女性类风湿关节炎DNA甲基化特征

DNA methylome signature in female patients with rheumatoid arthritis

目的应用基因芯片技术对类风湿关节炎(RA)DNA甲基化特征进行研究,探讨DNA甲基化在RA发病机制中的作用。方法随机选取本院门诊确诊为RA的12例女性患者作为RA组,体检的12名健康女性作为对照组,采用Infinium公司的基因芯片对两组受试者进行全基因组CpG岛DNA甲基化检测,筛选差异甲基化位点,采用Gene Ontology(GO)分析和Pathway分析对筛选基因进行功能分类和通路分析。结果RA组与对照组相比,共有24183个CpG位点甲基化水平发生改变(P<0.05),其中有13672个高甲基化位点,10511个低甲基化位点。RA组显著差异甲基化位点共191个,共对应着115个基因,其中高甲基化基因如IL-26、PCSK6、MICB、NCF4、GALNT9、PHF19、ADAMTS4、ACTN1等,低甲基化基因如CYP2E1、SMAD3、SLC1A1、CD44、AGPAT1、KCNQ1、AHRR等。GO生物学过程分析显示,差异甲基化基因参与生物学过程富集于:细胞因子介导的信号通路、炎症反应、核转录因子-κB(NF-κB)信号通路、免疫反应调节、T细胞活化、透明质酸的代谢等;Pathway分析显示,RA组特异的差异甲基化基因与沙门菌感染、Toll样受体信号通路、炎性肠病、NF-κB信号通路、TRP通道的炎性介质调节、趋化因子信号通路、TNF信号通路、破骨细胞分化、系统性红斑狼疮等信号通路有关。结论DNA异常甲基化可能参与了RA的发生发展,异常甲基化的基因可能成为RA评估发病、疾病进展和疾病严重程度的生物标记物或预测因子,也有望成为RA治疗的潜在靶点。

Objective To explore the role of DNA methylation in the pathogenesis of rheumatoid arthritis(RA)by gene chip technology.Methods 12 female patients with RA diagnosed in our outpatient department were randomly selected as the RA group,and 12 healthy women were selected in the same hospital as the normal control group.Using gene chip of infinium,we measured the whole blood of all subjects for detecting DNA methylation and screening the aberrant methylation sites of DNA.We also analyzed the function of abnormal methylation genes by using Gene Ontology(GO)analysis and Pathway analysis.ResultsThere were 24183 significantly differential methylated sites in RA than normal control groups,where 13672 were high methylation sites,10511 low methylation sites.There were 191 significantly different methylation sites in RA,corresponding to 115 genes.Among them,hypermethylated genes included IL-26,PCSK6,MICE,NCF4,GALNT9,PHF19,ADAMTS4,ACTN1,etc.,hypomethylated included CYP2E1,SMAD3,SLC1A1,CD44,AGPAT1,KCNQ1,AHRR,etc.GO biological process analysis showed that aberrant methylation genes mainly involved in cytokine mediated signaling pathway,inflammatory response,nuclear factor kappa B signaling pathway,immune response regulation,T cell activation,hyaluronic acid metabolism,and so on.Pathway analysis demonstrated that aberrant methylation genes played a part in Salmonella infection,toll like receptor signaling pathway,inflammatory bowel disease,NF-κB signaling pathway,inflammatory mediators regulation of TRP pathway,chemokine signaling pathway,TNF signaling pathway,osteoclast differentiation,systemic lupus erythematosus,and so forth.Conclusions Abnormal DNA methylation may be involved in the occurrence and development of RA.Methylation signatures specific to RA clinical outcomes may be utilized as biomarkers or predictors of exposure,disease progression,and disease severity,as well as potential therapeutic targets for RA.