Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

JD Campbell; C Yau; R Bowlby; Y Liu; K Brennan; H Fan; AM Taylor; C Wang; V Walter; R Akbani; LA Byers; CJ Creighton; C Coarfa; J Shih; AD Cherniack; O Gevaert; M Prunello; H Shen; P Anur; J Chen; H Cheng; DN Hayes; S Bullman; CS Pedamallu; AI Ojesina; S Sadeghi; KL Mungall; AG Robertson; C Benz; A Schultz; RS Kanchi; CM Gay; A Hegde; L Diao; J Wang; W Ma; P Sumazin; HS Chiu; TW Chen; P Gunaratne; L Donehower; JS Rader; R Zuna; H Al-Ahmadie; AJ Lazar; ER Flores; KY Tsai; JH Zhou; AK Rustgi; E Drill; R Shen; CK Wong; SJ Caesar-Johnson; JA Demchok; I Felau; M Kasapi; ML Ferguson; CM Hutter; HJ Sofia; R Tarnuzzer; Z Wang; L Yang; JC Zenklusen; J Zhang; S Chudamani; J Liu; L Lolla; R Naresh; T Pihl; Q Sun; Y Wan; Y Wu; J Cho; T DeFreitas; S Frazer; N Gehlenborg; G Getz; DI Heiman; J Kim; MS Lawrence; P Lin; S Meier; MS Noble; G Saksena; D Voet; H Zhang; B Bernard; N Chambwe; V Dhankani; T Knijnenburg; R Kramer; K Leinonen; Y Liu; M Miller; S Reynolds; I Shmulevich; V Thorsson; W Zhang; BM Broom; AM Hegde

Journal article

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

JD Campbell, C Yau, R Bowlby, Y Liu, K Brennan, H Fan, AM Taylor, C Wang, V Walter, R Akbani, LA Byers, CJ Creighton, C Coarfa, J Shih, AD Cherniack, O Gevaert, M Prunello, H Shen, P Anur, J Chen Show all

Cell Reports | CELL PRESS | Published : 2018

DOI: 10.1016/j.celrep.2018.03.063

Open access

Abstract

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previou..

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University of Melbourne Researchers

Christopher Hovens Author

Anthony Costello Author

Michael Lawrence Author

Niall Corcoran Author

Grants

Awarded by National Institutes of Health

Funding Acknowledgements

We are grateful to the patients who contributed to this study, and the support of the TCGA Steering Committee and Project Team, especially Samantha Caesar-Johnson and Ina Felau. This work was supported by the following grants from the NIH: U54 HG003273, U54 HG003067, U54 HG003079, U24 CA143799, U24 CA143835, U24 CA143840, U24 CA143843, U24 CA143845, U24 CA143848, U24 CA143858, U24 CA143866, U24 CA143867, U24 CA143882, U24 CA143883, U24 CA144025, and P30 CA016672, and NIDCD intramural project ZIA-DC-000074.