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基于生物信息学分析鉴定糖尿病足溃疡相关基因。

Identification of autophagy-related genes in diabetic foot ulcer based on bioinformatic analysis.

机构信息

Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China.

School of Public Health, Southern Medical University, Guangzhou, China.

出版信息

Int Wound J. 2024 Mar;21(3):e14476. doi: 10.1111/iwj.14476. Epub 2023 Nov 1.

DOI:10.1111/iwj.14476
PMID:37909396
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10898398/
Abstract

Diabetic foot ulcer (DFU) complications involve autophagy dysregulation. This study aimed to identify autophagy-related bioindicators in DFU. Differentially expressed genes (DEGs) between DFU and healthy samples were analysed from the Gene Expression Omnibus (GEO) datasets, GSE7014 and GSE29221. The roles of autophagy-related DEGs were investigated using protein-protein interaction (PPI) networks, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, Gene Ontology (GO) enrichment, and Gene Set Enrichment Analysis (GSEA). Immune cell infiltration's correlation with these DEGs was also assessed. From the Human Autophagy Database (HADB), 232 autophagy-related genes (ARGs) were identified, with an intersection of 17 key DEGs between GSE7014 and GSE29221. These genes are involved in pathways like autophagy-animal, NOD-like receptor signalling, and apoptosis. In the protein network, epidermal growth factor receptor (EGFR) and phosphatase and tensin homologue (PTEN) showed significant interactions with ARGs. Survival analysis indicated the prognostic importance of calpain 2 (CAPN2), integrin subunit beta 1 (ITGB1), and vesicle-associated membrane protein 3 (VAMP3). Lower immune scores were observed in the type 2 diabetes mellitus (DM2) group than in controls. Autophagy and ARGs significantly influence DFU pathophysiology.

摘要

糖尿病足溃疡 (DFU) 并发症涉及自噬失调。本研究旨在鉴定 DFU 中的自噬相关生物标志物。从基因表达综合数据库 (GEO) 数据集 GSE7014 和 GSE29221 中分析 DFU 与健康样本之间的差异表达基因 (DEGs)。使用蛋白质-蛋白质相互作用 (PPI) 网络、京都基因与基因组百科全书 (KEGG) 途径、基因本体论 (GO) 富集和基因集富集分析 (GSEA) 研究自噬相关 DEGs 的作用。还评估了这些 DEGs 与免疫细胞浸润的相关性。从人类自噬数据库 (HADB) 中确定了 232 个自噬相关基因 (ARGs)，GSE7014 和 GSE29221 之间有 17 个关键 DEGs 重叠。这些基因参与自噬动物、NOD 样受体信号和细胞凋亡等途径。在蛋白质网络中，表皮生长因子受体 (EGFR) 和磷酸酶和张力蛋白同源物 (PTEN) 与 ARGs 显示出显著的相互作用。生存分析表明钙蛋白酶 2 (CAPN2)、整合素亚基β 1 (ITGB1) 和囊泡相关膜蛋白 3 (VAMP3) 的预后重要性。与对照组相比，2 型糖尿病 (DM2) 组的免疫评分较低。自噬和 ARGs 显著影响 DFU 病理生理学。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8386/10898398/a622affc61b9/IWJ-21-e14476-g004.jpg
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