Epigenomic profiling of circulating chromatin for early detection and monitoring of neuroendocrine prostate cancer.
Authors: Semaan Karl , Nawfal Rashad , Eid Marc , Clark Travis , El Hajj Chehade Razane , Canniff John , Phillips Noa , Machaalani Marc , Cordeiro Paulo , Saliby Renee Maria , El Zarif Talal , Kuczmarski Katelyn , Lee Gwo-Shu Mary , Berchuck Jacob E , Pomerantz Mark , Painter Corrie , Barrett J. Carl , Choueiri Toni K. , Freedman Matthew , Baca Sylvan C. 
Published: February 2025

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Background:
Neuroendocrine prostate cancer (NEPC) is an aggressive subtype of prostate cancer that can arise after androgen blockade. Early detection of NEPC has prognostic and therapeutic implications but remains challenging. Neuroendocrine (NE) transformation is spatially heterogeneous, with co-existing NE and adenocarcinoma (AD) components across a patient's disease burden, leading to underdiagnosis using tumor biopsy. Moreover, treatment response assessment with cross-sectional imaging cannot distinguish changes in co-existing NE and AD components. To address these challenges, we developed a non-invasive approach to monitor NE transformation in patients with prostate AD (PRAD) through profiling of circulating chromatin.
Methods:
Plasma samples were collected longitudinally from patients initially diagnosed with PRAD who later developed NEPC at the Dana-Farber Cancer Institute. Chromatin immunoprecipitation and sequencing on cell-free DNA (cfChIP-seq) was performed for H3K27ac, a histone modification enriched at active promoters and enhancers. To separately quantify circulating chromatin derived from NE and AD components in a given patient, we measured H3K27ac at NE-specific enhancers (NE-score) and androgen receptor binding sites (AD-score), respectively. Whole genome sequencing was performed to estimate the cfDNA tumor fraction (TF) using ichorCNA. To evaluate cfChIP-seq for monitoring NEPC treatment response, we calculated changes in NE-score and TF for each pair of consecutive plasma draws after NE transformation. We then compared these changes during intervals of disease progression, stability, or response using the Kruskal-Wallis test.
Results:
This study included 32 plasma samples from 5 patients, with 14 pre-NE and 18 post-NE diagnosis, collected between December 2016 and April 2022. The NE-score was significantly elevated in post-NE compared to pre-NE samples (Wilcoxon sum rank p<0.01). NE-scores between consecutive draws increased at times of disease progression, changed minimally with disease stability, and decreased during response (median change: 16 vs. 2.0 vs. -32%, resp.; p=0.035). Importantly, changes in TF, which reflects an aggregate of AD and NE-derived tumor DNA, were less pronounced (11 vs. -0.5 vs. -13%, resp.; p=0.3). The AD-score was positively correlated with PSA levels (R=0.59; p<0.001). In 2 patients with plasma collected within 3 months prior to NE transformation, NE scores increased prior to pathologic diagnosis of NEPC. Another case revealed an increase in AD-score and PSA accompanied by a decrease in NE-score when a patient stopped ADT and started platinum-based chemotherapy for NEPC.
Conclusions:
Epigenomic profiling of circulating chromatin may enable early detection of NEPC and monitoring of NE and AD components in metastatic prostate cancer.