Omics and therapy - A basis for precision medicine

Molecular Oncology

Volumn 6, Issue 2, 2012, Pages 128-139

  Garay, Joseph P ^a   Gray, Joe W ^a  

^a Oregon Health and Science University Department of Biomedical Engineering   (United States)

Author keywords

Genomics; Personalized medicine; Targeted therapy

Indexed keywords

CETUXIMAB; CRIZOTINIB; DASATINIB; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ERLOTINIB; IMATINIB; INIPARIB; LAPATINIB; MOLECULAR MARKER; NILOTINIB; OLAPARIB; PANITUMUMAB; SORAFENIB; SUNITINIB; TAMOXIFEN; TRASTUZUMAB;

ACUTE LYMPHOBLASTIC LEUKEMIA; ANTINEOPLASTIC ACTIVITY; BREAST CANCER; CANCER GENETICS; CANCER RESISTANCE; CANCER THERAPY; CHRONIC MYELOID LEUKEMIA; CONTROLLED STUDY; GASTROINTESTINAL TUMOR; GENE INTERACTION; GENETIC POLYMORPHISM; GENOME ANALYSIS; GENOMICS; GLIOMA; HUMAN; HUMAN GENOME PROJECT; KIDNEY TUMOR; LUNG NON SMALL CELL CANCER; MELANOMA; MOLECULARLY TARGETED THERAPY; NEUROBLASTOMA; NONHUMAN; ORGANIZATION AND MANAGEMENT; OVARY CANCER; OVARY CARCINOMA; PANCREAS CANCER; PRIORITY JOURNAL; REVIEW; STOMACH CARCINOMA; TUMOR MICROENVIRONMENT;

EID: 84860495296     PISSN: 15747891     EISSN: 18780261     Source Type: Journal    
DOI: 10.1016/j.molonc.2012.02.009     Document Type: Review

References (113)

1. Abukhdeir A.M., Vitolo M.I., Argani P., De Marzo A.M., Karakas B., Konishi H., Gustin J.P., Lauring J., Garay J.P., Pendleton C., Konishi Y., Blair B.G., Brenner K., Garrett-Mayer E., Carraway H., Bachman K.E., Park B.H. Tamoxifen-stimulated growth of breast cancer due to p21 loss. Proc. Natl. Acad. Sci. U S A 2008, 105:288-293.
2. Alizadeh A.A., Eisen M.B., Davis R.E., Ma C., Lossos I.S., Rosenwald A., Boldrick J.C., Sabet H., Tran T., Yu X., Powell J.I., Yang L., Marti G.E., Moore T., Hudson J., Lu L., Lewis D.B., Tibshirani R., Sherlock G., Chan W.C., Greiner T.C., Weisenburger D.D., Armitage J.O., Warnke R., Levy R., Wilson W., Grever M.R., Byrd J.C., Botstein D., Brown P.O., Staudt L.M. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000, 403:503-511.
3. Bello D., Webber M.M., Kleinman H.K., Wartinger D.D., Rhim J.S. Androgen responsive adult human prostatic epithelial cell lines immortalized by human papillomavirus 18. Carcinogenesis 1997, 18:1215-1223.
4. Berns K., Horlings H.M., Hennessy B.T., Madiredjo M., Hijmans E.M., Beelen K., Linn S.C., Gonzalez-Angulo A.M., Stemke-Hale K., Hauptmann M., Beijersbergen R.L., Mills G.B., van de Vijver M.J., Bernards R. A functional genetic approach identifies the PI3K pathway as a major determinant of trastuzumab resistance in breast cancer. Cancer Cell 2007, 12:395-402.
5. Bhatia R., Holtz M., Niu N., Gray R., Snyder D.S., Sawyers C.L., Arber D.A., Slovak M.L., Forman S.J. Persistence of malignant hematopoietic progenitors in chronic myelogenous leukemia patients in complete cytogenetic remission following imatinib mesylate treatment. Blood 2003, 101:4701-4707.
6. Bissell M.J., Hines W.C. Why don't we get more cancer? A proposed role of the microenvironment in restraining cancer progression. Nat. Med. 2011, 17:320-329.
7. Bresler S.C., Wood A.C., Haglund E.A., Courtright J., Belcastro L.T., Plegaria J.S., Cole K., Toporovskaya Y., Zhao H., Carpenter E.L., Christensen J.G., Maris J.M., Lemmon M.A., Mosse Y.P. Differential inhibitor sensitivity of anaplastic lymphoma kinase variants found in neuroblastoma. Sci. Transl Med. 2011, 3:108ra114.
8. Buchdunger E., Zimmermann J., Mett H., Meyer T., Muller M., Druker B.J., Lydon N.B. Inhibition of the Abl protein-tyrosine kinase in vitro and in vivo by a 2-phenylaminopyrimidine derivative. Cancer Res. 1996, 56:100-104.
9. Burgess M.R., Skaggs B.J., Shah N.P., Lee F.Y., Sawyers C.L. Comparative analysis of two clinically active BCR-ABL kinase inhibitors reveals the role of conformation-specific binding in resistance. Proc. Natl. Acad. Sci. U S A 2005, 102:3395-3400.
10. Carter P., Presta L., Gorman C.M., Ridgway J.B., Henner D., Wong W.L., Rowland A.M., Kotts C., Carver M.E., Shepard H.M. Humanization of an anti-p185HER2 antibody for human cancer therapy. Proc. Natl. Acad. Sci. U S A 1992, 89:4285-4289.
11. Cassier P.A., Gelderblom H., Stacchiotti S., Thomas D., Maki R.G., Kroep J.R., van der Graaf W.T., Italiano A., Seddon B., Domont J., Bompas E., Wagner A.J., Blay J.Y. Efficacy of imatinib mesylate for the treatment of locally advanced and/or metastatic tenosynovial giant cell tumor/pigmented villonodular synovitis. Cancer 2011.
12. Cerami E., Demir E., Schultz N., Taylor B.S., Sander C. Automated network analysis identifies core pathways in glioblastoma. PLoS One 2010, 5:e8918.
13. Cerami E.G., Gross B.E., Demir E., Rodchenkov I., Babur O., Anwar N., Schultz N., Bader G.D., Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011, 39:D685-D690.
14. Chin K., DeVries S., Fridlyand J., Spellman P.T., Roydasgupta R., Kuo W.L., Lapuk A., Neve R.M., Qian Z., Ryder T., Chen F., Feiler H., Tokuyasu T., Kingsley C., Dairkee S., Meng Z., Chew K., Pinkel D., Jain A., Ljung B.M., Esserman L., Albertson D.G., Waldman F.M., Gray J.W. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 2006, 10:529-541.
15. Chu I., Blackwell K., Chen S., Slingerland J. The dual ErbB1/ErbB2 inhibitor, lapatinib (GW572016), cooperates with tamoxifen to inhibit both cell proliferation- and estrogen-dependent gene expression in antiestrogen-resistant breast cancer. Cancer Res. 2005, 65:18-25.
16. Collisson E.A., Sadanandam A., Olson P., Gibb W.J., Truitt M., Gu S., Cooc J., Weinkle J., Kim G.E., Jakkula L., Feiler H.S., Ko A.H., Olshen A.B., Danenberg K.L., Tempero M.A., Spellman P.T., Hanahan D., Gray J.W. Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nat. Med. 2011, 17:500-503.
17. Condeelis J., Pollard J.W. Macrophages: obligate partners for tumor cell migration, invasion, and metastasis. Cell 2006, 124:263-266.
18. le Coutre P., Mologni L., Cleris L., Marchesi E., Buchdunger E., Giardini R., Formelli F., Gambacorti-Passerini C. In vivo eradication of human BCR/Abl-positive leukemia cells with an Abl kinase inhibitor. J. Natl. Cancer Inst. 1999, 91:163-168.
19. Demetri G.D., von Mehren M., Blanke C.D., Van den Abbeele A.D., Eisenberg B., Roberts P.J., Heinrich M.C., Tuveson D.A., Singer S., Janicek M., Fletcher J.A., Silverman S.G., Silberman S.L., Capdeville R., Kiese B., Peng B., Dimitrijevic S., Druker B.J., Corless C., Fletcher C.D., Joensuu H. Efficacy and safety of imatinib mesylate in advanced gastrointestinal stromal tumors. N. Engl. J. Med. 2002, 347:472-480.
20. Dow L.E., Premsrirut P.K., Zuber J., Fellmann C., McJunkin K., Miething C., Park Y., Dickins R.A., Hannon G.J., Lowe S.W. A pipeline for the generation of shRNA transgenic mice. Nat. Protoc. 2012, 7:374-393.
21. Druker B.J., Lydon N.B. Lessons learned from the development of an Abl tyrosine kinase inhibitor for chronic myelogenous leukemia. J. Clin. Invest. 2000, 105:3-7.
22. Druker B.J., Tamura S., Buchdunger E., Ohno S., Segal G.M., Fanning S., Zimmermann J., Lydon N.B. Effects of a selective inhibitor of the Abl tyrosine kinase on the growth of Bcr-Abl positive cells. Nat. Med. 1996, 2:561-566.
23. Druker B.J., Talpaz M., Resta D.J., Peng B., Buchdunger E., Ford J.M., Lydon N.B., Kantarjian H., Capdeville R., Ohno-Jones S., Sawyers C.L. Efficacy and safety of a specific inhibitor of the BCR-Abl tyrosine kinase in chronic myeloid leukemia. N. Engl. J. Med. 2001, 344:1031-1037.
24. Druker B.J., Guilhot F., O'Brien S.G., Gathmann I., Kantarjian H., Gattermann N., Deininger M.W., Silver R.T., Goldman J.M., Stone R.M., Cervantes F., Hochhaus A., Powell B.L., Gabrilove J.L., Rousselot P., Reiffers J., Cornelissen J.J., Hughes T., Agis H., Fischer T., Verhoef G., Shepherd J., Saglio G., Gratwohl A., Nielsen J.L., Radich J.P., Simonsson B., Taylor K., Baccarani M., So C., Letvak L., Larson R.A. Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia. N. Engl. J. Med. 2006, 355:2408-2417.
25. Dybdal N., Leiberman G., Anderson S., McCune B., Bajamonde A., Cohen R.L., Mass R.D., Sanders C., Press M.F. Determination of HER2 gene amplification by fluorescence in situ hybridization and concordance with the clinical trials immunohistochemical assay in women with metastatic breast cancer evaluated for treatment with trastuzumab. Breast Cancer Res. Treat. 2005, 93:3-11.
26. Eichhorn P.J., Gili M., Scaltriti M., Serra V., Guzman M., Nijkamp W., Beijersbergen R.L., Valero V., Seoane J., Bernards R., Baselga J. Phosphatidylinositol 3-kinase hyperactivation results in lapatinib resistance that is reversed by the mTOR/phosphatidylinositol 3-kinase inhibitor NVP-BEZ235. Cancer Res. 2008, 68:9221-9230.
27. Farmer H., McCabe N., Lord C.J., Tutt A.N., Johnson D.A., Richardson T.B., Santarosa M., Dillon K.J., Hickson I., Knights C., Martin N.M., Jackson S.P., Smith G.C., Ashworth A. Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature 2005, 434:917-921.
28. Fong P.C., Boss D.S., Yap T.A., Tutt A., Wu P., Mergui-Roelvink M., Mortimer P., Swaisland H., Lau A., O'Connor M.J., Ashworth A., Carmichael J., Kaye S.B., Schellens J.H., de Bono J.S. Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. N. Engl. J. Med. 2009, 361:123-134.
29. Furukawa T., Duguid W.P., Rosenberg L., Viallet J., Galloway D.A., Tsao M.S. Long-term culture and immortalization of epithelial cells from normal adult human pancreatic ducts transfected by the E6E7 gene of human papilloma virus 16. Am. J. Pathol. 1996, 148:1763-1770.
30. Gee J.M., Harper M.E., Hutcheson I.R., Madden T.A., Barrow D., Knowlden J.M., McClelland R.A., Jordan N., Wakeling A.E., Nicholson R.I. The antiepidermal growth factor receptor agent gefitinib (ZD1839/Iressa) improves antihormone response and prevents development of resistance in breast cancer in vitro. Endocrinology 2003, 144:5105-5117.
31. Graham J., Muhsin M., Kirkpatrick P. Cetuximab. Nat. Rev. Drug Discov. 2004, 3:549-550.
32. Groffen J., Stephenson J.R., Heisterkamp N., de Klein A., Bartram C.R., Grosveld G. Philadelphia chromosomal breakpoints are clustered within a limited region, BCR, on chromosome 22. Cell 1984, 36:93-99.
33. Guo J., Si L., Kong Y., Flaherty K.T., Xu X., Zhu Y., Corless C.L., Li L., Li H., Sheng X., Cui C., Chi Z., Li S., Han M., Mao L., Lin X., Du N., Zhang X., Li J., Wang B., Qin S. Phase II, open-label, single-arm trial of imatinib mesylate in patients with metastatic melanoma harboring c-Kit mutation or amplification. J. Clin. Oncol. 2011, 29:2904-2909.
34. Gustin J.P., Karakas B., Weiss M.B., Abukhdeir A.M., Lauring J., Garay J.P., Cosgrove D., Tamaki A., Konishi H., Konishi Y., Mohseni M., Wang G., Rosen D.M., Denmeade S.R., Higgins M.J., Vitolo M.I., Bachman K.E., Park B.H. Knockin of mutant PIK3CA activates multiple oncogenic pathways. Proc. Natl. Acad. Sci. U S A 2009, 106:2835-2840.
35. Hanahan D., Weinberg R.A. The hallmarks of cancer. Cell 2000, 100:57-70.
36. Harley C.B., Futcher A.B., Greider C.W. Telomeres shorten during ageing of human fibroblasts. Nature 1990, 345:458-460.
37. Heiser L.M., Sadanandam A., Kuo W.L., Benz S.C., Goldstein T.C., Ng S., Gibb W.J., Wang N.J., Ziyad S., Tong F., Bayani N., Hu Z., Billig J.I., Dueregger A., Lewis S., Jakkula L., Korkola J.E., Durinck S., Pepin F., Guan Y., Purdom E., Neuvial P., Bengtsson H., Wood K.W., Smith P.G., Vassilev L.T., Hennessy B.T., Greshock J., Bachman K.E., Hardwicke M.A., Park J.W., Marton L.J., Wolf D.M., Collisson E.A., Neve R.M., Mills G.B., Speed T.P., Feiler H.S., Wooster R.F., Haussler D., Stuart J.M., Gray J.W., Spellman P.T. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc. Natl. Acad. Sci. U S A 2011.
38. Heyer J., Kwong L.N., Lowe S.W., Chin L. Non-germline genetically engineered mouse models for translational cancer research. Nat. Rev. Cancer 2010, 10:470-480.
39. Hodgson J.G., Malek T., Bornstein S., Hariono S., Ginzinger D.G., Muller W.J., Gray J.W. Copy number aberrations in mouse breast tumors reveal loci and genes important in tumorigenic receptor tyrosine kinase signaling. Cancer Res. 2005, 65:9695-9704.
40. Hollstein M., Sidransky D., Vogelstein B., Harris C.C. p53 mutations in human cancers. Science 1991, 253:49-53.
41. Hudis C.A. Trastuzumab - Mechanism of action and use in clinical practice. N. Engl. J. Med. 2007, 357:39-51.
42. Hudziak R.M., Schlessinger J., Ullrich A. Increased expression of the putative growth factor receptor p185HER2 causes transformation and tumorigenesis of NIH 3T3 cells. Proc. Natl. Acad. Sci. U S A 1987, 84:7159-7163.
43. Hudziak R.M., Lewis G.D., Winget M., Fendly B.M., Shepard H.M., Ullrich A. p185HER2 monoclonal antibody has antiproliferative effects in vitro and sensitizes human breast tumor cells to tumor necrosis factor. Mol. Cell Biol. 1989, 9:1165-1172.
44. Iyer R., Bharthuar A. A review of erlotinib - An oral, selective epidermal growth factor receptor tyrosine kinase inhibitor. Expert Opin. Pharmacother. 2010, 11:311-320.
45. Jacks T., Remington L., Williams B.O., Schmitt E.M., Halachmi S., Bronson R.T., Weinberg R.A. Tumor spectrum analysis in p53-mutant mice. Curr. Biol. 1994, 4:1-7.
46. Johnston S., Pippen J., Pivot X., Lichinitser M., Sadeghi S., Dieras V., Gomez H.L., Romieu G., Manikhas A., Kennedy M.J., Press M.F., Maltzman J., Florance A., O'Rourke L., Oliva C., Stein S., Pegram M. Lapatinib combined with letrozole versus letrozole and placebo as first-line therapy for postmenopausal hormone receptor-positive metastatic breast cancer. J. Clin. Oncol. 2009, 27:5538-5546.
47. Jones S., Zhang X., Parsons D.W., Lin J.C., Leary R.J., Angenendt P., Mankoo P., Carter H., Kamiyama H., Jimeno A., Hong S.M., Fu B., Lin M.T., Calhoun E.S., Kamiyama M., Walter K., Nikolskaya T., Nikolsky Y., Hartigan J., Smith D.R., Hidalgo M., Leach S.D., Klein A.P., Jaffee E.M., Goggins M., Maitra A., Iacobuzio-Donahue C., Eshleman J.R., Kern S.E., Hruban R.H., Karchin R., Papadopoulos N., Parmigiani G., Vogelstein B., Velculescu V.E., Kinzler K.W. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 2008, 321:1801-1806.
48. Junttila T.T., Akita R.W., Parsons K., Fields C., Lewis Phillips G.D., Friedman L.S., Sampath D., Sliwkowski M.X. Ligand-independent HER2/HER3/PI3K complex is disrupted by trastuzumab and is effectively inhibited by the PI3K inhibitor GDC-0941. Cancer Cell 2009, 15:429-440.
49. Kalinsky K., Jacks L.M., Heguy A., Patil S., Drobnjak M., Bhanot U.K., Hedvat C.V., Traina T.A., Solit D., Gerald W., Moynahan M.E. PIK3CA mutation associates with improved outcome in breast cancer. Clin. Cancer Res. 2009, 15:5049-5059.
50. Kantarjian H., Giles F., Wunderle L., Bhalla K., O'Brien S., Wassmann B., Tanaka C., Manley P., Rae P., Mietlowski W., Bochinski K., Hochhaus A., Griffin J.D., Hoelzer D., Albitar M., Dugan M., Cortes J., Alland L., Ottmann O.G. Nilotinib in imatinib-resistant CML and Philadelphia chromosome-positive ALL. N. Engl. J. Med. 2006, 354:2542-2551.
51. Kato S., Endoh H., Masuhiro Y., Kitamoto T., Uchiyama S., Sasaki H., Masushige S., Gotoh Y., Nishida E., Kawashima H., Metzger D., Chambon P. Activation of the estrogen receptor through phosphorylation by mitogen-activated protein kinase. Science 1995, 270:1491-1494.
52. Kessler J.D., Kahle K.T., Sun T., Meerbrey K.L., Schlabach M.R., Schmitt E.M., Skinner S.O., Xu Q., Li M.Z., Hartman Z.C., Rao M., Yu P., Dominguez-Vidana R., Liang A.C., Solimini N.L., Bernardi R.J., Yu B., Hsu T., Golding I., Luo J., Osborne C.K., Creighton C.J., Hilsenbeck S.G., Schiff R., Shaw C.A., Elledge S.J., Westbrook T.F. A SUMOylation-dependent transcriptional subprogram is required for Myc-driven tumorigenesis. Science 2012, 335:348-353.
53. Kindler T., Breitenbuecher F., Marx A., Beck J., Hess G., Weinkauf B., Duyster J., Peschel C., Kirkpatrick C.J., Theobald M., Gschaidmeier H., Huber C., Fischer T. Efficacy and safety of imatinib in adult patients with c-kit-positive acute myeloid leukemia. Blood 2004, 103:3644-3654.
54. King C.R., Kraus M.H., Aaronson S.A. Amplification of a novel v-erbB-related gene in a human mammary carcinoma. Science 1985, 229:974-976.
55. de Klein A., van Kessel A.G., Grosveld G., Bartram C.R., Hagemeijer A., Bootsma D., Spurr N.K., Heisterkamp N., Groffen J., Stephenson J.R. A cellular oncogene is translocated to the Philadelphia chromosome in chronic myelocytic leukaemia. Nature 1982, 300:765-767.
56. Knowlden J.M., Hutcheson I.R., Jones H.E., Madden T., Gee J.M., Harper M.E., Barrow D., Wakeling A.E., Nicholson R.I. Elevated levels of epidermal growth factor receptor/c-erbB2 heterodimers mediate an autocrine growth regulatory pathway in tamoxifen-resistant MCF-7 cells. Endocrinology 2003, 144:1032-1044.
57. Konishi H., Karakas B., Abukhdeir A.M., Lauring J., Gustin J.P., Garay J.P., Konishi Y., Gallmeier E., Bachman K.E., Park B.H. Knock-in of mutant K-ras in nontumorigenic human epithelial cells as a new model for studying K-ras mediated transformation. Cancer Res. 2007, 67:8460-8467.
58. Konishi H., Mohseni M., Tamaki A., Garay J.P., Croessmann S., Karnan S., Ota A., Wong H.Y., Konishi Y., Karakas B., Tahir K., Abukhdeir A.M., Gustin J.P., Cidado J., Wang G.M., Cosgrove D., Cochran R., Jelovac D., Higgins M.J., Arena S., Hawkins L., Lauring J., Gross A.L., Heaphy C.M., Hosokawa Y., Gabrielson E., Meeker A.K., Visvanathan K., Argani P., Bachman K.E., Park B.H. Mutation of a single allele of the cancer susceptibility gene BRCA1 leads to genomic instability in human breast epithelial cells. Proc. Natl. Acad. Sci. U S A 2011, 108:17773-17778.
59. Kopper L. Lapatinib: a sword with two edges. Pathol. Oncol. Res. 2008, 14:1-8.
60. Kumar A., White T.A., MacKenzie A.P., Clegg N., Lee C., Dumpit R.F., Coleman I., Ng S.B., Salipante S.J., Rieder M.J., Nickerson D.A., Corey E., Lange P.H., Morrissey C., Vessella R.L., Nelson P.S., Shendure J. Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers. Proc. Natl. Acad. Sci. U S A 2011, 108:17087-17092.
61. Kute T., Lack C.M., Willingham M., Bishwokama B., Williams H., Barrett K., Mitchell T., Vaughn J.P. Development of Herceptin resistance in breast cancer cells. Cytometry A 2004, 57:86-93.
62. Lin E.Y., Li J.F., Gnatovskiy L., Deng Y., Zhu L., Grzesik D.A., Qian H., Xue X.N., Pollard J.W. Macrophages regulate the angiogenic switch in a mouse model of breast cancer. Cancer Res. 2006, 66:11238-11246.
63. Liu C.G., Calin G.A., Meloon B., Gamliel N., Sevignani C., Ferracin M., Dumitru C.D., Shimizu M., Zupo S., Dono M., Alder H., Bullrich F., Negrini M., Croce C.M. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc. Natl. Acad. Sci. U S A 2004, 101:9740-9744.
64. Loi S., Haibe-Kains B., Majjaj S., Lallemand F., Durbecq V., Larsimont D., Gonzalez-Angulo A.M., Pusztai L., Symmans W.F., Bardelli A., Ellis P., Tutt A.N., Gillett C.E., Hennessy B.T., Mills G.B., Phillips W.A., Piccart M.J., Speed T.P., McArthur G.A., Sotiriou C. PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer. Proc. Natl. Acad. Sci. U S A 2010, 107:10208-10213.
65. Luo Y., Zhou H., Krueger J., Kaplan C., Lee S.H., Dolman C., Markowitz D., Wu W., Liu C., Reisfeld R.A., Xiang R. Targeting tumor-associated macrophages as a novel strategy against breast cancer. J. Clin. Invest. 2006, 116:2132-2141.
66. Luo J., Emanuele M.J., Li D., Creighton C.J., Schlabach M.R., Westbrook T.F., Wong K.K., Elledge S.J. A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Cell 2009, 137:835-848.
67. Lynch T.J., Bell D.W., Sordella R., Gurubhagavatula S., Okimoto R.A., Brannigan B.W., Harris P.L., Haserlat S.M., Supko J.G., Haluska F.G., Louis D.N., Christiani D.C., Settleman J., Haber D.A. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N. Engl. J. Med. 2004, 350:2129-2139.
68. Ma W.W., Adjei A.A. Novel agents on the horizon for cancer therapy. CA Cancer J. Clin. 2009, 59:111-137.
69. Margolin A.A., Nemenman I., Basso K., Wiggins C., Stolovitzky G., Dalla Favera R., Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinform. 2006, 7(Suppl. 1):S7.
70. Maser R.S., Choudhury B., Campbell P.J., Feng B., Wong K.K., Protopopov A., O'Neil J., Gutierrez A., Ivanova E., Perna I., Lin E., Mani V., Jiang S., McNamara K., Zaghlul S., Edkins S., Stevens C., Brennan C., Martin E.S., Wiedemeyer R., Kabbarah O., Nogueira C., Histen G., Aster J., Mansour M., Duke V., Foroni L., Fielding A.K., Goldstone A.H., Rowe J.M., Wang Y.A., Look A.T., Stratton M.R., Chin L., Futreal P.A., DePinho R.A. Chromosomally unstable mouse tumours have genomic alterations similar to diverse human cancers. Nature 2007, 447:966-971.
71. Metzker M.L. Sequencing technologies - The next generation. Nat. Rev. Genet. 2010, 11:31-46.
72. van Miltenburg M.H., Jonkers J. Using genetically engineered mouse models to validate candidate cancer genes and test new therapeutic approaches. Curr. Opin. Genet. Dev. 2012.
73. Motzer R.J., Hoosen S., Bello C.L., Christensen J.G. Sunitinib malate for the treatment of solid tumours: a review of current clinical data. Expert Opin. Investig. Drugs 2006, 15:553-561.
74. Neve R.M., Chin K., Fridlyand J., Yeh J., Baehner F.L., Fevr T., Clark L., Bayani N., Coppe J.P., Tong F., Speed T., Spellman P.T., DeVries S., Lapuk A., Wang N.J., Kuo W.L., Stilwell J.L., Pinkel D., Albertson D.G., Waldman F.M., McCormick F., Dickson R.B., Johnson M.D., Lippman M., Ethier S., Gazdar A., Gray J.W. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 2006, 10:515-527.
75. Nowell P.C., Hungerford D.A. A minute chromosome in human chronic granulocytic leukemia. Science 1960, 132:1497.
76. Olive K.P., Tuveson D.A., Ruhe Z.C., Yin B., Willis N.A., Bronson R.T., Crowley D., Jacks T. Mutant p53 gain of function in two mouse models of Li-Fraumeni syndrome. Cell 2004, 119:847-860.
77. Olive K.P., Jacobetz M.A., Davidson C.J., Gopinathan A., McIntyre D., Honess D., Madhu B., Goldgraben M.A., Caldwell M.E., Allard D., Frese K.K., Denicola G., Feig C., Combs C., Winter S.P., Ireland-Zecchini H., Reichelt S., Howat W.J., Chang A., Dhara M., Wang L., Ruckert F., Grutzmann R., Pilarsky C., Izeradjene K., Hingorani S.R., Huang P., Davies S.E., Plunkett W., Egorin M., Hruban R.H., Whitebread N., McGovern K., Adams J., Iacobuzio-Donahue C., Griffiths J., Tuveson D.A. Inhibition of Hedgehog signaling enhances delivery of chemotherapy in a mouse model of pancreatic cancer. Science 2009, 324:1457-1461.
78. O'Shaughnessy J., Osborne C., Pippen J.E., Yoffe M., Patt D., Rocha C., Koo I.C., Sherman B.M., Bradley C. Iniparib plus chemotherapy in metastatic triple-negative breast cancer. N. Engl. J. Med. 2011, 364:205-214.
79. Penzel R., Sers C., Chen Y., Lehmann-Muhlenhoff U., Merkelbach-Bruse S., Jung A., Kirchner T., Buttner R., Kreipe H.H., Petersen I., Dietel M., Schirmacher P. EGFR mutation detection in NSCLC-assessment of diagnostic application and recommendations of the German Panel for Mutation Testing in NSCLC. Virchows Arch. 2011, 458:95-98.
80. Pinkel D., Segraves R., Sudar D., Clark S., Poole I., Kowbel D., Collins C., Kuo W.L., Chen C., Zhai Y., Dairkee S.H., Ljung B.M., Gray J.W., Albertson D.G. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 1998, 20:207-211.
81. Pohlmann P.R., Mayer I.A., Mernaugh R. Resistance to trastuzumab in breast cancer. Clin. Cancer Res. 2009, 15:7479-7491.
82. Prahallad A., Sun C., Huang S., Di Nicolantonio F., Salazar R., Zecchin D., Beijersbergen R.L., Bardelli A., Bernards R. Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR. Nature 2012.
83. Prat A., Perou C.M. Deconstructing the molecular portraits of breast cancer. Mol. Oncol. 2011, 5:5-23.
84. Presta L.G., Chen H., O'Connor S.J., Chisholm V., Meng Y.G., Krummen L., Winkler M., Ferrara N. Humanization of an anti-vascular endothelial growth factor monoclonal antibody for the therapy of solid tumors and other disorders. Cancer Res. 1997, 57:4593-4599.
85. Qian B.Z., Pollard J.W. Macrophage diversity enhances tumor progression and metastasis. Cell 2010, 141:39-51.
86. Ronnov-Jessen L., Petersen O.W., Bissell M.J. Cellular changes involved in conversion of normal to malignant breast: importance of the stromal reaction. Physiol. Rev. 1996, 76:69-125.
87. Root D.E., Hacohen N., Hahn W.C., Lander E.S., Sabatini D.M. Genome-scale loss-of-function screening with a lentiviral RNAi library. Nat. Methods 2006, 3:715-719.
88. Saltz L., Easley C., Kirkpatrick P. Panitumumab. Nat. Rev. Drug Discov. 2006, 5:987-988.
89. Schena M., Shalon D., Davis R.W., Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470.
90. Shaw A.T., Yasothan U., Kirkpatrick P. Crizotinib. Nat. Rev. Drug Discov. 2011, 10:897-898.
91. Sieweke M.H., Thompson N.L., Sporn M.B., Bissell M.J. Mediation of wound-related Rous sarcoma virus tumorigenesis by TGF-beta. Science 1990, 248:1656-1660.
92. Slamon D.J., Leyland-Jones B., Shak S., Fuchs H., Paton V., Bajamonde A., Fleming T., Eiermann W., Wolter J., Pegram M., Baselga J., Norton L. Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. N. Engl. J. Med. 2001, 344:783-792.
93. Sorlie T., Perou C.M., Tibshirani R., Aas T., Geisler S., Johnsen H., Hastie T., Eisen M.B., van de Rijn M., Jeffrey S.S., Thorsen T., Quist H., Matese J.C., Brown P.O., Botstein D., Eystein Lonning P., Borresen-Dale A.L. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl. Acad. Sci. U S A 2001, 98:10869-10874.
94. Soule H.D., Maloney T.M., Wolman S.R., Peterson W.D., Brenz R., McGrath C.M., Russo J., Pauley R.J., Jones R.F., Brooks S.C. Isolation and characterization of a spontaneously immortalized human breast epithelial cell line, MCF-10. Cancer Res. 1990, 50:6075-6086.
95. Spurdle A.B., Healey S., Devereau A., Hogervorst F.B., Monteiro A.N., Nathanson K.L., Radice P., Stoppa-Lyonnet D., Tavtigian S., Wappenschmidt B., Couch F.J., Goldgar D.E. ENIGMA-evidence-based network for the interpretation of germline mutant alleles: an international initiative to evaluate risk and clinical significance associated with sequence variation in BRCA1 and BRCA2 genes. Hum. Mutat. 2012, 33:2-7.
96. Stein B., Smith B.D. Treatment options for patients with chronic myeloid leukemia who are resistant to or unable to tolerate imatinib. Clin. Ther. 2010, 32:804-820.
97. Steinberg M. Dasatinib: a tyrosine kinase inhibitor for the treatment of chronic myelogenous leukemia and Philadelphia chromosome-positive acute lymphoblastic leukemia. Clin. Ther. 2007, 29:2289-2308.
98. Taylor B.S., Schultz N., Hieronymus H., Gopalan A., Xiao Y., Carver B.S., Arora V.K., Kaushik P., Cerami E., Reva B., Antipin Y., Mitsiades N., Landers T., Dolgalev I., Major J.E., Wilson M., Socci N.D., Lash A.E., Heguy A., Eastham J.A., Scher H.I., Reuter V.E., Scardino P.T., Sander C., Sawyers C.L., Gerald W.L. Integrative genomic profiling of human prostate cancer. Cancer Cell 2010, 18:11-22.
99. The Cancer Genome Atlas Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008, 455:1061-1068.
100. The Cancer Genome Atlas Integrated genomic analyses of ovarian carcinoma. Nature 2011, 474:609-615.
101. Tseng P.H., Wang Y.C., Weng S.C., Weng J.R., Chen C.S., Brueggemeier R.W., Shapiro C.L., Chen C.Y., Dunn S.E., Pollak M., Chen C.S. Overcoming trastuzumab resistance in HER2-overexpressing breast cancer cells by using a novel celecoxib-derived phosphoinositide-dependent kinase-1 inhibitor. Mol. Pharmacol. 2006, 70:1534-1541.
102. Vaske C.J., Benz S.C., Sanborn J.Z., Earl D., Szeto C., Zhu J., Haussler D., Stuart J.M. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 2010, 26:i237-i245.
103. van't Veer L.J., Bernards R. Enabling personalized cancer medicine through analysis of gene-expression patterns. Nature 2008, 452:564-570.
104. Vogelstein B., Kinzler K.W. Cancer genes and the pathways they control. Nat. Med. 2004, 10:789-799.
105. Wagle N., Berger M.F., Davis M.J., Blumenstiel B., DeFelice M., Pochanard P., Ducar M., Van Hummelen P., MacConaill L.E., Hahn W.C., Meyerson M., Gabriel S.B., Garraway L.A. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov. 2012, 82-93.
106. Walsh T., Lee M.K., Casadei S., Thornton A.M., Stray S.M., Pennil C., Nord A.S., Mandell J.B., Swisher E.M., King M.C. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc. Natl. Acad. Sci. U S A 2010, 107:12629-12633.
107. Weber M., Davies J.J., Wittig D., Oakeley E.J., Haase M., Lam W.L., Schubeler D. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 2005, 37:853-862.
108. Wilhelm S., Carter C., Lynch M., Lowinger T., Dumas J., Smith R.A., Schwartz B., Simantov R., Kelley S. Discovery and development of sorafenib: a multikinase inhibitor for treating cancer. Nat. Rev. Drug Discov. 2006, 5:835-844.
109. Wyckoff J., Wang W., Lin E.Y., Wang Y., Pixley F., Stanley E.R., Graf T., Pollard J.W., Segall J., Condeelis J. A paracrine loop between tumor cells and macrophages is required for tumor cell migration in mammary tumors. Cancer Res. 2004, 64:7022-7029.
110. Xia W., Bacus S., Hegde P., Husain I., Strum J., Liu L., Paulazzo G., Lyass L., Trusk P., Hill J., Harris J., Spector N.L. A model of acquired autoresistance to a potent ErbB2 tyrosine kinase inhibitor and a therapeutic strategy to prevent its onset in breast cancer. Proc. Natl. Acad. Sci. U S A 2006, 103:7795-7800.
111. Yang X., Boehm J.S., Yang X., Salehi-Ashtiani K., Hao T., Shen Y., Lubonja R., Thomas S.R., Alkan O., Bhimdi T., Green T.M., Johannessen C.M., Silver S.J., Nguyen C., Murray R.R., Hieronymus H., Balcha D., Fan C., Lin C., Ghamsari L., Vidal M., Hahn W.C., Hill D.E., Root D.E. A public genome-scale lentiviral expression library of human ORFs. Nat. Methods 2011, 8:659-661.
112. Zhang J., Yang P.L., Gray N.S. Targeting cancer with small molecule kinase inhibitors. Nat. Rev. Cancer 2009, 9:28-39.
113. Zhang S., Huang W.C., Li P., Guo H., Poh S.B., Brady S.W., Xiong Y., Tseng L.M., Li S.H., Ding Z., Sahin A.A., Esteva F.J., Hortobagyi G.N., Yu D. Combating trastuzumab resistance by targeting SRC, a common node downstream of multiple resistance pathways. Nat. Med. 2011, 17:461-469.