ArticleCancer research2025
Plasma Cell-Free DNA Chromatin Immunoprecipitation Profiling Depicts Phenotypic and Clinical Heterogeneity in Advanced Prostate Cancer.
Article in Cancer research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Lutetium-177-PSMA-617 or cabazitaxel in metastatic prostate cancer: circulating tumor DNA analysis of the randomized phase 2 TheraP trial.Nature medicine · 2025Trial
- Reappraising the topology of cell-free fetal DNA in maternal blood toward improved prenatal genetic diagnostics.Science advances · 2026Review
- Plasma nucleosome profiling reports on tumor burden and molecular subtypes in small cell lung cancer.The Journal of clinical investigation · 2026Article
- Using Disease-Agnostic Genomic Liquid Biopsy in Complex Diagnoses: Real-Life Example of cfChIP-Seq in a Fever of Unknown Origin.JCO precision oncology · 2026Article
- Circulating Tumor DNA as Emerging Predictive and Prognostic Biomarker in Prostate Cancer.Cancers · 2026Review
- Integrated inference of cancer gene expression from cell-free plasma chromatin.bioRxiv : the preprint server for biology · 2026Article
- Epigenetic plasticity and chemoresistance in cancer: mechanisms, biomarkers, and translational opportunities for real-world evidence.Frontiers in cell and developmental biology · 2026Review
- Immune signaling as a determinant of cellular identity and tissue function.Frontiers in immunology · 2026Review
- SNAP: Streamlined Nextflow Analysis Pipeline for Immunoprecipitation-Based Epigenomic Profiling of Circulating Chromatin.bioRxiv : the preprint server for biology · 2025Article
- Simulating cell-free chromatin using preclinical cancer models for liquid biopsy applications.iScience · 2025Article
- Plasma epigenomic profiling reveals treatment-emergent squamous transformation in prostate cancer.NPJ precision oncology · 2025Article
- Intraindividual epigenetic heterogeneity underlying phenotypic subtypes of advanced prostate cancer.Nature communications · 2025Article
- CRISPR screening identifies regulators of enhancer-mediated androgen receptor transcription in advanced prostate cancer.Cell reports · 2025Article
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Authors and funding
21 authors.
Funding
Abstract
Cell phenotype underlies prostate cancer presentation and treatment resistance and can be regulated by epigenomic features. However, the osteotropic tendency of prostate cancer limits access to metastatic tissue, meaning most prior insights into prostate cancer chromatin biology are from preclinical models that do not fully represent disease complexity. Noninvasive chromatin immunoprecipitation of histones in plasma cell-free DNA (cfDNA) in humans may enable the capture of disparate prostate cancer phenotypes. In this study, we analyzed activating promoter- and enhancer-associated H3K4me2 from cfDNA in metastatic prostate cancer enriched for divergent patterns of metastasis and diverse clinical presentation. H3K4me2 density across prostate cancer genes, accessible chromatin, and lineage-defining transcription factor-binding sites correlated strongly with ctDNA fraction-demonstrating capture of prostate cancer-specific biology and informing the development of a statistical framework to adjust for ctDNA fraction. Chromatin hallmarks mirrored synchronously measured clinicogenomic features: bone- versus liver-predominant disease, serum PSA, biopsy-confirmed histopathologic subtype, and RB1 deletions convergently indicated phenotype segregation along an axis of differential androgen receptor activity and neuroendocrine identity. Detection of lineage switching after sequential progression on systemic therapy in select patients indicates potential use for individualized resistance monitoring. Epigenomic footprints of metastasis-induced normal tissue destruction were evident in bulk cfDNA from two patients. Finally, a public epigenomic resource was generated using a distinct chromatin marker that has not been widely investigated in prostate cancer. These results provide insights into the adaptive molecular landscape of aggressive prostate cancer and endorse plasma cfDNA chromatin profiling as a biomarker source and biological discovery tool. Significance: Plasma cell-free chromatin immunoprecipitation sequencing enables phenotypic dissection of lethal prostate cancer and is a practical tool for biomarker discovery while overcoming prior limitations of access to relevant tissue and reliance on model systems.
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