类风湿关节炎外周血单核细胞circRNA-miRNA-mRNA网络构建及关键基因预测

Construction of circrRNA-miRNA-mRNA Network of Peripheral Blood Monocytes in Rheumatoid Arthritis and Prediction of Key Genes

目的探索类风湿关节炎(RA)外周血单核细胞中环状RNA(circRNA)-微小RNA(miRNA)-信使RNA(mRNA)网络及关键基因。方法在基因表达数据库GEO中获取相关数据集GSE189338、GSE124373、GSE55457,通过R语言Limma包、edgeR包对circRNA、miRNA及mRNA进行差异表达分析,根据ceRNA网络关联数据通过Cytoscape3.8.0软件构建circRNA-miRNA-mRNA网络;通过R语言pheatmap包、reshape2包、ggpubr包对ceRNA网络节点进行热图和箱线图分析,并对差异表达的mRNA进行GO富集和KEGG通路分析。结果筛选出58个差异表达circRNA、35个差异表达miRNA及150个差异表达mRNA;根据ceRNA网络关联数据并运用Cytoscape 3.7.1软件,最终筛选出10个circRNA、8个miRNA和38个mRNA构建circRNA-miRNA-mRNA可视化网络;通过对ceRNA网络节点进行箱线图分析,在RA中发现高表达circRNA5个,低表达circRNA4个,高表达miRNA4个,低表达miRNA4个,高表达mRNA17个,低表达mRNA7个;GO分析共得到条目289个,其中生物学过程(BP)主要富集于B细胞活化、分化及增殖、淋巴细胞分化等252个条目中,细胞定位(CC)主要富集在质膜外侧、RNA聚合酶Ⅱ转录抑制物复合体等5个条目中,分子功能(MF)主要富集在纤连蛋白结合、细胞因子结合、受体配体活性等32个条目中;KEGG分析显示,差异mRNA主要富集在造血细胞谱系、原发性免疫缺陷、B细胞受体信号通路、Toll样受体信号通路、T细胞受体信号通路等。结论共发现10种circRNA及其相关的ceRNA网络在RA发病中的作用,这些基因及相关通路可为RA的诊断治疗提供新靶点。

Objective To explore the circular RNA(circRNA)-microRNA(miRNA)-messenger RNA(mRNA)network and key genes in peripheral blood mononuclear cells patients with rheumatoid arthritis(RA).Methods The relevant data sets GSE189338,GSE124373 and GSE55457 were obtained from the gene expression database GEO.The differential expression of circRNA,miRNA and mRNA was analyzed by R language Limma package and edgeR package.According to the ceRNA network association data,the circRNA-miRNA-mRNA network was constructed by Cytoscape 3.8.0 software.The heat map and box plot analysis of ceRNA network nodes were carried out by R language pheatmap package,reshape 2 package and ggpubr package,and the differentially expressed mRNAs were analyzed by GO enrichment and KEGG pathway analysis.Results A total of 58 differentially expressed circRNAs,35 differentially expressed miRNAs and 150 differentially expressed mRNAs were screened out.According to the ceRNA network correlation data and using Cytoscape 3.7.1 software,10 circRNAs,8 miRNAs and 38 mRNAs were finally screened to construct a circRNA-miRNA-mRNA visualization network;through the box plot analysis of ceRNA network nodes,5 circRNAs with high expression,4 circRNAs with low expression,4 miRNA with high expression,4 miRNA with low expression,17 mRNA with high expression and 7 mRNA with low expression were found in RA.A total of 289 items were obtained by GO analysis.Among them,biological process(BP)was mainly enriched in 252 items such as B cell activation,differentiation and proliferation,lymphocyte differentiation,etc.,and cell localization(CC)was mainly enriched in 5 items such as plasma membrane lateral,RNA polymerase II transcriptional inhibitor complex,etc.,while molecular function(MF)was mainly enriched in 32 items such as fibronectin binding,cytokine binding,receptor ligand activity,etc.;KEGG analysis showed that differential mRNA was mainly enriched in hematopoietic cell lineage,primary immunodeficiency,B cell receptor signaling pathway,Toll-like receptor signaling pathway,T cell receptor signaling pathway,etc.Conclusion A total of 10 circRNAs and their related ceRNA networks were found in the pathogenesis of RA.These genes and related pathways can provide new targets for the diagnosis and treatment of RA.