Identification of miRNAs-genes regulatory network in diabetic nephropathy based on bioinformatics analysis

Abstract

MicroRNAs (miRNAs) play a great contribution to the development of diabetic nephropathy (DN). The aim of this study was to explore potential miRNAs-genes regulatory network and biomarkers for the pathogenesis of DN using bioinformatics methods.Gene expression profiling data related to DN (GSE1009) was obtained from the Gene Expression Omnibus (GEO) database, and then differentially expressed genes (DEGs) between DN patients and normal individuals were screened using GEO2R, followed by a series of bioinformatics analyses, including identifying key genes, conducting pathway enrichment analysis, predicting and identifying key miRNAs, and establishing regulatory relationships between key miRNAs and their target genes.A total of 600 DEGs associated with DN were identified. An additional 7 key DEGs, including 6 downregulated genes, such as vascular endothelial growth factor α (VEGFA) and COL4A5, and 1 upregulated gene (CCL19), were identified in another dataset (GSE30528) from glomeruli samples. Pathway analysis showed that the down- and upregulated DEGs were enriched in 14 and 6 pathways, respectively, with 7 key genes mainly involved in extracellular matrix-receptor interaction, PI3K/Akt signaling, focal adhesion, and Rap1 signaling. The relationships between miRNAs and target genes were constructed, showing that miR-29 targeted COL4A and VEGFA, miR-200 targeted VEGFA, miR-25 targeted ITGAV, and miR-27 targeted EGFR.MiR-29 and miR-200 may play important roles in DN. VEGFA and COL4A5 were targeted by miR-29 and VEGFA by miR-200, which may mediate multiple signaling pathways leading to the pathogenesis and development of DN.

Figure 1

Differentially expressed genes (DEGs) common to GSE1009 and GSE30122. (A) Venn diagram of the up- and downregulated DEGs in GSE1009 and GSE30122. (B) Venn diagram of the hub genes identified in GSD1009 and the DEGs in glomerular tissues identified in GSE30122.

Figure 2

(A) GO analysis of the downregulated DEGs in DN (top 10). (B) GO analysis of the upregulated DEGs in DN (top 10). BP = biological process, CC = cellular component, DEGs = differentially expressed genes, DN = diabetic nephropathy, GO = gene ontology, MF = molecular function.

Figure 3

(A) MiRNA–protein interaction network between targeting miRNAs and the downregulated DEGs. The V-shaped nodes represent the key miRNAs (degree >12). The color gradient represents the degree (top 10 miRNAs). The round nodes represent the downregulated genes related to the key miRNAs or other miRNAs. (B) MiRNA–protein interaction network between targeting miRNAs and the upregulated DEGs. The triangle nodes represent the key miRNAs (degree >12). The color gradient represents the degree (top 10 miRNAs). The round nodes represent the upregulated genes related to the key miRNAs or other miRNAs. DEGs = differentially expressed genes, miRNAs = microRNAs.

Figure 4

Global network diagram of the interactions between the key miRNAs and their target genes. The diamond nodes represent the 9 key miRNAs. The hexagonal nodes represent the 5 hub genes (ITGB5 and CCL19 did not correspond to the miRNAs). The large round nodes represent genes associated with the 9 key miRNAs, and the small round nodes represent the other upregulated genes and miRNAs. miRNAs = microRNAs.

Figure 5

Schematic diagram of potential miRNAs-genes regulatory network in DN. DN = diabetic nephropathy, miRNAs = microRNAs.