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

Abstract 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 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 (2Suppl): Abstract nr A010.