Identification of novel long non-coding RNAs deregulated in hepatocellular carcinoma using RNA-sequencing

// Davide Degli Esposti 1 , Hector Hernandez-Vargas 1 , Catherine Voegele 2 , Nora Fernandez-Jimenez 1 , Nathalie Forey 2 , Brigitte Bancel 3, 4 , Florence Le Calvez-Kelm 2 , James McKay 2 , Philippe Merle 3, 5 , Zdenko Herceg 1 1 Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France 2 Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC), Lyon, France 3 Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Lyon Cedex, France 4 Hospices Civils de Lyon, Service d’Anatomopathologie, Groupement Hospitalier Lyon Nord, Lyon, France 5 Hospices Civils de Lyon, Service d’Hépatologie et de Gastroentérologie, Groupement Hospitalier Lyon Nord, Lyon, France Correspondence to: Zdenko Herceg, e-mail: HercegZ@iarc.fr Keywords: hepatocellular carcinoma, long non-coding RNA, gene networks, enhancer-associated RNAs, RNA-sequencing Received: September 17, 2015 Accepted: January 20, 2016 Published: February 13, 2016 ABSTRACT Functional characterization of long non-coding RNAs (lncRNAs) and their pathological relevance is still a challenging task. Abnormal expression of a few long non-coding RNAs have been found associated with hepatocellular carcinoma, with potential implications to both improve our understanding of molecular mechanism of liver carcinogenesis and to discover biomarkers for early diagnosis or therapy. However, the understanding of the global role of lncRNAs during HCC development is still in its infancy. In this study, we produced RNA-Seq data from 23 liver tissues (controls, cirrhotic and HCCs) and applied statistical and gene network analysis approaches to identify and characterize expressed lncRNAs. We detected 5,525 lncRNAs across different tissue types and identified 57 differentially expressed lncRNAs in HCC compared with adjacent non-tumour tissues using stringent criteria (FDR<0.05, Fold Change>2). Using weighted gene co-expression network analysis (WGCNA), we found that differentially expressed lncRNAs are co-expressed with genes involved in cell cycle regulation, TGF-β signalling and liver metabolism. Furthermore, we found that more than 20% of differentially expressed lncRNAs are associated to actively transcribed enhancers and that the co-expression patterns with their closest genes change dramatically during HCC development. Our study provides the most comprehensive compendium of lncRNAs expressed in HCC, as well as in control or cirrhotic livers. Our results identified both known oncogenic lncRNAs (such as H19 and CRNDE) and novel lncRNAs involved in cell cycle deregulation and liver metabolism deficits occurring during HCC development.