Bioinformatics analysis of differentially expressed genes in diabetic foot ulcer and preliminary experimental verification

Abstract

Background Molecular changes are closely related to the pathogenesis and healing process of diabetic foot ulcers (DFUs), and are crucial for the early prediction and intervention of DFU. Methods Bioinformatics analysis was performed in this study to identify the key differentially expressed genes (DEGs) in DFU, analyze their functions and function modes, and conduct preliminary experimental verification to determine the potential pivotal genes in the pathogenesis of DFU. Two datasets, GSE68183 and GSE80178, were obtained from the Gene Expression Omnibus (GEO). DEGs were obtained using GEO2R. Six co-expressed DEGs (co-DEGs) were obtained by R language analysis. The co-DEGs were constructed by using STRING and Cytoscape 3.7.2 to construct a protein-protein interaction (PPI) network, and two hub genes, NHLRC3 and BNIP3 , were identified. The BNIP3 gene was selected for further analysis. Co-DEGs were used for Gene Ontology (GO) function analysis using the WebGestalt database, and BNIP3 -related biological processes focused on mitochondrial protein decomposition. GO function analysis of the BNIP3 gene and its interacting genes was carried out using the cluster profile package and org.hs.eg. db package of the R language and its biological process was enriched in the cell response to external stimuli and autophagy. Results BNIP3 and its interacting genes were retrieved from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and KEGG pathway enrichment analysis was performed using the WebGestalt database. The results showed that BNIP3 was significantly correlated with mitochondrial autophagy and the FoxO signaling pathway. The miRDB and TargetScan databases were used to identify the relevant microRNAs (miRNAs) regulating the BNIP3 gene, and it was found that miRNA-182 may be involved in the targeted regulation of BNIP3. Western blot analysis was performed to determine the abnormal expression of BNIP3 . Conclusions Our study found that the BNIP3 gene may be a new biomarker and intervention target for DFU.

The role of programmed cell death in diabetic foot ulcers

“…The lncRNA taurine upregulated gene 1 (TUG1) restores EPC function in response to high glucose treatment by regulating miR‐29c‐3p/PDGF‐BB/Wnt signalling, the overexpression of TUG1 significantly increases the expression of the autophagy‐related protein LC3, the autophagy inhibitor CQ attenuates this effect, and the effect of TUG1 on EPCs is at least partially mediated by the autophagy pathway 71 . Bioinformatics analysis identified BNIP3 as a differentially expressed gene in DFU based on the GEO microarray public database, and showed that the BNIP3 gene was highly expressed in DFU and that its expression in HG‐induced HUVECs was significantly upregulated, which indicated that the BNIP3 gene may be a target for the treatment of diabetic foot ulcers 72 . Autophagy as a widely studied programmed cell death, its role in DFUs still needs further study.…”

“… 71 Bioinformatics analysis identified BNIP3 as a differentially expressed gene in DFU based on the GEO microarray public database, and showed that the BNIP3 gene was highly expressed in DFU and that its expression in HG‐induced HUVECs was significantly upregulated, which indicated that the BNIP3 gene may be a target for the treatment of diabetic foot ulcers. 72 Autophagy as a widely studied programmed cell death, its role in DFUs still needs further study.…”

Multi-target mechanism of polyherbal extract to treat diabetic foot ulcer based on network pharmacology and molecular docking

“…Wound healing is frequently mediated by growth factors and cytokines generated by cells stimulated through immune response (9). Long-term high glucose levels cause aberrant expression of several molecules, including vascular endothelial growth factor (VEGF), hypoxia-inducible factor 1 (HIF1), and anti-inflammatory factors (10).…”

“…Long-term high glucose levels cause aberrant expression of several molecules, including vascular endothelial growth factor (VEGF), hypoxia-inducible factor 1 (HIF1), and anti-inflammatory factors (10). This leads to bad angiogenesis and prolonged inflammation (9). Although there are numerous diabetic wound therapies available, only a few can improve oxygen delivery at the microvascular level (8).…”

Identifying and Validating GSTM5 as an Immunogenic Gene in Diabetic Foot Ulcer Using Bioinformatics and Machine Learning

“…This process is typically facilitated by growth factors and cytokines released by specialized cells that become activated as part of the immune response. 9 Sawaya et al observed that in cases of DFU, the transcription factors FOMI1 and STAT3, which support the survival of immune cells, are suppressed. This ultimately hinders the process of wound healing in diabetic patients.…”