FOXA2/AP-1 drives prostate cancer lineage plasticity [ChIP-seq]

FOXA (Forkhead Box Protein A) family proteins function as pioneer transcription factors by loosening the compact chromatin structure and facilitating access for other transcription factors. The role of FOXA1 has been intensively studied in normal prostate epithelial cells and the adenocarcinoma subtype of prostate cancer (PCa) where it acts as a critical pioneer factor for the chromatin binding of androgen receptor (AR). Recent studies have indicated the emergence of FOXA2 as an adaptive response to AR signaling inhibition, particularly in prostate tumors that have undergone lineage reprogramming to a neuroendocrine PCa subtype. However, the molecular basis for this transition from FOXA1 to FOXA2 and its role in regulating the development of PCa lineage plasticity remains unclear. In this study, we show that FOXA2 binds to distinct chromatin regions in multiple AR-null PCa models with different molecular subtypes and that its binding is dependent on an epigenetic factor, LSD1. More importantly, we demonstrate that FOXA2 can function as a major pioneer factor of JUN and govern the chromatin binding of AP-1 complex in PCa exhibiting lineage plasticity. Mechanistically, differential reprogramming of JUN activates lineage-specific super-enhancers that may promote PCa progression by enhancing cell state transitions to multiple lineages. Overall, our study reveals a pivotal function of the LSD1-FOXA2 axis in rewiring AP-1 to induce differential transcriptional reprogramming required for PCa lineage plasticity. Overall design: ChIP-seq analysis of H3K27Ac in PC3 cells. ChIP-seq analysis of FOXA2, JUN, and FOSL1 in PC3 cells treated with siFOXA2 versus siNTC. ChIP-seq analysis of FOXA2 treated with vehicle versus LSD1 inhibitor (ORY-1001, C12) in PC3cells. ChIP-seq analyses of H3K4me2 in NCI-H660 cells. ChIP-seq analyses of FOXA2 in NCI-H660 cells with vehicle versus LSD1 inhibitor (ORY-1001). ChIP-seq analyses of JUN in NCI-H660 cells treated with siFOXA2 versus siNTC. ATAC analysis in PC3 and NCI-H660 cells. ChIP-seq analyses of FOXA2, JUN in LNCaP cells stably expressing FOXA2. ChIP-seq analysis of FOXA2 treated with vehicle versus LSD1 inhibitor (ORY-1001) in DKO cells.