Abstract A079: A single-cell RNA expression atlas of metastatic prostate cancer: tumor cell evolution from AR sensitive to castration resistance

Abstract Background: Metastatic prostate cancer, a leading cause of prostate cancer mortality, exhibits therapy-induced tumor cells plasticity and associated intra-tumoral and organ-specific heterogeneity. Patients with alterations of tumor suppressor genes (TSGs) represent a hard-to-treat subgroup that often progresses to metastatic castration resistant prostate cancer (mCRPC) and neuroendocrine (NE) prostate cancer (NEPC). To understand the molecular mechanisms of mCRPC/NEPC progression and develop targeted therapies, we developed an AR positive patient-derived metastasis model that harbors TSGs alterations in TP53, PTEN, and RB1 (termed PDM136). Upon intracardiac injection in NSG mice, PDM136 develops bone, liver and adrenal metastases with AR+NE- histological phenotypes; tumor cells became heterogeneous with ARlowNE-, AR-NE+, AR-NE- subgroups following castration. Interestingly, bone metastatic tumors are mainly ARlowNE- and AR-NE-, while the majority of liver metastases are AR-NE+, recapitulating the major phenotypes of bone and liver metastasis in mCRPC patients. Methods: To understand global changes in tumor cell evolution across during castration, we profiled the single-cell transcriptomes of 70, 000 cells encompassing intact, early castrated, intermediate castrated and later castrated stages from bone, liver and adrenal metastases. Clustering, velocity and trajectory analyses were performed. Pseudo-bulk differential expression analyses were used to identify cell states, enriched pathways, and distinct castration-responsive tumor cell populations. Results: We identified 14 unique clusters representing heterogeneous cell states. Velocity and trajectory analysis of specific clusters suggested castration-associated plasticity. The transition from castration sensitive to castration resistance is associated with decreased AR signature and increased NE signature in a subset of neuroendocrine clusters marked by high expression of SOX2 and ASCL1. Tumor cells in liver metastases switched to a NE state earlier than bone and adrenal metastases. Many clusters also maintained a transition state during the development of castration resistance marked by dual negativity for AR and NE signatures. The transition state in bone metastases showed an upregulation of TGFb, notch and Wnt pathways that trigger EMT and stemness. Conclusions: These results suggest that while prostate tumor cells harboring TSGs are initially AR sensitive, they can achieve castration resistance via different mechanisms. Our study highlights the significance of using clinically relevant animal models to assess variable mechanisms that drive progression of mCRPC. Observed cellular plasticity and intra-/inter-tumor heterogeneity suggest that combination therapies targeting multiple pathways may be crucial for the effective management of mCRPC. Citation Format: JuanJuan I. Yin, Anson Ku, Chennan Li, Joseph Twohig, Tri Truong, Dana Vargas, Adam Sowalsky. A single-cell RNA expression atlas of metastatic prostate cancer: tumor cell evolution from AR sensitive to castration resistance abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86 (2Suppl): Abstract nr A079.