Systematic Identification of Combinatorial Drivers and Targets in Cancer Cell Lines

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Tabchy, Adel ^a   Eltonsy, Nevine ^a   Housman, David E ^b   Mills, Gordon B ^a  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

1 (1 CYANO 1 METHYLETHYL) 3 METHYL 8 (3 QUINOLINYL)IMIDAZO[4,5 C]QUINOLIN 2(1H,3H) ONE; 2 (6 AMINO 9 PURINYLMETHYL) 5 METHYL 3 (2 METHYLPHENYL) 3H QUINAZOLIN 4 ONE; 4 [2 (4 AMINO 1,2,5 OXADIAZOL 3 YL) 1 ETHYL 7 (3 PIPERIDINYLMETHOXY) 1H IMIDAZO[4,5 C]PYRIDIN 4 YL] 2 METHYL 3 BUTYN 2 OL; 9 (1 ANILINOETHYL) 7 METHYL 2 MORPHOLINOPYRIDO[1,2 A]PYRIMIDIN 4 ONE; ANTINEOPLASTIC AGENT; BEX 235; CL 387; ERLOTINIB; GSK 105961; GSK 1059615; GSK 1070916; GSK 2080806; GSK 2080806A; GSK 2119563A; GSK 2126458; GSK 461364; GSK 661637; GSK 923295; LAPATINIB; NERATINIB; PACLITAXEL; TEMSIROLIMUS; TGX221; TRAMETINIB; UNCLASSIFIED DRUG;

APC GENE; ARTICLE; CANCER CELL CULTURE; CANCER RESISTANCE; CDKN2A GENE; CONCENTRATION RESPONSE; CONTROLLED STUDY; DRUG EFFICACY; DRUG TARGETING; ERBB2 GENE; GENE ACTIVITY; GENE CLUSTER; GENE MUTATION; GENOTYPE; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; IGF1R GENE; MEK GENE; ONCOGENE; ONCOGENE K RAS; PI3K GENE; PTEN GENE; SINGLE NUCLEOTIDE POLYMORPHISM; TARGET CELL DESTRUCTION; VALIDITY;

CELL LINE, TUMOR; CELL LINEAGE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DRUG RESISTANCE, NEOPLASM; DRUG SCREENING ASSAYS, ANTITUMOR; GENOMICS; HUMANS; MOLECULAR TARGETED THERAPY; MUTATION; TUMOR MARKERS, BIOLOGICAL;

EID: 84875943737     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0060339     Document Type: Article

References (36)

1. Druker BJ, Talpaz M, Resta DJ, Peng B, Buchdunger E, et al. (2001) Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia. N Engl J Med 344: 1031-7.
2. Gorre ME, Mohammed M, Ellwood K, Hsu N, Paquette R, et al. (2001) Clinical resistance to STI-571 cancer therapy caused by BCR-ABL gene mutation or amplification. Science 293: 876-80.
3. Poulikakos PI, Zhang C, Bollag G, Shokat KM, Rosen N, (2010) RAF inhibitors transactivate RAF dimers and ERK signalling in cells with wild-type BRAF. Nature 464: 427-30.
4. Poulikakos PI, Persaud Y, Janakiraman M, Kong X, Ng C, et al. (2011) RAF inhibitor resistance is mediated by dimerization of aberrantly spliced BRAF(V600E). Nature 480: 387-90.
5. Chandarlapaty S, Sawai A, Scaltriti M, Rodrik-Outmezguine V, Grbovic-Huezo O, et al. (2011) AKT inhibition relieves feedback suppression of receptor tyrosine kinase expression and activity. Cancer Cell 19: 58-71.
6. Muranen T, Selfors LM, Worster DT, Iwanicki MP, Song L, et al. (2012) Inhibition of PI3K/mTOR leads to adaptive resistance in matrix-attached cancer cells. Cancer Cell 21: 227-39.
7. Blumberg HM, Burman WJ, Chaisson RE, Daley CL, Etkind SC, et al. (2003) American Thoracic Society/Centers for Disease Control and Prevention/Infectious Diseases Society of America: treatment of tuberculosis. Am J Respir Crit Care Med 167: 603-62.
8. Mitnick CD, Shin SS, Seung KJ, Rich ML, Atwood SS, et al. (2008) Comprehensive treatment of extensively drug-resistant tuberculosis. N Engl J Med 359: 563-74.
9. Thompson MA, Aberg JA, Cahn P, Montaner JS, Rizzardini G, et al. (2010) Antiretroviral treatment of adult HIV infection: 2010 recommendations of the International AIDS Society-USA panel. JAMA 304: 321-33.
10. Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, et al. (2006) A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 10: 515-27.
11. Greshock J, Bachman KE, Degenhardt YY, Jing J, Wen YH, et al. (2010) Molecular target class is predictive of in vitro response profile. Cancer Res 70: 3677-86.
12. McDermott U, Sharma SV, Dowell L, Greninger P, Montagut C, et al. (2007) Identification of genotype-correlated sensitivity to selective kinase inhibitors by using high-throughput tumor cell line profiling. Proc Natl Acad Sci U S A 104: 19936-41.
13. Kim N, He N, Kim C, Zhang F, Lu Y, et al. (2012) Systematic analysis of genotype-specific drug responses in cancer. Int J Cancer 000: 1-9.
14. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, et al. (2011) COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 39: D945-50.
15. Eisen MB, Spellman PT, Brown PO, Botstein D, (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14863-8.
16. Solit DB, Garraway LA, Pratilas CA, Sawai A, Getz G, et al. (2006) BRAF mutation predicts sensitivity to MEK inhibition. Nature 439: 358-62.
17. Shaw RJ, Cantley LC, (2006) Ras, PI(3)K and mTOR signalling controls tumour cell growth. Nature 441: 424-30.
18. Halilovic E, She QB, Ye Q, Pagliarini R, Sellers WR, et al. (2010) PIK3CA mutation uncouples tumor growth and cyclin D1 regulation from MEK/ERK and mutant KRAS signaling. Cancer Res 70: 6804-14.
19. Mellinghoff IK, Wang MY, Vivanco I, Haas-Kogan DA, Zhu S, et al. (2005) Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors. N Engl J Med 353: 2012-24.
20. Dang L, White DW, Gross S, Bennett BD, Bittinger MA, et al. (2009) Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 462: 739-44.
21. Figueroa ME, Abdel-Wahab O, Lu C, Ward PS, Patel J, et al. (2010) Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 18: 553-67.
22. Ciriello G, Cerami E, Sander C, Schultz N, (2012) Mutual exclusivity analysis identifies oncogenic network modules. Genome Res 22: 398-406.
23. Migliardi G, Sassi F, Torti D, Galimi F, Zanella ER, et al. (2012) Inhibition of MEK and PI3K/mTOR Suppresses Tumor Growth but Does Not Cause Tumor Regression in Patient-Derived Xenografts of RAS-Mutant Colorectal Carcinomas. Clin Cancer Res 18: 2515-2525.
24. Chapman PB, Hauschild A, Robert C, Haanen JB, Ascierto P, et al. (2011) Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation. N Engl J Med 364: 2507-16.
25. Cancer Genome Atlas Research Network, (2011) Integrated genomic analyses of ovarian carcinoma. Nature 474: 609-15.
26. Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, et al. (2012) Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483: 570-5.
27. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, et al. (2012) The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483: 603-7.
28. Weinstein IB, (2002) Cancer. Addiction to oncogenes-the Achilles heal of cancer. Science 297: 63-4.
29. Soda M, Choi YL, Enomoto M, Takada S, Yamashita Y, et al. (2007) Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature 448: 561-6.
30. Cheung LW, Hennessy BT, Li J, Yu S, Myers AP, et al. (2011) High Frequency of PIK3R1 and PIK3R2 Mutations in Endometrial Cancer Elucidates a Novel Mechanism for Regulation of PTEN Protein Stability. Cancer Discov 1: 170-185.
31. Pao W, Chmielecki J, (2010) Rational, biologically based treatment of EGFR-mutant non-small-cell lung cancer. Nat Rev Cancer 10: 760-774.
32. Khambata-Ford S, Garrett CR, Meropol NJ, Basik M, Harbison CT, et al. (2007) Expression of epiregulin and amphiregulin and K-ras mutation status predict disease control in metastatic colorectal cancer patients treated with cetuximab. J Clin Oncol 25: 3230-7.
33. Knudson AG Jr, (1971) Mutation and cancer: statistical study of retinoblastoma. Proc Natl Acad Sci U S A 68: 820-3.
34. Vogel CL, Cobleigh MA, Tripathy D, Gutheil JC, Harris LN, et al. (2002) Efficacy and safety of trastuzumab as a single agent in first-line treatment of HER2-overexpressing metastatic breast cancer. J Clin Oncol 20: 719-26.
35. Gerber DE, Minna JD, (2010) ALK inhibition for non-small cell lung cancer: from discovery to therapy in record time. Cancer Cell 18: 548-51.
36. Hanahan D, Weinberg RA, (2000) The hallmarks of cancer. Cell 100: 57-70.