m^(6)A相关基因在激素性股骨头坏死中的生物信息学分析  

Bioinformatics analysis of m^(6)A-associated genes in steroid-induced osteonecrosis of the femoral head

作　　者：令狐熙涛 桂佳琦 梁卓智[2] 瓦庆德 黄帅 Linghu Xitao;Gui Jiaqi;Liang Zhuozhi;Wa Qingde;Huang Shuai(Department of Orthopedics,Second Affiliated Hospital of Zunyi Medical University,Zunyi 563000,Guizhou Province,China;Department of Orthopedics,Second Affiliated Hospital of Guangzhou Medical University,Guangzhou 510260,Guangdong Province,China)

机构地区：[1]遵义医科大学第二附属医院骨外科,贵州省遵义市563000 [2]广州医科大学附属第二医院骨科,广东省广州市510260

出　　处：《中国组织工程研究》2024年第36期5811-5816,共6页Chinese Journal of Tissue Engineering Research

基　　金：广州市科技计划项目(2023A03J0405),项目负责人:黄帅;贵州省科技计划项目(黔科合基础一ZK[2021]重点007),项目负责人:瓦庆德。

摘　　要：背景:m^(6)A修饰与股骨头坏死的发生发展相关,但在激素性股骨头坏死中的作用尚不清楚。目的:基于GEO数据库,采用生物信息学方法分析激素性股骨头坏死中表达差异的m^(6)A基因及互作miRNAs,探寻其潜在发病机制。方法:在GEO数据库中检索并下载与激素性股骨头坏死相关的mRNA表达谱数据集(GSE123568),通过R软件对数据集进行差异基因筛选及GO功能、KEGG通路富集分析。识别差异基因中的m^(6)A差异表达基因(m^(6)A-DEGs)并对其进行GO功能与KEGG通路富集分析,比较m^(6)A-DEGs的表达量并分析它们之间的相关性。最后通过Cytoscape构建m^(6)A-DEGs的PPI互作网络及筛选核心基因。使用TargetScan,miRTarBase和miRBD数据库预测m^(6)A-DEGs相关的潜在miRNAs,同时使用ChIPBase及hTFtarget数据库预测7个核心基因潜在转录因子,然后分别构建m^(6)A-miRNA与转录因子m^(6)A调控网络。最后使用数据集GSE74089验证7个核心m^(6)A-DEGs的表达水平。结果与结论:①从数据集中共筛选出2460个差异表达的基因,其中1455个上调,1005个下调。②从数据集中筛选出了14个m^(6)A-DEGs,包括3个下调和11个上调基因,m^(6)A-DEGs在激素性股骨头坏死中的表达具有显著差异(P<0.05),Spearman分析表明它们之间具有一定相关性。③m^(6)A-DEGs的GO和KEGG富集分析主要集中在骨髓细胞分化与发育、免疫受体与细胞因子受体活性、破骨细胞分化、AMPK与白细胞介素17信号通路。④m^(6)A-DEGs前7个核心基因包括YTHDF3,YTHDF1,YTHDF2,ALKBH5,METTL3,HNRNPA2B1及HNRNPC,它们在miRTarBase,miRDB和TargetScan数据库中共有44个miRNA重叠,在ChIPBase及hTFtarget数据库中共有79个重叠转录因子。⑤在GSE74089数据集中有6个核心m^(6)A-DEGs的表达水平与GSE123568数据集一致。⑥结果证实,根据生物信息学方法筛选的7个m^(6)A-DEGs可能通过调控多个miRNA、转录因子和AMPK及白细胞介素17信号通路表达,进而影响激�BACKGROUND:m^(6)A modification has been confirmed to play an important role in the occurrence and development of osteonecrosis of the femoral however,the role of m^(6)A modification patterns in steroid-induced osteonecrosis of the femoral head remains unknown.OBJECTIVE:Bioinformatics analysis was performed based on the Gene Expression Omnibus(GEO)database to analyze the differential expression of the m^(6)A gene in steroid-induced osteonecrosis of the femoral head,predict the downstream targeted miRNAs,and investigate the potential pathogenesis.METHODS:Expressing profiles of mRNA data of steroid-induced osteonecrosis of the femoral head were downloaded from GEO database(GSE123568).Differentially expressed genes(DEGs),Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis were performed using the R software.After obtaining these differentially methylated m^(6)A genes(m^(6)A-DEGs),we analyzed GO function and KEGG pathway enrichment and compared the correlation among the m^(6)A-DEGs typing according to gene expression.The protein-protein interaction network and core gene subnetwork of m^(6)A-DEGs were constructed using Cytoscape software.The m^(6)A-DEGs-associated potential miRNAs were predicted using the TargetScan,miRTarBase,and miRBD databases.Simultaneously,ChIPBase and hTFtarget databases were used to predict potential transcription factors of seven core genes,then m^(6)A-miRNA and transcription factor-m^(6)A regulatory networks were constructed separately.Finally,the expression levels of the seven core m^(6)A-DEGs were verified by using the GSE74089 dataset.RESULTS AND CONCLUSION:(1)A total of 2460 common DEGs were screened out from datasets,among which 1455 genes were upregulated and 1005 genes were downregulated.(2)A total of 14 m^(6)A-DEGs were identified in the datasets.Among them,11 m^(6)A-DEGs were up-regulated and 3 m^(6)A-DEGs were down-regulated.Differential gene expression was considered significant for m^(6)A-DEGs in steroid-induced osteonecrosis of the femoral

关 键 词：激素性股骨头坏死 m^(6)A甲基化 微小RNA 转录因子 生物信息学 差异基因 基因调控网络 核心基因 

分 类 号：R459.9[医药卫生—治疗学] R318[医药卫生—临床医学] R681.8