基于生物信息学分析湿性年龄相关性黄斑变性的氧化应激相关基因及靶向防治中药筛选

目的 利用生物信息学方法筛选湿性年龄相关性黄斑变性（wet age-related macular degeneration,w AMD）的氧化应激相关差异表达基因及靶向中药，以期为wAMD的预防和治疗提供新思路。方法 从GEO数据库中筛选数据集，利用R软件limma包筛选差异基因，从Genecard数据库筛选氧化应激差异基因，并利用韦恩图得到共有基因。应用Metascape对氧化应激差异基因进行基因本体（gene ontology,GO）和京都基因与基因组百科全书（Kyoto encyclopedia of genes and genomes,KEGG）分析，并通过String数据库构建蛋白质相互作用（protein-protein interaction,PPI）网络，再通过Cytoscape软件筛选出wAMD中氧化应激的关键（Hub）基因。采用GSE103060数据集验证Hub基因的差异表达。利用Coremine Medical预测靶向中药。结果 经筛选共得到差异表达基因1 874个，其中上调基因747个，下调基因1 127个。KEGG富集分析表明，差异表达基因主要富集于细胞外基...

Analysis of oxidative stress-related genes in wAMD based on bioinformatics and screening of targeted traditional Chinese medicine for prevention and treatment

Objective Using bioinformatics methods to screen differential expression genes related to oxidative stress in wet age-related macular degeneration (wAMD) and to identify targeted traditional Chinese medicine strategies, in order to provide new insights into the prevention and treatment of wAMD. Methods Datasets were selected from the GEO database, and differential genes were screened using the limma package in R software. Differential oxidative stress genes were selected from the Genecard database, and common genes were obtained using a Venn diagram. Metascape was used for gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analysis of differential oxidative stress genes. A protein-protein interaction (PPI) network was constructed through the String database, and hub genes related to oxidative stress in wAMD were screened using Cytoscape software. The differential expression of hub genes was validated using the GSE103060 dataset. Coremine Medical was used to predict targeted traditional Chinese medicines. Results After screening, a total of 1 874 differentially expressed genes (DEGs) were identified, including 747 upregulated genes and 1 127 downregulated genes. KEGG enrichment analysis indicated that DEGs were mainly enriched in extracellular matrix-receptor interactions, focal adhesion kinase pathways, the Hippo signaling pathway, the advanced glycation end products- receptor for advanced glycation end products (AGE-RAGE) signaling pathway, calcium signaling pathways, and phosphatidylinositol-3-hydroxykinase/protein kinase B (PI3K/Akt) signaling pathways. Eight Hub genes closely related to oxidative stress in wAMD were selected through the PPI network: IL6, EGFR,HIF1A, APOE, FN1, PPARG, EDN1, and NGF. The significant differential expression of these Hub genes was validated in the GSE103060 dataset. Coremine Medical predicted that Renshen (Ginseng Radix et Rhizoma), Huangqi (Astragali Radix), Goqizi (Lycii Fructus), Danshen (Salviae Miltiorrhizae Radix et Rhizoma), Yinxingye (Ginkgo Folium), and other Chinese medicines could be used as targeted preventive or therapeutic measures for wAMD. Conclusion Through the exploration and bioinformatic analysis of wAMD chips, differential genes were mainly enriched in pathways related to oxidative stress and genes associated with oxidative stress in wAMD. Ginseng Radix et Rhizoma, Astragali Radix, Lycii Fructus, Salviae Miltiorrhizae Radix et Rhizoma,Ginkgo Folium and 26 other traditional Chinese medicines were identified as preferred options for preventing or treating oxidative stress in wAMD. It will be of great significance for understanding and exploring traditional Chinese medicine approaches to the prevention and treatment of wAMD.