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主管单位 工业和信息化部 主办单位 哈尔滨工业大学 主编 任南琪 国际刊号ISSN 1672-5565 国内刊号CN 23-1513/Q

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引用本文:刘艳玲,刘静,童明琼,范娜,王晓玥,孙婉.COPD 差异表达基因的生物信息学分析及在LUSC样本中的表达[J].生物信息学,2022,20(4):294-302.
LIU Yanling,LIU Jing,TONG Mingqiong,FAN Na,WANG Xiaoyue,SUN Wan.Bioinformatics analysis of differentially expressed genes in COPD and their differential expression in LUSC[J].Chinese Journal of Bioinformatics,2022,20(4):294-302.
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COPD 差异表达基因的生物信息学分析及在LUSC样本中的表达
刘艳玲,刘静,童明琼,范娜,王晓玥,孙婉
(德州学院 医药与护理学院,山东 德州 253023)
摘要:
为确定慢性阻塞性肺病(COPD)的分子标记物及COPD与肺鳞状细胞癌(LUSC)共存的差异表达基因,探寻COPD合并肺癌的预测因子,发现新的治疗靶点。本研究采用生物信息学方法,从GEO数据库中筛选3套基因芯片数据集,挖掘COPD患者小气道上皮细胞(SAEC)的差异表达基因(DEG)以及潜在的生物标记物,并通过基因本体(GO)、京都基因与基因组百科全书(KEGG)富集分析预测DEGs的功能及参与的代谢途径。继而对DEGs构建PPI网络,使用Cytoscape软件筛选子模块和Hub基因,并将Hub基因通过TCGA数据库分析其在LUSC中的差异表达情况及差异基因间的相关性。结果共获得52个上调基因和24个下调基因,代谢通路主要集中在细胞色素P450对外源物质的代谢、化学致癌、花生四烯酸代谢及甲状腺激素合成四条途径上,通过Cytoscape软件从PPI网络中筛选得到2个功能模块和10个Hub基因,进一步验证发现其中5个基因在TCGA数据库中的LUSC样本中同样差异表达。由此推测SPP1、ALDH3A1、SPRR3、KRT6A和SPRR1B 可能为COPD 分子标记物及COPD与LUSC共存的DEGs,从而为研究COPD和LUSC的发病机制及二者潜在关系奠定良好的基础。
关键词:  COPD  差异表达基因  生物信息学分析  LUSC
DOI:10.12113/202104020
分类号:Q343.1
文献标识码:A
基金项目:德州学院博士科研基金项目(No.2019xgrc25).
Bioinformatics analysis of differentially expressed genes in COPD and their differential expression in LUSC
LIU Yanling,LIU Jing,TONG Mingqiong,FAN Na,WANG Xiaoyue,SUN Wan
(School of Medicine and Nursing,Dezhou University,Dezhou 253023,Shandong,China)
Abstract:
In order to determine the molecular markers of chronic obstructive pulmonary disease (COPD) and the differential expression genes(DEGs) of COPD and lung squamous cell carcinoma(LUSC), explore the predictors of COPD and lung cancer, and find new therapeutic targets, three gene expression datasets were selected from GEO database, and DEGs and potential biomarkers of small airway epithelial cells(SAECs) of COPD were extracted based on bioinformatics method. The functions and metabolic pathways of DEGs were predicted by Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomic(KEGG). Then, the modules and hub genes were screened by Cytoscape from PPI networks. Lastly, the difference expression of hub genes in LUSC and the correlation of the differential genes were analyzed using TCGA database. Results showed that 52 up-regulated and 24 down-regulated genes were obtained. These 76 DEGs were mainly related to metabolism of xenobiotics by cytochrome P450, chemical carcinogenesis, arachidonic acid metabolism, and thyroid hormone synthesis. Then two functional modules and ten hub genes were screened from PPI network by Cytoscape. Further analysis showed that five of the ten hub genes were DEGs in LUSC samples in TCGA database. So SPP1, ALDH3A1, SPRR3, KRT6A,and SPRR1Bmay be molecular markers in COPD and DEGs in both COPD and LUSC,which lays a foundation for the research of pathogenesis of COPD and LUSC and corresponding relations.
Key words:  COPD  Differentially expressed genes  Bioinformatics analysis  LUSC

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