Distinct treatment-induced neuroendocrine prostate cancer subtypes predict prognosis

With limited treatment options for advanced CRPC exhibiting an NEPC phenotype, we aimed to elucidate the mechanisms of adeno-to-neuroendocrine lineage transition to guide the development of effective therapeutic strategies. By integrating single-cell RNA sequencing data from fresh human CRPC cases, we identified three distinct neuroendocrine subtypes in CRPC: a REST-dependent subtype (NE I), an N-Myc-dependent subtype (NE II), and a combined N-Myc/REST subtype (NE I+II) among 5,797 neuroendocrine-like epithelial cells.

These subtypes were validated through multiplex immunofluorescence staining. Single-cell trajectory analysis uncovered N-Myc and REST as key transcription factors driving these distinct neuroendocrine lineages, and multi-omics time course analysis of publicly available transcriptomic data further recapitulated the N-Myc and REST lineage progression. Notably, we observed PSMA loss in the N-Myc lineage and identified STMN1 as a biomarker for PSMA-negative NEPC.