Abstract Introduction: Upon prolonged anti-androgen treatment, 15-20% of castration resistant prostate cancer (CRPC) progresses to poorly differentiated, androgen-independent neuroendocrine prostate cancer (NEPC) that express neural markers. Studies on clinical samples have elucidated distinct DNA methylome of NEPC tumors compared to other subtypes, suggesting the importance of epigenetic regulation in lineage plasticity of advanced CRPCs.EZH2, catalyzer of repressive H3K27me3, is reported to be overexpressed in NEPC and has been studied as a therapeutic target in advanced prostate cancer. Although evidence from embryonic stem cell studies suggest possible interplay between the two mechanisms, how it contributes to lineage plasticity in advanced CRPCs is unaddressed. Methods: DNA methylome and H3K27me3 of patient-derived xenografts/organoids and murine model with MYCN induction and Pten/Rb1 co-loss (PRN) were analyzed. DNA methylome upon EZH2 deletion and H3K27me3 profile upon DNMT1 deletion was studied in human and murine NEPC models. To understand their transcriptional impact, expression profiles were analyzed upon EZH2/DNMT1 deletion. Results: Both DNA methylome and H3K27me3 profile shifts during progression of CRPC to NEPC. H3K27me3 was enriched at hypomethylated regions of NEPC Vs. CRPC tumors across models and was independent of genomic context. EZH2 loss changed DNA methylome in NEPC at regions known to have differential DNA methylation during lineage plasticity. Neuron-related genes were hypomethylated and upregulated while, morphogenesis-related and bivalent genes were hypermethylated and downregulated upon EZH2 deletion. Conversely, DNMT1 deletion altered H3K27me3 landscape in NEPC. Neuron-related genes and bivalent genes were downregulated and enriched with H3K27me3 but upregulated and had depleted H3K27me3 in CRPC upon DNMT1 deletion. H3K4me3 was also decreased upon DNMT1 knockout in NEPC at these regions suggesting loss of bivalency. Short-term DNMT inhibition in NEPC PDX showed similarly altered H3K27me3 as noted in DNMT deleted NEPCs. Conclusions: DNMT1 and EZH2 activity overlaps and together reprograms the epigenome during lineage plasticity of advanced CRPCs. EZH2 loss was partially compensated by DNMT activity leading to further neuroendocrine differentiation while DNMT1 loss shifted H3K27me3 leading to suppression of neuron-related genes. Citation Format: Richa Singh, Varadha Balaji Venkadakrishnan, Eddie Imada, Nicholas J. Brady, Yasutaka Yamada, Luigi Marchionni, Brian D. Robinson, David S. Rickman, Himisha Beltran. Cooperativity between DNMT and EZH2 activity drives neuroendocrine phenotype in advanced prostate cancer abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1359.
Singh et al. (2026) studied this question.