Abstract PS2-11-03: Fish-positive circulating tumor cells persist after effective therapy in estrogen receptor positive breast cancer: insights into genomic mechanisms of endocrine resistance

Abstract Background: Estrogen receptor (ER) positive breast cancer is commonly treated with endocrine therapy, yet resistance to estrogen deprivation remains a significant clinical challenge. Using custom FISH probes designed to detect tumor-specific genomic alterations, we identified circulating tumor cells (CTCs) of true tumor origin in early-stage luminal breast cancer patients. Longitudinal analysis revealed that 80% of patients had FISH-positive CTCs after completing therapy and while on antiestrogen treatment, despite no clinical evidence of disease. This finding suggests that standard endocrine therapy is insufficient to eradicate all malignant clones, indicating the persistence of therapy-resistant tumor cells. Methods: Primary tumor DNA was analyzed using the Oncoscan microarray platform to identify somatic copy-number alterations (SCNAs). Custom FISH probes targeting these alterations were applied to peripheral blood samples before and after therapy. Immunofluorescence characterization of CTCs was performed to assess epithelial and mesenchymal phenotypes as well as ER expression status. Genomic profiling focused on identifying drivers of proliferation, known ER resistance genes, and ER transcriptional regulators. Results: Immunofluorescence revealed that CTCs were highly heterogeneous, displaying both epithelial and mesenchymal phenotypes. ER expression among CTCs was variable: while some CTCs were ER-positive, a significant proportion showed reduced or absent ER staining. This heterogeneity suggests that loss or downregulation of ER is a key mechanism of resistance, allowing tumor cells to persist despite antiestrogen therapy. Genomic profiling of parent tumors demonstrated multiple, overlapping mechanisms supporting both proliferation and endocrine resistance. All tumors harbored several genomic alterations known to drive proliferation, most commonly involving MCL1, NTRK1, SDHC, SDHD, CHEK1, ATM, and BCL6. Every tumor exhibited at least one established mechanism of ER resistance, with frequent alterations in ATM and PIK3CA, and additional recurrent changes in AKT3, MTOR, and ARID1A. Several tumors also had alterations in genes directly involved in ER transcriptional regulation, notably ARID1A and SPEN. Conclusions: The persistence of FISH-positive CTCs in the majority of patients after therapy—despite no clinical evidence of disease—highlights the insufficiency of current endocrine regimens. The underlying genomic complexity, characterized by multiple drivers of proliferation, redundant ER resistance mechanisms, and disruption of ER regulatory pathways, underpins the survival and persistence of CTCs. These findings underscore the need for therapeutic strategies that address the multifaceted and overlapping nature of endocrine resistance in luminal breast cancer. Citation Format: K. Baldwin, K. von Maltzan, A. Zulli, M. Richard, J. Abdulsattar, D. Maroni, P. T. Greipp, R. Knudson, Mayo Cytogenetics Core, S. P. Thayer. Fish-positive circulating tumor cells persist after effective therapy in estrogen receptor positive breast cancer: insights into genomic mechanisms of endocrine resistance 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 PS2-11-03.