Abstract PD7-05: Gut Microbiota Signatures are Associated with Response in Triple Negative Breast Cancer Patients Treated with Standard Neoadjuvant Chemotherapy

Abstract Introduction: Our understanding of the microbiome’s role in cancer has expanded significantly, revealing how differences in the diversity and composition of gut microbiota contribute to the variability in treatment responses among cancer patients. Its role in driving triple-negative breast cancer (TNBC) and resistance to immunotherapy is still not fully understood. We hypothesized that dysbiosis (loss of diversity, depletion of beneficial obligate anaerobes, blooms of pathobionts) in TNBC is associated with poor treatment response. Methods: From August 2017 to June 2025, 49 newly diagnosed TNBC patients (median age, 52 years) undergoing standard neoadjuvant chemotherapy (NAC) were enrolled in an observational prospective study at 3 sites, Hackensack University Medical Center-John Theurer Cancer Center, Georgetown Lombardi Comprehensive Cancer Center and Yale Cancer Center. Stool samples were collected from patients before, during and after NAC (prior to surgery). Shallow shotgun sequencing was performed and annotated taxonomically using MetaPhlAn v4.1. Treatment response criteria included pathologic complete response (pCR) and residual cancer burden (RCB). Fecal microbiota transplantation (FMT) of stool samples from responders and non-responders was performed in antibiotic-treated C57BL/6 mice using the E0771 TNBC model. Each donor stool was given to 3-4 recipients. Results: To assess whether microbial dysbiosis predicts early relapse and impacts response after NAC, we compared gut microbiota profiles at diagnosis in responders (RCB-0, pCR) and non-responders (RCB-II, non-pCR). Using pairwise comparisons (adj p<0.05), we found that opportunistic pathobionts (Actinomyces dentalis) associated with resistance to immune checkpoint inhibitors were enriched (fold change, FC>4) in non-responders. In contrast, beneficial gut commensals including short chain fatty acid (SCFA) producers, Lachnospira pectinoschiza (FC>10), a novel pectin degrading bacterium, and Bilophila wadsworthia (FC>14), were more prevalent in responders. Having identified distinct gut microbiota profiles predictive of outcome at diagnosis, we assessed whether NAC modulated the composition of gut microbiota in responders and non-responders. Taxa associated with favorable outcomes (Eubacterium ramulus (FC>74), Subdoligranulum sp. (FC>4), Peptoniphilus (FC>29)) were identified in responders whereas immunosuppressive bacteria (e.g. Enterocloster asparagiformis (FC>12)) were abundant in non-responders after NAC. Random Forest classifier and SHapley Additive exPlanations (post-hoc explainability method) validated the contribution of both pre- and post-bacterial taxa to outcome. To establish causality, we humanized antibiotic-treated mice with stool contents collected from responders and non-responders (pre-NAC). E0771-mice transplanted with stool contents from non-responders had higher tumor volumes (n=3 donors,1929 mm3 ± 244.7, donors) compared to mice transplanted from responders (n=2 donors, 1365 mm3 ± 131.6) after 25 days (p<0.06). Conclusions: We identified an enrichment of opportunistic pathobionts in non-responders contrasting with a higher prevalence of beneficial commensals, including SCFA producers in responders at diagnosis. These initial differences persist and evolve after NAC, with better responses correlating with specific beneficial taxa and worse responses associated with the persistence or emergence of potentially immunosuppressive bacteria. Our FMT studies suggest a causal link between gut microbiota and TNBC progression. These findings suggest that distinct gut microbiota are predictive of TNBC treatment response, further justifying its potential as a prognostic biomarker and a target for therapeutic intervention. Citation Format: A. A. Aptekmann, L. L. Montgomery, I. Colorado, K. Goldgirsh, E. Corapi, S. Hyman, M. Brito, C. McGuire, A. Akand, R. L. Mehta, R. Carbone, M. Zupa, M. Davidson, C. Isaacs, C. B. Mainor, D. Graham, M. J. Goldfischer, L. Pusztai, R. Feinman. Gut Microbiota Signatures are Associated with Response in Triple Negative Breast Cancer Patients Treated with Standard Neoadjuvant Chemotherapy [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 PD7-05.