Abstract:Background and Aims Breast cancer is the most prevalent malignancy in women worldwide, and chemotherapy is one of the most important treatment modalities for breast cancer. Recent studies have shown that chemotherapy may exert anti-tumor effects by enhancing anti-tumor immunity in the tumor microenvironment. Therefore, this study was conducted to identify the changes in tumor-associated macrophages (TAMs) and relevant genes before and after neoadjuvant chemotherapy (NAC) in breast cancer patients by bioinformatics analysis and to evaluate the effect of NAC on immune functions in breast cancer patients.Methods Information searching was performed by entering "Breast Cancer", "TAMs", "Chemotherapy" and selecting the human breast cancer tissue in the GEO database, and the GSE134600 dataset was selected for analysis. Differentially expressed genes (DEGs) in tissue samples from breast cancer patients before and after NAC were screened by R package (limma function). GO function enrichment and KEGG pathway analysis were performed for all DRGs. The protein interaction network of DEGs was visualized by Cytoscape software, and hub genes were screened and 10 hub genes were analyzed for mutations by cBioPortal. Immune cell distribution and correlation in GSE134600 data were evaluated using the R package “CIBERSORT”.Results A total of 751 DEGs (409 up-regulated and 342 down-regulated genes) were identified before and after NAC for breast cancer. The biology of DEGs was analyzed by GO enrichment for biological process（BP）, cellular component（CC）, and molecular function（MF）. In BP function, they were mainly enriched in type I interferon(IFN-I) signaling pathway/viral response and defense and viral life cycle; in CC function, they were mainly enriched in extrinsic components of cell membrane and cytoplasmic side of cell membrane; in MF function, they were mainly enriched in cytokine receptor binding, double-stranded RNA binding and lipopeptide binding. In the analysis of KEGG pathway enrichment, DEGs were mainly enriched in influenza A (H1N1), measles, hepatitis C, coronavirus disease COVID-19, NF-κB signaling pathway, EBV virus infection, NOD-like receptor signaling pathway, and amoeba disease signaling pathway. The top 10 hub genes with the highest degree of interaction with TAMs before and after NAC for breast cancer were screened by CytoHubba plug-in: IFIT1, ISG15, MX1, MX2, IRF7, RSAD2, IFIT3, IFI35, IFI6, and IFITM1. Multi-omics analysis revealed that IFIT1, MX1 and MX2 were mainly deletion mutations, IFIT1 mainly had deep gene deletion, while MX1 and MX2 were mainly associated with gene amplifications. The content of M0 macrophages, CD8+T cells and M2 macrophages in breast cancer tissues decreased after NAC, and M0 macrophages were positively correlated with memory B cells (r=0.64) and negatively correlated with unactivated CD4+ memory T cells (r=-0.66).Conclusion The identified DEGs associated with TAMs in breast cancer patients before and after NAC are closely related to interferon signaling pathway, suggesting that interferon signaling pathway may play an important role by altering TAMs in NAC. Meanwhile, M0 macrophages are significantly altered before and after NAC, indicating that chemotherapy may regulate the immune response to tumor by changing the distribution of M0 macrophages and immune function.