Chemotherapy as a shaper of immune communication in the triple-negative breast cancer microenvironment.

Abstract

3093 Background: Triple-negative breast cancer (TNBC) is a highly immunogenic disease and exhibits among the highest levels of immune infiltration compared with other breast cancer subtypes. These characteristics, coupled with the lack of effective targeted therapies, have made TNBC a key candidate for immunotherapy in selected clinical settings. While chemotherapy remains a mainstay of treatment, its immunomodulatory effects on the tumor immune microenvironment (TIME) remain poorly understood. This study computationally models immune cell to immune cell communication using Single-cell RNA sequencing data to identify immune driver cells and their interactions, and how they are altered by chemotherapy in TNBC. Methods: Single-cell RNA sequencing data of over 200,000 tumor cells from TNBC patients’ tumor samples were obtained from the Gene Expression Omnibus database. They were analyzed to comprehensively characterize the TIME before and after chemotherapy. We also considered healthy breast tissue to establish immune pathways unique to TNBC pathogenesis. We employed unsupervised clustering analysis, reciprocal principal component analysis with annotation from the NIH Center of Immunology for immune cell identifiers. Communication probability, interaction strength, and pathway information flow were computed, and differential signaling was evaluated using Wilcoxon rank-sum tests ( p < 0.05). Multiple hypothesis testing was also accounted for by Bonferroni-adjusted p-values to control false positives. Results: Immune activity within the TIME was minimal in healthy breast tissue, highlighting signaling pathways specific to TNBC pathogenesis. In contrast, there was an increased immune response in tumors after chemotherapy. Pathways with the highest communication activity included MHC-I/II, CCL, MIF, and CD99 signaling. Notably, CD86 signaling, which correlates with PD-L1 expression, and CD45 signaling were significantly activated after chemotherapy in TNBC. Additionally, CD23 signaling, associated with antitumor immunity, was enhanced following chemotherapy. Natural killer cells emerged as the key immune cell type mediating outgoing signals through annexin, IL16, CX3C, and CD99 pathways, which were largely inactive before treatment. Conclusions: Our findings demonstrate that chemotherapy reprograms the TIME in TNBC by enhancing intercellular communication among immune cells and upregulating pro-immune signaling pathways. This remodeling of the TIME suggests potential targets for novel immunotherapeutic discoveries and immune-checkpoint modulation in TNBC.