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W. Rathmell
Last active: 11/27/2019

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

Chiu HS, Somvanshi S, Patel E, Chen TW, Singh VP, Zorman B, Patil SL, Pan Y, Chatterjee SS, Cancer Genome Atlas Research Network, Sood AK, Gunaratne PH, Sumazin P
Cell Rep. 2018 23 (1): 297-312.e12

PMID: 29617668 · PMCID: PMC5906131 · DOI:10.1016/j.celrep.2018.03.064

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 inferred tumor suppressor) and TUG1 and WT1-AS (inferred onco-lncRNAs) dysregulated cancer genes and altered proliferation of breast and gynecologic cancer cells. Our analysis indicates that, although most lncRNAs are dysregulated in a tumor-specific manner, some, including OIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergistically dysregulate cancer pathways in multiple tumor contexts.

Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

MeSH Terms (9)

Cell Line Cell Line, Tumor Gene Expression Regulation, Neoplastic Gene Regulatory Networks Genes, Tumor Suppressor Humans Neoplasms Oncogenes RNA, Long Noncoding

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