基于生物信息学方法筛选及验证慢性阻塞性肺疾病中的焦亡相关基因

Screening and validation of pyroptosis-related genes in COPD based on bioinformatics methods

  • 摘要: 目的:利用生物信息学方法筛选并分析慢性阻塞性肺疾病(慢阻肺)与焦亡相关的关键基因。方法:首先对慢阻肺数据集GSE38974 进行差异分析,得到差异基因后与焦亡相关基因取交集,最终获取焦亡相关的差异基因(DEprGs);对DEprGs进行GO 和KEGG 功能富集分析以及PPI分析;应用Cytoscape软件及其插件cytohubba的4种算法分析PPI的结果并取交集得出关键基因;用GSE38974、GSE47460 数据集再次验证关键基因后筛选出最有意义的核心基因;12 只C57BL/6 小鼠分别于空气和烟草烟雾暴露24周后采用HE染色观察小鼠肺组织病理改变,并运用实时荧光定量聚合酶链式反应(RT-qPCR)在动物模型中验证最关键基因的差异性表达。结果:GSE38974与焦亡相关基因取交集共得到32个DEprGs,PPI进一步分析后得到7个关键基因;使用GSE38974及GSE47460两个数据集再次验证7个关键基因,在两个数据集中同时表达且有显著差异(P<0.01)的核心基因仅有2个,即NAIPHDAC6,其中NAIP上调,HDAC6下调;HE染色可见烟草烟雾暴露组(烟熏组)小鼠较空气暴露组(空气组)肺泡变薄且断裂融合,肺泡腔明显扩大,炎症细胞浸润明显,烟熏组小鼠平均肺泡间距明显大于空气组(P<0.05);生物信息学分析的结果与核心基因实验验证结果一致,且相关性分析显示NAIPHDAC6 与小鼠的平均肺泡间距相关(P<0.05)。结论:在慢阻肺中,细胞焦亡相关基因NAIP 高表达,可能参与慢阻肺的发生和发展;而HDAC6 低表达,可能是潜在的保护因素。

     

    Abstract: Objective: To screen and analyze the key genes related to pyroptosis in chronic obstructive pulmonary disease(COPD)by bioinformatics.Methods: Firstly, differential analysis was performed on chronic obstructive pulmonary disease data set GSE38974, and intersection of the obtained differential genes and pyroptosis related genes was used to obtain the differentially expressed pyroptosis-related genes (DEprGs).GO and KEGG functional enrichment analysis and PPIanalysis were performed for DEprGs.Four algorithms of Cytoscape software and cytohubba were applied to analyze PPIresults and intersection of key genes were obtained.GSE38974 and GSE47460 data sets were used to verify key genes again and select the most significant core genes.Twelve C57BL/6 mice were exposed respectively to air and tobacco smoke for 24 weeks, and the pathological changes of mouse lung tissues were observed by HE staining.Real-time fluorescence quantitative polymerase chain reaction(RT-qPCR)was used to verify the differential expressions of the most critical genes in the animal model.Results: A total of 32 DEprGs were obtained by the intersection of GSE38974 and pyroptosis genes, and 7 key genes were obtained by further analysis of PPI.Seven key genes were verified again with GSE38974 and GSE47460 data sets.Only two core genes, NAIP and HDAC6, were expressed with significant differences (P<0.01) in the two data sets. NAIP was up-regulated, HDAC6 was downregulated.HE staining showed that compared with the air exposure group, the alveolar wall in the tobacco smoke exposure group was thinner, fractured and fused; the alveolar cavity was significantly enlarged and the inflammatory cell infiltration was obvious.The mean linear intercept in the smoking group was significantly higher than that in the air group (P<0.05).The results of bioinformatics analysis were consistent with the results of core gene test,and correlation analysis showed that NAIP and HDAC6 were correlated with the mean alveolar spacing of mice (P<0.05).Conclusion: In COPD, NAIP is highly expressed in COPD,which may be involved in the occurrence and development of COPD.The low expression of HDAC6 may be a potential protective factor.

     

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