scholarly journals The dynamics of cell-free DNA from urine and blood after a full marathon

2021 ◽  
Author(s):  
Yasuhiro Shishikura ◽  
Katsuyuki Tokinoya ◽  
Yuichi Aita ◽  
Nanami Sekine ◽  
Takehito Sugasawa ◽  
...  
Keyword(s):  
Creatine Kinase ◽  
Acute Exercise ◽  
Fragment Size ◽  
White Blood Cells ◽  
Healthy Male ◽  
Cell Free Dna ◽  
Extracellular Traps ◽  
Free Dna ◽  
Blood And Urine Samples ◽  
Male Subjects

AbstractPurposeCell-free DNA (cfDNA) has been investigated as a minimally invasive biomarker for many diseases, particularly cancer. An increase in cfDNA has been observed during exercise. Neutrophil extracellular traps (NETs) may be the origin of cfDNA in response to acute exercise, but the mechanisms of generation of cfDNA during exercise remain unclear. In this study we investigated the dynamics of serum and urinary cfDNA levels and determined the relevance of other biomarkers to serum and urinary cfDNA levels and fragment size after a full marathon.MethodsSamples were collected from 23 healthy male subjects. Blood and urine samples were collected before and immediately, two hours, and one day after the full marathon. The measurements included serum and urinary cfDNA, creatine kinase, myoglobin, creatinine, white blood cells, platelets, and lactoferrin from blood, and amylase, albumin, and creatinine from urine.ResultsSerum and urinary cfDNA levels increased after a full marathon. Creatine kinase, myoglobin, and creatinine in blood, and albumin and creatinine in urine also increased significantly after a full marathon. Serum cfDNA showed peak values about 180 bp after the full marathon. Values over 1000 bp were present at two hours post-marathon. Urinary cfDNA showed peak values from 35 bp to 50 bp after the full marathon. Values over 1000 bp appeared at Immediately and two hours post marathon.ConclusionThis study revealed that both serum and urinary cfDNA levels transiently increased after a full marathon. In addition, these cfDNA fragment varied in size.

Cell free DNA as an evolving liquid biopsy biomarker for initial diagnosis and therapeutic nursing in Cancer- An evolving aspect in Medical Biotechnology

2020 ◽  
Vol 21 ◽  
Author(s):  
Suman Kumar Ray ◽  
Sukhes Mukherjee
Keyword(s):  
Tumor Cells ◽  
Liquid Biopsy ◽  
Cancer Metastasis ◽  
Nuclear Dna ◽  
Fragment Size ◽  
Body Fluids ◽  
Response To Therapy ◽  
Significant Information ◽  
Cell Free Dna ◽  
Free Dna

: Cell-free DNA (cfDNA) is present in numerous body fluids in addition to initiates generally from blood cells. It is undoubtedly the utmost promising tool among all components of liquid biopsy. Liquid biopsy is a specialized method investigating the nonsolid biological tissue by revealing of circulating cells, cell free DNA etc. that enter body fluids. Since, cancer cells disengage from compact tumors circulate in peripheral blood, evaluating blood of cancer patients holds the opportunities for capture and molecular level analysis of various tumor-derived constituents. Cell free DNA samples can deliver a significant perceptions into oncology, for instance tumor heterogeneity, instantaneous tumor development, response to therapy and treatment, comprising immunotherapy and mechanisms of cancer metastasis. Malignant growth at any phase can outhouse tumor cells in addition to fragments of neoplasticity causing DNA into circulatory system giving noble sign of mutation in the tumor at sampling time. Liquid biopsy distinguishes diverse blood based evolving biomarkers comprising circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) or cfDNA, circulating RNA (cfRNA) and exosomes. Cell free DNA are little DNA fragments found circulating in plasma or serum, just as other fluids present in our body. Cell free DNA involves primarily double stranded nuclear DNA and mitochondrial DNA, present both on a surface level and in the lumen of vesicles. The probable origins of the tumor-inferred portion of cfDNA are apoptosis or tumor necrosis, lysis of CTCs or release of DNA from the tumor cells into circulation. The evolution of innovations, refinement and improvement in therapeutics for determination of cfDNA fragment size and its distribution provide significant information related with pathological conditions of the cell, thus emerging as promising indicator for clinical output in medical biotechnology.

Cell-free DNA concentration and fragment size fraction correlate with FDG PET/CT-derived parameters in NSCLC patients

2021 ◽  
Author(s):  
JM. González de Aledo-Castillo ◽  
S. Casanueva-Eliceiry ◽  
A. Soler-Perromat ◽  
D. Fuster ◽  
V. Pastor ◽  
...  
Keyword(s):  
Fdg Pet ◽  
Fragment Size ◽  
Size Fraction ◽  
Cell Free Dna ◽  
Dna Concentration ◽  
Free Dna ◽  
Pet Ct ◽  
Fdg Pet Ct ◽  
Nsclc Patients

Modeling cell-free DNA fragment size densities for non-invasive detection of cancer.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 3058-3058
Author(s):  
Jacob Carey ◽  
Bryan Chesnick ◽  
Denise Butler ◽  
Michael Rongione ◽  
Giovanni Parmigiani ◽  
...  
Keyword(s):  
Fragment Size ◽  
Length Distribution ◽  
Mixture Component ◽  
Base Pairs ◽  
Machine Model ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Genome Wide ◽  
Low Coverage

3058 Background: Circulating cell-free DNA (cfDNA) is largely nucleosomal in origin with typical fragment lengths of 167 base-pairs reflecting the length of DNA wrapped around-the histone and H1 linker. Given the nucleosomal origin of cfDNA, we have previously used low coverage whole genome sequencing to evaluate DNA fragmentation profiles to sensitively and specifically detect tumor-derived DNA with altered fragment lengths or coverage. Methods: Here we evaluate the use of Bayesian finite mixtures to model the fragment length distribution and demonstrate how the parameters from these models can be useful to distinguish between individuals with and without cancer. We examined the number of cfDNA fragments by size ranging from 100-220bp and approximated the mixture component location, scale, and weight using Markov Chain Monte Carlo. The performance of the method was determined using a ten-fold, ten repeat cross-validation of Gradient Boosted Machine model using 1) our previously described genome-wide fragmentation profile approach, 2) the parameters from the mixture model and 3) a combination of approaches 1) and 2) as features. Results: In this study of 215 cancer patients and 208 cancer-free individuals, we observed cross-validated AUCs of 1) 0.94, 2) 0.95, and 3) 0.97 among the three approaches. Conclusions: Our findings indicate that parsimonious mixture models may improve detection of cancer in conjunction with fragmentation profile analyses across the genome.

scholarly journals The influence of biological and lifestyle factors on circulating cell-free DNA in blood plasma

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Nicole Laurencia Yuwono ◽  
Kristina Warton ◽  
Caroline Elizabeth Ford
Keyword(s):  
Acute Exercise ◽  
Blood Collection ◽  
Occupational Hazard ◽  
Biological Factors ◽  
Cell Free Dna ◽  
Biological Sex ◽  
Hazard Exposure ◽  
Free Dna ◽  
Complete Reporting ◽  
Circulating Cell Free Dna

Research and clinical use of circulating cell-free DNA (cirDNA) is expanding rapidly; however, there remain large gaps in our understanding of the influence of lifestyle and biological factors on the amount of cirDNA present in blood. Here, we review 66 individual studies of cirDNA levels and lifestyle and biological factors, including exercise (acute and chronic), alcohol consumption, occupational hazard exposure, smoking, body mass index, menstruation, hypertension, circadian rhythm, stress, biological sex and age. Despite technical and methodological inconsistences across studies, we identify acute exercise as a significant influence on cirDNA levels. Given the large increase in cirDNA induced by acute exercise, we recommend that controlling for physical activity prior to blood collection is routinely incorporated into study design when total cirDNA levels are of interest. We also highlight appropriate selection and complete reporting of laboratory protocols as important for improving the reproducibility cirDNA studies and ability to critically evaluate the results.

Neutrophil Extracellular Traps May Contribute to the Pathogenesis in Adult-onset Still Disease

2019 ◽  
Vol 46 (12) ◽  
pp. 1560-1569 ◽  
Author(s):  
Mi-Hyun Ahn ◽  
Jae Ho Han ◽  
Young-Jun Chwae ◽  
Ju-Yang Jung ◽  
Chang-Hee Suh ◽  
...  
Keyword(s):  
Immunohistochemical Analysis ◽  
Serum Levels ◽  
Neutrophil Extracellular Traps ◽  
Polymorphonuclear Neutrophils ◽  
Adult Onset ◽  
Cell Free Dna ◽  
Extracellular Traps ◽  
Free Dna ◽  
Still Disease

Objective.Release of neutrophil extracellular traps (NET) has been described as an effector mechanism of polymorphonuclear neutrophils in several inflammatory diseases. Thus, this study was performed to evaluate the role of NET in the pathogenesis of adult-onset Still disease (AOSD).Methods.We determined the serum levels of NET molecules and investigated their associations with clinical disease activities in patients with AOSD. Further, we analyzed the differences in the NETosis response in AOSD patients compared to healthy controls (HC). To explore the in vivo involvement of NET in AOSD, we performed immunohistochemical analysis of skin and lymph node (LN) biopsies for proteins related to NET in patients with active AOSD.Results.Serum levels of cell-free DNA, myeloperoxidase (MPO)-DNA complex, and α-defensin were significantly increased in patients with AOSD compared to HC. Serum levels of the NET molecules, cell-free DNA, MPO-DNA, and α-defensin were correlated with several disease activity markers for AOSD. In followup of patients with AOSD after treatment with corticosteroid, the levels of cell-free DNA and α-defensin decreased significantly. On immunohistochemistry, neutrophil elastase–positive and MPO-positive inflammatory cells were detected in skin and LN of patients with AOSD, and were expressed in fiber form in the lesions. The serum from patients with active AOSD induced NETosis in neutrophils from HC. NET molecules induced interleukin 1β production in monocytes, representing a novel mechanism in the pathogenesis of AOSD.Conclusion.The findings presented here suggest that NET may contribute to the inflammatory response and pathogenesis in AOSD.

scholarly journals Neutrophil-Extracellular Traps, Cell-Free DNA, and Immunothrombosis in Companion Animals: A Review

2019 ◽  
Vol 57 (1) ◽  
pp. 6-23 ◽  
Author(s):  
Robert Goggs ◽  
Unity Jeffery ◽  
Dana N. LeVine ◽  
Ronald H. L. Li
Keyword(s):  
Companion Animals ◽  
High Mobility ◽  
Extracellular Dna ◽  
Death Process ◽  
Cell Free Dna ◽  
Pathogen Invasion ◽  
Extracellular Traps ◽  
Trap Formation ◽  
Free Dna ◽  
Extracellular Trap

Immunothrombosis is a potentially beneficial physiological process that aids innate immunity and host defense against pathogen invasion. However, this process can also be damaging when it occurs to excess or in critical blood vessels. Formation of extracellular traps by leukocytes, particularly neutrophils, is central to our understanding of immunothrombosis. In addition to degranulation and phagocytosis, extracellular traps are the third mechanism by which neutrophils combat potential pathogens. These traps consist of extracellular DNA decorated with bactericidal cellular proteins, including elastase, myeloperoxidase, and cathepsins. Neutrophils can release these structures as part of a controlled cell-death process or via a process termed vital NETosis that enables the cells to extrude DNA but remain viable. There is accumulating evidence that NETosis occurs in companion animals, including dogs, horses, and cats, and that it actively contributes to pathogenesis. Numerous studies have been published detailing various methods for identification and quantification of extracellular trap formation, including cell-free DNA, measurements of histones and proteins such as high-mobility group box–1, and techniques involving microscopy and flow cytometry. Here, we outline the present understanding of these phenomena and the mechanisms of extracellular trap formation. We critically review the data regarding measurement of NETosis in companion animals, summarize the existing literature on NETosis in veterinary species, and speculate on what therapeutic options these insights might present to clinicians in the future.

scholarly journals Molecular characterisation of longitudinally collected circulating cell-free DNA in HPV+ve and HPV-ve oropharyngeal cancer

2020 ◽  
Author(s):  
John P Thomson ◽  
Sophie J Warlow ◽  
Martyna Adamowicz ◽  
Helen Thain ◽  
Kate Cuschieri ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Clinical Decision Making ◽  
Fragment Size ◽  
Clinical Care ◽  
Significant Risk ◽  
Post Treatment ◽  
Response To Therapy ◽  
Cell Free Dna ◽  
Tissue Biopsy ◽  
Free Dna

Oropharyngeal squamous cell carcinoma (OPSCC) is an increasing global health problem and is divided into two types dependent on association with human papillomavirus (HPV), with a more favourable prognosis in virus-associated tumours. Current methods of establishing viral aetiology, assessing response to therapy and clinical monitoring rest on tissue biopsy, clinical examination and post-treatment imaging. However, tissue biopsy is invasive and carries significant risk of morbidity, and post-treatment scans are frequently indeterminate. Analysis of cell-free DNA (cfDNA) from the circulation provides a minimally invasive method for detecting and monitoring cancer-derived DNA fragments, with the potential for enhancing clinical care. Through the longitudinal collection of 166 blood samples in 67 OPSCC patients we evaluate the utility of three cfDNA analysis methods: droplet digital PCR (ddPCR) and fragment size analysis in both HPV+ve and HPV-ve disease, and ultra-deep sequencing in patients with HPV-ve disease. We show that ddPCR analysis of cfDNA for five HPV types (16, 18, 31, 33 & 35) is strongly concordant with existing clinical assays (p16 immunohistochemistry (IHC) and quantitative PCR analysis of solid tumour tissue) and that cfDNA fragment size was reduced in OPSCC patients compared to healthy controls. Sequential ddPCR measurements of cfDNA HPV copy number showed a decrease to undetectable levels in all 30 HPV+ve patients in at least one of their post-treatment samples and a corresponding increase in cfDNA fragment size in patients who had a complete response to chemoradiotherapy. In two HPV+ve patients, clinical decision-making based on HPV ddPCR of cfDNA may have led to earlier detection of relapse in one patient or avoided surgical exploration in a second patient, which led to resection of tissue that did not harbour malignancy. In HPV-ve disease, ultra-deep sequencing identified tumour-derived somatic mutations of circulating cfDNA in genes such as TP53 and members of the ERBB family that are potential markers of therapeutic responsiveness and patient prognosis. Together our data suggest that analysis of circulating cfDNA can enhance current clinical strategies for assessing therapeutic response and disease monitoring in both HPV+ve and HPV-ve OPSCC.

scholarly journals Enrichment of short mutant cell-free DNA fragments enhanced detection of pancreatic cancer

2018 ◽  
Author(s):  
Xiaoyu Liu ◽  
Lingxiao Liu ◽  
Yuan Ji ◽  
Changyu Li ◽  
Tao Wei ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Early Stage ◽  
Fragment Size ◽  
New Technology ◽  
Mutant Cell ◽  
Circulating Tumor Dna ◽  
Clinical Settings ◽  
Cell Free Dna ◽  
Free Dna ◽  
Target Capture

Analysis of cell-free DNA (cfDNA) is promising for broad applications in clinical settings, but with significant bias towards late-stage cancers. Although recent studies have discussed the diverse and degraded nature of cfDNA molecules, little is known about its impact on the practice of cfDNA analysis. Here we reported a new targeted sequencing by combining single-strand library preparation and target capture (SLHC-seq). By applying the new technology in plasma cfDNA from pancreatic cancer patients, we achieved higher efficiency in analysis of mutations than previously reported using other detection assays. SLHC-seq rescued short or damaged cfDNA fragments along to increase the sensitivity and accuracy of circulating-tumor DNA detection. Most importantly, we found that the small mutant fragments are prevalent in early-stage patients, which provides strong evidence for fragment size-based early detection of pancreatic cancer. Collectively, the new pipeline enhanced our understanding of cfDNA biology and provide new insights for liquid biopsy.

scholarly journals Circulating Neutrophil Extracellular Traps in the Pathogenesis of Acute Chest Syndrome of Sickle Cell Disease

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 3556-3556
Author(s):  
Ravi Vats ◽  
Egemen Tutuncuoglu ◽  
Jesus Tejero ◽  
Cheryl A Hillery ◽  
Mark T Gladwin ◽  
...  
Keyword(s):  
Sickle Cell Disease ◽  
Lung Injury ◽  
Sickle Cell ◽  
Neutrophil Extracellular Traps ◽  
Acute Chest Syndrome ◽  
Cell Disease ◽  
Cell Free Dna ◽  
Extracellular Traps ◽  
Free Dna ◽  
Platelet Aggregates

Introduction: Acute chest syndrome (ACS) is a type of acute lung injury and among the primary reasons for mortality and morbidity among Sickle Cell Disease (SCD) patients. Although epidemiologic evidence suggests that vaso-occlusion in the lung may serve as an antecedent to ACS, the cellular, molecular and biophysical mechanism of ACS is incompletely understood. Our recent findings revealed that the lung vaso-occlusion is enabled by the entrapment of embolic neutrophil-platelet aggregates in the pulmonary arterioles of transgenic humanized SCD mice. Recent evidence also suggests a role for neutrophil extracellular traps (NETs) in ACS. NETs are web-like structures of decondensed nuclear DNA decorated with citrullinated-histones (H3-cit) and neutrophil granule proteins. Interestingly, circulating nucleosomes and NETs fragments are elevated in SCD patient blood and the levels correlate with onset of ACS, however, the molecular mechanism that promotes generation of circulating NETs and the role of circulating NETs in promoting ACS remains poorly understood. Materials and Methods: Townes knock-in humanized SS (hα/hα:βS/βS) and AS (hα/hα:βA/βS) mice were used as SCD and control mice, respectively. SS and AS mice were intravenously (IV) administered 10 µmole/kg Oxy-Hb followed by Sytox orange, FITC-dextran or fluorescent anti-mouse mAbs against Ly6G, CD49b, H3cit, and neutrophil elastase for in vivo visualization of extracellular DNA, blood vessels, neutrophils, platelets and NETs, respectively. Pulmonary microcirculation was monitored using multi-photon-excitation enabled quantitative fluorescence intravital lung microscopy (qFILM). Results and Discussion: IV Oxy-Hb triggered the occlusion of pulmonary arterioles by neutrophil-platelet aggregates leading to loss of pulmonary blood flow in SCD but not control mice. Surprisingly, pulmonary vaso-occlusion in SCD mice was accompanied by the arrival of circulating cell free DNA (CFD) and NETs fragments into the pulmonary circulation. The cell free DNA (CFD) and NETs fragments entered the lung through the arterial circulation suggesting that they originated outside of lung. These cell free DNA (CFD) and NETs fragments contributed to lung vaso-occlusion and injury by promoting neutrophil-platelet aggregation in the lung arterioles. Conclusion: These findings reveal for the first time that circulating cell free DNA (CFD) and NETs fragments originating outside of lung contribute to pathogenesis of ACS. Currently, experiments are underway to identify the innate immune pathways that promote circulating NETs dependent lung injury in SCD. Disclosures Gladwin: Globin Solutions, Inc: Patents & Royalties: Provisional patents for the use of recombinant neuroglobin and heme-based molecules as antidotes for CO poisoning; United Therapeutics: Patents & Royalties: Co-inventor on an NIH government patent for the use of nitrite salts in cardiovascular diseases ; Bayer Pharmaceuticals: Other: Co-investigator.

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