Whole-Transcriptome Sequencing Identifies Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs Associated with CHOL

Abstract

To systematically evaluate the whole-transcriptome sequencing data of cholangiocarcinoma (CHOL) to gain more insights into the transcriptomic landscape and molecular mechanism of this cancer, we performed whole-transcriptome sequencing 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. In total, 2,895 differentially expressed messenger RNAs (dif-mRNAs), 56 differentially expressed microRNAs (dif-miRNAs), 151 differentially expressed long non-coding RNAs (dif-lncRNAs), and 110 differentially expressed circular RNAs (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 downregulated hsa-miR-144-3p were significantly enriched in the competing endogenous RNA (ceRNA) complex network, which also included 7 upregulated and 13 downregulated circRNAs, 7 upregulated lncRNAs, and 90 upregulated and 40 downregulated mRNAs. Moreover, most of the DEGs and a few of the 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.

circPARD3 drives malignant progression and chemoresistance of laryngeal squamous cell carcinoma by inhibiting autophagy through the PRKCI-Akt-mTOR pathway

“…RNA sequencing technology was provided by Novogene (Beijing, China). Differentially expressed circRNAs, miRNAs, and mRNAs were analyzed as previous reported [ 15 ] (Additional file 1 : Table S7–9).…”

Circular RNA circDNM3OS Functions as a miR-145-5p Sponge to Accelerate Cholangiocarcinoma Growth and Glutamine Metabolism by Upregulating MORC2

“… 17 , 21 , 22 Moreover, whole-transcriptome sequencing has revealed that there are 110 differentially expressed circRNAs in CCA tissues in contrast to adjacent normal tissues. 23 Previous study uncovered that circRNA circ_0000284 aroused the malignant phenotype of CCA cells. 21 Also, circRNA circCDR1as exerted a promoting impact on the malignancy of CCA cells through sponging miR-641.…”

Emerging roles of long noncoding RNAs in cholangiocarcinoma: Advances and challenges

“…However, few studies have utilized circRNA-containing whole-transcriptome sequencing technology, which allows accurate examination of the transcriptomic landscape of CCA. Chu et al [105] explored the molecular mechanisms of CCA by performing circRNA-containing whole-transcriptome sequencing and validation with the TCGA database. In this study, miR-144-3p was identified to be located in the center of the ceRNA network and might play an important role in the pathogenesis of CCA.…”