Plasma contains ultrashort single-stranded DNA in addition to nucleosomal cell-free DNA

Cheng, Jordan; Morselli, Marco; Wei, Huang; Heo, You Jeong; Pinheiro-Ferreira, Thalyta; Li, Feng; Fang, Wei; Kim, Yong; He, Hua‐Jun; Cole, Kenneth D.; Su, Wu‐Chou; Pellegrini, Matteo; Wong, David T.

doi:10.1016/j.isci.2022.104554

Cited by 22 publications

(40 citation statements)

References 33 publications

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“…While more research is needed, this represents an alternative view to the view in which the presence of mono-nucleosomes is ascribed mainly to apoptosis. In addition to HMW cfDNA and mono-nucleosomes, a growing number of studies are demonstrating the presence of sub-nucleosomal and ultrashort, single-stranded cfDNA fragments in body fluids [ 106 , 184 , 252 , 460 , 461 , 462 , 463 , 464 ]. Whether these shortened cfDNA fragments represent short fragments released from cells or extracellularly digested products of longer fragments is not yet clear.…”

Section: Biological Factors That Affect Cfdna Measurementsmentioning

confidence: 99%

New Perspectives on the Importance of Cell-Free DNA Biology

et al. 2022

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Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.

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Section: Biological Factors That Affect Cfdna Measurementsmentioning

confidence: 99%

New Perspectives on the Importance of Cell-Free DNA Biology

et al. 2022

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“…It has become increasingly clear during the last years that another cfDNA population exists in plasma that might exhibit diagnostic potential: ultrashort single-stranded cfDNA fragments up to 100 bp [ 20 , 167 , 168 , 169 , 170 ]. These fragments are often omitted by conventional library preparation due to the adapter ligation process that needs double strands and/or applied size selection procedures.…”

Section: Epigenetic-based Biomarkers In Liquid Biopsymentioning

confidence: 99%

“…An early study employing single-stranded library preparation and subsequent sequencing demonstrated that short cfDNA molecules directly footprint TFBS occupancy [ 20 ]. Recent efforts optimizing different DNA extraction and library preparation procedures independently demonstrated the presence of this novel population of cfDNA molecules that might inform on gene regulatory regions and DNA secondary structures [ 168 , 169 , 170 ].…”

Section: Epigenetic-based Biomarkers In Liquid Biopsymentioning

confidence: 99%

Tracing the Origin of Cell-Free DNA Molecules through Tissue-Specific Epigenetic Signatures

et al. 2022

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All cell and tissue types constantly release DNA fragments into human body fluids by various mechanisms including programmed cell death, accidental cell degradation and active extrusion. Particularly, cell-free DNA (cfDNA) in plasma or serum has been utilized for minimally invasive molecular diagnostics. Disease onset or pathological conditions that lead to increased cell death alter the contribution of different tissues to the total pool of cfDNA. Because cfDNA molecules retain cell-type specific epigenetic features, it is possible to infer tissue-of-origin from epigenetic characteristics. Recent research efforts demonstrated that analysis of, e.g. methylation patterns, nucleosome occupancy, and fragmentomics determined the cell- or tissue-of-origin of individual cfDNA molecules. This novel tissue-of origin-analysis enables to estimate the contributions of different tissues to the total cfDNA pool in body fluids and find tissues with increased cell death (pathologic condition), expanding the portfolio of liquid biopsies towards a wide range of pathologies and early diagnosis. In this review, we summarize the currently available tissue-of-origin approaches and point out the next steps towards clinical implementation.

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“…Furthermore, some studies demonstrated that a considerable population of plasma cfDNA fragments centered at ~50 bp was present in the plasma DNA pool using modified single-stranded DNA library preparations. These included combining high-affinity magnetic bead-based DNA extraction with single-stranded DNA sequencing library preparation [27] and adjusting the concentration of isopropanol to retain the low molecular weight nucleic acids for downstream analysis [28] . Notably, such ultrashort cfDNA fragments were found to be enriched in the accessible chromatin regions of blood cells, particularly in promoter regions that potentially harbor G-quadruplex (G4) DNA secondary structures [Figure 1, Bottom left].…”

Section: Short Cfdna Moleculesmentioning

confidence: 99%

“…Notably, such ultrashort cfDNA fragments were found to be enriched in the accessible chromatin regions of blood cells, particularly in promoter regions that potentially harbor G-quadruplex (G4) DNA secondary structures [Figure 1, Bottom left]. G4-positive promoter chromatin accessibility was reportedly decreased in cancer patients, potentially providing another type of biomarker for cancer detection [27] . (Top) Cell-free DNA (cfDNA) is a mixture of fragments released from various healthy and diseased cells in different tissues.…”

Section: Short Cfdna Moleculesmentioning

confidence: 99%

Emerging frontiers of cell-free DNA fragmentomics

2022

Extracell Vesicles Circ Nucleic Acids

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Analysis of cell-free DNA (cfDNA) in the blood has shown promise for monitoring a variety of biological processes. Plasma cfDNA is a mixture comprising DNA molecules released from various bodily tissues, mediated by characteristic DNA fragmentations occurring during cell death. Fragmentation of cfDNA is non-random and contains tissue-of-origin information, which has been demonstrated in circulating fetal, tumoral, and transplanted organ-derived cfDNA molecules. Many studies have elucidated a plurality of fragmentomic markers for noninvasive prenatal, cancer, and organ transplantation assessment, such as fragment sizes, fragment ends, end motifs, and nucleosome footprints. Recently, researchers have further revealed the large population of previously unidentified long cfDNA molecules (kilobases in size) in the plasma DNA pool. This review focuses on the emerging biological properties of cfDNA, together with a discussion on its potential clinical implications.

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Plasma contains ultrashort single-stranded DNA in addition to nucleosomal cell-free DNA

Cited by 22 publications

References 33 publications

New Perspectives on the Importance of Cell-Free DNA Biology

New Perspectives on the Importance of Cell-Free DNA Biology

Tracing the Origin of Cell-Free DNA Molecules through Tissue-Specific Epigenetic Signatures

Emerging frontiers of cell-free DNA fragmentomics

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