Abstract 2099: N-Myc-mediated epigenetic reprogramming drives lineage plasticity in advanced prostate cancer
Authors: Adeline Berger, Nicholas Brady, Rohan Bareja, Brian Robinson, Vincenza Conteduca, Michael Augello, Loredana Puca, Adnan Ahmed, Xiaodong Lu, Inah Hwang, Alyssa Bagadion, Andrea Sboner, Olivier Elemento, Jihye Paik, Jindan Yu, Christopher Barbieri, Noah Dephoure, Himisha Beltran, David S. Rickman
Journal: Cancer Research (2019)

Abstract Background: Despite recent advances in the development of highly effective androgen receptor (AR)-directed therapies for the treatment of prostate cancer, nearly 37% of patients develop resistance. A further third of these patients progress to develop aggressive neuroendocrine prostate cancer (NEPC) for which no effective therapies exist. Lineage plasticity, a process by which differentiated cells lose their identity and acquire alternative lineage programs, has been proposed as a mechanism of resistance to targeted therapies in epithelial tumors such as prostate cancer. Although epigenetic deregulation has been implicated as a driver of the epithelial to neuronal switch observed in NEPC, the molecular programs are poorly understood. Previously, we observed that the majority of NEPC and 20% of castration-resistant prostate cancer (CRPC) aberrantly overexpress the transcription factor MYCN (N-Myc). Despite this frequent occurrence, the role of N-Myc in driving lineage plasticity and the epigenetic mechanisms which regulate disease progression remain to be elucidated. Methods: We analyzed overall survival and whole transcriptome data from a cohort of over 200 prostate cancer patients, including the largest-to-date population of NEPC patients. We also analyzed epigenetic modifications along with the N-Myc transcriptome, cistrome and chromatin-bound interactome by performing ChIP-seq, RNA-seq and RIME in a combination of mouse models, human prostate cancer cell lines, and NEPC patient-derived organoids. Results: Expression of MYCN in CRPC and NEPC patients correlates with reduced overall survival. NEPC tumors are significantly enriched for stem cell genes associated with normal neuroendocrine cell precursors, embryonic stem cells and neural lineage-defining genes from activated neural stem cells. The integration of next-generation sequencing data revealed that the N-Myc cistrome is androgen-dependent and drives a transcriptional program leading to epithelial plasticity and the acquisition of clinically relevant neuronal lineage markers. Our data also reveal that N-Myc interacting proteins as well as AR co-factors and pioneering factors (e.g. FOXA1 and HOXB13) explain the observed dynamic binding of N-Myc. Interestingly, histone marks and EZH2 activity specifically associated with lineage-defining genes were reprogrammed by N-Myc. Finally, we demonstrated that N-Myc-induced gene expression and epigenetic changes accurately classify our patient cohort. Conclusions: We describe a novel role for N-Myc in prostate cancer, characterized by changes in the N-Myc cistrome and cooperation with AR co-factors, as well as reprogramming of the epigenome in an androgen context-dependent manner. This reprogramming is associated with induction of a lineage plastic state and a switch towards a neural identity that favors the development of AR independence and NEPC. Citation Format: Adeline Berger, Nicholas Brady, Rohan Bareja, Brian Robinson, Vincenza Conteduca, Michael Augello, Loredana Puca, Adnan Ahmed, Xiaodong Lu, Inah Hwang, Alyssa Bagadion, Andrea Sboner, Olivier Elemento, Jihye Paik, Jindan Yu, Christopher Barbieri, Noah Dephoure, Himisha Beltran, David S. Rickman. N-Myc-mediated epigenetic reprogramming drives lineage plasticity in advanced prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2099.