Abstract A010: MBD4 regulates FOXA1 lineage-specific enhancers to promote prostate tumorigenesis and progression

BACKGROUND: Like many cancers, prostate cancer (PCa) relies on tissue- and lineage-specific transcription factors essential for normal tissue function and tumor progression. A key master factor is the androgen receptor (AR), which regulates prostate tissue identity and differentiation, maintaining normal, growth-suppressive, prostate-specific luminal programs via androgen response elements (AREs). However, during tumorigenesis, AR is co-opted to drive oncogenic transcription programs, including reprogramming factors like FOXA1 and HOXB13. Despite AR’s critical role, the mechanisms and functional implications of both its oncogenic and growth-suppressive programs in PCa remain incompletely understood. We hypothesized that the methyl-CpG reader and DNA repair protein MBD4 safeguards lineage trajectories by restraining pioneer factor engagement. METHODS: We performed an epigenetic-focused CRISPR screen (2,508 genes) in an LNCaP ARE-activated model to nominate the regulators of AR programs. We engineered MBD4 knockout and inducible overexpression models and profiled chromatin and transcription by ATAC-seq; CUT&RUN (AR, FOXA1, H3K27ac, H3K4me3, H3K27me3); and RNA-seq across AR+ and AR- lines. Proliferation and lineage-identity programs were also evaluated in normal mouse prostate organoids. Clinical relevance was assessed using multi-cohort patient transcriptomes and cancer-dependency datasets. RESULTS: MBD4 emerged as a gatekeeper of the AR/ARE-mediated growth-suppressive program. MBD4 loss increased chromatin accessibility and enhancer acetylation at FOXA1-enriched loci, with FOXA1 binding expanding upon loss and decreasing with MBD4 overexpression. MBD4 localized to AR/FOXA1 enhancers and limited FOXA1 engagement. Functionally, MBD4 knockout accelerated proliferation in AR+ lines and slowed growth in AR- lines (e.g., PC3, DU145). In normal mouse prostate organoids, MBD4 disruption biased luminal epithelial identity programs and reprogrammed enhancer architecture. Across patient cohorts, MBD4 expression and dependency patterns tightly tracked with AR status/lineage, linking lineage context to chromatin plasticity. CONCLUSIONS: MBD4 acts as a gatekeeper of the AR/ARE-mediated growth-suppressive program by limiting lineage-specific enhancers and restraining FOXA1 engagement. Loss of MBD4 promotes FOXA1-driven reprogramming and lineage plasticity, nominating the MBD4–FOXA1 axis as a potential therapeutic target. AI DISCLOSURE: Generative AI was used to help draft the wording of this abstract; all content was supplied, reviewed, and approved by the authors. Citation Format: Xuanrong Chen, Janny Villa-Pulgarin, Jiansheng Wu, Un In Chan, Jude Owiredu, Anjali Yadav, Andrea Sboner, Christopher Barbieri. MBD4 regulates FOXA1 lineage-specific enhancers to promote prostate tumorigenesis and progression [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 A010.