Single-Cell and Spatial Transcriptomic Profiling Reveals Epithelial Functional States and Fibroblast Phenotypes in Hormone Therapy–Naïve Localized Prostate Cancer

Localized prostate cancers are heterogeneous and multifocal, with diverse outcomes. Current prognostic methods are epithelium-centric, overlooking the complex cellular landscape within the tumor microenvironment (TME). To further characterize the heterogeneity of the TME, we performed a comprehensive analysis of cancerous and adjacent-benign cores from 24 patients with hormone therapy-naïve localized prostate cancer using single-cell RNA sequencing (scRNA-seq). Integrating copy-number variation and transcriptional signatures enabled epithelial cell classification across a malignant spectrum, revealing widespread molecular perturbation. The analysis revealed patient-unique and shared luminal states and an expansion of club cell phenotypes, suggesting luminal dedifferentiation. Detailed annotation of stromal phenotypes, with a focus on fibroblasts, identified a perineural fibroblast population. Spatial transcriptomics elucidated the precise anatomic distribution of cancer-associated fibroblasts within the prostate cancer TME. Together, this study provides a valuable foundation for advancing the understanding of prostate cancer pathobiology and developing a comprehensive cellular model of the disease. SIGNIFICANCE: Development of a single-cell RNA-sequencing and spatial transcriptomics cellular reference of localized prostate cancer enables identification of a spectrum of malignant epithelial phenotypes and discovery of a perineural class of fibroblast.