非梗阻性无精子症的生物信息学分析

Bioinformatics analysis of non-obstructive azoospermia

目的利用整合生物信息学筛选非梗阻性无精子症(NOA)组织相关的生物标志物及其调控途径,揭示其潜在的分子机制。方法从GEO(Gene Expression Omnibus)数据库中获得GSE145467,GSE25518和GSE9210的基因表达谱矩阵,提取了正常生精的睾丸活检样本10例,无精子症患者睾丸活检样本76例。对这三个GEO芯片数据整合归一化并进行批次矫正后取交集。使用R软件鉴定正常生精样本组织(NS)与NOA之间的差异表达基因(DEGs),对差异表达的基因进行GO富集分析和KEGG通路富集分析,获取关键通路。然后基于在线工具(STRING)构建蛋白质与蛋白质相互作用网络图(PPI)。最后利用Cytoscape中的Cytohubba对枢纽基因(HUB基因)进行筛选。结果共筛选出489个常见的DEGs,包括10个上调基因和479个下调基因。它们通过对一些重要的途径,包括糖代谢,脂肪酸代谢,炭代谢、氨基酸合成、细胞周期及肌肉萎缩等的调控来参与精子发生。利用在线生物信息学工具String成功构建PPI网络图并使用Cytoscape筛选出网络中前30个关键基因(HUB genes)。包括BUB1、BIRC5、TTK、HMMR、RACGAP1、NEK2、DYNLL2、PBK、KIF15、UBB、KIF18A、OIP5、PTTG1、SPAG5、CKS2、CEP55、CDKN3、HIST1H2BA、TYMS、KPNA2、SGOL2、KIF2B、H2AFJ、DNALI1、SYCP1、SMC1B、DNAI1、DYNLRB2、FKBP6、SYCP3,这些基因都是下调基因。结论识别上述HUB基因和通路将有助于我们更好地理解NOA的发生机制,并为疾病的诊治提供潜在的生物标记物和治疗靶点。

Objective To screen NOA-related biomarkers and pathways using integrated bioinformatics,and elucidate its potential molecular mechanisms.Methods The gene expression profile matrices(GSE145467,GSE25518 and GSE9210)were obtained from GEO(Gene Expression Omnibus)database.Ten testicular biopsy samples of normal spermatogenic patients and 76 testicular biopsy samples of azoospermia patients were obtained.The online tool Sangerbox was used to normalize their integration and perform batch correction,and the Venn diagram to visualize the intersection genes of the three data sets.The R package"Limma"was run to identify differentially expressed genes(DEGs)between normal spermatogenic tissues(NS)and non-obstructive azoospermia tissues(NOA).For the functional annotations of common DEGs,the GO and KEGG pathway enrichment analysis were performed based on the DAVID database using R software.Protein-protein interaction network diagram(PPI)was constructed based on the online tool(STRING).The HUB genes were screened by Cytohubba in Cytoscape..Results CA total of 489 common DEGs were screened,including 10 upregulated genes and 479 downregulated genes in 3 data sets.They participated in spermatogenesis by regulating some important pathways,such as sugar metabolism,fatty acid metabolism,carbon metabolism,amino acid synthesis,cell cycle and muscle atrophy.We further identified the top 30 HUB genes of the PPI network,including BUB1,BIRC5,TTK,HMMR,RACGAP1,NEK2,DYNLL2,PBK,KIF15,UBB,KIF18 A,OIP5,PTTG1,SPAG5,CKS2,CEP55,CDKN3,HIST1 H2 BA,TYMS,KPNA2,SGOL2,KIF2 B,H2 AFJ,DNALI1,SYCP1,SMC1 B,DNAI1,DYNLRB2,FKBP6,SYCP3,these genes are all down-regulated genes.Conclusion The identified Hub genes and pathways will help us better understand the mechanism of azoospermia,and provide potential diagnostic biomarkers and therapeutic targets for azoospermia patients.