Identification of Key Genes of Human Advanced Diabetic Nephropathy Independent of Proteinuria by Transcriptome Analysis

Abstract

Background Diabetic nephropathy (DN) is the leading cause of ESRD. Emerging evidence indicated that proteinuria may not be the determinant of renal survival in DN. The aim of the current study was to provide molecular signatures apart from proteinuria in DN by an integrative bioinformatics approach. Method Affymetrix microarray datasets from microdissected glomerular and tubulointerstitial compartments of DN, healthy controls, and proteinuric disease controls including minimal change disease and membranous nephropathy were extracted from open-access database. Differentially expressed genes (DEGs) in DN versus both healthy and proteinuric controls were identified by limma package, and further defined by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Hub genes were checked by protein-protein interaction networks. Results A total of 566 glomerular and 581 tubulointerstitial DEGs were identified in DN, which were commonly differentially expressed compared to normal controls and proteinuric disease controls. The upregulated DEGs in both compartments were significantly enriched in GO biological process associated with fibrosis, inflammation, and platelet dysfunction, and largely located in extracellular space, including matrix and extracellular vesicles. Pathway analysis highlighted immune system regulation. Hub genes of the upregulated DEGs negatively correlated with estimated glomerular filtration rate (eGFR). While the downregulated DEGs and their hub genes in tubulointerstitium were enriched in pathways associated with lipid metabolism and oxidation, which positively correlated with eGFR. Conclusions Our study identified pathways including fibrosis, inflammation, lipid metabolism, and oxidative stress contributing to the progression of DN independent of proteinuria. These genes may serve as biomarkers and therapeutic targets.