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

Kai-Jian Chu, Yu-Shui Ma, Xiao-Hui Jiang, Ting-Miao Wu, Zhi-Jun Wu, Zhi-Zhen Li, Jing-Han Wang, Qing-Xiang Gao, Bin Yi, Yi Shi, Hui-Min Wang, Li-Peng Gu, Su-Qing Zhang, Gao-Ren Wang, Ji-Bin Liu, Da Fu, Xiao-Qing Jiang, Kai-Jian Chu, Yu-Shui Ma, Xiao-Hui Jiang, Ting-Miao Wu, Zhi-Jun Wu, Zhi-Zhen Li, Jing-Han Wang, Qing-Xiang Gao, Bin Yi, Yi Shi, Hui-Min Wang, Li-Peng Gu, Su-Qing Zhang, Gao-Ren Wang, Ji-Bin Liu, Da Fu, Xiao-Qing Jiang

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.

Keywords: CHOL; DEG; ceRNA; miR-144-3p; spliceosome.

Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.

Figures

Graphical abstract
Graphical abstract
Figure 1
Figure 1
Heatmaps of Differentially Expressed Molecules (A–D) Heatmaps of differentially expressed mRNAs (A), differentially expressed miRNAs (B), differentially expressed lncRNAs (C), and differentially expressed circRNAs (D). Red indicates upregulation, and green indicates downregulation.
Figure 2
Figure 2
Analysis of Gene Ontology Biological Process (GO-BP) and KEGG Pathway Top 20 pathways or GO-BP terms enriched by upregulated or downregulated mRNAs. (A) Top 20 GO-BP terms enriched by upregulated genes. (B) Top 20 GO-BP terms enriched by downregulated genes. (C) Top 20 pathways enriched by upregulated genes. (D) Top 20 pathways enriched by downregulated genes.
Figure 3
Figure 3
Four Modules Extracted from Protein-Protein Interaction (PPI) Network and GO-BP Enrichment Analysis Four modules extracted from PPI network and GO-BP enrichment analysis of genes in these four modules. (A) Significant clustered modules from the PPI network. Orange prism indicates upregulated genes. Node size corresponded to degree value; larger node has higher degree value. (B) Top 10 GO-BP terms enriched by genes in those four modules.
Figure 4
Figure 4
Bubble Maps of KEGG Pathway Enrichment (A) Pathways enriched by genes regulated by differentially expressed miRNAs. (B) Pathways enriched by genes regulated by differentially expressed lncRNAs. (C) Pathways enriched by genes regulated by differentially expressed circRNAs.
Figure 5
Figure 5
The lncRNA-miRNA-mRNA Network Orange prism represents the upregulated genes, green circle indicates downregulated genes, red triangle indicates upregulated miRNAs, green arrow shows the downregulated miRNAs, and white quadrilateral indicates the upregulated lncRNAs.
Figure 6
Figure 6
circRNA-miRNA-mRNA Network Orange prism represents the upregulated genes, green circle represents downregulated genes, red triangle indicates the upregulated miRNAs, green arrow indicates the downregulated miRNAs, white quadrilateral indicates the upregulated circRNA, and white hexagon indicates downregulated circRNA.
Figure 7
Figure 7
The Competing Endogenous RNA (ceRNA) Network Orange prism indicates the upregulated gene, green circle indicates the downregulated gene, red triangle indicates the upregulated miRNA, green arrow indicates the downregulated miRNA, yellow square indicates the upregulated lncRNA, white square indicates upregulated circRNA, and white hexagon indicates downregulated circRNA.

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