Genome-wide analysis of long noncoding RNA and mRNA co-expression profile in intrahepatic cholangiocarcinoma tissue by RNA sequencing

// Wenhui Yang 1, 2 , Yuan Li 3 , Xia Song 2 , Jun Xu 2 , Jun Xie 1 1 Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, China 2 Shanxi Province Cancer Hospital, Affiliated Cancer Hospital of Shanxi Medical University, Taiyuan, Shanxi, China 3 Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China Correspondence to: Jun Xu, email: junxuty@163.com Jun Xie, email: junxie@sxmu.edu.cn Keywords: intrahepatic cholangiocarcinoma, long noncoding RNA, co-expression, RNA sequencing Received: January 10, 2017      Accepted: February 13, 2017      Published: February 24, 2017 ABSTRACT Long noncoding RNAs (lncRNAs), which are pervasively transcribed in the genome, are emerging in molecular biology as crucial regulators of cancer. RNA-seq data were downloaded from GEO of NCBI and further analyzed to identify novel targets in intrahepatic cholangiocarcinoma (iCCA).We investigated differences in lncRNA and mRNA profiles between 7 pairs of iCCA and adjacent normal tissues. 230 lncRNAs were differentially expressed more than four-fold change in iCCA tissues. Among these, 97 were upregulated and 133 downregulated relatively to normal tissues. Moreover, 169 lncRNAs and 597 mRNAs formed the lncRNA-mRNA co-expression network which consist 766 network nodes and 769 connection edges. Bioinformatics analysis identified these dysregulated lncRNAs were associated with cholesterol homeostasis, insoluble fraction and lipid binding activity and were enriched in complement and coagulation cascades and PPAR signaling pathway. These results uncovered the landscape of iCCA-associated lncRNAs and co-expression network, providing insightful information about dysregulated lncRNAs in iCCA.