Circular RNA expression in pancreatic ductal adenocarcinoma

Abstract

The regulatory roles of circular RNAs (circRNAs) in cancer are attracting increasing attention. The aim of the present study was to explore the roles of circRNAs in pancreatic ductal adenocarcinoma (PDAC) using microarray data. The circRNA and microRNA (miRNA) microarray data were downloaded from Gene Expression Omnibus. A total of 256 differentially expressed circRNAs were obtained by analyzing the circRNA microarray data from 26 pairs of PDAC and adjacent normal tissues. Differentially expressed miRNAs were analyzed using a dataset of 6 PDAC tissues and 5 non-neoplastic pancreas samples (GSE43796); 20 differentially expressed miRNAs were detected. circRNA/miRNA interactions were predicted between differentially expressed circRNAs and miRNAs using miRanda and RNAhybrid algorithms and 51 circRNA/miRNA interactions were obtained. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis using gene symbols of differentially expressed circRNAs demonstrated that 41 circRNAs were enriched in 17 pathways. Subnetworks that were associated with apoptosis or proliferation were extracted from the 17 pathways and a new network was constructed using Cytoscape software, which identified that mitogen-activated protein kinase, PI3K/AKT and WNT/β-catenin signaling pathways may be associated with PDAC development. In conclusion, 256 differentially expressed circRNAs and 20 differentially expressed miRNAs were identified in PDAC tissues compared with normal tissues; the circRNA/miRNA interactions and the networks of KEGG pathways provided a global view of the function of these differentially expressed circRNAs and miRNAs.

Keywords: circular RNA; microRNA; pancreatic cancer; pathway analysis.

Figure 1.

Overview of the microarray datasets. (A) Box plots of the distributions of normalized signal intensities of the circRNA datasets. (B) Box plots for the distributions of normalized signal intensities of the miRNA datasets. (C) Scatter plots of the circRNA microarray signal values of between PDAC and adjacent normal tissues. Red dots represent upregulated circRNAs compared with normal tissues; green dots represent downregulated circRNAs compared with normal tissues; black dots represent equally expressed circRNAs. (D) Scatter plots of the miRNA microarray signal values between PDAC and normal tissues. Red dots represent upregulated miRNAs compared with normal tissues; green dots represent downregulated miRNAs compared with normal tissues; black dots represent equally expressed miRNAs. (E) Volcano plot of circRNA datasets. Red dots represent differentially expressed circRNAs. (F) Volcano plot of miRNA datasets. Red dots represent differentially expressed miRNAs. circRNA, circular RNA; miRNA, microRNA; PDAC, pancreatic ductal adenocarcinoma.

Figure 2.

Networks of circRNA/miRNA interactions predicted using miRanda and RNAhybrid software. Red circles represent upregulated circRNAs; green circles represent downregulated circRNAs; pink squares represent upregulated miRNAs; light green squares represent downregulated miRNAs. The size of the circles and squares represents the fold-change of the genes. circRNA, circular RNA; miRNA, microRNA.

Figure 3.

Network of KEGG pathways and circRNA host gene symbols. Red circles represent upregulated circRNA host genes; green circles represent downregulated circRNA host genes; the size of the circles represents the fold-change of the circRNAs. As both hsa_circ_0000676 and hsa_circ_0000679 are derived from ABCC1, they are indicated as ABCC1^# and ABCC1*, respectively. circRNA, circular RNA; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure 4.

Pathways associated with apoptosis or proliferation. Orange ellipses represent the host gene symbols for differentially expressed circRNAs and gray ellipses represent the downstream genes regulated by parental genes of the circRNAs in the KEGG pathways; green solid lines represent a direct activation effect; green dotted lines represent an indirect activation effect; red solid lines represent a direct inhibition effect; red dotted lines represent an indirect inhibition effect. circRNA, circular RNA; KEGG, Kyoto Encyclopedia of Genes and Genomes; +p, phosphorylation; -p, dephosphorylation.