摘 要: 目的 筛选矽肺患者肺组织差异表达基因作为矽肺的潜在生物标志物,探索其在早期诊断、治疗和发病机制中的可能价值。方法 从PubMed网站检索矽肺病人和健康对照人群生物样本mRNA测序数据,筛选两组数据中的差异表达基因,对其进行基因本体(GO)和基因组百科全书(KEGG)分析以及蛋白质与蛋白质相互作用(PPI)鉴定,利用Cytoscape软件中MCODE插件进行聚类分析评估PPI网络关键模块,利用CytoHubba插件筛选hub基因,搜索其他矽肺病以及相关疾病数据中hub基因表达情况。采集矽肺患者、接触矽尘健康工人和无接尘健康对照人群血清样本,以定时荧光定量聚合酶链式反应(RT-qPCR)检测7个差异表达基因相对表达水平,验证生物信息学结果。结果 筛选出244个上调差异表达基因,566个下调差异表达基因,其中SPP1、TIMP1、VCAM1,IFNG、SERPINE1、IGF1 6个上调hub基因及DNAI2、DNAI1,CCDC114、RSPH4A、RSPH1、DNAAF3 6个下调hub基因与矽肺发生发展有密切关系。SPP1、TIMP1、VCAM1、SERPINE1、IGF1、DNAI1和CCDC114基因经RT-qPCR实验验证在矽肺患者血清中存在差异表达;与对照组相比,矽肺组除DNAI1外,其余基因表达趋势均与生物信息学结果一致。结论 经过筛选验证出的SPP1、TIMP1、VCAM1、SERPINE1、IGF1、DNAI1和CCDC114在矽肺病人中存在差异表达,这些基因在生物过程、分子功能及细胞组分中发挥着重要作用,参与炎症、肿瘤、代谢的相关通路,有可能作为矽肺的潜在生物标志物。 |
关键词: 矽肺 差异表达基因 生物信息学 mRNA |
中图分类号: R135.2
文献标识码: A
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基金项目: 国家自然科学基金联合基金项目(U21A20334);河北省重点研发计划项目(192777129D) |
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Screening of silicosis differential genes based on bioinformatics and verificating in vivo |
LU Ya-ru,ZHAI Yue-song,CUI Jie,LI Xiang,WANG Ting-ting,HAO Xiao-hui,GUO Ling-li,LIU He-liang,WANG Hong-li
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School of Public Health,North China University of Science and Technology,Tangshan,Hebei 063210,China
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Abstract: Objective To screen the differentially expressed genes in the lung tissues of silicosis patients as potential biomarkers of silicosis,and to explore its possible value in early diagnosis,treatment and pathogenesis of silicosis. Methods According to the differences in mRNA sequencing data of biological samples from silicosis patients and healthy controls retrieved from PubMed website,the differentially expressed genes in the two groups were screened,give the analyses of GO,KEGG analysis and PPI,then,using MCODE plug-in Cytoscape software for the cluster analysis and evaluation of the key modules of PPI network,using CytoHubba plug-in to screen hub gene and search hub gene expression in other silicosis and related disease data sets. Serum samples of silicosis patients,healthy workers exposed to silica dust and healthy control population without silica dusts exposure were collected,and the relative expression levels of 7 differentially expressed genes were detected by RT-qPCR to verify the results from bioinformatics. Results The results showed that a total of 244 up-regulated differentially expressed genes and 566 down-regulated differentially expressed genes were screened,among them,SPP1,TIMP1,VCAM1,IFNG,SERPINE1,IGF1 six up-regulated hub genes and DNAI2,DNAI1,CCDC114,RSPH4A,RSPH1,DNAAF3 six down-regulated hub genes are closely related to the occurrence and development of silicosis. Additionally,there were some differential expression of SPP1,TIMP1,VCAM1,SERPINE1,IGF1,DNAI1 and CCDC114 genes in serum of silicosis patients was verified by RT-qPCR,but compared with control group,the gene expression trends of silicosis group were consistent with the bioinformatics results except for DNAI1. Conclusion The results suggested that SPP1,TIMP1,VCAM1,SERPINE1,IGF1,DNAI1 and CCDC114 which have been screened and verified,are differentially expressed in patients with silicosis,these genes play an important roles in the biological processes,molecular function and cellular components,and involved in pathways related to inflammation,tumor,and metabolism,and may be used as the potential biomarkers for silicosis. |
Keywords: silicosis differentially expressed genes bioinformatics mRNA |