Single-Cell Analysis Reveals Pre-Existing Basal-Associated Epithelial States in Metastatic Hormone-Naïve Prostate Cancer

Metastatic hormone-naïve prostate cancer (mHNPC) is a clinically aggressive form of prostate cancer characterized by early systemic dissemination and poor long-term outcomes; however, the intrinsic epithelial cell states present at diagnosis remain poorly defined. In this study, we performed single-cell transcriptomic profiling of diagnostic prostate biopsy specimens from five patients with treatment-naïve mHNPC using Fixed RNA Profiling. Integrated and case-specific analyses characterized epithelial heterogeneity and lineage-associated transcriptional programs. Across 17,825 high-quality single cells, epithelial heterogeneity was identified in all cases. In addition to luminal androgen receptor (AR)-dependent epithelial cells, reproducible basal-associated epithelial populations with reduced AR signaling and stem-like transcriptional features were observed across tumors. Epithelial–mesenchymal transition (EMT)-related transcriptional programs were detected across multiple epithelial states with inter-case variability without forming a distinct EMT cluster, whereas no transcriptionally discrete neuroendocrine epithelial cluster was identified at baseline. These findings demonstrate that treatment-naïve mHNPC harbors pre-existing basal-associated epithelial states that contribute to intrinsic tumor heterogeneity at diagnosis. The presence of AR-low and stem-like epithelial populations prior to systemic therapy suggests a potential role for lineage plasticity in the aggressive biological behavior of metastatic prostate cancer.