Abstract 432: Evolution of drug tolerance and resistance to endocrine therapy and CDK4/6 inhibitors in ER+ breast cancer

Abstract Inhibitors of CDK4/6 kinases provide a significant clinical benefit among estrogen receptor positive (ER+) breast cancer patients with advanced disease when combined with endocrine therapies (e.g., fulvestrant, letrozole). However, drug resistance to this combination therapy arises in many individuals. Some drivers have been defined that are responsible for a fraction of refractory disease, but for >50% of cases, the underlying cause of disease progression remains unknown. While inducing cell death in cancer cells is an ideal drug outcome, growing evidence indicates CDK4/6 inhibitors (CDK4/6i) can contribute to disease management by forcing cancer cells into permanent cell cycle arrest through a process known as geroconversion. We hypothesize that acquired resistance can arise from cells that are drug-tolerant and fail to complete geroconverstion, instead only entering a state of quiescence for a limited time before returning to proliferation. Here we investigate the molecular networks and their regulators that are responsible for differential outcomes in combined hormone and CDK4/6i treatment, and the synergistic effects of these drugs on geroconversion in ER+ breast cancer models. Employing a combination of bulk and single-cell RNA- and ATAC-seq, we have generated temporal maps of the transcriptional evolution of underlying regulator networks that cultivate a resistant state in MCF7 ER+ breast cancer cells. We validated our top findings in patient tumor samples and propose targets for novel therapeutic approaches. Our phenotypic and bulk sequencing assays displayed synergistic effects between drugs, resulting in a more rapid repression of cell cycle genes in combined therapy during early timepoints (<5 day), as well as a more durable suppression of S-phase entry at later time points (>15 days). By applying sci-RNA-seq we identified gene expression patterns that are specific to these drug-tolerant subpopulations, which we have validated at the protein level. Interestingly, we found that endocrine therapy imposed a distinct chromatin and transcriptional landscape detectable as early as 9 days of treatment which persisted through 40 days of treatment. Activated genes included cell surface proteins that could distinguish this drug-tolerant population and demarcate the bottleneck period between initial response and inevitable progression. Our evidence suggests that while endocrine therapy alone can induce both apoptosis and senescence, the additional layer of proliferative suppression afforded by CDK4/6i further delays the evolution and expansion of endocrine resistant cells that emerge. Future directions aim to validate our putative biomarkers of drug resistance using 3D patient-derived organoid models, in vivo xenografts, and additional patient clinical data to assess the robustness of the drug resistance signatures we have identified. Citation Format: Justin Rendleman, Matthew Pressler, Joanna Yeung, Lauren Anderson, Arnold Ou, Junyue Cao, Andrew Koff, Sarat Chandarlapaty, Viviana Risca. Evolution of drug tolerance and resistance to endocrine therapy and CDK4/6 inhibitors in ER+ 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 432.