New Perspectives on the Importance of Cell-Free DNA Biology

Abstract

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.

Cell-Free DNA in Plasma and Serum Indicates Disease Severity and Prognosis in Blunt Trauma Patients

“…Various mechanisms are discussed by which cfDNA is released from cells including damaged cells, dying or dead cells, as well as cells otherwise stimulated [ 23 ]—among others apoptosis, necrosis, suicidal and vital NETosis with consecutive release of neutrophil extracellular traps (NETs), erythroblast enucleation, phagocytosis, oncosis [ 25 , 26 ] and direct tissue damage from trauma [ 11 , 27 , 41 ]. cfDNA release into the blood stream may occur early after acute damage, and—despite the short half-life of 15 min to 2 h [ 20 , 24 , 31 ]—plasma levels may remain elevated for hours or days depending on the extent and dynamics of the trauma and the appearance of complications [ 41 , 42 ] in the further course.…”

“…Cell-free DNA (cfDNA) in the blood has recently gained increasing interest [ 10 ], as it is elevated in serum and plasma under physiological processes [ 11 ] such as pregnancy [ 12 ] and physical exercise [ 13 ] or during pathological processes, such as infections and sepsis [ 14 ], myocardial and other organ infarctions [ 15 , 16 ], autoimmune disorders [ 17 ], organ transplantation, thermal injuries [ 18 , 19 ], several types of cancers [ 20 , 21 ], surgery [ 20 , 22 ], as well as trauma [ 17 , 23 ]. The exact mechanism of cfDNA release from cells is still unclear [ 23 ]; however, apoptosis, necrosis, suicidal and vital NETosis with consecutive release of neutrophil extracellular traps (NETs) [ 24 ], erythroblast enucleation, phagocytosis and oncosis [ 25 , 26 ], as well as direct tissue damage from trauma are considered as potential sources [ 11 , 27 ]. As so-called danger-associated molecular patterns (DAMPs) [ 28 ], cfDNA is increased after traumatic injuries and plays a major role in the pathophysiology of the posttraumatic systemic inflammatory response commencing immediately after injury and contributing to post-injury complications [ 19 , 29 , 30 ].…”

“…The prediction of outcome in patients experiencing trauma in a variety of scenarios has been studied extensively [ 14 , 22 , 25 , 31 , 32 , 33 ], and cfDNA levels are associated with the severity of trauma and the prevalence of complications [ 20 ]. Due to the short half-life and stability of mono-nucleosomal cfDNA, from 15 min to 2 h [ 20 , 24 , 31 ], it could serve as a suitable marker in the critical emergency phase [ 20 , 31 ].…”

Application of PCR-based approaches for evaluation of cell-free DNA fragmentation in colorectal cancer

“…Circulating cell-free DNA in blood plasma is an attractive source of genomic and epigenomic biomarkers with fragmentation features being one of the dimensions. Various biological factors have been shown to alter cfDNA fragmentation, including the positioning of nucleosomes and chromatin state in cells of origin (Ivanov et al, 2015;Snyder et al, 2016;Bronkhorst et al, 2022;van der Pol et al, 2022).…”

In Vitro Analysis of Biological Activity of Circulating Cell-Free DNA Isolated from Blood Plasma of Schizophrenic Patients and Healthy Controls—Part 2: Adaptive Response

“…The source of cfDNA in the blood are the body’s cells that have died earlier due to necrosis or apoptosis. In addition, the living cells excrete DNA fragments into the medium in the form of particles of various size [ 1 , 2 , 3 , 4 , 5 , 6 , 7 ].…”