结直肠癌组织联合单细胞转录组测序筛选结直肠癌特异性细胞通讯

BulkRNA-Seq combined with scRNA-Seq screens colorectal cancer-specific cellular communications

目的结直肠癌组织联合单细胞转录组测序筛选特异性细胞通讯。方法首先从GEO数据库下载结直肠癌组织测序数据(GSE110225、GSE87211)和单细胞测序数据(GSE132465);接着利用R语言limma包对组织测序数据进行差异分析,并对差异基因进行功能富集分析,STRING数据库和Cytoscape软件筛选核心基因;最后TSNE降维法对单细胞测序数据进行细胞注释,R语言CellChat包做结直肠癌细胞通讯分析,确定核心基因中参与的核心细胞通讯,并加以分析。结果获得结直肠癌差异基因303个,功能富集在趋化因子介导的信号通路、细胞对趋化因子的反应等方面;信号通路主要富集在细胞因子和受体的相互作用、趋化因子信号通路等方面;筛选后获得15个核心基因,主要参与趋化因子(Chemokine C-X-C motif ligand,CXCL)细胞通讯,巨噬细胞、单核细胞和成纤维细胞是信号发出者,内皮细胞是媒介,T细胞、B细胞和组织干细胞是影响者。结论CXCL信号通路在结直肠癌的发生发展中起着重要的细胞通讯作用。

Objective Colorectal cancer tissue combined with single-cell transcriptome sequencing to screen for specific cellular communication.Methods GEO database downloads colorectal cancer tissue sequencing data(GSE110225,GSE87211)and single-cell sequencing data(GSE132465).Then,the R language limma package is used to perform differential analysis on the tissue sequencing data and functional enrichment analysis on the differential genes,and the STRING database and Cytoscape software to screen the core genes.Finally,the TSNE downscaling method was used to perform cellular annotation on single-cell sequencing data,and the R language CellChat package was used to do colorectal cancer cellular communication analysis to identify the core cellular communication involved in the core genes and analyze.Results Three hundred and three colorectal cancer differential genes were obtained,with functional enrichment in chemokine-mediated signaling pathways,cellular responses to chemokines,etc.Signaling pathways were mainly enriched in cytokine-receptor interactions,chemokine signaling pathways,etc.Fifteen core genes were obtained from the screening and were mainly involved in chemokine(Chemokine C-X-C motif ligand,CXCL)cellular communication,with macrophages,monocytes and fibroblasts as signal senders,endothelial cells as mediators,and T cells,B cells and tissue stem cells as effectors.Conclusion The CXCL signaling pathway plays an important role in cellular communication in colorectal cancer development.