Peter Ulz
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Peter Ulz
@ulzpeter.bsky.social
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Computational Biologist @ Freenome
Interested in cfDNA, cancer, genomics
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Reposted by Peter Ulz
teiflab.bsky.social
Interesting new preprint on nucleosome spacing from cfDNA [Johnston et al., 2024] biorxiv.org/content/10.1.... The authors refer to NRL changes 10n -> 10n-5 bp. Earlier we showed that NRL decreases in cancer more continuously, context-specific [Jacob et al., 2024] link.springer.com/article/10.1...
Circulating cell-free DNA (cfDNA) liquid biopsies offer a powerful, non-invasive approach for cancer diagnostics, leveraging DNA fragments primarily released during apoptosis. In this process, nucleosome-bound DNA is protected, while linker DNA is cleaved, generating fragments around 166 base pairs. Using droplet digital PCR (ddPCR) on cfDNA samples from 88 breast and colorectal cancer patients, we uncovered highly consistent nucleosome breakpoints across patients, significantly impacting the sensitivity of somatic mutation assays and underscoring the value of precise nucleosome positioning data. Here, we introduce an advanced fragmentomics method with probabilistic nucleosome protection scoring, enabling high-resolution mapping of nucleosome positions and cfDNA breakpoints. Our results reveal that while the 166 bp fragment size is common to both euchromatin and heterochromatin, it masks distinct nucleosome spacing patterns linked to two chromatin fiber conformations, T1 and T2 topoisomers. This insight enhances understanding of chromatin's role in cfDNA fragmentation, advancing diagnostic potential for liquid biopsy assays. We have generated high-resolution nucleosome maps in paired tumour and normal tissues from the same breast cancer patients using MNase-assisted histone H3 ChIP-seq and compared them with the corresponding cfDNA from blood plasma. This analysis has detected single-nucleosome repositioning at key regulatory regions in a patient-specific manner and common cancer-specific patterns across patients. The nucleosomes gained in tumour versus normal tissue were particularly informative of cancer pathways, with ~ 20-fold enrichment at CpG islands, a large fraction of which marked promoters of genes encoding DNA-binding proteins. The tumour tissues were characterised by a 5–10 bp decrease in the average distance between nucleosomes (nucleosome repeat length, NRL), which is qualitatively similar to the differences between pluripotent and differentiated cells. This effect was correlated with gene activity, differential DNA methylation and changes in local occupancy of linker histone variants H1.4 and H1X. Our study offers a novel resource of high-resolution nucleosome maps in breast cancer patients and reports for the first time the effect of systematic decrease of NRL in paired tumour versus normal breast tissues from the same patient. Our findings provide a new mechanistic understanding of nucleosome repositioning in tumour tissues that can be valuable for patient diagnostics, stratification and monitoring.
November 19, 2024 at 12:50 PM