过敏性鼻炎患者异常甲基化状态分析和关键基因/信号通路的确认

Identification of key genes and pathway involved in allergic rhinitis by DNA methylation analysis

目的通过搜集数据库,进行生物信息学(甲基化组学)分析,确定过敏性鼻炎患者与健康对照的差异甲基化基因(DMGs),进而探讨DMGs中关键基因及富集通路在过敏性鼻炎发病中可能的重要机制和作用。方法从GEO数据库中获取过敏性鼻炎患者和健康对照者的甲基化组学数据集(GSE100386,GSE50222),然后进行一系列生物信息学分析。首先利用R语言进行PCA分析,筛选差异甲基化位点DMCs及DMGs(阈值:Δβ=0.1,P<0.05)。利用STRING(10.0)进行蛋白互作分析,最后利用基因集富集分析(GSEA)对关键基因及其相关通路进行富集分析。结果经过PCA分析,GSE100386数据不显著被排除。GSE50222中花粉季外过敏性鼻炎患者和对照组相比共有2847个差异甲基化CpGs,对应1594个DMGs,花粉季中过敏性鼻炎患者和对照组相比共有950个差异甲基化CpGs,对应530个DMGs,Venn图显示其中重叠基因共458个。经过PPI分析得到STAT3、IL5、TP53、HDAC9、SMAD3等hub基因。GSEA分析发现关键DMGs所富集的Th17 cell differentiation、Notch signaling pathway、Focal adhesion、Th1 and Th2 cell differentiation等信号通路的显著富集。结论本研究所确认的关键基因/信号通路可能为过敏性鼻炎发病的DNA甲基化调控机制研究提供重要的线索。

OBJECTIVE To identify the key differentially methylation genes(DMGs) in allergic rhinitis(AR) patient and explore their potential pathway in the molecular mechanism of AR by bioinformatics research.METHODS Gene Expression Omnibus(GEO) datasets(GSE100386,GSE50222) of allergic rhinitis patients vs.healthy controls were obtained from GEO database.PCA analysis was performed by R.DMGs were screened under threshold of the mean difference in beta difference(Δ)≥±0.1 and P<0.05.Then we conducted protein protein interaction(PPI) analysis using STRING(10.0).Gene set enrichment analysis(GSEA) was applied to identify key genes and associated pathways.RESULTS After PCA analysis,only GSE50222 was meaningful for next analysis.Outside pollen season,there are 2847 differential methylation CpGs in AR patients compared with the control group,corresponding to 1594 DMGs.During pollen season,there are 950 differential methylation CpGsin AR patients compared with the control group,corresponding to 530 DMGs.Venn diagram showed there are 458 overlap genes.After PPI network analysis,STAT3,IL5,TP53,HDAC9,SMAD3 ect.were identified as hub genes.On the other hand,GSEA analysis found the DMGs are mostly involved in Th17 cell differentiation,Notch signaling pathway,Focal adhesion,Th1 and Th2 cell differentiation pathway and so on.CONCLUSION The key genes and the involved pathways identified by present bioinformatics analysis will provide the evidence of DNA methylation mechanism of AR.