Analysis of circRNA-mRNA expression profiles and functional enrichment in diabetes mellitus based on high throughput sequencing

Abstract

To study the pathogenesis of diabetes mellitus (DM) and identify new biomarkers, high-throughput RNA sequencing provides a technical means to explore the regulatory network of MD gene expression. To better elucidate the genetic basis of DM, we analysed the circRNA and mRNA expression profiles in serum samples from diabetic patients. The circRNAs and mRNAs with abnormal expression in the DM group and non-diabetic group (NDM) were classified by RNA sequencing and differential expression analysis. The circRNA-miRNA-mRNA regulatory network reveals the mechanism by which competitive endogenous RNAs (ceRNAs) regulate gene expression. The biological functions and interactions of circRNA and mRNA were analysed by gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Differential expression analysis showed that 441 circRNAs (366 up-regulated, 75 down-regulated) and 683 mRNAs (354 up-regulated, 329 down-regulated) were significantly differentially expressed in the DM group compared with the NDM group. Screening of the differential genes at the nodes of the interaction network showed that a single circRNA could interact with multiple miRNAs and then jointly regulate more mRNAs. In addition, the expressions of circRNA CNOT6 and AXIN1 as well as mRNA STAT3, MYD88, and B2M were associated with the progression of diabetes. Enrichment pathway analysis indicated that differentially expressed circRNA and mRNA may participate in Nod-like receptor signalling pathway, insulin signalling pathway, sphinolipid metabolism pathway, and ribosome pathway, and play a role in the pathogenesis of diabetes. This study provides a theoretical basis for elucidating the molecular mechanism of DM occurrence and development at circRNA and mRNA levels.

Keywords: ceRNA; circRNA; diabetes; mRNA.

FIGURE 1

Differentially expressed circRNA and mRNA in diabetes mellitus (DM) and NDM. (A,B) Each dot in the figure represents an mRNA or circRNA. The horizontal axis represents Log2 (fold change) of the multiple difference in RNA expression between the two groups. The ordinate is the negative log of the change in RNA expression. (B,C) The differentially expressed circRNAs or mRNAs were bidirectional clusterings with groups. The colour depth represented the expression level of genes, red represented high expression level, and blue represented low expression level. (E) Red nodes, green nodes, and blue nodes represent circRNA, miRNA, and mRNA, respectively

FIGURE 2

Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis results. (A‐C) GO enrichment analysis of downregulated (A) and upregulated (B) messenger RNAs and circular RNAs (C) of target genes. The abscissa is the GO classification and the ordinate is the number of target genes. (D,E) The bubble map of Kyoto Encyclopedia of Genes and Genomes enrichment analysis; (A) Messenger RNAs (mRNAs) predicted by differentially expressed circular RNAs; (B) differentially expressed mRNAs; the repeated pathways have been marked with red arrows). The abscissa is the enrichment factor (differential mRNA enriched into the pathway/background genes of the pathway), the ordinate is the description of the corresponding pathway, the bubble size is the number of differential genes, and the bubble colour is the enrichment significance P value