Bioinformatics Analysis Of Differentially Expressed Genes In Diabetic Foot Ulcers And Preliminary Experimental Verification

Objective:The bioinformatics analysis method was used to find the key differentially expressed genes in DFU,analyze their functions and function modes,and conduct preliminary experimental verification.Methods:1.Obtain two data sets about DFU from the GEO database,use GEO2 R to obtain differentially expressed genes(Padj < 0.05),and draw a Venn Diagram using R language(FC.cutoff <-1.2,GSE80178 data set Padj < 0.05,GSE68183 data set,P < 0.05),and co-expressed differentially expressed genes were obtained.2.GO functional enrichment analysis was performed for co-expressed differentially expressed genes through the Web Gestalt database(P < 0.05).3.The co-expressed differentially expressed genes were imported into STRING to construct a protein interaction network(set interaction score ≥ 0.9).The data were exported through STRING,analyzed by Cytoscape software,and the Top10 Hub genes were searched by cyto Hubba plug-in.4.GO function analysis and visualization of BNIP3 gene and its related Hub genes were performed from BP,MF,and CC levels using cluster profile package and org.hs.eg.db package of R language(Padj < 0.05).5.KEGG enrichment analysis of the BNIP3 gene and its related Hub gene was performed through Web Gestalt(P < 0.05);the KEGG database was used to search for BNIP3-related signaling pathways.mi RDB was used to search for related mi RNAs regulating the BNIP3 gene(Target Score≥90).BNIP3-related mi RNAs were searched using Target Scan.6.WB was used to detect the relative expression of BNIP3 protein in HUVEC cells treated with different concentrations of HG for 24 h and 72h(P < 0.05 was statistically significant).Results:1.Two data sets of GSE68183 and GSE80178 were obtained from GEO,and 6differentially expressed genes were obtained by analysis.Through GO function analysis and PPI network analysis,two key genes of NHLRC3 and BNIP3 were obtained.BNIP3 gene was selected for further analysis.2.GO enrichment analysis was performed on 6 co-DEGs,and BP associated with BNIP3 included mitochondrial protein catabolism,negative regulation of mitochondrial fusion and mitochondrial membrane permeability,and granzyme-mediated apoptotic signaling pathway,intrinsic apoptotic signaling pathway of hypoxia reaction,etc.BNIP3-related CC was mainly in the mitochondrial membrane.GO function analysis of BNIP3 and its interacting genes showed that CC level was significantly enriched in the autophagosome membrane,the autophagosome,and vacuolar membrane.At the MF level,the ubiquitin-binding protein ligase and ubiquitin-like protein ligase were significantly enriched.BP level was significantly enriched in the response of cells to external stimuli,autophagy,and the utilization of the autophagy mechanism.3.KEGG enrichment analysis showed that BNIP3 was significantly correlated with autophagy,mitochondrial autophagy,and Fox O signaling pathway.mi RNA-182 may be involved in the targeted regulation of BNIP3.4.The expression level of BNIP3 protein in HUVEC cells increased significantly with the increase of glucose concentration and the extension of intervention time.Conclusion:1.BNIP3 gene was highly expressed in DFU;The protein expression level of BNIP3 in HG-treated HUVEC cells increased with the increase of glucose concentration and intervention time.2.BNIP3 is mainly involved in autophagy and mitochondrial autophagy.3.BNIP3 is regulated by Fox O signaling pathway,and mi RNA-182 may be involved in the targeted regulation of BNIP3.