基于加权基因共表达网络分析探讨新型冠状病毒肺炎患者女性和男性的免疫机制差异  

Analysis and exploration on different immunopathological mechanisms for COVID-19 female and male patients based on weighted gene co-expression network

作　　者：窦雪 张维[1] 任心怡 何杰[1] Dou Xue;Zhang Wei;Ren Xinyi;He Jie(Department of Pulmonary and Critical Care Medicine,the First Affiliated Hospital of Chengdu Medical College,Chengdu 610500,China)

机构地区：[1]成都医学院第一附属医院呼吸与危重症医学科,成都610500

出　　处：《国际呼吸杂志》2022年第17期1314-1324,共11页International Journal of Respiration

基　　金：四川省医学科研课题计划基金项目(S21054)。

摘　　要：目的通过生物信息学方法筛选出患新型冠状病毒肺炎(COVID-19)的女性和男性的差异基因,寻找COVID-19男女患者间的免疫机制的不同。方法从GEO数据库下载3个COVID-19数据集(GSE152641、GSE157103、GSE157789),在GSE152641中,运用R软件进行差异基因分析和加权基因共表达网络分析,将上述所得的基因进行功能富集分析、蛋白质相互作用网络分析以及免疫细胞浸润分析,并使用cytoscape软件进行数据可视化,用cytohubba工具筛选出核心基因LCK,用皮尔森相关性分析分别分析在男性和女性患者中LCK与22种免疫细胞的关系,在GSE157103数据集中验证LCK的表达及男女患者间免疫细胞浸润的差异。应用统一流形逼近与投影算法对GSE157789数据集中的单细胞测序数据降维,分析LCK在男女患者全血中调节性T细胞的差异表达。结果在GSE152641数据集中共筛选出差异基因27个,加权基因共表达网络分析关键模块基因382个,两者的基因富集于淋巴细胞激活的调节、T细胞激活、淋巴细胞分化等生物学过程和功能中。同时这些基因在原发性免疫缺陷、细胞因子与细胞因子相互作用以及病毒蛋白与细胞因子受体相互作用等通路均有富集。免疫细胞浸润分析提示与男性患者相比,女性患者的未活化CD4^(+)记忆T细胞占比更高(P=0.003),而巨噬细胞M0型和中性粒细胞占比更低(P值均<0.05);cytohubba工具筛选出核心基因为LCK,在女性患者中为低表达;在男性和女性患者中,核心基因LCK的表达量与中性粒细胞占比均呈正相关关系(cor=0.50,P=0.01;cor=0.77,P=0.005)。在GSE157103验证集中,女性患者全血LCK的表达也低于男性患者(P<0.05),且女性患者的中性粒细胞占比也低于男性(P=0.025)。GSE157789数据集中LCK主要在调节性T细胞中表达,女性患者调节性T细胞中的LCK相对表达量低于男性患者(t=32.83,P<0.001)。结论女性与男性COVID-19患者的免疫机制具有性Objective To screen out the differential genes between female and male with COVID-19 by means of bioinformatics method,and to investigate difference in the immune mechanisms between them.Methods Three COVID-19 datasets(GSE152641,GSE157103,and GSE157789)were downloaded from the GEO database.R software was used for differential gene analysis and weighted gene co-expression network analysis in GSE152641,and the above-obtained genes were analyzed for functional enrichment analysis,protein interaction network analysis,and immune cell infiltration analysis.Cytoscape software was applied for data visualization,and cytohubba tool was applied to screen out the hub gene LCK.Pearson correlation analysis was applied to analyze the relationship between LCK and 22 sorts of immune cells in male and female patients.The expression of LCK and the difference in immune cell infiltration between male and female patients were verified in the GSE157103 dataset.The Unified Manifold Approximation and Projection Algorithm(UMAP)was applied to reduce the dimension of single-cell sequencing data in the GSE157789 dataset,and the differential expressions of LCK regulatory T cells in the whole blood of male and female patients were analyzed.Results A total of 27 differential genes and 382 genes of WGCNA were acquired from the GSE152641 dataset,and such two types of genes were found to be enriched in the regulation of lymphocyte activation and T cell activation,lymphocyte differentiation,etc.Moreover,these genes were found to be enriched in primary immune deficiency,cytokine-cytokine interaction and viral protein-cytokine receptor interaction.Immune cell infiltration analysis showed that female patients had a higher proportion of T cells CD4^(+) memory resting(P=0.003),while their proportion of macrophages M0 and neutrophils was lower(all P value<0.05).LCK,the core gene screened by the tool cytohubba,was lowly expressed in female patients.The expression of the core gene LCK in male and female patients was positively correlated with the proportio

关 键 词：新型冠状病毒肺炎 生物信息学分析 免疫细胞 性别特异性 

分 类 号：R563.1[医药卫生—呼吸系统] Q811.4[医药卫生—内科学]