Crosstalk between the polycomb repressive complex 2 and DNA methylation mediates neuroendocrine prostate cancer lineage plasticity [ChIP-Seq]

Acquired changes in DNA methylation have been proposed as a mechanism underlying epigenetic plasticity in several cancer types. In prostate cancer, methylation changes are dynamic, with preclinical studies pointing to a tumor suppressor role of the DNA methyltransferase DNMT1 in early stage, in contrast to an oncogenic function of DNMT1 in later stage. The importance of DNA methylation dynamics during normal development and cell lineage fate decisions also points to DNA methylation having a critical function in lineage plasticity, yet the mechanisms by which DNA methylation changes drives lineage transitions in prostate cancer is not well understood. DNA methylation can directly repress gene expression but also cooperate with other epigenetic pathways to modulate downstream transcriptional activity. The enhancer of zeste homolog 2 (EZH2) protein is a subunit of the polycomb repressive complex 2 (PRC2) and catalyzer of the repressive histone 3 lysine 27 tri-methylation (H3K27me3) mark that also acts to suppress downstream transcriptional activity and has also been implicated in lineage plasticity. EZH2 is overexpressed in castration-resistant prostate cancer (CRPC) including NEPC and is an emerging therapeutic target. Although, the compensatory relationship between DNA methylation and EZH2 has been shown in embryonic stem cell studies and in some cancer types during acquired treatment resistance or immune evasion, how DNA methylation and EZH2/PRC2 interact to modulate prostate cancer lineage plasticity has not been characterized. In this study, we address the potential crosstalk between epigenetic pathways in advanced prostate cancer and demonstrate how DNA methylation and H3K27me3 profiles overlap and cooperate to reprogram the epigenome during prostate cancer lineage plasticity. Using both mouse and patient-derived models, we highlight the compensatory roles of these two repressive machineries during progression of CRPC towards a NE-lineage state. We predict their specific impact on NEPC progression by assessing the associated molecular alterations following genetic and pharmacological perturbations of each.