Identification of marker genes in diabetic wounds by DNA microarray study

Abstract

ABSTRACT. This study aimed to identify marker genes in diabetic wounds using a dataset based on a DNA microarray of dermal lymphatic endothelial cells, and our results provide a basic understanding of diabetic wounds through further study of these differentially expressed genes (DEGs). From the Gene Expression Omnibus database, we downloaded a gene expression microarray (GSE38396) that includes 8 samples: 4 normal controls and 4 disease samples (type II diabetes). We then identified genes that were differentially expressed between normal and disease samples using packages in R language, constructed a proteinprotein interaction (PPI) network and analyzed modules in the network. In addition, phylogenetic analysis was performed by MEGA to find the most conserved genes. Two hundred and thirteen genes were identified as being differentially expressed between normal and disease samples, and we constructed a PPI network that included 213 pairs of proteins. We then identified a module including 20 genes, the function of which was Identification of marker genes in diabetic wounds significantly enriched in wounding response. Lastly, the most conserved genes, CD44 and CCL5, were identified through phylogenetic analysis. In summary, we found differentially expressed marker genes, a wounding response-related module, and the most important genes CD44 and CCL5. Our findings suggest new approaches to therapies for diabetic wounds.

[Retracted] MicroRNA‐133b Inhibition Restores EGFR Expression and Accelerates Diabetes‐Impaired Wound Healing

“…Studies have used microarrays to detect genetic contributors to diabetes-impaired wound healing. Consequently, several relevant genes such as CD44 , CCL5 , and IL-6 [ 21 , 22 ]—which play vital structural and functional roles in the regulation of diabetic wound progression—have been identified. Based on transcriptomic microarray data from DFUs and nondiabetic foot skin samples and subsequent DEG identification and GO and KEGG enrichment analyses, we identified EGFR as a potentially critical player in delayed wound healing in DFUs.…”

Identification of key genes involved in type 2 diabetic islet dysfunction: a bioinformatics study

“…Shao et al [13] identified that the glucocorticoid was central in the pathogenesis of type 2 diabetes from three GEO datasets by integrated method including DEGs screen, gene functional enrichment, PPI network analyses, drug–gene interactions and genetic association of DEGs. Ni et al [14] identified key genes in the diabetic wounds from one GEO dataset using a bioinformatics approach incorporating DEG screen, PPI network and phylogenetic analysis. Chen et al [15] used the gene expression profiles from GEO datasets and identified candidate genes for type 2 diabetes and obesity by screening of genes, GO and pathway analysis.…”

Overview of Transcriptomic Research on Type 2 Diabetes: Challenges and Perspectives

“…A better understanding of the gene expression changes’ role in diabetic complications might provide novel insights into the genome function mechanisms in T2D, making it possible to define the risk groups for a severe course of disease and to prevent its microvascular and macrovascular complications. The CD44 and CCL5 genes were found to be associated with wound healing in diabetic patients when analyzing the transcriptome of dermal lymphatic endothelial cells [ 79 ]. CCL5 is a chemokine that is a chemoattractant for inflammatory cells that release pro-angiogenic factors, stimulating wound vascularization [ 80 ].…”