Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas

Clinical Cancer Research

Volumn 21, Issue 3, 2015, Pages 632-641

  Seiwert, Tanguy Y ^a,b   Zuo, Zhixiang ^a   Keck, Michaela K ^a   Khattri, Arun ^a   Pedamallu, Chandra S ^c,d   Stricker, Thomas ^e   Brown, Christopher ^f   Pugh, Trevor J ^c,d   Stojanov, Petar ^c   Cho, Juok ^c   Lawrence, Michael S ^c   Getz, Gad ^c   Brägelmann, Johannes ^a   DeBoer, Rebecca ^a   Weichselbaum, Ralph R ^a   Langerman, Alexander ^a   Portugal, Louis ^a   Blair, Elizabeth ^a   Stenson, Kerstin ^a   Lingen, Mark W ^a   Cohen, Ezra E W ^a   Vokes, Everett E ^a   White, Kevin P ^a,b   Hammerman, Peter S ^c,d   more..

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^d DANA FARBER CANCER INSTITUTE   (United States)

^e VANDERBILT UNIVERSITY   (United States)

^f UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 2A; EPHRIN RECEPTOR A2; EPIDERMAL GROWTH FACTOR RECEPTOR; FIBROBLAST GROWTH FACTOR RECEPTOR 1; FIBROBLAST GROWTH FACTOR RECEPTOR 2; FIBROBLAST GROWTH FACTOR RECEPTOR 3; K RAS PROTEIN; NOTCH RECEPTOR; NOTCH1 RECEPTOR; PROTEIN P53;

ADULT; ADVANCED CANCER; ARTICLE; CANCER LOCALIZATION; CCND1 GENE; CDKN2A GENE; COMPARATIVE STUDY; CONTROLLED STUDY; CUL3 GENE; DDR2 GENE; DDX3X GENE; EGFR GENE; EPHA2 GENE; EXON; FEMALE; FGFR1 GENE; FGFR2 GENE; FGFR3 GENE; GENE AMPLIFICATION; GENE DOSAGE; GENE MUTATION; GENE TARGETING; GENETIC DIFFERENCE; GENOME ANALYSIS; HEAD AND NECK SQUAMOUS CELL CARCINOMA; HUMAN; MAJOR CLINICAL STUDY; MALE; MLL2 GENE; MLL3 GENE; NOTCH GENE; NOTCH1 GENE; NSD1 GENE; ONCOGENE K RAS; PAPILLOMAVIRUS INFECTION; PIK3CA GENE; SOMATIC MUTATION; TUMOR GENE; TUMOR SUPPRESSOR GENE; AGED; CANCER STAGING; CARCINOMA, SQUAMOUS CELL; COHORT ANALYSIS; COMPLICATION; COPY NUMBER VARIATION; GENE EXPRESSION PROFILING; GENOMICS; HEAD AND NECK NEOPLASMS; HUMAN PAPILLOMAVIRUS TYPE 16; HUMAN PAPILLOMAVIRUS TYPE 18; METABOLISM; MIDDLE AGED; MORTALITY; MUTATION; PAPILLOMAVIRIDAE; PATHOLOGY; PROGNOSIS; PROTEIN PROTEIN INTERACTION; RISK FACTOR; SIGNAL TRANSDUCTION; VIRUS INFECTION;

ADULT; AGED; CARCINOMA, SQUAMOUS CELL; COHORT STUDIES; DNA COPY NUMBER VARIATIONS; FEMALE; GENE EXPRESSION PROFILING; GENOMICS; HEAD AND NECK NEOPLASMS; HUMAN PAPILLOMAVIRUS 16; HUMAN PAPILLOMAVIRUS 18; HUMANS; MALE; MIDDLE AGED; MUTATION; NEOPLASM STAGING; PAPILLOMAVIRIDAE; PAPILLOMAVIRUS INFECTIONS; PROGNOSIS; PROTEIN INTERACTION MAPS; RISK FACTORS; SIGNAL TRANSDUCTION; TUMOR VIRUS INFECTIONS;

EID: 84961289657     PISSN: 10780432     EISSN: 15573265     Source Type: Journal    
DOI: 10.1158/1078-0432.CCR-13-3310     Document Type: Article

References (50)

1. Siegel R, Ward E, Brawley O, Jemal A. Cancer statistics, 2011: the impact of eliminating socioeconomic and racial disparities on premature cancer deaths. CA Cancer J Clin 2011;61:212-36.
2. Vokes EE, Weichselbaum RR, Lippman SM, Hong WK. Head and neck cancer. N Engl J Med 1993;328:184-94.
3. Ang KK, Harris J, Wheeler R, Weber R, Rosenthal DI, Nguyen-Tân PF, et al. Human papillomavirus and survival of patients with oropharyngeal cancer. N Engl J Med 2010;363:24-35.
4. Chaturvedi AK, Engels EA, Pfeiffer RM, Hernandez BY, Xiao W, Kim E, et al. Human papillomavirus and rising oropharyngeal cancer incidence in the United States. J Clin Oncol 2011;29:4294-301.
5. Hayes DN, Grandis JR, El-Naggar AK. The CancerGenome Atlas: integrated analysis of genome alterations in squamous cell carcinoma of the head and neck. J Clin Oncol 2013;31 (suppl; abstr 6009).
6. Chung CH, Parker JS, Karaca G, Wu J, Funkhouser WK, Moore D, et al. Molecular classification of head and neck squamous cell carcinomas using patterns of gene expression. Cancer Cell 2004;5:489-500.
7. Leemans CR, Braakhuis BJM, Brakenhoff RH. The molecular biology of head and neck cancer. Nat Rev Cancer 2010;11:9-22.
8. Slebos RJ, Yi Y, Ely K, Carter J, Evjen A, Zhang X, et al. Gene expression differences associated with human papillomavirus status in head and neck squamous cell carcinoma. Clin Cancer Res 2006;12:701-9.
9. Posner MR, Hershock DM, Blajman CR, Mickiewicz E, Winquist E, Gorbounova V, et al. Cisplatin and fluorouracil alone or with docetaxel in head and neck cancer. N Engl J Med 2007;357:1705-15.
10. Vermorken JB, Stöhlmacher-Williams J, Davidenko I, Licitra L, Winquist E, Villanueva C, et al. Cisplatin and fluorouracil with or without panitumumab in patients with recurrent or metastatic squamous-cell carcinoma of the head and neck (SPECTRUM): an open-label phase 3 randomised trial. Lancet Oncol 2013;14:697-710.
11. Vokes EE, Seiwert TY. EGFR-directed treatments in SCCHN. Lancet Oncol 2013;14:672-3.
12. Stransky N, Egloff AM, Tward AD, Kostic AD, Cibulskis K, Sivachenko A, et al. The mutational landscape of head and neck squamous cell carcinoma. Science 2011;333:1157-60.
13. Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, Li RJ, et al. Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science 2011;333:1154-7.
14. Pickering CR, Zhang J, Yoo SY, Bengtsson L, Moorthy S, Neskey DM, et al. Integrative genomic characterization of oral squamous cell carcinoma identifi es frequent somatic drivers. Cancer Discov 2013;3:770-81.
15. Lui VW, Hedberg ML, Li H, Vangara BS, Pendleton K, Zeng Y, et al. Frequent mutation of the PI3K pathway in head and neck cancer de fines predictive biomarkers. Cancer Discov 2013;3:761-9.
16. Killela PJ, Reitman ZJ, Jiao Y, Bettegowda C, Agrawal N, Diaz LA Jr, et al. TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal. Proc Natl Acad Sci U S A 2013;110:6021-6.
17. Sotlar K, Diemer D, Dethleffs A, Hack Y, Stubner A, Vollmer N, et al. Detection and typing of human papillomavirus by e6 nested multiplex PCR. J Clin Microbiol 2004;42:3176-84.
18. Zuo Z, Keck MK, Khattri A, Patel RD, Walter KZ, Lingen MW, et al. Multimodality determination of HPV status in head and neck cancers (HNC) and development of an HPV signature. J Clin Oncol 31 (suppl; abstr 6008).
19. Meyer M, Kircher M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc 2010;2010:pdb.prot5448.
20. Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature 2012;489:519-25.
21. Cibulskis K, McKenna A, Fennell T, Banks E, DePristo M, Getz G. ContEst: estimating cross-contamination of human samples in next-generation sequencing data. Bioinformatics 2011;27:2601-2.
22. Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotech 2013;31:213-9.
23. Jia P, Zhao Z. VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data. PLoS Comput Biol 2014;10:e1003460.
24. Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, et al. Cancer-specifi c high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res 2009;69:6660-7.
25. Li J, Lupat R, Amarasinghe KC, Thompson ER, Doyle MA, Ryland GL, et al. CONTRA: copy number analysis for targeted resequencing. Bioinformatics 2012;28:1307-13.
26. Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, et al. Mutational heterogeneity in cancer and the search for new cancerassociated genes. Nature 2013;499:214-8.
27. Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC, et al. Initial genome sequencing and analysis of multiple myeloma. Nature 2011;471:467-72.
28. Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol 2011;12:R41.
29. - tumors. Genome Med 2013;5:49.
30. Cappellen D, De Oliveira C, Ricol D, de Medina S, Bourdin J, Sastre-Garau X, et al. Frequent activating mutations of FGFR3 in human bladder and cervix carcinomas. Nat Genet 1999;23:18-20.
31. Liao RG, Jung J, Tchaicha J, Wilkerson MD, Sivachenko A, Beauchamp EM, et al. Inhibitor-sensitive FGFR2 and FGFR3 mutations in lung squamous cell carcinoma. Cancer Res 2013;73:5195-205.
32. Wagle N, Berger MF, Davis MJ, Blumenstiel B, Defelice M, Pochanard P, et al. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov 2012;2:82-93.
33. Andre F, Ranson M, Dean E, Varga A, Noll R, Stockman PK, et al. Results of a phase I study of AZD4547, an inhibitor of fibroblast growth factor receptor (FGFR), in patients with advanced solid tumors 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia LB-145.
34. Wolf J, LoRusso PM, Camidge RD, Perez JM, Tabernero J, Hidalgo M, et al. A phase I dose escalation study ofNVP-BGJ398, a selective pan FGFR inhibitor in genetically preselected advanced solid tumors 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): LB-122.
35. Singh D, Chan JM, Zoppoli P, Niola F, Sullivan R, Castano A, et al. Transforming fusions of FGFR and TACC genes in human glioblastoma. Science 2012;337:1231-5.
36. Parker BC, Annala MJ, Cogdell DE, Granberg KJ, Sun Y, Ji P, et al. The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma. J Clin Invest 2013;123:855-65.
37. Williams SV, Hurst CD, Knowles MA. Oncogenic FGFR3 gene fusions in bladder cancer. Hum Mol Genet 2013;22:795-803.
38. Smith G, Bounds R, Wolf H, Steele RJC, Carey FA, Wolf CR. Activating K-Ras mutations out with "hotspot" codons in sporadic colorectal tumours - implications for personalised cancer medicine. Br J Cancer 2010;102: 693-703.
39. Massarelli E, Varella-Garcia M, Tang X, Xavier AC, Ozburn NC, Liu DD, et al. KRAS mutation is an important predictor of resistance to therapy with epidermal growth factor receptor tyrosine kinase inhibitors in non -small cell lung cancer. Clin Cancer Res 2007;13:2890-6.
40. Licitra L, Mesia R, Rivera F, Remenár E, Hitt R, Erfán J, et al. Evaluation of EGFR gene copy number as a predictive biomarker for the efficacy of cetuximab in combinationwith chemotherapy in the first-line treatment of recurrent and/or metastatic squamous cell carcinoma of the head and neck: EXTREME study. Ann Onc 2011;22:1078-87.
41. Weiss J, Sos ML, Seidel D, Peifer M, Zander T, Heuckmann JM, et al. Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer. Sci Transl Med 2010;2:62ra93.
42. Young RJ, Rischin D, Fisher R, McArthur GA, Fox SB, Peters LJ, et al. Relationship between epidermal growth factor receptor status, p16 (INK4A), and outcome in head and neck squamous cell carcinoma. J Clin Oncol 2011;20:1230-7.
43. Jones DT, Jäger N, Kool M, Zichner T, Hutter B, Sultan M, et al. Dissecting the genomic complexityunderlyingmedulloblastoma. Nature 2012;488:100-5.
44. Pugh TJ, Weeraratne SD, Archer TC, Pomeranz Krummel DA, Auclair D, Bochicchio J, et al. Medulloblastoma exome sequencing uncovers subtypespecific somatic mutations. Nature 2012;488:106-10.
45. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 2011;476:298-303.
46. Grasso CS, Wu YM, Robinson DR, Cao X, Dhanasekaran SM, Khan AP, et al. The mutational landscape of lethal castration-resistant prostate cancer. Nature 2012;487:239-43.
47. Kim Y, Hammerman PS, Kim J, Yoon J-A. Integrative and comparative genomic analysis of lung squamous cell carcinomas in East Asians. J Clin Oncol 2014;32:121-8.
48. Jaramillo MC, Zhang DD. The emerging role of the Nrf2-Keap1 signaling pathway in cancer. Genes Dev 2013;27:2179-91.
49. An J, Mo D, Liu H, Veena MS, Srivatsan ES, Massoumi R, et al. Inactivation of the CYLD Deubiquitinase by HPV E6 mediates hypoxia-induced NF-κB activation. Cancer Cell 2008;14:394-407.
50. Meissner B, Kridel R, Lim RS, Rogic S, Tse K, Scott DW, et al. The E3 ubiquitin ligase UBR5 is recurrently mutated in mantle cell lymphoma. Blood 2013;121:3161-4.