Diabetic kidney disease-predisposing proinflammatory and profibrotic genes identified by weighted gene co-expression network analysis (WGCNA)

Abstract

Diabetic kidney disease (DKD) is one of the most serious microvascular complications of diabetes. Despite enormous efforts, the underlying underpinnings of DKD remain incompletely appreciated. We sought to perform novel and informative bioinformatic analysis to explore the molecular mechanism of DKD. The gene expression profiles of GSE142025, GSE30528, and GSE30529 datasets were downloaded from the Gene Expression Omnibus database. After the GSE142025 data set was preprocessed, a gene co-expression network was constructed by weighted gene co-expression network analysis (WGCNA), and hub genes were selected in the key modules. Meanwhile, differentially expressed genes (DEGs) upregulated commonly were identified between the GSE30528 and GSE30529 datasets. Then, pathway and process enrichment analysis were performed for hub genes and commonly upregulated DEGs. Next, candidate targets were identified by comparing hub genes to commonly upregulated DEGs. Finally, reverse-transcription quantitative polymerase chain reaction (RT-qPCR) was carried out to validate the expression of candidate targets, and protein-protein interaction (PPI) network was constructed. A total of 17 modules were clustered by WGCNA, and the most significant turquoise module was selected. Based upon MM > 0.7 and GM > 0.7, 313 hub genes were screened out in turquoise module. Functional analysis of these 313 genes demonstrated their enrichment in pathways involved in leukocyte differentiation, cell morphogenesis, lymphocyte activation, vascular development, collagen synthesis, chemotaxis, and chemokine signaling. A total of 115 commonly upregulated DEGs were identified between the GSE30528 and GSE30529 datasets. Intriguingly, a total of six proinflammatory and profibrotic candidate targets were selected and validated in DKD mice in vivo, including CCR2, MOXD1, COL6A3, COL1A2, PYCARD, and C7. Based on WGCNA and DEG analysis of DKD datasets, six DKD-predisposing candidate targets were uncovered. The data suggest that inflammation and fibrosis are key mechanisms of DKD, and future studies may determine the causal link between the six proinflammatory and profibrotic genes and DKD.

Keywords: diabetic kidney disease; differentially expressed gene; weighted gene co-expression network analysis.