目的探索视网膜缺血再灌注损伤(RIRI)中潜在的免疫细胞相关生物标志物。
方法从基因表达综合数据库下载RIRI基因表达谱数据集GSE20521，筛选其差异表达基因(DEGs)。对GSE20521基因集进行GSEA富集分析和ImmuCellAI免疫细胞浸润分析，获得富集通路和免疫细胞浸润相关信息。采用WGCNA及Pearson相关分析筛选与免疫浸润相关程度最高的模块及候选基因。构建候选基因蛋白互作(PPI)网络，并基于CytoHubba插件筛选关键基因。
结果RIRI组GSEA显著富集通路包括γ干扰素(IFN-γ)信号通路、凋亡、肿瘤坏死因子α/核因子κB信号通路、IFN-α信号通路、补体途径、白细胞介素6-信号传导及转录激活蛋白3(IL-6-STAT3)、IL-2-STAT5信号通路及炎症反应等。ImmuCellAI评估结果显示，RIRI组cDC2细胞、单核细胞来源DC细胞、M2巨噬细胞及CD8_Tc细胞比例较正常对照组显著升高(均 P<0.05)；pDC细胞、CD4_T细胞、CD4_Tm细胞、辅助性T细胞、调节性T细胞、滤泡性B细胞、嗜酸性粒细胞比例较正常对照组显著降低(均 P<0.05)；在RIRI和正常视网膜样本中共筛选出144个DEGs；将DEGs与枢纽模块中基因取交集共获得140个候选基因；GO分析显示细胞因子的正向调节、白细胞介导的免疫反应、伤口愈合、适应性免疫反应、烟酰胺腺嘌呤二核苷酸磷酸氧化复合物、趋化因子结合等均显著富集。KEGG分析共富集50条途径，包括吞噬体、百日咳、利什曼病、肺结核及补体和凝血级联等。基于PPI网络及Cyto-Hubba不同算法进行基因筛选，最终获得3个关键基因，即 Cd68、 Tlr2和 Hmox1。
结论生物信息学分析结果显示RIRI组织和正常视网膜组织存在不同的免疫微环境，RIRI与多种免疫细胞浸润存在相关性。
ObjectiveTo investigate the potential biomarkers associated with immune cells in retinal ischemia-reperfusion injury (RIRI).
MethodsThe RIRI gene expression profile dataset GSE20521 was obtained from the Gene Expression Omnibus database, and the differentially expressed genes (DEGs) were screened.The GSE20521 gene set was subjected to Gene Set Enrichment Analysis (GSEA) and Immune Cell Abundance Identifier (ImmuCellAI), yielding information pertaining to enriched pathways and immune cell infiltration.The Weighted Correlation Network Analysis (WGCNA) and Pearson correlation analysis were employed to identify the hub modules and candidate genes exhibiting the strongest correlation with immune infiltration.Subsequently, the protein-protein interaction (PPI) network of candidate genes was constructed, and key genes were screened using CytoHubba plugin.
ResultsThe significant GSEA enrichment pathways in the RIRI group including the interferon-γ (IFN-γ), apoptosis, tumor necrosis factor-α/nuclear factor-κB, IFN-α, complement pathway, interleukin-6 (IL-6)-(signal transducer and activator of transcription 3)(STAT3) and IL2-STAT5 signaling pathways, as well as inflammatory response.Compared with the normal control group, the results of ImmuCellAI evaluation revealed significant increases in the proportions of cDC2 cells, monocyte-derived DC cells, M2 macrophages, and CD8_Tc cells and decreases in the proportions of pDC cells, CD4_T cells, CD4_Tm cells, helper T cells, regulatory T cells, follicular B cells, and eosinophils in the RIRI group (all at P<0.05).A total of 144 DEGs were obtained between the two groups of samples.Taking the intersection of DEGs and hub module genes, 140 candidate genes were obtained.GO analysis showed significant enrichment of positive regulation of cytokine production, leukocyte mediated immunity, wound healing, adaptive immune response, niacinamide adenine dinucleotide phosphate oxidase complex, and chemokine binding, etc.KEGG analysis enriched 50 pathways, including phagosome, pertussis, leishmaniasis tuberculosis, and complement and coagulation cascades.Three key genes were finally obtained, namely Cd68, Tlr2 and Hmox1, which were screened by PPI and different CytoHubba algorithms.
ConclusionsThe bioinformatics analysis reveals a distinct immune microenvironment in the retina of the RIRI group and normal control group, suggesting a correlation between RIRI and infiltration of multiple immune cell types.
王文婷,梁娜,哈文静,等. 免疫浸润在视网膜缺血再灌注损伤中作用的生物信息学分析[J]. 中华实验眼科杂志,2024,42(11)：997-1005.
DOI:10.3760/cma.j.cn115989-20231026-00152版权归中华医学会所有。
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除非特别声明，本刊刊出的所有文章不代表中华医学会和本刊编委会的观点。
王文婷：实施研究、分析数据、论文撰写；梁娜：分析解释数据；哈文静：分析数据、指导实验；彭绍民：指导研究、论文修改审阅
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