基于单细胞转录组探讨新型冠状病毒感染后慢性疲劳综合征与炎症反应、氧化应激、细胞凋亡之间分子机制及其潜在干预中药预测  

Exploration on molecular mechanisms between chronic fatigue syndrome after COVID-19 and inflammatory response,oxidative stress and apoptosis based on single cell transcriptome and prediction of potential intervention in traditional Chinese medicine

作　　者：黎祖鸣 封杰妮 陈雪如 卢月[2] 黄涛亮 李际强[2] 杨荣源[2,3,4] 陈剑坤 刘云涛 LI Zuming;FENG Jieni;CHEN Xueru;LU Yue;HUANG Taoliang;LI Jiqiang;YANG Rongyuan;CHEN Jiankun;LIU Yuntao(The Second Clinical Medical College,Guangzhou University of Chinese Medicine,Guangzhou 510405,China;The Second Affiliated Hospital,Guangzhou University of Chinese Medicine(Guangdong Provincial Hospital of Chinese Medicine),Guangzhou 510120,China;National Key Laboratory of Traditional Chinese Medicine Syndrome,Guangzhou 510120,China;Guangdong Provincial Key Laboratory of Traditional Chinese Medicine Emergency Research,Guangzhou 510120,China)

机构地区：[1]广州中医药大学第二临床医学院,广东广州510405 [2]广州中医药大学第二附属医院(广东省中医院),广东广州510120 [3]中医证候全国重点实验室,广东广州510120 [4]广东省中医急症研究重点实验室,广东广州510120

出　　处：《中草药》2024年第11期3774-3788,共15页Chinese Traditional and Herbal Drugs

基　　金：国家中医药管理局中医药创新团队及人才支持计划项目(ZYYCXTD-D-202203);国家中医药管理局项目(2023ZYLCYJ02-21);广东省重点领域研发计划项目(2023B1111020003);广东省中医院重点实验室专项(JZ2020ZZ01,YN2023JZ02,KF2023JZ06);广州市科技局市校院联合资助项目-广州市中西医结合防治新发突发传染病重点实验室(202201020382);中华中医药学会临床研究项目(2023DEPLHGG-06);广东省中医院朝阳人才科研专项资助(ZY2022KY10,ZY2022YL04)。

摘　　要：目的通过分析新型冠状病毒感染后(简称“新冠后”)慢性疲劳综合征(chronic fatigue syndrome,CFS)患者与正常受试者的单细胞转录组数据,探讨新冠后CFS与炎症反应、氧化应激和细胞凋亡之间的分子机制,并预测调控关键基因的潜在中药,为治疗新冠后CFS提供理论支持。方法使用R语言4.2.1中的“Seurat”包处理新冠后CFS患者与正常受试者的外周血单细胞测序数据,“CellChat”包进行细胞通讯分析,“scMetabolism”包评估细胞代谢特征,综合5种算法(AddModuleScore、AUCell、UCell、singscore和ssGSEA)计算新冠后CFS患者与正常受试者中5种免疫细胞炎症反应、氧化应激和细胞凋亡评分,并比较两者间的差异。使用“scCODE”包鉴定各类免疫细胞在正常受试者与新冠后CFS患者之间的差异表达(differential expression,DE)基因。Upset图分析得到新冠后CFS炎症反应相关基因(inflammatory response related genes,IRGs)、氧化应激相关基因(oxidative stress related genes,OSRGs)和细胞凋亡相关基因(apoptosis related genes,ARGs)。使用“ClusterProfiler”包分别对IRGs、OSRGs、ARGs进行基因本体生物学过程(gene ontology biological process,GOBP)富集分析。基于STRING数据库及Cytoscape软件构建“IRGs-OSRGs-ARGs”分子交互复杂网络,使用cytoHubba插件筛选关键基因。利用COREMINE数据库预测调控关键基因的中药,并通过古今医案云平台统计中药的性味归经、药物功效分类。结果共鉴定出5种免疫细胞,分别为B细胞、CD4^(+)T细胞、CD8^(+)T细胞、NK细胞和单核细胞。相比于正常受试者,新冠后CFS患者的细胞通讯更为丰富且强度更大,两者之间并无明显差异的细胞代谢特征。新冠后CFS患者中各类免疫细胞的炎症反应、氧化应激和细胞凋亡评分普遍高于正常受试者。共得到33个IRGs、17个OSRGs和54个ARGs。“IRGs-OSRGs-ARGs”分子交互网络显示,IRGs、OSRGs和ARGs之间存在密切联�Objective To explore the molecular mechanism between chronic fatigue syndrome(CFS)after coronavirus disease 2019(COVID-19)and inflammatory response,oxidative stress,apoptosis by analyzing the single cell transcriptome data of patients with CFS after COVID-19 and normal subjects,and predict potential traditional Chinese medicines that regulate key genes,providing theoretical support for the treatment of CFS after COVID-19.Methods The“Seurat”package in R language 4.2.1 was used to process peripheral blood single cell sequencing data of CFS after COVID-19 patients and normal subjects;the“CellChat”package was used to analyze cell communication;and the“scMetabolism”package was used to evaluate cell metabolic characteristics.Five algorithms(AddModuleScore,AUCell,UCell,singscore and ssGSEA)were synthesized to calculate the inflammatory response,oxidative stress,apoptosis scores of five immune cells in CFS after COVID-19 patients and normal subjects,and the differences between them were compared.The“scCODE”package was used to identify differentially expressed(DE)genes between normal subjects and CFS after COVID-19 patients in various types of immune cells.Upset plot analysis showed that inflammatory response related genes(IRGs),oxidative stress related genes(OSRGs)and apoptosis related genes(ARGs)were involved in CFS after COVID-19.“ClusterProfiler”package was used to perform gene ontology biological process(GOBP)enrichment analysis on IRGs,OSRGs and ARGs respectively.STRING database and Cytoscape software were used to construct“IRGs-OSRGs-ARGs”molecular interaction complex network diagram.The cytoHubba plug-in was used to screen for key genes.COREMINE database was used to predict traditional Chinese medicine regulating key genes,and qi,flavours,meridian affinity,and drug efficacy classification were counted through the cloud platform of ancient and modern medical records.Results Five types of immune cells were identified,including B cells,CD4^(+)T cells,CD8^(+)T cells,NK cells,and monocytes.Cell-

关 键 词：新型冠状病毒感染 慢性疲劳综合征 单细胞转录组 炎症反应 氧化应激 细胞凋亡 甘草 人参 黄芩 鱼腥草 郁金 丹参 

分 类 号：R285[医药卫生—中药学]