Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function

Christopher R. Cabanski, Nicole Maher, Ha X. Dang, Jessica M. Silva-Fisher, Corinne E. Rauck, Danielle Cicka, Christopher Maher

Research output: Contribution to journalArticle

52 Scopus citations

Abstract

A growing number of gene-centric studies have highlighted the emerging significance of lncRNAs in cancer. However, these studies primarily focus on a single cancer type. Therefore, we conducted a pan-cancer analysis of lncRNAs comparing tumor and matched normal expression levels using RNA-Seq data from ~ 3,000 patients in 8 solid tumor types. While the majority of differentially expressed lncRNAs display tissue-specific expression we discovered 229 lncRNAs with outlier or differential expression across multiple cancers, which we refer to as ’onco-lncRNAs’. Due to their consistent altered expression, we hypothesize that these onco-lncRNAs may have conserved oncogenic and tumor suppressive functions across cancers. To address this, we associated the onco-lncRNAs in biological processes based on their co-expressed protein coding genes. To validate our predictions, we experimentally confirmed cell growth dependence of 2 novel oncogenic lncRNAs, onco-lncRNA-3 and onco-lncRNA-12, and a previously identified lncRNA CCAT1. Overall, we discovered lncRNAs that may have broad oncogenic and tumor suppressor roles that could significantly advance our understanding of cancer lncRNA biology.

Original languageEnglish
Pages (from-to)628-642
Number of pages15
JournalRNA Biology
Volume12
Issue number6
DOIs
StatePublished - Jan 1 2015

Keywords

  • Bioinformatics
  • Cancer genomics
  • LncRNA
  • Transcriptome

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