Identification of Biological Targets of Therapeutic Intervention for Diabetic Nephropathy with Bioinformatics Approach

We aimed to discover the potential microRNA (miRNA) targets for diabetic nephropathy (DN) treatment. The microarray data of GSE1009 was downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between DN patients and normal individuals were analyzed using limma package. The significant miRNAs targeting DEGs were collected based on Web-based Gene Set Enrichment Analysis Toolkit (WebGestalt) system. Then we predicted the protein-protein interaction (PPI) pairs regulated by significant miRNAs and constructed the PPI pairs-miRNA network using Cytoscape software. Besides, the significant function modules were explored using Molecular Complex Detection (MCODE) and Biological Networks Gene Ontology (BiNGO) plugin. Total 752 DEGs were obtained, including 318 down-regulated ones and 434 up-regulated ones. There were 10 significant miRNAs, among which miRNA-25 was the most significant. The PPI pairs-miRNA network was established with 103 PPI pairs and 10 miRNAs. Three function modules were obtained, including module A involved with miRNA-29, module B with miRNA-106 and module C with miRNA-124A and miRNA-21B. MiRNA-25, 29, 124 and 21 play key roles in DN progression and these miRNAs may be potential targets for DN treatment.