Abstract PS3-12-15: Mapping the imprint of taxane chemotherapy on the metastatic microenvironment in HR+ breast cancer with single cell and spatial profiling

Abstract Introduction: The tumor microenvironment (TME) plays a prominent role in critical elements of breast cancer progression including metastatic dissemination and therapeutic response and resistance. Differences between efficacy of checkpoint inhibitors as monotherapies as compared to combinations with conventional chemotherapies or antibody drug conjugates promotes the hypothesis that cancer-directed therapies not only impact tumor cells directly but also shape TME dynamics with potentially pivotal consequences on therapeutic response. Unfortunately, the impact of even common therapies on TME interactions as they occur in patients remains incompletely defined, particularly in HR+ metastatic breast cancer (MBC). Methods: Here, we leveraged recent advances in single-cell and spatial profiling techniques to address this shortcoming. Biopsy cores of liver metastases from 40 patients with HR+ MBC were profiled with both single-nucleus RNA sequencing (snRNA-seq) and Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH). Results: Integrating the snRNA-seq and MERFISH profiles yielded detailed description of the composition, gene expression profiles/programs and spatial organization of HR+ liver metastases. Of the 40 biopsies, 32 were from patients previously treated with taxanes: 16 in the adjuvant setting (treatment-biopsy interval 18-222 months; mean 84); 10 in both the adjuvant and metastatic settings (interval 0-61 months; mean 18); and 6 only in the metastatic setting (interval 1-48 months; mean 20). Multiple gene expression profiles were increased in biopsies from patients exposed in the metastatic setting only. The malignant cells from these were characterized by enriched oxidative phosphorylation (Wilcoxon rank sum p=0.022), glycolysis (p=0.029), and hypoxia (p=0.033) gene sets as well as increased MYC regulon activity. Correspondingly, the TME was enriched for HIF1A regulon activity as well as SPP1+ lipid-scavenging (p = 0.047) and angiogenic (p=0.035) macrophages, pericytes (p=0.031), lymphatic endothelial cells (p=0.009), and proliferating endothelial cells (p=0.003). Integrated spatial analyses revealed that this phenotype was elevated in regions of metastatic involvement compared to the adjacent normal liver (e.g. p=0.002 for lipid-scavenging macrophages), while interferon-induced inflammatory macrophages were relatively depleted (p=0.040). Conclusions: Taken together, these data not only furnish a detailed atlas of liver metastases in HR+ breast cancer, a common and clinically important site of metastatic spread with adverse prognostic implications in the most common, but seemingly least immunogenic, breast cancer subtype, but also map the imprint of taxane-based chemotherapy. We identify the setting of taxane exposure as a critical determinant of the impact of this key therapeutic class, with specific relevance in combination with immunotherapy, on the TME. Notably, taxane exposure limited to the metastatic setting was associated with a hypoxic/angiogenic and immunosuppressive/immune-excluded TME, even compared to cases with taxane treatment in both the adjuvant and metastatic setting, highlighting opportunities for future clinical translation. Citation Format: R. Strasser, Y. Tam, R. M. Oscanoa, Å. Segerstolpe, J. Nelson, C. McCann, L. DelloStritto, A. Frangieh, K. Helvie, S. Vigneau, A. R. Thorner, K. Nguyen, S. Strauss, N. U. Lin, S. M. Tolaney, S. Farhi, B. E. Johnson, N. Wagle, J. Klughammer, D. L. Abravanel. Mapping the imprint of taxane chemotherapy on the metastatic microenvironment in HR+ breast cancer with single cell and spatial profiling [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS3-12-15.