Integrated analysis of circular RNA-associated ceRNA network in pancreatic ductal adenocarcinoma

Abstract

Circular RNAs (circRNAs) have displayed dysregulated expression in several types of cancer. However, the functions of the majority of circRNAs in pancreatic ductal adenocarcinoma (PDAC) remain unknown. The present study aimed to investigate the expression, functions and molecular mechanisms of circRNAs in PDAC. The circRNAs, mRNAs and the microRNA (miRNAs) expression profiles were obtained from three Gene Expression Omnibus microarray datasets, and a circRNA-miRNA-mRNA and circRNA-miRNA-hubgene network was established. The interactions between proteins were analyzed using the Search Tool for the Retrieval of Interacting Genes/Proteins database, and hubgenes were identified using the MCODE plugin. A total of eight differentially expressed circRNAs (DEcircRNAs), 44 differentially expressed miRNAs (DEmiRNAs), and 2,052 differentially expressed mRNAs (DEmRNAs) were identified. The present study successfully constructed a circRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network based on four circRNAs, six miRNAs and 111 mRNAs in PDAC. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathways analyses indicated that DEmRNAs may participate in the pathogenesis and progression of PDAC. The protein-protein interaction network and module analysis identified six hubgenes (THBS1, FN1, TIMP3, TGFB2, ITGA1 and ITGA3). Furthermore, the circRNA-miRNA-hubgene regulatory modules were constructed based on the three DEcircRNAs, one DEmiRNAs and five DEmRNAs. In conclusion, the results of the present study improve the current understanding of the pathogenesis of PDAC.

Keywords: Gene Expression Omnibus; circular RNA; competitive endogenous RNA; pancreatic ductal adenocarcinoma.

Figure 1.

Flowchart of ceRNA network analysis. circRNA, circular RNA; MREs, miRNA response elements; miRNAs, micro RNAs; ceRNA, competing endogenous RNA; PPI network, protein-protein interaction network; GO, gene ontology; KEGG, kyto encyclopedia of genes and genomes.

Figure 2.

Volcano plot of DEGs of the three microarray datasets. (A) GSE79634 (circRNAs). (B) GSE69362 (circRNAs). (C) GSE60980 (miRNAs). (D) GSE60980 (mRNAs). Red indicates upregulated DEGs and green indicates downregulated DEGs. DEGs, differentially expressed genes.

Figure 3.

Heatmap of the DEcircRNAs on the GSE79634 and GSE69362 microarray datasets. (A) All DEcircRNAs. (B) Eight DEcircRNAs with robust rank aggregation method. The node color changes gradually from green to red in ascending order according to the log2(foldchange) of genes. DEcircRNAs, differentially expressed circRNAs.

Figure 4.

Structural patterns of the seven circRNAs. (A) hsa_circ_0013912, (B) hsa_circ_0006220, (C) hsa_circ_0043278, (D) hsa_circ_0000977, (E) hsa_circ_0001666, (F) hsa_circ_0013587. Different colors in the circular structure of the circRNA represents the position of the exon.

Figure 5.

ceRNA network of circRNA-miRNA-mRNA in pancreatic ductal adenocarcinoma. The network consisting of four circRNA nodes, six miRNA nodes, 111 mRNA nodes. Triangles indicate circRNAs, rounded rectangles indicate miRNA, and octagons indicate mRNA. The nodes highlighted in red represent upregulation and the nodes in blue represent downregulation. circRNA, circular RNA; miRNA, micro RNA.

Figure 6.

Identification of hubgenes from the PPI network with the MCODE algorithm. This network consists of 37 nodes and 36 edges. (A) The PPI network of 111 genes. (B) The PPI network of six hubgenes that were extracted from (A).

Figure 7.

circRNA-miRNA-hubgene network. The network consisting of three circRNAs, one miRNAs, and five hubgenes. Green indicates circRNAs, yellow indicates miRNA, and blue indicates mRNA. Diamonds indicate circRNAs, rounded rectangles indicate miRNA, and ellipses indicate mRNA.