基于生物信息学分析免疫紊乱在类风湿关节炎发病机制中的作用

Role of immune disordeRin pathogenesis of rheumatoid arthritis:a bioinformatics analysis

目的探讨免疫紊乱在类风湿关节炎(RA)发病机制中的作用。方法在GEO数据库下载3个人类RA滑膜组织基因芯片数据。使用limma包筛选RA相关差异表达基因后,进行通路和功能富集分析,并通过权重基因共表达网络分析(WGCNA)法筛选关键模块。筛选RA差异表达基因中与免疫相关的差异表达基因及关键基因,针对3个RA数据集进行免疫细胞浸润分析,再采用Pearson相关分析关键基因与免疫细胞的相关性;在GEO数据库下载RA小鼠外周血单细胞测序数据,以验证关键基因在免疫细胞中的表达。结果共筛选差异表达基因632个,其中上调的差异表达基因369个,下调的差异表达基因263个。WGCNA分析共获得4个模块,其中绿松石模块包含基因最多,同时与蓝色和棕色模块有较高的相关性,基因显著富集在趋化因子信号通路、细胞因子与细胞因子受体的相互作用、原发性免疫缺陷、T细胞受体信号传导途径、RA等通路。RA滑膜组织中细胞毒性T细胞、1型调节性T细胞、B淋巴细胞、CD8+T淋巴细胞、中央记忆型T细胞浸润比例增多;共筛选到234个免疫相关的差异表达基因,前5个最关键的B淋巴细胞免疫相关基因为CR2、PAX5、CCL19、UBASH3A、TRAT1,表达量均与B淋巴细胞矩阵呈正相关(均P<0.05)。验证结果显示,RA组和正常组B淋巴细胞中CR2、PAX5、UBASH3A基因的表达量差异有统计学意义(均P<0.05)。结论免疫紊乱与RA发病机制密切相关,B淋巴细胞、CD8+T淋巴细胞以及CR2、PAX5、UBASH3A基因可能在RA的发生中发挥了关键作用。

Objective To explore the role of immune disordeRin the pathogenesis of rheumatoid arthritis(RA).Methods Three microarray data sets of human RA synovial tissues were downloaded from the GEO database.AfteRscreening foRRA-related differentially expressed genes(DEGs)by limma package,pathway and function enrichment analysis was conducted,and weighted gene co-expression network analysis(WGCNA)was used to screen the key module.The immune-related DEGs and key genes were screened among the RA-related DEGs,and immune cell infiltration assay was performed on the three RA data sets,then Pearson correlation analysis was applied to the correlation between key genes and immune cells;the peripheral blood single cell sequencing data of RA mice were downloaded from the GEO database to verify the expression of key genes in immune cells.Results Totally 632 DEGs were identified,including 369 up-regulated DEGs and 263 down-regulated DEGs.According to WGCNA analysis,fouRmodules were obtained,among which Turquoise module possessed maximum genes and highly correlated with blue module and brown module,and the genes were Turquoise module enriched in chemokine signaling pathway,interaction between cytokine and cytokine receptor,primary immune deficiency,T cell receptoRsignaling pathway,RA and otheRpathways.The infiltration proportions of cytotoxic T cells,type 1 regulatory T cells,B lymphocytes,CD8+T lymphocytes and central memory T cells were increased in RA synovial tissues;a total of 234 immune-related DEGs were screened,and the top five most important genes related to B lymphocyte immune included CR2,PAX5,CCL19,UBASH3A and TRAT1,and the expression of the genes positively correlated with B lymphocyte array(all P<0.05).The verification results showed that there were statistically significant differences in the expression of CR2,PAX5 and UBASH3A genes in B lymphocytes between the RA group and the normal group(all P<0.05).Conclusion Immune disordeRis closely related to the pathogenesis of RA,B lymphocyte,CD8+T lymphocyte,as well as CR2,PAX5 and UBASH3A genes may play a pivotal role in the occurrence of RA.