Whole-transcriptome sequencing identifies key differentially expressed mRNAs, miRNAs, lncRNAs and circRNAs associated with cholangiocarcinoma

Abstract To systematically evaluates the whole-transcriptome sequencing data of cholangiocarcinoma (CHOL) to gain more insights into the transcriptomic landscape and molecular mechanism of this cancer, whole-transcriptome sequencing was performed based on the tumorous (C) and their corresponding non-tumorous adjacent to the tumors (CP) from eight CHOL patients. Subsequently, differential expression analysis was performed on the C and CP groups, followed by functional interaction prediction analysis to investigate gene-regulatory circuits in CHOL. In addition, The Cancer Genome Atlas (TCGA) for CHOL data was used to validate the results. Totally, 2895 dif-mRNAs, 56 dif-miRNAs, 151 dif-lncRNAs, and 110 dif-circRNAs were found in CHOL samples compared with controls. Enrichment analysis on those differentially expressed genes (DEGs) related to miRNA, lncRNA and circRNA also identified the function of spliceosome. The down-regulated hsa-miR-144-3p were significantly enriched in the ceRNA complex network, which also included 7 up- and 13 down-regulated circRNAs, 7 up-regulated lncRNAs, 90 up- and 40 down-regulated mRNAs. Moreover, most of DEGs and a few of miRNAs (such as hsa-miR-144-3p) were successfully validated by TCGA data. The genes involved in RNA splicing and protein degradation processes, and miR-144-3p may play fundamental roles in the pathogenesis of CHOL.