ArticleTumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine2013
Characterization of H3K9me3- and H4K20me3-associated circulating nucleosomal DNA by high-throughput sequencing in colorectal cancer.
Article in Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis that pooled it.
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Who cites it
34 citing papers in PubMed, 1 synthesis or guideline pooled it, 66 citations in OpenAlex.
- Genomic and epigenomic biomarkers in colorectal cancer: From diagnosis to therapy.Advances in cancer research · 2021Pooled it
- Liquid biopsy epigenetics: establishing a molecular profile based on cell-free DNA.Molecular oncology · 2026Review
- Unlocking the Epigenetic Landscape of Colorectal Cancer: A Step Toward Epigenetics to Precision.Sub-cellular biochemistry · 2026Review
- Review
- Unveiling Alterations of Epigenetic Modifications and Chromatin Architecture Leading to Lipid Metabolic Reprogramming during the Evolutionary Trastuzumab Adaptation of HER2-Positive Breast Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Pathogenesis and biomarkers of colorectal cancer by epigenetic alteration.Intestinal research · 2024Review
- Detecting colorectal cancer using genetic and epigenetic biomarkers: screening and diagnosis.Journal of medicine and life · 2024Review
- The changing face of circulating tumor DNA (ctDNA) profiling: Factors that shape the landscape of methodologies, technologies, and commercialization.Medizinische Genetik : Mitteilungsblatt des Berufsverbandes Medizinische Genetik e.V · 2023Article
- Loss of SUV420H2-Dependent Chromatin Compaction Drives Right-Sided Colon Cancer Progression.Gastroenterology · 2023Article
- Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review.Frontiers in genetics · 2023Review
- The roles of histone modifications in tumorigenesis and associated inhibitors in cancer therapy.Journal of the National Cancer Center · 2022Review
- Distinct histone H3 modification profiles correlate with aggressive characteristics of salivary gland neoplasms.Scientific reports · 2022Article
- New Perspectives on the Importance of Cell-Free DNA Biology.Diagnostics (Basel, Switzerland) · 2022Review
- Epigenetic Alteration in Colorectal Cancer: A Biomarker for Diagnostic and Therapeutic Application.Global medical genetics · 2022Review
- Combinatorial Power of cfDNA, CTCs and EVs in Oncology.Diagnostics (Basel, Switzerland) · 2022Review
- Mass spectrometry-based characterization of histones in clinical samples: applications, progress, and challenges.The FEBS journal · 2022Review
- ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin.Nature biotechnology · 2021Article
- Epigenetic Alterations in the Gastrointestinal Tract: Current and Emerging Use for Biomarkers of Cancer.Gastroenterology · 2021Review
- Epigenetic Landscape of Liquid Biopsy in Colorectal Cancer.Frontiers in cell and developmental biology · 2021Review
- Histone Modifications and their Role in Colorectal Cancer (Review).Pathology oncology research : POR · 2020Review
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Modified histone tails in nucleosomes circulating in the blood bear the potential as cancer biomarkers. Recently, using chromatin immunopecipitation (ChIP)-related quantitative PCR, we described reduced plasma levels of the two pericentric heterochromatin-specific histone methylation marks H3K9me3 and H4K20me3 in patients with colorectal cancer (CRC). Here, by utilizing ChIP-related high-throughput sequencing, we further characterized these modifications in circulation. Plasma DNA from nucleosomes immunoprecipitated by H3K9me3- and H4K20me3-specific antibodies from patients with CRC (N = 15) and healthy subjects (N = 15) was subjected to the Roche 454 FLX sequencing, and the generated array of ChIP-enriched sequences were compared to the human reference genome. The total number of nucleosomes, of sequence reads and of diverse DNA repetitive elements were statistically compared between the study groups. Total nucleosome amount was not different in both groups. Concerning both histone modifications, lower numbers of sequence reads were detected in CRC patients as compared with healthy controls (medians in H3K9me3: 32 vs. 61; p < 0.01; in H4K20me3: 54 vs. 88; p < 0.01). Size of fragments was not different in both groups. Most abundant sequences were repetitive LINE and SINE elements while simple repeats, LTR, DNA, SAT, and low complexity elements were less frequent. Best discrimination between both groups was achieved by total number of H3K9me3 reads (AUC 0.90) and H3K9me3 LINE elements L1 (AUC 0.93) und L2 (AUC 0.91). The present results confirm earlier findings of lower H3K9me3 levels in CRC and show LINE elements to be the most frequent and best discriminative markers on modified histones.
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