Whole Transcriptome Sequencing Analyzes the Interactions of mRNAs and ncRNAs in Cholangiocarcinoma.

Background: Cholangiocarcinoma is a common hepatic malignant tumor with an unfavorable prognosis. Therefore, we systematically evaluated the transcriptomic landscape of CHOL by whole transcriptome sequencing technology in this study and constructed a ceRNA network associated with CHOL.

Methods: First, whole transcriptome sequencing between the tumor tissues of CHOL and adjacent cancer tissues adjacent to the tumors from six patients with CHOL was performed. Then, a differential expression analysis between the CHOL group and adjacent cancer group was performed to screen significant markers. Subsequently, target gene predictive analysis and co-expression analysis were implemented to construct a ceRNA and protein-protein interaction network in CHOL, and enrichment analysis was performed to investigate gene-related molecular pathways.

Results: The results showed that there were 761 differentially expressed mRNAs, 47 differentially expressed miRNAs, 61 differentially expressed lncRNAs, and 1481 differentially expressed circRNAs in the adjacent cancer group compared with the CHOL group, respectively. Enrichment analysis of differentially expressed mRNAs showed that the PI3K-Akt, calcium, and MAPK signaling pathways were significantly enriched. Hsa-miR-196b-5p can be a sponge to adsorb lncRNA H19 and 101 downregulated mRNAs, constructing an lncRNA-miRNA-mRNA network. Hsa_circ_0025636, hsa_circ_0057335, hsa-miR-96-5p, and hsa-miR-196b-5p were involved in the circRNA-miRNA-mRNA network. Moreover, five core genes were obtained through PPI interaction analysis, which also played an important role in the ceRNA network.

Conclusions: This study systematically presents a transcriptomic landscape of CHOL and identifies lncRNA/circRNA-associated ceRNA networks that could provide insights for future treatment and prognosis of CHOL, laying a certain foundation for the study of molecular mechanisms and providing novel ideas for its prognosis and treatment.