Analysis of macrophage marker genes and their functions in triple negative breast cancer based on single cell sequencing / 医学研究生学报

ABSTRACT

ObjectiveAs 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.MethodsFirstly, 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-1R, HLA-DQA1, OLR1 and LAPTM5 were further obtained. The overall survival rate of TNBC patients with high expression of CSF-1R, HLA-DQA1 and OLR1 was higher than those with low expression. Moreover, the expression levels of CSF-1R, LAPTM5 and OLR1 were positively correlated with the immune infiltration of macrophages.ConclusionMarkers may be an important target for conquering tumors in the future. In addition, CSF-1R, 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.