Identification of a novel immune landscape signature as effective diagnostic markers related to immune cell infiltration in diabetic nephropathy

Abstract

BackgroundThe study aimed to identify core biomarkers related to diagnosis and immune microenvironment regulation and explore the immune molecular mechanism of diabetic nephropathy (DN) through bioinformatics analysis.MethodsGSE30529, GSE99325, and GSE104954 were merged with removing batch effects, and different expression genes (DEGs) were screened at a criterion |log2FC| >0.5 and adjusted P <0.05. KEGG, GO, and GSEA analyses were performed. Hub genes were screened by conducting PPI networks and calculating node genes using five algorithms with CytoHubba, followed by LASSO and ROC analysis to accurately identify diagnostic biomarkers. In addition, two different GEO datasets, GSE175759 and GSE47184, and an experiment cohort with 30 controls and 40 DN patients detected by IHC, were used to validate the biomarkers. Moreover, ssGSEA was performed to analyze the immune microenvironment in DN. Wilcoxon test and LASSO regression were used to determine the core immune signatures. The correlation between biomarkers and crucial immune signatures was calculated by Spearman analysis. Finally, cMap was used to explore potential drugs treating renal tubule injury in DN patients.ResultsA total of 509 DEGs, including 338 upregulated and 171 downregulated genes, were screened out. “chemokine signaling pathway” and “cell adhesion molecules” were enriched in both GSEA and KEGG analysis. CCR2, CX3CR1, and SELP, especially for the combination model of the three genes, were identified as core biomarkers with high diagnostic capabilities with striking AUC, sensitivity, and specificity in both merged and validated datasets and IHC validation. Immune infiltration analysis showed a notable infiltration advantage for APC co-stimulation, CD8+ T cells, checkpoint, cytolytic activity, macrophages, MHC class I, and parainflammation in the DN group. In addition, the correlation analysis showed that CCR2, CX3CR1, and SELP were strongly and positively correlated with checkpoint, cytolytic activity, macrophages, MHC class I, and parainflammation in the DN group. Finally, dilazep was screened out as an underlying compound for DN analyzed by CMap.ConclusionsCCR2, CX3CR1, and SELP are underlying diagnostic biomarkers for DN, especially in their combination. APC co-stimulation, CD8+ T cells, checkpoint, cytolytic activity, macrophages, MHC class I, and parainflammation may participate in the occurrence and development of DN. At last, dilazep may be a promising drug for treating DN.

Bioinformatics led discovery of biomarkers related to immune infiltration in diabetes nephropathy

“…CX3CR1 is upregulated in diabetic kidneys, and in streptozotocin-induced mouse models of diabetes, CX3CR1 deficiency reduces extracellular matrix deposition, which in turn affects the expression of CCL2. [ 22 ] A and activation of Smad2/3 in the glomeruli of diabetic mice, thereby alleviating proteinuria and podocyte loss in diabetic kidneys. Studies have shown that the early stage of glomerular growth in diabetic rats is accompanied by an increase in the expression of proto-oncogenes c-fos and c-jun [ 23 ] ; Meanwhile, the peroxisome proliferator-activating receptor γ-activating compound thiazolidinedione prevents the activation of the high glucose-induced TGF-1 gene by interacting with the activated protein kinase Cc-Fos-TGF-1 promoter cascade in mesangial cells (MCs) [ 24 , 25 ] ; The study found that CXCL10 reduced collagen production by renal fibroblasts in response to high glucose and TGF-|A, suggesting that CXCL10 can inhibit downstream signaling of the TGF-|A receptor pathway.…”

Role of MCP-1 as an inflammatory biomarker in nephropathy

“…Activation of the MCP-1/CCR2 axis induces chemotaxis and activation of inflammatory cells and initiates a series of signaling cascades in renal fibrosis ( 25 ). It mediates and promotes renal fibrosis by recruiting monocytes and promotes the activation and transdifferentiation of macrophages ( 26 ). The rationale for targeting MCP-1/CCR2 to treat human related diseases is to use drugs to block MCP-1 or CCR2 and inhibit the activation and conduction of the MCP-1/CCR2 axis, thereby reducing inflammatory cells and proinflammatory cytokines.…”

The Role of Immune Cells in DKD: Mechanisms and Targeted Therapies

“…The significance of DGKH and POLR2B in DKD requires further validation. Handi Zhou et al 143 identified CCR2, CX3CR1, and SELP as potential diagnostic biomarkers for DKD, which were associated with checkpoints, cytolytic activity, macrophages, MHC class I molecules, and paraneoplastic inflammation.…”

“…The significance of DGKH and POLR2B in DKD requires further validation. Handi Zhou et al 143 Although bioinformatics analyses have yielded various results, small sample sizes and database limitations mean that the findings often require validation using basic experimental methods.…”