生物信息学方法鉴定角膜炎中铁死亡相关的枢纽基因和通路。
Identification of hub genes and pathways of ferroptosis in keratitis by bioinformatics methods.
机构信息
Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China.
The Sixth Affiliated Hospital of Jinan University, Jinan University, Dongguan, China.
出版信息
Front Cell Infect Microbiol. 2023 Jan 31;13:1103471. doi: 10.3389/fcimb.2023.1103471. eCollection 2023.
BACKGROUND
Fungal keratitis is a common blinding eye disease, and Fusarium is one of the main species that cause fungal keratitis. As is well known, oxidative stress plays an important role in Fusarium keratitis and it is also a significant initiating factor of ferroptosis. But the relationship between Fusarium keratitis and ferroptosis is currently unclear. This study aimed to speculate and validate potential ferroptosis-related genes in Fusarium keratitis using bioinformatics analysis, which provided ideas for further research on its specific mechanism and new targets for its treatment.
METHODS
The microarray expression profiling dataset (GSE58291) came from Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) were obtained by the limma package of the R software. The DEGs were performed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Then, the DEGs were intersected with the genes in the ferroptosis database. The top 5 hub genes were obtained by the protein-protein interaction (PPI) network analysis and the cytoHubba plug-in of Cytoscape software. The hub genes were subjected to GSEA analysis. Then we analyzed the immune infiltration of the samples by CIBERSORT and ssGSEA algorithm. Finally, we validated the mRNA of hub genes by qPCR.
RESULTS
A total of 1,368 DEGs were identified and 26 ferroptosis-related DEGs were obtained. At the same time, ferroptosis-related pathways were enriched by GO and KEGG using DEGs. HMOX1, CYBB, GPX2, ALOX5 and SRC were obtained by the PPI network analysis and the cytoHubba plug-in of Cytoscape software. The iron metabolism and immune response related pathways were enriched using GSEA. They included hematopoietic cell lineage, lysosome and FC gamma R mediated phagocytosis. T cells follicular helper, monocytes, macrophages and mast cells might play an important role in Fusarium keratitis using analysis of immune infiltration. Finally, qPCR confirmed that the expression of HMOX1, CYBB, ALOX5 mRNA in the DON group was significantly elevated, while the expression of GPX2 were significantly decreased.
CONCLUSIONS
Ferroptosis may play an important role in Fusarium keratitis. HMOX1, CYBB, ALOX5 and GPX2 may be key ferroptosis-related genes in the pathogenesis of Fusarium keratitis.
背景
真菌性角膜炎是一种常见的致盲眼病，其中镰刀菌是引起真菌性角膜炎的主要菌种之一。众所周知，氧化应激在镰刀菌角膜炎中起着重要作用，也是铁死亡的重要启动因素。但是，镰刀菌角膜炎与铁死亡之间的关系目前尚不清楚。本研究旨在通过生物信息学分析推测和验证镰刀菌角膜炎中的潜在铁死亡相关基因，为进一步研究其具体机制和治疗新靶点提供思路。
方法
从基因表达综合数据库（GEO）中获取微阵列表达谱数据集（GSE58291）。使用 R 软件中的 limma 包获取差异表达基因（DEGs）。对 DEGs 进行基因本体论（GO）和京都基因与基因组百科全书（KEGG）富集分析。然后，将 DEGs 与铁死亡数据库中的基因进行交集。使用 Cytoscape 软件中的蛋白质-蛋白质相互作用（PPI）网络分析和 cytoHubba 插件获得前 5 个枢纽基因。对枢纽基因进行 GSEA 分析。然后，我们使用 CIBERSORT 和 ssGSEA 算法分析样本的免疫浸润情况。最后，通过 qPCR 验证枢纽基因的 mRNA。
结果
共鉴定出 1368 个 DEGs，获得了 26 个铁死亡相关的 DEGs。同时，GO 和 KEGG 通路富集分析发现 DEGs 与铁死亡相关。通过 PPI 网络分析和 Cytoscape 软件中的 cytoHubba 插件获得 HMOX1、CYBB、GPX2、ALOX5 和 SRC。GSEA 分析发现铁代谢和免疫反应相关通路富集，包括造血细胞谱系、溶酶体和 FCγR 介导的吞噬作用。通过免疫浸润分析发现 T 细胞滤泡辅助、单核细胞、巨噬细胞和肥大细胞可能在镰刀菌角膜炎中发挥重要作用。最后，qPCR 证实 DON 组 HMOX1、CYBB、ALOX5mRNA 的表达显著升高，而 GPX2 的表达显著降低。
结论
铁死亡可能在镰刀菌角膜炎中发挥重要作用。HMOX1、CYBB、ALOX5 和 GPX2 可能是镰刀菌角膜炎发病机制中的关键铁死亡相关基因。
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