Abstract Cancer patients are particularly susceptible to infections. Approximately 20-60% of patients may receive antibiotics at some point during their therapy, including perioperative care and periods of neutropenia. Retrospective studies suggest that antibiotics negatively impact outcomes in various cancers. A pilot study focused on breast cancer (BC) indicated that HER2+ BC patients experience greater reductions in survival following antibiotic exposure than HER2-negative cases. While this effect is thought to arise from disruptions in the host microbiota, the underlying mechanisms remain poorly defined. We previously demonstrated that microbiota signaling modulates innate immune cells in different tumor types, with consequences for the efficacy of chemotherapy and immunotherapy. However, HER2+ BC patients receive targeted therapies such as anti-HER2 antibodies with small-molecule tyrosine kinase inhibitors in case of therapy resistance. Therefore, the impact of microbiota specifically on HER2 therapies requires further study. To address this knowledge gap, we investigate how microbiota disruption, induced by antibiotics, affects responses to HER2-targeted therapies using mouse preclinical models. We utilized orthotopic HER2+ breast cancer mouse models, administered an oral broad-spectrum antibiotic cocktail (ABX) to deplete the microbiota, and employed HER2-targeted antibody (anti-HER2/neu) and small molecule (neratinib) therapies, along with high-throughput spectral flow cytometry, to assess treatment efficacy and the immune mechanisms of response. While antibiotic treatment alone did not alter tumor growth, it significantly impaired responses to HER2 therapies. Notably, the efficacy of anti-HER2 was partially diminished, while the response to neratinib was completely abrogated. To mimic clinical scenarios, we administered oral ciprofloxacin (cipro) or amoxicillin/clavulanic acid (amox/clav), examples of antibiotics commonly given to patients, and neratinib. Cipro mirrored the ABX effect, fully halting the neratinib response, whereas amox/clav induced a partial impairment. Given that cipro and amox/clav target fewer bacteria than the ABX cocktail, these findings suggest that both the abundance and composition of the microbiota play a role in the efficacy of HER2 therapy. Next, we examined whether disrupting microbiota with antibiotics influences the immune response linked to HER2+ BC treatments. We thoroughly profiled immune cell subsets in tumors and the circulation after HER2-targeted therapy. In control (H2O) mice, both HER2 therapies led to immune remodeling of the tumor microenvironment, characterized by a decrease in tumor-associated neutrophils and macrophages, along with increased infiltration of NK, CD8+, and CD4+ T cells. In contrast, ABX-treated mice failed to exhibit the same immune shifts, particularly in response to neratinib, with only marginal changes observed after treatment with anti-HER2/neu. Interestingly, a similar reduction in neutrophils post-therapy occurs in blood from H2O and ABX tumor-bearing mice. In contrast, NK cells are systemically reduced in untreated ABX animals compared to those in H2O-treated mice and do not recover after therapy, which could explain the lack of recruitment of these cells to the tumor bed in ABX mice and suggest a role of these cells in therapy efficacy. Overall, our results demonstrate that antibiotic-induced disruption of the gut microbiota impairs HER2+ breast cancer therapy and the immune response associated with treatment efficacy, both systemically and locally within the tumor bed. These findings underscore innate immune pathways and microbiota-based strategies as potential therapeutic targets to mitigate the detrimental effects of antibiotics in HER2+ BC patients. Citation Format: R. E. Araya, L. J. Parker, P. Mitra, N. Erlichman, P. Chalasani, R. Li. Microbiota disruption with oral antibiotics has a detrimental effect on HER2+ breast cancer therapy efficacy 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 PS3-12-02.
Araya et al. (Tue,) studied this question.