The unique molecular mechanism of diabetic nephropathy: a bioinformatics analysis of over 250 microarray datasets

Abstract

Background/Aims Diabetic nephropathy (DN) is one of the main causes of end-stage kidney disease worldwide. Emerging studies have suggested that its pathogenesis is distinct from nondiabetic renal diseases in many aspects. However, it still lacks a comprehensive understanding of the unique molecular mechanism of DN. Methods A total of 255 Affymetrix U133 microarray datasets (Affymetrix, Santa Calra, CA, USA) of human glomerular and tubulointerstitial tissues were collected. The 22 215 Affymetrix identifiers shared by the Human Genome U133 Plus 2.0 and U133A Array were extracted to facilitate dataset pooling. Next, a linear model was constructed and the empirical Bayes method was used to select the differentially expressed genes (DEGs) of each kidney disease. Based on these DEG sets, the unique DEGs of DN were identified and further analyzed using gene ontology and pathway enrichment analysis. Finally, the protein–protein interaction networks (PINs) were constructed and hub genes were selected to further refine the results. Results A total of 129 and 1251 unique DEGs were identified in the diabetic glomerulus (upregulated n = 83 and downregulated n = 203) and the diabetic tubulointerstitium (upregulated n = 399 and downregulated n = 874), respectively. Enrichment analysis revealed that the DEGs in the diabetic glomerulus were significantly associated with the extracellular matrix, cell growth, regulation of blood coagulation, cholesterol homeostasis, intrinsic apoptotic signaling pathway and renal filtration cell differentiation. In the diabetic tubulointerstitium, the significantly enriched biological processes and pathways included metabolism, the advanced glycation end products–receptor for advanced glycation end products signaling pathway in diabetic complications, the epidermal growth factor receptor (EGFR) signaling pathway, the FoxO signaling pathway, autophagy and ferroptosis. By constructing PINs, several nodes, such as AGR2, CSNK2A1, EGFR and HSPD1, were identified as hub genes, which might play key roles in regulating the development of DN. Conclusions Our study not only reveals the unique molecular mechanism of DN but also provides a valuable resource for biomarker and therapeutic target discovery. Some of our findings are promising and should be explored in future work.

Glutathione Peroxidase 4 Is a Predictor of Diabetic Kidney Disease Progression in Type 2 Diabetes Mellitus

“…A high glucose transport state in DKD exacerbates ROS production and results in oxidative stress [ 39 , 40 ]. Previous studies found that ROS played a central role in ferroptosis [ 41 , 42 ], and a microarray study found that the ferroptosis pathway was significantly enriched in the kidney tubulointerstitium of DKD patients [ 43 ]. GPX4 is the key regulator for ferroptosis and plays an antioxidant role in preventing lipid peroxidation.…”

Alterations in Protein Translation and Carboxylic Acid Catabolic Processes in Diabetic Kidney Disease

“…In our exploratory analysis, five genes in the carboxylic acid catabolism pathway were found to drive clustering in human subjects according to their DKD progression. This pathway has been previously identified as dysregulated in the tubulointerstitium of human diabetic kidneys [ 34 ]. In our study, increased expression of ACADVL, ACACB, and ACOX1 were associated with reduced progression in our carboxylic acid group 1.…”

Anti-Diabesity Middle Eastern Medicinal Plants and Their Action Mechanisms

“…Accumulative indication suggests that some herbal extracts with hypoglycemic properties may have beneficial effects on some processes associated with a decline in renal function, as well as reducing the severity of nephropathy in T2D experimental animals. Table 1 summarizes the most commonly used anti-nephropathy herbals [ 114 ]. Based on various experimental studies, traditional medicinal plants and their bioactive constituents control the cellular processes involved in the initiation of nephropathy owing to their significant pharmacological activities; however, their efficacy has not yet been explored in animal test models and in clinical studies.…”

“…e changes may result from the effects of excess glucose directly on kidney cells or indirectly through pathways that involve development of oxidants and advanced glycation end-products [109][110][111]. Chronic hyperglycemia accelerates the activation of the formation of advanced glycation end-products (AGEs), polyol pathway, and protein kinase C pathway [110][111][112][113][114].…”