Abstract 2735: The role of ca2 in regulating 3d chromatin structure in tamoxifen resistant breast cancer

Abstract Background: Estrogen receptor-positive breast cancer frequently develops resistance to tamoxifen in one third of patients, driven by various mechanisms. Our work has linked 3D chromatin alterations to this resistance. However, most of the work in 3D chromatin regulation was mostly conducted in in vitro cell culture system. It is becoming very clear that to expand the characterization of 3D genome organization in patient samples is an emerging task. Hypothesis: We hypothesize that 3D chromatin alterations, including compartment switching, TAD reorganization, and dysregulated chromatin looping, drive tamoxifen resistance (TR) in breast cancer. Looping-mediated genes may play critical roles in resistance and serve as potential therapeutic targets. Methods and Results: To investigate the role of 3D chromatin changes in tamoxifen resistance, we performed Hi-C profiling on normal tissues (NTs), primary tumors (PTs), and tamoxifen-treated recurrent tumors (RTs), uncovering significant chromatin alterations. These included 46.8% A-to-B and 32.8% B-to-A compartment switching from NTs to PTs, and 58.3% B-to-A flipping during PT-to-RT progression. TAD analysis identified RT-specific Neo and Fuse alterations as well as tumor-specific chromatin loops. CA2 was identified as a enhancer-promoter looping (EPL)-mediated gene with its higher expression linked to poor relapse-free survival in endocrine-treated patients. Functional studies using the CA2 inhibitor brinzolamide demonstrated its ability to reduce cell viability, loop intensity, and CA2 expression in MCF7TR and T47DTR cells. In vivo, brinzolamide significantly reduced tumor growth in tamoxifen-resistant cell-derived xenograft (CDX) models. Additionally, CRISPR deletion of CA2 EPL enhancer region in MCF7TR cells resulted in a marked reduction in cellular viability, gene expression and protein expression. Conclusion: Our findings suggest CA2 as a key looping-mediated gene play an oncogenic role in driving tamoxifen resistance in breast cancer. Our study yields significant mechanistic insights into the role and clinical relevance of 3D chromatin architecture in tamoxifen resistant breast cancer. Citation Format: Lavanya Choppavarapu, Kun Fang, Tianxiang Liu, Aigbe G. Ohihoin, Victor X. Jin. The role of ca2 in regulating 3d chromatin structure in tamoxifen resistant 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 2735.