title: Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function.
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.
authors: a The Genome Institute; Washington University School of Medicine ; St. Louis , MO USA.
authors: Christopher R
authors: CR
authors: Cabanski
authors: Nicole M
authors: NM
authors: White
authors: Ha X
authors: HX
authors: Dang
authors: Jessica M
authors: JM
authors: Silva-Fisher
authors: Corinne E
authors: CE
authors: Rauck
authors: Danielle
authors: D
authors: Cicka
authors: Christopher A
authors: CA
authors: Maher
mesh_terms: D045744:Cell Line, Tumor; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D006801:Humans; D009369:Neoplasms / Q000378:metabolism*; D062085:RNA, Long Noncoding / Q000378:metabolism*
chemical_list: C579842:CCAT1 long noncoding RNA, human; D062085:RNA, Long Noncoding; C000602202:onco-lncRNA-12, human; C000602203:onco-lncRNA-3, human
keywords: Cancer genomics; bioinformatics; lncRNA; transcriptome