摘要
目的·利用生物信息学方法研究系统性红斑狼疮(systemic lupus erythematosus,SLE)患者免疫细胞亚群的代谢通路活化水平。方法·从基因表达综合数据库(Gene Expression Omnibus,GEO)中下载SLE患者和正常人外周血单个核细胞(peripheral blood mononuclear cell,PBMC)的基因表达矩阵,以及SLE患者和正常人外周血中T细胞和B细胞亚群相应的基因表达矩阵,对测序数据进行标准化后筛选差异表达基因(differentially-expressed gene,DEG)。应用Enrichr在线富集工具对差异表达基因进行通路分析,并通过比对分析确定共同上调通路。借助基因集富集分析(gene set enrichment analysis,GSEA)软件对全基因表达矩阵进行通路富集分析。对SLE和正常人PBMC的转录测序数据进行免疫细胞的构成比例分析。对目的通路进行基因表达注释。运用基于转座酶和高通量测序的染色质分析(assay for transposase-accessible chromatin using sequencing,ATAC-seq)技术检测SLE患者和正常人B细胞中糖酵解相关基因的染色质开放性情况。结果·(1)维恩图展示SLE患者PBMC基因表达谱(GSE169080、GSE144390以及GSE139350)富集了139个共同上调的通路,GSEA分析结果显示其中包括糖酵解、氧化磷酸化(oxidative phosphorylation,OXPHOS)以及脂肪酸氧化(fatty acid oxidation,FAO)在内的多条代谢通路在SLE患者中上调。(2)免疫细胞比例构成分析发现,与正常人相比,SLE患者外周血中T细胞、B细胞以及NK细胞的比例较高;SLE患者T细胞和B细胞中多个代谢通路关键酶基因的表达水平均较正常人高。(3)SLE患者和正常人外周血B细胞的ATAC-seq结果显示,糖酵解关键酶基因SLC2A3、PKM以及LDHA的开放性在SLE患者中更高。(4)SLE患者B细胞亚群的代谢通路GSEA分析结果和代谢通路可视化分析显示,记忆B细胞和浆母细胞的多个代谢通路水平均较初始B细胞高。结论·SLE患者转录水平的多条代谢通路均发生改变,效应B细胞的代谢通路活化水平较初始B细胞高。
Objective·To study the metabolic pathway activity level of the immune cell subsets in the patients with systemic lupus erythematosus(SLE) by bioinformatics analysis. Methods·The matrix expression data of PBMCs collected from SLE patients and healthy controls were downloaded from Gene Expression Omnibus(GEO) Datasets, as well as the transcriptome data of T cell and B cell subsets from SLE patients and healthy controls. The differentially-expressed genes(DEGs) were identified in the standardized sequence data. Pathway enrichment analysis of DEGs was performed by online Enrichr tools, and the common up-regulated pathways were determined by comparative analysis. Gene set enrichment analysis(GSEA) was used to identify pathways that were enriched in the experiment processed with the whole gene expression matrix. RNA-seq data from PBMCs samples of SLE patients and healthy controls were used to characterize the immune cell composition. The targeted pathway was annotated with gene expression. Assay for transposase-accessible chromatin using sequencing(ATAC-seq) technique was performed to detect the chromatin accessibility of glycolysis-related genes in SLE patients and healthy controls. Results·(1) Venn diagram depicted 139common upregulated pathways in GSE169080, GSE144390 and GSE139350 data sets, and GSEA results showed that multiple classical metabolic pathways, including glycolysis, oxidative phosphorylation(OXPHOS) and fatty acid oxidation(FAO), were upregulated in SLE patients.(2) Immune cell composition analysis of PBMCs showed that the proportions of T cells, B cells and NK cells were higher in SLE patients, and the expression of genes encoding multiple enzymes of metabolic pathway in T cells and B cells were higher than those in healthy controls.(3) Compared to healthy controls, the intensity of ATAC-seq signal was significantly enhanced at transcriptional regulatory sites of SLC2A3, PKM and LDHA in peripheral B cells from SLE patients.(4) GSEA results and visualization analysis of metabolic pathways of SLE B cell subsets showed that the memory B cells and plasmablasts displayed a higher metabolic state than na?ve B cells. Conclusion·Multiple metabolic pathways are altered in SLE patients and the metabolic level of effector B cells is higher than na?ve B cells in SLE patients.
作者
韩夏夏
蒋扬
顾霜霜
戴黛
沈南
HAN Xiaxia;JIANG Yang;GU Shuangshuang;DAI Dai;SHEN Nan(Department of Rheumatology,Renji Hospital,Shanghai Jiao Tong University School of Medicine,Shanghai Institute of Rheumatology,Shanghai 200127,China)
出处
《上海交通大学学报（医学版）》
CAS
CSCD
北大核心
2022年第9期1197-1207,共11页
Journal of Shanghai Jiao tong University:Medical Science
基金
国家自然科学基金(31630021,31930037,82071843,81901637)
上海市高水平地方高校创新团队(SSMU-ZDCX 20180100)。
