Abstract A081: FOXA1 Lysine methylation remodels its chromatin binding and restrains oncogenic reprogramming in prostate cancer

Abstract Background: FOXA1 acts as a pioneer transcription factor that enhances chromatin accessibility and facilitates androgen receptor (AR) binding in prostate cancer (PCa). In the stage of castration-resistant prostate cancer (CRPC), FOXA1 undergoes chromatin remodeling that promotes tumor progression and therapy resistance. Our recent findings revealed that the chromatin binding of FOXA1 is destabilized by SETD7-mediated lysine 270 methylation and stabilized by LSD1-mediated demethylation. However, how FOXA1 methylation status influences global FOXA1 binding landscape, AR signaling, and other transcriptional programs in CRPC remain unclear. Methods: We firstly used AlphaFold structural modeling tool to predict the direct interaction between LSD1/SETD7 and FOXA1. To further define the functional role of FOXA1 K270 methylation, we generated stable cell lines expressing either inducible wildtype FOXA1 or the methylation-defective K270R mutant with knockdown of endogenous FOXA1. Integrated ChIP-seq and RNA-seq analyses were performed to evaluate changes in global FOXA1 chromatin occupancy, AR binding dynamics in response to AR-targeted therapies, super-enhancer landscape, and downstream transcriptional programs. We then determined effects of a clinical relevant LSD1 inhibitor bomedemstat, on FOXA1 chromatin binding and oncogenic reprogramming in cell lines and xenograft models. Results: AlphaFold modeling revealed that the amine oxidase domain of LSD1 interacts closely with the wing2 loop region of FOXA1. The K270R mutant exhibited expanded FOXA1 chromatin occupancy and altered AR chromatin binding in response to enzalutamide. Transcriptomic profiling showed upregulation of E2F, MYC, and other cell cycle-associated pathways in K270R mutant cells. Pharmacologic inhibition of LSD1 with bomedemstat globally reduced FOXA1 chromatin binding, suppressed E2F signaling, and decreased xenograft tumor growth in FOXA1-high CRPC models. Conclusions: Our study identifies FOXA1 K270 methylation as a critical molecular brake that restricts FOXA1 chromatin binding and its oncogenic transcriptional activities. LSD1 inhibition that restores FOXA1 methylation can restrict FOXA1 chromatin binding, repress FOXA1-activated E2F signaling, and reduce tumor growth. These findings provide a strong rationale for targeting the LSD1-FOXA1 axis as a therapeutic strategy in the AR/FOXA1-high CRPC tumors. Citation Format: Songqi Zhang, Mingyu Liu, Yaozong Su, Jaeweon Jeong, HyeonYeong Sun, Mannan Nouri, Dong Han, Shuai Gao, Jill A. Macoska, Steven P. Balk, Changmeng Cai. FOXA1 Lysine methylation remodels its chromatin binding and restrains oncogenic reprogramming in 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(2_Suppl):Abstract nr A081.