Abstract Background: Triple negative breast cancer (TNBC) is among the most aggressive and lethal breast cancer subtypes, disproportionately affecting young women and women of African ancestry. Most patients do not respond to current immunotherapy and chemotherapy regimens. Resistance is driven not only by tumor genetics but also by environmental pressures within the tumor microenvironment, including hypoxia, chronic inflammation, and suppressive stromal signals, which collectively reshape tumor-immune interactions and foster immune evasion. These factors promote metastasis and therapy failure, yet the molecular mechanisms connecting hypoxia to immunosuppression remain unclear. Patients with hypoxic TNBC have limited treatment options, highlighting an urgent need for strategies that can reprogram the tumor microenvironment and restore immune function. Here, we identify BACH1 as a key non-HIF hypoxia-responsive regulator that links cellular stress adaptation with immune escape in TNBC. Methods: We leveraged an integrated multi-omics approach to investigate hypoxia-induced plasticity and immune evasion in TNBC. Single-cell RNA sequencing and spatial transcriptomics mapped hypoxia-driven transcriptional changes in murine TNBC models and human xenografts. ATAC-seq and motif analysis identified accessible chromatin regions and key regulatory networks. Functional roles of BACH1 were assessed using CRISPR-mediated knockout and overexpression under hypoxic conditions. In vivo experiments with immune-competent and immune-deficient models distinguished tumor-intrinsic from host-dependent effects. Immune profiling by single-cell RNAseq, proteomics, and flow cytometry characterized immune activation in tumors and draining lymph nodes. We tested therapeutic reprogramming by treating tumors with hemin, an FDA-approved drug that promoted BACH1 degradation. Finally, artificial intelligence classifiers based on BACH1 activity signatures were developed and validated in independent breast cancer cohorts from Yale, the University of Chicago, and I-SPY 2. Results: BACH1 was robustly stabilized and induced by hypoxia in multiple TNBC cell lines and patient-derived organoids, independent of canonical HIF signaling. Unlike HIF1A, which supports cell survival during acute hypoxia, BACH1 drives stem-like transition states, enabling rapid shifts into pre-metastatic states and providing an alternative adaptation to hypoxic stress. This mechanism significantly impacts immune regulation, with critical consequences for tumor-immune interactions and therapy resistance. Notably, these BACH1-high stem-like states negatively correlate with T-cell infiltration in patient tumors across breast cancer cohorts, predicting immune exclusion and therapy resistance. Consistent with this observation, loss of BACH1 in cancer cells promoted an immune-inflamed tumor phenotype characterized by enhanced T-cell recruitment and activation, an increased CD8⁺/Treg ratio, decreased early stage tumor growth and significantly reduced lung metastasis in a syngeneic model. Conversely, re-expression of BACH1 restored T-cell exclusion in knockout tumors. Flow cytometry profiling revealed that BACH1-deficient tumors triggered early and sustained T-cell activation, while limiting T-cell PD-1 expression in tumor-draining lymph nodes. Mechanistically, BACH1 acts in part by repressing the Type I interferon alpha locus, suppressing immunostimulatory macrophages and promoting T cell exhaustion in tumor-draining lymph nodes. Genetic BACH1 knockout combined with immune checkpoint blockade potentiated therapeutic efficacy. Short-course hemin treatment reproduced the effects of genetic BACH1 deletion, enhancing T-cell priming and synergizing with immunotherapy. In contrast, continuous hemin dosing was immunosuppressive, highlighting the importance of precise therapeutic timing. Together, genetic loss and optimized pharmacologic inhibition of BACH1 sensitized TNBC tumors to checkpoint blockade. To identify patients likely to benefit from BACH1-targeted therapy, AI models trained on xenograft-derived BACH1 signatures were developed. These models predicted immune exclusion and resistance more effectively than bulk BACH1 mRNA levels, which is confounded by expression in immune cells. Elevated BACH1 activity correlated with poor T-cell infiltration and immunotherapy resistance across breast cancer cohorts. Stratifying patients by BACH1 activity provided high associative value for checkpoint inhibitor response and identified individuals with hypoxic TNBC who may benefit from BACH1-targeted treatment. Significance: This study identifies BACH1 as a central regulator of hypoxia-driven transcriptional plasticity and immune evasion in TNBC. By coordinating hypoxia, chromatin remodeling, and interferon suppression, BACH1 promotes metastatic and immunotherapy-resistant tumor states. Inhibition of BACH1 restores interferon signaling, enhances immune cell infiltration, and increases sensitivity to checkpoint blockade, suggesting BACH1 as a promising therapeutic target. We also present an AI-based biomarker strategy that stratifies patients by BACH1 activity, supporting clinical translation. Overall, these findings establish non-HIF hypoxia sensors as key drivers of tumor adaptation and position BACH1 as an actionable target to reprogram the tumor microenvironment and improve immunotherapy outcomes in aggressive cancers. Citation Format: Long Chi Nguyen, Madeline Henn Bungert, Emily Shi, Christopher Dann, Buu Truong, Kent Schechter, Dongbo Yang, Thomas Jiyoung Li, Eva Suarez, Wenchao Liu, Geetha P. Yerradoddi, Margarite D. Matossian, Joana Pinheiro, Jinjun Gao, Yoo Jane Han, Anran Li, Andrea Ziblat, Jing Zhang, Mitsuyo Matsumoto, Yan Li, Yingming Zhao, Scott Andre Oakes, Jingshu Wang, Thomas F. Gajewski, Olufunmilayo I. Olopade, Kazuhiko Igarashi, Frederick Matthew Howard, Jonathan A. Trujillo, Marsha Rich Rosner. BACH1 drives hypoxia-induced stem-like transition states and immune evasion in breast cancer abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts) ; 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86 (8Suppl): Abstract nr NG01.
Nguyen et al. (Fri,) studied this question.