Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

HS Chiu; S Somvanshi; E Patel; TW Chen; VP Singh; B Zorman; SL Patil; Y Pan; SS Chatterjee; 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; R Akbani; BM Broom; AM Hegde; Z Ju; RS Kanchi; A Korkut; J Li; H Liang; S Ling; W Liu; Y Lu; GB Mills; KS Ng; A Rao; M Ryan; J Wang; JN Weinstein; J Zhang; A Abeshouse; J Armenia; D Chakravarty; WK Chatila; I de Bruijn; J Gao; BE Gross; ZJ Heins; R Kundra; K La; M Ladanyi; A Luna; MG Nissan; A Ochoa; SM Phillips; E Reznik; F Sanchez-Vega; C Sander; N Schultz; R Sheridan; SO Sumer; Y Sun; BS Taylor; J Wang; H Zhang; P Anur; M Peto

Journal article

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

HS Chiu, S Somvanshi, E Patel, TW Chen, VP Singh, B Zorman, SL Patil, Y Pan, SS Chatterjee, SJ Caesar-Johnson, JA Demchok, I Felau, M Kasapi, ML Ferguson, CM Hutter, HJ Sofia, R Tarnuzzer, Z Wang, L Yang, JC Zenklusen Show all

Cell Reports | CELL PRESS | Published : 2018

DOI: 10.1016/j.celrep.2018.03.064

Abstract

Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles in cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling their effects on the activity of transcription factors, RNA-binding proteins, and microRNAs in 5,185 TCGA tumors and 1,019 ENCODE assays. Our predictions included hundreds of candidate onco- and tumor-suppressor lncRNAs (cancer lncRNAs) whose somatic alterations account for the dysregulation of dozens of cancer genes and pathways in each of 14 tumor contexts. To demonstrate proof of concept, we showed that perturbations targeting OIP5-AS1 (an..

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University of Melbourne Researchers

Christopher Hovens Author

Anthony Costello Author

Michael Lawrence Author

Alex Boussioutas Author

Grants

Awarded by National Institutes of Health

Funding Acknowledgements

We acknowledge support from the European Union's Horizon 2020 Research and Innovation Programme 668858; Taiwan Ministry of Science and Technology grant MOST-106-2311-B-182-005; and NIH grants 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. The results published here are, in part, based upon data generated by the TCGA pilot project established by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI).