title: Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets.
abstract: Hepatocellular carcinoma (HCC) is an aggressive and deadly cancer. The molecular pathogenesis of the disease remains poorly understood. To better understand HCC biology and explore potential biomarkers and therapeutic targets, we investigated the whole transcriptome of HCC. Considering the genetic heterogeneity of HCC, four datasets from four studies consisting of 15 pairs of HCC and adjacent normal samples were analyzed. We observed that the number of lncRNAs expressed in each HCC sample was consistently greater than the adjacent normal sample. Moreover, 15 lncRNAs were identified expressed in five to seven HCC tissues but were not detected in any adjacent normal tissue. Differential expression analysis detected 35 up- and 80 down-regulated lncRNAs in HCC samples compared with adjacent normal samples. In addition, five differentially expressed lncRNAs were predicted to play a role in oxidation and reduction process. With regard to splicing alterations, we identified nine highly recurrent differential splicing events belonging to eight genes USO1, RPS24, CCDC50, THNSL2, NUMB, FN1 (two events), SLC39A14 and NR1I3. Of them, splicing alterations of SLC39A14 and NR1I3 were reported for the association with HCC for the first time. The splicing dysregulation in HCC may be influenced by three splicing factors ESRP2, CELF2 and SRSF5 which were significantly down-regulated in HCC samples. This study revealed uncharacterized aspects of HCC transcriptome and identified important lncRNAs and splicing isoforms with the potential to serve as biomarkers and therapeutic targets for the disease.
authors.affiliation: Informatics, MSD China R&D, Beijing, China.|MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Informatics, MSD China R&D, Beijing, China.
authors.forename: Xiaoqiao
authors.initials: X
authors.lastname: Liu
authors.affiliation: MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China. zhangxg@tsinghua.edu.cn.|School of Life Sciences, Tsinghua University, Beijing, China. zhangxg@tsinghua.edu.cn.
authors.forename: Xuegong
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Informatics, MSD China R&D, Beijing, China. ronghua_chen@merck.com.|Research IT, Merck and Co., Inc., Boston, MA, USA. ronghua_chen@merck.com.
authors.forename: Ronghua
authors.initials: R
authors.lastname: Chen
mesh_terms: D017398:Alternative Splicing; D006528:Carcinoma, Hepatocellular / Q000235:genetics; D027682:Cation Transport Proteins / Q000235:genetics*; D000090702:Constitutive Androstane Receptor; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics*; D010084:Oxidation-Reduction; D062085:RNA, Long Noncoding / Q000235:genetics*; D018160:Receptors, Cytoplasmic and Nuclear / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D027682:Cation Transport Proteins; D000090702:Constitutive Androstane Receptor; C000716327:NR1I3 protein, human; D062085:RNA, Long Noncoding; D018160:Receptors, Cytoplasmic and Nuclear; C497524:SLC39A14 protein, human
keywords: Alternative splicing; HCC; Long noncoding RNA (lncRNA); RNA-Seq