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.