Neoadjuvant androgen signaling inhibition promotes the emergence of mixed basal/club-like cancer identity cells in prostate cancer tumors

Background: Therapies targeting androgen signaling are a cornerstone of high-risk prostate cancer treatment. Recently published evidence from the ARNEO trial (NCT03080116) shows that treatment intensification with androgen receptor signaling inhibitors (ARSIs) added to standard androgen deprivation therapy (ADT) significantly reduces residual cancer burden but does not decrease the risk of biochemical recurrence. Here we set out to investigate how cancer cells maintain viability under androgen signaling inhibition treatment pressure. Methods: We analyzed spatial, single-cell, and bulk transcriptomics data from 124 patient tumors across multiple clinical trials treated with neoadjuvant ADT or ADT+ARSIs for three months before surgery. We used matched data modalities from 57 untreated patient tumors as controls. Patient-matched pre- and post-treatment spatial transcriptomics data were available for 10 patients. Results: Our results show that three months of androgen signaling inhibition promotes the emergence of cancer cells with a mixed KRT5 +/ TP63 + basal and PIGR +/ KLF5 + club cell identity. Spatial transcriptomics data show that this adaptation is particularly pronounced in the residual tumor regions of ADT+ARSI-treated tumors. These cells exhibit an immunomodulatory transcriptional profile, characterized by upregulation of major histocompatibility complex (MHC) class I (HLA-A, HLA-B, HLA-E) and II ( CD74 , HLA-DRA , HLA-DRB1 ) genes, as well as interferon-stimulated genes ( IFITM1 , IFITM2 , IFITM3 ). The transcriptomics signature of these cells can be identified in metastatic castration-resistant tumors that lack androgen signaling or neuroendocrine characteristics, where their presence is associated with pro-inflammatory chemokine signaling activity. We show that sustained in vitro stimulation with a soluble pro-inflammatory factor is sufficient to induce features of this identity and that its emergence is associated with reduced sensitivity to AR-targeted therapies. Conclusion: Neoadjuvant androgen signaling inhibition promotes the emergence of mixed basal/club-like identity prostate cancer cells with an immunomodulatory transcriptional signature.