figshare
Browse
1/1
2 files

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

Version 3 2015-10-16, 03:44
Version 2 2015-10-16, 03:44
Version 1 2015-06-03, 00:00
dataset
posted on 2015-10-16, 03:44 authored by Christopher R Cabanski, Nicole M White, Ha X Dang, Jessica M Silva-Fisher, Corinne E Rauck, Danielle Cicka, Christopher A Maher

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.

History