Cancer vulnerabilities unveiled by genomic loss

Cell

Volumn 150, Issue 4, 2012, Pages 842-854

  Nijhawan, Deepak ^a,b,d   Zack, Travis I ^a,b,c   Ren, Yin ^b   Strickland, Matthew R ^a   Lamothe, Rebecca ^a   Schumacher, Steven E ^a,b   Tsherniak, Aviad ^b   Besche, Henrike C ^d   Rosenbluh, Joseph ^a,b,d   Shehata, Shyemaa ^a   Cowley, Glenn S ^b   Weir, Barbara A ^b   Goldberg, Alfred L ^d   Mesirov, Jill P ^b   Root, David E ^b   Bhatia, Sangeeta N ^b,d,e   Beroukhim, Rameen ^a,b,d   Hahn, William C ^a,b,d  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c HARVARD UNIVERSITY   (United States)

^d HARVARD MEDICAL SCHOOL   (United States)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEASOME;

19SPSMC1 GENE; ARTICLE; BMP8A GENE; CANCER GENETICS; CANCER SUSCEPTIBILITY; CELL PROLIFERATION; COPY NUMBER ALTERATIONS YIELDING CANCER LIABILITIES OWING TO PARTIAL LOSS GENE; COPY NUMBER VARIATION; CPT1B GENE; EEF1A1 GENE; EEF2 GENE; EIF2B2 GENE; GENE; GENE LOSS; GENE REPRESSION; GENOME; GENOME ANALYSIS; GENOMIC INSTABILITY; HPGD GENE; HUMAN; LSM4 GENE; NONHUMAN; PCNA GENE; PHF5A GENE; POLG GENE; POLR2F GENE; PRIORITY JOURNAL; PSMA4 GENE; PSMC2 GENE; PSMD2 GENE; PSMD5 GENE; PUF60 GENE; RBM17 GENE; RIBOSOME; RNA INTERFERENCE; RPS11 GENE; RPS15 GENE; SF3A2 GENE; SMC2 GNE; SMU1 GENE; SNRNP70 GENE; SNRPB GENE; SPLICEOSOME; TIE1 GENE; TUMOR GENE; USPL1 GENE; ZNF583 GENE;

EID: 84865227709     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2012.07.023     Document Type: Article

References (37)

1. C. Aghajanian, S. Soignet, D.S. Dizon, C.S. Pien, J. Adams, P.J. Elliott, P. Sabbatini, V. Miller, M.L. Hensley, and S. Pezzulli A phase I trial of the novel proteasome inhibitor PS341 in advanced solid tumor malignancies Clin. Cancer Res. 8 2002 2505 2511 (Pubitemid 34856332)
2. A. Ashworth, C.J. Lord, and J.S. Reis-Filho Genetic interactions in cancer progression and treatment Cell 145 2011 30 38
3. J. Barretina, G. Caponigro, N. Stransky, K. Venkatesan, A.A. Margolin, S. Kim, C.J. Wilson, J. Lehár, G.V. Kryukov, and D. Sonkin The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity Nature 483 2012 603 607
4. Y. Benjamini, and Y. Hochberg Controlling the false discovery rate: a practical and powerful approach to multiple testing J. R. Stat. Soc. Ser. B Methodol. 57 1995 289 300
5. R. Beroukhim, C.H. Mermel, D. Porter, G. Wei, S. Raychaudhuri, J. Donovan, J. Barretina, J.S. Boehm, J. Dobson, and M. Urashima The landscape of somatic copy-number alteration across human cancers Nature 463 2010 899 905
6. M.S. Brose, P. Volpe, M. Feldman, M. Kumar, I. Rishi, R. Gerrero, E. Einhorn, M. Herlyn, J. Minna, and A. Nicholson BRAF and RAS mutations in human lung cancer and melanoma Cancer Res. 62 2002 6997 7000 (Pubitemid 35424092)
7. H.E. Bryant, N. Schultz, H.D. Thomas, K.M. Parker, D. Flower, E. Lopez, S. Kyle, M. Meuth, N.J. Curtin, and T. Helleday Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase Nature 434 2005 913 917 (Pubitemid 40559005)
8. Cancer Genome Atlas Research Network Integrated genomic analyses of ovarian carcinoma Nature 474 2011 609 615
9. H.W. Cheung, G.S. Cowley, B.A. Weir, J.S. Boehm, S. Rusin, J.A. Scott, A. East, L.D. Ali, P.H. Lizotte, and T.C. Wong Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer Proc. Natl. Acad. Sci. USA 108 2011 12372 12377
10. G.Q. Daley, R.A. Vanetten, and D. Baltimore Induction of chronic myelogenous leukemia in mice by the P210BCR/ABL gene of the Philadelphia chromosome Science 247 1990 824 830
11. S. Elsasser, M. Schmidt, and D. Finley Characterization of the proteasome using native gel electrophoresis Methods Enzymol. 398 2005 353 363 (Pubitemid 41578897)
12. H. Farmer, N. McCabe, C.J. Lord, A.N. Tutt, D.A. Johnson, T.B. Richardson, M. Santarosa, K.J. Dillon, I. Hickson, and C. Knights Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy Nature 434 2005 917 921 (Pubitemid 40559006)
13. D. Finley Recognition and processing of ubiquitin-protein conjugates by the proteasome Annu. Rev. Biochem. 78 2009 477 513
14. E. Frei III Gene deletion: a new target for cancer-chemotherapy Lancet 342 1993 662 664
15. M. Funakoshi, R.J. Tomko Jr., H. Kobayashi, and M. Hochstrasser Multiple assembly chaperones govern biogenesis of the proteasome regulatory particle base Cell 137 2009 887 899
16. M.J. Garnett, E.J. Edelman, S.J. Heidorn, C.D. Greenman, A. Dastur, K.W. Lau, P. Greninger, I.R. Thompson, X. Luo, and J. Soares Systematic identification of genomic markers of drug sensitivity in cancer cells Nature 483 2012 570 575
17. W.G. Kaelin Jr. The concept of synthetic lethality in the context of anticancer therapy Nat. Rev. Cancer 5 2005 689 698
18. T. Kaneko, J. Hamazaki, S. Iemura, K. Sasaki, K. Furuyama, T. Natsume, K. Tanaka, and S. Murata Assembly pathway of the mammalian proteasome base subcomplex is mediated by multiple specific chaperones Cell 137 2009 914 925
19. A.F. Kisselev, and A.L. Goldberg Monitoring activity and inhibition of 26S proteasomes with fluorogenic peptide substrates Methods Enzymol. 398 2005 364 378 (Pubitemid 41578898)
20. J. Liu, G. Yang, J.A. Thompson-Lanza, A. Glassman, K. Hayes, A. Patterson, R.T. Marquez, N. Auersperg, Y. Yu, and W.C. Hahn A genetically defined model for human ovarian cancer Cancer Res. 64 2004 1655 1663 (Pubitemid 38428686)
21. R. Marcotte, K.R. Brown, F. Suarez, A. Sayad, K. Karamboulas, P.M. Krzyzanowski, F. Sircoulomb, M. Medrano, Y. Fedyshyn, and J.L.Y. Koh Essential gene profiles in breast, pancreatic, and ovarian cancer cells Cancer Discov. 2 2012 172 189
22. C.H. Mermel, S.E. Schumacher, B. Hill, M.L. Meyerson, R. Beroukhim, and G. Getz GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers Genome Biol. 12 2011 R41
23. S. Park, J. Roelofs, W. Kim, J. Robert, M. Schmidt, S.P. Gygi, and D. Finley Hexameric assembly of the proteasomal ATPases is templated through their C termini Nature 459 2009 866 870
24. Y. Ren, H.W. Cheung, G. von Maltzhan, A. Agrawal, G.S. Cowley, B.A. Weir, J.S. Boehm, P. Tamayo, A.M. Karst, and J.F. Liu Targeted tumor-penetrating siRNA nanocomplexes for credentialing the ovarian cancer target ID4 Sci. Transl. Med. 4 2012 147ra112
25. P.G. Richardson, P. Sonneveld, M.W. Schuster, D. Irwin, E.A. Stadtmauer, T. Facon, J.L. Harousseau, D. Ben-Yehuda, S. Lonial, H. Goldschmidt Assessment of Proteasome Inhibition for Extending Remissions (APEX) Investigators Bortezomib or high-dose dexamethasone for relapsed multiple myeloma N. Engl. J. Med. 352 2005 2487 2498 (Pubitemid 41007864)
26. J. Roelofs, S. Park, W. Haas, G. Tian, F.E. McAllister, Y. Huo, B.H. Lee, F. Zhang, Y.G. Shi, S.P. Gygi, and D. Finley Chaperone-mediated pathway of proteasome regulatory particle assembly Nature 459 2009 861 865
27. Y. Saeki, A. Toh-E, T. Kudo, H. Kawamura, and K. Tanaka Multiple proteasome-interacting proteins assist the assembly of the yeast 19S regulatory particle Cell 137 2009 900 913
28. C.L. Sawyers Making progress through molecular attacks on cancer Cold Spring Harb. Symp. Quant. Biol. 70 2005 479 482 (Pubitemid 44124904)
29. D.M. Smith, H. Fraga, C. Reis, G. Kafri, and A.L. Goldberg ATP binds to proteasomal ATPases in pairs with distinct functional effects, implying an ordered reaction cycle Cell 144 2011 526 538
30. M. Soda, Y.L. Choi, M. Enomoto, S. Takada, Y. Yamashita, S. Ishikawa, S.I. Fujiwara, H. Watanabe, K. Kurashina, and H. Hatanaka Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer Nature 448 2007 561 566 (Pubitemid 47206930)
31. N.L. Solimini, J. Luo, and S.J. Elledge Non-oncogene addiction and the stress phenotype of cancer cells Cell 130 2007 986 988 (Pubitemid 47422308)
32. M.R. Stratton, P.J. Campbell, and P.A. Futreal The cancer genome Nature 458 2009 719 724
33. D. Thompson, K. Hakala, and G.N. DeMartino Subcomplexes of PA700, the 19 S regulator of the 26 S proteasome, reveal relative roles of AAA subunits in 26 S proteasome assembly and activation and ATPase activity J. Biol. Chem. 284 2009 24891 24903
34. I.B. Weinstein, and A.K. Joe Mechanisms of disease: Oncogene addiction - a rationale for molecular targeting in cancer therapy Nat. Clin. Pract. Oncol. 3 2006 448 457 (Pubitemid 44203817)
35. R. Zhang, and Y. Lin DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes Nucleic Acids Res. 37 Database issue 2009 D455 D458
36. Moffat, J., Grueneberg, D.A., Yang, X., Kim, S.Y., Kloepfer, A.M., Hinkle, G., Piqani, B., Eisenhaure, T.M., Luo, B., Grenier, J.K., et al. (2006). A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124, 1283-1298.
37. Ortiz-Estevez, M., De Las Rivas, J., Fontanillo, C., and Rubio, A. (2011). Segmentation of genomic and transcriptomic microarrays data reveals major correlation between DNA copy number aberrations and gene-loci expression. Genomics 97, 86-93.