单细胞RNA测序联合实验验证树突状细胞在慢性阻塞性肺疾病中的核心基因  

Single-cell RNA sequencing combined experimental verifies the core genes of dendritic cells in chronic obstructive pulmonary disease

作　　者：薛廷 郑乐婷[2] 董菲 周广[1] 钟小宁[1] XUE Ting;ZHENG Leting;DONG Fei;ZHOU Guang;ZHONG Xiaoning(Department of Respiratory and Critical Care Medicine,First Affiliated Hospital of Guangxi Medical University,Nanning 530021,China;Department of Rheumatology and Immunology,First Affiliated Hospital of Guangxi Medical University,Nanning 530021,China)

机构地区：[1]广西医科大学第一附属医院呼吸与危重症医学科,广西南宁530021 [2]广西医科大学第一附属医院风湿免疫科,广西南宁530021

出　　处：《细胞与分子免疫学杂志》2024年第2期97-105,共9页Chinese Journal of Cellular and Molecular Immunology

基　　金：国家自然科学基金(82070044,82360012)。

摘　　要：目的 单细胞RNA测序(scRNA-Seq)联合实验验证树突状细胞在慢性阻塞性肺疾病(COPD)中的核心基因。方法从基因表达数据集(GEO)数据库下载单细胞数据GSE173896和芯片数据GSE38974。GSE173896进行质控、批次矫正、降维聚类、细胞类型注释及组间树突状细胞差异表达基因(DC-DEG)鉴定。GSE38974差异分析得到的差异基因(DEG)与DC-DEG取交集获取共有DC-DEG,评估共有DC-DEG对COPD的诊断效能和共有DC-DEG富集分析及其与GSE38974免疫细胞浸润中激活的树突状细胞(DC)、浆细胞样树突状细胞(pDC)和Th17细胞的相关性。肺气肿小鼠模型肺组织对共有DC-DEG的mRNA表达量进行实验验证。结果 GSE173896得到组间DC-DEG 18个,GSE38974得到646个DEG,两者取交集得到3个DC-DEG,包括白细胞介素1受体拮抗剂(IL1RN)、 S100钙结合蛋白A8(S100A8)和S100A9,曲线下面积(AUC)值分别为0.841、 0.804和0.966。基因本体论分析(GO)和京都基因与基因组百科全书(KEGG)主要富集于慢性炎症反应、含胶原蛋白的细胞外基质、晚期糖基化终产物受体(RAGE)结合、 Toll样受体(TLR)结合、白细胞介素17(IL-17)信号通路等。IL1RN、 S100A8和S100A9均与激活的DC、 pDC及Th17细胞呈正相关。实验验证结果显示肺气肿小鼠肺组织IL1RN、 S100A8和S100A9的mRNA相对表达量上调。结论 IL1RN、 S100A8和S100A9可能是DC在COPD发病机制中的核心基因,为后续COPD的免疫治疗提供潜在靶点和理论依据。Objective Single-cell RNA sequencing(scRNA-Seq)and experimental verifies core genes of dendritic cells in chronic obstructivepulmonary disease(COPD).Methods scRNA-seqdataGSE173896andchipdata GSE38974were extracted from the Gene Expression Omnibus(GEO)database.GSE173896 was used to perform quality control,batch correction,dimensionality reduction clustering,cell type annotation and dendritic cell differentially expressed genes(DC-DEGs)identification.DEGs from the analysis of GSE38974 were intersected with DC-DEGs to obtain the common DC-DEGs.The diagnostic efficacy of the common DC-DEGs for COPD and their enrichment analysis were conducted.The correlation of the common DC-DEGs with activated dendritic cell(DCs),plasmacytoid dendritic cell(pDCs)and type 17 T helper(Th17)cells were analyzed.The mRNA expression level of the common DC-DEGs in the lung tissue of emphysema mice was verified.ResultsFrom GSE173896,18 DC-DEGs were obtained between groups and from GSE38974,646 DEGs were obtained.The intersection of the two resulted in 3 common DC-DEGs,including interleukin 1 receptor antagonist 1(IL1RN),S100 calcicum-binding protein A8(S100A8)and S100A9.Their respective area under curve(AUC)values were 0.841,0.804 and 0.966.The GO and KEGG enrichment analysis mainly concentrated on chronic inflammatory response,collagencontaining extracellular matrix,receptor for advanced glycation end products(RAGE)binding,Toll-like receptor(TLR)binding and interleukin 17(IL-17)signaling pathway.IL1RN,S100A8 and S100A9 were positively correlated with activated DCs,pDCs and Th17 cells.The results showed that the mRNA relative expression levels of IL1RN,S100A8 and S100A9 were up-regulated in the lung tissue of emphysema mice.Conclusion IL1RN,S100A8 and S100A9 may be the core genes of DCs in the pathogenesis of COPD,which potentially provide targets and a theoretical basis for subsequent COPD immunotherapy.

关 键 词：慢性阻塞性肺疾病(COPD) 单细胞RNA测序(scRNA-Seq) 树突状细胞(DC) 核心基因 

分 类 号：R563.3[医药卫生—呼吸系统] R364.5[医药卫生—内科学] R392.12[医药卫生—临床医学]