Epigenetic Plasticity in castration-resistant prostate cancer (CRPC) to neuroendocrine prostate cancer (NEPC) Transition

Despite the significant success of second-generation androgen receptor (AR) pathway inhibitors (ARPIs) (such as enzalutamide¹ and abiraterone²), castration-resistant prostate cancers (CRPC) progress under prolonged androgen deprivation³. A subset of CRPC tumors evade the pressure of targeted therapies by shedding their dependence on AR (AR-independent)⁴. These new clones harbor distinct molecular profiles and unlock a new phenotype associated with stem-cell-like and neuronal characteristics^5-10. Lineage plasticity underlies this transition to an alternative phenotype. This process is initially driven by molecular alterations creating clones with cellular plasticity, followed by additional events that lead to the treatment-emergent small-cell Neuroendocrine Prostate Cancer (tNEPC)¹¹. Most NEPC cases are diagnosed in advanced stages with metastasis explaining the high mortality rate ^11-15. While de novo NEPC are rare^{16, 17}, tNEPC account for approximately 20% of advanced, treatment-refractory CRPC cases^{5, 7, 18} and this number may further rise as a result of hormone therapies moving earlier in the line of treatment¹⁹.

The Epigenetic Landscape of NEPC

The genomic variations between CRPC and NEPC are limited, except for the frequent loss of tumor suppressors PTEN, RB1, and TP53. However, the progression to NEPC is accompanied by extensive transcriptional reprogramming ^{11, 15}, suggesting that the emergence of the neuroendocrine phenotype is driven predominantly by epigenetic dysregulation^20-23. Epigenetic plasticity controls cell fate by altering DNA accessibility to transcription factors and gene expression. The process is controlled through regulation of DNA methylation, nucleosome remodeling, and histone modifications²⁴. Altogether, alterations in the epigenome of CRPC tumors following AR-targeted therapies is characteristic of the progression to tNEPC.

Chromatin remodeling and the role of Transcription factors 

The progression of CRPC to tNEPC under the pressure of ARPIs is marked by significant chromatin remodeling, where the chromatin accessibility increases at regions regulating the stem-cell and neuronal pathways, to facilitate the binding of specific transcription factors (TFs). This creates the shift in gene expression patterns towards a neuronal phenotype. During the progression to NEPC, ASCL1, a neuronal-determinant TF, is central to driving lineage plasticity and neuronal lineage determination. ASCL1 expression, motif accessibility, and activity increase disproportionately following ARPIs, leading to the activation of stem-cell-like and neuronal programs. Notably, loss of ASCL1 in NEPC results in the significant loss of accessible chromatin and reversal of the neuronal state to luminal one²². ASCL1 further support the NEPC phenotype by reprogramming the cistrome of other pioneering TFs such as FOXA1²⁵ . Therefore, the transition from CRPC to NEPC provoked by ARPIs modify the transcriptional control of lineage specific transcription factors.

It is important to highlight the distinction among NEPC subtypes through their chromatin landscape, since each subtype will have its unique vulnerabilities that can be explored for therapeutic purposes. Although converging towards a neuronal program, neuronal-lineage determinant TFs such as ASCL1 and NEUROD1 orchestrate divergent chromatin remodeling trajectories that favor the neuroendocrine (NE) program. Further, investigations employing single-cell chromatin accessibility analyses in mouse models have unveiled two distinct clones, driven by ASCL1 or the stem-cell specific TF OCT11 (also known as POU2F3), which defines a non-NE subtype. These results emphasize the complexity of the epigenetic landscape in NEPC but also highlights the specificity of TFs' involvement in driving the NE phenotype, highlighting the nuanced interplay of epigenetic mechanisms in cancer progression.

Epigenetic modifiers 

Lineage determinant TFs guide specific chromatin remodelers and epigenetic modifiers to exert their influence, thereby establishing the desired cell fate. Epigenetic modifiers governing prostate cancer lineage switches are often dysregulated in NEPC, such as histone methyltransferase EZH2 and DNA methyltransferases^{26, 27}. EZH2, a core component of the Polycomb Repressive Complex 2 (PRC2), deposits methyl groups on lysine 27 of histone 3 (H3K27) to suppress transcription²⁸. EZH2 is over-expressed in NEPC compared to CRPC and plays a role in silencing the AR-driven luminal program. Interestingly, EZH2 has been reported to function in a non-canonical manner, in concert with an alternative AR program, to induce histone acetylation and facilitate the NE lineage conversion to activate stem-cell and NE programs ²³.

In parallel, the role of DNA methylation in distinguishing prostate cancer stages has become increasingly evident^{11, 29}. DNA methylome alterations is a hallmark of tNEPC, highlighting the unique epigenetic profile of these tumors¹¹.  In fact, a distinct DNA methylation pattern (combination of DNA hyper- and hypo-methylation) is associated with NEPC, which can be detected in circulating cell-free DNA (cfDNA), potentially serving as significant biomarkers^{29, 30}. However, whether NEPC subtypes can be distinguished with DNA methylation patterns remain to be elucidated. These intricate interactions between lineage-determining TFs and epigenetic modifiers underscore the complexity of prostate cancer progression and the development of lineage plasticity. Given the potential reversibility of epigenetic modifications, unraveling mechanisms controlling lineage plasticity could lead to the identification of therapeutic targets and the development of strategies to combat resistance to ARPIs.

Learn more:

These review articles summarise the transcriptional and epigenetic mechanisms governing prostate cancer lineage plasticity:

1. The Transcriptional and Epigenetic Landscape of Cancer Cell Lineage Plasticity | Cancer Discovery | American Association for Cancer Research (aacrjournals.org)
2. Epigenetics in prostate cancer: clinical implications - PMC (nih.gov)
3. Epigenetic reprogramming during prostate cancer progression: A perspective from development - PMC (nih.gov)

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