Abstract Background: Acquired resistance to androgen receptor (AR) -targeted therapies and the progression to metastatic-castrate resistant prostate cancer (CRPC) remains a significant clinical problem. Mechanisms of acquired resistance include lineage plasticity, by which CRPC tumors can become AR-negative and progress to neuroendocrine prostate cancer (NEPC). Clinical prognoses for patients with NEPC are poor and more work is needed to understand the underlying molecular mechanisms driving lineage plasticity and CRPC to NEPC progression. FOXA2, a key lineage-determining pioneer transcription factor (TF), is significantly upregulated in subsets of CRPC and the majority of NEPC patient tumors. However, little is known about the role of FOXA2 in regulating lineage plasticity and progression from CRPC to NEPC. Methods: We queried single-cell RNAseq data from CRPC patient tumors and performed RNAseq and immunohistochemical assessment in patient tumors from 2 independent cohort of patient tumors. In CRPC and NEPC patient-derived organoids, we assessed transcriptional, chromatin accessibility changes and TF/pioneer factor and SWI-SNF chromatin occupancy changes. We performed unbiased approach of rapid immunoprecipitation mass spectrometry of endogenous protein for FOXA2 in adenocarcinoma and NEPC models to identify chromatin-bound, FOXA2-interacting proteins. We validated FOXA2-co-factor protein-protein interacting using co-immunoprecipitation. Lastly, we generated knock-in degron alleles for FOXA2 in NEPC patient-derived organoids to understand how FOXA2 is required for NEPC maintenance. Results: In the CRPC tumors, high FOXA2 expression was correlated with high ONECUT2 and SOX2 expression, high NEPC score, low AR signaling score, and poorer patient prognosis. We also found that FOXA2 overexpression suppressed androgen signaling and reprograms the chromatin accessibility landscape to close AR binding sites and open chromatin related to neural reprogramming. Additionally, we found that FOXA2 interacts with the SWI-SNF complex, AR, and HOXB13 to redirect AR and HOXB13 DNA binding away from canonical AR-regulated sites. We found that FOXA2 is bound at regulatory regions of known NEPC driver genes and epigenetic modifiers. Lastly, we discovered that FOXA2 physically interacts with key NEPC TFs and epigenetic regulators, suggesting that these FOXA2 physical interactions are required for NEPC progression. Loss of FOXA2 was sufficient to suppress key NEPC genes. Conclusions: Overall, our data from murine and human models indicate that FOXA2 functions to suppress androgen signaling by redirecting AR and AR cofactor binding. Our data also shows that FOXA2 functions as a pioneer TF to redirect chromatin accessibility and, through its interaction with key NEPC-associated TFs and a chromatin-modifying protein complex, drives the NEPC-associated molecular program. These findings provide novel mechanistic insights underlying how FOXA2 regulates lineage plasticity and NEPC progression. Citation Format: Richard Garner, Nicholas Brady, Xuanrong Chen, Alessandra Ferri, Richa Singh, Kate Dunmore, Filippo Pederzolli, Hubert Pakula, Jagpreet Singh Nanda, Michael Freeman, Michael Haffner, Colm Morrissey, Brian Robinson, Antonio Marzio, Massimo Loda, Christopher Barbieri, David S. Rickman. FOXA2 reprograms AR signaling to promote lineage plasticity in advanced prostate cancer abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86 (2Suppl): Abstract nr PR033.
Garner et al. (2026) studied this question.