(19) TZZ ¥¥¥ _T (11) EP 2 423 332 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 29.02.2012 Bulletin 2012/09 C12Q 1/68 (2006.01) (21) Application number: 11180577.6 (22) Date of filing: 23.08.2007 (84) Designated Contracting States: (72) Inventors: AT BE BG CH CY CZ DE DK EE ES FI FR GB GR • Nakamura, Yusuke HU IE IS IT LI LT LU LV MC MT NL PL PT RO SE Tokyo, 113-8654 (JP) SI SK TR • Daigo, Yataro Designated Extension States: Tokyo, 113-8654 (JP) AL BA HR MK RS • Nakatsuru, Shuichi Kanagawa, 213-0012 (JP) (30) Priority: 25.08.2006 US 840376 P 14.03.2007 US 894801 P (74) Representative: Vossius & Partner Siebertstrasse 4 (62) Document number(s) of the earlier application(s) in 81675 München (DE) accordance with Art. 76 EPC: 07806302.1 / 2 061 900 Remarks: This application was filed on 08-09-2011 as a (71) Applicant: Oncotherapy Science, Inc. divisional application to the application mentioned Kawasaki-shi under INID code 62. Kanagawa 213-0012 (JP) (54) Prognostic markers and therapeutic targets for lung cancer (57) The present invention provides a diagnostic present invention provides methods and kits for identify- marker to detecting lung cancer. In particular, the present ing inhibitors of the interaction between KIF4A/ZNF549, invention provides lung cancer marker genes i.e. KIF4A, KIF4A/ZNF553, MAPJD/MYC, or FGFR1OP/WRNIP1 MAPJD, NPTX, or FGFR1OP. The present invention fur- which find utility in the treatment and prevention of lung. ther provides methods and kit for identifying compounds Alternatively, the present invention provides MAPJD as- for treating lung cancer as well as methods for predicting sociated with HAT complex as therapeutic target. a prognosis or diagnosis of lung cancer. In particular, the EP 2 423 332 A1 Printed by Jouve, 75001 PARIS (FR) EP 2 423 332 A1 Description Cross- Reference to Related Applications 5 [0001] The present application claims the benefit of U.S. Provisional Application No. 60/840,376, filed August 25, 2006, and U.S. Provisional Application No. 60/894,801, filed March 14, 2007, the entire disclosures of each of which are hereby incorporated herein by reference for all purposes. Technical Field 10 [0002] The present invention relates to methods for detecting and diagnosing cancer as well as methods for treating and preventing cancer. Background Art 15 [0003] Lung cancer is one of the most common and fatal cancers in the world (Greenlee RT et al. CA Cancer J Clin 2001;51:15-36.). A number of genetic alterations associated with development and progression of lung cancer, have been reported, but its precise molecular mechanisms still remain unclear (Sozzi G. Eur J Cancer 37 Suppl 7: S63-73.). Two major bistological-distinct types of lung cancer, non-small cell lung cancer (NSCLC) and small-cell lung cancer 20 (SCLC) have different pathophysiological and clinical features that suggest differences in the mechanism of their car- cinogenesis. SCLC accounts- for 15-20% of all lung cancers (Morita T et al. Acta Pathol Jpn 40: 665-75, 1990.; Simon GR et al. Chest 123 Suppl 1: S259-71, 2003.) and is categorized as neuroendocrine tumors of the lung with certain morphologic, ultra-structural, and immunohistochemical characteristics. However, detailed molecular characteristics of neuroendocrine tumors are still not well understood. Although patients with SCLC respond favorably to the 1st line multi- 25 agent chemotherapy, they often relapse in a short time. Hence, only 20% of patients with limited-stage disease (LD) can be cured with combined modality therapy and less than 5% of those with extensive-disease (ED) can achieve 5- year survival after the initial diagnosis (Chute JP et al. J Clin Oncol 17: 1794-801, 1999.; Sandler AB. Semin Oncol 30: 9-25, 2003.). Therefore, new therapeutic strategies such as molecular-targeted agents are eagerly awaited. [0004] Systemic chemotherapy is the main treatment for the majority of patients with NSCLC because most are 30 diagnosed with advanced inoperable disease. Within the last decade several newly-developed cytotoxic agents such as paclitaxel, docetaxel, gemcitabine, and vinorelbine have begun to offer multiple choices for treatment of patients with advanced lung cancer; however, each of those regimens confers only a modest survival benefit compared with cisplatin- based therapies (Schiller JH, et al. N Engl J Med 2002; 346:92-8.; Kelly K, et al. J Clin Oncol 2001:19:3210-8.). Hence, novel therapeutic strategies such as molecular-targeted dregs, antibodies, nucleic acid drugs and cancer vaccines, are 35 eagerly being sought. [0005] The long-term survival rate, even with complete clinical resections, remains unsatisfactory (Naruke T, et al. Ann Thorac Surg. 2001 Jun; 71(6): 1759-64.). Therefore, a better understanding of the molecular pathogenesis of lung cancer is an urgent issue in order to develop better diagnostic approaches and new molecular targeted therapies. Although the precise pathways involved in lung tumorigenesis remain unclear, some evidences indicate that tumor cells 40 express cell-surface markers unique to each histological type at particular stages of differentiation. Since cell-surface proteins are considered more accessible to immune mechanism and drug-delivery systems, identification of cancer- specific cell-surface and secretory proteins is likely to be an effective approach to development of novel diagnostic markers and therapeutic strategies. [0006] The genome-wide DNA microarray analysis is useful to obtain comprehensive gene expression profiles related 45 to detailed phenotypic and biological information in cancer cells (Golub TR, et al. Science. 1999 Oct 15;286(5439): 531-7.; Pomeroy SL, et al. Nature. 2002 Jan 24;415(6870):436-42.; van’t Veer LJ, et al. Nature. 2002 Jan 31;415(6871): 530-6.). This approach is also useful to identify unknown molecules involved in the pathways of carcinogenesis. Through gene-expression profile analysis of SCLCs and NSCLCs coupled with purification of cancer cell population by laser- microbeam microdissection (LMM) on a cDNA microarray consisting of about 30,000 genes, the present inventors 50 identified a number of potential molecular targets for diagnosis, treatment, and/or choice of therapy (Kikuchi T, et al. Oncogene. 2003 Apr 10;22(14):2192-205.; Int J Oncol. 2006 Apr;28(4):799-805.; Kakiuchi S, et al. Mol Cancer Res. 2003 May;1(7):485-99.; Hum Mol Genet. 2004 Dec 15;13(24):3029-43. Epub 2004 Oct 20.). To verify the biological and clinicopathological significance of the respective gene products, the present inventors have also been performing high- throughput screening of loss-of-function effects by means of the RNAi technique as well as tumor-tissue microarray 55 analysis of clinical lung-cancer materials (Suzuki C, et al. Cancer Res. 2003 Nov 1;63(21):7038-41.; Cancer Res, 2005 Dec 15;65(24):11314-25.; Ishikawa N, et al. Clin Cancer Res. 2004 Dec 15;10(24):8363-70.; Cancer Res. 2005 Oct 15; 65(20):9176-84.; Kato T, et al. Cancer Res. 2005;65(13):5638-46.; Furukawa C, et al. Cancer Res. 2005;65(16): 7102-10.). This systematic approach revealed that KIF4A (kinesin family member 4A) (GenBank Accession No. NM_ 2 EP 2 423 332 A1 012310) was frequently over-expressed in the great majority of SCLCs as well as in 40% of NSCLCs, and was essential to growth or progression of lung-cancers, that MAPJD (Myc-associated protein with JmjC domain) (C14orf169, chro- mosome 14 open reading frame 169; alias FLJ21802/N066 protein) (GenBank Accession NO. NM_024644) was over- expressed in the great majority of the NSCLCs, that Neural pentraxin I (NPTX1) (GenBank Accession No. NM_002522) 5 was frequently transactivated in primary lung cancers, and that the gene encoding fibroblast growth factor receptor 1 oncogene partner (FGFR10P alias FOP) (GenBank Accession No. NM_007045) was likely to over-express in the great majority of primary NSCLCs (WO2004/31413, WO2005/89735). [0007] Recent years, a new approach of cancer therapy using gene-specific siRNA was attempted in clinical trials (Burncrot D et al., Nat Chem Biol 2006 Dec, 2(12): 711-9). RNAi seems to have already earned a place among the 10 major technology platforms (Putral LN et al., Drug News Perspect 2006 Jul-Aug, 19(6): 317-24; Frantz S, Nat Rev Drug Discov 2006 Jul, 5(7): 528-9; Dykxhoom DM et al., Gene Ther 2006 Mar, 13(6): 541-52). Nevertheless, there are several challenges that need to be faced before RNAi can be applied in clinical use. These challenges include poor stability of RNA in vivo (Hall AH et al., Nucleic Acids Res 2004 Nov 15, 32(20): 5991-6000, Print 2004; Amarzguioui M et al., NuCleic Acids Res 2003 Jan 15, 31(2): 589-95), toxicity as an agent (Frantz S, Nat Rev Drug Discov 2006 Jul, 5(7): 15 528-9), mode of delivery, the precise sequence of the siRNA or shRNA used, and cell type specificity. It is a well-known fact that there are possible toxicities related to silencing of partially homologous genes or induction of the interferon response (Judge AD et al., Nat Biotechnol 2005 Apr, 23(4): 457-62, Epub 2005 Mar 20; Jackson AL & Linsley PS, Trends Genet 2004 Nov, 20(11): 521-4). So double-stranded molecules targeting cancer-specific genes must be devoid of adverse side-effects. 20 Summary of the Invention [0008] The present invention is based, at least in part, on the discovery of a specific expression pattern of a kinesin family member 4A (KIF4A) (GenBank Accession No. NM_012310), Myc-associated protein with JmjC domain (MAPJD) 25 (GenBank Accession No. NM_024644), Neuronal pentraxin I (NPTX1) (GenBank Accession No. NM_002522) and fibroblast growth factor receptor 1 oncogene partner (FGFR1OP) (GenBank Accession No.