Abstract 940: Integrated analysis of cfDNA fragmentomics, DNA methylation and cfRNA transcription in metastatic castration-resistant prostate cancer (mCRPC)
Authors: Dai Chao , Zhu Lisha , Huang Yong , Bonora Giancarlo , Zhou Kemin , Jia Shidong , Du Pan 
Published: March 2024

Abstract
Background Liquid biopsies based on cell-free DNA (cfDNA) analysis provide non-invasive clinical diagnostic insights. Recently, cfDNA fragmentomics has emerged as a tool for inferring epigenomic and transcriptional information from tumor-derived cfDNA. We conducted a comprehensive profiling of cfDNA fragmentomics, whole transcriptome sequencing (WTS), and genome-wide DNA methylation on two metastatic castration-resistant prostate cancer (mCRPC) samples to systematically investigate molecular aberrations in mCRPC.
Methods Two mCRPC patient plasma samples were extensively profiled using high-depth 150x whole-genome sequencing (WGS), 30x whole-genome methylation, and cfRNA WTS. CfDNA fragmentomics analysis was performed to assess androgen receptor (AR) transcriptional activity. We calculated fragment coverage around AR binding sites (ARBS) and quantified ARBS nucleosome profiling abnormality scores (ARBS scores) by comparing centric fragment coverage with normal plasma background. Additionally, we calculated fragment size entropy around AR promoter and enhancer regions to reflect AR gene expression activity. Fragmentomics-inferred gene activity was validated through promoter-targeted panels and WTS profiling of matched mCRPC samples.
Results Both mCRPC plasma samples exhibited significant ARBS nucleosome depletion. Sample A showed a higher ARBS score compared to Sample B. Interestingly, AR enhancer activity inferred from high-depth WGS and targeted panels was high in both samples, while AR promoter activity was high only in Sample A. Genome-wide DNA methylation revealed hypo-methylation in AR enhancer and ARBS regions in both samples, with Sample A showing more pronounced hypo-methylation. Copy number variation analysis indicated AR amplification in Sample A and RB1 loss in Sample B. Collectively, these findings suggest that Sample A may represent androgen receptor-dependent prostate cancer (ARPC), while Sample B may have developed resistance to androgen therapy, possibly indicating neuroendocrine prostate cancer (NEPC).
Conclusions This study, to our knowledge, is the first to combine high-depth WGS, promoter-targeted panels, WTS, and genome-wide DNA methylation to systematically study epigenomic and transcriptional dysregulation in mCRPC. The integration of mutation, copy number variation, fragmentomics, and DNA methylation profiling holds potential clinical utility for inferring prostate cancer subtypes, facilitating patient stratification, and guiding treatment selection.
Citation Format: Chao Dai, Lisha Zhu, Yong Huang, Giancarlo Bonora, Kemin Zhou, Shidong Jia, Pan Du. Integrated analysis of cfDNA fragmentomics, DNA methylation and cfRNA transcription in metastatic castration-resistant prostate cancer (mCRPC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 940.