Abstract PS2-11-04: Transcriptional Plasticity in Early Evolving Endocrine Therapy Resistance

Abstract Introduction: 70% of breast cancers express estrogen receptor (ER) alpha. Endocrine therapies (ET) initially form the backbone of their treatment, but more than one-third develop ET resistance. Most research on ET resistance focuses on pathways cooperating with high ER activity, but less on cellular diversity within ER-positive (ER+) tumors. We hypothesize that a fraction of cells with low ER expression in untreated ER+ tumors can resist tamoxifen, which is selected by treatment and can evolve towards adapted resistance. Methods: We performed single-cell RNA expression and chromatin accessibility analysis on ER+/HER2-negative patient-derived xenografts (PDX) treated with tamoxifen (50 mg/kg PO daily) or control for 6 weeks. Cell clusters were characterized using gene set enrichment analysis and trajectory analysis. Results: ESR1 expression correlated inversely with PIM3, PLK3, and IRAK2 kinase activity and positively with RET kinase activity in untreated tumors in multiple datasets (PMID: 34493872, 23000897, 34739872) and two PDX models. Trajectory analysis of the PDX1 model defined the closest trajectory between untreated and tamoxifen-treated cells through ESR1-low cell clusters, suggesting that tamoxifen resistance arises from an untreated ESR1-low population. The untreated ESR1-low cluster was again characterized by greater PIM3, PLK3, and IRAK2 kinase activity expression. In the PDX1 model, the untreated ESR1-low cluster also had higher expression of kinase signatures related to MAPK, PIK3CA, and NF-κB. The trajectory from untreated to tamoxifen-treated ESR1-low clusters was associated with lower activity of kinase signatures related to MAPK and NF-κB pathways, and increased HER2 kinase activity signature. Late-resistant cells at the endpoints of diverging trajectories regain expression of ESR1 but not ESR1-associated genes, and have decreased PIM3 kinase activity signature and increased BRAF and PIK3CA kinase activity signature expression. Conclusions: ESR1-low cells in untreated ER+ tumors may represent a funnel point in the development of ET resistance and consistently demonstrate enrichment of specific kinase signatures. In persisting on ET, these ESR1-low cells might seed ET-resistant trajectories with heterogeneous potential acquired driver kinase pathways. Early targeting of pathways enriched in ESR1-low cells in ER+ tumors in combination with ET could prevent or delay ET resistance. Further study is needed to determine the reproducibility of resistant trajectories and the efficacy of selectively targeting preexisting ESR-low cells. Citation Format: Y. N. Agrawal, S. Haase, A. A. Whitman, P. M. Spanheimer. Transcriptional Plasticity in Early Evolving Endocrine Therapy 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 PS2-11-04.