Structure of cell-free circulating DNA in plasma (ccfDNA) in healthy volunteers: evidence of a predominant nucleosomal form
Michaël Toublanc PhD defense
27.11.26 - 27.11.26
Circulating cell-free DNA (ccfDNA) is an increasingly used biomarker in liquid biopsy. However, detecting a tumour-associated alteration requires the fragment carrying it to reach the bloodstream and persist until sampling. This depends on its fragmentation and on the molecular forms in which it circulates, which remain poorly characterised.
This thesis aimed to characterise the organisation of ccfDNA in plasma using µLAS technology, which enables DNA concentration and size-based separation. We developed a multi-injection strategy that increased the analysed volume tenfold and lowered the limit of detection to 11 pg/mL. This increased sensitivity enabled the analysis of ccfDNA subpopulations isolated by plasma fractionation using size-exclusion chromatography, density-gradient ultracentrifugation and rate-zonal centrifugation, as well as by immunocapture.
In plasma from healthy donors, most ccfDNA exhibited properties consistent with free mono- and dinucleosomes. A minor population of longer fragments co-fractionated with larger plasma structures, including extracellular vesicles. Immunocapture targeting double-stranded DNA and histone H3 provided further evidence for the presence of circulating nucleosomes and showed that target accessibility depends on the plasma environment. Immunocapture of epigenetic marks (5-methylcytosine and H3K9me3) preferentially recovered longer fragments, revealing a size-dependent bias that should be considered when analysing epigenetic biomarkers.
Finally, analysis of plasma from a patient with pancreatic ductal adenocarcinoma revealed a different distribution of ccfDNA across plasma fractions compared with healthy donors. Although preliminary, this observation opens the way to investigating whether circulating tumour DNA displays a distinct macromolecular organisation and whether this organisation influences its persistence and detection in plasma.
published on 13.11.26