基于生物信息学分析药物治疗骨关节炎的潜在基因靶点

Potential gene targets of medication for osteoarthritis:an analysis based on bioinformatics

目的基于生物信息学方法分析药物治疗骨关节炎的潜在基因靶点。方法从基因表达综合数据库筛选出符合条件的微阵列芯片GSE41038、GSE55235、GSE55457、GSE82107,使用R语言软件筛选出差异表达基因(DEGs)。利用DAVID数据库进行DEGs的基因本体论(GO)功能富集分析、京都基因与基因组百科全书(KEGG)通路富集分析,利用STRING数据库和Cytoscape软件制作蛋白-蛋白相互作用(PPI)网络,并运用cytoHubba插件分析PPI网络中的中枢模块。基于DRUGBANK数据库与药物-基因相互作用数据库确定骨关节炎常用治疗药物及其靶基因,并将靶基因与中枢模块的关键基因取交集,选取4例骨关节炎患者(实验组)和4例关节创伤患者(对照组)的滑膜组织进行实时荧光定量PCR验证。结果共筛选出111个DEGs,其中表达上调基因55个、表达下调基因56个。DEGs的生物学过程主要与细胞黏附、免疫反应、凋亡过程的正向调控有关,细胞组分主要富集在细胞外区域、浆膜、细胞外间质等,分子功能主要富集在转录因子活性与特异性序列DNA结合、蛋白质同质化活性等方面;DEGs通过白细胞介素17信号通路、肿瘤坏死因子信号通路等信号通路参与骨关节炎滑膜炎症发展。PPI网络的中枢模块包含11个关键基因。共筛选出50种治疗骨关节炎的常用药物(塞来昔布、吲哚美辛、曲马多等)及263个药物靶基因。药物靶基因与中枢模块关键基因的交集基因为血管内皮生长因子A(VEGFA)、基质金属蛋白酶(MMP)1、MMP9、前列腺素内过氧化物合酶2(PTGS2)。实时荧光定量PCR结果显示,实验组滑膜组织中VEGFA、PTGS2的mRNA表达水平低于对照组,MMP9的mRNA表达水平高于对照组(均P<0.05),两组MMP1的mRNA表达水平差异无统计学意义(P>0.05)。结论VEGFA、MMP、PTGS2或为药物治疗骨关节炎的潜在基因靶点。

Objective To analyze the potential gene targets of medication for osteoarthritis based on bioinformatics.Methods Eligible microarray chips of GSE41038,GSE55235,GSE55457,and GSE82107 were screened from the Gene Expression Omnibus(GEO)database.The differentially expressed genes(DEGs)were screened by using R language software.The Gene Ontology(GO)functional enrichment analysis,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis were performed on DEGs by employing the DAVID database.The protein-protein interaction(PPI)network was produced by using the STRING database and Cytoscape software,and central module of PPI network was analyzed by CytoHubba plugin.Based on the DRUGBANK database and the Drug-Gene Interaction Database,the frequently used drugs for osteoarthritis and their target genes were determined,and the intersection of the target genes with the key genes of the central module was obtained.The synovial tissues of 4 osteoarthritis patients(experimental group)and 4 joint trauma patients(control group)were selected for verification by real-time fluorescence quantitative PCR.Results A total of 111 DEGs were screened,therein there were 55 genes with up-regulated expression,and 56 genes with down-regulated expression.The biological processes of DEGs were mainly related to cell adhesion,immune responses,and positive regulation of apoptosis process,the cellular components were mainly enriched in the extracellular region,serosa,and extracellular matrix,etc.,and the molecular functions mainly enriched in transcription factor activity and specific sequence DNA binding,protein homogeneity activity,etc.DEGs invovled in the development of osteoarthritis synovial inflammation through signaling pathways in terms of interleukin 17 signaling pathway and tumor necrosis factor signaling pathway,etc.The central module of PPI network contained 11 key genes.A total of 50 frequently used drugs for treating osteoarthritis were screened out,including celecoxib,indomethacin,tramadol,etc.,and 263 target genes of drugs were also screened out.The intersection genes between target genes of drugs and key genes of the central module were vascular endothelial growth factor A(VEGFA),matrix metalloproteinase(MMP)1,MMP9,and prostaglandin-endoperoxide synthase 2(PTGS2).The results of real-time fluorescence quantitative PCR revealed that the mRNA expressions of VEGFA and PTGS2 in the synovial tissues of the experimental group were lower than those of the control group,and the mRNA expression of MMP9 was higher than that of the control group(all P<0.05),but no statistically significant difference in the mRNA expression of MMP1 was found between the two groups(P>0.05).Conclusion VEGFA,MMP and PTGS2 may be the potential gene targets of medication for osteoarthritis.