基于实验研究和生物信息学筛选三种小鼠肺疾病的炎症相关关键基因
Identification of inflammation related key genes in three mouse lung diseases based on experimental studies and bioinformatics
王汉钦 1康慧敏 1周珂 1李柔 1陈适1
作者信息
- 1. 湖南师范大学医学院,长沙 410013
- 折叠
摘要
目的:应用RNA测序和生物信息学方法筛选小鼠矽肺、特发性肺纤维化(idiopathic pulmonary fibrosis,IPF)和慢性阻塞性肺部疾病(chronic obstructive pulmonary diseases,COPD)共同枢纽基因,以期为这三种肺部疾病的诊断和治疗提供新的实验依据.方法:建立小鼠矽肺模型并验证,提取矽肺小鼠肺组织进行RNA测序.采用limma包筛选差异表达基因(differentially expressed genes,DEGs),采用ggplot包绘制火山图;采用韦恩图筛选小鼠矽肺与IPF、COPD的共有DEGs;通过STRING数据库构建蛋白质-蛋白质相互作用(protein-protein interactions,PPI)网络识别DEGs中的关键基因;关键基因在矽肺、IPF和COPD小鼠中的表达水平通过qPCR和GEO数据集进行验证.结果:通过构建小鼠矽肺模型和小鼠肺组织RNA测序,结合IPF和COPD小鼠数据集,三种疾病共鉴定出8个共同的DEGs;qPCR结果显示,Cxcl10、MMP12、Lcn2在矽肺小鼠肺组织中显著增加,而Ctss水平无显著变化;在IPF和COPD的验证集中,Ctss、Cxcl10、MMP12、Lcn2均呈现高表达.结论:Cxcl10、MMP12、Lcn2是小鼠矽肺、IPF和COPD潜在的炎症相关关键基因.
Abstract
Objective RNA sequencing and bioinformatics methods were utilized to identify key genes associated with mouse silicosis,idiopathic pulmonary fibrosis(IPF),and chronic obstructive pulmonary disease(COPD).This research aims to establish a novel experimental foundation for diagnosing and treating chronic inflammatory lung diseases.Methods A mouse model of silicosis was established and validated,then RNA sequencing was conducted on the lung tissues of silicosis mice.Dif-ferentially expressed genes(DEGs)were identified using the limma package,volcano and heat maps were generated with the ggplot package.Common DEGs in silicosis,IPF,and COPD were identified using a Venn diagram.A protein-protein interaction(PPI)network was constructed using the STRING database to identify key genes among the DEGs.The expression of key genes in the lung tissues of silicosis mice was validated through qPCR assays,and the expression of key genes in IPF and COPD mice was validated using the GSE218997 and GSE76205 datasets.Results A mouse silicosis model was established and RNA se-quencing of mouse lung tissue was performed,in conjunction with datasets from IPF and COPD mice,a total of 8 common DEGs were identified across the three diseases.The qPCR results revealed a significant increase in Cxcl10,MMP12,and Lcn2 in the lung tissue of silicosis mice,while no significant change was observed in Ctss levels.In the validation sets of IPF and COPD,Ctss,Cxcl10,MMP12,and Lcn2 all showed high expression.Conclusion Cxcl10,MMP12,and Lcn2 are potential inflammation related key genes for mouse silicosis,IPF,and COPD.
关键词
矽肺病/特发性肺纤维化/慢性阻塞性肺部疾病/炎症/关键基因Key words
silicosis/idiopathic pulmonary fibrosis/chronic obstructive pulmonary diseases/inflammation/key gene引用本文复制引用
基金项目
国家自然科学基金(82173493)
湖南省自然科学基金(2023JJ30423)
出版年
2024
NETL
NSTL
万方数据