年龄相关性黄斑变性中特征基因的鉴定及其与免疫细胞浸润的关系。
The identification of signature genes and their relationship with immune cell infiltration in age-related macular degeneration.
机构信息
Department of Ophthalmology, The Tongnan District People's Hospital, Chongqing, China.
Department of Ophthalmology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
出版信息
Mol Biol Rep. 2024 Feb 23;51(1):339. doi: 10.1007/s11033-023-08969-2.
BACKGROUND
Age-related macular degeneration (AMD) is a prevalent source of visual impairment among the elderly population, and its incidence has risen in tandem with the increasing longevity of humans. Despite the progress made with anti-VEGF therapy, clinical outcomes have proven to be unsatisfactory.
METHOD
We obtained differentially expressed genes (DEGs) of AMD patients and healthy controls from the GEO database. GO and KEGG analyses were used to enrich the DEGs. Weighted gene coexpression network analysis (WGCNA) was used to identify modules related to AMD. SVM, random forest, and least absolute shrinkage and selection operator (LASSO) were employed to screen hub genes. Gene set enrichment analysis (GSEA) was used to explore the pathways in which these hub genes were enriched. CIBERSORT was utilized to analyze the relationship between the hub genes and immune cell infiltration. Finally, Western blotting and RT‒PCR were used to explore the expression of hub genes in AMD mice.
RESULTS
We screened 1084 DEGs in GSE29801, of which 496 genes were upregulated. These 1084 DEGs were introduced into the WGCNA, and 94 genes related to AMD were obtained. Seventy-nine overlapping genes were obtained by the Venn plot. These 79 genes were introduced into three machine-learning methods to screen the hub genes, and the genes identified by the three methods were TNC, FAP, SREBF1, and TGF-β2. We verified their diagnostic function in the GSE29801 and GSE103060 datasets. Then, the hub gene co-enrichment pathways were obtained by GO and KEGG analyses. CIBERSORT analysis showed that these hub genes were associated with immune cell infiltration. Finally, we found increased expression of TNC, FAP, SREBF1, and TGF-β2 mRNA and protein in the retinas of AMD mice.
CONCLUSION
We found that four hub genes, namely, FAP, TGF-β2, SREBF1, and TNC, have diagnostic significance in patients with AMD and are related to immune cell infiltration. Finally, we determined that the mRNA and protein expression of these hub genes was upregulated in the retinas of AMD mice.
背景
年龄相关性黄斑变性（AMD）是老年人视力障碍的一个常见原因，随着人类寿命的延长，其发病率也在上升。尽管抗血管内皮生长因子（VEGF）治疗取得了进展，但临床结果仍不尽如人意。
方法
我们从 GEO 数据库中获得 AMD 患者和健康对照的差异表达基因（DEGs）。GO 和 KEGG 分析用于富集 DEGs。加权基因共表达网络分析（WGCNA）用于识别与 AMD 相关的模块。SVM、随机森林和最小绝对收缩和选择算子（LASSO）用于筛选枢纽基因。基因集富集分析（GSEA）用于探索这些枢纽基因富集的途径。CIBERSORT 用于分析枢纽基因与免疫细胞浸润的关系。最后，Western 印迹和 RT-PCR 用于探索 AMD 小鼠中枢纽基因的表达。
结果
我们在 GSE29801 中筛选出 1084 个 DEG，其中 496 个基因上调。这些 1084 个 DEG 被引入 WGCNA，得到与 AMD 相关的 94 个基因。Venn 图获得 79 个重叠基因。这 79 个基因被引入三种机器学习方法筛选枢纽基因，三种方法鉴定的基因均为 TNC、FAP、SREBF1 和 TGF-β2。我们在 GSE29801 和 GSE103060 数据集验证了它们的诊断功能。然后，通过 GO 和 KEGG 分析获得枢纽基因的共富集途径。CIBERSORT 分析表明，这些枢纽基因与免疫细胞浸润有关。最后，我们发现 AMD 小鼠视网膜中 TNC、FAP、SREBF1 和 TGF-β2mRNA 和蛋白表达增加。
结论
我们发现 FAP、TGF-β2、SREBF1 和 TNC 这四个枢纽基因在 AMD 患者中有诊断意义，与免疫细胞浸润有关。最后，我们确定这些枢纽基因在 AMD 小鼠视网膜中的 mRNA 和蛋白表达上调。
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