基于单细胞测序分析三阴性乳腺癌中巨噬细胞标记基因及其功能

Analysis of macrophage marker genes and their functions in triple negative breast cancer based on single cell sequencing

目的寻找有效的肿瘤标记物是目前研究的热点。通过单细胞测序方法明确三阴性乳腺癌(TNBC)组织中巨噬细胞的标记基因,并分析标记基因可能参与的生物学过程和其中的关键基因。方法运用GEO数据库下载数据集GSE118389获得所需的单细胞数据,并利用PCA和t-SNE的降维,获得15个亚群细胞,进而获得不同亚群细胞的标记基因。再对巨噬细胞的标记基因进行基因本体论和京都基因与基因组百科全书富集分析,分析这些基因可能参与的生物学过程。最后通过构建蛋白-蛋白互作网络,寻找各个网络中的关键基因,利用Kaplan-Meier Plotter数据库对关键基因行预后分析,运用肿瘤免疫评估数据库对关键基因表达水平与TNBC癌组织中巨噬细胞浸润状态进行相关性分析。结果共获得244个巨噬细胞的标记基因,主要富集于嗜中性粒细胞脱颗粒、中性粒细胞激活、酰胺绑定、肽绑定和细胞黏附分子结合等过程,进一步获得4个关键基因CSF1R、HLA-DQA1、OLR1和LAPTM5。其中CSF1R、HLA-DQA1、OLR1高表达的TNBC患者总体生存率高于低表达者;CSF1R、LAPTM5、OLR1基因表达水平与巨噬细胞免疫浸润呈正相关。结论标记物未来可能作为攻克肿瘤的重要靶点。此外,CSF1R、HLA-DQA1、OLR1可以作为有效的生物标志物预测TNBC患者预后,可以为TNBC患者的靶向治疗与免疫治疗提供思路。

Objective As the search for effective tumor markers has been the focus of current research,this paper aims to identify the macrophage marker genes in triple negative breast cancer(TNBC)tissue by single cell sequencing,and to analyze its biological processes and the key genes involved.Methods Firstly,the GEO database was used to download the data set GSE118389 to obtain the required single cell data,and the dimension reduction of PCA and T-SNE was used to obtain 15 subsets of cells,and the marker genes of different subsets of cells were obtained.Then,gene ontology(GO)and KEGG enrichment analysis was performed on the macrophage marker genes to analyze the biological processes in which these genes may be involved.Finally,a protein-protein interaction(PPI)network was constructed to find key genes in each network,and the Kaplan-Meier Plotter database was used to analyze the prognosis of key genes,and the tumor immune assessment(TIMER)database was used to analyze the correlation between the expression level of key genes and the infiltration state of macrophages in TNBC cancer tissues.ResultsA total of 244 macrophage marker genes were obtained,mainly in the processes of neutrophil degranulation,neutrophil activation,amide binding,peptide binding and cell adhesion molecule binding,and four key genes CSF-1 R,HLA-DQA1,OLR1 and LAPTM5 were further obtained.The overall survival rate of TNBC patients with high expression of CSF-1 R,HLA-DQA1 and OLR1 was higher than those with low expression.Moreover,the expression levels of CSF-1 R,LAPTM5 and OLR1 were positively correlated with the immune infiltration of macrophages.Conclusion Markers may be an important target for conquering tumors in the future.In addition,CSF-1 R,HLA-DQA1 and OLR1 can be used as an effective biomarker to predict the prognosis of TNBC patients and provide ideas for targeted therapy and immunotherapy for them.