# Patent

## Title
Antibodies that recognize the 85P1B3 protein useful in treatment and detection of cancer

## Abstract

A novel gene (designated 85P1B3) and its encoded protein are described. While 85P1B3 exhibits tissue specific expression in normal adult tissue, it is aberrantly expressed in multiple cancers including set forth in Table 1. Consequently, 85P1B3 provides a diagnostic and/or therapeutic target for cancers. The 85P1B3 gene or fragment thereof, or its encoded protein or a fragment thereof, can be used to elicit an immune response.

## Background
This application claims the benefit of U.S. provisional patent application Ser. No. 60/228,432, filed Aug. 28, 2000, the entire contents of which are hereby incorporated herein by reference.


SUBMISSION ON COMPACT DISC
The contents of the following submission on compact discs are incorporated herein by reference in its entirety: A compact disc copy of the Sequence Listing (COPY 1) (file name: 5115820028.txt, date recorded: Feb. 13, 2003, size: 216 KB); a duplicate compact disc copy of the Sequence Listing (COPY 2) (file name: 5115820028.txt, date recorded: Feb. 13, 2003, size: 216 KB); a computer readable form copy of the Sequence Listing (CRF COPY) (file name: 5115820028.txt, date recorded: Feb. 13, 2003, size: 216 KB).
FIELD OF THE INVENTION
The invention described herein relates to a novel gene and its encoded protein, termed 85P1B3, and to diagnostic and therapeutic methods and compositions useful in the management of various cancers that express 85P1B3.
BACKGROUND OF THE INVENTION
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.
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.
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.
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.
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 1996 September 2 (9): 1445–51), STEAP (Hubert, et al., Proc Natl Acad Sci USA. 1999 Dec. 7; 96(25): 14523–8) and prostate stem cell antigen (PSCA) (Reiter et al., 1998, Proc. Natl. Acad. Sci. USA 95: 1735).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 lung and bronchial cancers.
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.
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.
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.
Local excision of ductal carcinoma in situ (DCFS) 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.
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.
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.
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.
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
The present invention relates to a novel gene, designated 85P1B3, that is over-expressed in multiple cancers listed in Table 1. Northern blot expression analysis of 85P1B3 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 85P1B3 are provided. The tissue-related profile of 85P1B3 in normal adult tissues, combined with the over-expression observed in prostate and other tumors, shows that 85P1B3 is aberrantly over-expressed in at least some cancers, and thus serves as a useful diagnostic and/or therapeutic target for cancers of the tissues such as those listed in Table 1.
The invention provides polynucleotides corresponding or complementary to all or part of the 85P1B3 genes, mRNAs, and/or coding sequences, preferably in isolated form, including polynucleotides encoding 85P1B3-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 85P1B3-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 85P1B3 genes or mRNA sequences or parts thereof, and polynucleotides or oligonucleotides that hybridize to the 85P1B3 genes, mRNAs, or to 85P1B3-encoding polynucleotides. Also provided are means for isolating cDNAs and the genes encoding 85P1B3. Recombinant DNA molecules containing 85P1B3 polynucleotides, cells transformed or transduced with such molecules, and host-vector systems for the expression of 85P1B3 gene products are also provided. The invention further provides antibodies that bind to 85P1B3 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.
The invention further provides methods for detecting the presence and status of 85P1B3 polynucleotides and proteins in various biological samples, as well as methods for identifying cells that express 85P1B3. A typical embodiment of this invention provides methods for monitoring 85P1B3 gene products in a tissue or hematology sample having or suspected of having some form of growth dysregulation such as cancer.
The invention further provides various immunogenic or therapeutic compositions and strategies for treating cancers that express 85P1B3 such as prostate cancers, including therapies aimed at inhibiting the transcription, translation, processing or function of 85P1B3 as well as cancer vaccines.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. 85P1B3 SSH sequence. The 85P1B3 SSH sequence contains 259 bp. (SEQ ID. NO.: 724) and it's alignment with a fragment of the Homo sapiens Opa-interacting protein OIP5 (SEQ ID NO: 725) cDNA.
FIG. 2. The cDNA (SEQ ID. NO.:727) and amino acid sequence (SEQ ID. NO.:728) of 85P1B3. The start methionine is underlined. The open reading frame extends from nucleic acid 13 to 702 including the stop codon.
FIG. 3. Amino acid sequence of 85P1B3 (SEQ ID. NO.:728). The 85P1B3 protein has 229 amino acids.
FIG. 4. Sequence alignment of 85P1B3 (SEQ ID NO: 728) with GenBank accession number AAC39561.1 (AF025441), Opa-interacting protein OIP5 (SEQ ID. NO.:731).
FIG. 5. Hydrophilicity amino acid profile of 85P1B3 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 through the ExPasy molecular biology server.
FIG. 6. Hydropathicity amino acid profile of 85P1B3 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 through the ExPasy molecular biology server.
FIG. 7. Percent accessible residues amino acid profile of 85P1B3 determined by computer algorithm sequence analysis using the method of Janin (Janin J., 1979 Nature 277:491–492) accessed on the ProtScale website through the ExPasy molecular biology server.
FIG. 8. Average flexibility amino acid profile of 85P1B3 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 through the ExPasy molecular biology server.
FIG. 9. Beta-turn amino acid profile of 85P1B3 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 through the ExPasy molecular biology server.
FIG. 10. RT-PCR analysis of 85P1B3 expression. First strand cDNA was prepared from vital pool 1 (VP1: liver, lung and kidney), vital pool 2 (VP2, pancreas, spleen and stomach), prostate xenograft pool (LAPC-4AD, LAPC-4AI, LAPC-9AD, LAPC-9AI), prostate cancer pool, bladder cancer pool, kidney cancer pool, colon cancer pool, lung cancer pool, ovary cancer pool, breast cancer pool, and cancer metastasis pool. Normalization was performed by PCR using primers to actin and GAPDH. Semi-quantitative PCR, using primers to 85P1B3, was performed at 26 and 30 cycles of amplification.
FIG. 11. Expression of 85P1B3 in normal human tissues. Two multiple tissue northern blots (Clontech) with 2 μg of mRNA/lane, were probed with the 85P1B3 SSH sequence. Size standards in kilobases (kb) are indicated on the side. The results show exclusive expression of an approximately 1.4 kb 85P1B3 transcript in testis but not in any other normal tissues.
FIG. 12. Expression of 85P1B3 in human cancer cell lines. RNA was extracted from a panel of human cancer cell lines. Northern blots with 10 μg of total RNA/lane were probed with the 85P1B3 SSH sequence. Size standards in kilobases (kb) are indicated on the side.
FIG. 13. Expression of 85P1B3 in human patient cancer specimens and cancer cell lines. Expression of 85P1B3 was assayed in a panel of human cancers (T) and their respective matched normal tissues (N) on RNA dot blots. 85P1B3 expression was detected in the cancers of the breast, prostate, uterus, cervix, stomach and lung. 85P1B3 was also found to be highly expressed in all human cancer cell lines tested.
FIG. 14. Expression of 85P1B3 in colon cancer patient specimens. RNA was extracted from colon cancer cell lines (CL), normal colon (N), colon tumors (T) and their normal adjacent tissues (Nat) derived from colon cancer patients. Northern blots with 10 μg of total RNA/lane were probed with the 85P1B3 SSH sequence. Size standards in kilobases (kb) are indicated on the side. Results show expression of 85P1B3 in 2 colon tumor specimens but not in the corresponding normal adjacent tissue. Expression is also seen in all 4 colon cancer cell lines (Colo 205, LoVo, T84, Caco-2). P1—Stage III, T2N1MX; P2—Stage III, T3N1MX.
FIG. 15. Expression of 85P1B3 in bladder cancer patient specimens. RNA was extracted from bladder cancer cell lines (CL), normal bladder (N), bladder tumors (T) and their normal adjacent tissue (Nat) derived from bladder cancer patients. Northern blot with 10 μg of total RNA/lane were probed with the 85P1B3 SSH sequence. Size standards in kilobases (kb) are indicated on the side. Results show expression of 85P1B3 in 3 of 5 bladder tumor specimens. Expression is also seen in all three bladder cancer cell lines, UM-UC-3, J82, and SCABER.
FIG. 16. Expression of 85P1B3 in lung cancer patient specimens. RNA was extracted from lung cancer cell lines (CL), normal lung (N), lung tumors (T) and their normal adjacent tissue (NAT) derived from lung cancer patients. Northern blot with 10 μg of total RNA/lane was probed with the 85P1B3 SSH sequence. Size standards in kilobases (kb) are indicated on the side. Results show expression of 85P1B3 in three lung tumor specimens. Expression is also seen in all lung cancer cell lines.
FIG. 17. Expression of 85P1B3 in Prostate Cancer Xenografts Following Castration. Male mice were injected with LAPC-9AD tumor cells. When tumor reached a palpable size (0.3–0.5 cm in diameter), mice were castrated and tumors harvested at different time points following castration. RNA was isolated from the xenograft tissues. Northern blots with 10 μg of total RNA/lane were probed with the 85P1B3 SSH fragment. Size standards in kilobases (kb) are indicated on the side. Results show expression of 85P1B3 is maintained following castration. A picture of the ethidium-bromide staining of the RNA gel is also presented. Hybridization of the same northern blot with the androgen-dependent gene TMPRSS2 confirms the quality of the androgen deprivation following castration.
FIG. 18. Expression of 85P1B3 in PC3 Cells Following Retroviral-Mediated Gene Delivery. PC3 cells were transduced with the pSRα retroviral vector encoding the 85P1B3 gene. Following selection with neomycin, the cells were expanded and RNA was extracted. Northern blot with 10 μg of total RNA/lane was probed with the 85P1B3 SSH sequence. Size standards in kilobases (kb) are indicated on the side. Results show expression of the 85P1B3 transcript driven from the retroviral LTR, which migrates slower than the endogenous 1.4 kb 85P1B3 transcript. LAPC-9A1 shows only expression of the endogenous 85P1B3, but not the pSRα transcript.
FIG. 19. Schematic diagram of the alignment of 85P1B3 with its splice variant. The region of homology between 85P1B3 and its splice variant 1 is marked with a hatched box. Regions specific for 85P1B3 are marked in white boxes, and the ones specific for the splice variant 1 as black boxes. The SSH sequence of 85P1B3 is also indicated by a white box.
FIG. 20. Western analysis of 85P1B3 expression with an anti-85P1B3 polyclonal antibody. Panel A. Detection of GST-85P1B3 with anti-GST-85P1B3 rabbit serum. 200 ng of GST-85P1B3 (amino acids 1–229) and 200 ng of GST alone were separated by SDS-PAGE and transferred to nitrocellulose. The blot was then incubated with indicated dilutions of anti-85P1B3 serum. Immunoreactive bands were detected by incubation with anti-rabbit IgG HPP-secondary antibody and visualized by enhanced chemiluminescence and exposure to autoradiography film. Shown with arrows is detection of the GST-85P1B3 protein and minimal detection of GST alone. Panel B. 293T cells were transiently transfected with either empty pCDNA 3.1 vector or pCDNA 3.1 carrying the 85P1B3 cDNA. Lysates of the cells were separated by SDS-PAGE and subjected to Western analysis as performed for the data in Panel A, with 2 μg/ml of purified anti-85P1B3 polyclonal antibody. Panel C. Western analysis was carried out as for the data in Panel B, but using an anti-His polyclonal antibody (Santa Cruz Biotechnology, Santa Cruz, Calif.). Arrows indicate the immunoreactive bands corresponding to His-tagged 85P1B3 protein.
FIG. 21. Secondary structure and transmembrane prediction for 85P1B3. Panel A. The secondary structure of 85P1B3 protein was predicted using the HNN—Hierarchical Neural Network method (Guermeur, 1997), accessed from the ExPasy molecular biology server. This method indicates the presence and location of alpha helices (h), extended strands (e), and random coils (c) from the primary protein sequence. The percent of the protein in a given secondary structure is also given. Panel B. Schematic representation of the probability of existence of transmembrane regions of 85P1B3 based on the TMpred algorithm of Hofmann and Stoffel which utilizes TMBASE (K. Hofmann, W. Stoffel. TMBASE-A database of membrane spanning protein segments Biol. Chem. Hoppe-Seyler 374:166, 1993). Stretches of amino acids approximately 17–33 amino acids in length with a value greater than 0 are potential transmembrane helices. This program indicates the presence of one helix in 85P1B3. Panel C. Schematic representation of the probability of the existence of transmembrane regions and the extracellular and intracellular orientation of 85P1B3 based on the algorithm of Sonnhammer, von Heijne, and Krogh (Erik, L. L., et al., A hidden Markov model for predicting transmembrane helices in protein sequences. In Proc. of Sixth Int. Conf. on Intelligent Systems for Molecular Biology, p 175–182 Ed J. Glasgow, et al., Menlo Park, Calif.: AAAI Press, 1998). This program indicates 85P1B3 to be an intracellular protein without transmembrane domains. These transmembrane prediction results are also summarized in Table XXV.



DETAILED DESCRIPTION OF THE INVENTION
Outline of Sections

    
    
        I.) Definitions
        II.) 85P1B3 Polynucleotides
        
            II.A.) Uses of 85P1B3 Polynucleotides
            
                II.A.1.) Monitoring of Genetic Abnormalities
                II.A.2.) Antisense Embodiments
                II.A.3.) Primers and Primer Pairs
                II.A.4.) Isolation of 85P1B3-Encoding Nucleic Acid Molecules
                II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector Systems
            
            
        
        
        III.) 85P1B3-related Proteins
        
            III.A.) Motif-bearing Protein Embodiments
            III.B.) Expression of 85P1B3-related Proteins
            III.C.) Modifications of 85P1B3-related Proteins
            III.D.) Uses of 85P1B3-related Proteins
        
        
        IV.) 85P1B3 Antibodies
        V.) 85P1B3 Cellular Immune Responses
        VI.) 85P1B3 Transgenic Animals
        VII.) Methods for the Detection of 85P1B3
        VIII.) Methods for Monitoring the Status of 85P1B3-related Genes and Their Products
        IX.) Identification of Molecules That Interact With 85P1B3
        X.) Therapeutic Methods and Compositions
        
            X.A.) Anti-Cancer Vaccines
            X.B.) 85P1B3 as a Target for Antibody-Based Therapy
            X.C.) 85P1B3 as a Target for Cellular Immune Responses
            
                X.C.1. Minigene Vaccines
                X.C.2. Combinations of CTL Peptides with Helper Peptides
                X.C.3. Combinations of CTL Peptides with T Cell Priming Agents
                X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL and/or HTL Peptides
            
            
            X.D.) Adoptive Immunotherapy
            X.E.) Administration of Vaccines for Therapeutic or Prophylactic Purposes
        
        
        XI.) Diagnostic and Prognostic Embodiments of 85P1B3.
        XII.) Inhibition of 85P1B3 Protein Function
        
            XII.A.) Inhibition of 85P1B3 With Intracellular Antibodies
            XII.B.) Inhibition of 85P1B3 with Recombinant Proteins
            XII.C.) Inhibition of 85P1B3 Transcription or Translation
            XII.D.) General Considerations for Therapeutic Strategies
        
        
        XIII.) KITS
    
    


I.) Definitions:
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.
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.
“Altering the native glycosylation pattern” is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence 85P1B3 (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 85P1B3. 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.
The term “analog” refers to a molecule which is structurally similar or shares similar or corresponding attributes with another molecule (e.g. a 85P1B3-related protein). For example an analog of the 85P1B3 protein can be specifically bound by an antibody or T cell that specifically binds to 85P1B3.
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-85P1B3 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.
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-85P1B3 antibodies and clones thereof (including agonist, antagonist and neutralizing antibodies) and anti-85P1B3 antibody compositions with polyepitopic specificity.
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.”
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, TAXOLTM, 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.
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.
“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).
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.
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 85P1B3 gene or that encode polypeptides other than 85P1B3 gene product or fragments thereof. A skilled artisan can readily employ nucleic acid isolation procedures to obtain an isolated 85P1B3 polynucleotide. A protein is said to be “isolated,” for example, when physical, mechanical or chemical methods are employed to remove the 85P1B3 protein from cellular constituents that are normally associated with the protein. A skilled artisan can readily employ standard purification methods to obtain an isolated 85P1B3 protein. Alternatively, an isolated protein can be prepared by chemical means.
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.
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.
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.
A “motif”, as in biological motif of an 85P1B3-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.
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.
“Pharmaceutically acceptable” refers to a non-toxic, inert, and/or composition that is physiologically compatible with humans or other mammals.
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).
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”.
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.
A “recombinant” DNA or RNA molecule is a DNA or RNA molecule that has been subjected to molecular manipulation in vitro.
“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).
“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.
An HLA “supermotif” is a peptide binding specificity shared by HLA molecules encoded by two or more HLA alleles.
As used herein “to treat” or “therapeutic” and grammatically related terms, refer to any improvement of any consequence of disease, such as prolonged survival, less morbidity, and/or a lessening of side effects which are the byproducts of an alternative therapeutic modality; full eradication of disease is not required.
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.
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.
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 85P1B3 protein shown in FIG. 2 or FIG. 3). An analog is an example of a variant protein.
The 85P1B3-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. Fusion proteins that combine parts of different 85P1B3 proteins or fragments thereof, as well as fusion proteins of a 85P1B3 protein and a heterologous polypeptide are also included. Such 85P1B3 proteins are collectively referred to as the 85P1B3-related proteins, the proteins of the invention, or 85P1B3. The term “85P1B3-related protein” refers to a polypeptide fragment or an 85P1B3 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.
II.) 85P1B3 Polynucleotides
One aspect of the invention provides polynucleotides corresponding or complementary to all or part of an 85P1B3 gene, mRNA, and/or coding sequence, preferably in isolated form, including polynucleotides encoding an 85P1B3-related protein and fragments thereof, DNA, RNA, DNA/RNA hybrid, and related molecules, polynucleotides or oligonucleotides complementary to an 85P1B3 gene or mRNA sequence or a part thereof, and polynucleotides or oligonucleotides that hybridize to an 85P1B3 gene, mRNA, or to an 85P1B3 encoding polynucleotide (collectively, “85P1B3 polynucleotides”). In all instances when referred to in this section, T can also be U in FIG. 2.
Embodiments of a 85P1B3 polynucleotide include: a 85P1B3 polynucleotide having the sequence shown in FIG. 2, the nucleotide sequence of 85P1B3 as shown in FIG. 2, wherein T is 1; 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 85P1B3 nucleotides comprise, without limitation:

    
    
        (a) a polynucleotide comprising or consisting of the sequence as shown in FIG. 2 (SEQ ID NO.: 727), wherein T can also be U;
        (b) a polynucleotide comprising or consisting of the sequence as shown in FIG. 2 (SEQ ID NO.: 727), from nucleotide residue number 13 through nucleotide residue number 699, wherein T can also be U;
        (c) a polynucleotide that encodes a 85P1B3-related protein whose sequence is encoded by cDNA contained in a plasmid deposited with American Type Culture Collection.
        (d) a polynucleotide that encodes an 85P1B3-related protein that is at least 90% homologous to the entire amino acid sequence shown in SEQ ID NO.:728;
        (e) a polynucleotide that encodes an 85P1B3-related protein that is at least identical to the entire amino acid sequence shown in SEQ ID NO: 728;
        (f) a polynucleotide that encodes at least one peptide set forth in Tables V–XVIII;
        (g) a polynucleotide that encodes a peptide region of at least 5 amino acids FIG. 3 in any whole number increment up to 229 that includes an amino acid position having a value greater than 0.5 in the Hydrophilicity profile of FIG. 5;
        (h) a polynucleotide that encodes a peptide region of at least 5 amino acids of FIG. 3 in any whole number increment up to 229 that includes an amino acid position having a value less than 0.5 in the Hydropathicity profile of FIG. 6;
        (i) a polynucleotide that encodes a peptide region of at least 5 amino acids of FIG. 3 in any whole number increment up to 229 that includes an amino acid position having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 7;
        (j) a polynucleotide that encodes a peptide region of at least 5 amino acids of FIG. 3 in any whole number increment up to 229 that includes an amino acid position having a value greater than 0.5 in the Average Flexibility profile on FIG. 8;
        (k) a polynucleotide that encodes a peptide region of at least 5 amino acids of FIG. 3 in any whole number increment up to 229 that includes an amino acid position having a value greater than 0.5 in the Beta-turn profile of FIG. 9;
        (l) a polynucleotide that is fully complementary to a polynucleotide of any one of (a)–(k);
        (m) a polynucleotide that selectively hybridizes under stringent conditions to a polynucleotide of (a)–(l); and
        (n) a polynucleotide of any of (a)–(m) or peptide of (o) (see immediately below) together with a pharmaceutical excipient and/or in a human unit dose form.
        Regarding item (n) immediately above, examples of embodiments of 85P1B3 polypeptides comprise, without limitation:
        (o) a peptide that is encoded by any of (a)–(k).
    
    


As used herein, a range is understood to specifically disclose all whole unit positions thereof.
Typical embodiments of the invention disclosed herein include 85P1B3 polynucleotides that encode specific portions of the 85P1B3 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, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, or 229 contiguous amino acids.
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 85P1B3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 10 to about amino acid 20 of the 85P1B3 protein shown in FIG. 2, or FIG. 3, polynucleotides encoding about amino acid 20 to about amino acid 30 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 30 to about amino acid 40 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 40 to about amino acid 50 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 50 to about amino acid 60 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 60 to about amino acid 70 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 70 to about amino acid 80 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 80 to about amino acid 90 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 90 to about amino acid 100 of the 85P1B3 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 85P1B3 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.
Polynucleotides encoding relatively long portions of the 85P1B3 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 85P1B3 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 85P1B3 sequence as shown in FIG. 2 or FIG. 3.
Additional illustrative embodiments of the invention disclosed herein include 85P1B3 polynucleotide fragments encoding one or more of the biological motifs contained within the 85P1B3 protein sequence, including one or more of the motif-bearing subsequences of the 85P1B3 protein set forth in Tables V–XVIII. In another embodiment, typical polynucleotide fragments of the invention encode one or more of the regions of 85P1B3 that exhibit homology to a known molecule. In another embodiment of the invention, typical polynucleotide fragments can encode one or more of the 85P1B3 N-glycosylation sites, cAMP and cGMP-dependent protein kinase phosphorylation sites, casein kinase II phosphorylation sites or N-myristoylation site and amidation sites.
II.A.) Uses of 85P1B3 Polynucleotides
II.A.1.) Monitoring of Genetic Abnormalities
The polynucleotides of the preceding paragraphs have a number of different specific uses. The human 85P1B3 gene maps to the chromosomal location set forth in Example 3. For example, because the 85P1B3 gene maps to this chromosome, polynucleotides that encode different regions of the 85P1B3 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(34): 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 85P1B3 protein provide new tools that can be used to delineate, with greater precision than previously possible, cytogenetic abnormalities in the chromosomal region that encodes 85P1B3 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)).
Furthermore, as 85P1B3 was shown to be highly expressed in prostate and other cancers, 85P1B3 polynucleotides are used in methods assessing the status of 85P1B3 gene products in normal versus cancerous tissues. Typically, polynucleotides that encode specific regions of the 85P1B3 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 85P1B3 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.
II.A.2.) Antisense Embodiments
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 85P1B3. 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 85P1B3 polynucleotides and polynucleotide sequences disclosed herein.
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., 85P1B3. See for example, Jack Cohen, Oligodeoxynucleotides, Antisense Inhibitors of Gene Expression, CRC Press, 1989; and Synthesis 1:1–5 (1988). The 85P1B3 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 85P1B3 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).
The 85P1B3 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 85P1B3 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 85P1B3 mRNA and not to mRNA specifying other regulatory subunits of protein kinase. In one embodiment, 85P1B3 antisense oligonucleotides of the present invention are 15 to 30-mer fragments of the antisense DNA molecule that have a sequence that hybridizes to 85P1B3 mRNA. Optionally, 85P1B3 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 85P1B3. Alternatively, the antisense molecules are modified to employ ribozymes in the inhibition of 85P1B3 expression, see, e.g., L. A. Couture & D. T. Stinchcomb; Trends Genet 12: 510–515 (1996).
II.A.3.) Primers and Primer Pairs
Further specific embodiments of these 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 85P1B3 polynucleotide in a sample and as a means for detecting a cell expressing a 85P1B3 protein.
Examples of such probes include polypeptides comprising all or part of the human 85P1B3 cDNA sequence shown in FIG. 2. Examples of primer pairs capable of specifically amplifying 85P1B3 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 85P1B3 mRNA.
The 85P1B3 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 85P1B3 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 85P1B3 polypeptides; as tools for modulating or inhibiting the expression of the 85P1B3 gene(s) and/or translation of the 85P1B3 transcript(s); and as therapeutic agents.
The present invention includes the use of any probe as described herein to identify and isolate a 85P1B3 or 85P1B3 related nucleic acid sequence from a naturally occurring source, such as humans or other mammals, as well as the isolated nucleic acid sequence per se, which would comprise all or most of the sequences found in the probe used.
II.A.4.) Isolation of 85P1B3-Encoding Nucleic Acid Molecules
The 85P1B3 cDNA sequences described herein enable the isolation of other polynucleotides encoding 85P1B3 gene product(s), as well as the isolation of polynucleotides encoding 85P1B3 gene product homologs, alternatively spliced isoforms, allelic variants, and mutant forms of the 85P1B3 gene product as well as polynucleotides that encode analogs of 85P1B3-related proteins. Various molecular cloning methods that can be employed to isolate full length cDNAs encoding an 85P1B3 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 85P1B3 gene cDNAs can be identified by probing with a labeled 85P1B3 cDNA or a fragment thereof. For example, in one embodiment, the 85P1B3 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 85P1B3 gene. The 85P1B3 gene itself can be isolated by screening genomic DNA libraries, bacterial artificial chromosome libraries (BACs), yeast artificial chromosome libraries (YACs), and the like, with 85P1B3 DNA probes or primers.
II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector Systems
The invention also provides recombinant DNA or RNA molecules containing an 85P1B3 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).
The invention further provides a host-vector system comprising a recombinant DNA molecule containing a 85P1B3 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 85P1B3 or a fragment, analog or homolog thereof can be used to generate 85P1B3 proteins or fragments thereof using any number of host-vector systems routinely used and widely known in the art.
A wide range of host-vector systems suitable for the expression of 85P1B3 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, 85P1B3 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 85P1B3 protein or fragment thereof. Such host-vector systems can be employed to study the functional properties of 85P1B3 and 85P1B3 mutations or analogs.
Recombinant human 85P1B3 protein or an analog or homolog or fragment thereof can be produced by mammalian cells transfected with a construct encoding a 85P1B3-related nucleotide. For example, 293T cells can be transfected with an expression plasmid encoding 85P1B3 or fragment, analog or homolog thereof, the 85P1B3 or related protein is expressed in the 293T cells, and the recombinant 85P1B3 protein is isolated using standard purification methods (e.g., affinity purification using anti-85P1B3 antibodies). In another embodiment, a 85P1B3 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 85P1B3 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 85P1B3 coding sequence can be used for the generation of a secreted form of recombinant 85P1B3 protein.
As discussed herein, redundancy in the genetic code permits variation in 85P1B3 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.
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)).
III.) 85P1B3-Related Proteins
Another aspect of the present invention provides 85P1B3-related proteins. Specific embodiments of 85P1B3 proteins comprise a polypeptide having all or part of the amino acid sequence of human 85P1B3 as shown in FIG. 2 or FIG. 3. Alternatively, embodiments of 85P1B3 proteins comprise variant, homolog or analog polypeptides that have alterations in the amino acid sequence of 85P1B3 shown in FIG. 2 or FIG. 3.
In general, naturally occurring allelic variants of human 85P1B3 share a high degree of structural identity and homology (e.g., 90% or more homology). Typically, allelic variants of the 85P1B3 protein contain conservative amino acid substitutions within the 85P1B3 sequences described herein or contain a substitution of an amino acid from a corresponding position in a homologue of 85P1B3. One class of 85P1B3 allelic variants are proteins that share a high degree of homology with at least a small region of a particular 85P1B3 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.
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 1995 May 19; 270(20):118826).
Embodiments of the invention disclosed herein include a wide variety of art-accepted variants or analogs of 85P1B3 proteins such as polypeptides having amino acid insertions, deletions and substitutions. 85P1B3 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., 3:4331 (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 85P1B3 variant DNA.
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.
As defined herein, 85P1B3 variants, analogs or homologs, have the distinguishing attribute of having at least one epitope that is “cross reactive” with a 85P1B3 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 85P1B3 variant also specifically binds to the 85P1B3 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 85P1B3 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.
Another class of 85P1B3-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 85P1B3 protein variants or analogs comprise one or more of the 85P1B3 biological motifs described herein or presently known in the art. Thus, encompassed by the present invention are analogs of 85P1B3 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.
As discussed herein, embodiments of the claimed invention include polypeptides containing less than the full amino acid sequence of the 85P1B3 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 85P1B3 protein shown in FIG. 2 or FIG. 3.
Moreover, representative embodiments of the invention disclosed herein include polypeptides consisting of about amino acid 1 to about amino acid 10 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 10 to about amino acid 20 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 20 to about amino acid 30 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 30 to about amino acid 40 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 40 to about amino acid 50 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 50 to about amino acid 60 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 60 to about amino acid 70 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 70 to about amino acid 80 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 80 to about amino acid 90 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 90 to about amino acid 100 of the 85P1B3 protein shown in FIG. 2 or FIG. 3, etc. throughout the entirety of the 85P1B3 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 85P1B3 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.
85P1B3-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 85P1B3-related protein. In one embodiment, nucleic acid molecules provide a means to generate defined fragments of the 85P1B3 protein (or variants, homologs or analogs thereof).
III.A.) Motif-Bearing Protein Embodiments
Additional illustrative embodiments of the invention disclosed herein include 85P1B3 polypeptides comprising the amino acid residues of one or more of the biological motifs contained within the 85P1B3 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., EpimatrixTM and EpimerTM, Brown University, and BIMAS).
Motif bearing subsequences of the 85P1B3 protein are set forth and identified in Table XIX.
Table XX sets forth several frequently occurring motifs based on pfam searches. 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.
Polypeptides comprising one or more of the 85P1B3 motifs discussed above are useful in elucidating the specific characteristics of a malignant phenotype in view of the observation that the 85P1B3 motifs discussed above are associated with growth dysregulation and because 85P1B3 is overexpressed in certain cancers (See, e.g., Table 1). 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)).
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 85P1B3 protein that are capable of optimally binding to specified HLA alleles (e.g., Table IV; EpimatrixTM and EpimerTM, Brown University and BIMAS.) 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.
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.
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(34): 201–212; Sette et al., J. Immunol. 2001 166(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.
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.
85P1B3-related proteins are embodied in many forms, preferably in isolated form. A purified 85P1B3 protein molecule will be substantially free of other proteins or molecules that impair the binding of 85P1B3 to antibody, T cell or other ligand. The nature and degree of isolation and purification will depend on the intended use. Embodiments of a 85P1B3-related proteins include purified 85P1B3-related proteins and functional, soluble 85P1B3-related proteins. In one embodiment, a functional, soluble 85P1B3 protein or fragment thereof retains the ability to be bound by antibody, T cell or other ligand.
The invention also provides 85P1B3 proteins comprising biologically active fragments of the 85P1B3 amino acid sequence shown in FIG. 2 or FIG. 3. Such proteins exhibit properties of the 85P1B3 protein, such as the ability to elicit the generation of antibodies that specifically bind an epitope associated with the 85P1B3 protein; to be bound by such antibodies; to elicit the activation of HTL or CTL; and/or, to be recognized by HTL or CTL.
85P1B3-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-85P1B3 antibodies, or T cells or in identifying cellular factors that bind to 85P1B3.
CTL epitopes can be determined using specific algorithms to identify peptides within an 85P1B3 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); EpimatrixTM and EpimerTM, Brown University and BIMAS). Illustrating this, peptide epitopes from 85P1B3 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 85P1B3 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 85P1B3 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.
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.
It is to be appreciated that every epitope predicted by the BIMAS site, EpimerTM and EpimatrixTM 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 85P1B3 protein. As used in this context “applied” means that the 85P1B3 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 85P1B3 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 I motif are within the scope of the invention.
III.B.) Expression of 85P1B3-Related Proteins
In an embodiment described in the examples that follow, 85P1B3 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 85P1B3 with a C-terminal 6×His (SEQ ID NO: 709) 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 85P1B3 protein in transfected cells. The secreted HIS-tagged 85P1B3 in the culture media can be purified, e.g., using a nickel column using standard techniques.
III.C.) Modifications of 85P1B3-Related Proteins
Modifications of 85P1B3-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 85P1B3 polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C-terminal residues of the 85P1B3. Another type of covalent modification of the 85P1B3 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 85P1B3 comprises linking the 85P1B3 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.
The 85P1B3-related proteins of the present invention can also be modified to form a chimeric molecule comprising 85P1B3 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 85P1B3 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 85P1B3. A chimeric molecule can comprise a fusion of a 85P1B3-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 85P1B3. In an alternative embodiment, the chimeric molecule can comprise a fusion of a 85P1B3-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 85P1B3 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, CH1, CH2 and CH3 regions of an IgG1 molecule. For the production of immunoglobulin fusions see, e.g., U.S. Pat. No. 5,428,130 issued Jun. 27, 1995.
III.D.) Uses of 85P1B3-Related Proteins
The proteins of the invention have a number of different specific uses. As 85P1B3 is highly expressed in prostate and other cancers, 85P1B3-related proteins are used in methods that assess the status of 85P1B3 gene products in normal versus cancerous tissues, thereby elucidating the malignant phenotype. Typically, polypeptides from specific regions of the 85P1B3 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 85P1B3-related proteins comprising the amino acid residues of one or more of the biological motifs contained within the 85P1B3 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, 85P1B3-related proteins that contain the amino acid residues of one or more of the biological motifs in the 85P1B3 protein are used to screen for factors that interact with that region of 85P1B3.
85P1B3 protein fragments/subsequences are particularly useful in generating and characterizing domain-specific antibodies (e.g., antibodies recognizing an extracellular or intracellular epitope of an 85P1B3 protein), for identifying agents or cellular factors that bind to 85P1B3 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.
Proteins encoded by the 85P1B3 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 85P1B3 gene product. Antibodies raised against an 85P1B3 protein or fragment thereof are useful in diagnostic and prognostic assays, and imaging methodologies in the management of human cancers characterized by expression of 85P1B3 protein, such as those listed in Table 1. Such antibodies can be expressed intracellularly and used in methods of treating patients with such cancers. 85P1B3-related nucleic acids or proteins are also used in generating HTL or CTL responses.
Various immunological assays useful for the detection of 85P1B3 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 85P1B3-expressing cells (e.g., in radioscintigraphic imaging methods). 85P1B3 proteins are also particularly useful in generating cancer vaccines, as further described herein.
IV.) 85P1B3 Antibodies
Another aspect of the invention provides antibodies that bind to 85P1B3-related proteins. Preferred antibodies specifically bind to a 85P1B3-related protein and do not bind (or bind weakly) to peptides or proteins that are not 85P1B3-related proteins. For example, antibodies bind 85P1B3 can bind 85P1B3-related proteins such as the homologs or analogs thereof.
85P1B3 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 85P1B3 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 85P1B3 is involved, such as advanced or metastatic prostate cancers.
The invention also provides various immunological assays useful for the detection and quantification of 85P1B3 and mutant 85P1B3-related proteins. Such assays can comprise one or more 85P1B3 antibodies capable of recognizing and binding a 85P1B3-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.
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.
In addition, immunological imaging methods capable of detecting prostate cancer and other cancers expressing 85P1B3 are also provided by the invention, including but not limited to radioscintigraphic imaging methods using labeled 85P1B3 antibodies. Such assays are clinically useful in the detection, monitoring, and prognosis of 85P1B3 expressing cancers such as prostate cancer.
85P1B3 antibodies are also used in methods for purifying a 85P1B3-related protein and for isolating 85P1B3 homologues and related molecules. For example, a method of purifying a 85P1B3-related protein comprises incubating an 85P1B3 antibody, which has been coupled to a solid matrix, with a lysate or other solution containing a 85P1B3-related protein under conditions that permit the 85P1B3 antibody to bind to the 85P1B3-related protein; washing the solid matrix to eliminate impurities; and eluting the 85P1B3-related protein from the coupled antibody. Other uses of the 85P1B3 antibodies of the invention include generating anti-idiotypic antibodies that mimic the 85P1B3 protein.
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 85P1B3-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 85P1B3 can also be used, such as a 85P1B3 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 85P1B3-related protein is synthesized and used as an immunogen.
In addition, naked DNA immunization techniques known in the art are used (with or without purified 85P1B3-related protein or 85P1B3 expressing cells) to generate an immune response to the encoded immunogen (for review, see Donnelly et al., 1997, Ann. Rev. Immunol. 15: 617–648).
The amino acid sequence of 85P1B3 as shown in FIG. 2 or FIG. 3 can be analyzed to select specific regions of the 85P1B3 protein for generating antibodies. For example, hydrophobicity and hydrophilicity analyses of the 85P1B3 amino acid sequence are used to identify hydrophilic regions in the 85P1B3 structure. Regions of the 85P1B3 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 85P1B3 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 85P1B3 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.
85P1B3 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 85P1B3-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.
The antibodies or fragments of the invention can also be produced, by recombinant means. Regions that bind specifically to the desired regions of the 85P1B3 protein can also be produced in the context of chimeric or complementarity determining region (CDR) grafted antibodies of multiple species origin. Humanized or human 85P1B3 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.
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 85P1B3 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 85P1B3 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 19 Dec. 2000; U.S. Pat. No. 6,150,584 issued 12 Nov. 2000; and, U.S. Pat. No. 6,114,598 issued 5 Sep. 2000). This method avoids the in vitro manipulation required with phage display technology and efficiently produces high affinity authentic human antibodies.
Reactivity of 85P1B3 antibodies with an 85P1B3-related protein can be established by a number of well known means, including Western blot, immunoprecipitation, ELISA, and FACS analyses using, as appropriate, 85P1B3-related proteins, 85P1B3-expressing cells or extracts thereof A 85P1B3 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 85P1B3 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).
V.) 85P1B3 Cellular Immune Responses
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.
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).
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.)
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).
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.
Various strategies can be utilized to evaluate cellular immunogenicity, including:
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.
2) Immunization of HLA transgenic mice (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.
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 5 ICr release involving peptide-sensitized targets, T cell proliferation, or lymphokine release.
VI.) 85P1B3 Transgenic Animals
Nucleic acids that encode a 85P1B3-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 85P1B3 can be used to clone genomic DNA that encodes 85P1B3. The cloned genomic sequences can then be used to generate transgenic animals containing cells that express DNA that encode 85P1B3. 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 12 Apr. 1988, and U.S. Pat. No. 4,870,009 issued 26 Sep. 1989. Typically, particular cells would be targeted for 85P1B3 transgene incorporation with tissue-specific enhancers.
Transgenic animals that include a copy of a transgene encoding 85P1B3 can be used to examine the effect of increased expression of DNA that encodes 85P1B3. 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.
Alternatively, non-human homologues of 85P1B3 can be used to construct a 85P1B3 “knock out” animal that has a defective or altered gene encoding 85P1B3 as a result of homologous recombination between the endogenous gene encoding 85P1B3 and altered genomic DNA encoding 85P1B3 introduced into an embryonic cell of the animal. For example, cDNA that encodes 85P1B3 can be used to clone genomic DNA encoding 85P1B3 in accordance with established techniques. A portion of the genomic DNA encoding 85P1B3 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 85P1B3 polypeptide.
VII.) Methods for the Detection of 85P1B3
Another aspect of the present invention relates to methods for detecting 85P1B3 polynucleotides and 85P1B3-related proteins, as well as methods for identifying a cell that expresses 85P1B3. The expression profile of 85P1B3 makes it a diagnostic marker for metastasized disease. Accordingly, the status of 85P1B3 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 85P1B3 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.
More particularly, the invention provides assays for the detection of 85P1B3 polynucleotides in a biological sample, such as serum, bone, prostate, and other tissues, urine, semen, cell preparations, and the like. Detectable 85P1B3 polynucleotides include, for example, a 85P1B3 gene or fragment thereof, 85P1B3 mRNA, alternative splice variant 85P1B3 mRNAs, and recombinant DNA or RNA molecules that contain a 85P1B3 polynucleotide. A number of methods for amplifying and/or detecting the presence of 85P1B3 polynucleotides are well known in the art and can be employed in the practice of this aspect of the invention.
In one embodiment, a method for detecting an 85P1B3 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 85P1B3 polynucleotides as sense and antisense primers to amplify 85P1B3 cDNAs therein; and detecting the presence of the amplified 85P1B3 cDNA. Optionally, the sequence of the amplified 85P1B3 cDNA can be determined.
In another embodiment, a method of detecting a 85P1B3 gene in a biological sample comprises first isolating genomic DNA from the sample; amplifying the isolated genomic DNA using 85P1B3 polynucleotides as sense and antisense primers; and detecting the presence of the amplified 85P1B3 gene. Any number of appropriate sense and antisense probe combinations can be designed from the nucleotide sequence provided for the 85P1B3 (FIG. 2) and used for this purpose.
The invention also provides assays for detecting the presence of an 85P1B3 protein in a tissue or other biological sample such as serum, semen, bone, prostate, urine, cell preparations, and the like. Methods for detecting a 85P1B3-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 85P1B3-related protein in a biological sample comprises first contacting the sample with a 85P1B3 antibody, a 85P1B3-reactive fragment thereof, or a recombinant protein containing an antigen binding region of a 85P1B3 antibody; and then detecting the binding of 85P1B3-related protein in the sample.
Methods for identifying a cell that expresses 85P1B3 are also within the scope of the invention. In one embodiment, an assay for identifying a cell that expresses a 85P1B3 gene comprises detecting the presence of 85P1B3 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 85P1B3 riboprobes, Northern blot and related techniques) and various nucleic acid amplification assays (such as RT-PCR using complementary primers specific for 85P1B3, 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 85P1B3 gene comprises detecting the presence of 85P1B3-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 85P1B3-related proteins and cells that express 85P1B3-related proteins.
85P1B3 expression analysis is also useful as a tool for identifying and evaluating agents that modulate 85P1B3 gene expression. For example, 85P1B3 expression is significantly upregulated in prostate cancer, and is expressed in cancers of the tissues listed in Table 1. Identification of a molecule or biological agent that inhibits 85P1B3 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 85P1B3 expression by RT-PCR, nucleic acid hybridization or antibody binding.
VIII.) Methods for Monitoring the Status of 85P1B3-Related Genes and Their Products
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 85P1B3 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 85P1B3 in a biological sample of interest can be compared, for example, to the status of 85P1B3 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 85P1B3 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. 1996 Dec. 9; 376(2):306–14 and U.S. Pat. No. 5,837,501) to compare 85P1B3 status in a sample.
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 85P1B3 expressing cells) as well as the level, and biological activity of expressed gene products (such as 85P1B3 mRNA, polynucleotides and polypeptides). Typically, an alteration in the status of 85P1B3 comprises a change in the location of 85P1B3 and/or 85P1B3 expressing cells and/or an increase in 85P1B3 mRNA and/or protein expression.
85P1B3 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 85P1B3 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 85P1B3 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 85P1B3 gene), Northern analysis and/or PCR analysis of 85P1B3 mRNA (to examine, for example alterations in the polynucleotide sequences or expression levels of 85P1B3 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 85P1B3 proteins and/or associations of 85P1B3 proteins with polypeptide binding partners). Detectable 85P1B3 polynucleotides include, for example, a 85P1B3 gene or fragment thereof, 85P1B3 mRNA, alternative splice variants, 85P1B3 mRNAs, and recombinant DNA or RNA molecules containing a 85P1B3 polynucleotide.
The expression profile of 85P1B3 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 85P1B3 provides information useful for predicting susceptibility to particular disease stages, progression, and/or tumor aggressiveness. The invention provides methods and assays for determining 85P1B3 status and diagnosing cancers that express 85P1B3, such as cancers of the tissues listed in Table 1. For example, because 85P1B3 mRNA is so highly expressed in prostate and other cancers relative to normal prostate tissue, assays that evaluate the levels of 85P1B3 mRNA transcripts or proteins in a biological sample can be used to diagnose a disease associated with 85P1B3 dysregulation, and can provide prognostic information useful in defining appropriate therapeutic options.
The expression status of 85P1B3 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 85P1B3 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.
As described above, the status of 85P1B3 in a biological sample can be examined by a number of well-known procedures in the art. For example, the status of 85P1B3 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 85P1B3 expressing cells (e.g. those that express 85P1B3 mRNAs or proteins). This examination can provide evidence of dysregulated cellular growth, for example, when 85P1B3-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 85P1B3 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 μg 154(2 Pt 1):474–8).
In one aspect, the invention provides methods for monitoring 85P1B3 gene products by determining the status of 85P1B3 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 85P1B3 gene products in a corresponding normal sample. The presence of aberrant 85P1B3 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.
In another aspect, the invention provides assays useful in determining the presence of cancer in an individual, comprising detecting a significant increase in 85P1B3 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 85P1B3 mRNA can, for example, be evaluated in tissue samples including but not limited to those listed in Table 1. The presence of significant 85P1B3 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 85P1B3 mRNA or express it at lower levels.
In a related embodiment, 85P1B3 status is determined at the protein level rather than at the nucleic acid level. For example, such a method comprises determining the level of 85P1B3 protein expressed by cells in a test tissue sample and comparing the level so determined to the level of 85P1B3 expressed in a corresponding normal sample. In one embodiment, the presence of 85P1B3 protein is evaluated, for example, using immunohistochemical methods. 85P1B3 antibodies or binding partners capable of detecting 85P1B3 protein expression are used in a variety of assay formats well known in the art for this purpose.
In a further embodiment, one can evaluate the status of 85P1B3 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 85P1B3 may be indicative of the presence or promotion of a tumor. Such assays therefore have diagnostic and predictive value where a mutation in 85P1B3 indicates a potential loss of function or increase in tumor growth.
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 85P1B3 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 7 Sep. 1999, and U.S. Pat. No. 5,952,170 issued 17 Jan. 1995).
Additionally, one can examine the methylation status of the 85P1B3 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-1 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.
Gene amplification is an additional method for assessing the status of 85P1B3. 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.
Biopsied tissue or peripheral blood can be conveniently assayed for the presence of cancer cells using for example, Northem, dot blot or RT-PCR analysis to detect 85P1B3 expression. The presence of RT-PCR amplifiable 85P1B3 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).
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 85P1B3 mRNA or 85P1B3 protein in a tissue sample, its presence indicating susceptibility to cancer, wherein the degree of 85P1B3 mRNA expression correlates to the degree of susceptibility. In a specific embodiment, the presence of 85P1B3 in prostate or other tissue is examined, with the presence of 85P1B3 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 85P1B3 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 85P1B3 gene products in the sample is an indication of cancer susceptibility (or the emergence or existence of a tumor).
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 85P1B3 mRNA or 85P1B3 protein expressed by tumor cells, comparing the level so determined to the level of 85P1B3 mRNA or 85P1B3 protein expressed in a corresponding normal tissue taken from the same individual or a normal tissue reference sample, wherein the degree of 85P1B3 mRNA or 85P1B3 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 85P1B3 is expressed in the tumor cells, with higher expression levels indicating more aggressive tumors. Another embodiment is the evaluation of the integrity of 85P1B3 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.
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 85P1B3 mRNA or 85P1B3 protein expressed by cells in a sample of the tumor, comparing the level so determined to the level of 85P1B3 mRNA or 85P1B3 protein expressed in an equivalent tissue sample taken from the same individual at a different time, wherein the degree of 85P1B3 mRNA or 85P1B3 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 85P1B3 expression in the tumor cells over time, where increased expression over time indicates a progression of the cancer. Also, one can evaluate the integrity 85P1B3 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.
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 85P1B3 gene and 85P1B3 gene products (or perturbations in 85P1B3 gene and 85P1B3 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 85P1B3 gene and 85P1B3 gene products (or perturbations in 85P1B3 gene and 85P1B3 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.
In one embodiment, methods for observing a coincidence between the expression of 85P1B3 gene and 85P1B3 gene products (or perturbations in 85P1B3 gene and 85P1B3 gene products) and another factor associated with malignancy entails detecting the overexpression of 85P1B3 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 85P1B3 mRNA or protein and PSA mRNA or protein overexpression (or PSCA or PSM expression). In a specific embodiment, the expression of 85P1B3 and PSA mRNA in prostate tissue is examined, where the coincidence of 85P1B3 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.
Methods for detecting and quantifying the expression of 85P1B3 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 85P1B3 mRNA include in situ hybridization using labeled 85P1B3 riboprobes, Northern blot and related techniques using 85P1B3 polynucleotide probes, RT-PCR analysis using primers specific for 85P1B3, 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 85P1B3 mRNA expression. Any number of primers capable of amplifying 85P1B3 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 85P1B3 protein can be used in an immunohistochemical assay of biopsied tissue.
IX.) Identification of Molecules that Interact with 85P1B3
The 85P1B3 protein and nucleic acid sequences disclosed herein allow a skilled artisan to identify proteins, small molecules and other agents that interact with 85P1B3, as well as pathways activated by 85P1B3 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 21 Sep. 1999, U.S. Pat. No. 5,925,523 issued 20 Jul. 1999, U.S. Pat. No. 5,846,722 issued 8 Dec. 1998 and U.S. Pat. No. 6,004,746 issued 21 Dec. 1999. Algorithms are also available in the art for genome-based predictions of protein function (see, e.g., Marcotte, et al., Nature 402: 4 November 1999, 83–86).
Alternatively one can screen peptide libraries to identify molecules that interact with 85P1B3 protein sequences. In such methods, peptides that bind to 85P1B3 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 85P1B3 protein.
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 85P1B3 protein sequences are disclosed for example in U.S. Pat. No. 5,723,286 issued 3 Mar. 1998 and U.S. Pat. No. 5,733,731 issued 31 Mar. 1998.
Alternatively, cell lines that express 85P1B3 are used to identify protein—protein interactions mediated by 85P1B3. Such interactions can be examined using immunoprecipitation techniques (see, e.g., Hamilton B J, et al. Biochem. Biophys. Res. Commun. 1999, 261:646–51). 85P1B3 protein can be immunoprecipitated from 85P1B3-expressing cell lines using anti-85P1B3 antibodies. Alternatively, antibodies against His-tag can be used in a cell line engineered to express fusions of 85P1B3 and a His-tag (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.
Small molecules and ligands that interact with 85P1B3 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 85P1B3'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 85P1B3-related ion channel, protein pump, or cell communication functions are identified and used to treat patients that have a cancer that expresses 85P1B3 (see, e.g., Hille, B., Ionic Channels of Excitable Membranes 2nd Ed., Sinauer Assoc., Sunderland, Mass., 1992). Moreover, ligands that regulate 85P1B3 function can be identified based on their ability to bind 85P1B3 and activate a reporter construct. Typical methods are discussed for example in U.S. Pat. No. 5,928,868 issued 27 Jul. 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 85P1B3 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 modulators which activate or inhibit 85P1B3.
An embodiment of this invention comprises a method of screening for a molecule that interacts with an 85P1B3 amino acid sequence shown in FIG. 2 or FIG. 3, comprising the steps of contacting a population of molecules with the 85P1B3 amino acid sequence, allowing the population of molecules and the 85P1B3 amino acid sequence to interact under conditions that facilitate an interaction, determining the presence of a molecule that interacts with the 85P1B3 amino acid sequence, and then separating molecules that do not interact with the 85P1B3 amino acid sequence from molecules that do. In a specific embodiment, the method further comprises purifying, characterizing and identifying a molecule that interacts with the 85P1B3 amino acid sequence. The identified molecule can be used to modulate a function performed by 85P1B3. In a preferred embodiment, the 85P1B3 amino acid sequence is contacted with a library of peptides.
X.) Therapeutic Methods and Compositions
The identification of 85P1B3 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 contemplated herein, 85P1B3 functions as a transcription factor involved in activating tumor-promoting genes or repressing genes that block tumorigenesis.
Accordingly, therapeutic approaches that inhibit the activity of the 85P1B3 protein are useful for patients suffering from a cancer that expresses 85P1B3. These therapeutic approaches generally fall into two classes. One class comprises various methods for inhibiting the binding or association of the 85P1B3 protein with its binding partner or with other proteins. Another class comprises a variety of methods for inhibiting the transcription of the 85P1B3 gene or translation of 85P1B3 mRNA.
X.A.) Anti-Cancer Vaccines
The invention provides cancer vaccines comprising a 85P1B3-related protein or 85P1B3-related nucleic acid. In view of the expression of 85P1B3, cancer vaccines prevent and/or treat 85P1B3-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).
Such methods can be readily practiced by employing a 85P1B3-related protein, or an 85P1B3-encoding nucleic acid molecule and recombinant vectors capable of expressing and presenting the 85P1B3 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 June 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 85P1B3 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 85P1B3 immunogen contains a biological motif, see e.g., Tables V–XVIII, or a peptide of a size range from 85P1B3 indicated in FIG. 5, FIG. 6, FIG. 7, FIG. 8, and FIG. 9.
The entire 85P1B3 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.
In patients with 85P1B3-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.
Cellular Vaccines:
CTL epitopes can be determined using specific algorithms to identify peptides within 85P1B3 protein that bind corresponding HLA alleles (see e.g., Table IV; EpimerTM and EpimatrixTM, Brown University and, BIMAS, and SYFPEITHI). In a preferred embodiment, the 85P1B3 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.
Antibody-Based Vaccines
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 85P1B3 protein) so that an immune response is generated. A typical embodiment consists of a method for generating an immune response to 85P1B3 in a host, by contacting the host with a sufficient amount of at least one 85P1B3 B cell or cytotoxic T-cell epitope or analog thereof; and at least one periodic interval thereafter re-contacting the host with the 85P1B3 B cell or cytotoxic T-cell epitope or analog thereof. A specific embodiment consists of a method of generating an immune response against a 85P1B3-related protein or a man-made multiepitopic peptide comprising: administering 85P1B3 immunogen (e.g. the 85P1B3 protein or a peptide fragment thereof, an 85P1B3 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 PADRETM 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 85P1B3 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 85P1B3 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.
Nucleic Acid Vaccines:
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 85P1B3. Constructs comprising DNA encoding a 85P1B3-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 85P1B3 protein/immunogen. Alternatively, a vaccine comprises a 85P1B3-related protein. Expression of the 85P1B3-related protein immunogen results in the generation of prophylactic or therapeutic humoral and cellular immunity against cells that bear 85P1B3 protein. Various prophylactic and therapeutic genetic immunization techniques known in the art can be used. 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).
For therapeutic or prophylactic immunization purposes, proteins of the invention can be expressed via 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 85P1B3-related protein into the patient (e.g., intramuscularly or intradermally) to induce an anti-tumor response.
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 elicits 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.
Thus, gene delivery systems are used to deliver a 85P1B3-related nucleic acid molecule. In one embodiment, the full-length human 85P1B3 cDNA is employed. In another embodiment, 85P1B3 nucleic acid molecules encoding specific cytotoxic T lymphocyte (CTL) and/or antibody epitopes are employed.
Ex Vivo Vaccines
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 85P1B3 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 85P1B3 peptides to T cells in the context of MHC class I or II molecules. In one embodiment, autologous dendritic cells are pulsed with 85P1B3 peptides capable of binding to MHC class I and/or class II molecules. In another embodiment, dendritic cells are pulsed with the complete 85P1B3 protein. Yet another embodiment involves engineering the overexpression of the 85P1B3 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 85P1B3 can also be engineered to express immune modulators, such as GM-CSF, and used as immunizing agents.
X. B.) 85P1B3 as a Target for Antibody-Based Therapy
85P1B3 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 85P1B3 is expressed by cancer cells of various lineages relative to corresponding normal cells, systemic administration of 85P1B3-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 85P1B3 are useful to treat 85P1B3-expressing cancers systemically, either as conjugates with a toxin or therapeutic agent, or as naked antibodies capable of inhibiting cell proliferation or function.
85P1B3 antibodies can be introduced into a patient such that the antibody binds to 85P1B3 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 85P1B3, inhibition of ligand binding or signal transduction pathways, modulation of tumor cell differentiation, alteration of tumor angiogenesis factor profiles, and/or apoptosis.
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 85P1B3 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. 85P1B3), the cytotoxic agent will exert its known biological effect (i.e. cytotoxicity) on those cells.
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-85P1B3 antibody) that binds to a marker (e.g. 85P1B3) 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 85P1B3, comprising conjugating the cytotoxic agent to an antibody that immunospecifically binds to a 85P1B3 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.
Cancer immunotherapy using anti-85P1B3 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., ZevalinTM, IDEC Pharmaceuticals Corp. or BexxarTM, Coulter Pharmaceuticals), while others involve co-administration of antibodies and other therapeutic agents, such as HerceptinTM (trastuzumab) with paclitaxel (Genentech, Inc.). To treat prostate cancer, for example, 85P1B3 antibodies can be administered in conjunction with radiation, chemotherapy or hormone ablation.
Although 85P1B3 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.
Cancer patients can be evaluated for the presence and level of 85P1B3 expression, preferably using immunohistochemical assessments of tumor tissue, quantitative 85P1B3 imaging, or other techniques that reliably indicate the presence and degree of 85P1B3 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.
Anti-85P1B3 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-85P1B3 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-85P1B3 mAbs that exert a direct biological effect on tumor growth are useful to treat cancers that express 85P1B3. 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-85P1B3 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.
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 85P1B3 antigen with high affinity but exhibit low or no antigenicity in the patient.
Therapeutic methods of the invention contemplate the administration of single anti-85P1B3 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-85P1B3 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-85P1B3 mAbs are administered in their “naked” or unconjugated form, or can have a therapeutic agent(s) conjugated to them.
Anti-85P1B3 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-85P1B3 antibody preparation, via an acceptable route of administration such as intravenous injection (IV), typically at a dose in the range of about 0. I 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.
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-85P1B3 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 85P1B3 expression in the patient, the extent of circulating shed 85P1B3 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.
Optionally, patients should be evaluated for the levels of 85P1B3 in a given sample (e.g. the levels of circulating 85P1B3 antigen and/or 85P1B3 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 (for example, urine cytology and/or ImmunoCyt levels in bladder cancer therapy, or by analogy, serum PSA levels in prostate cancer therapy).
Anti-idiotypic anti-85P1B3 antibodies can also be used in anti-cancer therapy as a vaccine for inducing an immune response to cells expressing a 85P1B3-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-85P1B3 antibodies that mimic an epitope on a 85P1B3-related protein (see, for example, Wagner et al., 1997, Hybridoma 16: 3340; 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.
X.C.) 85P1B3 as a Target for Cellular Immune Responses
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.
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 tripalmitoyl-5-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))
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 85P1B3 antigen, or derives at least some therapeutic benefit when the antigen was tumor-associated.
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 PADRETM (Epimmune, San Diego, Calif.) molecule (described e.g., in U.S. Pat. No. 5,736,142).
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.
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.
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 34 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.
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.
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.
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.
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.
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.
7.) Where the sequences of multiple variants of the same target protein are present, 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.
X.C.1. Minigene Vaccines
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.
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 85P1B3, the PADRE® universal helper T cell epitope (or multiple HTL epitopes from 85P1B3), and an endoplasmic reticulum-translocating signal sequence can be engineered. A vaccine may also comprise epitopes that are derived from other TAAs.
The immunogenicity of a multi-epitopic minigene can be confirmed 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.
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.
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.
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.
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.
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.
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.
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 (PADRETM, 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.
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.
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, BioTechniques 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.
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.
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 confirmed in transgenic mice in an analogous manner.
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.
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.
X.C.2. Combinations of CTL Peptides with Helper Peptides
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.
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.
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.
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., PADRETM, 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.
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.
X.C.3. Combinations of CTL Peptides with T Cell Priming Agents
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.
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.
X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL and/or HTL Peptides
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 ProgenipoietinTM (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.
The DC can be pulsed ex vivo with a cocktail of peptides, some of which stimulate CTL responses to 85P1B3. 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 85P1B3.
X.D. Adoptive Immunotherapy
Antigenic 85P1B3-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.
X.E. Administration of Vaccines for Therapeutic or Prophylactic Purposes
Pharmaceutical and vaccine compositions of the invention are typically used to treat and/or prevent a cancer that expresses or overexpresses 85P1B3. 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.
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 85P1B3. 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.
For therapeutic use, administration should generally begin at the first diagnosis of 85P1B3-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 85P1B3, a vaccine comprising 85P1B3-specific CTL may be more efficacious in killing tumor cells in patient with advanced disease than alternative embodiments.
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.
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.
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.
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.
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.
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.
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.
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.
A human unit dose form of a composition is typically included in a pharmaceutical composition that comprises a human unit dose of an acceptable carrier, in one embodiment an aqueous carrier, and is administered in a volume/quantity 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). For example a peptide dose for initial immunization can be from about 1 to about 50,000 μg, generally 100–5,000 μg, for a 70 kg patient. For example, for nucleic acids an initial immunization may be performed using an expression vector 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 34 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. For antibodies, a reatment generally involves repeated administration of the anti-85P1B3 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. Moreover, 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-85P1B3 mAb preparation represents an acceptable dosing regimen. As appreciated by those of skill in the art, various factors can influence the ideal dose in a particular case. Such factors include, for example, half life of a composition, the binding affinity of an Ab, the immunogenicity of a substance, the degree of 85P1B3 expression in the patient, the extent of circulating shed 85P1B3 antigen, the desired steady-state 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.
In one embodiment, human unit dose forms of polynucleotides comprise a suitable dosage range or effective amount that provides any therapeutic effect. As appreciated by one of ordinary skill in the art a therapeutic effect depends on a number of factors, including the sequence of the polynucleotide, molecular weight of the polynucleotide and route of administration. Dosages are generally selected by the physician or other health care professional in accordance with a variety of parameters known in the art, such as severity of symptoms, history of the patient and the like. Generally, for a polynucleotide of about 20 bases, a dosage range may be selected from, for example, an independently selected lower limit such as about 0.1, 0.25, 0.5, 1, 2, 5, 10, 20, 30, 40, 50, 60, 80, 100, 200, 300, 400 or 500 mg/kg up to an independently selected upper limit, greater than the lower limit, of about 60, 80, 100, 200, 300, 400, 500, 750, 1000, 1500, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000 or 10,000 mg/kg. For example, a dose may be about any of the following: 0.1 to 100 mg/kg, 0.1 to 50 mg/kg, 0.1 to 25 mg/kg, 0.1 to 10 mg/kg, 1 to 500 mg/kg, 100 to 400 mg/kg, 200 to 300 mg/kg, 1 to 100 mg/kg, 100 to 200 mg/kg, 300 to 400 mg/kg, 400 to 500 mg/kg, 500 to 1000 mg/kg, 500 to 5000 mg/kg, or 500 to 10,000 mg/kg. Generally, parenteral routes of administration may require higher doses of polynucleotide compared to more direct application to the nucleotide to diseased tissue, as do polynucleotides of increasing length.
In one embodiment, human unit dose forms of T-cells comprise a suitable dosage range or effective amount that provides any therapeutic effect. As appreciated by one of ordinary skill in the art, a therapeutic effect depends on a number of factors. Dosages are generally selected by the physician or other health care professional in accordance with a variety of parameters known in the art, such as severity of symptoms, history of the patient and the like. A dose may be about 104 cells to about 106 cells, about 106 cells to about 108 cells, about 108 to about 1011 cells, or about 108 to about 5×1010 cells. A dose may also about 106 cells/m2 to about 1010 cells/m2, or about 106 cells/m2 to about 108 cells/m2.
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.
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.
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%.
For aerosol administration, immunogenic peptides are preferably supplied in finely divided form along with a surfactant and propellant. Typical percentages of peptides are about 0.01%–20% by weight, preferably about 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 about 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 about 0.1%–20% by weight of the composition, preferably about 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.
XI.) Diagnostic and Prognostic Embodiments of 85P1B3.
As disclosed herein, 85P1B3 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).
85P1B3 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. August; 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 1999 July 4(1):99–102 and Minimoto et al., Cancer Detect Prev 2000; 24(1):1–12). Therefore, this disclosure of the 85P1B3 polynucleotides and polypeptides (as well as the 85P1B3 polynucleotide probes and anti-85P1B3 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.
Typical embodiments of diagnostic methods which utilize the 85P1B3 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 85P1B3 polynucleotides described herein can be utilized in the same way to detect 85P1B3 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 85P1B3 polypeptides described herein can be utilized to generate antibodies for use in detecting 85P1B3 overexpression or the metastasis of prostate cells and cells of other cancers expressing this gene.
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 85P1B3 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 85P1B3-expressing cells (lymph node) is found to contain 85P1B3-expressing cells such as the 85P1B3 expression seen in LAPC-4 and LAPC9, xenografts isolated from lymph node and bone metastasis, respectively, this finding is indicative of metastasis.
Alternatively 85P1B3 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 85P1B3 or express 85P1B3 at a different level are found to express 85P1B3 or have an increased expression of 85P1B3 (see, e.g., the 85P1B3 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 85P1B3) such as PSA, PSCA etc. (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3): 233–237 (1996)).
Just as PSA polynucleotide fragments and polynucleotide variants are employed by skilled artisans for use in methods of monitoring PSA, 85P1B3 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 85P1B3 polynucleotide fragment is used as a probe to show the expression of 85P1B3 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. 1996 November–December 11(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 85P1B3 polynucleotide shown in SEQ ID NO: 701) under conditions of high stringency.
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. 85P1B3 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 85P1B3 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 85P1B3 polypeptide shown in SEQ ID NO: 703).
As shown herein, the 85P1B3 polynucleotides and polypeptides (as well as the 85P1B3 polynucleotide probes and anti-85P1B3 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 1. Diagnostic assays that measure the presence of 85P1B3 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 85P1B3 polynucleotides and polypeptides (as well as the 85P1B3 polynucleotide probes and anti-85P1B3 antibodies used to identify the presence of these molecules) must be employed to confirm metastases of prostatic origin.
Finally, in addition to their use in diagnostic assays, the 85P1B3 polynucleotides disclosed herein have a number of other utilities such as their use in the identification of oncogenetic associated chromosomal abnormalities in the chromosomal region to which the 85P1B3 gene maps (see Example 3 below). Moreover, in addition to their use in diagnostic assays, the 85P1B3-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 1996 Jun. 28; 80(1–2): 63–9).
Additionally, 85P1B3-related proteins or polynucleotides of the invention can be used to treat a pathologic condition characterized by the over-expression of 85P1B3. 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 85P1B3 antigen. Antibodies or other molecules that react with 85P1B3 can be used to modulate the function of this molecule, and thereby provide a therapeutic benefit.
XII.) Inhibition of 85P1B3 Protein Function
The invention includes various methods and compositions for inhibiting the binding of 85P1B3 to its binding partner or its association with other protein(s) as well as methods for inhibiting 85P1B3 function.
XII.A.) Inhibition of 85P1B3 with Intracellular Antibodies
In one approach, a recombinant vector that encodes single chain antibodies that specifically bind to 85P1B3 are introduced into 85P1B3 expressing cells via gene transfer technologies. Accordingly, the encoded single chain anti-85P1B3 antibody is expressed intracellularly, binds to 85P1B3 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).
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 (SEQ ID NO: 708) 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.
In one embodiment, intrabodies are used to capture 85P1B3 in the nucleus, thereby preventing its activity within the nucleus. Nuclear targeting signals are engineered into such 85P1B3 intrabodies in order to achieve the desired targeting. Such 85P1B3 intrabodies are designed to bind specifically to a particular 85P1B3 domain. In another embodiment, cytosolic intrabodies that specifically bind to the 85P1B3 protein are used to prevent 85P1B3 from gaining access to the nucleus, thereby preventing it from exerting any biological activity within the nucleus (e.g., preventing 85P1B3 from forming transcription complexes with other factors).
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 6 Jul. 1999).
XII.B.) Inhibition of 85P1B3 with Recombinant Proteins
In another approach, recombinant molecules bind to 85P1B3 and thereby inhibit 85P1B3 function. For example, these recombinant molecules prevent or inhibit 85P1B3 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 85P1B3 specific antibody molecule. In a particular embodiment, the 85P1B3 binding domain of a 85P1B3 binding partner is engineered into a dimeric fusion protein, whereby the fusion protein comprises two 85P1B3 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 85P1B3, whereby the dimeric fusion protein specifically binds to 85P1B3 and blocks 85P1B3 interaction with a binding partner. Such dimeric fusion proteins are further combined into multimeric proteins using known antibody linking technologies.
XII.C.) Inhibition of 85P1B3 Transcription or Translation
The present invention also comprises various methods and compositions for inhibiting the transcription of the 85P1B3 gene. Similarly, the invention also provides methods and compositions for inhibiting the translation of 85P1B3 mRNA into protein.
In one approach, a method of inhibiting the transcription of the 85P1B3 gene comprises contacting the 85P1B3 gene with a 85P1B3 antisense polynucleotide. In another approach, a method of inhibiting 85P1B3 mRNA translation comprises contacting the 85P1B3 mRNA with an antisense polynucleotide. In another approach, a 85P1B3 specific ribozyme is used to cleave the 85P1B3 message, thereby inhibiting translation. Such antisense and ribozyme based methods can also be directed to the regulatory regions of the 85P1B3 gene, such as the 85P1B3 promoter and/or enhancer elements. Similarly, proteins capable of inhibiting a 85P1B3 gene transcription factor are used to inhibit 85P1B3 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.
Other factors that inhibit the transcription of 85P1B3 by interfering with 85P1B3 transcriptional activation are also useful to treat cancers expressing 85P1B3. Similarly, factors that interfere with 85P1B3 processing are useful to treat cancers that express 85P1B3. Cancer treatment methods utilizing such factors are also within the scope of the invention.
XII.D.) General Considerations for Therapeutic Strategies
Gene transfer and gene therapy technologies can be used to deliver therapeutic polynucleotide molecules to tumor cells synthesizing 85P1B3 (i.e., antisense, ribozyme, polynucleotides encoding intrabodies and other 85P1B3 inhibitory molecules). A number of gene therapy approaches are known in the art. Recombinant vectors encoding 85P1B3 antisense polynucleotides, ribozymes, factors capable of interfering with 85P1B3 transcription, and so forth, can be delivered to target tumor cells using such gene therapy approaches.
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.
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 85P1B3 to a binding partner, etc.
In vivo, the effect of a 85P1B3 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.
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.
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).
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.
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.
XIII.) Kits
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 85P1B3-related protein or a 85P1B3 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.
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.
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
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 85P1B3 Gene
To isolate genes that are involved in the progression of androgen dependent (AD) prostate cancer to androgen independent (AI) cancer, we conducted an experiment 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.
The gene 85P1B3 was derived from an LAPC-4 AD (3 days post-castration) minus LAPC-4 AD subtraction. The SSH DNA sequence of 319 bp (FIG. 1) is a fragment of the Opa-Interacting Protein 5 gene (OIP-5).
Materials and Methods
LAPC Xenografts and Human Tissues:
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.
Cell Lines:
Human cell lines (e.g., HeLa) were obtained from the ATCC and were maintained in DMEM with 5% fetal calf serum.
RNA Isolation:
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.








Oligonucleotides:



The following HPLC purified oligonucleotides were used.


 









DPNCDN (cDNA synthesis primer):




5′TTTTGATCAAGCTT303′
(SEQ ID NO: 714)


 


Adaptor 1:


5′CTAATACGACTCACTATAGGGCTCGAGCGGCCGCCCGGGCAG3′
(SEQ ID NO: 715)


3′GGCCCGTCCTAG5′
(SEQ ID NO: 716)


 


Adaptor 2:


5′GTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAG3′
(SEQ ID NO: 717)


3′CGGCTCCTAG5′
(SEQ ID NO: 718)


 


PCR primer 1:


5′CTAATACGACTCACTATAGGGC3′
(SEQ ID NO: 719)


 


Nested primer (NP)1:


5′TCGAGCGGCCGCCCGGGCAGGA3′
(SEQ ID NO: 720)


 


Nested primer (NP)2:


5′AGCGTGGTCGCGGCCGAGGA3′
(SEQ ID NO: 721)






Suppression Subtractive Hybridization:
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.
The gene 85P1B3 was derived from an LAPC-4 AD (3 days post-castration) minus LAPC-4 AD subtraction. The SSH DNA sequence (FIG. 1) was identified.
The cDNA derived from an LAPC-4 AD tumor (grown in intact male mouse) was used as the source of the “driver” cDNA, while the cDNA from the LAPC-4 AD tumor (3 days post-castration) 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.
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.
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.
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.
PCR Amplification, Cloning and Sequencing of Gene Fragments Generated from SSH:
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.
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.
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 NC1-CGAP databases.
RT-PCR Expression Analysis:
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.
Normalization of the first strand cDNAs from multiple tissues was performed by using the primers 5′atatcgccgcgctcgtcgtcgacaa3′ (SEQ ID NO: 722) and 5′agccacacgcagctcattgtagaagg 3′ (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.
To determine expression levels of the 85P1B3 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.
A typical RT-PCR expression analysis is shown in FIG. 10. 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. Strong expression of 85P1B3 was observed in xenograft pool, bladder cancer pool, kidney cancer pool, colon cancer pool, lung cancer pool, breast cancer pool, ovary cancer pool, and cancer metastasis pool. Lower levels of expression were observed in VP1, VP2, and prostate cancer pool.
Example 2
Full Length Cloning of 85P1B3
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.
The gene 85P1B3 was derived from an LAPC-4 AD (3 days post-castration minus LAPC-4 AD) (no castration) subtraction. The SSH DNA sequence (FIG. 1) was designated 85P1B3. cDNA clone 85P1B3-clone A (FIG. 2) was identified by screening a human testis library (Display Target, Pangene) using the 85P1B3 SSH DNA sequence. The cDNA (clone A) of 1,262 bp revealed an ORF encoding 229 amino acids (FIG. 2 and FIG. 3). The nucleotide and protein sequence of 85P1B3 corresponds to the OIP-5 gene (FIG. 4). The 85P1B3 protein is predicted to be cytoplasmic using the PSORT program (URL psort.nibb.ac.jp:8800/form.html).
Example 3
Chromosomal Localization
Chromosomal localization can implicate genes in disease pathogenesis. Several chromosome mapping approaches are available in the art, 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.). 85P1B3 maps to chromosome 15q14, using 85P1B3 sequence and the NCBI BLAST tool
The chromosomal localization of 85P1B3 was also determined using the GeneBridge4 Human/Hamster radiation hybrid (RH) panel (Walter et al., 1994; Nature Genetics 7:22)(Research Genetics, Huntsville Ala.).
The following PCR primers were used:









(SEQ ID NO:732)











85P1B3.1
5′ catgggactctgcatcttaattcc 3′




 









(SEQ ID NO:733)










85P1B3.2
5′ caggttcaggctttattgctgtct 3′






The resulting 85P1B3 mapping vector for the 93 radiation hybrid panel DNAs (100100010101000101000000000000110100000012101100001011100100001011100010010101100110110110101), the 85P1B3 gene was localized to chromosome 15q13.2- q14.
Of note, chromosome 15q13.2- q14 is a region implicated in cancers (Tomlinson et al., Gastroenterology 1999 April; 116(4):789–95).
Example 4
Expression Analysis of 85P1B3 in Normal Tissues and Patient Specimens
Analysis of 85P1B3 by RT-PCR is shown in FIG. 10. Strong expression of 85P1B3 is observed in xenograft pool, bladder cancer pool, kidney cancer pool, colon cancer pool, lung cancer pool, breast cancer pool, ovary cancer pool, and cancer metastasis pool. Lower levels of expression are observed in VP1, VP2, and prostate cancer pool.
Extensive Northern blot analysis of 85P1B3 in 16 human normal tissues demonstrated that 85P1B3 expression is reminiscent of a cancer-testis gene (FIG. 11). A 1.4 kb transcript was detected in testis but not in any other normal tissues. 85P1B3 expression was also shown in prostate cancer xenografts and in all cancer cell lines tested, such as in the cancers of the prostate (LAPC 4AD, LAPC 4AI, LAPC 9AD, LAPC 9AI, LNCaP, PC-3, DU145, Tsu-Prl and LAPC-4 CL), bladder (HT1197, SCaBER, UM-UC-3, TCCSUP, J82, 5637), 293T cell line, Ewing's sarcoma (EWS), brain (PFSK-1, T98G), bone (SK-ES-1, HOS, U-2 OS, RD-ES), lung (CALU-1, A427, NCI-H82, NCI-H146), kidney (769-P, A498, CAKI-1, SW839), breast (CAMA-1, DU4475, MCF-7, MDA-MB-435s), testicular (NTERRA-2, NCC1T, TERA-1, TERA-2), ovarian (OV-1063, PA-1, SW 626), pancreas (PANC-1, Bx PC-3, HPAC, Capan-1), colon (Caco-2, LoVo, T84, Colo205), and cervical (A431) (FIG. 12). These results indicate that 85P1B3 is a testis-specific gene that is upregulated in multiple cancers.
Expression of 85P1B3 was assayed in a panel of human patient tumors (T) and their respective matched normal tissues (N) on RNA dot blots (FIG. 13). 85P1B3 expression was seen in the cancers of the breast, prostate, uterus, ovary, cervix, stomach and lung. The expression detected in normal adjacent tissues (isolated from diseased tissues) but not in normal tissues (isolated from healthy donors) may indicate that these tissues are not fully normal and that 85P1B3 may be expressed in early stage tumors. 85P1B3 was also found to be highly expressed in all human cancer cell lines tested, HeLa (cervical carcinoma), Daudi (Burkitt's lymphoma), K562 (CML), HL-60 (PML), G361 (melanoma), A549 (lung carcinoma), MOLT4 (lymphoblastic leukemia), SW480 (colorectal carcinoma), and Raji (Burkitt's lymphoma).
Northern blot analysis on individual patient tumor specimens showed expression of 85P1B3 in two colon tumor tissues tested, and in the colon cancer cell lines Colo 205, LoVo, T84 and Caco-2, but not in normal colon (FIG. 14).
Expression of 85P1B3 was also detected in the tumors of 4 out of 5 bladder cancer patients, and in all three bladder cancer cell lines tested, but not in normal bladder (FIG. 15).
In lung cancer samples, 85P1B3 expression was observed in three lung tumor specimens, all three lung cancer cell lines tested, but not in normal lung (FIG. 16).
In order to assay for androgen regulation of 85P1B3 expression, LAPC-9AD tumor cells were injected in male mice (FIG. 17). When tumors reached a palpable size (0.3–0.5 cm in diameter), mice were castrated and tumors harvested at different time points. RNA was isolated from the xenograft tissues and Northern blots with 10 μg of total RNA/lane were probed with the 85P1B3 SSH fragment. Results showed that expression of 85P1B3 is not affected by androgen deprivation, and therefore, is not androgen-regulated.
The restricted expression of 85P1B3 in normal tissues and the expression detected in bladder cancer, kidney cancer, colon cancer, lung cancer, prostate cancer, ovarian cancer, and breast cancer indicate that 85P1B3 is a therapeutic and/or prophylactic target and a prognostic and/or diagnostic marker for human cancers.
Example 5
Production of Recombinant 85P1B3 in Prokaryotic Systems
To express recombinant 85P1B3 in prokaryotic cells, the full or partial length 85P1B3 cDNA sequences can be cloned into any one of a variety of expression vectors known in the art. One or more of the following regions of 85P1B3 are expressed in these constructs, amino acids 1 to 229; or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more contiguous amino acids from 85P1B3, variants, or analogs thereof.
A. In vitro Transcription and Translation Constructs:
pCRII: To generate 85P1B3 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 85P1B3 cDNA. The pCRII vector has Sp6 and T7 promoters flanking the insert to drive the transcription of 85P1B3 RNA for use as probes in RNA in situ hybridization experiments. These probes are used to analyze the cell and tissue expression of 85P1B3 at the RNA level. Transcribed 85P1B3 RNA representing the cDNA amino acid coding region of the 85P1B3 gene is used in in vitro translation systems such as the TnTTM Coupled Reticulolysate System (Promega, Corp., Madison, Wis.) to synthesize 85P1B3 protein.
B. Bacterial Constructs:
pGEX Constructs: To generate recombinant 85P1B3 proteins in bacteria that are fused to the Glutathione S-transferase (GST) protein, all or parts of the 85P1B3 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.). These constructs allow controlled expression of recombinant 85P1B3 protein sequences with GST fused at the amino-terminus and a six histidine epitope (6×His) (SEQ ID NO: 709) 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 anti-His antibodies. The 6×His tag (SEQ ID NO: 709) is generated by adding 6 histidine codons to the cloning primer at the 3′ end, e.g., of the open reading frame (ORF). A proteolytic cleavage site, such as the PreScissionTM recognition site in pGEX-6P-1, may be employed such that it permits cleavage of the GST tag from 85P1B3-related protein. The ampicillin resistance gene and pBR322 origin permits selection and maintenance of the pGEX plasmids in E. coli. 
In one embodiment, a GST-fusion protein encoding the full length 85P1B3 protein sequence (amino acids 1–229) was constructed and purified from induced bacteria. This preparation was then used as immunogen to generate a rabbit anti-85P1B3 polyclonal antibody (see the section entitled “Generation of 85P1B3 Polyclonal Antibodies”. As can be seen in FIG. 20A, the pAb strongly recognizes the original GST-fusion immunogen as well as 85P1B3 protein expressed in 293T cells (FIG. 20B and FIG. 20C).
pMAL Constructs: To generate, in bacteria, recombinant 85P1B3 proteins that are fused to maltose-binding protein (MBP), all or parts of the 85P1B3 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.). These constructs allow controlled expression of recombinant 85P1B3 protein sequences with MBP fused at the amino-terminus and a 6×His epitope tag at the carboxyl-terminus. The MBP and 6×His tags (SEQ ID NO: 709) 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 epitope tag (SEQ ID NO: 709) is generated by adding 6 histidine codons to the 3′ cloning primer. A Factor Xa recognition site permits cleavage of the pMAL tag from 85P1B3. 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.
pET Constructs: To express 85P1B3 in bacterial cells, all or parts of the 85P1B3 cDNA protein coding sequence are cloned into the pET family of vectors (Novagen, Madison, Wis.). These vectors allow tightly controlled expression of recombinant 85P1B3 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 (SEQ ID NO: 709) and S-TagTM that aid purification and detection of the recombinant protein. For example, constructs are made utilizing pET NusA fusion system 43.1 such that regions of the 85P1B3 protein are expressed as amino-terminal fusions to NusA.
C. Yeast Constructs:
pESC Constructs: To express 85P1B3 in the yeast species Saccharomyces cerevisiae for generation of recombinant protein and functional studies, all or parts of the 85P1B3 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 FlagTM or Myc epitope tags in the same yeast cell. This system is useful to confirm protein—protein interactions of 85P1B3. In addition, expression in yeast yields similar post-translational modifications, such as glycosylations and phosphorylations, that are found when expressed in eukaryotic cells.
pESP Constructs: To express 85P1B3 in the yeast species Saccharomyces pombe, all or parts of the 85P1B3 cDNA protein coding sequence are cloned into the pESP family of vectors. These vectors allow controlled high level of expression of a 85P1B3 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 FlagTM epitope tag allows detection of the recombinant protein with anti-FlagTM antibody.
Example 6
Production of Recombinant 85P1B3 in Eukaryotic Systems
A. Mammalian Constructs:
To express recombinant 85P1B3 in eukaryotic cells, the full or partial length 85P1B3 cDNA sequences can be cloned into any one of a variety of expression vectors known in the art. One or more of the following regions of 85P1B3 are expressed in these constructs, amino acids 1 to 229; or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more contiguous amino acids from 85P1B3, variants, or analogs thereof.
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-85P1B3 polyclonal serum, described herein.
pcDNA4/HisMax Constructs: To express 85P1B3 in mammalian cells, the 85P1B3 ORF, or portions thereof, of 85P1B3 are cloned into pcDNA4/HisMax Version A (Invitrogen, Carlsbad, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter and the SP16 translational enhancer. The recombinant protein has XpressTM and six histidine (6×His) (SEQ ID NO: 709) epitopes fused to the amino-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. 
pcDNA3.1/MycHis Constructs: To express 85P1B3 in mammalian cells, the 85P1B3 ORF, or portions thereof, of 85P1B3 with a 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 6×His epitope (SEQ ID NO: 709) fused to the carboxyl-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. 
pcDNA3.1/CT-GFP-TOPO Construct: To express 85P1B3 in mammalian cells and to allow detection of the recombinant proteins using fluorescence, the 85P1B3 ORF, or portions thereof, of 85P1B3 with a consensus Kozak translation initiation site are cloned into pcDNA3.1/CT-GFP-TOPO (Invitrogen, CA). Protein expression is driven from the cytomegalovirus (CMV) promoter. The recombinant proteins have the Green Fluorescent Protein (GFP) fused to the carboxyl-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. Additional constructs with an amino-terminal GFP fusion are made in pcDNA3.1INT-GFP-TOPO spanning the entire length of the 85P1B3 proteins.
PAPtag: The 85P1B3 ORF, or portions thereof of 85P1B3 are cloned into pAPtag-5 (GenHunter Corp. Nashville, Tenn.). This construct generates an alkaline phosphatase fusion at the carboxyl-terminus of the 85P1B3 proteins while fusing the IgGK signal sequence to the amino-terminus. Constructs are also generated in which alkaline phosphatase with an amino-terminal IgGK signal sequence is fused to the amino-terminus of 85P1B3 proteins. The resulting recombinant 85P1B3 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 85P1B3 proteins. Protein expression is driven from the CMV promoter and the recombinant proteins also contain myc and 6×His (SEQ ID NO: 709) epitopes fused at the carboxyl-terminus that facilitates detection and purification. The Zeocin resistance gene present in the vector allows for selection of mammalian cells expressing the recombinant protein and the ampicillin resistance gene permits selection of the plasmid in E. coli. 
ptag5: The 85P1B3 ORF, or portions thereof, of 85P1B3 was cloned into pTag-5. This vector is similar to pAPtag but without the alkaline phosphatase fusion. This construct generated 85P1B3 protein with an amino-terminal IgGK signal sequence and myc and 6×His epitope (SEQ ID NO: 709) tags at the carboxyl-terminus that facilitate detection and affinity purification. The resulting recombinant 85P1B3 protein was optimized for secretion into the media of transfected mammalian cells, and was used as immunogen or ligand to identify proteins such as ligands or receptors that interact with the 85P1B3 proteins. Protein expression is driven from the CMV promoter. The Zeocin resistance gene present in the vector allows for selection of mammalian cells expressing the protein, and the ampicillin resistance gene permits selection of the plasmid in E. coli. 
PsecFc: The 85P1B3 ORF, or portions thereof, of 85P1B3 are also cloned into psecFc. The psecFc vector was assembled by cloning the human immunoglobulin G1 (IgG) Fc (hinge, CH2, CH3 regions) into pSecTag2 (Invitrogen, California). This construct generates an IgG1 Fc fusion at the carboxyl-terminus of the 85P1B3 proteins, while fusing the IgGK signal sequence to N-terminus. 85P1B3 fusions utilizing the murine IgG1 Fc region are also used. The resulting recombinant 85P1B3 proteins are optimized for secretion into the media of transfected mammalian cells, and can be used as immunogens or to identify proteins such as ligands or receptors that interact with the 85P1B3 protein. Protein expression is driven from the CMV promoter. The hygromycin resistance gene present in the vector allows for selection of mammalian cells that express the recombinant protein, and the ampicillin resistance gene permits selection of the plasmid in E. coli. 
pSRα Constructs: To generate mammalian cell lines that express 85P1B3, or portions thereof, constitutively, the ORF of 85P1B3 was cloned into pSRα constructs. 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, 85P1B3, into the host cell-lines. Protein expression is driven from a long terminal repeat (LTR). The Neomycin resistance gene present in the vector 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. FIG. 18 shows expression of 85P1B3 using the pSRα retroviral vector in the prostate cancer cell line PC3. 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.
Additional pSRα constructs are made that fuse an epitope tag such as the FLAGTM tag to the carboxyl-terminus of 85P1B3 sequences to allow detection using anti-Flag antibodies. For example, the FLAGTM sequence 5′ gat tac aag gat gac gac gat aag 3′ (SEQ ID NO: 734) is added to cloning primer at the 3′ end of the ORF. Additional pSRα constructs are made to produce both amino-terminal and carboxyl-terminal GFP and myc/6×His (SEQ ID NO: 709) fusion proteins of the full-length 85P1B3 proteins.
Additional Viral Vectors: Additional constructs are made for viral-mediated delivery and expression of 85P1B3. High virus titer leading to high level expression of 85P1B3 is achieved in viral delivery systems such as adenoviral vectors and herpes amplicon vectors. The 85P1B3 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, 85P1B3 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.
Regulated Expression Systems: To control expression of 85P1B3 in mammalian cells, coding sequences of 85P1B3, or portions thereof, 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 85P1B3. These vectors are thereafter used to control expression of 85P1B3 in various cell lines such as SCaBER, NIH 3T3, 293 or rat-1 cells.
B. Baculovirus Expression Systems
To generate recombinant 85P1B3 proteins in a baculovirus expression system, 85P1B3 ORF, or portions thereof, are cloned into the baculovirus transfer vector pBlueBac 4.5 (Invitrogen), which provides a His-tag at the N-terminus. Specifically, pBlueBac-85P1B3 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 85P1B3 protein is then generated by infection of HighFive insect cells (Invitrogen) with purified baculovirus. Recombinant 85P1B3 protein can be detected using anti-85P1B3 or anti-His-tag antibody. 85P1B3 protein can be purified and used in various cell-based assays or as immunogen to generate polyclonal and monoclonal antibodies specific for 85P1B3.
Example 7
Antigenicity Profiles and Secondary Structure
FIG. 5, FIG. 6, FIG. 7, FIG. 8, and FIG. 9 depict graphically five amino acid profiles of the 85P1B3 amino acid sequence, each assessment available by accessing the ProtScale website on the ExPasy molecular biology server.
These profiles: FIG. 5, Hydrophilicity, (Hopp T. P., Woods K. R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824–3828); FIG. 6, Hydropathicity, (Kyte J., Doolittle R. F., 1982. J. Mol. Biol. 157:105–132); FIG. 7, Percentage Accessible Residues (Janin J., 1979 Nature 277:491–492); FIG. 8, Average Flexibility, (Bhaskaran R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res. 32:242–255); FIG. 9, 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 85P1B3 protein. Each of the above amino acid profiles of 85P1B3 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.
Hydrophilicity (FIG. 5), Hydropathicity (FIG. 6) and Percentage Accessible Residues (FIG. 7) 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.
Average Flexibility (FIG. 8) and Beta-turn (FIG. 9) 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.
Antigenic sequences of the 85P1B3 protein indicated, e.g., by the profiles set forth in FIG. 5, FIG. 6, FIG. 7, FIG. 8, and/or FIG. 9 are used to prepare immunogens, either peptides or nucleic acids that encode them, to generate therapeutic and diagnostic anti-85P1B3 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, 24, 25, 30, 35, 40, 45, 50 or more than 50 contiguous amino acids, or the corresponding nucleic acids that encode them, from the 85P1B3 protein. In particular, peptide immunogens of the invention can comprise, a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 229 that includes an amino acid position having a value greater than 0.5 in the Hydrophilicity profile of FIG. 5; a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 229 that includes an amino acid position having a value less than 0.5 in the Hydropathicity profile of FIG. 6; a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 229 that includes an amino acid position having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 7; a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 229 that includes an amino acid position having a value greater than 0.5 in the Average Flexibility profile on FIG. 8; and, a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to 229 that includes an amino acid position having a value greater than 0.5 in the Beta-turn profile of FIG. 9. 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.
The secondary structure of 85P1B3, namely the predicted presence and location of alpha helices, extended strands, and random coils, is predicted from the primary amino acid sequence using the HNN—Hierarchical Neural Network method (Guermeur, 1997), accessed from the ExPasy molecular biology server. The analysis indicates that 85P1B3 is composed of 36.8% alpha helix, 13.97% extended strand, and 49.34% random coil (FIG. 21A).
Analysis for the potential presence of transmembrane domains in 85P1B3 was carried out using a variety of transmembrane prediction algorithms accessed from the ExPasy molecular biology server. A potential transmembrane domain composed of amino acids 129–149 is predicted by the TMpred program (FIG. 21B). HMMTop predicts a transmembrane region from amino acids 134–158. The SOSUI and TMHMM (FIG. 21C) programs predict that 85P1B3 is a soluble protein without transmembrane domains. The results of the transmembrane predictions are summarized in Table XXV.
Example 8
Generation of 85P1B3 Polyclonal Antibodies
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 85P1B3 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. 5, FIG. 6, FIG. 7, FIG. 8, or FIG. 9 for amino acid profiles that indicate such regions of 85P1B3).
For example, 85P1B3 recombinant bacterial fusion proteins or peptides encoding hydrophilic, flexible, beta-turn regions of the 85P1B3 sequence, such as amino acids 1–77 and 190–229 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 190–206 of 85P1B3 is conjugated to KLH and used to immunize the rabbit. Alternatively the immunizing agent may include all or portions of the 85P1B3 protein, analogs or fusion proteins thereof. For example, the 85P1B3 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.
In one embodiment, a GST-fusion protein encoding the full length 85P1B3 protein sequence was produced and purified and used as immunogen (see the section entitled “Production of 85P1B3 in Prokaryotic Systems”). Shorter sequences are also fused to GST in order to direct antibody to specific regions of the protein such as amino acids 1–77 to generate amino-terminal specific antibodies. Other recombinant bacterial fusion proteins that may be employed include maltose binding protein, LacZ, thioredoxin, NusA, or an immunoglobulin constant region (see the section entitled “Production of 85P1B3 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., Umes, M., Grosmaire, L., Damle, N., and Ledbetter, L. (1991) J. Exp. Med. 174, 561–566).
In addition to bacterial derived fusion proteins, mammalian expressed protein antigens are also used. These antigens are expressed from mammalian expression vectors such as the Tag5 and Fc-fusion vectors (see the section entitled “Production of Recombinant 85P1B3 in Eukaryotic Systems”), and retain post-translational modifications such as glycosylations found in native protein. In one embodiment, a predicted antigenic region of 85P1B3, amino acids 190–229, is cloned into the Tag5 mammalian secretion vector. The recombinant protein is purified by metal chelate chromatography from tissue culture supernatants of 293T cells stably expressing the recombinant vector. The purified Tag5 85P1B3 protein is then used as immunogen.
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).
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.
To test reactivity and specificity of immune serum, such as the rabbit serum raised from immunization with GST-85P1B3 full length fusion protein, the full-length 85P1B3 cDNA was cloned into pCDNA 3.1 myc-his expression vector (Invitrogen, see the Example entitled “Production of Recombinant 85P1B3 in Eukaryotic Systems”). After transfection of the constructs into 293T cells, cell lysates were probed with the anti-85P1B3 serum and with anti-His antibody (Santa Cruz Biotechnologies, Santa Cruz, Calif.) to determine specific reactivity to denatured 85P1B3 protein using the Western blot technique. As can be seen in FIG. 20B, the anti-85P1B3 pAb specifically recognized 85P1B3 protein expressed in 293T cells that is the same molecular weight as that detected by the anti-His Ab (FIG. 20C). Recognition of native protein by the antiserum is determined by immunoprecipitation and flow cytometric analyses of 293T and other recombinant 85P1B3-expressing cells. In addition, specificity of the antiserum is tested by Western blot, immunoprecipitation, fluorescent microscopy, and flow cytometric techniques using cells that endogenously express 85P1B3.
To purify the anti-serum derived from the GST-85P1B3 immunized rabbit, the serum was passed over an affinity column composed of GST to remove anti-GST reactive antibodies. The serum was then further purified by protein G affinity chromatography to isolate the IgG fraction. Serum from rabbits immunized with other fusion proteins, such as MBP fusion proteins, are purified by depletion of antibodies reactive to 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 9
Generation of 85P1B3 Monoclonal Antibodies (mAbs)
In one embodiment, therapeutic mAbs to 85P1B3 comprise those that react with epitopes of the protein that would disrupt or modulate the biological function of 85P1B3, for example those that would disrupt its interaction with ligands or proteins that mediate or are involved in its biological activity. Therapeutic mAbs also comprise those which specifically bind epitopes of 85P1B3 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 85P1B3 protein or regions of the 85P1B3 protein predicted to be antigenic from computer analysis of the amino acid sequence (see, e.g., FIG. 5, FIG. 6, FIG. 7, FIG. 8, or FIG. 9, and the Example entitled “Antigenicity Profiles”).
Immunogens include peptides, recombinant bacterial proteins, and mammalian expressed Tag 5 proteins and human and murine IgG FC fusion proteins. To generate mAbs to 85P1B3, mice are first immunized intraperitoneally (IP) with, typically, 10–50 μg of protein immunogen mixed in complete Freund's adjuvant. Mice are then subsequently immunized IP every 2–4 weeks with, typically, 10–50 μg of antigen mixed in incomplete Freund's adjuvant. Alternatively, MPL-TDM adjuvant is used in immunizations. In addition, a DNA-based immunization protocol is employed in which a mammalian expression vector encoding 85P1B3 sequence is used to immunize mice by direct injection of the plasmid DNA. For example, either pCDNA 3.1 encoding the full length 85P1B3 cDNA, amino acids 1–77, or 190–229 of 85P1B3 (predicted to be antigenic from sequence analysis, see, e.g., FIG. 5, FIG. 6, FIG. 7, FIG. 8 or FIG. 9) fused at the amino-terminus to an IgK leader sequence and at the carboxyl-terminus to the coding sequence of murine or human IgG Fc region, is used. This protocol is used alone and in combination with protein 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, fluorescence microscopy, 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).
In one embodiment for generating 85P1B3 monoclonal antibodies, a glutathione-S-transferase (GST) fusion protein encoding the full length 85P1B3 protein is expressed and purified. A cleavage fragment encoding 85P1B3 specific amino acids is then used as immunogen in which GST is removed by site-specific proteolysis. Balb C mice are initially immunized intraperitoneally with 25 μg of the 85P1B3 cleavage protein mixed in complete Freund's adjuvant. Mice are subsequently immunized every two weeks with 25 μg of 85P1B3 cleavage protein mixed in incomplete Freund's adjuvant for a total of three immunizations. The titer of serum from immunized mice is determined by ELISA using the full length GST-fusion protein and the cleaved immunogen. Reactivity and specificity of serum to full length 85P1B3 protein is monitored by Western blotting, immunoprecipitation and flow cytometry using 293T cells transfected with an expression vector encoding the 85P1B3 cDNA. Other recombinant 85P1B3-expressing cells (see e.g., the Example entitled “Production of 85P1B3 in Eukaryotic Systems”) or cells endogenously expressing 85P1B3 are also used. Mice showing the strongest reactivity are rested and given a final injection of 85P1B3 cleavage protein in PBS and then sacrificed four days later. The spleens of the sacrificed mice are 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, immunoprecipitation, fluorescent microscopy, and flow cytometry to identify 85P1B3 specific antibody-producing clones.
The binding affinity of a 85P1B3 monoclonal antibody is determined using standard technologies. Affinity measurements quantify the strength of antibody to epitope binding and are used to help define which 85P1B3 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
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.
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.
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
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 and confirmation 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.
Computer Searches and Algorithms for Identification of Supermotif and/or Motif-Bearing Epitopes
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 85P1B3 set forth in FIGS. 2 and 3.
Computer searches for epitopes bearing HLA Class I or Class II supermotifs or motifs are performed as follows. All translated 85P1B3 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.
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:

“ΔG”=a1i×a2i×a3i . . . ×ani 

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.

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.
Selection of HLA-A2 Supertype Cross-Reactive Peptides
Complete protein sequences from 85P1B3 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).
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.
Selection of HLA-A3 Supermotif-Bearing Epitopes
The 85P1B3 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.
Selection of HLA-B7 Supermotif Bearing Epitopes
The 85P1B3 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.
Selection of A1 and A24 Motif-Bearing Epitopes
To further increase population coverage, HLA-A1 and -A24 epitopes can also be incorporated into vaccine compositions. An analysis of the 85P1B3 protein can also be performed to identify HLA-A1- and A24-motif-containing sequences.
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
Cross-reactive candidate CTL A2-supermotif-bearing peptides that are identified as described herein are selected to confirm in vitro immunogenicity. Confirmation is performed using the following methodology:
Target Cell Lines for Cellular Screening:
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 confirm the ability of peptide-specific CTLs to recognize endogenous antigen.
Primary CTL Induction Cultures:
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.
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 μg/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.
Setting up induction cultures: 0.25 ml cytokine-generated DC (at 1×105 cells/ml) 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.
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 β2 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.
Measurement of CTL Lytic Activity by 51Cr Release.
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.
Adherent target cells are removed from culture flasks with trypsin-EDTA. Target cells are labelled with 200 μCi of 51Cr sodium chromate (Dupont, Wilmington, Del.) for 1 hour at 37° C. Labelled 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 (10011) 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.

Maximum and spontaneous release are determined by incubating the labelled targets with 1% Trition 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.
In situ Measurement of Human IFNγ Production as an Indicator of Peptide-Specific and Endogenous Recognition
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.
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.
CTL Expansion.
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.
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.
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.
Immunogenicity can also be confirmed using PBMCs isolated from patients bearing a tumor that expresses 85P1B3. 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.
Evaluation of A*03/A11 Immunogenicity
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.
Evaluation of B7 Immunogenicity
Immunogenicity screening of the B7-supertype cross-reactive binding peptides identified as set forth herein are confirmed in a manner analogous to the confirmation of A2- and A3-supermotif-bearing peptides.
Peptides bearing other supermotifs/motifs, e.g., HLA-A1, HLA-A24 etc. are also confirmed using similar methodology
Example 13
Implementation of the Extended Supermotif to Improve the Binding Capacity of Native Epitopes by Creating Analogs
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.
Analoging at Primary Anchor Residues
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.
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.
Alternatively, a peptide is confirmed as binding one or all supertype members and then analogued to modulate binding affinity to any one (or more) of the supertype members to add population coverage.
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 500 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).
In the cellular screening of these peptide analogs, it is important to confirm that analog-specific CTLs are also able to recognize the wild-type peptide and, when possible, target cells that endogenously express the epitope.
Analoging of HLA-A3 and B7-Supermotif-Bearing Peptides
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.
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 confirmed as having A3-supertype cross-reactivity.
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).
Analoging at primary anchor residues of other motif and/or supermotif-bearing epitopes is performed in a like manner.
The analog peptides are then be confirmed 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.
Analoging at Secondary Anchor Residues
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.
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. Analogued peptides are additionally tested for the ability to stimulate a recall response using PBMC from patients with 85P1B3-expressing tumors.
Other Analoging Strategies
Another form of peptide analoguing, 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 1. Chen, John Wiley & Sons, England, 1999).
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 and Confirmation of 85P1B3-derived Sequences with HLA-DR Binding Motifs
Peptide epitopes bearing an HLA class II supermotif or motif are identified and confirmed as outlined below using methodology similar to that described for HLA Class I peptides.
Selection of HLA-DR-Supermotif-Bearing Epitopes.
To identify 85P1B3-derived, HLA class II HTL epitopes, the 85P1B3 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).
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.
The 85P1B3-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. 85P1B3-derived peptides found to bind common HLA-DR alleles are of particular interest.
Selection of DR3 Motif Peptides
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.
To efficiently identify peptides that bind DR3, target 85P1B3 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 confirmed as having 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.
DR3 binding epitopes identified in this manner are included in vaccine compositions with DR supermotif-bearing peptide epitopes.
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 DR3 binding.
Example 15
Immunogenicity of 85P1B3-Derived HTL Epitopes
This example determines immunogenic DR supermotif- and DR3 motif-bearing epitopes among those identified using the methodology set forth herein.
Immunogenicity of HTL epitopes are confirmed 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 85P1B3-expressing tumors.
Example 16
Calculation of Phenotypic Frequencies of HLA-supertypes in Various Ethnic Backgrounds to Determine Breadth of Population Coverage
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.
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].
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).
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 analagous approach can be used to estimate population coverage achieved with combinations of class II motif-bearing epitopes.
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.
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
This example confirms that CTL induced by native or analoged peptide epitopes identified and selected as described herein recognize endogenously synthesized, i.e., native antigens.
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 85P1B3 expression vectors.
The results demonstrate that CTL lines obtained from animals primed with peptide epitope recognize endogenously synthesized 85P1B3 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
This example illustrates the induction of CTLs and HTLs in transgenic mice, by use of a 85P1B3-derived CTL and HTL peptide vaccine compositions. The vaccine composition used herein comprise peptides to be administered to a patient with a 85P1B3-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.
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 confirm 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 syngenic irradiated LPS-activated lymphoblasts coated with peptide.
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)
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.
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: [(1/50,000)−(1/500,000)]×106=18 LU.
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 confirm 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 85P1B3-specific Vaccine
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.
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.
Epitopes are selected which, upon administration, mimic immune responses that are correlated with 85P1B3 clearance. The number of epitopes used depends on observations of patients who spontaneously clear 85P1B3. For example, if it has been observed that patients who spontaneously clear 85P1B3 generate an immune response to at least three (3) from 85P1B3 antigen, then three or four (34) epitopes should be included for HLA class I. A similar rationale is used to determine HLA class II epitopes.
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 from the BIMAS web site, at URL bimas.dcrt.nih.gov.
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.
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 85P1B3, 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.
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 85P1B3.
Example 20
Construction of “Minigene” Multi-Epitope DNA Plasmids
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.
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 85P1B3, are selected such that multiple supermotifs/motifs are represented to ensure broad population coverage. Similarly, HLA class II epitopes are selected from 85P1B3 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.
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.
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.
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.
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.
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
The degree to which a plasmid construct, for example a plasmid constructed in accordance with the previous Example, is able to induce immunogenicity is confirmed in vitro by determining 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).
Alternatively, immunogenicity is confirmed 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.
For example, to confirm 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.
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.
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.
To confirm 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.
DNA minigenes, constructed as described in the previous Example, can also be confirmed 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).
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.
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
Vaccine compositions of the present invention can be used to prevent 85P1B3 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 85P1B3-associated tumor.
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 Freunds 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 85P1B3-associated disease.
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 85P1B3 Sequences
A native 85P1B3 polyprotein sequence is analyzed, 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.
The vaccine composition will include, for example, multiple CTL epitopes from 85P1B3 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.
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 85P1B3, 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.
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
The 85P1B3 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 85P1B3 and such other antigens. For example, a vaccine composition can be provided as a single polypeptide that incorporates multiple epitopes from 85P1B3 as well as tumor-associated antigens that are often expressed with a target cancer associated with 85P1B3 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
Peptides of the invention may be used to analyze an immune response for the presence of specific antibodies, CTL or HTL directed to 85P1B3. 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.
In this example highly sensitive human leukocyte antigen tetrameric complexes (“tetramers”) are used for a cross-sectional analysis of, for example, 85P1B3 HLA-A*0201-specific CTL frequencies from HLA A*0201-positive individuals at different stages of disease or following immunization comprising an 85P1B3 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.
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 85P1B3 epitope, and thus the status of exposure to 85P1B3, or exposure to a vaccine that elicits a protective or therapeutic response.
Example 26
Use of Peptide Epitopes to Evaluate Recall Responses
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 85P1B3-associated disease or who have been vaccinated with an 85P1B3 vaccine.
For example, the class I restricted CTL response of persons who have been vaccinated may be analyzed. The vaccine may be any 85P1B3 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.
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.
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).
Target cell lines are autologous and allogeneic EBV-transformed B-LCL that are either purchased from the American Society for Histocompatibility and Immunogenetics (ASHI, Boston, Mass.) or established from the pool of patients as described (Guilhot, et al. J. Virol. 66:2670–2678, 1992).
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.
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 oftargets by detergent (2% Triton X-100; Sigma Chemical Co., St. Louis, Mo.). Spontaneous release is <25% of maximum release for all experiments.
The results of such an analysis indicate the extent to which HLA-restricted CTL populations have been stimulated by previous exposure to 85P1B3 or an 85P1B3 vaccine.
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 85P1B3 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
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:
A total of about 27 individuals are enrolled and divided into 3 groups:
Group I: 3 subjects are injected with placebo and 6 subjects are injected with 5 μg of peptide composition;
Group II: 3 subjects are injected with placebo and 6 subjects are injected with 50 μg peptide composition;
Group III: 3 subjects are injected with placebo and 6 subjects are injected with 500 μg of peptide composition.
After 4 weeks following the first injection, all subjects receive a booster inoculation at the same dosage.
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.
Safety: The incidence of adverse events is monitored in the placebo and drug treatment group and assessed in terms of degree and reversibility.
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.
The vaccine is found to be both safe and efficacious.
Example 28
Phase II Trials in Patients Expressing 85P1B3
Phase II trials are performed to study the effect of administering the CTL-HTL peptide compositions to patients having cancer that expresses 85P1B3. The main objectives of the trial are to determine an effective dose and regimen for inducing CTLs in cancer patients that express 85P1B3, 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:
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.
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 85P1B3.
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 85P1B3-associated disease.
Example 29
Induction of CTL Responses Using a Prime Boost Protocol
A prime boost protocol similar in its underlying principle to that used to confirm 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.
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 34 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.
Analysis of the results indicates that a magnitude of response sufficient to achieve a therapeutic or protective immunity against 85P1B3 is generated.
Example 30
Administration of Vaccine Compositions Using Dendritic Cells (DC)
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 85P1B3 protein from which the epitopes in the vaccine are derived.
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 ProgenipoietinTM (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.
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.
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 ProgenipoietinTM 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 ProgenipoietinTM 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 ProgenipoietinTM is typically estimated to be between 2–10%, but can vary as appreciated by one of skill in the art.
Ex vivo Activation of CTL/HTL Responses
Alternatively, ex vivo CTL or HTL responses to 85P1B3 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 and Confirming Motif-Bearing Peptides
Another method of identifying and confirming 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. 85P1B3. 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.
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 85P1B3 to isolate peptides corresponding to 85P1B3 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.
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
Sequences complementary to the 85P1B3-encoding sequences, or any parts thereof, are used to detect, decrease, or inhibit expression of naturally occurring 85P1B3. 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 85P1B3. 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 85P1B3-encoding transcript.
Example 33
Purification of Naturally-occurring or Recombinant 85P1B3 Using 85P1B3 Specific Antibodies
Naturally occurring or recombinant 85P1B3 is substantially purified by immunoaffinity chromatography using antibodies specific for 85P1B3. An immunoaffinity column is constructed by covalently coupling anti-85P1B3 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.
Media containing 85P1B3 are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of 85P1B3 (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/85P1B3 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 85P1B3
85P1B3, or biologically active fragments thereof, are labeled with 121 l 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 85P1B3, washed, and any wells with labeled 85P1B3 complex are assayed. Data obtained using different concentrations of 85P1B3 are used to calculate values for the number, affinity, and association of 85P1B3 with the candidate molecules. 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 items of information are hereby incorporated by reference herein in their entireties.
Example 35
In Vivo Assay for 85P1B3 Tumor Growth Promotion
The effect of the 85P1B3 protein on tumor cell growth can be confirmed in vivo by gene overexpression in a variety of cancer cells, including prostate, kidney and bladder. For example, SCID mice can be injected SQ on each flank with 1×106 prostate, kidney or bladder cancer cells (such as PC3, LNCaP, SCaBER, UM-UC-3, HT1376, RT4, T24, Caki, A-498 and SW839 cells) containing tkNeo empty vector or 85P1B3.
At least two strategies may be used: (1) Constitutive 85P1B3 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 5 Jul. 1989), adenovirus (such as Adenoviris 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. (2) Regulated expression under control of an inducible vector system, such as ecdysone, tet, etc., can be used provided such promoters are compatible with the host cell systems. Tumor volume is then monitored at the appearance of palpable tumors and is followed over time to validate that 85P1B3-expressing cells grow at a faster rate and that tumors produced by 85P1B3-expressing cells demonstrate characteristics of altered aggressiveness (e.g. enhanced metastasis, vascularization, reduced responsiveness to chemotherapeutic drugs). Additionally, mice can be implanted with the same cells orthotopically in the prostate, bladder or kidney to determine if 85P1B3 has an effect on local growth in the prostate, bladder or kidney or on the ability of the cells to metastasize, specifically to lungs or lymph nodes (Fu, X., et al., Int. J. Cancer, 1991. 49: p. 938–939; Chang, S., et al., Anticancer Res., 1997. 17: p. 3239–3242; Peralta, E. A., et al., J. Urol., 1999. 162: p. 1806–1811).
Furthermore, this assay is useful to confirm the 85P1B3 inhibitory effect of candidate therapeutic compositions, such as for example, 85P1B3 antibodies or intrabodies, and 85P1B3 antisense molecules or ribozymes.
Example 36
85P1B3 Monoclonal Antibody-Mediated Inhibition of Tumors In Vivo
The significant expression of 85P1B3 in cancer tissues, together with its restricted expression in normal tissues, makes 85P1B3 an excellent target for antibody therapy. In cases where the monoclonal antibody target is a cell surface protein, antibodies have been shown to be efficacious at inhibiting tumor growth (See, e.g., (Saffran, D., et al., PNAS 10:1073–1078). In cases where the target is not on the cell surface, such as PSA and PAP in prostate cancer, antibodies have also been shown to recognize and inhibit growth of cells expressing those proteins (Saffran, D. C., et al., Cancer and Metastasis Reviews, 1999. 18: p. 437–449). As with any cellular protein with a restricted expression profile, 85P1B3 is a target for T cell-based immunotherapy.
Accordingly, the therapeutic efficacy of anti-85P1B3 mAbs in human colon, kidney, bladder and prostate cancer mouse models is modeled in 85P1B3-expressing kidney, bladder or prostate cancer xenografts or cancer cell lines, such as those described in the Example entitled “In Vivo Assay for 85P1B3 Tumor Growth Promotion”, that have been engineered to express 85P1B3.
Antibody efficacy on tumor growth and metastasis formation is confirmed, e.g., in a mouse orthotopic in the prostate, colon, bladder or kidney cancer xenograft model. The antibodies can be unconjugated, or can be conjugated to a therapeutic modality, as appreciated in the art. It is confirmed that anti-85P1B3 mAbs inhibit formation of 85P1B3-expressing kidney, bladder and prostate tumors. Anti-85P1B3 mAbs also retard the growth of established orthotopic tumors and prolong survival of tumor-bearing mice. These results indicate the utility of anti-85P1B3 mAbs in the treatment of local and advanced stages of cancer. (See, e.g., Saffran, D., et al., PNAS 10:1073–1078.)
Administration of anti-85P1B3 mAbs retard established orthotopic tumor growth and inhibit metastasis to distant sites, resulting in a significant prolongation in the survival of tumor-bearing mice. These studies indicate that 85P1B3 is an attractive target for immunotherapy and demonstrate the therapeutic potential of anti-85P1B3 mAbs for the treatment of local and metastatic kidney, colon, bladder and prostate cancer.
This example demonstrates that unconjugated 85P1B3 monoclonal antibodies effectively to inhibit the growth of human bladder tumors grown in SCID mice; accordingly a combination of such efficacious monoclonal antibodies is also effective.
Example 37
Induction of a Specific CTL Response in Humans
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:
A total of about 27 individuals are enrolled and divided into 3 groups:
Group I: 3 subjects are injected with placebo and 6 subjects are injected with 5 μg of peptide composition;
Group II: 3 subjects are injected with placebo and 6 subjects are injected with 50 μg peptide composition;
Group III: 3 subjects are injected with placebo and 6 subjects are injected with 500 μg of peptide composition.
After 4 weeks following the first injection, all subjects receive a booster inoculation at the same dosage.
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.
Safety: The incidence of adverse events is monitored in the placebo and drug treatment group and assessed in terms of degree and reversibility.
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.
The vaccine is found to be both safe and efficacious.
Example 38
Splice Variants of 85P1B3
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 the same or a 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.
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.
Moreover, computer programs are available in the art that identify splice variants based on genomic sequences. Genomic-based variant identification programs include FgenesH (A. Salamov and V. Solovyev, “Ab initio gene finding in Drosophila genomic DNA,” Genome Research. 2000 April; 10(4):516–22); Grail and GenScan. For a general discussion of spice variant identification protocols see, e.g., Southan C., “A genomic perspective on human proteases,” FEBS Lett. 2001 Jun. 8; 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 USA. 2000 Nov. 7; 97(23):12690–3.
For variants identified by the EST-based method, Table XXI shows the nucleotide sequences of the splice variants. Figure Table XXII shows the alignment of the splice variant with the 85P1B3 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 85P1B3. Thus, for each splice variant, a variant's reading frame that encodes the longest single contiguous peptide homology between 85P1B3 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 three frame shifted amino acid translations of the splice variant for the identified reading frame orientation.
For variants identified by any one of the genomic sequence-based methods, Table XXI shows the nucleotide sequences of the splice variant. Figure Table XXII shows the alignment of the splice variant with the 85P1B3 nucleic acid sequence. Table XXIII displays the alignment of amino acid sequence of the predicted transcripts with 85P1B3. The genomic-based computer programs predict a transcript from genomic sequence, and not only predict exons but also set open reading frame as the first forward open reading frame. The predicted transcript does not contain 5′ or 3′ untranslated region (UTR). It starts with ATG and ends with a stop codon, TAG, TGA or TAA. In case the transcript is predicted on the reverse strand of the genomic sequence, the sequence of the transcript is reverse-complemented to the genomic sequence of the exons. Thus, the genomic-based programs provide the correct transcript sequence, with 5′ to 3′ orientation and +1 as the open reading frame. However, due to the possibility of inaccurate prediction of exons or the possibility of sequencing errors in genomic data, other peptides in other forward open reading frame can also be encoded by the variant. Table XXIV lays out all amino acid translations of the splice variant in each of the three forward reading frames.
To further confirm the parameters of a splice variant, 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. 1999 μg. 17; 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. 1997 Oct. 1; 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. 2001 Jan. 24; 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,” Biochim Biophys Acta. 1997 μg. 7; 1353(2): 191–8.
It is known in the art that genomic regions are upregulated in cancers. When the genomic region to which 85P1B3 maps is upregulated in a particular cancer, the splice variants of 85P1B3 are upregulated as well. Disclosed herein is that 85P1B3 has a particular expression profile. Splice variants of 85P1B3 that are structurally and/or functionally similar to 85P1B3 share this expression pattern, thus serving as tumor-associated markers/antigens.
Using the EST assembly approach, we identified one splice variants designated splice variant 1.







TABLE XXIA





Nucleotide sequence of splice variant 1. (SEQ ID NO: 701)

















1
TTTTTTTTTT CCTATCTAGC TATCTCTTAA AAACAAAAGC CATAGTAAAT GCATCAGAGA



 


61
TGGATATTCA AAATGTTCCT CTATCAGAAA AGATTGCAGA GGTAAAATTT CATGATGGTT


 


121
GTATGCTTTT TTAAAATACA GACAACTCTT GATAACTTCT ACCAATGAAC TTGGGCATGA


 


181
TGAAATGGCA TGATGCTCAA TAATCCTTTT TACTTGATTT GACCTTCCCT ATTGAATTTG


 


241
TAATGAAAAA CAAAATACTA AAACCACACT GTAAGGTATA GTTCAGGAAG AAAGGAAAAG


 


301
CTGCTCAACT GCTGCACTCC TGCATTCTCC TTTGTGCTGG GAATGGATAT CATCATCTTG


 


361
CCATAGAGGT GTCTTCTTTG CAAATACCTT GTAATTGCTC AACTGTCTCA GACATAAGAG


 


421
TGATGAAACA GTTATTAAGA ATTCCTGGCC GGGCGTGGTG GCTCACGCCT GTAATCCCAG


 


481
CACTTTGGCC TCGTGC
















TABLE XXIIA





Nucleotide sequence alignment of 85P1B3 with splice variant 1.















Score = 160 bits (83), Expect = 3e−36


Identities = 83/83 (100%)


Strand = Plus/Plus


 








 























TABLE XXIIIA





Amino acid sequence alignment of 85P1B3 and splice



variant 1.
















Score = 64.8 bits (135), Expect = 2e−08



Identities = 28/29 (96%)


Frame = +1/+3


 











85P1B3:
526
YLLKTKAIVNASEMDIQNVPLSEKIAELK
612





YLLKTKAIVNASEMDIQNVPLSEKIAE+K




(SEQ ID NO:704)


Vrnt 1:
21
YLLKTKAIVNASEMDIQNVPLSEKIAEVK
107




(SEQ ID NO:707)

















TABLE XXIVA







Peptide sequences from the translation of the nucleotide sequence



of splice variant 1.









Open reading




frame
Amino acid sequences





Frame 1
FFFSYLAIS*KQKP**MHQRWIFKMFLYQKRLQR*NFMMVVCFFKIQTTLDNFYQ*TWG*



(SEQ ID NO:705)
*NGMMLNNPFYLI*PSLLNL**KTKY*NHTVRYSSGRKEKLLNCCTPAFSFVLGMDIIIL



P*RCLLCKYLVIAQLSQT*E**NSY*EFLAGRGGSRL*SQHFGLV


 


Frame 2
FFFPI*LSLKNKSHSKCIRDGYSKCSSIRKDCRGKIS*WLYAFLKYRQLLITSTNELGDD


(SEQ ID NO:706)
EMA*CSIILFT*FDLPY*ICNEKQNTKTTL*GIVQEERKSCSTAALLHSPLCWEWISSSC



HRGVFFANTL*LLNCLRHKSDETVIKNSWPGVVAHACNPSTLASC


 


Frame 3
FFFLSSYLLKTKAIVNASEMDIQNVPLSEKIAEVKFHDGCMLF*NTDNS**LLPMNLGMM


(SEQ ID NO:707)
KWHDAQ*SFLLDLTFPIEFVMKNKILKPHCKV*FRKKGKAAQLLHSCILLCAGNGYHHLA



IEVSSLQIPCNCSTVSDIRVMKQLLRIPGRAWWLTPVIPALWPR





Note:


Frame 3 gives the longest subsequence that is identical with 85P1B3 amino acid sequence. In this Table each (*)indicates the product of a single codon, i.e., a single unknown amino acid or a stop codon.






Example 39
Expression Analysis of 85P1B3 Splice Variants in Normal Tissues and Patient Tumor Specimens
Expression of 85P1B3 described in Example 4 was performed using the 85P1B3 SSH sequence as a probe. This nucleic acid sequence spans region 701–1019 of the 85P1B3 gene, a region absent in the 85P1B3 splice variant 1 (FIG. 19). Therefore, the Northern blots described in FIG. 11, FIG. 12, FIG. 13, FIG. 14, FIG. 15, FIG. 16, FIG. 17, and FIG. 18 detected the transcript of 85P1B3 but not of splice variant 1.
A probe comprising region of homology between 85P1B3 and its splice variant 1 is generated (Probe 1). This region spans nucleotide positions 524–606 of 85P1B3 and 19–101 of splice variant 1. Normal tissue northern blots and patient cancer northern blots are probed with probe 1. The results have two bands, and show expression of the 1.2 kb transcript of 85P1B3 and the transcript of its splice variant 1.
In another study, a probe comprising a region present in the ORF of the splice variant but not in the ORF of 85P1B3 is generated (Probe 2). This region spans nucleotide positions 102496 of the splice variant 1. Normal tissue northern blots and patient cancer Northern blots are probed with probe 2. The results have single bands, and show expression of splice variant 1 but not the transcript of 85P1B3.
When 85P1B3 splice variant 1 is expressed in patient cancer specimens, and shows restricted expression in normal tissues, 85P1B3 splice variant 1 is a suitable cancer target for cancer diagnosis and therapy.
Example 40
Splice Variant Protein Characteristics
The present variant protein is understood to be partial, and thus to comprise domains of the full protein. Amino acids 7–35 of the 85P1B3 variant 1 protein align with amino acids 172–200 of 85P1B3 with 96% identity, while the remaining downstream amino acids diverge from the 85P1B3. This pattern of high homology to one section of the parent protein coupled to a high divergence from the remaining portions of the parent protein form the hallmark of a splice variant.
Protein blast analysis of variant 1 shows that the 85P1B3 variant is homologous to OIP5, a human protein known to be involved in adhesion and invasion of epithelial cells (Brooks G F et al, Mol Microbiol. 1991, 5:3063; Weel J F et al, J Exp Med. 1991, 173:1395), with 96% identity over 28 amino acids. Analysis by pFam or prosite failed to identify any motifs. However motif homology was observed to Glyoxalase 1 at aa 114–153 of the variant protein. Glyoxalase is a glutathione-mediating detoxifying enzyme, that protects cells from advanced glycation endproducts (AGEs) (Thornalley P J. Chem Biol Interact. 1998, 111:137). Glyoxalase is highly expressed in breast cancer cells (Rulli A et al, Breast Cancer Res Treat. 2001, 66:67).
Regarding localization, the 85P1B3 variant localizes to the cytoplasm (cytoplasmic 60.9% PSORT II) or the mitochondria (mitochondrial 0.519, PSORT).
Based on bioinformatic analysis (TMPred, Sosui) the 85P1B3 variant does not appear to contain transmembrane domains, but forms a soluble intracellular protein. Due to its homology to OIP5 and Glyoxalase 1, 85P1B3 is involved in the adhesion and invasion of epithelial cells, and has a cancer-related expression pattern.
Example 41
Homology Comparison of 85P1B3 to Known Sequences
The 85P1B3 protein of FIG. 3 has 229 amino acids with calculated molecular weight of 24.69 kDa, and pI of 7.02. 85P1B3 is predicted to be a mitochondrial (60.9%) or cytoplasmic (21.7) protein.
85P1B3 shows best homology to human Opa interacting protein 5 (gi 2815610) sharing 100% identity with that protein. Opacity associated proteins (Opa) were identified in Neisseria gonorrhoeae as outer membrane proteins that are involved in mediating the adhesion of Neisseria to mammalian cells and the invasion of human epithelial cells (Brooks G F et al, Mol Microbiol. 1991, 5:3063; Weel I F et al, J Exp Med. 1991, 173:1395). OPA proteins bind to membrane proteins, such as CD66 and carcinoembryonic antigen related cellular molecule (CEACAM), on the surface of human epithelial and mononuclear cells, thereby facilitating entry of Neisseria into mammalian host cells (Muenzner P et al, J. Biol. Chem. 2001, 276:24331; Chen T et al, J. Exp. Med. 1997, 185:1557). In order to delineate the role of Opa in adherence and invasion of human cells, Williams et al used a two yeast hybrid system to identify Opa interacting proteins (Williams J M et al, Mol. Microbiol. 1998, 27:171). Screening a human cDNA library for Opa interacting partners, they identified Opa interacting protein 5 or OIP5. OIP5 is an intracellular, cytoplasmic protein with homology to thyroid hormone receptor interacting protein-6 (TRIP6) (Williams J M & Rest R F. Ann N Y Acad. Sci. 1996, 797:288). TRIP6 is an intracellular signaling molecule that relays information to the nucleus thereby regulating gene expression (Zhao M et al, Gene Expr. 1999, 207; Wang Y et al, Gene. 1999, 234:403).
This information indicates that 85P1B3 can play a role in the adhesion and invasion of epithelial cells into adjacent tissues and basement membranes, and regulate transcription by transmitting cell surface signals to the nucleus.
Accordingly, when 85P1B3 functions as a regulator of cell adhesion and invasion, or as a modulator of transcription involved in activating genes associated with tumorigenesis or in blocking expression of genes that repress tumorigenesis, 85P1B3 is used for therapeutic, diagnostic, prognostic and/or preventative purposes.
Example 42
Identification and Confirmation of Potential Signal Transduction Pathways
Many mammalian proteins have been reported to interact with signaling molecules and to participate in regulating signaling pathways. (J. Neurochem. 2001; 76:217–223). In particular, OPA has been reported to associate with a phosphatase and surface receptors (Hauck C et al, Infect. Immun. 1999, 67:5490; Muenzner P et al, J. Biol. Chem. 2001, 276:24331). Using immunoprecipitation and Western blotting techniques, proteins are identified that associate with 85P1B3 and mediate signaling events. Several pathways known to play a role in cancer biology can be regulated by 85P1B3, 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, e.g., Western blotting techniques the ability of 85P1B3 to regulate these pathways is confirmed. Cells expressing or lacking 85P1B3 are either left untreated or stimulated with cytokines, androgen and anti-integrin 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. When 85P1B3 plays a role in the regulation of signaling pathways, whether individually or communally, it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.
To confirm that 85P1B3 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.

    
    
        1. NFkB-luc, NFkB/Rel; Ik-kinase/SAPK; growth/apoptosis/stress
        2. SRE-luc, SRF/TCF/ELK1; MAPK/SAPK; growth/differentiation
        3. AP-1-luc, FOS/JUN; MAPK/SAPK/PKC; growth/apoptosis/stress
        4. ARE-luc, androgen receptor; steroids/MAPK; growth/differentiation/apoptosis
        5. p53-luc, p53; SAPK; growth/differentiation/apoptosis
        6. CRE-luc, CREB/ATF2; PKA/p38; growth/apoptosis/stress
    
    


Gene-mediated effects can be 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 85P1B3 are mapped and used for the identification and validation of therapeutic targets. When 85P1B3 is involved in cell signaling, it is used as target for diagnostic, prognostic, preventative and/or therapeutic purposes.
Example 43
Involvement in Tumor Progression
The 85P1B3 gene can contribute to the growth of cancer cells. The role of 85P1B3 in tumor growth is confirmed 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 85P1B3. Parental cells lacking 85P1B3 and cells expressing 85P1B3 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 1, Evans S L. Anticancer Drugs. 1996, 7:288).
To confirm the role of 85P1B3 in the transformation process, its effect in colony forming assays is investigated. Parental NIH3T3 cells lacking 85P1B3 are compared to NHI-3T3 cells expressing 85P1B3 using a soft agar assay under stringent and more permissive conditions (Song Z. et al. Cancer Res. 2000; 60:6730).
To confirm the role of 85P1B3 in invasion and metastasis of cancer cells, a well-established assay is used, e.g., a Transwell Insert System assay (Becton Dickinson) (Cancer Res. 1999; 59:6010). Control cells, including prostate, colon, bladder and kidney cell lines lacking 85P1B3 are compared to cells expressing 85P1B3. 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.
85P1B3 can also play a role in cell cycle and apoptosis. Parental cells and cells expressing 85P1B3 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 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 85P1B3, 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. The modulation of cell death by 85P1B3 can play a critical role in regulating tumor progression and tumor load.
When 85P1B3 plays a role in cell growth, transformation, invasion or apoptosis, it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.
Example 44
Involvement in Angiogenesis
Angiogenesis or new capillary blood vessel formation is necessary for tumor growth (Hanahan D, Folkman J. Cell. 1996, 86:353; Folkman J. Endocrinology. 1998 139:441). Several assays have been developed to measure angiogenesis in vitro and in vivo, such as the tissue culture assays endothelial cell tube formation and endothelial cell proliferation. Using these assays as well as in vitro neo-vascularization, the role of 85P1B3 in angiogenesis, enhancement or inhibition, is confirmed.
For example, endothelial cells engineered to express 85P1B3 are evaluated using tube formation and proliferation assays. The effect of 85P1B3 is also confirmed in animal models in vivo. For example, cells either expressing or lacking 85P1B3 are implanted subcutaneously in immunocompromised mice. Endothelial cell migration and angiogenesis are evaluated 5–15 days later using immunohistochemistry techniques. When 85P1B3 affects angiogenesis, it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.
Example 45
Regulation of Transcription
The cytoplasmic localization of 85P1B3 and its similarity to TRIP5 support the use in accordance with the present invention of 85P1B3 as a modulator of the transcriptional regulation of eukaryotic genes. Regulation of gene expression is confirmed, e.g., by studying gene expression in cells expressing or lacking 85P1B3. For this purpose, two types of experiments are performed.
In the first set of experiments, RNA from parental and 85P1B3-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 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 (Chen K et al. Thyroid. 2001. 11:41.).
In the second set of experiments, specific transcriptional pathway activation is evaluated using commercially available (Stratagene) luciferase reporter constructs including: NFkB-luc, SRE-luc, ELKI-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.
When 85P1B3 plays a role in gene regulation, it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.
Example 46
Involvement in Cell Adhesion
Cell adhesion plays a critical role in tissue colonization and metastasis. 85P1B3 can participate in cellular organization, and as a consequence cell adhesion and motility. This is supported by the presence of an RGD motif in the N-terminal portion of 85P1B3 (see Table XIX). To confirm that 85P1B3 regulates cell adhesion, control cells lacking 85P1B3 are compared to cells expressing 85P1B3, using techniques previously described (see, e.g., Haier et al, Br. J. Cancer. 1999, 80:1867; Lehr and Pienta, J. Natl. Cancer Inst. 1998, 90:118). Briefly, in one embodiment, cells labeled with a fluorescent indicator, such as calcein, are incubated on tissue culture wells coated with media alone or with matrix proteins. Adherent cells are detected by fluorimetric analysis and percent adhesion is calculated. In another embodiment, cells lacking or expressing 85P1B3 are analyzed for their ability to mediate cell—cell adhesion using similar experimental techniques as described above. Both of these experimental systems are used to identify proteins, antibodies and/or small molecules that modulate cell adhesion to extracellular matrix and cell—cell interaction. Since cell adhesion plays a critical role in tumor growth, progression, and, colonization, when 85P1B3 is involved in these processes it serves as a diagnostic, prognostic, preventative and/or therapeutic modality.
Example 47
Protein—Protein Association
Two proteins with homology to 85P1B3, namely OIP5 and TRIP6, have been shown to interact with other proteins, thereby regulating signal transduction, gene transcription, and cell adhesion. Using immunoprecipitation techniques as well as two yeast hybrid systems, proteins are identified that associate with 85P1B3. Immunoprecipitates from cells expressing 85P1B3 and cells lacking 85P1B3 are compared for specific protein—protein associations.
Studies are performed to confirm the extent of association of 85P1B with effector molecules, such as receptors, adaptor proteins and SH2-containing proteins. Studies comparing 85P1B3 positive and 85P1B3 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.
In addition, protein—protein interactions are confirmed using two yeast hybrid methodology (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 85P1B3-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 85P1B3, and thus identifies therapeutic, prognostic, preventative and/or diagnostic targets for cancer. This and similar assays are also used to identify and screen for small molecules that interact with 85P1B3.
When 85P1B3 associates with proteins or small molecules it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.
Throughout this application, various website data content, publications, patent applications and patents are referenced. The disclosures of each of these references are hereby incorporated by reference herein in their entireties.
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.
Tables







TABLE I





Tissues that Express 85P1B3 When Malignant







Prostate


Bladder


Kidney


Colon


Lung


Ovary


Breast


Stomach


Uterus


Cervix
















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
















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 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



















TABLE IV A






POSITION
POSITION
POSITION


SUPERMOTIFS
2 (Primary Anchor)
3 (Primary Anchor)
C Terminus (Primary Anchor)







A1
TILVMS

FWY



(SEQ ID NO:748)


A2
LIVMATQ

IVMATL



(SEQ ID NO:749)

(SEQ ID NO:750)


A3
VSMATLI

RK



(SEQ ID NO:751)


A24
YFWIVLMT

FIYWLM



(SEQ ID NO:752)

(SEQ ID NO:753)


B7
P

VILFMWYA




(SEQ ID NO:754)


B27
RHK

FYLWMIVA




(SEQ ID NO:755)


B44
ED

FWYLIMVA




(SEQ ID NO:756)


B58
ATS

FWYLIVMA




(SEQ ID NO:757)


B62
QLIVMP

FWYMIVLA



(SEQ ID NO:758)

(SEQ ID NO:759)


MOTIFS


A1
TSM

Y


A1

DEAS
Y




(SEQ ID NO:806)


A2.1
LMVQIAT

VLIMAT



(SEQ ID NO:760)

(SEQ ID NO:761)


A3
LMVISATFCGD

KYRHFA



(SEQ ID NO:762)

(SEQ ID NO:763)


A11
VTMLISAGNCDF

KRYH



(SEQ ID NO:764)

(SEQ ID NO:765)


A24
YFWM

FLIW



(SEQ ID NO:766)

(SEQ ID NO:767)


A*3101
MVTALIS

RK



(SEQ ID NO:768)


A*3301
MVALFIST

RK



(SEQ ID NO:769)


A*6801
AVTMSLI

RK



(SEQ ID NO:770)


B*0702
P

LMFWYAIV





(SEQ ID NO:771)


B*3501
P

LMFWYIVA





(SEQ ID NO:772)


B51
P

LIVFWYAM





(SEQ ID NO:773)


B*5301
P

IMFWYALV





(SEQ ID NO:774)


B*5401
P

ATIVLMFWY





(SEQ ID NO:748)





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.













TABLE IV (B)







HLA CLASS II SUPERMOTIF









1
6
9





W, F, Y, V, .I, L
A, V, I, L, P, C, S, T
A, V, I, L, C, S, T, M, Y


























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




(SEQ ID




(SEQ ID




NO:776)




NO:777)



deleterious



W


R

WDE


DR1
preferred
MFLIVWY


PAMQ

VMATSPLIC
M

AVM




(SEQ ID


(SEQ ID

(SEQ ID




NO:778)


NO:779)

NO:780)



deleterious

C
CH
FD
CWD

GDE
D


DR7
preferred
MFLIVWY
M
W
A

IVMSACTPL
M

IV




(SEQ ID




(SEQ ID




NO:781)




NO:782)



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

(SEQ ID




NO:783)


motif b

LIVMFAY


DNQEST

KRH


preferred

(SEQ ID


(SEQ ID




NO:784)


NO:785)


DR

MFLIVWY




VMSTACPLI


Supermotif

(SEQ ID




(SEQ ID




NO:786




NO:787





Italicized residues indicate less preferred or “tolerated” residues.













TABLE IV (D)







POSITION

















SUPER












MOTIFS

1
2
3
4
5
6
7
8
C-terminus





A1






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  TILVM














  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  FWY









(SEQ ID





NO:788)


 


A2






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  LIVMATQ














  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  LIVMAT









(SEQ ID






(SEQ ID





NO:789)






NO:790)


 


A3
preferred





  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  VSMATLI




YFW(4/5)


YFW(3/5)
YFW(4/5)
P(4/5)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  RK









(SEQ ID





NO:791)


 



deleterious
DE (3/5);

DE




P (5/5)

(4/5)


 


A24






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  YFWIVLMT














  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  FIYWLM









(SEQ ID






(SEQ ID





NO:792)






NO:793)


 


B7
preferred
FWY (5/5),LIVM (3/5)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  P




FWY(4/5)




FWY(3/5)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  VILFMWYA








(SEQ ID







(SEQ ID




NO:794)







NO:795)


 



deleterious
DE (3/5);



DE
G
QN
DE




P(5/5);



(3/5)
(4/5)
(4/5)
(4/5)




G(4/5);




A(3/5);




QN(3/5)


 



B27






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  RHK













  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  FYLWMIVA
















(SEQ ID












NO:796)


 



B44






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  ED













  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  FWYLIMVA
















(SEQ ID












NO:797)


 



B58






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  ATS













  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  FWYLIVMA
















(SEQ ID












NO:798)


 



B62






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  QLIVMP













  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  FWYMIVLA










(SEQ ID





(SEQ ID






NO:799)





NO:800)



























TABLE IV E















9












or


POSITION:
1
2
3
4
5
6
7
8
C-terminus
C-terminus







A19-mer
preferred
GFYW(SEQ IDNO:801)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  STM




DEA
YFW

P
DEQN(SEQ IDNO:802)
YFW




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  Y






 



deleterious
DE

RHKLIVMP(SEQ IDNO:803)
A
G
A


 


A19-mer
preferred
GRHK(SEQ IDNO:804)
ASTCLIVM(SEQ IDNO:805)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  DEAS



(SEQ IDNO:806)
GSTC(SEQ IDNO:807)

ASTC(SEQ IDNO:808)
LIVM(SEQ IDNO:809)
DE




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  Y






 



deleterious
A
RHKDEPYFW(SEQ IDNO:810)

DE
PQN
RHK
PG
GP


 


A110-mer
preferred
YFW




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  STM




DEAQN(SEQ IDNO:811)
A
YFWQN(SEQ IDNO:812)

PASTC(SEQ IDNO:813)
GDE
P




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  Y






 



deleterious
GP

RHKGLIVM(SEQ IDNO:814)
DE
RHK
QNA
RHKYFW(SEQ IDNO:815)
RHK
A


 


A110-mer
preferred
YFW
STCLIVM(SEQ IDNO:816)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  DEAS



(SEQ IDNO:817)
A
YFW

PG
G
YFW




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  Y






 



deletetious
RHK
RHKDEPY


P
G

PRHK
QN





FW(SEQ IDNO:818)





(SEQ IDNO:819)


 


A2.19-mer
preferred
YFW




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  LMIVQAT




YFW
STC
YFW

A
P




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  VLIMAT









(SEQ IDNO:820)






(SEQ IDNO:821)


 



deleterious
DEP

DERKH(SEQ IDNO:822)


RKH
DERKH(SEQ IDNO:823)


 


A2.110-mer
preferred
AYFW




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  LMIVQAT



(SEQ IDNO:824)
LVIM(SEQ IDNO:825)
G

G

FYWLVIM(SEQ IDNO:826)





  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  VLIMAT



(SEQ IDNO:827)


 



deleterious
DEP

DE
RKHA(SEQ IDNO:828)
P

RKH
DERKLH(SEQ IDNO:829)
RKH


 


A3
preferred
RHK




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  LMVISATFCGD



(SEQ IDNO:830)
YFW
PRHKKYFW(SEQ IDNO:831)
A
YFW

P




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  KYRHFA



(SEQ IDNO:832)


 



deleterious
DEP

DE


 


A11
preferred
A




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  VTLMISAGNCDF



(SEQ IDNO:833)
YFW
YFW
A
YFW
YFW
P




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  KRYH



(SEQ IDNO:834)


 



deleterious
DEP





A
G


 


A249-mer
preferred
YFWRHK(SEQ IDNO:835)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  YFWM



(SEQ IDNO:836)

STC


YFW
YFW




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  FLIW



(SEQ IDNO:837)


 



deleterious
DEG

DE
G
QNP
DERHK(SEQ IDNO:838)
G
AQN


 


A2410-mer
preferred





  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  YFWM



(SEQ IDNO:839)

P
YFWP(SEQ IDNO:840)

P






  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  FLIW



(SEQ IDNO:841)


 



deleterious


GDE
QN
RHK
DE
A
QN
DEA


 


A3101
preferred
RHK




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  MVTALIS




YFW
P

YFW
YFW
AP




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  RK









(SEQ ID





NO:842)


 



deleterious
DEP

DE

ADE
DE
DE
DE


 


A3301
preferred





  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  MVALFIST




YFW



AYFW(SEQ IDNO:844)





  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  RK









(SEQ ID





NO:843)


 



deleterious
GP

DE


 


A6801
preferred
YFWSTC(SEQ IDNO:845)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  AVTMSLI



(SEQ IDNO:846)


YFWLIVM(SEQ IDNO:847)

YFW
P




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  RK






 



deleterious
GP

DEG

RHK


A


 


B0702
preferred
RHKFWY(SEQ IDNO:848)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  P




RHK

RHK
RHK
RHK
PA




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  LMFWYAIV



(SEQ IDNO:849)


 



deleterious
DEQNP(SEQ IDNO:850)

DEP
DE
DE
GDE
QN
DE


 


B3501
preferred
FWYLIVM(SEQ IDNO:851)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  P




FWY


FWY





  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  LMFWYIVA



(SEQ IDNO:852)


 



deleterious
AGP



G
G


 


B51
preferred
LIVMFWY(SEQ IDNO:856)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  P




FWY
STC
FWY

G
FWY




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  LIVFWYAM



(SEQ IDNO:853)


 



deleterious
AGPDERHKSTC(SEQ IDNO:854)



DE
G
DEQN(SEQ IDNO:855)
GDE


 


B5301
preferred
LIVMFWY(SEQ IDNO:856)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  P




FWY
STC
FWY

LIVMFWY(SEQ IDNO:857)
FWY




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  IMFWYALV



(SEQ IDNO:858)


 



deleterious
AGPQN(SEQ IDNO:859)




G
RHKQN(SEQ IDNO:860)
DE


 


B5401
preferred
FWY




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  P




FWYLIVM(SEQ IDNO:861)

LIVM(SEQ IDNO:862)

ALIVM(SEQ IDNO:863)
FWYAP(SEQ IDNO:864)




  
    1
    ⁢
    °
    ⁢
    
      
    
    ⁢
    Anchor
  
  ATIVLMFWY



(SEQ IDNO:865)


 



deleterious
GPQNDE(SEQ IDNO:866)

GDESTC(SEQ IDNO:867)

RHKDE(SEQ IDNO:868)
DE
QNDGE(SEQ IDNO:869)
DE





Italicized residues indicate less preferred or “tolerated” residues. The information in this Table is specific for 9-mers unless otherwise specified.














TABLE V







HLA Peptide Scoring Results—85P1B3—A1, 9-mers














Start
Subsequence Residue
Score (Estimate of Half Time of Disassociation of a Molecule




Rank
Position
Listing
Containing This Subsequence)
Seq.ID#















1
114
VLEAPFLVG
4.500
1.



 


2
192
LSEKIAELK
2.700
2.


 


3
87
LADSVHLAW
2.500
3.


 


4
27
AIDQASFTT
2.500
4.


 


5
164
LSSDKMVCY
1.500
5.


 


6
217
LSEVTPDQS
1.350
6.


 


7
182
ASEMDIQNV
1.350
7.


 


8
12
CATPPRGDF
1.000
8.


 


9
122
GIEGSLKGS
0.900
9.


 


10
196
IAELKEKIV
0.900
10.


 


11
141
GIPVGFHLY
0.500
11.


 


12
100
SLGAVVFSR
0.500
12.


 


13
184
EMDIQNVPL
0.500
13.


 


14
57
AEEPAAGPQ
0.450
14.


 


15
36
SMEWDTQVV
0.450
15.


 


16
46
GSSPLGPAG
0.300
16.


 


17
138
GSCGIPVGF
0.300
17.


 


18
13
ATPPRGDFC
0.250
18.


 


19
221
TPDQSKPEN
0.250
19.


 


20
23
GTERAIDQA
0.225
20.


 


21
61
AAGPQLPSW
0.200
21.


 


22
120
LVGIEGSLK
0.200
22.


 


23
169
MVCYLLKTK
0.200
23.


 


24
203
IVLTHNRLK
0.200
24.


 


25
56
GAEEPAAGP
0.180
25.


 


26
130
STYNLLFCG
0.125
26.


 


27
128
KGSTYNLLF
0.125
27.


 


28
140
CGIPVGFHL
0.125
28.


 


29
124
EGSLKGSTY
0.125
29.


 


30
109
VTNNVVLEA
0.125
30.


 


31
1
MAAQPLRHR
0.100
31.


 


32
2
AAQPLRHRS
0.100
32.


 


33
69
WLQPERCAV
0.100
33.


 


34
154
ALAALRGHF
0.100
34.


 


35
165
SSDKMVCYL
0.075
35.


 


36
31
ASFTTSMEW
0.075
36.


 


37
129
GSTYNLLFC
0.075
37.


 


38
149
YSTHAALAA
0.075
38.


 


39
66
LPSWLQPER
0.050
39.


 


40
136
FCGSCGIPV
0.050
40.


 


41
111
NNVVLEAPF
0.050
41.


 


42
150
STHAALAAL
0.050
42.


 


43
167
DKMVCYLLK
0.050
43.


 


44
49
PLGPAGLGA
0.050
44.


 


45
204
VLTHNRLKS
0.050
45.


 


46
163
CLSSDKMVC
0.050
46.


 


47
38
EWDTQVVKG
0.050
47.


 


48
152
HAALAALRG
0.050
48.


 


49
179
IVNASEMDI
0.050
49.


 


50
181
NASEMIDIQN
0.050
50.

















TABLE VI







HLA Peptide Scoring Results—85P1B3—A1, 10-mers














Start
Subsequence Residue
Score (Estimate of Half Time of Disassociation of a Molecule




Rank
Position
Listing
Containing This Subsequence)
Seq.ID#














1
217
LSEVTPDQSK
27.000
51.


 


2
36
SMEWDTQVVK
18.000
52.


 


3
196
IAELKEKIVL
4.500
53.


 


4
69
WLQPERCAVF
2.000
54.


 


5
114
VLEAPFLVGI
1.800
55.


 


6
17
RGDFCGGTER
1.250
56.


 


7
140
CGIPVGFHLY
1.250
57.


 


8
13
ATPPRGDFCG
1.250
58.


 


9
163
CLSSDKMVCY
1.000
59.


 


10
2
AAQPLRHRSR
1.000
60.


 


11
56
GAEEPAAGPQ
0.900
61.


 


12
57
AEEPAAGPQL
0.900
62.


 


13
122
GIEGSLKGST
0.900
63.


 


14
99
RSLGAVVFSR
0.750
64.


 


15
27
AIDQASFTTS
0.500
65.


 


16
90
SVHLAWDLSR
0.500
66.


 


17
184
EMDIQNVPLS
0.500
67.


 


18
150
STHAALAALR
0.500
68.


 


19
46
GSSPLGPAGL
0.300
69.


 


20
23
GTERAIDQAS
0.225
70.


 


21
119
FLVGIEGSLK
0.200
71.


 


22
202
KIVLTHNRLK
0.200
72.


 


23
186
DIQNVPLSEK
0.200
73.


 


24
65
QLPSWLQPER
0.200
74.


 


25
165
SSDKMVCYLL
0.150
75.


 


26
182
ASEMDIQNVP
0.135
76.


 


27
94
AWDLSRSLGA
0.125
77.


 


28
71
QPERCAVFQC
0.113
78.


 


29
87
LADSVHLAWD
0.100
79.


 


30
12
CATPPRGDFC
0.100
80.


 


31
11
RCATPPRGDF
0.100
81.


 


32
153
AALAALRGHF
0.100
82.


 


33
61
AAGPQLPSWL
0.100
83.


 


34
168
KMVCYLLKTK
0.100
84.


 


35
129
GSTYNLLFCG
0.075
85.


 


36
192
LSEKIAELKE
0.068
86.


 


37
116
EAPFLVGIEG
0.050
87.


 


38
155
LAALRGHFCL
0.050
88.


 


39
203
IVLTHNRLKS
0.050
89.


 


40
112
NVVLEAPFLV
0.050
90.


 


41
139
SCGIPVGFHL
0.050
91.


 


42
178
AIVNASEMDI
0.050
92.


 


43
26
RAIDQASFTT
0.050
93.


 


44
159
RGHFCLSSDK
0.050
94.


 


45
110
TNNVVLEAPF
0.050
95.


 


46
108
RVTNNVVLEA
0.050
96.


 


47
30
QASFTTSMEW
0.050
97.


 


48
113
VVLEAPFLVG
0.050
98.


 


49
120
LVGIEGSLKG
0.050
99.


 


50
137
CGSCGIPVGF
0.050
100.

















TABLE VII







HLA Peptide Scoring Results—85P1B3—A2, 9-mers














Start
Subsequence Residue
Score (Estimate of Half Time of Disassociation of a Molecule




Rank
Position
Listing
Containing This Subsequence)
Seq.ID#















1
113
VVLEAPFLV
910.291
101.



 


2
212
SLMKILSEV
591.888
102.


 


3
172
YLLKTKAIV
485.348
103.


 


4
69
WLQPERCAV
319.939
104.


 


5
86
VLADSVHLA
79.642
105.


 


6
134
LLFCGSCGI
65.622
106.


 


7
168
KMVCYLLKT
43.325
107.


 


8
78
FQCAQCHAV
32.438
108.


 


9
119
FLVGIEGSL
12.775
109.


 


10
112
NVVLEAPFL
10.281
110.


 


11
202
KIVLTHNRL
10.281
111.


 


12
195
KIAELKEKI
10.087
112.


 


13
162
FCLSSDKMV
7.727
113.


 


14
85
AVLADSVHL
6.916
114.


 


15
35
TSMEWDTQV
6.887
115.


 


16
156
AALRGHFCL
6.367
116.


 


17
54
GLGAEEPAA
4.968
117.


 


18
191
PLSEKIAEL
4.432
118.


 


19
33
FTTSMEWDT
3.571
119.


 


20
93
LAWDLSRSL
3.433
120.


 


21
115
LEAPFLVGI
3.014
121.


 


22
27
AIDQASFTT
2.377
122.


 


23
26
RAIDQASFT
2.334
123.


 


24
147
HLYSTHAAL
2.324
124.


 


25
136
FCGSCGIPV
2.088
125.


 


26
163
CLSSDKMVC
2.037
126.


 


27
42
QVVKGSSPL
1.869
127.


 


28
96
DLSRSLGAV
1.560
128.


 


29
179
IVNASEMDI
1.552
129.


 


30
101
LGAVVFSRV
1.466
130.


 


31
36
SMEWDTQVV
1.318
131.


 


32
205
LTHNRLKSL
1.160
132.


 


33
140
CGIPVGFHL
0.809
133.


 


34
62
AGPQLPSWL
0.767
134.


 


35
126
SLKGSTYNL
0.748
135.


 


36
165
SSDKMVCYL
0.706
136.


 


37
209
RLKSLMKIL
0.705
137.


 


38
150
STHAALAAL
0.682
138.


 


39
155
LAALRGHFC
0.645
139.


 


40
197
AELKEKIVL
0.630
140.


 


41
184
EMDIQNVPL
0.463
141.


 


42
129
GSTYNLLFC
0.410
142.


 


43
133
NLLFCGSCG
0.276
143.


 


44
132
YNLLFCGSC
0.273
144.


 


45
109
VTNNVVLEA
0.270
145.


 


46
177
KAIVNASEM
0.242
146.


 


47
100
SLGAVVFSR
0.199
147.


 


48
13
ATPPRGDFC
0.186
148.


 


49
198
ELKEKIVLT
0.184
149.


 


50
189
NVPLSEKIA
0.178
150.

















TABLE VIII







HLA Peptide Scoring Results—85P1B3—A2, 10-mers














Start
Subsequence Residue
Score (Estimate of Half Time of Disassociation of a Molecule




Rank
Position
Listing
Containing This Subsequence)
Seq.ID#















1
100
SLGAVVFSRV
132.149
151.



 


2
204
VLTHNRLKSL
83.527
152.


 


3
195
KIAELKEKIV
56.266
153.


 


4
133
NLLFCGSCGI
38.601
154.


 


5
104
VVFSRVTNNV
38.280
155.


 


6
112
NVVLEAPFLV
35.298
156.


 


7
154
ALAALRGHFC
27.324
157.


 


8
211
KSLMKILSEV
13.523
158.


 


9
164
LSSDKMVCYL
12.295
159.


 


10
114
VLEAPFLVGI
9.921
160.


 


11
181
NASEMDIQNV
9.109
161.


 


12
183
SEMDIQNVPL
6.301
162.


 


13
212
SLMKILSEVT
5.539
163.


 


14
78
FQCAQCHAVL
4.085
164.


 


15
85
AVLADSVHLA
3.699
165.


 


16
155
LAALRGHFCL
2.925
166.


 


17
35
TSMEWDTQVV
2.824
167.


 


18
26
RAIDQASFTT
2.461
168.


 


19
41
TQVVKGSSPL
2.166
169.


 


20
96
DLSRSLGAVV
2.139
170.


 


21
190
VPLSEKIAEL
2.017
171.


 


22
61
AAGPQLPSWL
1.632
172.


 


23
76
AVFQCAQCHA
1.608
173.


 


24
149
YSTHAALAAL
1.475
174.


 


25
128
KGSTYNLLFC
1.436
175.


 


26
178
AIVNASEMDI
1.435
176.


 


27
197
AELKEKIVLT
1.233
177.


 


28
126
SLKGSTYNLL
1.122
178.


 


29
108
RVTNNVVLEA
1.000
179.


 


30
34
TTSMEWDTQV
0.966
180.


 


31
187
IQNVPLSEKI
0.881
181.


 


32
139
SCGIPVGFHL
0.809
182.


 


33
111
NNVVLEAPFL
0.767
183.


 


34
169
MVCYLLKTKA
0.739
184.


 


35
173
LLKTKAIVNA
0.680
185.


 


36
147
HLYSTHAALA
0.541
186.


 


37
172
YLLKTKAIVN
0.520
187.


 


38
86
VLADSVHLAW
0.519
188.


 


39
125
GSLKGSTYNL
0.516
189.


 


40
3
AQPLRHRSRC
0.504
190.


 


41
95
WDLSRSLGAV
0.492
191.


 


42
170
VCYLLKTKAI
0.370
192.


 


43
216
ILSEVTPDQS
0.255
193.


 


44
146
FHLYSTHAAL
0.252
194.


 


45
162
FCLSSDKMVC
0.226
195.


 


46
88
ADSVHLAWDL
0.223
196.


 


47
82
QCHAVLADSV
0.222
197.


 


48
141
GIPVGFHLYS
0.214
198.


 


49
144
VGFHLYSTHA
0.204
199.


 


50
37
MEWDTQVVKG
0.193
200.

















TABLE IX







HLA Peptide Scoring Results - 85P1B3 - A3, 9-mers














Start
Subsequence Residue
Score (Estimate of Half Time of Disassociation of a Molecule




Rank
Position
Listing
Containing This Subsequence)
Seq. ID#















1
100
SLGAVVFSR
54.000
201.



 


2
168
KMVCYLLKT
4.050
202.


 


3
141
GIPVGFHLY
3.600
203.


 


4
147
HLYSTHAAL
3.000
204.


 


5
134
LLFCGSCGI
3.000
205.


 


6
126
SLKGSTYNL
2.700
206.


 


7
120
LVGIEGSLK
2.000
207.


 


8
169
MVCYLLKTK
1.500
208.


 


9
187
IQNVPLSEK
1.350
209.


 


10
212
SLMKILSEV
0.675
210.


 


11
119
FLVGIEGSL
0.608
211.


 


12
54
GLGAEEPAA
0.600
212.


 


13
154
ALAALRGHF
0.600
213.


 


14
86
VLADSVHLA
0.600
214.


 


15
209
RLKSLMKIL
0.450
215.


 


16
163
CLSSDKMVC
0.400
216.


 


17
160
GHFCLSSDK
0.300
217.


 


18
69
WLQPERCAV
0.300
218.


 


19
172
YLLKTKAIV
0.300
219.


 


20
37
MEWDTQVVK
0.300
220.


 


21
203
IVLTHNRLK
0.300
221.


 


22
202
KIVLTHNRL
0.270
222.


 


23
195
KIAELKEKI
0.270
223.


 


24
36
SMEWDTQVV
0.200
224.


 


25
184
EMDIQNVPL
0.180
225.


 


26
157
ALRGHFCLS
0.180
226.


 


27
114
VLEAPFLVG
0.180
227.


 


28
192
LSEKIAELK
0.150
228.


 


29
191
PLSEKIAEL
0.135
229.


 


30
113
VVLEAPFLV
0.135
230.


 


31
218
SEVTPDQSK
0.135
231.


 


32
179
IVNASEMDI
0.120
232.


 


33
76
AVFQCAQCH
0.100
233.


 


34
213
LMKILSEVT
0.100
234.


 


35
70
LQPERCAVF
0.090
235.


 


36
65
QLPSWLQPE
0.090
236.


 


37
85
AVLADSVHL
0.090
237.


 


38
42
QVVKGSSPL
0.090
238.


 


39
112
NVVLEAPFL
0.090
239.


 


40
109
VTNNVVLEA
0.090
240.


 


41
207
HNRLKSLMK
0.080
241.


 


42
204
VLTHNRLKS
0.080
242.


 


43
138
GSCGIPVGF
0.068
243.


 


44
198
ELKEKIVLT
0.068
244.


 


45
18
GDFCGGTER
0.060
245.


 


46
92
HLAWDLSRS
0.060
246.


 


47
49
PLGPAGLGA
0.060
247.


 


48
216
ILSEVTPDQ
0.045
248.


 


49
23
GTERAIDQA
0.045
249.


 


50
150
STHAALAAL
0.045
250.

















TABLE X







HLA Peptide Scoring Results - 85P1B3 - A3, 10-mers














Start
Subsequence Residue
Score (Estimate of Half Time of Disassociation of a Molecule




Rank
Position
Listing
Containing This Subsequence)
Seq. ID#















1
168
KMVCYLLKTK
67.500
251.



 


2
119
FLVGIEGSLK
45.000
252.


 


3
36
SMEWDTQVVK
20.000
253.


 


4
163
CLSSDKMVCY
6.000
254.


 


5
191
PLSEKIAELK
4.500
255.


 


6
65
QLPSWLQPER
4.000
256.


 


7
69
WLQPERCAVF
3.000
257.


 


8
114
VLEAPFLVGI
2.700
258.


 


9
90
SVHLAWDLSR
2.400
259.


 


10
186
DIQNVPLSEK
1.350
260.


 


11
147
HLYSTHAALA
1.000
261.


 


12
100
SLGAVVFSRV
0.900
262.


 


13
202
KIVLTHNRLK
0.900
263.


 


14
126
SLKGSTYNLL
0.900
264.


 


15
133
NLLFCGSCGI
0.900
265.


 


16
198
ELKEKIVLTH
0.810
266.


 


17
99
RSLGAVVFSR
0.608
267.


 


18
86
VLADSVHLAW
0.600
268.


 


19
204
VLTHNRLKSL
0.450
269.


 


20
157
ALRGHFCLSS
0.360
270.


 


21
173
LLKTKAIVNA
0.300
271.


 


22
154
ALAALRGHFC
0.200
272.


 


23
150
STHAALAALR
0.200
273.


 


24
108
RVTNNVVLEA
0.180
274.


 


25
178
AIVNASEMDI
0.180
275.


 


26
104
VVFSRVTNNV
0.150
276.


 


27
212
SLMKILSEVT
0.150
277.


 


28
217
LSEVTPDQSK
0.150
278.


 


29
76
AVFQCAQCHA
0.100
279.


 


30
85
AVLADSVHLA
0.090
280.


 


31
112
NVVLEAPFLV
0.090
281.


 


32
209
RLKSLMKILS
0.080
282.


 


33
141
GIPVGFHLYS
0.072
283.


 


34
172
YLLKTKAIVN
0.060
284.


 


35
96
DLSRSLGAVV
0.060
285.


 


36
54
GLGAEEPAAG
0.060
286.


 


37
92
HLAWDLSRSL
0.060
287.


 


38
216
ILSEVTPDQS
0.060
288.


 


39
195
KIAELKEKIV
0.045
289.


 


40
193
SEKIAELKEK
0.045
290.


 


41
113
VVLEAPFLVG
0.041
291.


 


42
125
GSLKGSTYNL
0.041
292.


 


43
166
SDKMVCYLLK
0.040
293.


 


44
206
THNRLKSLMK
0.040
294.


 


45
184
EMDIQNVPLS
0.036
295.


 


46
200
KEKIVLTHNR
0.036
296.


 


47
134
LLFCGSCGIP
0.030
297.


 


48
34
TTSMEWDTQV
0.030
298.


 


49
130
STYNLLFCGS
0.030
299.


 


50
41
TQVVKGSSPL
0.027
300.

















TABLE XI







HLA Peptide Scoring Results - 85P1B3 - A11, 9-mers














Start
Subsequence Residue
Score (Estimate of Half Time of Disassociation of a Molecule




Rank
Position
Listing
Containing This Subsequence)
Seq. ID#















1
120
LVGIEGSLK
2.000
301.



 


2
169
MVCYLLKTK
1.000
302.


 


3
187
IQNVPLSEK
0.600
303.


 


4
203
IVLTHNRLK
0.300
304.


 


5
100
SLGAVVFSR
0.240
305.


 


6
160
GHFCLSSDK
0.120
306.


 


7
37
MEWDTQVVK
0.120
307.


 


8
113
VVLEAPFLV
0.090
308.


 


9
218
SEVTPDQSK
0.090
309.


 


10
207
HNRLKSLMK
0.080
310.


 


11
76
AVFQCAQCH
0.040
311.


 


12
66
LPSWLQPER
0.040
312.


 


13
179
IVNASEMDI
0.040
313.


 


14
85
AVLADSVHL
0.030
314.


 


15
112
NVVLEAPFL
0.030
315.


 


16
42
QVVKGSSPL
0.030
316.


 


17
23
GTERAIDQA
0.030
317.


 


18
18
GDFCGGTER
0.024
318.


 


19
167
DKMVCYLLK
0.024
319.


 


20
109
VTNNVVLEA
0.020
320.


 


21
192
LSEKIAELK
0.020
321.


 


22
202
KIVLTHNRL
0.018
322.


 


23
9
RSRCATPPR
0.012
323.


 


24
91
VHLAWDLSR
0.012
324.


 


25
3
AQPLRHRSR
0.012
325.


 


26
54
GLGAEEPAA
0.012
326.


 


27
141
GIPVGFHLY
0.012
327.


 


28
195
KIAELKEKI
0.012
328.


 


29
189
NVPLSEKIA
0.010
329.


 


30
150
STHAALAAL
0.010
330.


 


31
156
AALRGHFCL
0.009
331.


 


32
177
KAIVNASEM
0.009
332.


 


33
212
SLMKILSEV
0.008
333


 


34
126
SLKGSTYNL
0.008
334.


 


35
147
HLYSTHAAL
0.008
335.


 


36
134
LLFCGSCGI
0.008
336.


 


37
172
YLLKTKAIV
0.006
337.


 


38
145
GFHLYSTHA
0.006
338.


 


39
70
LQPERCAVF
0.006
339.


 


40
130
STYNLLFCG
0.006
340.


 


41
108
RVTNNVVLE
0.006
341.


 


42
78
FQCAQCHAV
0.006
342.


 


43
209
RLKSLMKIL
0.006
343.


 


44
119
FLVGIEGSL
0.006
344.


 


45
205
LTHNRLKSL
0.005
345.


 


46
194
EKIAELKEK
0.005
346.


 


47
87
LADSVHLAW
0.004
347.


 


48
1
MAAQPLRHR
0.004
348.


 


49
154
ALAALRGHF
0.004
349.


 


50
151
THAALAALR
0.004
350.

















TABLE XII







HLA Peptide Scoring Results - 85P1B3 - A1, 10-mers














Start
Subsequence Residue
Score (Estimate of Half Time of Disassociation of a Molecule




Rank
Position
Listing
Containing This Subsequence)
Seq. ID#















1
168
KMVCYLLKTK
0.900
351.



 


2
90
SVHLAWDLSR
0.800
352.


 


3
119
FLVGIEGSLK
0.060
353.


 


4
36
SMEWDTQVVK
0.400
354.


 


5
150
STHAALAALR
0.200
355.


 


6
202
KIVLTHNRLK
0.180
356.


 


7
186
DIQNVPLSEK
0.120
357.


 


8
108
RVTNNVVLEA
0.120
358.


 


9
112
NVVLEAPFLV
0.090
359.


 


10
65
QLPSWLQPER
0.080
360.


 


11
159
RGHFCLSSDK
0.060
361.


 


12
99
RSLGAVVFSR
0.054
362.


 


13
166
SDKMVCYLLK
0.040
363.


 


14
76
AVFQCAQCHA
0.040
364.


 


15
191
PLSEKIAELK
0.040
365.


 


16
104
VVFSRVTNNV
0.040
366.


 


17
206
THNRLKSLMK
0.040
367.


 


18
200
KEKIVLTHNR
0.036
368.


 


19
85
AVLADSVHLA
0.030
369.


 


20
193
SEKIAELKEK
0.030
370.


 


21
217
LSEVTPDQSK
0.020
371.


 


22
169
MVCYLLKTKA
0.020
372.


 


23
17
RGDFCGGTER
0.012
373.


 


24
178
AIVNASEMDI
0.012
374.


 


25
205
LTHNRLKSLM
0.010
375.


 


26
34
TTSMEWDTQV
0.010
376.


 


27
41
TQVVKGSSPL
0.009
377.


 


28
86
VLADSVHLAW
0.008
378.


 


29
147
HLYSTHAALA
0.008
379.


 


30
148
LYSTHAALAA
0.008
380.


 


31
133
NLLFCGSCGI
0.006
381.


 


32
203
IVLTHNRLKS
0.006
382.


 


33
78
FQCAQCHAVL
0.006
383.


 


34
187
IQNVPLSEKI
0.006
384.


 


35
145
GFHLYSTHAA
0.006
385.


 


36
48
SPLGPAGLGA
0.006
386.


 


37
155
LAALRGHFCL
0.006
387.


 


38
11
RCATPPRGDF
0.006
388.


 


39
113
VVLEAPFLVG
0.006
389.


 


40
139
SCGIPVGFHL
0.006
390.


 


41
195
KIAELKEKIV
0.006
391.


 


42
171
CYLLKTKAIV
0.006
392.


 


43
43
VVKGSSPLGP
0.004
393.


 


44
163
CLSSDKMVCY
0.004
394.


 


45
100
SLGAVVFSRV
0.004
395.


 


46
135
LFCGSCGIPV
0.004
396.


 


47
196
IAELKEKIVL
0.004
397.


 


48
8
HRSRCATPPR
0.004
398.


 


49
189
NVPLSEKIAE
0.004
399.


 


50
126
SLKGSTYNLL
0.004
400.

















TABLE XIII







HLA Peptide Scoring Results - 85P1B3 - A24, 9-mers














Start
Subsequence Residue
Score (Estimate of Half Time of Disassociation of a Molecule




Rank
Position
Listing
Containing This Subsequence)
Seq. ID#















1
171
CYLLKTKAI
75.000
401.



 


2
202
KIVLTHNRL
14.400
402.


 


3
131
TYNLLFCGS
10.800
403.


 


4
140
CGIPVGFHL
10.080
404.


 


5
209
RLKSLMKIL
9.600
405.


 


6
119
FLVGIEGSL
8.400
406.


 


7
62
AGPQLPSWL
7.200
407.


 


8
89
DSVHLAWDL
7.200
408.


 


9
112
NVVLEAPFL
6.000
409.


 


10
42
QVVKGSSPL
6.000
410.


 


11
47
SSPLGPAGL
6.000
411.


 


12
85
AVLADSVHL
6.000
412.


 


13
156
AALRGHFCL
6.000
413.


 


14
93
LAWDLSRSL
5.760
414.


 


15
148
LYSTHAALA
5.000
415.


 


16
126
SLKGSTYNL
4.000
416.


 


17
184
EMDIQNVPL
4.000
417.


 


18
147
HLYSTHAAL
4.000
418.


 


19
79
QCAQCHAVL
4.000
419.


 


20
165
SSDKMVCYL
4.000
420.


 


21
205
LTHNRLKSL
4.000
421.


 


22
150
STHAALAAL
4.000
422.


 


23
128
KGSTYNLLF
4.000
423.


 


24
70
LQPERCAVF
3.600
424.


 


25
111
NNVVLEAPF
3.600
425.


 


26
195
KIAELKEKI
3.168
426.


 


27
138
GSCGIPVGF
2.800
427.


 


28
161
HFCLSSDKM
2.750
428.


 


29
12
CATPPRGDF
2.400
429.


 


30
154
ALAALRGHF
2.400
430.


 


31
188
QNVPLSEKI
2.376
431.


 


32
177
KAIVNASEM
1.650
432.


 


33
179
IVNASEMDI
1.500
433.


 


34
134
LLFCGSCGI
1.000
434.


 


35
20
FCGGTERAI
1.000
435.


 


36
105
VFSRVTNNV
0.840
436.


 


37
77
VFQCAQCHA
0.750
437.


 


38
197
AELKEKIVL
0.600
438.


 


39
107
SRVTNNVVL
0.600
439.


 


40
58
EEPAAGPQL
0.600
440.


 


41
166
SDKMVCYLL
0.560
441.


 


42
191
PLSEKIAEL
0.528
442.


 


43
29
DQASFTTSM
0.500
443.


 


44
145
GFHLYSTHA
0.500
444.


 


45
19
DFCGGTERA
0.500
445.


 


46
127
LKGSTYNLL
0.480
446.


 


47
26
RAIDQASFT
0.360
447.


 


48
175
KTKAIVNAS
0.336
448.


 


49
168
KMVCYLLKT
0.330
449.


 


50
99
RSLGAVVFS
0.300
450.

















TABLE XIV







HLA Peptide Scoring Results-85P1B3-A24, 10-mers














Start
Subsequence Residue
Score (Estimate of Half Time of Disassociation of a Molecule




Rank
Position
Listing
Containing This Subsequence)
Seq. ID#















1
171
CYLLKTKAIV
7.500
451.



 


2
131
TYNLLFCGSC
7.500
452.


 


3
190
VPLSEKIAEL
6.600
453.


 


4
196
IAELKEKIVL
6.000
454.


 


5
41
TQVVKGSSPL
6.000
455.


 


6
125
GSLKGSTYNL
6.000
456.


 


7
111
NNVVLEAPFL
6.000
457.


 


8
84
HAVLADSVHL
6.000
458.


 


9
61
AAGPQLPSWL
5.760
459.


 


10
139
SCGIPVGFHL
5.600
460.


 


11
165
SSDKMVCYLL
5.600
461.


 


12
148
LYSTHAALAA
5.000
462.


 


13
19
DFCGGTERAI
5.000
463.


 


14
46
GSSPLGPAGL
4.800
464.


 


15
92
HLAWDLSRSL
4.800
465.


 


16
126
SLKGSTYNLL
4.800
466.


 


17
164
LSSDKMVCYL
4.800
467.


 


18
118
PFLVGIEGSL
4.200
468.


 


19
155
LAALRGHFCL
4.000
469.


 


20
11
RCATPPRGDF
4.000
470.


 


21
78
FQCAQCHAVL
4.000
471.


 


22
149
YSTHAALAAL
4.000
472.


 


23
106
FSRVTNNVVL
4.000
473.


 


24
204
VLTHNRLKSL
4.000
474.


 


25
110
TNNVVLEAPF
3.600
475.


 


26
69
WLQPERCAVF
3.600
476.


 


27
153
AALAALRGHF
3.600
477.


 


28
137
CGSCGIPVGF
2.800
478.


 


29
97
LSRSLGAVVF
2.000
479.


 


30
187
IQNVPLSEKI
1.980
480.


 


31
178
AIVNASEMDI
1.500
481.


 


32
114
VLEAPFLVGI
1.500
482.


 


33
133
NLLFCGSCGI
1.500
483.


 


34
207
HNRLKSLMKI
1.100
484.


 


35
170
VCYLLKTKAI
1.000
485.


 


36
77
VFQCAQCHAV
0.750
486.


 


37
183
SEMDIQNVPL
0.720
487.


 


38
208
NRLKSLMKIL
0.720
488.


 


39
201
EKIVLTHNRL
0.720
489.


 


40
57
AEEPAAGPQL
0.720
490.


 


41
146
FHLYSTHAAL
0.600
491.


 


42
105
VFSRVTNNVV
0.600
492.


 


43
205
LTHNRLKSLM
0.600
493.


 


44
135
LFCGSCGIPV
0.500
494.


 


45
161
HFCLSSDKMV
0.500
495.


 


46
145
GFHLYSTHAA
0.500
496.


 


47
32
SFTTSMEWDT
0.500
497.


 


48
88
ADSVHLAWDL
0.480
498.


 


49
211
KSLMKILSEV
0.462
499.


 


50
26
RAIDQASFTT
0.360
500.

















TABLE XV







HLA Peptide Scoring Results-SSPIB3-B7, 9-mers














Start
Subsequence Residue
Score (Estimate of Half Time of Disassociation of a Molecule




Rank
Position
Listing
Containing This Subsequence)
Seq. ID#















1
85
AVLADSVHL
60.000
501.



 


2
156
AALRGHFCL
36.000
502.


 


3
112
NVVLEAPFL
20.000
503.


 


4
42
QVVKGSSPL
20.000
504.


 


5
62
AGPQLPSWL
12.000
505.


 


6
93
LAWDLSRSL
12.000
506.


 


7
150
STHAALAAL
4.000
507.


 


8
89
DSVHLAWDL
4.000
508.


 


9
202
KIVLTHNRL
4.000
509.


 


10
147
HLYSTHAAL
4.000
510.


 


11
126
SLKGSTYNL
4.000
511.


 


12
79
QCAQCHAVL
4.000
512.


 


13
205
LTHNRLKSL
4.000
513.


 


14
140
CGIPVGFHL
4.000
514.


 


15
119
FLVGIEGSL
4.000
515.


 


16
47
SSPLGPAGL
4.000
516.


 


17
209
RLKSLMKIL
4.000
517.


 


18
177
KAIVNASEM
3.000
518.


 


19
4
QPLRHRSRC
3.000
519.


 


20
179
IVNASEMDI
2.000
520.


 


21
97
LSRSLGAVV
2.000
521.


 


22
106
FSRVTNNVV
2.000
522.


 


23
184
EMDIQNVPL
1.200
523.


 


24
165
SSDKMVCYL
1.200
524.


 


25
197
AELKEKIVL
1.200
525.


 


26
113
VVLEAPFLV
1.000
526.


 


27
29
DQASFTTSM
1.000
527.


 


28
35
TSMEWDTQV
0.600
528.


 


29
117
APFLVGIEG
0.600
529.


 


30
212
SLMKILSEV
0.600
530.


 


31
157
ALRGHFCLS
0.600
531.


 


32
189
NVPLSEKIA
0.500
532.


 


33
103
AVVFSRVTN
0.450
533.


 


34
20
FCGGTERAI
0.400
534.


 


35
134
LLFCGSCGI
0.400
535.


 


36
107
SRVTNNVVL
0.400
536.


 


37
188
QNVPLSEKI
0.400
537.


 


38
127
LKGSTYNLL
0.400
538.


 


39
191
PLSEKIAEL
0.400
539.


 


40
166
SDKMVCYLL
0.400
540.


 


41
58
EEPAAGPQL
0.400
541.


 


42
142
IPVGFHLYS
0.400
542.


 


43
195
KIAELKEKI
0.400
543.


 


44
75
CAVFQCAQC
0.300
544.


 


45
155
LAALRGHFC
0.300
545.


 


46
48
SPLGPAGLG
0.300
546.


 


47
53
AGLGAEEPA
0.300
547.


 


48
69
WLQPERCAV
0.300
548.


 


49
80
CAQCHAVLA
0.300
549.


 


50
26
RAIDQASFT
0.300
550.

















TABLE XVI







HLA Peptide Scoring Results-85P1B3-B7, 10-mers














Start
Subsequence Residue
Score (Estimate of Half Time of Disassociation of a Molecule




Rank
Position
Listing
Containing This Subsequence)
Seq. ID#















1
190
VPLSEKIAEL
80.000
551.



 


2
106
FSRVTNNVVL
40.000
552.


 


3
61
AAGPQLPSWL
36.000
553.


 


4
84
HAVLADSVHL
12.000
554.


 


5
155
LAALRGHFCL
12.000
555.


 


6
46
GSSPLGPAGL
4.000
556.


 


7
111
NNVVLEAPFL
4.000
557.


 


8
92
HLAWDLSRSL
4.000
558.


 


9
78
FQCAQCHAVL
4.000
559.


 


10
204
VLTHNRLKSL
4.000
560.


 


11
139
SCGIPVGFHL
4.000
561.


 


12
149
YSTHAALAAL
4.000
562.


 


13
126
SLKGSTYNLL
4.000
563.


 


14
164
LSSDKMVCYL
4.000
564.


 


15
41
TQVVKGSSPL
4.000
565.


 


16
207
HNRLKSLMKI
4.000
566.


 


17
125
GSLKGSTYNL
4.000
567.


 


18
196
IAELKEKIVL
3.600
568.


 


19
15
PPRGDFCGGT
2.000
569.


 


20
48
SPLGPAGLGA
2.000
570.


 


21
4
QPLRHRSRCA
2.000
571.


 


22
142
IPVGFHLYST
2.000
572.


 


23
66
LPSWLQPERC
2.000
573.


 


24
85
AVLADSVHLA
1.500
574.


 


25
76
AVFQCAQCHA
1.500
575.


 


26
165
SSDKMVCYLL
1.200
576.


 


27
117
APFLVGIEGS
1.200
577.


 


28
88
ADSVHLAWDL
1.200
578.


 


29
183
SEMDIQNVPL
1.200
579.


 


30
178
AIVNASEMDI
1.200
580.


 


31
112
NVVLEAPFLV
1.000
581.


 


32
205
LTHNRLKSLM
1.000
582.


 


33
104
VVFSRVTNNV
1.000
583.


 


34
71
QPERCAVFQC
0.600
584.


 


35
157
ALRGHFCLSS
0.600
585.


 


36
181
NASEMDIQNV
0.600
586.


 


37
35
TSMEWDTQVV
0.600
587.


 


38
59
EPAAGPQLPS
0.600
588.


 


39
169
MVCYLLKTKA
0.500
589.


 


40
108
RVTNNVVLEA
0.500
590.


 


41
3
AQPLRHRSRC
0.450
591.


 


42
201
EKIVLTHNRL
0.400
592.


 


43
170
VCYLLKTKAI
0.400
593.


 


44
146
FHLYSTHAAL
0.400
594.


 


45
133
NLLFCGSCGI
0.400
595.


 


46
187
IQNVPLSEKI
0.400
596.


 


47
208
NRLKSLMKIL
0.400
597.


 


48
57
AEEPAAGPQL
0.360
598.


 


49
53
AGLGAEEPAA
0.300
599.


 


50
154
ALAALRGHFC
0.300
600.

















TABLE XVII







HLA Peptide Scoring Results-85P1B3-B35, 9-mers














Start
Subsequence Residue
Score (Estimate of Half Time of Disassociation of a Molecule




Rank
Position
Listing
Containing This Subsequence)
Seq. ID#















1
164
LSSDKMVCY
20.000
601.



 


2
177
KAIVNASEM
12.000
602.


 


3
209
RLKSLMKIL
6.000
603.


 


4
93
LAWDLSRSL
6.000
604.


 


5
89
DSVHLAWDL
5.000
605.


 


6
138
GSCGIPVGF
5.000
606.


 


7
47
SSPLGPAGL
5.000
607.


 


8
126
SLKGSTYNL
3.000
608.


 


9
12
CATPPRGDF
3.000
609.


 


10
156
AALRGHFCL
3.000
610.


 


11
106
FSRVTMNVV
3.000
611.


 


12
97
LSRSLGAVV
3.000
612.


 


13
31
ASFTTSMEW
2.500
613.


 


14
141
GIPVGFHLY
2.000
614.


 


15
128
KGSTYNLLF
2.000
615.


 


16
142
IPVGFHLYS
2.000
616.


 


17
35
TSMEWDTQV
2.000
617.


 


18
4
QPLRHRSRC
2.000
618.


 


19
70
LQPERCAVF
2.000
619.


 


20
202
KIVLTHNRL
2.000
620.


 


21
29
DQASFTTSM
2.000
621.


 


22
124
EGSLKGSTY
2.000
622.


 


23
195
KIAELKEKI
1.600
623.


 


24
165
SSDKMVCYL
1.500
624.


 


25
85
AVLADSVHL
1.500
625.


 


26
112
NVVLEAPFL
1.500
626.


 


27
61
AAGPQLPSW
1.500
627.


 


28
26
RAIDQASFT
1.200
628.


 


29
62
AGPQLPSWL
1.000
629.


 


30
119
FLVGIEGSL
1.000
630.


 


31
140
CGIPVGFHL
1.000
631.


 


32
154
ALAALRGHF
1.000
632.


 


33
42
QVVKGSSPL
1.000
633.


 


34
150
STHAALAAL
1.000
634.


 


35
205
LTHNRLKSL
1.000
635.


 


36
99
RSLGAVVFS
1.000
636.


 


37
79
QCAQCHAVL
1.000
637.


 


38
147
HLYSTHAAL
1.000
638.


 


39
111
NNVVLEAPF
1.000
639.


 


40
221
TPDQSKPEN
0.600
640.


 


41
198
ELKEKIVLT
0.600
641.


 


42
181
NASEMDIQN
0.600
642.


 


43
175
KTKAIVNAS
0.600
643.


 


44
125
GSLKGSTYN
0.500
644.


 


45
129
GSTYNLLFC
0.500
645.


 


46
149
YSTHAALAA
0.500
646.


 


47
182
ASEMDIQNV
0.450
647.


 


48
87
LADSVHLAW
0.450
648.


 


49
113
VVLEAPFLV
0.400
649.


 


50
20
FCGGTERAI
0.400
650.

















TABLE XVIII







HLA Peptide Scoring Results-85P1B3-B35, 10-mers














Start
Subsequence Residue
Score (Estimate of Half Time of Disassociation of a Molecule




Rank
Position
Listing
Containing This Subsequence)
Seq. ID#















1
190
VPLSEKIAEL
20.000
651.



 


2
106
FSRVTNNVVL
15.000
652.


 


3
97
LSRSLGAVVF
15.000
653.


 


4
164
LSSDKMVCYL
10.000
654.


 


5
46
GSSPLGPAGL
5.000
655.


 


6
149
YSTHAALAAL
5.000
656.


 


7
125
GSLKGSTYNL
5.000
657.


 


8
84
HAVLADSVHL
4.500
658.


 


9
153
AALAALRGHF
3.000
659.


 


10
61
AAGPQLPSWL
3.000
660.


 


11
35
TSMEWDTQVV
3.000
661.


 


12
155
LAALRGHFCL
3.000
662.


 


13
126
SLKGSTYNLL
3.000
663.


 


14
117
APFLVGIEGS
2.000
664.


 


15
140
CGIPVGFHLY
2.000
665.


 


16
59
EPAAGPQLPS
2.000
666.


 


17
205
LTHNRLKSLM
2.000
667.


 


18
4
QPLRHRSRCA
2.000
668.


 


19
66
LPSWLQPERC
2.000
669.


 


20
142
IPVGFHLYST
2.000
670.


 


21
163
CLSSDKMVCY
2.000
671.


 


22
211
KSLMKILSEV
2.000
672.


 


23
11
RCATPPRGDF
2.000
673.


 


24
48
SPLGPAGLGA
2.000
674.


 


25
181
NASEMDIQNV
1.800
675.


 


26
30
QASFTTSMEW
1.500
676.


 


27
165
SSDKMVCYLL
1.500
677.


 


28
111
NNVVLEAPFL
1.500
678.


 


29
196
IAELKEKIVL
1.350
679.


 


30
26
RAIDQASFTT
1.200
680.


 


31
207
HNRLKSLMKI
1.200
681.


 


32
204
VLTHNRLKSL
1.000
682.


 


33
137
CGSCGIPVGF
1.000
683.


 


34
86
VLADSVHLAW
1.000
684.


 


35
41
TQVVKGSSPL
1.000
685.


 


36
139
SCGIPVGFHL
1.000
686.


 


37
92
HLAWDLSRSL
1.000
687.


 


38
69
WLQPERCAVF
1.000
688.


 


39
78
FQCAQCHAVL
1.000
689.


 


40
110
TNNVVLEAPF
1.000
690.


 


41
195
KIAELKEKIV
0.800
691.


 


42
209
RLKSLMKILS
0.600
692.


 


43
15
PPRGDFCGGT
0.600
693.


 


44
71
QPERCAVFQC
0.600
694.


 


45
89
DSVHLAWDLS
0.500
695.


 


46
24
TERAIDQASF
0.450
696.


 


47
170
VCYLLKTKAI
0.400
697.


 


48
178
AIVNASEMDI
0.400
698.


 


49
133
NLLFCGSCGI
0.400
699.


 


50
187
IQNVPLSEKI
0.400
700.
















TABLE XIX





Motifs and Post-translational modifications

















N-glycosylation site



181–184 NASE (SEQ ID NO: 735)



Protein kinase C phosphorylation site



Number of matches: 4



1  24–26 TER



2 126–128 SLK



3 166–168 SDK



4 193–195 SEK



Casein kinase II phosphorylation site



Number of matches: 3



1  35–38 TSME (SEQ ID NO: 736)



2 183–186 SEMD (SEQ ID NO: 737)



3 225–228 SKPE (SEQ ID NO: 738)



N-myristoylation site



Number of matches: 5



1  23–28 GTERAI (SEQ ID NO: 739)



2 122–127 GIEGSL (SEQ ID NO: 740)



3 125–130 GSLKGS (SEQ ID NO: 741)



4 129–134 GSTYNL (SEQ ID NO: 742)



5 141–146 GIPVGF (SEQ ID NO: 743)



RGD Cell attachment sequence



17–19 RGD



Cytochrome c family heme-binding site signature



80–85 CAQCHA

















TABLE XX







Frequently Occurring Motifs











avrg. %

Potential


Name
identity
Description
Function





zf-C2H2
34%
Zinc finger, C2H2 type
Nucleic acid-





binding protein





functions as





transcription





factor, nuclear





location





probable


cytochrome b N
68%
Cytochrome b(N-
membrane




terminal)/b6/petB
bound oxidase,





generate





superoxide


ig
19%
Immunoglobuline domain
domains are





one hundred





amino acids





long and





include a





conserved





intradomain





disulfide bond.


WD40
18%
WD domain, G-beta repeat
tandem repeats





of 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 Repeat
short sequence





motifs involved





in protein-





protein





interactions


pkinase
23%
Protein kinase domain
conserved





catalytic 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





intracellular





signaling or as





constituents of





the





cytoskeleton


EGF
34%
EGF-like domain
30–40 amino-





acid long found





in the





extracellular





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




Ubiquinone/plastoquinone
associated.




(complex I), various chains
Involved in





proton





translocation





across the





membrane


efhand
24%
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 protease
Aspartyl or





acid proteases,





centered on a





catalytic





aspartyl residue


Collagen
42%
Collagen triple helix repeat
extracellular




(20 copies)
structural





proteins





involved in





formation of





connective





tissue. The





sequence





consists of the





G-X-Y and the





polypeptide





chains forms a





triple helix.


fn3
20%
Fibronectin type III domain
Located in the





extracellular





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 receptor
seven




(rhodopsin family)
hydrophobic





transmembrane





regions, with





the N-terminus





located





extracellularly





while the





C-terminus is





cytoplasmic.





Signal through





G proteins
















TABLE XXV







Protein Properties











Bioinformatic





Program
URL
Outcome














ORF
ORF Finder
http://www.ncbi.nlm.gov/gorf
13–702 (includes stop)


Protein Length


229 amino acids


Transmembrane region
TM Pred
http://www.ch.embnet.org/
one TM at aa 129–149



HMMTop
http://www.enzim.hu/hmmtop/
one TM at aa 134–158



Sosui
http://www.genome.ad.jp/SOSui/
indicates no TM, soluble





protein



TMHMM
http://www.cbs.dtu.dk/services/TMHMM
indicates no TM


Signal Peptide
Signal P
http://www.cbs.dtu.dk/services/SignalP/
indicates no signal


pI
pI/MW tool
http://www.expasy.ch/tools/
pI 7.02


Molecular weight
pI/MW tool
http://www.expasy.ch/tools/
24.69 kDa


Localization
PSORT
http://psort.nibb.ac.jp/
Cytoplasmic 65%





Mitochondrial 10%



PSORT II
http://psort.nibb.ac.jp/
Mitochondrial 60.9%





Cytoplamic 21.7%


Motifs
Pfam
http://www.sanger.ac.uk/Pfam/
no motif detected



Prints
http://www.biochem.ucl.ac.uk/
no significant motif



Blocks
http://www.blocks.fhcrc.org/
soybean trypsin inhibitor





protease family,





Cytochrome c



Prosite
http://www.genome.ad.jp/
Cytochrome c family,





heme binding signature

## Claims

1. An isolated monoclonal antibody or fragment thereof that specifically binds to a protein comprising the amino acid sequence of SEQ ID NO: 728, wherein the antibody or fragment thereof is conjugated to a diagnostic agent or a cytotoxic agent.

2. The antibody or fragment thereof of claim 1, wherein the antibody is a human antibody, a humanized antibody or a chimeric antibody.

3. The antibody or fragment thereof of claim 1, wherein the fragment is an Fab, F(ab′)2, Fv or sFv fragment.

4. The antibody or fragment thereof of claim 1, wherein the cytotoxic agent is selected from the group consisting of radioactive isotopes, chemotherapeutic agents and toxins.

5. The antibody or fragment thereof of claim 4, wherein the radioactive isotope is selected from the group consisting of 211At, 131I, 125I, 90Y, 186Re, 188Re, 153Sm, 212Bi, 32P and radioactive isotopes of Lu.

6. The antibody or fragment thereof of claim 4, wherein the chemotherapeutic agent is selected from the group consisting of actinomycin, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, gelonin, and calicheamicin.

7. The antibody or fragment thereof of claim 4, wherein the toxin is selected from the group consisting of diphtheria toxin, enomycin, phenomycin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A chain, mitogellin, modeccin A chain, and alpha-sarcin.

8. The antibody or fragment thereof of claim 1, wherein the antibody or fragment thereof further comprises a pharmaceutically acceptable carrier.