Abstract 2307: Targeted cell-free DNA methylation signature in metastatic castration-resistant prostate cancer
Authors: Wong Jodie , Tian Yijun , Bitaraf Amir , Hanson Claire , Larson Matthew , Lloyd Jennifer , Batten Julia , Agarwal Neeraj , Swami Umang , Neibling Anna , Tward Jonathan , Maughan Benjamin , Gupta Sumati , Kohli Manish , Wang Liang 
Published: June 2023

Abstract
Background: DNA methylation of cytosines in CpG sites serves as an important epigenetic regulator for gene expression. In prostate cancer (PC), differences in DNA methylation regions have been observed between normal and tumor cells. However, acquiring the samples to study these patterns can be challenging through standard biopsies. Therefore, liquid biopsies provide a minimally invasive method which can be utilized to investigate the methylome of PC patients. In this study, we used liquid biopsies from a well-defined group of PC patients to examine cell-free DNA (cfDNA) methylation signatures and determine their clinical significance in metastatic castration-resistant prostate cancer.
Methods: Plasma was prospectively collected from a cohort 108 PC patients representing localized PC (n=24), metastatic hormone-sensitive PC (mHSPC) (n=28), and metastatic castration resistant PC (mCRPC) (n=37 pre-, n=19 post- mCRPC treatments). cfDNA from the patient plasma was used for an enzymatic methylation sequencing (EM-seq) that targeted a panel of genes (n=441) implicated in prostate cancer biology. Methylation status at CpG islands of these genes were examined using Twist targeted cfDNA methylation assay. The Bismark program was used for methylation calling. Differentially methylated regions (DMRs) across various patient outcomes were assessed by linking the CpG methylation data from target genes to the associated clinical data.
Results: We identified DMRs in 305 out of the 411 target genes in the plasma epigenome when comparing the mCRPC to non-mCRPC states (localized PC and mHSPC) (false discovery rate, FDR &lt; 0.2). From these 305 genes, we found that in patients experiencing only PSA relapse after failure of mHSPC (biochemical mCRPC) versus patients with clinical progression (clinical mCRPC), 261 out of the 305 genes had DMRs (p &lt;0.05). We also compared DMRs before and after 3-months of treatment in the mCRPC state and found that 175 out of the 305 genes showed significant changes after 3-months of mCRPC-specific treatment. Furthermore, from these 175 genes, 24 genes showed significant methylation differences when comparing patients with and without disease progression during mCRPC treatment and 20 genes showed significant differences when comparing patients with neuroendocrine features to those with common adenocarcinoma of PC at the mCRPC state (p&lt;0.05). These differentially methylated genes include RUNX3, FOXA2, HIC1 and MYCN.
Conclusions: cfDNA-based liquid biopsies provide a minimally invasive method to investigate the methylome of mCRPC patients. Our observations that cfDNA methylation was correlated with disease progression provide evidence that DMRs across a select panel of genes may serve as predictive biomarker for poor response to therapy and survival.
Citation Format: Jodie Wong, Yijun Tian, Amir Bitaraf, Claire Hanson, Matthew Larson, Jennifer Lloyd, Julia Batten, Neeraj Agarwal, Umang Swami, Anna Neibling, Jonathan Tward, Benjamin Maughan, Sumati Gupta, Manish Kohli, Liang Wang. Targeted cell-free DNA methylation signature in metastatic castration-resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2307.