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E USOO7745.391 B2 (12) United States Patent (10) Patent No.: US 7,745,391 B2 Mintz et al. (45) Date of Patent: Jun. 29, 2010 (54) HUMAN THROMBOSPONDIN POLYPEPTIDE 5,283,317. A 2/1994 Saifer et al. 5,288,514. A 2/1994 Ellman (75) Inventors: Liat Mintz, East Brunswick, NJ (US); 5,328,470 A 7, 1994 Nabel et al. Hanging Xie, Lambertville, NJ (US); 5,384,261 A 1/1995 Winkler et al. Dvir Dahary, Tel-Aviv (IL); Erez 5,459,039 A 10/1995 Modrich et al. Levanon, Petach-Tikva (IL), Shiri 5,475,092 A 12/1995 Charietal. Freilich, Herzlia (IL); Nili Beck, Kfar 5,498,531 A 3, 1996 Jarrell Saba (IL); Wei-Yong Zhu, Plainsboro, 5,510,270 A 4/1996 Fodor et al. E"ESNI)s s 379- J. A ROMomoglio is et al.a (73) Assignee: Compugen Ltd., Tel-Aviv (IL) 5,585,089 A 12/1996 Queen et al. 5,585.499 A 12/1996 Chari et al. (*) Notice: Subject to any disclaimer, the term of this 5,631, 169 A 5/1997 Lakowicz et al. patent is extended or adjusted under 35 5,693,761 A 12/1997 Queen et al. U.S.C. 154(b) by 441 days. 5,693,762. A 12/1997 Queen et al. 5,695,937 A 12/1997 Kinzler et al. (21) Appl. No.: 11/443,428 5,846,545. A 12/1998 Chari et al. 5,854,033. A 12/1998 Lizardi (22) Filed: May 31, 2006 5,876,742 A 3/1999 Cochrum et al. (Under 37 CFR 1.47) 6,033,862. A 3/2000 Matsuda et al. (65) Prior Publication Data 6,049,728 A 4/2000 Chou et al. 6,727,063 B1 4/2004 Lander et al. .................. 435/6 US 2007/0083334 A1 Apr. 12, 2007 7,223,731 B2 * 5/2007 Lawler ............. ... 514/12 7.368,548 B2 * 5/2008 Dahary et al. .............. 536,231 Related U.S. Application Data 2002fO155615 A1 10, 2002 Novikov et al. (63) Continuation of application No. 10/242,799, filed on 2003.0118585 A1 6, 2003 Muller et al. Sep. 13, 2002, now abandoned. 2003/0176666 A1 9, 2003 Sutcliffe et al. (60) Provisional application No. 60/397,784, filed on Jul. 2004.0054268 A1 3, 2004 Esenaliev et al. 24, 2002, provisional application No. 60/384,096, 2004/0101876 A1 5, 2004 Mintz et al. filed on May 31, 2002, provisional application No. 2004/O127777 A1 7, 2004 Ruchiti et al. 60/371,494, filed on Apr. 11, 2002, provisional appli- 2004/O142325 A1 7, 2004 Mintz et al. cation No. 60/354.242, filed on Feb. 6, 2002, provi- 2004/0248157 Al 12/2004 Ayalon-Soffer et al. sional application No. 60/324,524, filed on Sep. 26, 2004/0265799 A1 12, 2004 Novik et al. 2001, provisional application No. 60/322,506, filed on 2005/O123538 A1 6/2005 Shemesh et al. Sep. 14, 2001, provisional application No. 60/322,359, 2005, 0186600 A1 8, 2005 Sella-Tavor et al. filed on Sep. 14, 2001, provisional application No. 60/322.285, filed on Sep. 14, 2001. (51) Int. Cl. (Continued) A6 IK 38/00 (2006.01) C07K I4/00 (2006.01) FOREIGN PATENT DOCUMENTS (52) U.S. Cl. .............................. 514/2; 514/12:530/350 EP 125O23 11, 1984 (58) Field of Classification Search ....................... None See application file for complete search history. (56) References Cited (Continued) U.S. PATENT DOCUMENTS OTHER PUBLICATIONS 4,215,051 A 7, 1980 Schroeder et al. 4,683.202 A 7, 1987 Mullis Lawler et al., J. Cell. Biol. 103: 1635-1648, 1986.* 4,704,692 A 11, 1987 Ladner 4,816,567 A 3/1989 Cabilly et al. (Continued) 4,868,103 A 9/1989 Stavrianopoulos et al. 4,873,316 A 10, 1989 Meade et al. Primary Examiner David J Steadman 4.946,778 A 8, 1990 Ladner et al. 4,987,071 A 1/1991 Cech et al. (57) ABSTRACT 5,093,246 A 3, 1992 Cech et al. 5,116,742 A 5, 1992 Cech et al. 5,143,854 A 9, 1992 Pirrung A human thrombospondin 1 protein, polynucleotide encod 5,208,020 A 5, 1993 Chari et al. ing the protein, and pharmaceutical composition thereof 5,223,409 A 6/1993 Ladner et al. gune p , and p p 5,225,539 A 7, 1993 Winter 5,272,057 A 12/1993 Smulson et al. 2 Claims, 25 Drawing Sheets US 7,745,391 B2 Page 2 U.S. PATENT DOCUMENTS Akhurst “TGF-B Antagonists: Why Suppress ATumor Suppressor?’’. The Journal of Clinical Investigation, 109(12): 1533-1536, 2002. 2005/023396.0 A1 10/2005 Kong-Beltran et al. Altschul et al. “Basic Local Alignment Search Tool”, Journal of 2006, OO68405 A1 3, 2006 Diber et al. molecular Biology, 215: 403-410, 1990. 2007/0082337 A1 4/2007 Sorek et al. Asadullah et al. “Interleukin-10 Therapy-Review of A New Approach'. Pharmacological Review, 55(2): 241-269, 2003. FOREIGN PATENT DOCUMENTS Attisano et al. “Signal Transduction by the TGF-B Superfamily”. EP 1841.87 6, 1985 Science, 296(5573): 1646-1647, 2002. EP 171496 2, 1986 Audic et al. “The Significance of Digital Gene Expression Profiles'. EP 173494 3, 1986 Genome Research, 7: 986-995, 1997. EP O519596 12/1992 Azios et al. “Expression of Herstatin, An Autoinhibitor of HER-2/ EP O770349 5, 1997 Neu, Inhibits Transactivation of HER-3 by HER-2 and Blocks EGF GB 2322941 9, 1998 Activation of the EGF Receptor'. Oncogene, 20(37): 5199-5232, WO WO 86.01533 3, 1986 2001. WO WO90,02809 3, 1990 Baker et al. "A Randomized Phase 2 Study of the Thrombospondin WO WO91/00906 1, 1991 Mimetic. Peptide ABT-510 in Patients With Advanced Soft Tissue WO WO91,06667 5, 1991 Sarcoma (STS)”, Journal of Clinical Onoclogy, Proceedings of the WO WO91f10741 7, 1991 ASCO Annual Meeting 2005, 23(16 Suppl.): 9013, Jun. 1, 2005. WO WO 91f17271 11, 1991 Abstract. WO WO92fO1047 1, 1992 Benson et al. “GenBank”. Nucleic Acids Research, 25(1): 1-6, 1997. WO WO92fO3917 3, 1992 p. 1-5. WO WO92fO3918 3, 1992 Bieche et al. “Overexpression of BRCA2 Gene in Sporadic Breast WO WO92.09690 6, 1992 Tumours”. Oncogen, 18: 5232-5238, 1999. WO WO92, 15679 9, 1992 Bihl et al. “Identification of a Novel IL-6 Isoform Binding to the WO WO92, 18619 10, 1992 Endogenous IL-6 Receptor'. American Journal of Respiratory Cell WO WO92/2O791 11, 1992 and Molecular Biology, 27: 48-56, 2002. WO WO93/O1288 1, 1993 Birchmeier et al. “Met, Metastasis, Motility and More', Nature WO WO94f10300 5, 1994 Reviews: Molecular Cell Biology, 4:915-925, 2003. WO WO 98.55510 12/1998 Blazar et al. “Ligation of 4-IBB (CDw137) Regulates Graft-Versus WO WO99, 18208 4f1999 Host Disease, Graft-Versus-Leukemia, and Graft Rejection in WO WO 99.51773 10, 1999 Allogeneic Bone Marrow Transplant Recipients'. The Journal of WO WO O2, 12341 2, 2002 Immunology, 166(5): 3174-3183, 2001. WO WO 03/020953 3, 2003 Boguski"Biosequence Exegesis”. Science, 286: 453-455, 1999. WO WO 2004/092.338 10, 2004 Boguski et al. “ESTablishing A Human Transcript Map”. Nature WO WO 2004/096979 11, 2004 WO WO 2004/096.980 11, 2004 Genetics, 10: 369-371, 1995. WO WO 2005/033133 4/2005 Bonfield etal. “A New DNA Sequence Assembly Program'. Nucleic WO WO 2005/0686.18 7/2005 Acids Research, 23(24): 4992-4999, 1995. WO WO 2005/071058 8, 2005 Bornstein “Diversity of Function Is Inherent in Matricellular Pro WO WO 2005/071059 8, 2005 teins: An Appraisal of Thrombospondin 1'. The Journal of Cell WO WO 2005,111634 11, 2005 Biology, 130(3): 503-506, Aug. 1995. WO WO 2005,113596 12/2005 Bornstein “Thrombospondins: Structure and Regulation of Expres sion'. The FASEB Journal, 6:3290-3299, 1992. Brattain et al. “The Type II Transforming Growth Factor-B Receptor OTHER PUBLICATIONS as A Tumor-Suppressor Gene'. Current Opinion in Oncology, 8(1): Chen et al., Mol Cell Prot 1:304-313, 2002.* 49-53, 1996. Tolsma et al., J. Cell Biol. 122:497-511, 1993.* Brett et al. “EST Comparison Indicates 3.8% of Human mRNAs Chen et al., Biochemistry 37.9976-9982, 1998.* Contain Possible Alternative Splice Forms', FEBS Letters, 474: “Agencourt 6578352 NIH MGC 41 Homo Sapiens cDNA Clone 83-86, 2000. IMAGE: 5467535 5", mRNA Sequence”, Database EMBL'Online!, Brierley etal. “IFN-O/B Receptor Interactions to Biologic Outcomes: Database Accession No. BM556795, 2002. Understanding the Circuitry”, Journal of Interferon and Cytokine “Agencourt 785234 NIH MGC 67 Homo Sapiens cDNA Clone Research, 22(8): 835-845, 2002. IMAGE: 61400985", mRNA Sequence”, Database EMBL'Online!, Brockmann et al. "Inhibition of Intracerebral Glioblastoma Growth Database Accession No. BU169315, 2002. by Local Treatment With the Scatter Factor/Hepatocyte Growth Fac “Agencourt 7952308 NIH MGC 72 Homo Sapiens cDNA Clone tor-Antagonist NK4'. Clinical Cancer Research, 9: 4578-4585, IMAGE: 6149711 5", mRNA Sequence”, Database EMBL'Online!, 2003. Database Accession No. BU171488, 2002. Buetow etal. “High-Throughput Development and Characterization “OTTHUMP00000031654 (Fragment), Database EMBL, Database of A Genomewide Collection of Gene-Based Single Nucleotide Accession No. Q9BQP0, 2001. Abstract. Polymorphism Markers by Chip-Based Matrix-Assisted Laser Abounader et al. “In Vivo Targeting of SF/HGF and C-Met Expres Desorption/Ionization Time-of-Flight Masss Spectrometry”. Proc. sion Via U1snRNA/Ribozymes Inhibits Glioma Growth and Natl. Acad. Sci. US, 98(2): 581-584, 2001. Esp. p. 581-583 A. Angiogenesis and Promotes Apoptosis'. The FASEB Journal, 16: Burgess et al.
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