Abstract 113: Decoding developmental programs driving tumorigenesis and immunotherapy resistance in triple-negative breast cancer
Authors: Rachel Gleyzer, Farnaz Khameneh, Zhen Qi, Wubing Zhang, Chloé B. Steen, Minji Kang, Maya Maalouf, Melanis Ghadimi, Makenna Lindsey, Sally Bobo, Thomas J. Lomis, Frederick M. Dirbas, Michael F. Clarke, Aaron M. Newman
Journal: Cancer Research (2025)

Abstract Background: Triple-negative breast cancer (TNBC), defined by a lack of hormone receptors and lack of HER2 amplification, is the deadliest subtype of breast cancer. TNBC kills 1 in 3 patients and while promising new drugs based on PARP inhibition and anti-PD1 immunotherapy can extend survival in selected patients, 30-40% of patients relapse or fail therapy. Increasing evidence suggests that TNBC tumors harbor stem-like tumorigenic cancer cells with high plasticity, capable of replenishing cancer cell populations and linked to adverse outcomes. Unfortunately, the phenotypic diversity, microenvironmental contexture, and functional significance of these cells remain poorly understood and available marker genes are not specific, precluding rational drug development. Methods: We created a multimodal single-cell RNA-seq atlas of 80 TNBC patients, including clinical covariates such as BRCA1/2 mutations, race/ethnicity, and prior treatment status. We then defined differentiation-associated malignant cell states using a novel interpretable deep learning approach for determining single-cell potency. We subsequently interrogated geospatial features, including localized microenvironments of less differentiated malignant cells, and linked them to immune checkpoint inhibitor (ICI) response. Results: Our quantitative analysis shows that TNBC is enriched in cancer cells with high developmental potency as compared to other breast cancer subtypes, consistent with its aggressive phenotype. Critically, we observed a strong association between enrichment of high potency cells and resistance to ICI treatment across human and mouse bulk expression data, both within TNBC and across other cancer types, a finding that we experimentally validated in a murine model of TNBC. In scRNA-seq and spatial transcriptomics data, we defined striking relationships between less differentiated cancer cells and context-dependent T cell states indicative of strong immunosuppressive capability. In line with this, we found that knockout of genes associated with immature cancer cells promotes TNBC cell killing by T cells in a co-culture CRISPR screen. Ongoing experiments include perturbations of novel therapeutic targets emerging from this work, with the goal of improving immunotherapy responses and ultimately extending patient survival. Conclusion: We anticipate that our approach will expand our understanding of developmental landscapes in TNBC and lead to new opportunities for developing targeted drugs in this devastating disease. Citation Format: Rachel Gleyzer,Farnaz Khameneh,Zhen Qi,Wubing Zhang,Chloé B. Steen,Minji Kang,Maya Maalouf,Melanis Ghadimi,Makenna Lindsey,Sally Bobo,Thomas J. Lomis,Frederick M. Dirbas,Michael F. Clarke,Aaron M. Newman. Decoding developmental programs driving tumorigenesis and immunotherapy resistance in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 113.