基于GEO数据库对类风湿关节炎差异表达基因的分析、验证及治疗中药预测

Analysis and Verification of Differentially Expressed Genes of RA Based on GEO Database and Predicted Chinese Medicinal for RA Treatment

目的:通过生物信息学方法获得类风湿关节炎(RA)的差异基因及所涉及途径,匹配预测治疗RA的潜在中药。方法:从GEO数据库下载类风湿性关节炎的基因芯片数据,确定RA样本中的差异基因、蛋白互作网络,并应用CytoHubba插件鉴定关键基因。对关键基因的GO功能和KEGG通路进行分析,阐明关键基因的生物学过程。同时采用RT-qPCR法检测CIA小鼠的脾脏差异基因表达情况对前面分析的结果进行验证。最后利用Coremine Medical数据库预测对关键基因具有显著调控作用的中药。结果:从GEO数据库获得类风湿性关节炎差异表达基因760个,GO和KEGG对其进行分析后获得CD4、CD86、TNF、CD80等核心基因20个。富集分析结果显示,白细胞活化、细胞因子介导、白细胞-细胞黏附、细胞因子活性及细胞黏附等通路对RA的发病至关重要。RT-qPCR实验结果证明,与Control组相比,CIA组小鼠脾脏的CD4、CD80、CD86表达程度升高,TNF-α表达程度降低,CD80表达变化最明显。采用COREMINE预测关键基因和通路,结果显示川牛膝、黄芪、灵芝、车前草、车前子和南星等可能针对CD4、CD86、TNF、CD80靶向治疗RA。结论:本研究明确了类风湿性关节炎的核心基因及基因所富集的通路,探讨了RA主要涉及的生物学过程,并用CIA小鼠验证了核心差异基因,为RA治疗的新靶点选择提供了支撑,预测了针对核心基因的靶向治疗中药,为治疗RA的靶向中药研究提供了依据。

Objective:To obtain the differential genes and related pathways of rheumatoid arthritis(RA)by bioinformatics method,and to match and predict the potential Chinese medicinal for RA treatment.Methods:Genomic microarray data of RA were downloaded from the GEO database to determine the differential genes and the protein interaction network,and CytoHubba plugin was used for the identification of the key genes.The GO function and the KEGG pathway of the key genes were analyzed to elucidate the biological processes of them.RT-qPCR was used to detect the expressions of differential genes in spleen of CIA mice to verify the results of previous analysis.Finally,the Coremine Medical database was applied to predict potential Chinese medicinal with significant regulation effect on the key genes.Results:760 differential genes of RA were obtained from GEO database,and 20 core genes,including CD4,CD86,TNF and CD80,were obtained after GO analysis and KEGG pathway analysis.The results of enrichment analysis of these genes showed that the pathways of leukocyte activation,cytokine mediation,leukocyte-cell adhesion,cytokine activity and cell adhesion were crucial to the pathogenesis of RA.The RT-qPCR results showed that compared with those in the Control group,the expressions of CD4,CD80 and CD86 in spleen of CIA mice were increased,whereas the expression of TNF-αwas decreased,and the change of CD80 expression was the most obvious.COREMINE predicted the key genes and the pathways,and the results showed that Cyathulae Radix,Astmgali Radix,Ganoderma lucidum,Plantaginis Herb,Semen Plantaginis and Arisaematis Rhizoma might target CD4,CD86,TNF and CD80 in treatment of RA.Conclusion:This study identified the core genes of RA and the pathways in which genes were enriched,it discussed the biological processes involved in RA,verified the core differential genes with CIA mice,provided evidence for new targets for RA treatment,predicted the targeted Chinese medicinal for the core genes,and provided an evidence for the research of targeted Chinese medicinal in treatment of RA.