摘要
目的基于单细胞RNA测序数据分析脑胶质瘤微环境中反应性星形细胞的浸润程度,并探讨其转录组学特征.方法基于GSE103224数据集(23793个细胞)和GSE138794数据集(20278个细胞)的脑胶质瘤单细胞RNA测序数据,应用R软件"Seurat"包分析特征表达基因.基于已建立的肿瘤相关反应性星形细胞特征基因,应用"Seurat"软件包中的"AddModuleScore"命令,计算每个细胞的特征基因表达评分,将表达评分显著升高者定义为肿瘤相关反应性星形细胞亚群(即目标亚群).并应用"Seurat"软件包中的"FindMarkers"命令,计算目标亚群间的差异表达基因[差异倍数>2.0倍(高表达)或<0.5倍(低表达),校正P<0.05].分析2个数据集中目标亚群相交集的上调基因,并参照DAVID数据库对上调基因进行功能注释功能富集.结果依据细胞特征基因表达,GSE103224和GSE138794数据集的细胞均可分为26个亚群,分别有4个和5个亚群为目标亚群,目标亚群的细胞数分别占总细胞数的15.6%(3712/23793)和16.5%(3347/20278).差异分析显示,GSE103224数据集中的4个目标亚群与其他亚群间存在229个差异基因,其中上调基因136个,下调基因93个;GSE138794数据集中,5个目标亚群与其他亚群间存在422个差异基因,其中上调基因270个,下调基因152个.2个数据集有交集的上调基因94个,下调基因50个.基因功能注释结果显示,有交集的94个上调基因与37个基因功能显著相关(FDR<0.05),主要包括免疫反应、小胶质细胞激活、ERK通路、肿瘤坏死因子通路、凋亡通路等.结论单细胞分析结果显示,脑胶质瘤微环境中普遍存在肿瘤相关反应性星形细胞,其功能可能与脑胶质瘤发生、发展过程中的免疫反应、ERK通路等相关.
Objective To analyze the infiltration degree of reactive astrocytes in glioma microenvironment based on single-cell RNA sequencing data,and to investigate its transcriptomic characteristics.Methods Single-cell RNA sequencing data from CSE103224(23793 cells)and GSE138794(20278 cells)datasets were used to analyze characteristic gene expression profile using R software"Seurat”package.Based on the established tumor-associated reactive astrocyte characteristic genes,the"AddModuleScore"command in the"Seurat"package was used to calculate the characteristic gene expression score of each cell,and those whose expression score increased significantly were defined as tumor-associated reactive astrocyte subsets(i.e.,target subsets).The"FindMarkers"command in the."Seurat"package was applied to identify differentially expressed genes between target subsets and others[fold change>2.0(high expression)or<0.5(low expression),adjusted P<0.05]among target markers.The up-regulated genes in the intersection of target subgroups in the two data sets were analyzed,and functional annotation of the up-regulated genes was analyzed according to the biological functions of DAVID database.Results According to the expression profiles,the cells in GSE103224 and GSEI 38794 data sets could be divided into 26 subgroups,with 4 and 5 target subsets respectively.The cells of the target subsets in GSE103224 and GSE138794 data sets accounted for 15.6%(3712/23793)and 16.5%(3347/20278)of the total cells respectively.Differential analysis showed that there were 229 differentially expressed genes between the 4 target subsets in the GSE103224 dataset and other subsets,among which 136 were up-regulated genes and 93 were down-regulated genes.In the GSE138794 dataset,there were 422 differential genes between the 5 target subsets and other subsets,among which there were 270 up-regulated genes and 152 down-regulated genes.There were 94 up-regulated genes and 50 down-regulated genes with intersection between the two data sets.Gene function annotation results showed that 94 overlapping up-regulated genes were significantly correlated with 37 gene functions(FDR<0.05),which mainly included immune response,microglia activation,ERK pathway,tumor necrosis factor pathway,apoptosis pathway,etc.Conclusion The results of single-cell analysis showed that tumor-related reactive astrocytes are common in the glioma microenvironment,and their functions may be related to the immune response and ERK pathway during the development of glioma.
作者
张传宝
金书丞
许钦
刘演
王洋洋
王曦
贾旺
Zhang Chuanbao;Jin Shucheng;Xu Qin;Liu Yan;Wang Yangyang;Wang Xi;Jia Wang(Neurosurgery Center,Beijing Tiantan Hospital,Capital Medical University,Beijing 100070,China)
出处
《中华神经外科杂志》
CSCD
北大核心
2023年第6期607-611,共5页
Chinese Journal of Neurosurgery
基金
国家自然科学基金(81802483)。
作者简介
通信作者:贾旺,Email:jiawangttyy@126.com。
