Identification and validation of immune-related biomarkers and potential regulators and therapeutic targets for diabetic kidney disease

Abstract

Background: Diabetic kidney disease (DKD) is a major complication of diabetes and the leading cause of end-stage renal disease worldwide. Renal inflammation and infiltration of immune cells contribute to the development and progression of DKD. Thus, the aim of the present study was to identify and validate immune-related biomarkers and analyze potential regulators including transcription factors (TFs), microRNAs (miRNAs), and drugs for DKD.

Methods: Immune-related genes from the ImmPort database and glomeruli samples from GSE1009 and GSE30528 were used to identify differentially expressed immune-related genes (DEIRGs) of DKD. The expression level and clinical correlation analyses of DEIRGs were verified in the Nephroseq database. Murine podocytes were cultured to construct the high glucose-induced podocyte injury model. The reliability of the bioinformatics analysis was experimentally validated by RT-qPCR in podocytes. Networks among DEIRGs, regulators, and drugs were constructed to predict potential regulatory mechanisms for DKD.

Results: DKD-associated DEIRGs were identified. CCL19 and IL7R were significantly upregulated in the DKD group and negatively correlated with glomerular filtration rate (GFR). GHR, FGF1, FYN, VEGFA, F2R, TGFBR3, PTGDS, FGF9, and SEMA5A were significantly decreased in the DKD group and positively correlated with GFR. RT-qPCR showed that the relative mRNA expression levels of GHR, FGF1, FYN, TGFBR3, PTGDS, FGF9, and SEMA5A were significantly down-regulated in the high glucose-induced podocyte injury group. The enriched regulators for DEIRGs included 110 miRNAs and 8 TFs. The abnormal expression of DEIRGs could be regulated by 16 established drugs.

Conclusions: This study identified immune-related biomarkers, regulators, and drugs of DKD. The findings of the present study provide novel insights into immune-related diagnosis and treatment of DKD.

Keywords: Diabetic kidney disease; Experimental validation; Immune-related biomarkers; Therapeutic drugs; Transcription factors; microRNAs.

Fig. 1

DEIRGs associated with DKD. The blue circle represents the differentially expressed genes (DEGs) of GSE1009, the red circle represents the DEGs of GSE30528, and the green circle represents the immune-related genes. The red box indicates that genes are upregulated in diabetic kidney disease (DKD) group while green box represents downregulated differentially expressed immune-related genes (DEIRGs) in DKD. “Changed” represents the expression of genes changed in opposite direction between GSE1009 and GSE30528

Fig. 2

The expression levels of DEIRGs a CCL 19, b IL7R, c GHR, d FGF1, e FYN, f VEGFA, g F2R, h TGFBR3, i PTGDS, j FGF9, and k SEMA5A in DKD and NC glomerular tissues. DEIRGs, differentially expressed immune-related genes; NC, normal control; DKD, diabetic kidney disease, ****P < 0.0001; ***P < 0.001; **P < 0.01

Fig. 3

The correlation analysis between DEIRGs a CCL 19, b IL7R, c GHR, d FGF1, e FYN, f VEGFA, g F2R, h TGFBR3, i PTGDS, j FGF9, k SEMA5A and GFR. DEIRGs, differentially expressed immune-related genes; GFR glomerular filtration rate

Fig. 4

The relative mRNA expression levels of a CCL 19, b IL7R, c GHR, d FGF1, e FYN, f VEGFA, g F2R, h TGFBR3, i PTGDS, j FGF9, and k SEMA5A in the NC and HG group. NC, normal control; HG, high-glucose; ns: P > 0.05; *P < 0.05; **P < 0.01

Fig. 5

The predicted miRNAs-experimentally validated DEIRGs-TFs network. The red circles represent validated differentially expressed immune-related genes (DEIRGs). The yellow circles represent microRNAs (miRNAs). The black circles represent transcription factors (TFs)

Fig. 6

Drugs-DEIRGs interaction network. The green round rectangles represent downregulated differentially expressed immune-related genes (DEIRGs) in DKD. The blue ellipses represent targeted therapy drugs. The black arrows represent that the drugs could increase the expression of target genes