慢性阻塞性肺疾病内质网应激特征基因筛选及免疫浸润表现

Screening of endoplasmic reticulum stress characteristic genes and immune infiltration manifestations in chronic obstructive pulmonary disease

  • 摘要: 目的:基于生物信息学、机器学习算法和实验验证揭示内质网应激(ERS)在慢性阻塞性肺疾病(COPD)中的核心基因。方法:从GEO数据库下载微阵列数据集GSE5058、GSE8545和GSE19407,以鉴定COPD吸烟者和非吸烟者气道上皮细胞之间的差异表达基因(DEGs),随后与ERS相关基因重叠后得到共有差异表达基因(ERs-DEGs)并进行富集分析。通过LASSO、SVM-RFE和RF 3种机器学习算法筛选ERS特征基因,并在GSE10006中验证和评估其诊断效能,随后进行免疫浸润分析、构建关键基因的lncRNA-miRNA-mRNA ceRNA网络和小鼠肺气肿模型肺组织mRNA表达量验证。结果:筛选出153个共有差异基因,其中74个基因表达上调,79个基因表达下调。GO和KEGG分析显示,ERs-DEGs主要富集于ERS反应、蛋白折叠及多个炎症信号通路,DO分析主要富集于肺血管闭塞性疾病、COPD等。免疫浸润分析提示,COPD样本与多种免疫细胞浸润高度相关。经机器学习算法最终共鉴定出4个特征基因(包括THBS1、BCL2、USP13RNFT2),且在训练集和验证集中均显示出良好的诊断效能。同时,选择共表达的mRNA和miRNA构建mRNA-miRNA相互作用网络。RT-PCR结果显示,与空气组小鼠比较,香烟烟雾暴露诱导的肺气肿小鼠肺组织THBS1RNFT2的mRNA表达水平升高,BCL2USP13的mRNA表达水平下降(均P<0.05)。结论:THBS1、BCL2、USP13RNFT2可能是COPD发病过程中ERS形成的核心基因,有望成为COPD免疫治疗的靶点。

     

    Abstract: Objective: To identify the core genes of endoplasmic reticulum stress (ERS) in chronic obstructive pulmonary disease (COPD) using the bioinformatics, various machine learning algorithms and experimental validation. Methods: The microarray data GSE5058, GSE8545, and GSE19407 were downloaded from the GEO database to identify differentially expressed genes (DEGs) between airway epithelial cells of COPD smokers and non-smokers, and then the common DEGs were obtained after overlapping with ERS-related genes and enriched for analysis. Three machine learning algorithms, LASSO, SVM-RFE, and RF, were used to screen the characteristic genes, and their diagnostic performance was verified and evaluated in the GSE10006. Subsequently, immunoinfiltration analysis was performed. Finally the lncRNA-miRNA-mRNA ceRNA network of key genes was constructed and the mRNA expression levels of lung tissue in the mouse emphysema model were verified. Results: A total of 153 common DEGs were screened, of which 74 genes were up-regulated and 79 genes were down-regulated. GO and KEGG analysis showed that ERs-DEGs were mainly enriched in ERS response, protein folding and multiple inflammatory signaling pathways, and DO analysis was mainly enriched in pulmonary vascular occlusive diseases and COPD and so on. Immunoinfiltration analysis showed that COPD samples were highly correlated with a variety of immune cell infiltrations. A total of 4 characteristic genes (including THBS1, BCL2, USP13 and RNFT2) were finally identified by machine learning algorithms, and they showed good diagnostic performance in both the training set and the validation set. At the same time, co-expressed mRNA and miRNA were selected to construct the mRNA-miRNA interaction network. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) results showed that compared with the air exposure group mice, the mRNA expression levels of THBS1 and RNFT2 in the lung tissues of emphysema mice induced by cigarette smoke exposure were increased, and the mRNA expression levels of BCL2 and USP13 were decreased (all P<0.05). Conclusion: THBS1, BCL2, USP13 and RNFT2 may be the core genes formed by ERS during the pathogenesis of COPD, and are expected to be targets for COPD immunotherapy.

     

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