From cancer genomes to oncogenic drivers, tumour dependencies and therapeutic targets

Nature Reviews Cancer

Volumn 12, Issue 8, 2012, Pages 572-578

  Eifert, Cheryl ^a   Powers, R Scott ^a  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADAM PROTEIN; BETA CATENIN; COMPLEMENTARY DNA; EPIDERMAL GROWTH FACTOR RECEPTOR 2; FIBROBLAST GROWTH FACTOR 19; JANUS KINASE 1; K RAS PROTEIN; MICRORNA; MONOCLONAL ANTIBODY; OLIGONUCLEOTIDE; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; PROMYELOCYTIC LEUKEMIA PROTEIN; PROTEIN TYROSINE KINASE; RETINOBLASTOMA BINDING PROTEIN 1; RETINOIC ACID RECEPTOR ALPHA; SCATTER FACTOR RECEPTOR; SHORT HAIRPIN RNA; SMAD4 PROTEIN; SMALL INTERFERING RNA; TRANSCRIPTION FACTOR PAX8; TRANSCRIPTION FACTOR YAP1; WNT PROTEIN;

CANCER CELL; CANCER CLASSIFICATION; CANCER GENETICS; CANCER THERAPY; CARCINOGENESIS; COLON CANCER; COLON POLYPOSIS; COMPARATIVE GENOMIC HYBRIDIZATION; COMPARATIVE STUDY; GASTROINTESTINAL CARCINOMA; GENE DOSAGE; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; GENETIC SCREENING; GLIOBLASTOMA; HUMAN; IN VITRO STUDY; IN VIVO STUDY; LIVER CELL CARCINOMA; MISSENSE MUTATION; MUTAGENESIS; NONHUMAN; ONCOGENE; OVARY CANCER; PANCREAS CANCER; PRIORITY JOURNAL; PROMYELOCYTIC LEUKEMIA; PROTEIN EXPRESSION; REVIEW; RNA INTERFERENCE; SCORING SYSTEM; SIGNAL TRANSDUCTION;

ANIMALS; CELL TRANSFORMATION, NEOPLASTIC; GENOME; HUMANS; MOLECULAR TARGETED THERAPY; MUTATION; NEOPLASMS;

EID: 84864326095     PISSN: 1474175X     EISSN: 14741768     Source Type: Journal    
DOI: 10.1038/nrc3299     Document Type: Review

References (54)

1. Kimura, H. et al. ALK fusion gene positive lung cancer and 3 cases treated with an inhibitor for ALK kinase activity. Lung Cancer 75, 66-72 (2012).
2. Ashworth, A. A synthetic lethal therapeutic approach: poly(ADP) ribose polymerase inhibitors for the treatment of cancers deficient in DNA double-strand break repair. J. Clin. Oncol. 26, 3785-3790 (2008).
3. Papaemmanuil, E. et al. Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. N. Engl. J. Med. 365, 1384-1395 (2011).
4. Parsons, D. W. et al. An integrated genomic analysis of human glioblastoma multiforme. Science 321, 1807-1812 (2008).
5. The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615 (2011).
6. Hammerman, P. S. Mutations in the DDR2 kinase gene identify a novel therapeutic target in squamous cell lung cancer. Cancer Discov. 1, 78-89 (2011).
7. Figueroa, M. E. et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 18, 553-567 (2010).
8. Schvartzman, J. M., Sotillo, R. & Benezra, R. Mitotic chromosomal instability and cancer: mouse modelling of the human disease. Nature Rev. Cancer 10, 102-115 (2010).
9. Snuderl, M. et al. Mosaic amplification of multiple receptor tyrosine kinase genes in glioblastoma. Cancer Cell 20, 810-817 (2011).
10. Zender, L. et al. Identification and validation of oncogenes in liver cancer using an integrative oncogenomic approach. Cell 125, 1253-1267 (2006). (Pubitemid 43929093)
11. Maser, R. S. et al. Chromosomally unstable mouse tumours have genomic alterations similar to diverse human cancers. Nature 447, 966-971 (2007). (Pubitemid 46975753)
12. Koudijs, M. J. et al. High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors. Genome Res. 21, 2181-2189 (2011).
13. Mattison, J. et al. Novel candidate cancer genes identified by a large-scale cross-species comparative oncogenomics approach. Cancer Res. 70, 883-895 (2010).
14. Starr, T. K. et al. A transposon-based genetic screen in mice identifies genes altered in colorectal cancer. Science 323, 1747-1750 (2009).
15. Cheung, H. W. et al. Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer. Proc. Natl Acad. Sci. USA 108, 12372-12377 (2011).
16. Sawey, E. T. et al. Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by Oncogenomic screening. Cancer Cell 19, 347-358 (2011).
17. Jones, S. et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321, 1801-1806 (2008).
18. TCGA. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008).
19. Cerami, E., Demir, E., Schultz, N., Taylor, B. S. & Sander, C. Automated network analysis identifies core pathways in glioblastoma. PLoS ONE 5, e8918 (2010).
20. Ciriello, G., Cerami, E., Sander, C. & Schultz, N. Mutual exclusivity analysis identifies oncogenic network modules. Genome Res. 22, 398-406 (2012).
21. Vaske, C. J. et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 26, i237-i245 (2010).
22. Oda, K. et al. PIK3CA cooperates with other phosphatidylinositol 3?-kinase pathway mutations to effect oncogenic transformation. Cancer Res. 68, 8127-8136 (2008).
23. Bansal, M. & Califano, A. Genome-wide dissection of posttranscriptional and posttranslational interactions. Methods Mol. Biol. 786, 131-149 (2012).
24. Sumazin, P. et al. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147, 370-381 (2011).
25. Carro, M. S. et al. The transcriptional network for mesenchymal transformation of brain tumours. Nature 463, 318-325 (2010).
26. Akavia, U. D. et al. An integrated approach to uncover drivers of cancer. Cell 143, 1005-1017 (2010).
27. Carter, H. et al. Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res. 69, 6660-6667 (2009).
28. Rueda, O. M. & Diaz-Uriarte, R. Finding recurrent copy number alteration regions: a review of methods. Curr. Bioinform. 5, 1-17 (2010).
29. Beroukhim, R. et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc. Natl Acad. Sci. USA 104, 20007-20012 (2007).
30. Karlsson, E. et al. High-resolution genomic analysis of the 11q13 amplicon in breast cancers identifies synergy with 8p12 amplification, involving the mTOR targets S6K2 and 4EBP1. Genes Chromosom. Cancer 50, 775-787 (2011).
31. Wu, G., Feng, X. & Stein, L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 11, R53 (2010).
32. Sweet-Cordero, A. et al. An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nature Genet. 37, 48-55 (2005). (Pubitemid 40070939)
33. Lee, J. S. et al. Application of comparative functional genomics to identify best-fit mouse models to study human cancer. Nature Genet. 36, 1306-1311 (2004).
34. Tward, A. D. et al. Distinct pathways of genomic progression to benign and malignant tumors of the liver. Proc. Natl Acad. Sci. USA 104, 14771-14776 (2007). (Pubitemid 350003218)
35. Kim, M. et al. Comparative oncogenomics identifies NEDD9 as a melanoma metastasis gene. Cell 125, 1269-1281 (2006). (Pubitemid 43949521)
36. Wartman, L. D. et al. Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression. J. Clin. Invest. 121, 1445-1455 (2011).
37. Ma, O. et al. MMP13, Birc2 (cIAP1), and Birc3 (cIAP2), amplified on chromosome 9, collaborate with p53 deficiency in mouse osteosarcoma progression. Cancer Res. 69, 2559-2567 (2009).
38. Cheng, L. et al. Rb inactivation accelerates neoplastic growth and substitutes for recurrent amplification of cIAP1, cIAP2 and Yap1 in sporadic mammary carcinoma associated with p53 deficiency. Oncogene 29, 5700-5711 (2010).
39. Overholtzer, M. et al. Transforming properties of YAP, a candidate oncogene on the chromosome 11q22 amplicon. Proc. Natl Acad. Sci. USA 103, 12405-12410 (2006). (Pubitemid 44267272)
40. Keng, V. W. et al. A conditional transposon-based insertional mutagenesis screen for genes associated with mouse hepatocellular carcinoma. Nature Biotech. 27, 264-274 (2009).
41. Starr, T. K. et al. A Sleeping Beauty transposon-mediated screen identifies murine susceptibility genes for adenomatous polyposis coli (Apc)-dependent intestinal tumorigenesis. Proc. Natl Acad. Sci. USA 108, 5765-5770 (2011).
42. March, H. N. et al. Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis. Nature Genet. 43, 1202-1209 (2011).
43. Rangarajan, A. & Weinberg, R. A. Comparative biology of mouse versus human cells: modelling human cancer in mice. Nature Rev. Cancer 3, 952-959 (2003). (Pubitemid 37500180)
44. Koh, J. L. et al. COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines. Nucleic Acids Res. 40, D957-D963 (2012).
45. Brough, R. et al. Functional viability profiles of breast Cancer. Cancer Discov. 1, 260-273 (2011).
46. Zuber, J. et al. RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 478, 524-528 (2011).
47. Scott, K. L. et al. Proinvasion metastasis drivers in early-stage melanoma are oncogenes. Cancer Cell 20, 92-103 (2011).
48. Zender, L. et al. An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer. Cell 135, 852-864 (2008).
49. Bric, A. et al. Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model. Cancer Cell 16, 324-335 (2009).
50. Luo, J., Solimini, N. L. & Elledge, S. J. Principles of cancer therapy: oncogene and non-oncogene addiction. Cell 136, 823-837 (2009).
51. Fellmann, C. et al. Functional identification of optimized RNAi triggers using a massively parallel sensor assay. Mol. Cell 41, 733-746 (2011).
52. Schreiber, S. L. et al. Towards patient-based cancer therapeutics. Nature Biotech. 28, 904-906 (2010).
53. Barretina, J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603-607 (2012).
54. Garnett, M. J. et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483, 570-575 (2012).