软骨细胞单细胞转录组数据的再挖掘揭示人骨关节炎病程中转录调控因子和代谢的时序变化  

Re-mining of Single-Cell RNA-Sequencing Data of Chondrocytes Reveals Changes in Transcriptional Regulators and Metabolism during Progression of Human Osteoarthritis

作　　者：施剑明 杜桂花[2] SHI Jian-ming;DU Gui-hua(Department of Orthopedics Trauma,No.1 People’s Hospital of Jingdezhen,Jingdezhen 330000,China;Department of Occupational Health and Toxicology,School of Public Health,Jiangxi Provincial Key Laboratory of Preventive Medicine,Nanchang University,Nanchang 330006,China)

机构地区：[1]景德镇市第一人民医院创伤骨科,江西景德镇333000 [2]南昌大学公共卫生学院劳动卫生与毒理学教研室,江西省预防医学重点实验室,南昌330006

出　　处：《南昌大学学报（医学版）》2023年第5期8-14,23,共8页Journal of Nanchang University：Medical Sciences

基　　金：江西省自然科学基金(20212BAB216074)。

摘　　要：目的基于单细胞测序(single-cell RNA sequencing,scRNA-seq)数据再挖掘分析探讨人骨关节炎(human osteoarthritis,hOA)进展中相关基因及生物学过程变化。方法从GEO数据库下载hOA软骨细胞scRNA-seq数据集,并使用R软件中Seurat、Monocle 2和CellCycleSoring等软件包对数据进行质量控制、标准化和归一化,并进行差异基因(特别是转录调控因子)、细胞周期及拟时轨迹分析,在此基础上对差异基因进行基因功能分析并解析涉及的生物学过程。结果scRNA-seq数据分析表明hOA发展初期存在细胞因子的产生和一氧化氮的生物合成等,晚期则伴随血管生成、胶原纤维形成和基质破坏,而细胞炎症反应伴随整个病理过程;差异基因分析筛选出多个新的随hOA进展发生表达水平动态改变的转录调控因子,如KMT2C、EGR2和EBF1;差异基因功能分析显示hOA进展伴随着软骨细胞的代谢改变,表现为氧化磷酸化相关基因表达水平增加,而糖酵解相关基因表达水平降低。结论基于hOA分级的软骨细胞拟时轨迹分析发现hOA进展过程中发生了包括转录调控因子在内的差异基因表达、生物学过程和细胞代谢方式的改变,可为临床开展阶段针对性临床干预和阻遏或逆转hOA进展的新疗法的开发提供了理论基础。Objective To explore the changes in relative gene expression and biological processes during the progression of human osteoarthritis(hOA)based on re-mining single-cell RNA sequencing(scRNA-seq)data.Methods The scRNA-seq dataset of hOA chondrocytes was download from GEO database,and quality control,standardization and normalization of the data were performed using Seurat,Monocle 2 and CellCycleSoring packages in R software.The differentially expressed genes(especially transcription regulators),cell cycle and trajectory were analyzed.Furthermore,the functions of the differentially expressed genes and the biological processes involved were analyzed.Results scRNA-seq analysis showed cytokines production and nitric oxide biosynthesis in the early stage of hOA,angiogenesis,collagen fiber formation and matrix destruction in the late stage,and cellular inflammatory response in the whole pathological process.The trajectory analysis of chondrocytes in hOA revealed the expression of many new transcriptional regulators,such as KMT2C,EGR2,and EBF1,which were dynamically changed along with the progression of hOA.Differential gene function analysis showed that the progression of hOA was accompanied by metabolic changes in chondrocytes,presented as increased expression of genes related to oxidative phosphorylation and decreased expression of genes related to glycolysis.Conclusion The trajectory analysis of chondrocytes based on hOA grades showed that differential gene expression,biological processes and cell metabolism were changed during the progression of hOA.Our results provide a theoretical basis for targeted clinical intervention and development of new therapies to block or reverse the progression of hOA.

关 键 词：单细胞测序 人骨关节炎 软骨细胞 转录因子 细胞代谢 

分 类 号：R684.3[医药卫生—骨科学]