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Nucleic Acid and Corresponding Protein Named 158P1D7 Useful in the Treatment and Detection of Bladder and Other Cancers

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Nucleic Acid and Corresponding Protein Named 158P1D7 Useful in the Treatment and Detection of Bladder and Other Cancers (19) & (11) EP 2 343 315 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 13.07.2011 Bulletin 2011/28 C07K 14/47 (2006.01) C12N 15/12 (2006.01) C12Q 1/68 (2006.01) A61K 38/17 (2006.01) (2006.01) (2006.01) (21) Application number: 10075689.9 C07K 16/18 A01K 67/027 A61K 39/00 (2006.01) C12N 15/11 (2006.01) (22) Date of filing: 10.02.2004 (84) Designated Contracting States: • Perez-Villar, Juan, J. AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Valencia 46530 (ES) HU IE IT LI LU MC NL PT RO SE SI SK TR • Morrison, Karen, Jane, Meyrick Santa Monica, CA 90403 (US) (30) Priority: 10.02.2003 US 446633 P • Faris, Mary Los Angeles, CA 90077 (US) (62) Document number(s) of the earlier application(s) in • Ge, Wangmao accordance with Art. 76 EPC: Culver City, CA 90230 (US) 04709923.9 / 1 594 892 • Gudas, Jean Los Angeles, CA 90049 (US) (71) Applicant: Agensys, Inc. • Kanner, Steven, B. Santa Monica, CA 90404 (US) SAnta Monica, CA 90403 (US) (72) Inventors: (74) Representative: Lord, Hilton David et al • Jakobovits, Aya Marks & Clerk LLP Beverly Hills, CA 90210 (US) 90 Long Acre • Morrison, Robert Kendall London WC2E 9RA (GB) Santa Monica, CA 90403 (US) • Raitano, Arthur B. Remarks: Los Angeles, CA 90066 (US) This application was filed on 01-10-2010 as a • Challita-Eid, Pia, M. divisional application to the application mentioned Encino, CA 91436 (US) under INID code 62. (54) Nucleic acid and corresponding protein named 158P1D7 useful in the t reatment and detection of bladder and other cancers (57) A polynucleotide that encodes 158P1D7 pro- tein, wherein the polynucleotide is: encodes a protein that can be used to immunise an an- (a) a polynucleotide comprising the sequence of SEQ ID imal or raise antibodies. Cells expressing the protein can NO:8, from nucleotide residue number 23 through 1210; be detected, or growth and/or survival of a cell expressing or the protein inhibited. (b) a polynucleotide comprising the sequence of SEQ ID NO:10, from nucleotide residue number 23 through 1612 EP 2 343 315 A2 Printed by Jouve, 75001 PARIS (FR) EP 2 343 315 A2 Description FIELD OF THE INVENTION 5 [0001] The invention described herein relates to novel nucleic acid sequences and thier encoded proteins, referred to as 158P1D7 and variants thereof, and to diagnostic and therapeutic methods and compositions useful in the man- agement of various cancers that express 158P1D7 and variants thereof. BACKGROUND OF THE INVENTION 10 [0002] 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 15 of the next century, cancer is predicted to become the leading cause of death. [0003] 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 20 100,000 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. [0004] Bladder cancers comprise a heterogeneous group of diseases. The main determinants of disease control and 25 survival are histology and extent of disease. The main codes for these factors include pathology classification, the International Classification of Diseases-Oncology (ICDO), and staging classification of extent of disease, the TNM clas- sification.(Table XXI). For a general discussion of bladder and other urogenital cancers, see, e.g., Volgelzang, et al, Eds. Comprehensive Textbook of Genitourinary Oncology, (Williams & Wilkins, Baltimore 1996), in particular pages 295-556. 30 [0005] Three primary types of tumors have been reported in the bladder. The most common type of bladder cancer is Transitional cell carcinoma (TCC); this accounts for about 90% of all bladder cancers. The second form of bladder cancer is squamous cell carcinoma, which accounts for about 8% of all bladder cancers where schistosomiasis is not endemic, and approximately 75% of bladder carcinomas where schistosomiasis is endemic. Squamous cell carcinomas tend to invade deeper layers of the bladder. The third type of bladder cancer is adenocarcinoma, which account for 1%- 35 2% of bladder cancers; these are primarily invasive forms of cancer. [0006] Bladder cancer is commonly detected and diagnosed using cytoscopy and urine cytology. However these methods demonstrate poor sensitivity. Relatively more reliable methods of detection currently used in the clinic include the bladder tumor antigen (BTA) stat test, NMP22 protein assay, telomerase expression and hyaluronic acid and hy- aluronidase (HA-HAase) urine test. The advantage of using such markers in the diagnosis of bladder cancer is their 40 relative high sensitivity in earlier tumor stages compared to standard cytology. [0007] For example, the BTA stat test has 60-80% sensitivity and 50-70% specificity for bladder cancer, while the HA- HAase urine test shows 90-92% sensitivity and 80-84% specificity for bladder cancer (J Urol 2001 165: 1067). In general, sensitivity for stage Ta tumors was 81% for nuclear matrix protein (NMP22), 70% for telomerase, 32% for bladder tumor antigen (BTA) and 26% for cytology (J Urol 2001 166:470; J Urol 1999, 161:810). Although the telomeric repeat assay 45 which measures telomerase activity is relatively sensitive, instability of telomerase in urine presently renders this detection method unreliable. [0008] Most bladder cancers recur in the bladder. Generally, bladder cancer is managed with a combination of transure- thral 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. 50 Radical cystectomy and urinary diversion is the most effective means to eliminate the cancer but carry an undeniable impact on urinary and sexual function. [0009] Intravesical bacilli Calmette-Guerin (BCG) is a common and efficacious immunotherapeutic agent used in the treatment of bladder cancer. BCG is also used as a prophylactic agent to prevent recurrence of bladder cancer. However, 30% of patients fail to respond to BCG therapy and go on to develop invasive and metastatic disease (Catalona et al. 55 J Urol 1987, 137:220-224). BCG-related side effects have been frequently observed such as drug-induced cystitis, risk of bacterial infection, and hematuria, amongst others. Other alternative immunotherapies have been used for the treat- ment of bladder cancer, such as KLH (Flamm et al. Urologe 1994; 33:138-143) interferons (Bazarbashi et al. J Surg Oncol. 2000; 74:181-4), and MAGE-3 peptide loaded dendritic cells (Nishiyama et al. Clin Cancer Res 2001; 7:23-31). 2 EP 2 343 315 A2 All these approaches are still experimental (Zlotta et al. Eur Urol 2000;37 Suppl 3:10-15). There continues to be a significant need for diagnostic and treatment modalities that are beneficial for bladder cancer patients. Furthermore, from a worldwide standpoint, several cancers stand out as the leading killers. In particular, carcinomas of the lung, prostate, breast, colon, pancreas, and ovary are primary causes of cancer death. These and virtually all other carcinomas 5 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, 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. 10 [0010] Prostate cancer is the fourth most prevalent cancer in men worldwide. 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. Unfor- 15 tunately, these treatments are ineffective for many and are often associated with undesirable consequences. [0011] 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. While previously identified markers such as PSA, PSM, PCTA and PSCA have 20 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.
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