Single-Cell Profiling Identifies the SPDEF/GAS5 Axis as a Potential Driver of Tamoxifen Resistance in Estrogen Receptor-Positive Breast Cancer

Background Estrogen receptor-positive (ER+) breast cancer is the most prevalent breast cancer subtype, and tamoxifen remains the cornerstone of adjuvant endocrine therapy. However, a significant proportion of patients eventually develop acquired tamoxifen resistance, leading to disease recurrence and progression. Methodology To characterize the cellular and molecular mechanisms underlying this resistance at single-cell resolution, we performed an integrative analysis of publicly available single-cell RNA sequencing data from 16 ER+ breast cancer specimens, comprising 13 treatment-naive primary tumors and three tamoxifen-resistant recurrent tumors. Following rigorous quality control, batch correction, and dimensionality reduction, we identified 11 major cell populations in the tumor microenvironment. Copy number variation inference using InferCNV was utilized to confirm the malignant identity of the epithelial cells. Results Gene Ontology Biological Process enrichment analysis revealed that recurrent malignant cells were significantly enriched for pathways associated with translation, chromatin remodeling, and cell division compared with primary tumor cells. Sub-clustering of malignant epithelial cells resolved nine distinct subpopulations, among which a GAS5+ (growth arrest-specific 5-positive) subpopulation was markedly expanded in tamoxifen-resistant recurrent tumors. This subpopulation exhibited distinctive metabolic reprogramming characterized by enhanced aerobic respiration and energy metabolism. Monocle2-based pseudotemporal trajectory analysis positioned GAS5+ cells at a terminally differentiated state, likely derived from CLDN3+ and CEACAM6+ tumor progenitor cells. Single-cell regulatory network inference using SCENIC identified SPDEF (SAM pointed domain-containing ETS transcription factor) as a putative key transcription factor specifically active in GAS5+ tumor cells, and SPDEF expression was highly enriched in this subcluster. Validation in The Cancer Genome Atlas breast cancer cohort demonstrated that high SPDEF expression was significantly associated with worse overall survival (log-rank p = 0.011). Conclusions These findings implicate the SPDEF-GAS5+ regulatory axis as a potential driver of tamoxifen resistance and a compelling candidate for future therapeutic targeting in ER+ breast cancer.