Single-cell profiling of patient-derived ovarian cancer organoids identifies epithelial states enriched after acute tamoxifen exposure

Background: Tamoxifen is used for hormone receptor-positive breast cancer, but its activity and response determinants in ovarian cancer remain incompletely defined. Integrating patient-derived organoids (PDOs) with single-cell RNA sequencing (scRNA-seq) may identify transcriptional states associated with endocrine response.Methods: Ovarian cancer tissues from 4 patients were cultured under Matrigel-based organoid conditions and profiled by scRNA-seq after tamoxifen treatment or matched untreated culture. Patient-adjusted generalized linear mixed-effects models identified treatment-enriched and treatment-reduced epithelial subclusters. Differential expression and gene set enrichment analyses were performed, and a 40-gene bidirectional treatment-enriched surviving (TES) state signature was scored using singscore. The TES score was evaluated in an exploratory manner in nine ovarian cancer cell lines with matched bulk RNA sequencing and tamoxifen viability assays, and further assessed in tamoxifen-treated, high-purity samples from The Cancer Genome Atlas breast invasive carcinoma (TCGA BRCA).Results: Integrated analysis of 11,999 single cells identified epithelial, fibroblast, macrophage, T-cell, dendritic cell, and B-cell compartments. Epithelial reclustering identified 5 states: EC1 and EC4 were operationally defined as treatment-enriched epithelial states, hereafter referred to as TES, recognizing that enrichment after treatment does not by itself prove a causal survival mechanism, whereas EC0, EC2, and EC3 were classified as treatment-reduced states (TRS). TES states showed inflammatory response, tumor necrosis factor α/nuclear factor κB signaling, complement activation, epithelial–mesenchymal transition, and lipid-associated programs, whereas TRS were enriched for cell-cycle, MYC/E2F, DNA repair, and oxidative phosphorylation pathways. The TES score correlated with tamoxifen area under the curve in ovarian cancer cell lines (Spearman ρ=0.733, p=0.0246) and stratified progression-free survival in TCGA BRCA samples (log-rank p=0.0035; hazard ratio, 3.179).Conclusion: Patient-derived ovarian cancer organoids identified heterogeneous epithelial states enriched after acute tamoxifen exposure. The derived transcriptional score showed exploratory association with tamoxifen response in ovarian cancer cell lines and progression-free survival in tamoxifen-treated breast cancer samples, warranting further validation.