Drug-Induced Epigenomic Plasticity Reprograms Circadian Rhythm Regulation to Drive Prostate Cancer toward Androgen Independence

Abstract

In prostate cancer, androgen receptor (AR)-targeting agents are very effective in various disease stages. However, therapy resistance inevitably occurs and little is known about how tumor cells adapt to bypass AR suppression. Here, we performed integrative multi-omics analyses on tissues isolated before and after 3 months of AR-targeting enzalutamide monotherapy from high-risk prostate cancer patients enrolled in a neoadjuvant clinical trial. Transcriptomic analyses demonstrated that AR inhibition drove tumors towards a neuroendocrine-like disease state. Additionally, epigenomic profiling revealed massive enzalutamide-induced reprogramming of pioneer factor FOXA1 – from inactive chromatin sites towards active cis-regulatory elements that dictate pro-survival signals. Notably, treatment-induced FOXA1 sites were enriched for circadian clock component ARNTL. Post-treatment ARNTL levels associated with poor outcome, and ARNTL knockout strongly decreased prostate cancer cell growth. Our data highlight a remarkable cistromic plasticity of FOXA1 following AR-targeted therapy, and revealed an acquired dependency on circadian regulator ARNTL, a novel candidate therapeutic target.

Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential

“…Finally, we employ machine learning to classify patient ARBS in a grouped analysis using LNCaP STARR-seq 12 , which has limitations to interpretability due to contextual differences between patients, constructs, and cell lines. However, we have recently observed a strong correlation between LNCaP STARR-seq data and H3K27ac signals in patient samples 62 , making such a predictive model relevant for clinical activity.…”

Epigenetic mechanisms underlying subtype heterogeneity and tumor recurrence in prostate cancer

“…Polycomb Repressor Complex 2 (PRC2, comprising EED and SUZ12) could transdifferentiate CSPC cells (LNCaP-AR) into NEPC and induce resistance to enzalutamide 27 . Recent clinical evidence supports that enzalutamide treatment in localized CSPC induces epigenomic plasticity 28 , by reprograming circadian rhythm regulation, which leads to the activation of cellular plasticity with the gain of NEPC-like features 28 . One may also consider the evidence that nitric oxide (NO) signaling acts as a driver of epigenetic reprogramming 29 , in the context of NO-signaling also inhibits the AR activity in prostate cancer cells 30 .…”

Polycomb Directed Cell Fate Decisions in Development and Cancer

“…It has been reported that the EZH2-T350 phosphorylation and consequent AR interaction plays an important role in the transition and differentiation from CRPC to more aggressive PCa phenotypes [ 176 ]. Therefore, these tumors become enzalutamide resistant, a second-generation ADT, and display neuroendocrine (NE) features [ 179 ]. They are associated with high levels of chromogranin A, enolase and synaptophysin in serum, accompanied by a reduction in prostate-specific antigens (PSAs), a stem or basal cell-like phenotype, altered kinase signaling, and/or characteristic epigenetic alterations.…”

“…Recently, FOXA1 has emerged as an enzalutamide-induced reprograming factor in high-risk PCa patients. Linder et al reported that AR inhibitory therapy induces the cistromic repositioning of FOXA1-promoting ARNTL expression level, a classical circadian rhythm regulator, which compensates for AR inhibition and induces cellular proliferation signals [ 179 ]. In addition, ATAC-seq and RNA-seq analysis demonstrated that ASCL1 , SOX2 and NEUROD1 expression are shared master regulators between neuroendocrine cancers.…”