Comparison of gene expression patterns across 12 tumor types identifies a cancer supercluster characterized by TP53 mutations and cell cycle defects

Oncogene

Volumn 34, Issue 21, 2015, Pages 2732-2740

  Martinez E ^a,b   Yoshihara, K ^a,c   Kim, H ^a   Mills, G M ^a   Trevino V ^b   Verhaak, R G W ^a  

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

^b SCHOOL OF ENGINEERING AND SCIENCES   (Mexico)

^c NIIGATA UNIVERSITY GRADUATE SCHOOL OF MEDICAL AND DENTAL SCIENCES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN B1; CYCLIN DEPENDENT KINASE INHIBITOR 2A; PROTEIN P53;

ACUTE MYELOBLASTIC LEUKEMIA; APOPTOSIS; ARTICLE; BLADDER CANCER; BLADDER CARCINOMA; BREAST CANCER; CANCER GENETICS; CELL CYCLE; CELL PROLIFERATION; COLON ADENOCARCINOMA; CONTROLLED STUDY; COPY NUMBER VARIATION; CYSTADENOCARCINOMA; DNA DAMAGE; DOUBLE STRANDED DNA BREAK; ENDOMETRIUM CARCINOMA; ESOPHAGUS CANCER; FEMALE; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE LOSS; GENE MUTATION; GENOMIC INSTABILITY; GLIOBLASTOMA; HEAD AND NECK SQUAMOUS CELL CARCINOMA; HUMAN; HUMAN CELL; HUMAN TISSUE; KIDNEY CANCER; KIDNEY CARCINOMA; LUNG ADENOCARCINOMA; MAJOR CLINICAL STUDY; MUTATION RATE; PHENOTYPE; PRIORITY JOURNAL; PROTEIN EXPRESSION; RECTUM CARCINOMA; SQUAMOUS CELL LUNG CARCINOMA; TUMOR SUPPRESSOR GENE; UPREGULATION; UTERINE CERVIX CANCER; GENE EXPRESSION PROFILING; GENETICS; HETEROZYGOSITY LOSS; MUTATION; NEOPLASM; PROCEDURES;

CELL CYCLE; CYCLIN B1; CYCLIN-DEPENDENT KINASE INHIBITOR P16; DNA DAMAGE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, P53; HUMANS; LOSS OF HETEROZYGOSITY; MUTATION; NEOPLASMS; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84930275553     PISSN: 09509232     EISSN: 14765594     Source Type: Journal    
DOI: 10.1038/onc.2014.216     Document Type: Article

References (43)

1. TCGA. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008; 455: 1061-1068.
2. Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR et al. The somatic genomic landscape of glioblastoma. Cell 2013; 155: 462-477.
3. TCGA. Integrated genomic analyses of ovarian carcinoma. Nature 2011; 474: 609-615.
4. TCGA. Comprehensive genomic characterization of squamous cell lung cancers. Nature 2012; 489: 519-525.
5. TCGA. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012; 487: 330-337.
6. TCGA. Comprehensive molecular portraits of human breast tumours. Nature 2012; 490: 61-70.
7. TCGA. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 2013; 499: 43-49.
8. TCGA. Genomic and epigenomic landscapes of adult De novo acute myeloid leukemia. N Engl J Med 2013; 368: 2059-2074.
9. TCGA. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 2014; 507: 315-322.
10. Perou CM, Sørlie T, Eisen MB, Van De Rijn M, Jeffrey SS, Rees CA et al. Molecular portraits of human breast tumours. Nature 2000; 406: 747-752.
11. Verhaak RG, Wouters BJ, Erpelinck CA, Abbas S, Beverloo HB, Lugthart S et al. Prediction of molecular subtypes in acute myeloid leukemia based on gene expression profiling. Haematologica 2009; 94: 131-134.
12. Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 2010; 17: 98-110.
13. Van De Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW et al. A geneexpression signature as a predictor of survival in breast cancer. N Engl J Med 2002; 347: 1999-2009.
14. Verhaak RG, Tamayo P, Yang JY, Hubbard D, Zhang H, Creighton CJ et al. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest 2013; 123: 517-525.
15. Valk PJ, Verhaak RG, Beijen MA, Erpelinck CA, Barjesteh Van Waalwijk Van Doorn-Khosrovani S, Boer JM et al. Prognostically useful gene-expression profiles in acute myeloid leukemia. N Engl J Med 2004; 350: 1617-1628.
16. Brunet JP, Tamayo P, Golub TR, Mesirov JP. Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci USA 2004; 101: 4164-4169.
17. Barbie DA, Tamayo P, Boehm JS, Kim SY, Moody SE, Dunn IF et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature 2009; 462: 108-112.
18. Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J et al. Inference of patientspecific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 2010; 26: I237-i245.
19. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005; 102: 15545-15550.
20. Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S et al. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc Natl Acad Sci USA 2012; 109: 2724-2729.
21. Yoshihara K, Shahmoradgoli M, Martínez E, Vegesna R, Kim H, Torres-Garcia W et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun 2013; 4: 2612.
22. Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T et al. Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol 2012; 30: 413-421.
23. Martinsson-Ahlzén HS, Liberal V, Grünenfelder B, Chaves SR, Spruck CH, Reed SI. Cyclin-dependent kinase-associated proteins Cks1 and Cks2 are essential during early embryogenesis and for cell cycle progression in somatic cells. Mol Cell Biol 2008; 28: 5698-5709.
24. Li J, Bennett K, Stukalov A, Fang B, Zhang G, Yoshida T et al. Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms. Mol Syst Biol 2013; 9: 705.
25. Zheng Y, Zhang C, Croucher DR, Soliman MA, St-Denis N, Pasculescu A et al. Temporal regulation of EGF signalling networks by the scaffold protein Shc1. Nature 2013; 499: 166-171.
26. Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci USA 2001; 98: 13790-13795.
27. Wolchok JD, Kluger H, Callahan MK, Postow MA, Rizvi NA, Lesokhin AM et al. Nivolumab plus ipilimumab in advanced melanoma. N Engl J Med 2013; 369: 122-133.
28. Hamid O, Robert C, Daud A, Hodi FS, Hwu WJ, Kefford R et al. Safety and tumor responses with lambrolizumab (anti-PD-1) in melanoma. N Engl J Med 2013; 369: 134-144.
29. Topalian SL, Hodi FS, Brahmer JR, Gettinger SN, Smith DC, McDermott DF et al. Safety, activity, and immune correlates of anti-PD-1 antibody in cancer. N Engl J Med 2012; 366: 2443-2454.
30. Hodi FS, O'Day SJ, McDermott DF, Weber RW, Sosman JA, Haanen JB et al. Improved survival with ipilimumab in patients with metastatic melanoma. N Engl J Med 2010; 363: 711-723.
31. Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 2009; 27: 1160-1167.
32. Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B et al. Pan-cancer patterns of somatic copy number alteration. Nat Genet 2013; 45: 1134-1140.
33. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001; 98: 5116-5121.
34. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012; 483: 603-607.
35. Everitt BS, Landau S, Leese M, Stahl D, Shewhart WA, Wilks SS. Cluster Analysis. John Wiley & Sons Ltd: West Sussex, UK, 2011.
36. Zheng S, Fu J, Vegesna R, Mao Y, Heathcock LE, Torres-Garcia W et al. A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival. Genes Dev 2013; 27: 1462-1472.
37. Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 2002; 99: 6567-6572.
38. Noble WS. What is a support vector machine? Nat Biotechnol 2006; 24: 1565-1567.
39. Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G et al. The Reactome pathway knowledgebase. Nucleic Acids Res 2014; 42(Database issue): D472-D477.
40. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. Data, information, knowledge and principle: Back to metabolism in KEGG. Nucleic Acids Res 2014; 42(Database issue): D199-D205.
41. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T et al. PID: The Pathway Interaction Database. Nucleic Acids Res 2009; 37(Database issue): D674-D679.
42. Rosner B. Percentage Points for a Generalized ESD Many Outlier Procedure. Technometrics 1983; 25: 165-172.
43. Team RC. RA: Language and Environment for Statistical Computing, Vol. 13. R Foundation for Statistical Computing: Vienna, Austria, 2013, pp 497-512.