ArticleMolecular oncology2023
Cell-free chromatin immunoprecipitation can determine tumor gene expression in lung cancer patients.
Article in Molecular oncology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 17 citations in OpenAlex.
- Reappraising the topology of cell-free fetal DNA in maternal blood toward improved prenatal genetic diagnostics.Science advances · 2026Review
- Transcription Factor Subtype Governs Response and Resistance to DLL3-Directed T-Cell Engagement in Small Cell Lung Cancer.bioRxiv : the preprint server for biology · 2026Article
- Liquid biopsy epigenetics: establishing a molecular profile based on cell-free DNA.Molecular oncology · 2026Review
- Integrated inference of cancer gene expression from cell-free plasma chromatin.bioRxiv : the preprint server for biology · 2026Article
- Open chromatin-guided interpretable machine learning reveals cancer-specific chromatin features in cell-free DNA.Communications biology · 2025Article
- Urine cf-nucleosomes: A non-invasive window into human physiology and disease.Cell genomics · 2025Article
- Circulating Cell-free DNA Fragmentomics Detection and Beyond.Aging and disease · 2025Review
- Cell-free epigenomes enhanced fragmentomics-based model for early detection of lung cancer.Clinical and translational medicine · 2025Article
- %dd-cfDNA: The New Frontier for Heart/Lung Transplant Surveillance?Transplant international : official journal of the European Society for Organ Transplantation · 2025Review
- Histone modifications of circulating nucleosomes are associated with changes in cell-free DNA fragmentation patterns.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Integration of Cell-Free DNA End Motifs and Fragment Lengths Can Identify Active Genes in Liquid Biopsies.International journal of molecular sciences · 2024Article
- Trans-Regulation of AlternativeCells · 2023Article
- Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation.Life science alliance · 2023Article
- Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications.Genes · 2023Review
- Clinical application of liquid biopsy based on circulating tumor DNA in non-small cell lung cancer.Frontiers in physiology · 2023Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell-free DNA (cfDNA) in blood plasma can be bound to nucleosomes that contain post-translational modifications representing the epigenetic profile of the cell of origin. This includes histone H3 lysine 36 trimethylation (H3K36me3), a marker of active transcription. We hypothesised that cell-free chromatin immunoprecipitation (cfChIP) of H3K36me3-modified nucleosomes present in blood plasma can delineate tumour gene expression levels. H3K36me3 cfChIP followed by targeted NGS (cfChIP-seq) was performed on blood plasma samples from non-small-cell lung cancer (NSCLC) patients (NSCLC, n = 8), small-cell lung cancer (SCLC) patients (SCLC, n = 4) and healthy controls (n = 4). H3K36me3 cfChIP-seq demonstrated increased enrichment of mutated alleles compared with normal alleles in plasma from patients with known somatic cancer mutations. Additionally, genes identified to be differentially expressed in SCLC and NSCLC tumours had concordant H3K36me3 cfChIP enrichment profiles in NSCLC (sensitivity = 0.80) and SCLC blood plasma (sensitivity = 0.86). Findings here expand the utility of cfDNA in liquid biopsies to characterise treatment resistance, cancer subtyping and disease progression.
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