DLMRFCWLM
39.291
228.

29
567
TLLMLNLLI
38.601
229.

30
77
AMGETALHI
30.893
230.

31
568
LLMLNLLIA
29.468
231.

32
420
ILGGPFHVL
28.290
232.

33
194
SLGNTVLHI
23.995
233.

34
125
VVNQNMNLV
23.795
234.

35
396
AIIILLVEV
21.996
235.

36
113
ELYEGQTAL
21.021
236.

37
512
FQTEDPEEL
20.016
237.

38
451
VVPMSFALV
19.657
238.

39
570
MLNLLIAMM
19.425
239.

40
159
LIYFGEHPL
15.979
240.

41
129
NMNLVRALL
15.428
241.

42
502
LGFASAFYI
13.665
242.

43
329
FCMLGAIYL
13.054
243.

44
202
ILILQPNKT
12.668
244.

45
339
YIICFTMCC
11.941
245.

46
393
VIGAIIILL
11.485
246.

47
528
MALFSTFEL
10.824
247.

48
473
QMLGPFTIM
10.342
248.

49
443
RLISASGEV
9.042
249.

50
556
SITYAAFAI
8.320
250.

[0854]

21

TABLE VII(B)

HLA Peptide Scoring Results-CaTrF2E11-A2, 9-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule Containing

Rank
Position
Listing
This Subsequence)
SEQ ID NO:

1
642
QLLYFIYSV
2249.173
251.

2
666
YLAMMVFAL
1310.882
252.

3
709
FLLVYLLFM
1069.625
253.

4
761
FLLDLFKLT
988.029
254.

5
659
YLAGIEAYL
540.469
255.

6
570
YLCAMVIFT
433.632
256.

7
264
FLLTHKKRL
363.588
257.

8
801
LLLNMLIAL
309.050
258.

9
710
LLVYLLFMI
236.595
259.

10
49
KQLAALLLV
210.038
260.

11
713
YLLFMIGYA
139.051
261.

12
440
LLLLKCARL
134.369
262.

13
646
FIYSVLVIV
132.749
263.

14
163
FQGAFRKGV
123.265
264.

15
777
MLSSTKYPV
118.238
265.

16
348
LLVAQGADV
118.238
266.

17
809
LMGETVGQV
104.685
267.

18
304
VLLDIAERT
94.168
268.

19
668
AMMVFALVL
88.939
269.

20
787
FIILLVTYI
83.474
270.

21
789
ILLVTYIIL
82.637
271.

22
643
LLYFIYSVL
71.470
272.

23
716
FMIGYASAL
70.971
273.

24
34
WEWPPCAPV
51.635
274.

25
602
RLAGEVITL
49.134
275.

26
286
CLPKALLNL
49.134
276.

27
795
IILTSVLLL
42.494
277.

28
650
VLVIVSAAL
36.316
278.

29
578
TLTAYYQPL
32.044
279.

30
826
KLQWATTIL
30.655
280.

31
800
VLLLNMLIA
29.468
281.

32
790
LLVTYIILT
29.137
282.

33
611
FTGVLFFFT
28.856
283.

34
73
CLTPLSFPC
28.814
284.

35
652
VIVSAALYL
27.464
285.

36
388
NQPHIVNYL
27.399
286.

37
674
LVLGWMNAL
27.042
287.

38
762
LLDLFKLTI
26.958
288.

39
819
KESKHIWKL
25.079
289.

40
613
GVLFFFTNI
24.386
290.

41
767
KLTIGMGDL
22.356
291.

42
897
YQYYGFSHT
21.131
292.

43
802
LLNMLIALM
19.425
293.

44
726
SLLNPCANM
18.382
294.

45
717
MIGYASALV
16.258
295.

46
657
ALYLAGIEA
15.898
296.

47
573
AMVIFTLTA
13.634
297.

48
794
YIILTSVLL
13.512
298.

49
792
VTYIILTSV
12.087
299.

50
667
LAMMVFALV
11.545
300.

[0855]

22

TABLE VIII(A)

lILA Peptide Scoring Results-83P2H3-A2, 10-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
529
ALFSTFELFL
1651.954
301.

2
576
AMMGDTHWRV
1393.938
302.

3
63
KLLKYEDCKV
900.698
303.

4
97
VLMEAAPELV
878.901
304.

5
427
VLIITYAFMV
685.783
305.

6
501
ILGFASAFYI
565.771
306.

7
624
GLGDRWFLRV
541.810
307.

8
336
YLLYIICFTM
490.421
308.

9
49
LLLAAKDNDV
437.482
309.

10
245
KLAGVEGNTV
243.432
310.

11
331
MLGAIYLLYI
224.357
311.

12
602
VMLERKLPRC
212.821
312.

13
240
GLTPFKLAGV
159.970
313.

14
429
IITYAFMVLV
142.093
314.

15
465
VMYFARGFQM
113.209
315.

16
473
QMLGPFTIMI
105.939
316.

17
568
LLMLNLLIAM
71.872
317.

18
377
YMTPKDDIRI
70.971
318.

19
420
ILGGPFHVLI
67.396
319.

20
87
ALYDNLEAAM
65.180
320.

21
43
RIWESPLLLA
53.466
321.

22
569
LMLNLLIAMM
51.908
322.

23
337
LLYIICFTMC
51.349
323.

24
204
ILQPNKTFAc
48.984
324.

25
105
LVFEPMTSEL
48.205
325.

26
180
RLLIEHGADI
38.601
326.

27
432
YAFMVLVTMV
37.815
327.

28
393
VIGAIIILLV
37.393
328.

29
307
ILDQTPVKEL
33.411
329.

30
456
FALVLGWCNV
27.950
330.

31
435
MVLVTMVMRL
27.042
331.

32
203
LILQPNKTFA
23.632
332.

33
11
LILCLWSKFC
23.632
333.

34
158
NLIYFGEHPL
21.362
334.

35
2
GLSLPKEKGL
21.362
335.

36
398
IILLVEVPDI
20.753
336.

37
194
SLGNTVLHIL
20.145
337.

38
367
LLQQKLLQEA
19.425
338.

39
567
TLLMLNLLIA
17.334

40
339
YIICFTMCCI
15.177
340.

41
490
LMRFCWLMAV
14.927
341.

42
124
AVVNQNMNLV
13.997
342.

43
443
RLISASGEVV
13.973
343.

44
77
AMGETALHIA
13.872
344.

45
96
MVLMEAAPEL
11.757
345.

46
564
IJATLLMLNL
11.485
346.

47
485
MIFGDLMRFC
10.871
347.

48
591
ELWRAQIVAT
10.669
348.

49
496
LMAVVTLGFA
10.031
349.

50
385
RLVGELVTVI
9.838
350.

[0856]

23

TABLE VIII(B)

HLA Peptide Scoring Results-CaTrF2E11-A2,10-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule Containing

Rank
Position
Listing
This Subsequence)
SEQ ID NO:

1
761
FLLDLFKLTI
2766.482
351.

2
709
FLLVYLLFMI
2368.734
352.

3
570
YLCAMVIFTL
1310.882
353.

4
641
FQLLYFIYSV
1048.989
354.

5
666
YLAMMVFALV
607.884
355.

6
634
SLFIDGSFQL
458.437
356.

7
897
YQYYGFSHTV
394.449
357.

8
436
KMYDLLLLKC
378.950
358.

9
643
LLYFIYSVLV
378.363
359

10
800
VLLLNMLIAL
309.050
360.

11
701
ILFKDLFRFL
280.832
361.

12
833
ILDIERSFPV
274.313
362.

13
716
FMIGYASALV
231.067
363.

14
50
QLAALLLVHV
159.970
364.

15
727
LLNPCANMKV
118.238
365.

16
789
ILLVTYIILT
107.808
366.

17
509
SLYDLSSLDT
97.770
367.

18
395
YLTENPHKKA
93.696
368.

19
457
VLNNDGLSPL
83.527
369.

20
541
MLAVEPINEL
83.527
370.

21
808
ALMGETVGQV
76.945
371.

22
705
DLFRFLLVYL
74.990
372.

23
777
MLSSTKYPVV
72.717
373.

24
801
LLLNMLIALM
71.872
374.

25
681
ALYFTRGLKL
68.360
375.

26
805
MLIALMGETV
57.937
376.

27
673
ALVLGWMNAL
49.134
377.

28
642
QLLYFIYSVL
48.610
378.

29
714
LLFMIGYASA
46.873
379.

30
130
NLFEGEDGSL
42.129
380.

31
689
KLTGTYSIMI
36.515
381.

32
827
LQWATTILDI
34.328
382.

33
794
YIILTSVLLL
31.077
383.

34
55
LLVHVGGGFL
25.966
384.

35
264
FLLTHKKRLT
25.367
385.

36
791
LVTYIILTSV
23.795
386.

37
659
YLAGIEAYLA
22.853
387.

38
609
TLFTGVLFFF
20.230
388.

39
796
ILTSVLLLNM
19.425
389.

40
623
DLFMKKCPGV
19.301
390.

41
347
ELLVAQGADV
19.301
391.

42
447
RLFPDSNLEA
18.382
392.

43
651
LVIVSAALYL
17.477
393.

44
759
STFLLDLFKL
14.645
394.

45
776
EMLSSTKYPV
13.939
395.

46
592
YPYRTTVDYL
12.724
396.

47
558
FGAVSFYINV
11.904
397.

48
42
VITTVALKQL
11.485
398.

49
788
IILLVTYIIL
11.363
399.

50
697
MIQKILFKDL
9.488
400.

[0857]

24

TABLE IX(A)

HLA Peptide Scoring Results-83P2H3-A3,9-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
10
GLILCLWSK
405.000
401.

2
254
VMFQHLMQK
300.000
402.

3
63
KLLKYEDCK
270.000
403.

4
214
QMYNLLLSY
60.000
404.

5
607
KLPRCLWPR
54.000
405.

6
292
LLELIITTK
45.000
406.

7
624
GLGDRWFLR
36.000
407.

8
484
KMIFGDLMR
36.000
408.

9
529
ALFSTFELF
30.000
409.

10
131
NLVRALLAR
18.000
410.

11
602
VMLERKLPR
18.000
411.

12
476
GPFTIMIQK
13.500
412.

13
331
MLGAIYLLY
12.000
413.

14
318
SLKWKRYGR
12.000
414.

15
576
AMMGDTHWR
9.000
415.

16
496
LMAVVILGF
9.000
416.

17
697
RLRQGTLRR
8.000
417.

18
400
LLVEVPDIF
6.750
418.

19
330
CMLGAIYLL
6.075
419.

20
678
SLPMPSVSR
6.000
420.

21
377
YMTPKDDIR
6.000
421.

22
658
DLDKDSVEK
6.000
422.

23
315
ELVSLKWKR
5.400
423.

24
474
MLGPFTIMI
5.400
424.

25
436
VLVTMVMRL
5.400
425.

26
553
FMYSITYAA
4.500
426.

27
485
MIFGDLMRF
4.500
427.

28
337
LLYIICFTM
4.500
428.

29
420
ILGGPFHVL
4.050
429.

30
501
ILGFASAFY
4.000
430.

31
459
VLGWCNVMY
4.000
431.

32
194
SLGNTVLHI
3.600
432.

33
306
QILDQTPVK
3.000
433.

34
201
HILILQPNK
3.000
434.

35
14
CLWSKFCRW
3.000
435.

36
399
ILLVEVPDI
2.700
436.

37
373
LQEAYMTPK
2.700
437.

38
638
DLNRQRIQR
2.400
438.

39
347
CIYRPLKPR
2.250
439.

40
473
QMLGPFTIM
2.025
440.

41
567
TLLMLNLLI
1.800
441.

42
77
AMGETALHI
1.800
442.

43
87
ALYDNLEAA
1.500
443.

44
599
ATTVMLERK
1.500
444.

45
500
VILGFASAF
1.350
445.

46
97
VLMEAAPEL
1.350
446.

47
113
ELYEGQTAL
1.350
447.

48
532
STFELFLTI
1.350
448.

49
181
LLIEHGADI
1.350
449.

50
426
HVLIITYAF
1.350
450.

[0858]

25

TABLE IX(B)

HLA Peptide Scoring Results-CaTrF2E11-A3,9-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule Containing

Rank
Position
Listing
This Subsequence)
SEQ ID NO:

1
436
KMYDLLLLK
900.000
451.

2
614
VLFFFTNIK
300.000
452.

3
696
IMIQKILFK
90.000
453.

4
692
GTYSIMIQK
67.500
454.

5
198
SLFDYGTYR
60.000
455.

6
609
TLFTGVLFF
60.000
456.

7
705
DLFRFLLVY
54.000
457.

8
701
ILFKDLFRF
45.000
458.

9
466
LMMAAKTGK
30.000
459.

10
727
LLNPCANMK
30.000
460.

11
261
LLPFLLTHK
30.000
461.

12
681
ALYFTRGLK
30.000
462.

13
395
YLTENPHKK
30.000
463.

14
549
ELLRDKWRK
27.000
464.

15
476
GIFQHIIRR
18.000
465.

16
260
GLLPFLLTH
12.150
466.

17
620
NIKDLFMKK
12.000
467.

18
678
WMNALYFTR
12.000
468.

19
759
STFLLDLFK
10.000
469.

20
885
GIINEDPGK
9.000
470.

21
838
RSFPVFLRK
6.750
471.

22
774
DLEMLSSTK
6.000
472.

23
333
ALHIAIERR
6.000
473.

24
239
KVFNRPILF
6.000
474.

25
290
ALLNLSNGR
6.000
475.

26
602
RLAGEVITL
5.400
476.

27
666
YLAMMVFAL
5.400
477.

28
668
AMMVFALVL
5.400
478.

29
643
LLYFIYSVL
4.500
479.

30
716
FMIGYASAL
4.050
480.

31
710
LLVYLLFMI
4.050
481.

32
642
QLLYFIYSV
4.050
482.

33
675
VLGWMNALY
4.000
483.

34
160
RMKLFQGAFR
4.000
484.

35
762
LLDLFKLTI
3.600
485.

36
700
KILFKDLFR
3.600
486.

37
462
GLSPLMMAA
2.700
487.

38
709
FLLVYLLFM
2.700
488.

39
801
LLLNMLIAL
2.700
489.

40
613
GVLFFFTNI
2.430
490.

41
575
VIFTLTAYY
2.000
491.

42
281
STGKTCLPK
2.000
492.

43
657
ALYLAGIEA
2.000
493.

44
286
CLPKALLNL
1.800
494.

45
578
TLTAYYQPL
1.800
495.

46
826
KLQWATTIL
1.800
496.

47
439
DLLLLKCAR
1.800
497.

48
789
ILLVTYIIL
1.800
498.

49
573
AMVIFTLTA
1.800
499.

50
790
LLVTYIILT
1.350
500.

[0859]

26

TABLE X(A)

HLA Peptide Scoring Results-83P2H3-A3,10-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
372
LLQEAYMTPK
135.000
501.

2
291
SLLELIITTK
101.250
502.

3
344
TMCCIYRPLK
60.000
503.

4
714
GLEDGESWEY
36.000
504.

5
292
LLELIITTKK
30.000
505.

6
254
VMFQHLMQKR
30.000
506.

7
400
LLVEVPDIFR
27.000
507.

8
330
CMLGAIYLLY
27.000
508.

9
484
KMIFGDLMRF
27.000
509.

10
529
ALFSTFELFL
18.000
510.

11
495
WLMAVVILGF
13.500
511.

12
459
VLGWCNVMYF
12.000
512.

13
12
ILCLWSKFCR
12.000
513.

14
624
GLGDRWFLRV
10.800
514.

15
553
FMYSITYAAF
10.000
515.

16
253
TVMIFQHLMQK
9.000
516.

17
10
GLILCLWSKF
9.000
517.

18
131
NLVRALLARR
9.000
518.

19
334
AIYLLYIICF
9.000
519.

20
181
LLIEHGADIR
9.000
520.

21
434
FMVLVTMVMR
9.000
521.

22
473
QMLGPFTIMI
8.100
522.

23
550
DLPFMYSITY
7.200
523.

24
98
LMEAAPELVF
6.000
524.

25
331
MLGAIYLLYI
5.400
525.

26
399
ILLVEVPDIF
4.500
526.

27
385
RLVGELVTVI
4.050
527.

28
652
HTRGSEDLDK
3.000
528.

29
337
LLYIICFTMC
3.000
529.

30
465
VMYFARGFQM
3.000
530.

31
14
CLWSKFCRWF
3.000
531.

32
420
ILGGPFHVLI
2.700
532.

33
427
VLIITYAFMV
2.700
533.

34
202
ILILQPNKTF
2.250
534.

35
209
KTFACQMYNL
2.025
535.

36
501
ILGFASAFYI
1.800
536.

37
490
LMRFCWLMAV
1.800
537.

38
423
GPFHVLIITY
1.800
538.

39
638
DLNRQRIQRY
1.800
539.

40
597
IVATTVMLER
1.800
540.

41
377
YMTPKDDIRL
1.800
541.

42
336
YLLYIICFTM
1.350
542.

43
240
GLTPFKLAGV
1.350
543.

44
194
SLGNTVLHIL
1.350
544.

45
576
AMMGDTHWRV
1.350
545.

46
307
ILDQTPVKEL
1.350
546.

47
601
TVMLERKLPR
1.200
547.

48
4
SLPKEKGLIL
1.200
548.

49
57
DVQALNKLLK
1.200
549.

50
532
STFELFLTII
1.012
550.

[0860]

27

TABLE X(B)

HLA Peptide Scoring Results-CaTrF2E11-A3,10-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Dissassociation of a Molecule Containing

Rank
Position
Listing
This Subsequence)
SEQ ID NO.

1
260
GLLPFLLTHK
202.500
551.

2
462
GLSPLMMAAK
135.000
552.

3
609
TLFTGVLFFF
67.500
553.

4
160
RMKFQGAFRK
60.000
554.

5
657
ALYLAGIEAY
30.000
555.

6
525
VLEILVYNSK
30.000
556.

7
726
SLLNPCANMK
30.000
557.

8
613
GVLFFFTNIK
27.000
558.

9
261
LLPFLLTHKK
20.000
559.

10
73
CLTPLSFPCR
18.000
560.

11
711
LVYLLFMIGY
18.000
561.

12
689
KLTGTYSIMI
16.200
562.

13
634
SLFIDGSFQL
9.000
563.

14
573
AMVIFTLTAY
9.000
564.

15
695
SIMIQKILFK
9.000
565.

16
436
KMYDLLLLKC
9.000
566.

17
602
RLAGEVITLF
6.750
567.

18
63
FLEPPPLAGF
6.750
568.

19
681
ALYFTRGLKL
6.000
569.

20
419
ALVAIADNTR
6.000
570.

21
650
VLVIVSAALY
6.000
571.

22
917
VVPRVVELNK
6.000
572.

23
761
FLLDLFKLTI
5.400
573.

24
687
GLKLTGTYSI
5.400
574.

25
314
NMREFINSPF
4.500
575.

26
618
FTNIKDLFMK
4.500
576.

27
570
YLCAMVIFTL
4.050
577.

28
709
FLLVYLLFMI
4.050
578.

29
673
ALVLGWMNAL
4.050
579.

30
700
KILFKDLFRF
4.050
580.

31
675
VLGWMNALYF
4.000
581.

32
92
GMADSSEGPR
3.600
582.

33
636
FIDGSFQLLY
3.600
583.

34
219
IIEKQPQSPK
3.000
584.

35
643
LLYFIYSVLV
3.000
585.

36
529
LVYNSKIENR
3.000
586.

37
785
VVFIILLVTY
3.000
587.

38
447
RLFPDSNLEA
3.000
588.

39
465
PLMMAAKTGK
3.000
589.

40
198
SLFDYGTYRH
3.000
590.

41
800
VLLLNMLIAL
2.700
591.

42
359
QARGRFFQPK
2.700
592.

43
585
PLEGTPPYPY
2.700
593.

44
474
KIGIFQHIIR
2.400
594.

45
813
TVGQVSKESK
2.000
595.

46
158
NLRMKFQGAF
1.800
596.

47
669
MMVFALVLGW
1.800
597.

48
54
LLLVHVGGGF
1.350
598.

49
541
MLAVEPINEL
1.350
599.

50
789
ILLVTYIILT
1.350
600.

[0861]

28

TABLE XI(A)

HLA Peptide Scoring Results-83P2H3-A11,9-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Dissassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
10
GLILCLWSK
3.600
601.

2
476
GPFTIMIQK
2.400
602.

3
63
KLLKYEDCK
1.800
603.

4
254
VMFQHLMQK
1.600
604.

5
58
VQALNKLLK
1.200
605.

6
599
ATTVMLERK
1.000
606.

7
172
CVNSEEIVR
0.800
607.

8
401
LVEVIPDIFR
0.800
608.

9
624
GLGDRWFLR
0.720
609.

10
484
KMIFGDLMR
0.720
610.

11
306
QILDQTPVK
0.600
611.

12
201
HILILQPNK
0.600
612.

13
435
MVLVTMVMR
0.600
613.

14
355
RTNNRTSPR
0.600
614.

15
373
LQEAYMTPK
0.600
615.

16
607
KLPRCLWPR
0.480
616.

17
697
RLRQGTLRR
0.480
617.

18
292
LLELIITTK
0.400
618.

19
132
LVRALLARR
0.400
619.

20
146
RATGTAFRR
0.360
620.

21
256
FQHLMQKRK
0.300
621.

22
602
VMLERKLPR
0.240
622.

23
646
RYAQAFHTR
0.240
623.

24
131
NLVRALLAR
0.240
624.

25
345
MCCIYRPLK
0.200
625.

26
297
ITTKKREAR
0.200
626.

27
312
PVKELVSLK
0.200
627.

28
13
LCLWSKFCR
0.180
628.

29
576
AMMGDTHWR
0.160
629.

30
318
SLKWKRYGR
0.160
630.

31
314
KELVSLKWK
0.135
631.

32
658
DLDKDSVEK
0.120
632.

33
462
WCNVMYFAR
0.120
633.

34
18
KFCRWFQRR
0.120
634.

35
293
LELIITTKK
0.090
635.

36
347
CIYRPLKPR
0.080
636.

37
598
VATTVMLER
0.080
637.

38
678
SLPMPSVSR
0.080
638.

39
342
CFTMCCIYR
0.080
639.

40
182
LIEHGADIR
0.080
640.

41
377
YMTPKDDIR
0.080
641.

42
315
ELVSLKWKR
0.072
642.

43
363
RDNTLLQQK
0.060
643.

44
426
HVLIITYAF
0.060
644.

45
392
TVIGAIIIL
0.060
645.

46
584
RVAHERDEL
0.060
646.

47
124
AVVNQNMNL
0.060
647.

48
248
GVEGNTVMF
0.060
648.

49
406
DIFRMGVTR
0.048
649.

50
638
DLNRQRIQR
0.048
650.

[0862]

29

TABLE XI(B)

HLA Peptide Scoring Results-CaTrF2E11-A11,9-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
692
GTYSIMIQK
12.000
651.

2
436
KMYDLLLLK
4.800
652.

3
759
STFLLDLFK
4.000
653.

4
281
STGKTCLPK
2.000
654.

5
885
GIINEDPGK
1.800
655.

6
696
IMIQKILFK
1.200
656.

7
476
GIFQHIIRR
0.960
657.

8
620
NIKIDLFMKK
0.800
658.

9
681
ALYFTRGLK
0.800
659.

10
614
VLFFFTNIK
0.800
660.

1
466
LMMAAKTGK
0.800
661.

12
700
KILFKDLFR
0.720
662.

3
394
NYLTENPHK
0.600
663.

14
727
LLNPCANMK
0.400
664.

15
395
YLTENPHKK
0.400
665.

16
420
LVAIADNTR
0.400
666.

17
745
TVPTYPSCR
0.400
667.

18
918
VPRVVELNK
0.400
668.

19
231
APQPPPILK
0.400
669.

20
830
ATTILDIER
0.400
670.

21
261
LLPFLLTHK
0.400
671.

22
262
LPFLLTHKK
0.400
672.

23
549
ELLRDKWRK
0.360
673.

24
41
PVITTVALK
0.300
674.

25
838
RSFPVFLRK
0.240
675.

26
160
RMKFQGAFR
0.240
676.

27
678
WMNALYFTR
0.240
677.

28
239
KVFNRPILF
0.240
678.

29
74
LTPLSFPCR
0.200
679.

30
619
TNIKDLFMK
0.180
680.

31
428
RENTKFVTK
0.180
681.

32
811
GETVGQVSK
0.180
682.

33
321
SPFRDIYYR
0.160
683.

34
198
SLFDYGTYR
0.160
684.

35
161
MKFQGAFRK
0.120
685.

36
214
RWRKKIIEK
0.120
686.

37
148
RPAGPGDGR
0.120
687.

38
8
GANLCFQVR
0.120
688.

39
871
RVDEVNWSH
0.120
689.

40
774
DLEMLSSTK
0.120
690.

41
332
TALHIAIER
0.120
691.

42
290
ALLNLSNGR
0.120
692.

43
353
GADVHAQAR
0.120
693.

44
3
RVVGPGANL
0.090
694.

45
613
GVLFFFTNI
0.090
695.

46
526
LEILVYNSK
0.090
696.

47
670
MVFALVLGW
0.080
697.

48
333
ALHIAIERR
0.080
698.

49
530
VYNSKIENR
0.080
699.

50
841
PVFLRKAFR
0.080
700.

[0863]

30

TABLE XII(A)

HLA Peptide Scoring Results—83P2H3—A11, 10-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
253
TVMFQHLMQK
8.000
701.

2
305
RQILDQTPVK
2.700
702.

3
632
RVEDRQDLNR
2.400
703.

4
652
HTRGSEDLDK
2.000
704.

5
601
TVMLERKLPR
1.600
705.

6
57
DVQALNKLLK
1.200
706.

7
597
IVATTVMLER
0.800
707.

8
125
VVNQNMNLVR
0.800
708.

9
291
SLLELIITTK
0.600
709.

10
292
LLELIITTKK
0.400
710.

11
344
TMCCIYRPLK
0.400
711.

12
372
LLQEAYMTPK
0.400
712.

13
699
RQGTLRRDLR
0.360
713.

14
311
TPVKELVSLK
0.300
714.

15
66
KYEDCKVHQR
0.240
715.

16
12
ILCLWSKFCR
0.240
716.

17
400
LLVEVPDIFR
0.240
717.

18
598
VATTVMLERK
0.200
718.

19
9
KGLILCLWSK
0.180
719.

20
350
RPLKPRTNNR
0.180
720.

21
341
ICFTMCCIYR
0.160
721.

22
215
MYNLLLSYDR
0.160
722.

23
376
AYMTPKDDIR
0.160
723.

24
254
VMFQHLMQKR
0.160
724.

25
54
KDNDVQALNK
0.120
725.

26
131
NLVRALLARR
0.120
726.

27
181
LLIEHGADIR
0.120
727.

28
434
FMVLVTMVMR
0.120
728.

29
209
KTFACQMYNL
0.120
729.

30
171
ACVNSEEIVR
0.120
730.

31
314
KELVSLKWKR
0.108
731.

32
255
MFQHLMQKRK
0.100
732.

33
575
IAMMGDTHWR
0.080
733.

34
296
IITTKKREAR
0.080
734.

35
585
VAHERDELWR
0.080
745.

36
33
RDEQNLLQQK
0.060
736.

37
392
TVIGAIIILL
0.060
747.

38
580
DTHWRVAHER
0.060
738.

39
584
RVAHERDELW
0.060
739.

40
411
GVTRFFGQTI
0.060
740.

41
401
LVEVPDIFRM
0.060
741.

42
45
WESPLLLAAK
0.060
742.

43
435
MVLVTMVMRL
0.060
743.

44
43
RIWESPLLLA
0.048
744.

45
418
QTILGGPFHV
0.045
745.

46
681
MPSVSRSTSR
0.040
746.

47
137
LARRASVSAR
0.040
747.

48
144
SARATGTAFR
0.040
748.

49
390
LVTVIGAIII
0.040
749.

50
451
VVPMSFALVL
0.040
750.

[0864]

31

TABLE XII(B)

HLA Peptide Scoring Results—CaTrF2E11—A11, 10-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
613
GVLFFFTNIK
9.000
751.

2
917
VVPRVVELNK
4.000
752.

3
160
RMKFQGAFRK
3.600
753.

4
618
FTNIKDLFMK
3.000
754.

5
813
TVGQVSKESK
2.000
755.

6
260
GLLPFLLTHK
1.800
756.

7
695
SIMIQKILFK
1.600
756.

8
462
GLSPLMMAAK
1.200
758.

9
529
LVYNSKIENR
0.800
759.

10
543
AVEPINELLR
0.800
760.

11
726
SLLNPCANMK
0.600
761.

12
862
GTPDRRWCFR
0.600
762.

13
394
NYLTENPHKK
0.600
763.

14
474
KIGIFQHIIR
0.480
764.

15
331
QTALHIAIER
0.400
765.

16
204
TYRHHSSDNK
0.400
766.

17
525
VLEILVYNSK
0.400
767.

18
219
IIEKQPQSPK
0.400
768.

19
261
LLPFLLTHKK
0.400
769.

20
40
APVITTVALK
0.300
770.

21
744
CTVPTYPSCR
0.300
771.

22
680
NALYFTRGLK
0.300
772.

23
213
KRWRKKIIEK
0.240
773.

24
92
GMADSSEGPR
0.240
774.

25
359
QARGRFFQPK
0.200
775.

26
423
IADNTRENTK
0.200
776.

27
289
KALLNLSNGR
0.180
777.

28
243
RPILFDIVSR
0.180
778.

29
548
NELLRDKWRK
0.180
779.

30
490
DTRHLSRKSK
0.150
780.

31
619
TNIKDLFMKK
0.120
781.

32
403
KADMRRQDSR
0.120
782.

33
419
ALVAIADNTR
0.120
783.

34
151
GPGDGRPNLR
0.120
784.

35
773
GDLEMLSSTK
0.090
785.

36
116
GTPGGEAFPL
0.090
786.

37
471
KTGKIGIFQH
0.090
787.

38
899
YYGFSHTVGR
0.080
788.

39
399
NPHKKADMRR
0.080
789.

40
465
PLMMAAKTGK
0.080
790.

41
829
WATTILDIER
0.080
791.

42
435
TKMYDLLLLK
0.080
792.

43
393
VNYLTENPHK
0.080
793.

44
73
CLTPLSFPCR
0.080
794.

45
711
LVYLLFMIGY
0.080
795.

46
677
GWMNALYFTR
0.072
796.

47
849
RSGEMVTVGK
0.060
797.

48
759
STFLLDLFKL
0.060
798.

49
840
FPVFLRKAFR
0.060
799.

50
692
GTYSIMIQKI
0.060
800.

[0865]

32

TABLE XIII(A)

HLA Peptide Scoring Results—83P2H3—A24, 9-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
269
TYGPLTSTL
288.000
801.

2
221
SYDRHGDHL
200.000
802.

3
335
IYLLYIICF
150.000
803.

4
554
MYSITYAAF
100.000
804.

5
622
EYGLGDRWF
100.000
805.

6
523
FYDYPMALF
100.000
806

7
376
AYMTPKDDI
75.000
807.

8
323
RYGRPYFCM
50.000
808.

9
106
VFEPMTSEL
39.600
809.

0
546
NYNVDLPFM
37.500
810.

1
88
LYDNLEAAM
30.000
811.

2
467
YFARGFQML
28.800
812.

3
561
AFAIIATLL
28.000
813.

14
466
MYFARGFQM
25.000
814.

15
522
HFYDYPMAL
24.000
815.

16
530
LFSTFELFL
20.000
816.

17
151
AFRRSPCNL
20.000
817.

18
210
TFACQMYNL
20.000
818.

19
161
YFGEHPLSF
12.000
819.

20
359
RTSPRDNTL
11.520
820.

21
174
NSEEIVRLL
10.080
821.

22
407
IFRMGVTRF
10.000
822.

23
699
RQGTLRRDL
9.600
823.

24
43
RIWESPLLL
9.600
824.

25
338
LYIICFTMC
9.000
825.

26
584
RVAHERDEL
8.800
826.

27
233
DLVPNHQGL
8.640
827.

28
195
LGNTVLHIL
8.400
828.

29
129
NMNLVRALL
8.400
829.

30
75
RGAMGETAL
8.000
830.

31
690
RSSANWERL
8.000
831.

32
97
VLMEAAPEL
7.920
832.

33
600
TTVMLERKL
7.920
833.

34
525
DYPMALFST
7.500
834.

35
533
TFELFLTII
7.500
835.

36
128
QNMNLVRAL
7.200
836.

37
3
LSLPKEKGL
7.200
837.

38
450
EVVPMSFAL
7.200
838.

39
90
DNLEAAMVL
7.200
839.

40
643
RIQRYAQAF
7.200
840.

41
566
ATLLMLNLL
7.200
841.

42
348
IYRPLKPRT
7.200
842.

43
57
DVQALNKLL
7.200
843.

44
482
IQKMIFGDL
6.720
844.

45
528
MALFSTFEL
6.600
845.

46
364
DNTLLQQKL
6.336
846.

47
563
AIIATLLML
6.000
847.

48
197
NTVLHILIL
6.000
848.

49
329
FCMLGAIYL
6.000
849.

50
596
QIVATTVML
6.000
850.

[0866]

33

TABLE XIII(B)

HLA Peptide Scoring Results—CaTrF2E11—A24, 9-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
782
KYPVVFIIL
1008.000
851.

2
563
FYINVVSYL
420.000
852.

3
793
TYIILTSVL
360.000
853.

4
502
AYGPVYSSL
336.000
854.

5
682
LYFTRGLKL
220.000
855.

6
719
GYASALVSL
200.000
856.

7
326
IYYRGQTAL
200.000
857.

8
569
SYLCAMVIF
150.000
858.

9
693
TYSIMIQKI
66.000
859.

10
432
KLVTKMYDL
60.000
860.

11
708
RFLLVYLLF
42.000
861.

12
635
LFIDGSFQL
36.000
862.

13
702
LFKDLFRFL
34.560
863.

14
760
TFLLDLFKL
33.000
864.

15
131
LFEGEDGSL
30.000
865.

16
375
YFGELPLSL
28.800
866.

17
706
LFRFLLVYL
24.000
867.

18
757
TFSTFLLDL
20.000
868.

19
373
YFYFGELPL
20.000
869.

20
593
PYRTTVDYL
20.000
870.

21
901
GFSHTVGRL
20.000
871.

22
616
FFFTNIKDL
20.000
872.

23
412
RGNTVLHAL
16.800
873.

24
169
KGVPNPIDL
14.400
874.

25
617
FFTNIKDLF
14.000
875.

26
610
LFTGVLFFF
14.000
876.

27
557
KFGAVSFYI
14.000
877.

28
826
KLQWATTIL
12.000
878.

29
3
RVVGPGANL
12.000
879.

30
534
KIENRHEML
12.000
880.

31
298
RNDTIPVLL
11.200
881.

32
543
AVEPINELL
10.080
882.

33
388
NQPHIVNYL
10.080
883.

34
71
GFCLTPLSF
10.000
884.

35
599
DYLRLAGEV
9.900
885.

36
542
LAVEPINEL
9.504
886.

37
798
TSVLLLNML
8.640
887.

38
694
YSIMIQKIL
8.400
888.

39
650
VLVIVSAAL
8.400
889.

40
628
KCPGVNSLF
8.400
890.

41
284
KTCLPKALL
8.000
891.

42
767
KLTIGMGDL
8.000
892.

43
341
RCKHYVELL
8.000
893.

44
955
KWRTDDAPL
8.000
894.

45
602
RLAGEVITL
8.000
895.

46
18
RGSCCSSRL
8.000
896.

47
595
RTTVDYLRL
8.000
897.

48
916
SVVPRVVEL
7.920
898.

49
645
YFIYSVLVI
7.500
899.

50
665
AYLAMMVFA
7.500
900.

[0867]

34

TABLE XIV(A)

HLA Peptide Scoring Results—83P2H3—A24, 10-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
323
RYGRPYFCML
480.000
901.

2
466
MYFARGFQML
288.000
902.

3
525
DYPMALFSTF
216.000
903.

4
622
EYGLGDRWFL
200.000
904.

5
160
IYFGEHPLSF
100.000
905.

6
114
LYEGQTALHI
75.000
906.

7
431
TYAFMVLVTM
35.000
907.

8
511
IFQTEDPEEL
33.000
908.

9
210
TFACQMYNLL
24.000
909.

10
650
AFHTRGSEDL
20.000
910.

11
328
YFCMLGAIYL
20.000
911.

12
407
IFRMGVTRFF
14.000
912.

13
522
HFYDYPMALF
12.000
913.

14
335
IYLLYIICFT
10.500
914.

15
481
MIQKMIFGDL
10.080
915.

16
492
RFCWLMAVVI
10.000
916.

17
503
GFASAFYIIF
10.000
917.

18
359
RTSPRDNTLL
9.600
918.

19
546
NYNVDLPFMY
9.000
919.

20
250
EGNTVMFQHL
8.640
920.

21
392
TVIGAIIILL
8.400
921.

22
343
FTMCCIYRPL
8.400
922.

23
128
QNMNLVRALL
8.400
923.

24
209
KTFACQMYNL
8.000
924.

25
338
LYIICFTMCC
7.500
925.

26
471
GFQMLGPFTI
7.500
926.

27
603
MLERKLPRCL
7.200
927.

28
419
TILGGPFHVL
7.200
928.

29
29
WAQSRDEQNL
7.200
929.

30
428
LIITYAFMVL
7.200
930.

31
127
NQNMNLVRAL
7.200
931.

32
173
VNSEEIVRLL
6.720
932.

33
96
MVLMEAAPEL
6.600
933.

34
348
IYRPLKPRTN
6.000
934.

35
391
VTVIGAIIIL
6.000
935.

36
4
SLPKEKGLIL
6.000
936.

37
542
DGPANYNVDL
6.000
937.

38
329
FCMLGAIYLL
6.000
938.

39
670
GCPFSPHLSL
6.000
939.

40
562
FAIIATLLML
6.000
940.

41
271
GPLTSTLYDL
6.000
941.

42
694
NWERLRQGTL
6.000
942.

43
616
SGICGREYGL
6.000
943.

44
484
KMIFGDLMRF
6.000
944.

45
435
MVLVTMVMRL
6.000
945.

46
151
AFRRSPCNLI
6.000
946.

47
310
QTPVKELVSL
6.000
947.

48
158
NLIYFGEHPL
6.000
948.

49
595
AQIVATTVML
6.000
949.

50
123
IAVVNQNMNL
6.000
950.

[0868]

35

TABLE XIV(B)

HLA Peptide Scoring Results—CaTrF2E11—A24, 10-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
782
KYPVVFIILL
600.000
1

2
658
LYLAGIEAYL
420.000
2

3
665
AYLAMMVFAL
300.000
3

4
793
TYIILTSVLL
300.000
4

5
693
TYSIMIQKIL
280.000
5

6
719
GYASALVSLL
240.000
6

7
374
FYFGELPLSL
240.000
7

8
372
GYFYFGELPL
200.000
8

9
599
DYLRLAGEVI
75.000
9

10
432
KFVTKMYDLL
60.000
10

11
635
LFIDGSFQLL
51.840
11

12
644
LYFIYSVLVI
50.000
12

13
327
YYRGQTALHI
50.000
13

14
122
AFPLSSLANL
30.000
14

15
715
LFMIGYASAL
30.000
15

16
562
SFYINVVSYL
28.000
16

17
702
LFKDLFRFLL
24.000
17

18
706
LFRFLLVYLL
24.000
18

19
615
LFFFTNIKDL
20.000
19

20
839
SFPVFLRKAF
18.000
20

21
169
KGVPNPIDLL
14.400
21

22
616
FFFTNIKDLF
14.000
22

23
387
TNQPHIVNYL
12.096
23

24
757
TFSTFLLDLF
12.000
24

25
101
RAGPGEVAEL
10.560
25

26
240
VFNRPILFDI
10.500
26

27
563
FYINVVSYLC
10.500
27

28
542
LAVEPINELL
10.080
28

29
928
SNPDEVVVPL
10.080
29

30
786
VFIILLVTYI
9.000
30

31
896
TYQYYGFSHT
9.000
31

32
317
EFINSPFRDI
9.000
32

33
173
NPIDLLESTL
8.640
33

34
697
MIQKILFKDL
8.640
34

35
166
AFRKGVPNPI
8.400
35

36
649
SVLVIVSAAL
8.400
36

37
642
QLLYFIYSVL
8.400
37

38
748
TYPSCRDSET
8.250
38

39
408
RQDSRGNTVL
8.000
39

40
252
RGSTADLDGL
8.000
40

41
712
VYLLFMIGYA
7.500
41

42
569
SYLCAMVIFT
7.500
42

43
708
RFLLVYLLFM
7.500
43

44
285
TCLPKALLNL
7.200
44

45
673
ALVLGWMNAL
7.200
45

46
577
FTLTAYYQPL
7.200
46

47
46
VALKQLAALL
7.200
47

48
65
EPPPLAGFCL
7.200
48

49
647
IYSVLVIVSA
7.000
49

50
915
SSVVPRVVEL
6.600
50

[0869]

36

TABLE XV(A)

HLA Peptide Scoring Results—83P2H3—B7, 9-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
452
VPMSFALVL
240.000
951.

2
671
CPFSPHLSL
120.000
952.

3
5
LPKEKGLIL
80.000
953.

4
311
TPVKELVSL
80.000
954.

5
543
GPANYNVDL
80.000
955.

6
124
AVVNQNMNL
60.000
956.

7
324
YGRPYFCML
40.000
957.

8
31
QSRDEQNLL
40.000
958.

9
560
AAFAIIATL
36.000
959.

10
584
RVAHERDEL
30.000
960.

11
450
EVVPMSFAL
20.000
961.

12
57
DVQALNKLL
20.000
962.

13
392
TVIGAIIIL
20.000
963.

14
102
APELVFEPM
18.000
964.

15
151
AFRRSPCNL
12.000
965.

16
528
MALFSTFEL
12.000
966.

17
128
QNMNLVRAL
12.000
967.

18
566
ATLLMLNLL
12.000
968.

19
211
FACQMYNLL
12.000
969.

20
565
IATLLMLNL
12.000
970.

21
212
ACQMYNLLL
12.000
971.

22
329
FCMLGAIYL
12.000
972.

23
97
VLMEAAPEL
12.000
973.

24
30
AQSRDEQNL
12.000
974.

25
563
AIIATLLML
12.000
975.

26
699
RQGTLRRDL
6.000
976.

27
623
YGLGDRWFL
6.000
977.

28
420
ILGGPFHVL
6.000
978.

29
300
KKREARQIL
6.000
979.

30
129
NMNLVRALL
6.000
980.

31
458
LVLGWCNVM
5.000
981.

32
690
RSSANWERL
4.000
982.

33
702
TLRRDLRGI
4.000
983.

34
364
DNTLLQQKL
4.000
984.

35
284
DSSGDEQSL
4.000
985.

36
165
HPLSFAACV
4.000
986.

37
353
KPRTNNRTS
4.000
987.

38
3
LSLPKEKGL
4.000
988.

39
379
TPKDDIRLV
4.000
989.

40
330
CMLGAIYLL
4.000
990.

41
197
NTVLHILIL
4.000
991.

42
436
VLVTMVMRL
4.000
992.

43
378
MTPKDDIRL
4.000
993.

44
285
SSGDEQSLL
4.000
994.

45
75
RGAMGETAL
4.000
995.

46
195
LGNTVLHIL
4.000
996.

47
80
ETALHIAAL
4.000
997.

48
617
GICGREYGL
4.000
998.

49
113
ELYEGQTAL
4.000
999.

50
596
QIVATTVML
4.000
1000.

[0870]

37

TABLE XV(B)

HLA Peptide Scoring Results—CaTrF2E11—B7, 9-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence
SEQ ID NO:

1
40
APVITTVAL
240.000
1001.

2
151
GPGDGRPNL
120.000
1002.

3
123
FPLSSLANL
80.000
1003.

4
783
YPVVPIILL
80.000
1004.

5
117
TPGGEAFPL
80.000
1005.

6
75
TPLSFPCRL
80.000
1006.

7
279
EPSTGKTCL
80.000
1007.

8
99
GPRAGPGEV
40.000
1008.

9
250
VSRGSTADL
40.000
1009.

10
668
AMMVFALVL
36.000
1010.

11
170
GVPNPIDLL
30.000
1011.

12
3
RVVGPGANL
30.000
1012.

13
229
APAPQPPPI
24.000
1013.

14
929
NPDEVVVPL
24.000
1014.

15
674
LVLGWMNAL
20.000
1015.

16
916
SVVPRVVEL
20.000
1016.

17
433
FVTKMYDLL
20.000
1017.

18
188
VPGPKKAPM
20.000
1018.

19
1
MPRVVGPGA
20.000
1019.

20
56
LVHVGGGFL
20.000
1020.

21
542
LAVEPINEL
18.000
1021.

22
543
AVEPINELL
18.000
1022.

23
455
EAVLNNDGL
12.000
1023.

24
46
VALKQLAAL
12.000
1024.

25
770
IGMGDLEML
12.000
1025.

26
680
NALYFTRGL
12.000
1026.

27
69
LAGFCLTPL
12.000
1027.

28
47
ALKQLAALL
12.000
1028.

29
102
AGPGEVAEL
12.000
1029.

30
720
YASALVSLL
12.000
1030.

31
629
CPGVNSLFI
8.000
1031.

32
66
PPPLAGFCL
8.000
1032.

33
932
EVVVPLDSM
7.500
1033.

34
284
KTCLPKALL
6.000
1034.

35
20
SCCSSRLRL
6.000
1035.

36
14
QVRERGSCC
5.000
1036.

37
566
NVVSYLCAM
5.000
1037.

38
706
LFRFLLVYL
4.000
1038.

39
694
YSIMIQKIL
4.000
1039.

40
600
YLRLAGEVI
4.000
1040.

41
371
GGYFYFGEL
4.000
1041.

42
440
LLLLKCARL
4.000
1042.

43
795
IILTSVLLL
4.000
1043.

44
716
FMIGYASAL
4.000
1044.

45
650
VLVIVSAAL
4.000
1045.

46
607
VITLFTGVL
4.000
1046.

47
43
ITTVALKQL
4.000
1047.

48
434
VTKMYDLLL
4.000
1048.

49
578
TLTAYYQPL
4.000
1049.

50
61
GGFLEPPPL
4.000
1050.

[0871]

38

TABLE XVI(A)

HLA Peptide Scoring Results—83P2H3—B7, 10-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:+HZ,1/47

+TA,11
271
GPLTSTLYDL
80.000
1051.

2
630
FLRVEDRQDL
60.000
1052.

3
706
DLRGIINRGL
40.000
1053.

4
412
VTRFFGQTIL
40.000
1054.

5
52
AAKDNDVQAL
36.000
1055.

6
560
AAFAIIATLL
36.000
1056.

7
451
VVPMSFALVL
20.000
1057.

8
476
GPFTIMIQKM
20.000
1058.

9
96
MVLMEAAPEL
20.000
1059.

10
172
CVNSEEIVRL
20.000
1060.

11
392
TVIGAIIILL
20.000
1061.

12
105
LVFEPMTSEL
20.000
1062.

13
206
QPNKTFACQM
20.000
1063.

14
435
MVLVTMVMRL
20.000
1064.

15
128
QNMNLVRALL
18.000
1065.

16
559
YAAFAIIATL
12.000
1066.

17
329
FCMLGAIYLL
12.000
1067.

18
29
WAQSRDEQNL
12.000
1068.

19
562
FAIIATLLML
12.000
1069.

20
150
TAFRRSPCNL
12.000
1070.

21
599
ATTVMLERKL
12.000
1071.

22
30
AQSRDEQNLL
12.000
1072.

23
123
IAVVNQNMNL
12.000
1073.

24
595
AQIVATTVML
12.000
1074.

25
343
FTMCCIYRPL
12.000
1075.

26
565
IATLLMLNLL
12.000
1076.

27
211
FACQMYNLLL
12.000
1077.

28
529
ALFSTFELFL
12.000
1078.

29
101
AAPELVFEPM
9.000
1079.

30
326
RPYFCMLGAI
8.000
1080.

31
670
GCPFSPHLSL
6.000
1081.

32
702
TLRRDLRGII
6.000
1082.

33
679
LPMPSVSRST
6.000
1083.

34
419
TILGGPFHVL
6.000
1084.

35
132
LVRALLARRA
5.000
1085.

36
426
HVLIITYAFM
5.000
1086.

37
178
IVRLLIEHGA
5.000
1087.

38
472
FQMLGPFTIM
4.500
1088.

39
564
IIATLLMLNL
4.000
1089.

40
493
FCWLMAVVIL
4.000
1090.

41
4
SLPKEKGLIL
4.000
1091.

42
127
NQNMNLVRAL
4.000
1092.

43
616
SGICGREYGL
4.000
1093.

44
220
LSYDRHGDHL
4.000
1094.

45
310
QTPVKELVSL
4.000
1095.

46
359
RTSPRDNTLL
4.000
1096.

47
2
GLSLPKEKGL
4.000
1097.

48
364
DNTLLQQKLL
4.000
1098.

49
542
DGPANYNVDL
4.000
1099.

50
40
QQKRIWESPL
4.000
1100.

[0872]

39

TABLE XVI(B)

HLA Peptide Scoring Results—CaTrF2E11—B7, 10-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
229
APAPQPPPIL
360.000
1101.

2
445
CARLFPDSNL
180.000
1102.

3
190
GPKKAPMDSL
120.000
1103.

4
504
GPVYSSLYDL
80.000
1104.

5
592
YPYRTTVDYL
80.000
1105.

6
173
NIPDLLESTL
80.000
1106.

7
65
EPPPLAGFCL
80.000
1107.

8
296
NGRNDTIPVL
40.000
1108.

9
667
LAMMVFALVL
36.000
1109.

10
99
GPRAGPGEVA
30.000
1110.

11
449
FPDSNLEAVL
24.000
1111.

12
485
EVTDEDTRHL
20.000
1112.

13
433
FVTKMYDLLL
20.000
1113.

14
249
IVSRGSTADL
20.000
1114.

15
651
LVIVSAALYL
20.000
1115.

16
649
SVLVIVSAAL
20.000
1116.

17
45
TVALKQLAAL
20.000
1117.

18
952
YPRKWRTDDA
20.000
1118.

19
606
EVITLFTGVL
20.000
1119.

20
150
AGPGDGRPNL
18.000
1120.

21
231
APQPPPILKV
18.000
1121.

22
542
LAVEPINELL
12.000
1122.

23
39
CAPVITTVAL
12.000
1123.

24
46
VALKQLAALL
12.000
1124.

25
47
ALKQLAALLL
12.000
1125.

26
673
ALVLGWMNAL
12.000
1126.

27
101
RAGPGEVAEL
12.000
1127.

28
501
WAYGPVYSSL
12.000
1128.

29
681
ALYFTRGLKL
12.000
1129.

30
589
TPPYPYRTTV
6.000
1130.

31
541
MLAVEPINEL
6.000
1131.

32
19
GSCCSSRLRL
6.000
1132.

33
169
KGVPNPIDLL
6.000
1133.

34
237
ILKVFNRPIL
6.000
1134.

35
670
MVFALVLGWM
5.000
1135.

36
187
VVPGPKKAPM
5.000
1136.

37
718
IGYASALVSL
4.000
1137.

38
434
VTKMYDLLLL
4.000
1138.

39
1
MPRVVGPGAN
4.000
1139.

40
577
FTLTAYYQPL
4.000
1140.

41
252
RGSTADLDGL
4.000
1141.

42
900
YGFSHTVGRL
4.000
1142.

43
794
YIILTSVLLL
4.000
1143.

44
325
DIYYRGQTAL
4.000
1144.

45
759
STFLLDLFKL
4.000
1145.

46
570
YLCAMVIFTL
4.000
1146.

47
339
ERRCKHYVEL
4.000
1147.

48
55
LLVHVGGGFL
4.000
1148.

49
42
VITTVALKQL
4.000
1149.

50
253
GSTADLDGLL
4.000
1150.

[0873]

40

TABLE XVII(A)

HLA Peptide Scoring Results-83P2H3-B35,9-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
5
LPKEKGLIL
120.000
1151.

2
31
QSRDEQNLL
45.000
1152.

3
551
LPFMYSITY
40.000
1153.

4
379
TPKDDIRLV
36.000
1154.

5
311
TPVKELVSL
30.000
1155.

6
516
DPEELGHFY
24.000
1156.

7
452
TPMSFALVL
20.000
1157.

8
526
YPMALFSTF
20.000
1158.

9
615
RSGICGREY
20.000
1159.

10
671
CPFSPHLSL
20.000
1160.

11
543
GPANYNVDL
20.000
1161.

12
285
SSGDEQSLL
15.000
1162.

13
353
KPRTNNRTS
12.000
1163.

14
102
APELVFEPM
12.000
1164.

15
154
RSPCNLIYF
10.000
1165.

16
690
RSSANWERL
10.000
1166.

17
673
FSPHLSLPM
10.000
1167.

18
446
SASGEVVPM
9.000
1168.

19
144
SARATGTAF
9.000
1169.

20
284
DSSGDEQSL
7.500
1170.

21
360
TSPRDNTLL
7.500
1171.

22
608
LPRCLWPRS
6.000
1172.

23
369
QQKLLQEAY
6.000
1173.

24
81
TALHIAALY
6.000
1174.

25
639
LNRQRIQRY
6.000
1175.

26
59
QALNKLLKY
6.000
1176.

27
432
YAFMVLVTM
6.000
1177.

28
562
FAIIATLLM
6.000
1178.

29
3
LSLPKEKGL
5.000
1179.

30
547
YNYDLPFMY
4.000
1180.

31
326
RPYFCMLGA
4.000
1181.

32
165
HPLSFAACV
4.000
1182.

33
247
AGVEGNTVM
4.000
1183.

34
539
TIIDGPANY
4.000
1184.

35
43
RIWESPLLL
4.000
1185.

36
350
RPLKPRTNN
4.000
1186.

37
324
YGRPYFCML
3.000
1187.

38
173
VNSEEIVRL
3.000
1188.

39
713
RGLEDGESW
3.000
1189.

40
565
IATLLMLNL
3.000
1190.

41
585
VAHERDELW
3.000
1191.

42
174
NSEEIVRLL
3.000
1192.

43
528
MALFSTFEL
3.000
1193.

44
211
FACQMYNLL
3.000
1194.

45
482
IQKMIFGDL
3.000
1195.

46
512
FQTEDPEEL
3.000
1196.

47
560
AAFAIIATL
3.000
1197.

48
504
FASAFYIIF
3.000
1198.

49
584
RVAHERDEL
3.000
1199.

50
454
MSFALVLGW
2.500
1200.

[0874]

41

TABLE XVII(B)

HLA Peptide Scoring Results-CaTrF2E11-B35,9-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Dissociation of a Molecule Containing

Rank
Position
Listing
This Subsequence)
SEQ ID NO:

1
366
QPKDEGGYF
180.000
1201.

2
194
APMDSLFDY
80.000
1202.

3
584
QPLEGTPPY
80.000
1203.

4
188
VPGPKKAPM
40.000
1204.

5
151
GPGDGRPNL
40.000
1205.

6
592
YPYRTTVDY
40.000
1206.

7
117
TPGGEAFPL
30.000
1207.

8
783
YPVVFIILL
20.000
1208.

9
40
APVITTVAL
20.000
1209.

10
840
FPVFLRKAF
20.000
1210.

11
279
EPSTGKTCL
20.000
1211.

12
233
QPPPILKVF
20.000
1212.

13
123
FPLSSLANL
20.000
1213.

14
75
TPLSFPCRL
20.000
1214.

15
523
ASVLEILVY
15.000
1215.

16
197
DSLFDYGTY
15.000
1216.

17
817
VSKESKHIW
15.000
1217.

18
250
VSRGSTADL
15.000
1218.

19
929
NPDEVVVPL
12.000
1219.

20
99
GPRAGPGEV
12.000
1220.

21
320
NSPFRDIYY
10.000
1221.

22
229
APAPQPPPI
8.000
1222.

23
629
CPGVNSLFI
8.000
1223.

24
508
SSLYDLSSL
7.500
1224.

25
253
GSTADLDGL
7.500
1225.

26
341
RCKHYVELL
6.000
1226.

27
430
NTKFVTKMY
6.000
1227.

28
287
LPKALLNLS
6.000
1228.

29
1
MPRVVGPGA
6.000
1229.

30
542
LAVEPINEL
6.000
1230.

31
550
LLRDKWRKF
6.000
1231.

32
603
LAGEVITLF
6.000
1232.

33
190
GPKKAPMDS
6.000
1233.

34
694
YSIMIQKIL
5.000
1234.

35
633
NSLFIDGSF
5.000
1235.

36
758
FSTFLLDLF
5.000
1236.

37
798
TSVLLLNML
5.000
1237.

38
779
SSTKYPVVF
5.000
1238.

39
173
NPIDLLEST
4.000
1239.

40
307
DIAERTGNM
4.000
1240.

41
689
KLTGTYSIM
4.000
1241.

42
142
SPADASRPA
4.000
1242.

43
661
AGIEAYLAM
4.000
1243.

44
686
RGLKLTGTY
4.000
1244.

45
243
RPILFDIVS
4.000
1245.

46
469
AAKTGKIGI
3.600
1246.

47
595
RTTVDYLRL
3.000
1247.

48
602
RLAGEVITL
3.000
1248.

49
69
LAGFCLTPL
3.000
1249.

50
664
EAYLAMMVF
3.000
1250.

[0875]

42

TABLE XVIII(A)

HLA Peptide Scoring Results-83P2H3-B35,10-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule

Rank
Position
Listing
Containing This Subsequence)
SEQ ID NO:

1
423
GPFHVLIITY
40.000
1251.

2
206
QPNKTFACQM
40.000
1252.

3
476
GPFTIMIQKM
40.000
1253.

4
52
AAKDNDVQAL
27.000
1254.

5
271
GPLTSTLYDL
20.000
1255.

6
235
VPNHQGLTPF
20.000
1256.

7
326
RPYFCMLGAI
16.000
1257.

8
445
ISASGEVVPM
15.000
1258.

9
5
LPKEKGLILC
12.000
1259.

10
101
AAPELVFEPM
12.000
1260.

11
594
RAQIVATTVM
12.000
1261.

12
220
LSYDRHGDHL
10.000
1262.

13
447
ASGEVVPMSF
10.000
1263.

14
284
DSSGDEQSLL
7.500
1264.

15
482
IQKMIIFGDLM
6.000
1265.

16
369
QQKLLQEAYM
6.000
1266.

17
246
LAGVIEGNTVM
6.000
1267.

18
69
DCKVHQRGAM
6.000
1268.

19
686
RSTSRSSANW
5.000
1269.

20
143
VSARATGTAF
5.000
1270.

21
29
WAQSRDEQNL
4.500
1271.

22
630
FLRVEDRQDL
4.500
1272.

23
87
ALYDNLEAAM
4.000
1273.

24
90
DNLEAAMVLM
4.000
1274.

25
123
IAVVNQNMNL
3.000
1275.

26
562
FAIIATLLML
3.000
1276.

27
150
TAFRRSPCNL
3.000
1277.

28
560
AAFAIIATLL
3.000
1278.

29
528
MALFSTFELF
3.000
1279.

30
3
LSLPKEKGLI
3.000
1280.

31
359
RTSPRDNTLL
3.000
1281.

32
211
FACQMYNLLL
3.000
1282.

33
412
VTRFFGQTIL
3.000
1283.

34
545
ANYNVDLPFM
3.000
1284.

35
40
QQKRIWESPL
3.000
1285.

36
565
IATLLMLNLL
3.000
1286.

37
559
YAAFAIIATL
3.000
1287.

38
706
DLRGIINRGL
3.000
1288.

39
274
TSTLYDLTEI
3.000
1289.

40
484
KMIFGDLMRF
3.000
1290.

41
190
RAQDSLGNTV
2.400
1291.

42
340
IICFTMCCIY
2.000
1292.

43
330
CMLGAIYLLY
2.000
1293.

44
472
FQMLGPFTIM
2.000
1294.

45
679
LPMPSVSRST
2.000
1295.

46
519
ELGHFYDYPM
2.000
1296.

47
251
GNTVMFQHLM
2.000
1297.

48
213
CQMYNLLLSY
2.000
1298.

49
58
VQALNKLLKY
2.000
1299.

50
568
LLMLNLLIAM
2.000
1300.

[0876]

43

TABLE XVIII(B)

HLA Peptide Scoring Results-CaTrF2E11-B35,10-mers

Score (Estimate of Half Time of

Start
Subsequence Residue
Disassociation of a Molecule Containing

Rank
Position
Listing
This Subsequence)
SEQ ID NO:

1
366
QPKDEGGYFY
240.000
1301.

2
190
GPKKAPMDSL
60.000
1302.

3
890
DPGKNETYQY
60.000
1303.

4
173
NPIDLLESTL
40.000
1304.

5
494
LSRKSKDWAY
30.000
1305.

6
532
NSKIENRHEM
30.000
1306.

7
749
YPSCRDSETF
30.000
1307.

8
592
YPYRTTVDYL
20.000
1308.

9
65
EPPPLAGFCL
20.000
1309.

10
84
SSADGPGAGM
20.000
1310.

11
504
GPVYSSLYDL
20.000
1311.

12
123
FPLSSLANLF
20.000
1312.

13
229
APAPQPPPIL
20.000
1313.

14
193
KAPMDSLFDY
12.000
1314.

15
336
IAIERRCKHY
12.000
1315.

16
497
KSKDWAYGPV
12.000
1316.

17
561
VSFYINVVSY
10.000
1317.

18
639
GSFQLLYFIY
10.000
1318.

19
725
VSLLNPCANM
10.000
1319.

20
522
EASVLEILVY
9.000
1320.

21
101
RAGPGEVAEL
9.000
1321.

22
445
CARLFPDSNL
9.000
1322.

23
469
AAKTGKIGIF
9.000
1323.

24
918
VPRVVELNKN
9.000
1324.

25
507
YSSLYDLSSL
7.500
1325.

26
820
ESKHIWKLQW
7.500
1326.

27
449
FPDSNLEAVL
6.000
1327.

28
542
LAVEPINELL
6.000
1328.

29
952
YPRKWRTDDA
6.000
1329.

30
314
NMREFINSPF
6.000
1330.

31
1
MPRVVGPGAN
6.000
1331.

32
287
LPKALLNLSN
6.000
1332.

33
99
GPRAGPGEVA
6.000
1333.

34
660
LAGIEAYLAM
6.000
1334.

35
915
SSVVPRVVEL
5.000
1335.

36
114
ESGTPGGEAF
5.000
1336.

37
694
YSIMIQKILF
5.000
1337.

38
19
GSCCSSRLRL
5.000
1338.

39
778
LSSTKYPVVF
5.000
1339.

40
253
GSTADLDGLL
5.000
1340.

41
568
VSYLCAMVIF
5.000
1341.

42
434
VTKMYDLLLL
4.500
1342.

43
231
APQPPPILKV
4.000
1343.

44
458
LNNDGLSPLM
4.000
1344.

45
661
AGIEAYLAMM
4.000
1345.

46
589
TPPYPYRTTV
4.000
1346.

47
783
YPVVFIILLV
4.000
1347.

48
6
GPGANLCFQV
4.000
1348.

49
700
KILFKDLFRF
3.000
1349.

50
501
WAYGPVYSSL
3.000
1350.

[0877]

44

TABLE XLX (A)

Motif-bearing Subsequences of the 83P2H3 Protein

Post translational modifications

N-glycosylation site

1
208-211 NKTF

2
358-361 NRTS

cAMP- and cGMP-dependent protein kinase phosphorylation site

1
25-28 RRES

2
139-142 RRAS

3
263-266 RKHT

Protein kinase C phosphorylation site

1
144-146 SAR

2
298-300 TTK

3
299-301 TKK

4
318-320 SLK

5
361-363 SPR

6
379-381 TPK

7
688-690 TSR

8
702-704 TLR

Casein kinase II phosphorylation site

1
32-35 SRDE

2
276-279 TLYD

3
281-284 TEID

4
285-288 SSGD

5
286-289 SGDE

6
291-294 SLLE

7
361-364 SPRD

8
379-382 TPKD

9
532-535 STFE

10
539-542 TIID

N-myristoylation site

1
10-15 GLILCL

2
248-253 GVEGNT

3
714-719 GLEDGE

Motifs and Domains:

Ank repeat
aa 44 76

aa 78 . . 108

aa 116 . . 148

aa 162 . . 194

Ion transport
aa 409 . . 578

[0878]

45

TABLE XIX (B)

Motif-bearing Subsequences of the CaTrF2E11 Protein

Post translational modifications

N-glycosylation site

Number of matches: 5

1
233-236 NLSN

2
239-242 NDTI

3
683-686 NCTV

4
816-819 NWSH

5
834-837 NETY

cAMP- and cGMP-dependent protein kinase phosphorylation site

210-213 KRLT

Protein kinase C phosphorylation site

Number of matches: 8

1
144-146 TYR

2
166-168 SPK

3
207-209 THK

4
222-224 TGK

5
412-414 TGK

6
222-224 TGK

7
412-414 TGK

8
435-437 SRK

Casein kinase II phosphorylation site

Number of matches: 17

1
24-27 SSAD

2
82-85 SPAD

3
121-124 TLYE

4
138-141 SLFD

5
194-197 STAD

6
213-216 TDEE

7
392-395 SNLE

8
427-430 TDED

9
449-452 SLYD

10
454-457 SSLD

11
458-461 TCGE

12
464-467 SVLE

13
473-476 SKIE

14
536-539 TTVD

15
691-694 SCRD

16
772-775 TILD

17
868-871 SNPD

Tyrosine kinase phosphorylation site

436-443 RKSKDWAY

N-myristoylation site

Number of matches: 5

1
30-35 GAGMAD

2
32-37 GMADSS

3
56-61 GTPGGE

4
627-632 GLKLTG

5
881-886 GNPRCD

Motifs and Domains

Ankyrin binding domain

aa 329-361

aa 376-408

aa 461-493

Transmembrane domain

aa 561-583

aa 605-622

aa 638-660

aa 672-697

aa 707-725

aa 783-811

[0879]

46

TABLE XX

Frequently Occurring Motifs

avrg. %

Name
identity
Description
Potential Function

zf-C2H2
34%
Zinc finger,
Nucleic acid-binding

C2H2 type
protein functions as

transcription factor,

nuclear location

probable

cytochrome_b—
68%
Cytochrome b(N-
membrane bound

N

terminal)/b6/petB
oxidase, generate

superoxide

ig
19%
Immunoglobulin
domains are one

domain
hundred amino acids

long and include a

conserved intradomain

disulfide bond.

WD40
18%
WD domain,
tandem repeats of

G-beta repeat
about 40 residues,

each containing a

Trp-Asp motif.

Function in signal

transduction and

protein interaction

PDZ
23%
PDZ domain
may function in

targeting signaling

molecules to

sub-membranous sites

LRR
28%
Leucine Rich
short sequence motifs

Repeat
involved in protein-

protein interactions

pkinase
23%
protein kinase
conserved catalytic

domain
core common to both

serine/threonine and

tyrosine protein

kinases containing an

ATP binding site and

a catalytic site

PH
16%
PH domain
pleckstrin homology

involved in intra-

cellular signaling or

as constituents of

the cytoskeleton

EGF
34%
EGF-like domain
30-40 amino-acid long

found in the extra-

cellular domain of

membrane-bound

proteins or in

secreted proteins

rvt
49%
Reverse

transcriptase (RNA-

dependent DNA

polymerase)

ank
25%
Ank repeat
Cytoplasmic protein,

associates integral

membrane proteins to

the cytoskeleton

oxidored_ql
32%
NADH-
membrane associated.

Ubiquinone/
Involved in proton

plastoquinone
tanslocation across

(complex I),
the membrane

various chains

efhand
4%
EF hand
calcium-binding

domain, consists of

a12 residue loop

flanked on both sides

by a 12 residue alpha-

helical domain

rvp
79%
Retroviral aspartyl
Aspartyl or acid

protease
proteases, centered on

a catalytic aspartyl

residue

Collagen
42%
Collagen triple helix
extracellular structural

repeat (20 copies)
proteins involved in

formation of connec-

tive tissue. The

sequence consists of

the G-X-Y and the

polypeptide chains

forms a triple helix.

fn3
20%
Fibronectin type
Located in the extra-

III domain
cellular ligand-binding

region of receptors and

is about 200 amino

acid residues long with

two pairs of cysteines

involved in disulfide

bonds

7tm_1
19%
7 transmembrane
seven hydrophobic

receptor (rhodopsin
transmembrane

family)
regions, with the N-

terminus located extra-

cellularly while the

C-terminus is

cytoplasmic. Signal

through G proteins

[0880]

47

TABLE XXIA

Nucleotide sequence of splice variant A for PCaT.

1
GGTTCTGCAA GCCACACATG GCCTCACTGC ATGTTTTTCT TCTTTTTTAA CAATCCTTTT

61
AAAAAATGTA GAAACCCTTT TCAGTTCAAA GGCCACACCA AAGCAGGTCA GGTAGATCTG

121
GTCCACAGGC CATAGATAGC CAATCCCTGT CCCAGAGGTG GAGCTGTGAG ACTTGTCGGG

181
GTGAGACCTG TTAGAGGCTG GATGGGGCAA TTGCTTGGGG AATNTGTGCA GATGTTCTCT

241
GCCTCCTGCT CCTTCTAGAT GATTTTTGGG CGACCTGATG CGATTCTGCT GGCTGATGGC

301
TGTGGTCATC CTGGGGCTTT GCTTCAGGTA ATCATCTGTC CAGGGACCAG GGGCCATGGC

361
AGGGGAAGAG ATGAGGAAGT TTAGGGGGCA CTGGCNCTGG CTAAACTTGG GGAGGAGGAG

421
TAATGCAGAG ATNCAGAGGA GACCTAT

[0881]

48

TABLE XXIIA

Nucleotide sequence alignment of Variant A with PCaT.

Score=106 bits (55), Expect=1e-19

Identities=69/71 (97%), Gaps 2/71 (2%)

Strand=Plus/Plus

PCaT:
1651
agatgatttttggcgacctgatgcgattctgctggctgatggctgtggtcatcct-ggg
1708

|||||||||||||
|||||||||||||||||||||||||||||||||||||||||||||

Vrnt A:
257
agatgatttttgggcgacctgatgcgattctgctggctgatggctgtggtcatcctgggg
316

PCaT:
1709
ctttgcttcag 1719

|||||||||||

Vrnt A:
317
ctttgcttcag 327

[0882]

49

TABLE XXIIA

Longest amino acid sequence alignment of Variant A

and PCaT.

Score=42.8 bits (87), Expect=0.16

Identities=16/16 (100%)

Frame=+3/+2

PCaT:
1662
GDLMRFCWLMAVVILG
1709

GDLMRFCWLMAVVTILG

Vrnt A:
269
GDLMRFCWLMAVVILG
316

[0883]

50

TABLE XXIVA

Peptide sequences from the translation of the nucleotide sequence of va-

riant A.

Open reading frame
Amino acid sequences

Frame 1
GSASHTWPHCMFFFFFNNPFKKCRNPFQFKGHTKAGQVDLVHRP*IANPCPRGG

AVRLVGVRPVRGWMGQLLGE*VQMFSASCSF*MIFGRPDAILLADGCGHPGALL

QVIICPGTRGHGRGRDEEV*GALALAKLGEEE*CRD*EETY

Frame 2
VLQATHGLTACFSSFLTILLKNVETLFSSKATPKQVR*IWSTGHR*PIPVPEVE

L*DLSG*DLLEAGWGNCLGN*CRCSLPPAPSR*FLGDLMRFCWLMAVVILGLCF

R*SSVQGPGAMAGEEMRKFRGHW*WLNLGRRSNAE*QRRP

Frame 3
FCKPHMASLHVFLLF*QSF*KM*KPFSVQRPHQSRSGRSGPQAIDSQSLSQRWS

CETCRGETC*RLDGAIAWG*CADVLCLLLLLDDFWAT*CDSAG*WLWSSWGFAS

GNHLSRDQGPWQGKR*GSLGGTG*G*TWGGGVMQR*RGDL

Note: Frame 2 gives the longest subsequence that is identical with PCaT amino acid sequence. In this Table each (*)indicates a single unknown amino acid.

[0884]

51

TABLE XXIB

Nucleotide sequence of splice Variant B for PCaT.

1
ATTCTGCTGG CTGATGGCTG TGGTCATCCT GGGCTTGCTT CAGCCTTCTA TATCATCTTC

61
CAGACAGAGG ACCCCGAGAG CTAGGCCACT TCTACGACTA CCCCACGCCC CTGTCCGGCA

121
CCTTCGAGCT GTTCCTTACC ATCATCGATG GCCCAGCCAA CTACAACGTG GACCTGCCCT

181
TCGTGTACAG CATCACCTAT GCTGCCTTTG CCATCATCGC CACACTGCTC ATGCTCAACC

241
TCCTCATTGC CATGATGGGC GACACTCACT GGCGAGTGGC CCATGAGCGG GATGAGCTGT

301
GGAGGGCCCA GATTGTGGCC ACCACGGTGA TGCTGGAGCG GAAGCTGCCT CGCTGCCTGT

361
GGCCTCGCTC CGGGATCTGC GGANNCGGGA GTATGGCCTG GGAGACCGCT GGTCCCTCGG

421
CGCGCTGGAA GAACAGGCAA CGATCTCAAC CGGCAGCGGA TCCAACGCCA CCGCACAGGC

481
CTTCCACACC CGGGGCTCCT GAGGATTCGG CCCCCAGACT CAGTGCAAAC AACTAGAGCT

541
GGCGCTGTCC CTTTCAGCCC CAGCGTGTCC CCTTCCTAAT TGCGCTCAAG GTCCCGAAAG

601
TACCTTCCCG TAGACGTGCC AATGGGCGCA AGCGCTCCGG GCAAGGCGGC CCCTGCCGGA

661
GAAGACCTGC GTGGCGACCA CTCCACCAGG GGCTCCGGAC GCACCGCGAA GCTGGGATAT

721
CCAGAACCGA CGCGTGTCCC ACCTGGCCCG GACCTGGCCC CCATTACCGG GGGGCCAACG

781
ACACAAACCG AAACCCAGGA GCCATCCCGG CCAGGGGAAA CAGCGGCCCC ACGCCGAACA

841
TCCTCG

[0885]

52

TABLE XMIB

Nucleotide sequence alignment of Variant B with PCaT.

Score=798 bits (415), Expect=0.0

Identities=542/573 (94%), Gaps=15/573 (2%)

Strand=Plus/Plus

PCaT:
1676
attctgctggctgatggctgtggtcatcctgggctttgcttcagccttctatatcatctt
1735

|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Vrnt B:
1
attctgctggctgatggctgtggtcatcctgggcttgcttcagccttctatatcatctt
59

PCat:
1736
ccagacagaggaccccgaggagctaggccacttctacgactaccccatggccctgttcag
1795

|||||||||||||||||||||||||||||||||||||||||||||||||||||||

Vrnt B:
60
ccagacagaggaccccgagagctaggccacttctacgactaccccacgcccctgtccgg
118

PCaT:
1796
caccttcgagctgttccttaccatcatcgatggcccagccaactacaacgtggacctgcc
1855

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Vrnt B:
119
caccttcgagctgttccttaccatcatcgatggcccagccaactacaacgtggacctgcc
178

PCaT:
1856
cttcatgtacagcatcacctatgctgcctttgccatcatcgccacactgctcatgctcaa
1915

|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Vrnt B:
179
cttcgtgtacagcatcacctatgctgcctttgccatcatcgccacactgctcatgctcaa
238

PCaT:
1916
cctcctcattgccatgatgggcgacactcactggcgagtggcccatgagcgggatgagct
1975

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Vrnt B:
239
cctcctcattgccatgatgggcgacactcactggcgagtggcccatgagcgggatgagct
298

PCaT:
1976
gtggagggcccagattgtggccaccacggtgatgctggagcggaagctgcctcgctgcct
2035

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Vrnt B:
299
gtggagggcccagattgtggccaccacggtgatgctggagcggaagctgcctcgctgcct
358

PCaT:
2036
gtggcctcgctccgggatctgcggacgggagtatggcctgggagaccgctggttcct
2092

||||||||||||||||||||||||| |||||||||||||||||||||||||||||||

Vrnt B:
359
gtggcctcgctccgggatctgcgganncgggagtatggcctgggagaccgctggtccctc
418

PCaT:
2093
-gcg-ggtggaag-acaggcaa-gatctcaaccggcagcggatccaacgctacgcacag
2147

|||||||||||||||||||||||||||||||||||||||||||||||||||||

Vrnt B:
419
ggcgcgctggaagaacaggcaacgatctcaaccggcagcggatccaacgccaccgcacag
478

PCaT:
2148
gccttccacacccggggct-ctgaggatttgg-acaaagactcagtggaaaaactagag
2204

|||||||||||||||||||||||||||||| | |||||||||||||||||||||

Vrnt B:
479
gccttccacacccggggctcctgaggattcggcccccagactcagtgcaaacaactagag
538

PCaT:
2205
ctgg-gctgtccc-ttcagcccccacctgtccc 2235

||||||||||||||||||||| |||||||

Vrnt B:
539
ctggcgctgtccctttcagccccagcgtgtccc 571

[0886]

53

Table XXIIIB

Longest amino acid sequence alignment of Variant B and PCaT.

Score = 243 bits (525), Expect(6) = 5e-77

Identities = 98/104 (94%)

Frame = +3/+3

PCaT:
1749
PEELGHFYDYPMALFSTFELFLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIA
1928

P ELGHFYDYP L

TFELFLTIIDGPANYNVDLPF+YSITYAAFAIIATLLMLNLLIA

Vrnt B:
72
PRELGHFYDYPTPLSGTFELFLTIIDGPANYNVDLPFVYSITYAAFAIIATLLMLNLLIA
251

PCaT:
1929
MMGDTHWRVAHERCELWRAQIVATTVMLERKLPRCLWPRSGICG
2060

MMGDTHWRVAHERDELWPAQIVATTVMLERKLPRCLWPRSGICG

Vrnt B:
252
MMGDTHWRVAHERDELWRAQIVATTVMLERKLPRCLWPRSGICG
383

[0887]

54

Table XXIVB

Peptide sequences from the translation of the nucleotide sequence of variant

B.

Open reading frame
Amino acid sequences

Frame 1
ILLADGCGHPGLASAFYIIFQTEDPES*ATSTTTPRPCPAPSSCSLPSSMAQPTTT

WTCPSCTASPMLPLPSSPHCSCSTSSLP*WATLTGEWPMSGMSCGGPRLWPPR*CW

SGSCLAACGLAPGSA**GVWPGRPLVPRRAGRTGNDLNRQRIQRHRTGLPHPGLLR

IRPPDSVQTTRAGAVPFSPSVSPS*LRSRSRKYLPVDVPMGASAPGKGAPAGEDLR

GDHSTRGSGRTAKLGYPEPTRVPPGPDLAPITGGPTTQTETQEPSRPGETAAPRRTSS

Frame 2
FCWLMAVVILGLLQPSISSSRQRTPRARPLLRLPHAPVRHLRAVPYHHRWPSQLQR

GPALRVQHHLCCLCHHRHTAHAQPPGCHDGRHSLASGP*AG*AVEGPDCGHHGDAG

AEAASLPVASLRDLR*REYGLGDRWSLGALEEQATISTGSGSNATAQAFHTRGS*G

FGPQTQCKQLELALSLSAPACPLPNCAQGPESTFP*TCQWAQALRARGPLPEKTCV

ATTPPGAPCAPRSWDIQNRRVSHLARTWPPLPGGQRHKPKPRSHPGQGKQRPHAEHP

Frame 3
SAG*WLWSSWACFSLLYHLPDRGPRELGHFYDYPTPLSGTFELFLTIIDGPANYNV

DLPFVYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATTVMLE

RKLPRCLWPRSGICG*GSMAWETAGPSARWKNRQRSQPAADPTPPHRPSTPGAPED

SAPRLSANN*SWRCPFQPQRVPFLIALKVPKVPSRRRANGRKRSGQGGPCRRRPAW

RPLHQGLRTHREAGISRTDACPTWPGPGPHYRGANDTNRNPFGAIPARGNSGPTPNIL

Note: Frame 3 gives the longest subsequence that is identical with PCaT amino acid sequence. In this Table each (*) indicates a single unknown amino acid.

[0888]

55

Table XXTC

Nucleotide sequence of splice Variant C for PCaT. ″.

1
TTTATTTTCT CCAGGAATAT ATATTGATAT TCTAAGTGGG ATGTTTATAT TTATAAGTGG

61
CCTTTATGTC TGTAGGGTCA AAATATCTGG GAGCCCTTAA AAGCCCTTTC TATTTGCTTT

121
CTCTGGTGCC TGTGCTCCTG GGAATGGGGC TTCTGCTTCC TGTCTTTCTC CTGCCTCTGG

181
CCTCGCTGCG TCATGCATGT TQGGTCATTG GGTAAAGAAT TGTTGGTCTC AAGCTCTATC

241
AACTCTCTCC CACTGAAGAA GGTCAACAAA GGCTGCCCTA CCCCTACCTC TGTCTGCGCC

301
CAGCCTCATC TCTGACTTCT CCTTTTGTTC CCATACGCAG ATTGTGGCCA CCACGGTGAT

361
GCTGGAGCGG AAGCTGCCTC GCTGCCTGTG GCCTCGCTCC GGGATCTGCG GACGGGAGTA

421
TGGCCTGGGA GACCGCTGGT TCCTGCGGTG AGTGATATGC GGGGGTAGGT GTCCCCTCAG

481
AAGCCTCATC GGCAGGGTAT CCCCCTGCTC AGACAGCTTC CGGCTCCTGG GTTCCCTGTG

541
CAGGCCTGTG TGCTCCCTAG GCTCTATGCT TGTTGATTGA GCTGGTGAGG AAGGGGTCCC

601
GTTTGGAGCT CAGACTTCCC AAAGCATCCA GGGAGTCTGT GGCAGAGCCT GCTGCTTTCT

661
GAGGCCTAGC TGCCAAGGGG CCAGTTACCC AGGCATNCAC CATGGGNTNC AGAAAAGNGG

721
AAAAGGCCAG CAATGGCGGT GGAT

[0889]

56

Table XXILC

Nucleotide sequence alignment of Variant C with PCaT.

Score = 214 bits (111), Expect = 4e−52

Identities = 111/111 (100%)

Strand = Plus/Plus

PCaT:
1986
cagattgtggccaccacggtgatgctggagcggaagctgcctcgctgcctgtggcctcgc
2045

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Vrnt C:
338
cagattgtggccaccacggtgatgctggagcggaagctgcctcgctgcctgtggcctcgc
397

PCaT:
2046
tccgggatctgcggacgggagtatggcctgggagaccgctggttcctgcgg
2096

||||||||||||||||||||||||||||||||||||||||||||||||||||||

Vrnt C:
398
tccgggatctgcggacgggagtatggcctgggagaccgctggttcctgcgg
448

[0890]

57

Table XXIIIC

Longest amino acid sequence alignment of Variant C

and PCaT.

Score = 97.3 bits (206), Expect = 6e−18

Identities = 37/37 (100%)

Frame = +3/+2

PCaT:

1986
QIVATTVMLERKLPRCLWPRSGICGREYGLGDRWFLR
2096

QIVATTVMLERKLPRCLWPRSGICGREYGLGDRWFLR

Vrnt C:

338
QIVATTVMLERKLPRCLWPRSGICGREYGLGDRWFLR
448

[0891]

58

!Table XXIVC

Peptide sequences from the translation of the nucleotide sequence of va-

riant C.

Open reading frame
Amino acid sequences

Frame 1
FIFSRNIY*YSKWDVYIYKWPLCL*GQNIWEPLKALSICFLWCLCSWEWGFCFLSFS

CLWPGCVMDVGSLGKELLVSSSINSLPLKKVNKGCPTPTSVCAQPHL*LLLLFPYAD

CGHHGDAGAEAASLPVASLRDLRTGVWPGRPLVPAVSDMRG*VSPEKPHRQGIPLLR

QLPAPGFPVEACVLPRLYAC*LSW*GRGPVWSSDFPKHPGSLWQSLLLSEA*LPRGQ

LPRH*PW**EK*KRPAMAVD

Frame 2
LFSPGIYIDILSGMFIFISGLYVCRVKISGSP*KPFLFAFSGACAPGNGASASCLSP

ASGLAASWMLGHWVKNCWSQALSTLSH*RRSTKAALPLPLSAPSLISDFSFCSHTQI

VATTVMLERKLPRCLWPRSGICGREYGLGDRWFLR*VICGGRCPLRSLIGRVSPCSD

SFRLLGSLWRPVCSLGSMLVD*AGEEGVPFGAQTSQSIQGVCGRACCFLRPSCQGAS

YPG*HHG*QK*GKGQQWRW

Frame 3
YGLQEYILIG*VGCLYL*VAFMSVGSKYLGALKSPFYLLSLVPVLLGMGLLLPVFLL

PLAWLRHGCWVIG*RIVGLKLYQLSPTEEGQQRLPYPYLCLRPASSLTSPFVPIRRL

WPPR*CWSGSCLAACGLAPGSADGSMAWETAGSCGE*YAGVGVP*EASSAGYPPAQT

ASGSWVPCGGLCAP*ALCLLIELVRKGSRLELRLPKASRESVAEPAAF*GLAAKGPV

TQA*TMG*RK*EKASNGGG

Note: Frame 2 gives the longest subsequence that is identical with PCaT amino acid sequence. In this Table each (*) indicates a single unknown amino acid.

Nucleic acids and corresponding proteins entitled 83P2H3 and CaTrF2E11 useful in treatment and detection of cancer

Information

Publication Number

Date Filed

Date Published

Inventors

CPC

US Classifications

International Classifications

Abstract

Description

Claims

Parent Case Info

Provisional Applications (1)