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Walczak K, Grzybowska-Adamowicz J, Stawski R, Brzezińska O, Zmysłowska A, Nowak D. Response of Circulating Free Cellular DNA to Repeated Exercise in Men with Type 1 Diabetes Mellitus. J Clin Med 2024; 13:5859. [PMID: 39407919 PMCID: PMC11477321 DOI: 10.3390/jcm13195859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 09/02/2024] [Accepted: 09/26/2024] [Indexed: 10/20/2024] Open
Abstract
Background: Intense exercise leads to neutrophil extracellular traps (NETs) formation, which triggers cell disintegration. NET, as well as other processes of apoptosis, necrosis, and spontaneous secretion, result in increased levels of cell-free DNA (cf-DNA) in the circulation. An increment of cf-DNA is also observed in autoimmune diseases, such as type 1 diabetes mellitus (T1DM). Repeated exhaustive exercises are an impulse for physiological adaptation; therefore, in this case-control study, we compared the exercise-induced increase in cf-DNA in men with T1DM and healthy controls to determine the development of the tolerance to exercise. Methods: Volunteers performed a treadmill run to exhaustion at a speed matching 70% of their personal VO2 max at three consecutive visits, separated by a 72 h resting period. Blood was collected before and after exercise for the determination of plasma cell-free nuclear and mitochondrial DNA (cf n-DNA, cf mt-DNA) by real-time PCR, blood cell count and metabolic markers. Results: Each bout of exhaustive exercise induced a great elevation of cf n-DNA levels. An increase in cf mt-DNA was observed after each run. However, the significance of the increase was noted only after the second bout in T1DM participants (p < 0.02). Changes in cf-DNA concentration were transient and returned to baseline values during 72 h of resting. The exercise-induced increment in circulating cf n-DNA and cf mt-DNA was not significantly different between the studied groups (p > 0.05). Conclusions: Cf-DNA appears to be a sensitive marker of inflammation, with a lower post-exercise increase in individuals with T1DM than in healthy men.
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Affiliation(s)
- Konrad Walczak
- Department of Internal Medicine and Nephrodiabetology, Medical University of Lodz, 90-549 Lodz, Poland
| | | | - Robert Stawski
- Department of Clinical Physiology, Medical University of Lodz, 92-215 Lodz, Poland
| | - Olga Brzezińska
- Department of Rheumatology, Medical University of Lodz, 90-549 Lodz, Poland
| | - Agnieszka Zmysłowska
- Department of Clinical Genetics, Medical University of Lodz, 92-213 Lodz, Poland
| | - Dariusz Nowak
- Department of Clinical Physiology, Medical University of Lodz, 92-215 Lodz, Poland
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2
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Lang HM, Duffourc MM, Bazyler CD, Ramsey MW, Gentles JA. The Relationship Between Cell-Free DNA and Resistance Training Volume Load. J Strength Cond Res 2024; 38:1008-1012. [PMID: 38373069 DOI: 10.1519/jsc.0000000000004751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
ABSTRACT Lang, HM, Duffourc, MM, Bazyler, CD, Ramsey, MW, and Gentles, JA. The relationship between cell-free DNA and resistance training volume load. J Strength Cond Res 38(6): 1008-1012, 2024-The primary purpose of this study was to assess the sensitivity of cell-free DNA (cf-DNA) to different resistance training volume loads. The secondary purpose was to examine the relationship between change in cf-DNA and relative strength. Researchers hypothesized that (a) cf-DNA concentrations would increase with increasing volume load and (b) increases in relative strength would result in predicted decreases to %Δ of cf-DNA. Thirty subjects were recruited for this study, 15 men and 15 women. Blood was collected through venous draws into 4-ml vacutainers at 3 time points: immediately before (T1), after 3 sets (T2), and after 6 sets (T3) of the back squat exercise. A critical alpha of 0.05 was set for inferential statistics. A repeated-measures ANOVA showed that cf-DNA increased significantly from T1 (407.72 ± 320.83) to T2 (1,244.6 ± 875.83) ( p < 0.01) and T1 (407.72 ± 320.83) to T3 (1,331.15 ± 1,141.66) ( p < 0.01), whereas no difference was found from T2 to T3 ( p = 1.00). The linear regression model used to examine the predictive capabilities relative strength had on cf-DNA %Δ from T1 to T3 was found to be significant ( p = 0.04; R2 = 0.15). The results of this study demonstrate the short response of cf-DNA in relation to variations in resistance training volume load. Results also demonstrated the positive relationship between relative strength and cf-DNA %Δ. The current study builds on the body of research that cf-DNA provides insight regarding the level of immune response after exercise training.
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Affiliation(s)
- Henry M Lang
- Department of Exercise Science, University of Mary, Bismarck, North Dakota
| | - Michelle M Duffourc
- Department of Pharmacology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee; and
| | - Caleb D Bazyler
- Department of Exercise and Sport Science, East Tennessee State University, Johnson City, Tennessee
| | - Michael W Ramsey
- Department of Exercise and Sport Science, East Tennessee State University, Johnson City, Tennessee
| | - Jeremy A Gentles
- Department of Exercise and Sport Science, East Tennessee State University, Johnson City, Tennessee
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3
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Nogiec CD, Karlic R, Taborda E, Dunkelbarger S, Fridlich O, Dor Y, Polak P, Li R. Exercise-Induced Cell-Free DNA Correlates with Energy Expenditure in Multiple Exercise Protocols. Med Sci Sports Exerc 2024; 56:813-821. [PMID: 38109167 DOI: 10.1249/mss.0000000000003363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
PURPOSE Exercise-induced cell-free DNA (ei-cfDNA) has been studied in response to various types of exercise. Its correlation with exercise intensity and duration has been observed consistently. However, comprehensive measurements and exploration of the tissue of origin are lacking. The aim of this study is to establish precise connections between exercise variables and the distribution of tissue of origin, aiming to provide further evidence supporting its use as a biomarker for exercise. METHODS Twelve self-identified active adults (six men and six women) performed a crossover study starting with either endurance testing or resistance testing under different intensities and protocols. We obtained blood before and after each exercise session and measured the levels of cfDNA and determined its tissue of origin utilizing cell type-specific DNA methylation patterns in plasma. RESULTS We found that when duration and intensity are fixed, ei-cfDNA fold change correlates with energy expenditure ( P = 0.001) in endurance testing and years trained ( P = 0.001) in resistance testing. Most of the ei-cfDNA comes from increases in white blood cells (~95%) where neutrophils make up the majority (~74%) and the distribution is different between exercise modalities and protocols. CONCLUSIONS This study highlights the potential of exercise-induced cfDNA as a biomarker for exercise, showing correlations with energy expenditure and a consistent pattern of tissue origin. Additional research is needed to investigate potential sex differences in the response of cfDNA to exercise, further exploring its clinical implications.
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Affiliation(s)
| | - Rosa Karlic
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, CROATIA
| | - Eddie Taborda
- Department of Health Sciences, Northeastern University, Boston, MA
| | | | - Ori Fridlich
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, ISRAEL
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, ISRAEL
| | | | - Rui Li
- Department of Health Sciences, Northeastern University, Boston, MA
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Chmielecki A, Bortnik K, Galczynski S, Kopacz K, Padula G, Jerczynska H, Stawski R, Nowak D. Interleukin-4 during post-exercise recovery negatively correlates with the production of phagocyte-generated oxidants. Front Physiol 2023; 14:1186296. [PMID: 38192745 PMCID: PMC10773862 DOI: 10.3389/fphys.2023.1186296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 11/02/2023] [Indexed: 01/10/2024] Open
Abstract
Exhaustive run induced a biphasic oxidative response of circulating phagocytes in 16 amateur sportsmen. The first phase involved an increment just after exercise of enhanced whole blood chemiluminescence normalized per phagocyte count, whereas in the second phase a decrement from 1 h post-exercise and ongoing till 24 h. We tested whether plasma Interleukin IL-4, IL-8, IL-10 and Tumor Necrosis Factor α concentrations change in response to exhaustive run and whether there are associations between their levels and delta resting. Moreover, IL-8 and IL-10 significantly increased immediately post-exercise and after 1 h, but later normalized. Tumor necrosis factor α rose by 1.1-times only just after exercise. However, none of these cytokines showed any correlation with the investigated chemiluminescence. Exercise did not alter plasma concentrations of IL-4. However, pre-exercise IL-4 negatively correlated with measured luminescence just after exercise (ρ = -0.54, p < 0.05), and also tended to be negatively associated with decrements of the second phase at 1 h post-exercise ρ = -0.45, p = 0.08. It is suggested that plasma IL-4, by a negative association with blood phagocytes oxidants production, could be involved in the maintenance of proper balance between oxidants and anti-oxidants during strenuous exercise and post-exercise recovery.
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Affiliation(s)
| | | | - Szymon Galczynski
- Academic Laboratory of Movement and Human Physical Performance “DynamoLab”, Medical University of Lodz, Łódź, Poland
| | - Karolina Kopacz
- Academic Laboratory of Movement and Human Physical Performance “DynamoLab”, Medical University of Lodz, Łódź, Poland
| | - Gianluca Padula
- Academic Laboratory of Movement and Human Physical Performance “DynamoLab”, Medical University of Lodz, Łódź, Poland
| | - Hanna Jerczynska
- Central Scientific Laboratory, Medical University of Lodz, Łódź, Poland
| | - Robert Stawski
- Department of Clinical Physiology, Medical University of Lodz, Łódź, Poland
| | - Dariusz Nowak
- Department of Clinical Physiology, Medical University of Lodz, Łódź, Poland
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Haller N, Reichel T, Zimmer P, Behringer M, Wahl P, Stöggl T, Krüger K, Simon P. Blood-Based Biomarkers for Managing Workload in Athletes: Perspectives for Research on Emerging Biomarkers. Sports Med 2023; 53:2039-2053. [PMID: 37341908 PMCID: PMC10587296 DOI: 10.1007/s40279-023-01866-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2023] [Indexed: 06/22/2023]
Abstract
At present, various blood-based biomarkers have found their applications in the field of sports medicine. This current opinion addresses biomarkers that warrant consideration in future research for monitoring the athlete training load. In this regard, we identified a variety of emerging load-sensitive biomarkers, e.g., cytokines (such as IL-6), chaperones (such as heat shock proteins) or enzymes (such as myeloperoxidase) that could improve future athlete load monitoring as they have shown meaningful increases in acute and chronic exercise settings. In some cases, they have even been linked to training status or performance characteristics. However, many of these markers have not been extensively studied and the cost and effort of measuring these parameters are still high, making them inconvenient for practitioners so far. We therefore outline strategies to improve knowledge of acute and chronic biomarker responses, including ideas for standardized study settings. In addition, we emphasize the need for methodological advances such as the development of minimally invasive point-of-care devices as well as statistical aspects related to the evaluation of these monitoring tools to make biomarkers suitable for regular load monitoring.
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Affiliation(s)
- Nils Haller
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University of Mainz, Mainz, Germany
- Department of Sport and Exercise Science, University of Salzburg, Salzburg, Austria
| | - Thomas Reichel
- Department of Exercise Physiology and Sports Therapy, Institute of Sports Science, Justus-Liebig-University Gießen, Giessen, Germany
| | - Philipp Zimmer
- Division of Performance and Health (Sports Medicine), Institute for Sport and Sport Science, TU Dortmund University, Dortmund, Germany
| | - Michael Behringer
- Department of Sports Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Patrick Wahl
- Department of Exercise Physiology, German Sport University Cologne, Cologne, Germany
| | - Thomas Stöggl
- Department of Sport and Exercise Science, University of Salzburg, Salzburg, Austria
- Red Bull Athlete Performance Center, Salzburg, Austria
| | - Karsten Krüger
- Department of Exercise Physiology and Sports Therapy, Institute of Sports Science, Justus-Liebig-University Gießen, Giessen, Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University of Mainz, Mainz, Germany.
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6
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Peng WW, Liu Y, Sha HH, Wen SD, Fang Y, Zhou GR. Relationship between plasma circulating cell-free DNA concentration and treatment outcomes including prognosis in patients with advanced non-small cell lung cancer. BMC Pulm Med 2023; 23:348. [PMID: 37710221 PMCID: PMC10503004 DOI: 10.1186/s12890-023-02586-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/27/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND Some research found that elevated plasma cell-free DNA (cfDNA) concentrations and poor prognosis are associated in non-small cell lung cancer (NSCLC). However, more studies need to be carried out to verify this conclusion. Therefore, this study investigated the relationship between cfDNA concentration and treatment outcomes including prognosis in patients with advanced NSCLC. METHODS We retrospectively collected medical records and cfDNA data from 160 patients with advanced NSCLC. Progression-free survival (PFS) were calculated using the Kaplan-Meier method and were compared between groups using the log rank test. Cox regression analysis was used for estimating the independent predictors of PFS. And we used logistic regression to evaluate the relationship between baseline biomarkers and efficacy. In our study, BT1 cfDNA, BT2 cfDNA, and BT3 cfDNA were defined as cfDNA concentration before the first treatment (baseline cfDNA concentration), cfDNA concentration before the second treatment, and cfDNA concentration before the third treatment, respectively. RESULTS Patients with low cfDNA (BT1 cfDNA < 15 (ng/mL)) were reported a significantly prolonged median progression-free survival (mPFS) compared with patients with patients with high cfDNA (BT1 cfDNA ≥ 15(ng/mL)) (mPFS: 14.6 vs. 8.3 months, P = 0.002), as well as patients with neutrophil/lymphocyte ratio (NLR)<2.98 (mPFS: 13.1 vs. 7.9 months, P = 0.023). In addition, Cox proportional hazards regression analysis identified independent indicators associated with PFS including BT1 cfDNA ≥ 15 (ng/mL), NLR ≥ 2.98 and extrapulmonary metastasis. The best cut-off value for BT3 cfDNA for predicting disease progression is 41.46 (ng/mL) (Area Under the Curve (AUC): 0.652, 95%CI: 0.516-0.788), achieving 90.7% sensitivity and 37.5% specificity for the prediction of disease progression. BT3 cfDNA (OR = 6.08, 95% CI: 1.94-19.57, P = 0.002) was an independent factor for disease progression in patients with advanced NSCLC. CONCLUSIONS BT1 cfDNA may be a biomarker to assess the prognosis of advanced NSCLC. Patients with advanced NSCLC with lower cfDNA and NLR before treatment had a better prognosis. Increased BT3 cfDNA concentration was an independent factor of disease progression in advanced NSCLC patients. These findings may assist in identifying high-risk patients and guiding treatment strategies.
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Affiliation(s)
- Wei-Wei Peng
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Baiziting 42, Nanjing, 210009, Jiangsu, China
| | - Ying Liu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Baiziting 42, Nanjing, 210009, Jiangsu, China
| | - Huan-Huan Sha
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Baiziting 42, Nanjing, 210009, Jiangsu, China
| | - Shao-Di Wen
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Baiziting 42, Nanjing, 210009, Jiangsu, China
| | - Ying Fang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Baiziting 42, Nanjing, 210009, Jiangsu, China.
| | - Guo-Ren Zhou
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Baiziting 42, Nanjing, 210009, Jiangsu, China.
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7
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Rose KM, Huelster HL, Meeks JJ, Faltas BM, Sonpavde GP, Lerner SP, Ross JS, Spiess PE, Grass GD, Jain RK, Kamat AM, Vosoughi A, Wang L, Wang X, Li R. Circulating and urinary tumour DNA in urothelial carcinoma - upper tract, lower tract and metastatic disease. Nat Rev Urol 2023; 20:406-419. [PMID: 36977797 DOI: 10.1038/s41585-023-00725-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2023] [Indexed: 03/30/2023]
Abstract
Precision medicine has transformed the way urothelial carcinoma is managed. However, current practices are limited by the availability of tissue samples for genomic profiling and the spatial and temporal molecular heterogeneity observed in many studies. Among rapidly advancing genomic sequencing technologies, non-invasive liquid biopsy has emerged as a promising diagnostic tool to reproduce tumour genomics, and has shown potential to be integrated in several aspects of clinical care. In urothelial carcinoma, liquid biopsies such as plasma circulating tumour DNA (ctDNA) and urinary tumour DNA (utDNA) have been investigated as a surrogates for tumour biopsies and might bridge many shortfalls currently faced by clinicians. Both ctDNA and utDNA seem really promising in urothelial carcinoma diagnosis, staging and prognosis, response to therapy monitoring, detection of minimal residual disease and surveillance. The use of liquid biopsies in patients with urothelial carcinoma could further advance precision medicine in this population, facilitating personalized patient monitoring through non-invasive assays.
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Affiliation(s)
- Kyle M Rose
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Heather L Huelster
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Joshua J Meeks
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Bishoy M Faltas
- Department of Hematology/Oncology, Weill-Cornell Medicine, New York, NY, USA
| | - Guru P Sonpavde
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Seth P Lerner
- Department of Urology, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc, Cambridge, MA, USA
- Departments of Urology and Pathology, Upstate Medical University, Syracuse, NY, USA
| | - Philippe E Spiess
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - G Daniel Grass
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Rohit K Jain
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Ashish M Kamat
- Department of Urology, MD Anderson Cancer Center, Houston, TX, USA
| | - Aram Vosoughi
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Liang Wang
- Department of Tumour Biology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Xuefeng Wang
- Department of Biostatistics/Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Roger Li
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA.
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, FL, USA.
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8
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Fridlich O, Peretz A, Fox-Fisher I, Pyanzin S, Dadon Z, Shcolnik E, Sadeh R, Fialkoff G, Sharkia I, Moss J, Arpinati L, Nice S, Nogiec CD, Ahuno ST, Li R, Taborda E, Dunkelbarger S, Fridlender ZG, Polak P, Kaplan T, Friedman N, Glaser B, Shemer R, Constantini N, Dor Y. Elevated cfDNA after exercise is derived primarily from mature polymorphonuclear neutrophils, with a minor contribution of cardiomyocytes. Cell Rep Med 2023:101074. [PMID: 37290439 DOI: 10.1016/j.xcrm.2023.101074] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 08/25/2022] [Accepted: 05/15/2023] [Indexed: 06/10/2023]
Abstract
Strenuous physical exercise causes a massive elevation in the concentration of circulating cell-free DNA (cfDNA), which correlates with effort intensity and duration. The cellular sources and physiological drivers of this phenomenon are unknown. Using methylation patterns of cfDNA and associated histones, we show that cfDNA in exercise originates mostly in extramedullary polymorphonuclear neutrophils. Strikingly, cardiomyocyte cfDNA concentration increases after a marathon, consistent with elevated troponin levels and indicating low-level, delayed cardiac cell death. Physical impact, low oxygen levels, and elevated core body temperature contribute to neutrophil cfDNA release, while muscle contraction, increased heart rate, β-adrenergic signaling, or steroid treatment fail to cause elevation of cfDNA. Physical training reduces neutrophil cfDNA release after a standard exercise, revealing an inverse relationship between exercise-induced cfDNA release and training level. We speculate that the release of cfDNA from neutrophils in exercise relates to the activation of neutrophils in the context of exercise-induced muscle damage.
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Affiliation(s)
- Ori Fridlich
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ayelet Peretz
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ilana Fox-Fisher
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Sheina Pyanzin
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ziv Dadon
- Jesselson Integrated Heart Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Eilon Shcolnik
- Jesselson Integrated Heart Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Ronen Sadeh
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel; The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Israel
| | - Gavriel Fialkoff
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel; The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Israel
| | - Israa Sharkia
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel; The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Israel
| | - Joshua Moss
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ludovica Arpinati
- Institute of Pulmonary Medicine, Hadassah Medical Center and Hebrew University of Jerusalem, Israel
| | - Shachar Nice
- Heidi Rothberg Sport Medicine Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Christopher D Nogiec
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Bouvé College of Health Sciences, Northeastern University, Boston, MA, USA
| | - Samuel Terkper Ahuno
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rui Li
- Bouvé College of Health Sciences, Northeastern University, Boston, MA, USA
| | - Eddie Taborda
- Bouvé College of Health Sciences, Northeastern University, Boston, MA, USA
| | - Sonia Dunkelbarger
- Bouvé College of Health Sciences, Northeastern University, Boston, MA, USA
| | - Zvi G Fridlender
- Institute of Pulmonary Medicine, Hadassah Medical Center and Hebrew University of Jerusalem, Israel
| | - Paz Polak
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Nir Friedman
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel; The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Israel
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Naama Constantini
- Heidi Rothberg Sport Medicine Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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Natalia A, Zhang L, Sundah NR, Zhang Y, Shao H. Analytical device miniaturization for the detection of circulating biomarkers. NATURE REVIEWS BIOENGINEERING 2023; 1:1-18. [PMID: 37359772 PMCID: PMC10064972 DOI: 10.1038/s44222-023-00050-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 06/28/2023]
Abstract
Diverse (sub)cellular materials are secreted by cells into the systemic circulation at different stages of disease progression. These circulating biomarkers include whole cells, such as circulating tumour cells, subcellular extracellular vesicles and cell-free factors such as DNA, RNA and proteins. The biophysical and biomolecular state of circulating biomarkers carry a rich repertoire of molecular information that can be captured in the form of liquid biopsies for disease detection and monitoring. In this Review, we discuss miniaturized platforms that allow the minimally invasive and rapid detection and analysis of circulating biomarkers, accounting for their differences in size, concentration and molecular composition. We examine differently scaled materials and devices that can enrich, measure and analyse specific circulating biomarkers, outlining their distinct detection challenges. Finally, we highlight emerging opportunities in biomarker and device integration and provide key future milestones for their clinical translation.
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Affiliation(s)
- Auginia Natalia
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Li Zhang
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Noah R. Sundah
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
| | - Yan Zhang
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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10
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Li H, Lu S, Zhou Z, Zhu X, Shao Y. Role of Circulating Tumor DNA in Colorectal Cancer. Methods Mol Biol 2023; 2695:227-236. [PMID: 37450122 DOI: 10.1007/978-1-0716-3346-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Colorectal cancer (CRC) is a very common gastrointestinal tumor, ranking second in the global cause of cancer death. Because of the invasive nature of biopsy and cannot reflect the heterogeneity of tumor or monitor the dynamic progress of tumor, it is necessary to induce a novel noninvasive method to improve the current treatment strategies of colorectal cancer. Among all the components of liquid biopsy, circulating tumor DNA (ctDNA) may have the best future. CtDNA maintains the same genomic characteristics as those in matched tumor tissues, so it allows quantitative evaluation and analysis of mutation load in body fluid. Furthermore, because the half-life of ctDNA is from 16 min to several hours in circulation, the circulating ctDNA can be measured repeatedly within a certain period to monitor the response of CRC to treatment, the occurrence of drug resistance, and the diagnosis of recurrence.
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Affiliation(s)
- Haotian Li
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Sheng Lu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zidong Zhou
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiaocheng Zhu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yong Shao
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
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11
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Bronkhorst AJ, Ungerer V, Oberhofer A, Gabriel S, Polatoglou E, Randeu H, Uhlig C, Pfister H, Mayer Z, Holdenrieder S. New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:2147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
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.
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Affiliation(s)
- Abel J. Bronkhorst
- Munich Biomarker Research Center, Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, D-80636 Munich, Germany
| | | | | | | | | | | | | | | | | | - Stefan Holdenrieder
- Munich Biomarker Research Center, Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, D-80636 Munich, Germany
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12
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Dehnen D, Neuberger E, In der Schmitten J, Giagkou E, Simon P, Botzenhardt S. cfDNA as a surrogate marker for COVID-19 severity in patients with influenza-like symptoms with and without SARS-CoV-2 infections in general practice: a study protocol for a prospective cohort study. BMJ Open 2022; 12:e058647. [PMID: 35710258 PMCID: PMC9207575 DOI: 10.1136/bmjopen-2021-058647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
INTRODUCTION The clinical course of patients with a SARS-CoV-2 (COVID-19) infection varies widely, from symptom-free to severe courses that can lead to death. Laboratory values of SARS-CoV-2 patients such as lymphocyte counts or C-reactive protein (CRP) do not allow a prediction of the actual course of the disease. To identify a possible predictive marker for the differentiation and prognosis of illness with influenza-like symptoms with and without SARS-CoV-2 infections in general practice, we will analyse the concentrations of cell-free DNA (cfDNA) levels, laboratory and clinical parameters, temperature, oxygen saturation, breathing rate and concomitant symptoms in patients with flu-like symptoms with and without a SARS-CoV-2 infection. METHODS AND ANALYSIS This is a single-centre, two-arm, parallel longitudinal cohort study with a total of 44 patients. 22 patients with flu-like symptoms without a SARS-CoV-2 infection and 22 patients with flu-like symptoms with a SARS-CoV-2 infection will be recruited. The primary objective is to compare cfDNA levels in ambulatory patients in general practice with flu-like symptoms with SARS-CoV-2 infection with those with influenza like symptoms without a SARS-CoV-2 infection during the disease (day 7 and day 14). The secondary objective is to determine whether there is a correlation between cfDNA concentrations on the one hand, and laboratory and clinical parameters on the other hand. cfDNA, differential blood count, high-sensitive CRP and erythrocyte sedimentation rate will be measured in blood samples, concomitant symptoms will be surveyed via a self-assessment questionnaire, and oxygen saturation, breathing rate and examination of the lungs will be reported by treating physicians. ETHICS AND DISSEMINATION Ethical approval was issued on 1 March 2021 by the Ethics Committee Essen under the number 21-9916-BO. Findings will be published in peer-reviewed open-access journals and presented at national and international conferences. TRIAL REGISTRATION NUMBER DRKS00024722.
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Affiliation(s)
- Dorothea Dehnen
- Institute of General Practice, Medical Faculty, University of Duisburg-Essen Faculty of Medicine, Essen, Germany
| | - Elmo Neuberger
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg Universitat Mainz, Mainz, Germany
| | - Jürgen In der Schmitten
- Institute of General Practice, Medical Faculty, University of Duisburg-Essen Faculty of Medicine, Essen, Germany
| | - Ekaterini Giagkou
- Institute of General Practice, Medical Faculty, University of Duisburg-Essen Faculty of Medicine, Essen, Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg Universitat Mainz, Mainz, Germany
| | - Suzan Botzenhardt
- Institute of General Practice, Medical Faculty, University of Duisburg-Essen Faculty of Medicine, Essen, Germany
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13
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Bell LR, Gabbett TJ, Davis GM, Wallen MP, O’Brien BJ. Stubborn Exercise Responders-Where to Next? Sports (Basel) 2022; 10:sports10060095. [PMID: 35736835 PMCID: PMC9229615 DOI: 10.3390/sports10060095] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/03/2022] [Accepted: 06/08/2022] [Indexed: 11/17/2022] Open
Abstract
There is a wide variance in the magnitude of physiological adaptations after resistance or endurance training. The incidence of “non” or “poor” responders to training has been reported to represent as high as 40% of the project’s sample. However, the incidence of poor responders to training can be ameliorated with manipulation of either the training frequency, intensity, type and duration. Additionally, global non-response to cardio-respiratory fitness training is eliminated when evaluating several health measures beyond just the target variables as at least one or more measure improves. More research is required to determine if altering resistance training variables results in a more favourable response in individuals with an initial poor response to resistance training. Moreover, we recommend abandoning the term “poor” responders, as ultimately the magnitude of change in cardiorespiratory fitness in response to endurance training is similar in “poor” and “high” responders if the training frequency is subsequently increased. Therefore, we propose “stubborn” responders as a more appropriate term. Future research should focus on developing viable physiological and lifestyle screening tests that identify likely stubborn responders to conventional exercise training guidelines before the individual engages with training. Exerkines, DNA damage, metabolomic responses in blood, saliva and breath, gene sequence, gene expression and epigenetics are candidate biomarkers that warrant investigation into their relationship with trainability. Crucially, viable biomarker screening tests should show good construct validity to distinguish between different exercise loads, and possess excellent sensitivity and reliability. Furthermore “red flag” tests of likely poor responders to training should be practical to assess in clinical settings and be affordable and non-invasive. Early identification of stubborn responders would enable optimization of training programs from the onset of training to maintain exercise motivation and optimize the impact on training adaptations and health.
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Affiliation(s)
- Leo R. Bell
- Institute of Health and Wellbeing, Federation University, Mount Helen, VIC 3350, Australia; (L.R.B.); (T.J.G.); (G.M.D.); (M.P.W.)
| | - Tim J. Gabbett
- Institute of Health and Wellbeing, Federation University, Mount Helen, VIC 3350, Australia; (L.R.B.); (T.J.G.); (G.M.D.); (M.P.W.)
- Gabbett Performance Solutions, Brisbane, QLD 4011, Australia
| | - Gregory M. Davis
- Institute of Health and Wellbeing, Federation University, Mount Helen, VIC 3350, Australia; (L.R.B.); (T.J.G.); (G.M.D.); (M.P.W.)
| | - Matthew P. Wallen
- Institute of Health and Wellbeing, Federation University, Mount Helen, VIC 3350, Australia; (L.R.B.); (T.J.G.); (G.M.D.); (M.P.W.)
- Caring Futures Institute, College of Nursing and Health Sciences, Flinders University, Adelaide, SA 5000, Australia
| | - Brendan J. O’Brien
- Institute of Health and Wellbeing, Federation University, Mount Helen, VIC 3350, Australia; (L.R.B.); (T.J.G.); (G.M.D.); (M.P.W.)
- Correspondence:
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14
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Feasibility of Cell-Free DNA Measurement from the Earlobe during Physiological Exercise Testing. Diagnostics (Basel) 2022; 12:diagnostics12061379. [PMID: 35741187 PMCID: PMC9222055 DOI: 10.3390/diagnostics12061379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
Abstract
Circulating, cell-free DNA (cfDNA) has been discussed as an upcoming blood-based biomarker in exercise physiology, reflecting important aspects of exercise load. cfDNA blood sampling has evolved from elaborate venous to efficient capillary sampling from the fingertips. In this study, we aimed to evaluate the principal feasibility of cfDNA blood sampling from the earlobe. Therefore, we obtained cfDNA concentrations from the fingertips, earlobe, and the antecubital vein during physiological exercise testing. Significantly higher concentrations were obtained from the earlobe compared to fingertip samples. All of the measurement methods showed good to excellent repeatability (ICCs of 0.85 to 0.93). In addition, the control experiments revealed that repeated sampling from the earlobe but not from the fingertips increased cfDNA at rest. In summary, cfDNA sampling is feasible for all sampling sources. However, at rest, cfDNA collected from the earlobe tend to increase over time in the absence of physical load, potentially limiting this sampling method.
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15
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Dumić J, Cvetko A, Abramović I, Šupraha Goreta S, Perović A, Njire Bratičević M, Kifer D, Sinčić N, Gornik O, Žarak M. Changes in Specific Biomarkers Indicate Cardiac Adaptive and Anti-inflammatory Response of Repeated Recreational SCUBA Diving. Front Cardiovasc Med 2022; 9:855682. [PMID: 35360010 PMCID: PMC8964121 DOI: 10.3389/fcvm.2022.855682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveRecreational SCUBA (rSCUBA) diving has become a highly popular and widespread sport. Yet, information on molecular events underlying (patho)physiological events that follow exposure to the specific environmental conditions (hyperbaric conditions, coldness, immersion, and elevated breathing pressure), in which rSCUBA diving is performed, remain largely unknown. Our previous study suggested that repeated rSCUBA diving triggers an adaptive response of cardiovascular and immune system. To elucidate further molecular events underlying cardiac and immune system adaptation and to exclude possible adverse effects we measured blood levels of specific cardiac and inflammation markers.MethodsThis longitudinal intervention study included fourteen recreational divers who performed five dives, one per week, on the depth 20–30 m that lasted 30 min, after the non-dive period of 5 months. Blood samples were taken immediately before and after the first, third, and fifth dives. Copeptin, immunoglobulins A, G and M, complement components C3 and C4, and differential blood count parameters, including neutrophil-to-lymphocyte ratio (NLR) were determined using standard laboratory methods. Cell-free DNA was measured by qPCR analysis and N-glycans released from IgG and total plasma proteins (TPP), were analyzed by hydrophilic interaction ultra-performance liquid chromatography.ResultsCopeptin level increased after the first dive but decreased after the third and fifth dive. Increases in immunoglobulins level after every dive and during whole studied period were observed, but no changes in C3, C4, and cfDNA level were detected. NLR increased only after the first dive. IgG and TPP N-glycosylation alterations toward anti-inflammatory status over whole studied period were manifested as an increase in monogalyctosylated and core-fucosylated IgG N-glycans and decrease in agalactosylated TPP N-glycans.ConclusionrSCUBA diving practiced on a regular basis promotes anti-inflammatory status thus contributing cardioprotection and conferring multiple health benefits.
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Affiliation(s)
- Jerka Dumić
- Department of Biochemistry and Molecular Biology, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Ana Cvetko
- Department of Biochemistry and Molecular Biology, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Irena Abramović
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Sandra Šupraha Goreta
- Department of Biochemistry and Molecular Biology, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Antonija Perović
- Department of Laboratory Diagnostics, Dubrovnik General Hospital, Dubrovnik, Croatia
| | | | - Domagoj Kifer
- Department of Biophysics, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Nino Sinčić
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Olga Gornik
- Department of Biochemistry and Molecular Biology, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Marko Žarak
- Clinical Department of Laboratory Diagnostics, Dubrava University Hospital, Zagreb, Croatia
- *Correspondence: Marko Žarak,
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16
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Yin L, Guo Z, Wang T, Wang X. Increase of circulating cfDNA by chronic training or overtraining in human and rat and its possible mechanisms. Sci Sports 2022. [DOI: 10.1016/j.scispo.2021.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Novel Diagnostic Biomarkers in Colorectal Cancer. Int J Mol Sci 2022; 23:ijms23020852. [PMID: 35055034 PMCID: PMC8776048 DOI: 10.3390/ijms23020852] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/27/2021] [Accepted: 01/03/2022] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is still a leading cause of cancer death worldwide. Less than half of cases are diagnosed when the cancer is locally advanced. CRC is a heterogenous disease associated with a number of genetic or somatic mutations. Diagnostic markers are used for risk stratification and early detection, which might prolong overall survival. Nowadays, the widespread use of semi-invasive endoscopic methods and feacal blood tests characterised by suboptimal accuracy of diagnostic results has led to the detection of cases at later stages. New molecular noninvasive tests based on the detection of CRC alterations seem to be more sensitive and specific then the current methods. Therefore, research aiming at identifying molecular markers, such as DNA, RNA and proteins, would improve survival rates and contribute to the development of personalized medicine. The identification of “ideal” diagnostic biomarkers, having high sensitivity and specificity, being safe, cheap and easy to measure, remains a challenge. The purpose of this review is to discuss recent advances in novel diagnostic biomarkers for tumor tissue, blood and stool samples in CRC patients.
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18
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Chmielecki A, Bortnik K, Galczynski S, Padula G, Jerczynska H, Stawski R, Nowak D. Exhaustive Exercise Increases Spontaneous but Not fMLP-Induced Production of Reactive Oxygen Species by Circulating Phagocytes in Amateur Sportsmen. BIOLOGY 2022; 11:103. [PMID: 35053101 PMCID: PMC8773189 DOI: 10.3390/biology11010103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/22/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Strenuous exercise alters the oxidative response of blood phagocytes to various agonists. However, little is known about spontaneous post exercise oxidant production by these cells. In this cross-over trial, we tested whether an exhaustive treadmill run at a speed corresponding to 70% of VO2max affects spontaneous and fMLP-provoked oxidant production by phagocytes in 18 amateur sportsmen. Blood was collected before, just after, and 1, 3, 5 and 24 h post exercise for determination of absolute and normalized per phagocyte count spontaneous (a-rLBCL, rLBCL) and fMLP-induced luminol-enhanced whole blood chemiluminescence (a-fMLP-LBCL, fMLP-LBCL). a-rLBCL and rLBCL increased by 2.5- and 1.5-times just after exercise (p < 0.05) and then returned to baseline or decreased by about 2-times at the remaining time-points, respectively. a-fMLP-LBCL increased 1.7- and 1.6-times just after and at 3 h post-exercise (p < 0.05), respectively, while fMLP-LBCL was suppressed by 1.5- to 2.3-times at 1, 3, 5 and 24 h post-exercise. No correlations were found between elevated post-exercise a-rLBCL, a-fMLP-LBCL and run distance to exhaustion. No changes of oxidants production were observed in the control arm (1 h resting instead of exercise). Exhaustive exercise decreased the blood phagocyte-specific oxidative response to fMLP while increasing transiently spontaneous oxidant generation, which could be a factor inducing secondary rise in antioxidant enzymes activity.
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Affiliation(s)
- Adam Chmielecki
- Sports Centre, Medical University of Lodz, 6-go Sierpnia 69, 90-645 Lodz, Poland; (A.C.); (K.B.)
| | - Krzysztof Bortnik
- Sports Centre, Medical University of Lodz, 6-go Sierpnia 69, 90-645 Lodz, Poland; (A.C.); (K.B.)
| | - Szymon Galczynski
- Academic Laboratory of Movement and Human Physical Performance “DynamoLab”, Medical University of Lodz, Pomorska 251, 92-216 Lodz, Poland; (S.G.); (G.P.)
| | - Gianluca Padula
- Academic Laboratory of Movement and Human Physical Performance “DynamoLab”, Medical University of Lodz, Pomorska 251, 92-216 Lodz, Poland; (S.G.); (G.P.)
| | - Hanna Jerczynska
- Central Scientific Laboratory, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland;
| | - Robert Stawski
- Department of Clinical Physiology, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland;
| | - Dariusz Nowak
- Department of Clinical Physiology, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland;
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19
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Yuwono NL, Warton K, Ford CE. The influence of biological and lifestyle factors on circulating cell-free DNA in blood plasma. eLife 2021; 10:e69679. [PMID: 34752217 PMCID: PMC8577835 DOI: 10.7554/elife.69679] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/23/2021] [Indexed: 01/02/2023] Open
Abstract
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.
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Affiliation(s)
- Nicole Laurencia Yuwono
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women's and Children's Health, Faculty of Medicine & Health, University of New South WalesSydneyAustralia
| | - Kristina Warton
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women's and Children's Health, Faculty of Medicine & Health, University of New South WalesSydneyAustralia
| | - Caroline Elizabeth Ford
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women's and Children's Health, Faculty of Medicine & Health, University of New South WalesSydneyAustralia
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20
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Tsoi KM, Gokgoz N, Darville-O'Quinn P, Prochazka P, Malekoltojari A, Griffin AM, Ferguson PC, Wunder JS, Andrulis IL. Detection and utility of cell-free and circulating tumour DNA in bone and soft-tissue sarcomas. Bone Joint Res 2021; 10:602-610. [PMID: 34558310 PMCID: PMC8479566 DOI: 10.1302/2046-3758.109.bjr-2021-0014.r1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Aims Cell-free DNA (cfDNA) and circulating tumour DNA (ctDNA) are used for prognostication and monitoring in patients with carcinomas, but their utility is unclear in sarcomas. The objectives of this pilot study were to explore the prognostic significance of cfDNA and investigate whether tumour-specific alterations can be detected in the circulation of sarcoma patients. Methods Matched tumour and blood were collected from 64 sarcoma patients (n = 70 samples) prior to resection of the primary tumour (n = 57) or disease recurrence (n = 7). DNA was isolated from plasma, quantified, and analyzed for cfDNA. A subset of cases (n = 6) underwent whole exome sequencing to identify tumour-specific alterations used to detect ctDNA using digital droplet polymerase chain reaction (ddPCR). Results Cell-free was present in 69 of 70 samples above 0.5 ng/ml. Improved disease-free survival was found for patients with lower cfDNA levels (90% vs 48% at one-year for ≤ 6 ng/ml and > 6 ng/ml, respectively; p = 0.005). Digital droplet PCR was performed as a pilot study and mutant alleles were detectable at 0.5% to 2.5% of the wild type genome, and at a level of 0.25 ng tumour DNA. Tumour-specific alterations (ctDNA) were found in five of six cases. Conclusion This work demonstrates the feasibility and potential utility of cfDNA and ctDNA as biomarkers for bone and soft-tissue sarcomas, despite the lack of recurrent genomic alterations. A larger study is required to validate these findings. Cite this article: Bone Joint Res 2021;10(9):602–610.
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Affiliation(s)
- Kim M Tsoi
- University of Toronto Musculoskeletal Oncology Unit, Sinai Health System, Toronto, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Surgery, University of Toronto, Toronto, Canada
| | - Nalan Gokgoz
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | | | - Patrick Prochazka
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Ainaz Malekoltojari
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Anthony M Griffin
- University of Toronto Musculoskeletal Oncology Unit, Sinai Health System, Toronto, Canada
| | - Peter C Ferguson
- University of Toronto Musculoskeletal Oncology Unit, Sinai Health System, Toronto, Canada.,Department of Surgery, University of Toronto, Toronto, Canada
| | - Jay S Wunder
- University of Toronto Musculoskeletal Oncology Unit, Sinai Health System, Toronto, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Surgery, University of Toronto, Toronto, Canada
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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21
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Huebner H, Lubrich H, Blum S, Antoniadis S, Lermann J, Ekici A, Fasching PA, Beckmann MW, Ruebner M, Burghaus S. Comparison of methods for isolation and quantification of circulating cell-free DNA from patients with endometriosis. Reprod Biomed Online 2021; 43:788-798. [PMID: 34493460 DOI: 10.1016/j.rbmo.2021.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/13/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
RESEARCH QUESTION Which is the optimal extraction method for isolating and quantifying circulating cell-free DNA (ccfDNA) from patients with endometriosis? Endometriosis is a common benign disease, associated with pain, infertility and reduced quality of life. Endometriosis is also a known risk factor for various cancers. Robust biomarkers for early detection and prediction of prognosis, however, are lacking. CcfDNA is an easy to obtain biomarker associated with prognosis of cancer patients and enables non-invasive analysis of somatic mutations. Recently, elevated levels of ccfDNA were detected in patients with endometriosis. DESIGN Two different ccfDNA extraction methods were compared: Maxwell RSC ccfDNA plasma kit (Maxwell) and QiAamp minElute ccfDNA mini kit (QIAamp). The ccfDNA and circulating mitochondrial DNA (mtDNA) quantities from 34 patients diagnosed with endometriosis were analysed. Fluorometric measurement and quantitative reverse transcription polymerase chain reaction (qRT-PCR) of short and long ALU and mtDNA fragments were used to quantiy ccfDNA. RESULTS The yield of ccfDNA isolated with the Maxwell method was significantly higher compared with the QIAamp method (P < 0.0001). Integrity of ccfDNA was significantly higher in the QIAamp isolate (P < 0.0001). Recovered mtDNA was not significantly different between both extraction methods used. CONCLUSIONS The choice of extraction method can significantly influence the ccfDNA output and integrity. Both methods, however, enabled isolation of sufficient ccfDNA for further downstream applications. With this approach, isolation of ccfDNA could enable the non-invasive detection and analysis of somatic mutation within endometriosis tissue.
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Affiliation(s)
- Hanna Huebner
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Hannah Lubrich
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Simon Blum
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Sophia Antoniadis
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Johannes Lermann
- Department of Obstetrics and Gynecology, Klinikum Klagenfurt am Wörthersee, Austria
| | - Arif Ekici
- Institute of Human Genetics, Erlangen University Hospital, Friedrich-Alexander University, Erlangen-Nürnberg, Erlangen, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Matthias Ruebner
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Stefanie Burghaus
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Endometriosis Center for Franconia, Friedrich-Alexander University Erlangen-Nürnberg, Germany.
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cfDNA Changes in Maximal Exercises as a Sport Adaptation Predictor. Genes (Basel) 2021; 12:genes12081238. [PMID: 34440412 PMCID: PMC8392318 DOI: 10.3390/genes12081238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 01/16/2023] Open
Abstract
Changes of circulating free plasma DNA (cfDNA) are associated with different types of tissue injury, including those induced by intensive aerobic and anaerobic exercises. Observed changes are dependent from induced inflammation, and thus it may be a potential marker for athletic overtraining. We aimed to identify the response of cfDNA to different types of exercise, with association to exercise intensity as a potential marker of exercise load. Fifty volunteers (25 athletes and 25 physically active men) were assigned to the study and performed maximal aerobic (Bruce test) and anaerobic (Wingate Anaerobic Test) test. Blood samples for cfDNA analysis were collected at four time-points: before, 2-5 min after, 30 min after and 60 min after each type of maximal physical activity. The two-way ANOVA revealed a significant effect of group factor on serum cfDNA concentrations (32.15% higher concentration of cfDNA in the athletes). In turn the results of the post hoc test for the interaction of the repeated measures factor and the group showed that while the concentration of cfDNA decreased by 40.10% in the period from 30 min to 60 min after exercise in the control group, the concentration of cfDNA in the group of athletes remained at a similar level. Our analysis presents different responses depending on the intensity and duration of exercise. Our observations imply that formation of cfDNA is associated with response to physical activity but only during maximal effort.
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The relevance of liquid biopsy in surgical oncology: The application of perioperative circulating nucleic acid dynamics in improving patient outcomes. Surgeon 2021; 20:e163-e173. [PMID: 34362650 DOI: 10.1016/j.surge.2021.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 06/13/2021] [Accepted: 06/23/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Liquid biopsy is gaining increasing clinical utility in the management of cancer patients. The main components of a liquid biopsy are circulating nucleic acids, circulating tumour cells and extracellular vesicles such as exosomes. Circulating nucleic acids including cell free DNA (cfDNA) and circulating tumour DNA (ctDNA) in particular have been the focus of recent attention as they have demonstrated excellent potential in cancer screening, provision of prognostic information and in genomic profiling of a tumour without the need for repeated tissue biopsies. The aim of this review was to explore the current evidence in relation to the use of liquid biopsy in the perioperative setting and identify ways in which liquid biopsy may be applied in the future. METHODS This narrative review is based on a comprehensive literature search up to the 1st of June 2020 for papers relevant to the application of liquid biopsy in surgical oncology, focusing particularly on the perioperative period. RESULTS Recent evidence has demonstrated that perioperative liquid biopsy can accurately stratify patients' risk of recurrence compared to conventional biomarkers. Attention to the perioperative dynamics of liquid biopsy components can potentially provide new understanding of the complex relationship between surgery and cancer outcome. In addition, careful evaluation of liquid biopsy components in the perioperative window may provide important diagnostic and therapeutic information for cancer patients. CONCLUSION The rapidly evolving concept of the liquid biopsy has the potential to become the cornerstone for decision making around surveillance and adjuvant therapies the era of personalised medicine.
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Donor-derived Cell-free DNA in Solid-organ Transplant Diagnostics: Indications, Limitations, and Future Directions. Transplantation 2021; 105:1203-1211. [PMID: 33534526 DOI: 10.1097/tp.0000000000003651] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The last few years have seen an explosion in clinical research focusing on the use of donor-derived cell-free DNA (dd-cfDNA) in solid-organ transplants (SOT). Although most of the literature published so far focuses on kidney transplants, there are several recent as well as ongoing research studies on heart, lung, pancreas, and liver transplants. Though initially studied as a noninvasive means of identifying subclinical or acute rejection in SOT, it is rapidly becoming clear that instead of being a specific marker for allograft rejection, dd-cfDNA is more appropriately described as a marker of severe injury, although the most common cause of this injury is allograft rejection. Multiple studies in kidney transplants have shown that although sensitivity for the diagnosis of antibody-mediated rejection is excellent, it is less so for T-cell-mediated rejection. It is possible that combining dd-cfDNA with other novel urine- or blood-based biomarkers may increase the sensitivity for the diagnosis of rejection. Irrespective of the cause, though, elevated dd-cfDNA seems to portend adverse allograft prognosis and formation of de novo donor-specific antibody. Although current data do not lend themselves to a clear conclusion, ongoing studies may reveal the utility of serial surveillance for the management of SOT as following levels of dd-cfDNA over time may provide windows of opportunity to intervene early and before irreversible allograft injury. Finally, cost-effectiveness studies will be needed to guide the ideal incorporation of dd-cfDNA into routine clinical practice.
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Optimization of Preanalytical Variables for cfDNA Processing and Detection of ctDNA in Archival Plasma Samples. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5585148. [PMID: 34307658 PMCID: PMC8285169 DOI: 10.1155/2021/5585148] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/23/2021] [Indexed: 12/19/2022]
Abstract
DNA released from cells into the peripheral blood is known as cell-free DNA (cfDNA), representing a promising noninvasive source of biomarkers that could be utilized to manage Diffuse Large B-Cell Lymphoma (DLBCL), among other diseases. The procedure for purification and handling of cfDNA is not yet standardized, and various preanalytical variables may affect the yield and analysis of cfDNA, including the purification kits, blood collection tubes, and centrifugation regime. Therefore, we aimed to investigate the impact of these preanalytical variables on the yield of cfDNA by comparing three different purification kits DNeasy Blood & Tissue Kit (Qiagen), QIAamp Circulating Nucleic Acid Kit (Qiagen), and Quick-cfDNA Serum & Plasma Kit (Zymo Research). Two blood collection tubes (BCTs), EDTA-K2 and Cell-Free DNA (Streck), stored at four different time points before plasma was separated and cfDNA purified, were compared, and for EDTA tubes, two centrifugation regimes at 2000 × g and 3000 × g were tested. Additionally, we have tested the utility of long-term archival blood samples from DLBCL patients to detect circulating tumor DNA (ctDNA). We observed a higher cfDNA yield using the QIAamp Circulating Nucleic Acid Kit (Qiagen) purification kit, as well as a higher cfDNA yield when blood samples were collected in EDTA BCTs, with a centrifuge regime at 2000 × g. Moreover, ctDNA detection was feasible from archival plasma samples with a median storage time of nine years.
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Liquid Biopsy Is a Promising Tool for Genetic Testing in Idiopathic Pulmonary Fibrosis. Diagnostics (Basel) 2021; 11:diagnostics11071202. [PMID: 34359285 PMCID: PMC8305941 DOI: 10.3390/diagnostics11071202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/21/2021] [Accepted: 06/27/2021] [Indexed: 01/24/2023] Open
Abstract
Liquid biopsy, which allows the isolation of circulating cell-free (ccf) DNA from blood, is an emerging noninvasive tool widely used in oncology for diagnostic and prognosis purposes. Previous data have shown that serum cfDNA discriminates idiopathic pulmonary fibrosis (IPF) from other interstitial lung diseases. Our study aimed to measure plasma levels of ccfDNA in 59 consecutive therapy-naive and clinically stable IPF patients. The single nucleotide polymorphism (SNP) of the MUC5B gene promoter (rs35705950), associated with increased susceptibility of developing IPF, has been sought in plasma cfDNA and genomic DNA for comparison. Thirty-five age- and sex-matched healthy volunteers were recruited as the control group. Our results show that concentrations of small-size ccfDNA fragments were significantly higher in IPF patients than in controls and inversely correlated with lung function deterioration. Moreover, the median level of 104 ng/mL allowed discriminating patients with mild disease from those more advanced. The rs35705950 polymorphism was found in 11.8% of IPF patients and 8% of controls, with no differences. Complete concordance between ccfDNA and genomic DNA was detected in all control samples, while four out of seven IPF cases (57%) carrying the rs35705950 polymorphism were discordant from genomic DNA (7% of total IPF). Liquid biopsy is a suitable tool with optimistic expectations of application in the field of IPF. In analogy with cancer biology, finding some discrepancies between ccfDNA and genomic DNA in IPF patients suggests that the former may convey specific genetic information present in the primary site of the disease.
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27
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Trumpff C, Michelson J, Lagranha CJ, Taleon V, Karan KR, Sturm G, Lindqvist D, Fernström J, Moser D, Kaufman BA, Picard M. Stress and circulating cell-free mitochondrial DNA: A systematic review of human studies, physiological considerations, and technical recommendations. Mitochondrion 2021; 59:225-245. [PMID: 33839318 PMCID: PMC8418815 DOI: 10.1016/j.mito.2021.04.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/23/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023]
Abstract
Cell-free mitochondrial DNA (cf-mtDNA) is a marker of inflammatory disease and a predictor of mortality, but little is known about cf-mtDNA in relation to psychobiology. A systematic review of the literature reveals that blood cf-mtDNA varies in response to common real-world stressors including psychopathology, acute psychological stress, and exercise. Moreover, cf-mtDNA is inducible within minutes and exhibits high intra-individual day-to-day variation, highlighting the dynamic regulation of cf-mtDNA levels. We discuss current knowledge on the mechanisms of cf-mtDNA release, its forms of transport ("cell-free" does not mean "membrane-free"), potential physiological functions, putative cellular and neuroendocrine triggers, and factors that may contribute to cf-mtDNA removal from the circulation. A review of in vitro, pre-clinical, and clinical studies shows conflicting results around the dogma that physiological forms of cf-mtDNA are pro-inflammatory, opening the possibility of other physiological functions, including the cell-to-cell transfer of whole mitochondria. Finally, to enhance the reproducibility and biological interpretation of human cf-mtDNA research, we propose guidelines for blood collection, cf-mtDNA isolation, quantification, and reporting standards, which can promote concerted advances by the community. Defining the mechanistic basis for cf-mtDNA signaling is an opportunity to elucidate the role of mitochondria in brain-body interactions and psychopathology.
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Affiliation(s)
- Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Jeremy Michelson
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Claudia J Lagranha
- University of Pittsburgh, School of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, Pittsburgh, PA, United States
| | - Veronica Taleon
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Kalpita R Karan
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Gabriel Sturm
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Daniel Lindqvist
- Faculty of Medicine, Department of Clinical Sciences, Psychiatry, Lund University, Lund, Sweden; Office of Psychiatry and Habilitation, Region Skåne, Sweden
| | - Johan Fernström
- Faculty of Medicine, Department of Clinical Sciences, Psychiatry, Lund University, Lund, Sweden
| | - Dirk Moser
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - Brett A Kaufman
- University of Pittsburgh, School of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, Pittsburgh, PA, United States
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Medical Center, New York, USA; New York State Psychiatric Institute, NY, USA.
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Neuberger EWI, Brahmer A, Ehlert T, Kluge K, Philippi KFA, Boedecker SC, Weinmann-Menke J, Simon P. Validating quantitative PCR assays for cfDNA detection without DNA extraction in exercising SLE patients. Sci Rep 2021; 11:13581. [PMID: 34193884 PMCID: PMC8245561 DOI: 10.1038/s41598-021-92826-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 06/07/2021] [Indexed: 01/10/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) has been investigated as a screening tool for many diseases. To avoid expensive and time-consuming DNA isolation, direct quantification PCR assays can be established. However, rigorous validation is required to provide reliable data in the clinical and non-clinical context. Considering the International Organization for Standardization, as well as bioanalytical method validation guidelines, we provide a comprehensive procedure to validate assays for cfDNA quantification from blood plasma without DNA isolation. A 90 and 222 bp assay was validated to study the kinetics of cfDNA after exercise in patients with systemic lupus erythematosus (SLE). The assays showed ultra-low limit of quantification (LOQ) with 0.47 and 0.69 ng/ml, repeatability ≤ 11.6% (95% CI 8.1-20.3), and intermediate precision ≤ 12.1% (95% CI 9.2-17.7). Incurred sample reanalysis confirmed the precision of the procedure. The additional consideration of pre-analytical factors shows that centrifugation speed and temperature do not change cfDNA concentrations. In SLE patients cfDNA increases ~ twofold after a walking exercise, normalizing after 60 min of rest. The established assays allow reliable and cost-efficient quantification of cfDNA in minute amounts of plasma in the clinical setting. Additionally, the assay can be used as a tool to determine the impact of pre-analytical factors and validate cfDNA quantity and quality of isolated samples.
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Affiliation(s)
- Elmo W I Neuberger
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Alexandra Brahmer
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Tobias Ehlert
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Katrin Kluge
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Keito F A Philippi
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Simone C Boedecker
- Department of Rheumatology and Nephrology, University Medical Center Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Julia Weinmann-Menke
- Department of Rheumatology and Nephrology, University Medical Center Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany.
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29
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De Vlaminck I. The Proportion of Donor-Specific Cell-Free DNA in Blood as a Marker of Transplant Rejection: Not an Absolute. Clin Chem 2021; 66:1257-1258. [PMID: 32968783 DOI: 10.1093/clinchem/hvaa199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 08/06/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY
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30
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Paracchini L, D’Incalci M, Marchini S. Liquid Biopsy in the Clinical Management of High-Grade Serous Epithelial Ovarian Cancer-Current Use and Future Opportunities. Cancers (Basel) 2021; 13:2386. [PMID: 34069200 PMCID: PMC8156052 DOI: 10.3390/cancers13102386] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
The lack of a sensitive and specific biomarker and the limits relating to the single primary tumor sampling make it difficult to monitor high-grade serous epithelial ovarian cancer (HGS-EOC) over time and to capture those alterations that are potentially useful in guiding clinical decisions. To overcome these issues, liquid biopsy has emerged as a very promising tool for HGS-EOC. The analysis of circulating tumor DNA appears to be feasible and studies assessing specific pathogenic mutations (i.e., TP53) or copy number alterations have shown a sufficient degree of sensitivity and specificity to be realistically used to monitor the effectiveness of antitumor therapy. Liquid biopsy can also provide potential important information on the mechanisms of sensitivity and resistance, e.g., by the determination of the reversion of BRCA mutations. Perspective studies are needed to test whether the application of liquid biopsy will significantly improve HGS-EOC management and patients' survival.
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Affiliation(s)
- Lara Paracchini
- Department of Biomedical Sciences, Humanitas University, 20072 Pieve Emanuele, Italy;
- IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy;
| | - Maurizio D’Incalci
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
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31
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Ungerer V, Bronkhorst AJ, Van den Ackerveken P, Herzog M, Holdenrieder S. Serial profiling of cell-free DNA and nucleosome histone modifications in cell cultures. Sci Rep 2021; 11:9460. [PMID: 33947882 PMCID: PMC8096822 DOI: 10.1038/s41598-021-88866-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
Abstract
Recent advances in basic research have unveiled several strategies for improving the sensitivity and specificity of cell-free DNA (cfDNA) based assays, which is a prerequisite for broadening its clinical use. Included among these strategies is leveraging knowledge of both the biogenesis and physico-chemical properties of cfDNA towards the identification of better disease-defining features and optimization of methods. While good progress has been made on this front, much of cfDNA biology remains uncharted. Here, we correlated serial measurements of cfDNA size, concentration and nucleosome histone modifications with various cellular parameters, including cell growth rate, viability, apoptosis, necrosis, and cell cycle phase in three different cell lines. Collectively, the picture emerged that temporal changes in cfDNA levels are rather irregular and not the result of constitutive release from live cells. Instead, changes in cfDNA levels correlated with intermittent cell death events, wherein apoptosis contributed more to cfDNA release in non-cancer cells and necrosis more in cancer cells. Interestingly, the presence of a ~ 3 kbp cfDNA population, which is often deemed to originate from accidental cell lysis or active release, was found to originate from necrosis. High-resolution analysis of this cfDNA population revealed an underlying DNA laddering pattern consisting of several oligo-nucleosomes, identical to those generated by apoptosis. This suggests that necrosis may contribute significantly to the pool of mono-nucleosomal cfDNA fragments that are generally interrogated for cancer mutational profiling. Furthermore, since active steps are often taken to exclude longer oligo-nucleosomes from clinical biospecimens and subsequent assays this raises the question of whether important pathological information is lost.
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Affiliation(s)
- Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany
| | - Abel J Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany
| | | | - Marielle Herzog
- Belgian Volition SRL, 22 Rue Phocas Lejeune, Parc Scientifique Crealys, 5032, Isnes, Belgium
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany.
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32
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Neuberger EWI, Hillen B, Mayr K, Simon P, Krämer-Albers EM, Brahmer A. Kinetics and Topology of DNA Associated with Circulating Extracellular Vesicles Released during Exercise. Genes (Basel) 2021; 12:522. [PMID: 33918465 PMCID: PMC8065814 DOI: 10.3390/genes12040522] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 12/22/2022] Open
Abstract
Although it is widely accepted that cancer-derived extracellular vesicles (EVs) carry DNA cargo, the association of cell-free circulating DNA (cfDNA) and EVs in plasma of healthy humans remains elusive. Using a physiological exercise model, where EVs and cfDNA are synchronously released, we aimed to characterize the kinetics and localization of DNA associated with EVs. EVs were separated from human plasma using size exclusion chromatography or immuno-affinity capture for CD9+, CD63+, and CD81+ EVs. DNA was quantified with an ultra-sensitive qPCR assay targeting repetitive LINE elements, with or without DNase digestion. This model shows that a minute part of circulating cell-free DNA is associated with EVs. During rest and following exercise, only 0.12% of the total cfDNA occurs in association with CD9+/CD63+/CD81+EVs. DNase digestion experiments indicate that the largest part of EV associated DNA is sensitive to DNase digestion and only ~20% are protected within the lumen of the separated EVs. A single bout of running or cycling exercise increases the levels of EVs, cfDNA, and EV-associated DNA. While EV surface DNA is increasing, DNAse-resistant DNA remains at resting levels, indicating that EVs released during exercise (ExerVs) do not contain DNA. Consequently, DNA is largely associated with the outer surface of circulating EVs. ExerVs recruit cfDNA to their corona, but do not carry DNA in their lumen.
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Affiliation(s)
- Elmo W. I. Neuberger
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (B.H.); (P.S.)
| | - Barlo Hillen
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (B.H.); (P.S.)
| | - Katharina Mayr
- Institute of Developmental Biology and Neurobiology, Extracellular Vesicles Research Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (K.M.); (E.-M.K.-A.)
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (B.H.); (P.S.)
| | - Eva-Maria Krämer-Albers
- Institute of Developmental Biology and Neurobiology, Extracellular Vesicles Research Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (K.M.); (E.-M.K.-A.)
| | - Alexandra Brahmer
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (B.H.); (P.S.)
- Institute of Developmental Biology and Neurobiology, Extracellular Vesicles Research Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany; (K.M.); (E.-M.K.-A.)
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Walczak K, Stawski R, Perdas E, Brzezinska O, Kosielski P, Galczynski S, Budlewski T, Padula G, Nowak D. Circulating cell free DNA response to exhaustive exercise in average trained men with type I diabetes mellitus. Sci Rep 2021; 11:4639. [PMID: 33633280 PMCID: PMC7907132 DOI: 10.1038/s41598-021-84201-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 02/09/2021] [Indexed: 12/20/2022] Open
Abstract
It is believed that neutrophils extracellular traps (NETs) formation is responsible for the increase in cf DNA after exercise. Since T1DM is accompanied by enhanced NETs generation, we compared exercise-induced increase in cf DNA in 14 men with T1DM and 11 healthy controls and analyzed its association with exercise load. Subjects performed a treadmill run to exhaustion at speed corresponding to 70% of their personal VO2max. Blood was collected before and just after exercise for determination of plasma cf nuclear and mitochondrial DNA (cf n-DNA, cf mt-DNA) by real-time PCR, blood cell count and metabolic markers. Exercise resulted in the increase in median cf n-DNA from 3.9 ng/mL to 21.0 ng/mL in T1DM group and from 3.3 ng/mL to 28.9 ng/mL in controls. Median exercise-induced increment (∆) in cf n-DNA did not differ significantly in both groups (17.8 ng/mL vs. 22.1 ng/mL, p = 0.23), but this variable correlated with run distance (r = 0.66), Δ neutrophils (r = 0.86), Δ creatinine (r = 0.65) and Δ creatine kinase (r = 0.77) only in controls. Pre- and post-exercise cf mt-DNA were not significantly different within and between groups. These suggest low usefulness of Δ cf n-DNA as a marker of exercise intensity in T1DM men.
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Affiliation(s)
- Konrad Walczak
- Department of Internal Medicine and Nephrodiabetology, Medical University of Lodz, Lodz, Poland
| | - Robert Stawski
- Department of Clinical Physiology, Medical University of Lodz, Lodz, Poland
| | - Ewelina Perdas
- Department of Clinical Physiology, Medical University of Lodz, Lodz, Poland
| | - Olga Brzezinska
- Department of Rheumatology, Medical University of Lodz, Lodz, Poland
| | - Piotr Kosielski
- Academic Laboratory of Movement and Human Physical Performance, Medical University of Lodz, Lodz, Poland
| | - Szymon Galczynski
- Academic Laboratory of Movement and Human Physical Performance, Medical University of Lodz, Lodz, Poland
| | - Tomasz Budlewski
- Department of Rheumatology, Medical University of Lodz, Lodz, Poland
| | - Gianluca Padula
- Academic Laboratory of Movement and Human Physical Performance, Medical University of Lodz, Lodz, Poland
| | - Dariusz Nowak
- Department of Clinical Physiology, Medical University of Lodz, Lodz, Poland.
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Luo H, Wei W, Ye Z, Zheng J, Xu RH. Liquid Biopsy of Methylation Biomarkers in Cell-Free DNA. Trends Mol Med 2021; 27:482-500. [PMID: 33500194 DOI: 10.1016/j.molmed.2020.12.011] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 02/09/2023]
Abstract
Liquid biopsies, in particular, analysis of cell-free DNA (cfDNA), have emerged as a promising noninvasive diagnostic approach in oncology. Abnormal distribution of DNA methylation is one of the hallmarks of many cancers and methylation changes occur early during carcinogenesis. Systemic analysis of cfDNA methylation profiles is being developed for cancer early detection, monitoring for minimal residual disease (MRD), predicting treatment response and prognosis, and tracing the tissue origin. This review highlights the advantages and disadvantages of ctDNA profiling for noninvasive diagnosis of early-stage cancers and explores recent advances in the clinical application of ctDNA methylation assays. We also summarize the technologies for ctDNA methylation analysis and provide a brief overview of the bioinformatic approaches for analyzing DNA methylation sequencing data.
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Affiliation(s)
- Huiyan Luo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Wei Wei
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Ziyi Ye
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jiabo Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Rui-Hua Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.
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35
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Changes in plasma hydroxyproline and plasma cell-free DNA concentrations after higher- versus lower-intensity eccentric cycling. Eur J Appl Physiol 2021; 121:1087-1097. [PMID: 33439308 DOI: 10.1007/s00421-020-04593-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/18/2020] [Indexed: 12/29/2022]
Abstract
PURPOSE We examined changes in plasma creatine kinase (CK) activity, hydroxyproline and cell-free DNA (cfDNA) concentrations in relation to changes in maximum voluntary isometric contraction (MVIC) torque and delayed-onset muscle soreness (DOMS) following a session of volume-matched higher- (HI) versus lower-intensity (LI) eccentric cycling exercise. METHODS Healthy young men performed either 5 × 1-min HI at 20% of peak power output (n = 11) or 5 × 4-min LI eccentric cycling at 5% of peak power output (n = 9). Changes in knee extensor MVIC torque, DOMS, plasma CK activity, and hydroxyproline and cfDNA concentrations before, immediately after, and 24-72 h post-exercise were compared between groups. RESULTS Plasma CK activity increased post-exercise (141 ± 73.5%) and MVIC torque decreased from immediately (13.3 ± 7.8%) to 48 h (6.7 ± 13.5%) post-exercise (P < 0.05), without significant differences between groups. DOMS was greater after HI (peak: 4.5 ± 3.0 on a 10-point scale) than LI (1.2 ± 1.0). Hydroxyproline concentration increased 40-53% at 24-72 h after both LI and HI (P < 0.05). cfDNA concentration increased immediately after HI only (2.3 ± 0.9-fold, P < 0.001), with a significant difference between groups (P = 0.002). Lack of detectable methylated HOXD4 indicated that the cfDNA was not derived from skeletal muscle. No significant correlations were evident between the magnitude of change in the measures, but the cfDNA increase immediately post-exercise was correlated with the maximal change in heart rate during exercise (r = 0.513, P = 0.025). CONCLUSION Changes in plasma hydroxyproline and cfDNA concentrations were not associated with muscle fiber damage, but the increased hydroxyproline in both groups suggests increased collagen turnover. cfDNA may be a useful metabolic-intensity exercise marker.
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Hagstrom AD, Yuwono N, Warton K, Ford CE. Sex Bias in Cohorts Included in Sports Medicine Research. Sports Med 2021; 51:1799-1804. [PMID: 33400219 DOI: 10.1007/s40279-020-01405-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2020] [Indexed: 10/22/2022]
Affiliation(s)
- Amanda D Hagstrom
- Department of Exercise Physiology, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Nicole Yuwono
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, A/Prof Caroline Ford, Sydney, NSW, 2052, Australia
| | - Kristina Warton
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, A/Prof Caroline Ford, Sydney, NSW, 2052, Australia
| | - Caroline E Ford
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, A/Prof Caroline Ford, Sydney, NSW, 2052, Australia.
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Barefoot ME, Lindberg MR, Wellstein A. Decoding the Tissue of Origin of Cellular Damage from Cell-Free DNA in Liquid Biopsies. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11669-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Jaworski JJ, Morgan RD, Sivakumar S. Circulating Cell-Free Tumour DNA for Early Detection of Pancreatic Cancer. Cancers (Basel) 2020; 12:E3704. [PMID: 33317202 PMCID: PMC7763954 DOI: 10.3390/cancers12123704] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/04/2020] [Indexed: 01/11/2023] Open
Abstract
Pancreatic cancer is a lethal disease, with mortality rates negatively associated with the stage at which the disease is detected. Early detection is therefore critical to improving survival outcomes. A recent focus of research for early detection is the use of circulating cell-free tumour DNA (ctDNA). The detection of ctDNA offers potential as a relatively non-invasive method of diagnosing pancreatic cancer by using genetic sequencing technology to detect tumour-specific mutational signatures in blood samples before symptoms manifest. These technologies are limited by a number of factors that lower sensitivity and specificity, including low levels of detectable ctDNA in early stage disease and contamination with non-cancer circulating cell-free DNA. However, genetic and epigenetic analysis of ctDNA in combination with other standard diagnostic tests may improve early detection rates. In this review, we evaluate the genetic and epigenetic methods under investigation in diagnosing pancreatic cancer and provide a perspective for future developments.
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Affiliation(s)
- Jedrzej J. Jaworski
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK;
| | - Robert D. Morgan
- Department of Medical Oncology, Christie NHS Foundation Trust, Manchester M20 4BX, UK;
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Shivan Sivakumar
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
- Department of Medical Oncology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
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Exploration of cell-free DNA (cfDNA) recovery for touch deposits. Forensic Sci Int Genet 2020; 51:102431. [PMID: 33260058 DOI: 10.1016/j.fsigen.2020.102431] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 11/12/2020] [Accepted: 11/15/2020] [Indexed: 12/15/2022]
Abstract
Although touch deposit DNA is widely used in forensic casework, its cellular and acellular contents and their biological origins are poorly understood. There is evidence that the cell-free component of DNA deposited by handling may contribute substantial genetic information; however, most research into touch DNA recovery does not separate cellular and cell-free fractions or seek to characterize their contents. This work is an important early step in developing methods to isolate the cfDNA from biological material deposited by handling. Size-filtration as a separation technique was determined to be prone to DNA loss, even on optimized control samples of pure ladder DNA. Centrifugal separation was optimized to determine minimum speed and time required to reliably remove all cellular debris from the material collected by rinsing donor hands. To determine if the centrifugal force risked rupturing shed corneocyte cells and releasing cellular DNA into the supernatant, DNA levels were measured, and cells were visualized microscopically before and after centrifugation of hand rinses. Heated buccal cells were used as a positive control to demonstrate cell rupture would be detected with these methods. Following the determination of a suitable separation technique, an investigation into purification methods for cfDNA was conducted. DNA recovery using three kits for plasma cfDNA, one for PCR clean-up and one for genomic DNA were assessed on both ladder DNA to simulate cfDNA fragments and on collected hand deposit supernatants from both unwashed and washed hands. Purification methods designed for recovery of short DNA fragments from plasma yielded the highest recovery percentage across sample types, with BioChain cfPure performing the best. Donors' hands were shown to shed high levels of cfDNA, which were better recovered with a method for short fragments than with a traditional genomic technique often used on touch DNA samples.
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40
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Wei M, Ye M, Dong K, Dong R. Circulating tumor DNA in neuroblastoma. Pediatr Blood Cancer 2020; 67:e28311. [PMID: 32729220 DOI: 10.1002/pbc.28311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/10/2020] [Accepted: 03/19/2020] [Indexed: 12/20/2022]
Abstract
As a sympathetic nervous system-derived tumor, aggressive neuroblastoma (NB) is currently attracting interest from researchers seeking diagnostic and prognostic markers via less invasive procedures. The analysis of circulating tumor DNA (ctDNA) in peripheral blood can provide genetic information from multiple tumor lesions and is not dependent on a surgical procedure. The identification of genetic alterations, chromosomal variations, and hypermethylation contained within plasma DNA yields clinical value in the diagnosis, risk stratification, monitoring of treatment effects, and survival prediction for patients. With the widespread application of genome sequencing, droplet digital polymerase chain reaction, and other advanced technologies, the detection of ctDNA may guide therapeutic schedules, enhance the quality of life, and improve the prognosis for patients with NB.
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Affiliation(s)
- Meng Wei
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China
| | - Mujie Ye
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China
| | - Kuiran Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China
| | - Rui Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China
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Circulating Tumor DNA as a Novel Biomarker Optimizing Chemotherapy for Colorectal Cancer. Cancers (Basel) 2020; 12:cancers12061566. [PMID: 32545750 PMCID: PMC7352651 DOI: 10.3390/cancers12061566] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/22/2022] Open
Abstract
Liquid biopsy is a minimally invasive method for detecting soluble factors, including circulating tumor DNA (ctDNA), in body fluids. ctDNA carrying tumor-specific genetic or epigenetic alterations is released into circulation from tumor cells. ctDNA in the plasma contains somatic mutations that have occurred in the tumor, and reflects tumor progression and therapeutic effects promptly and accurately. Furthermore, ctDNA is useful for early detection of recurrence and estimation of prognosis and may be utilized for diagnosis and personalized medicine for treatment selection. Thus, in the near future, it will be possible to select the most appropriate treatment based on real-time genetic information using ctDNA.
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Delmonico L, Alves G, Bines J. Cell free DNA biology and its involvement in breast carcinogenesis. Adv Clin Chem 2020; 97:171-223. [PMID: 32448434 DOI: 10.1016/bs.acc.2019.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Liquid biopsy represents a procedure for minimally invasive analysis of non-solid tissue, blood and other body fluids. It comprises a set of analytes that includes circulating tumor cells (CTCs) and circulating free DNA (cfDNA), RNA, long noncoding RNA (lncRNA) and micro RNA (miRNA), as well as extracellular vesicles. These novel analytes represent an alternative tool to complement diagnosis and monitor and predict response to treatment of the tumoral process and may be used for other disease processes such viral and parasitic infection. This review focuses on the biologic and molecular characteristics of cfDNA in general and the molecular changes (mutational and epigenetic) proven useful in oncologic practice for diagnosis, monitoring and treatment of breast cancer specifically.
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Affiliation(s)
- Lucas Delmonico
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Gilda Alves
- Laboratório de Marcadores Circulantes, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - José Bines
- Instituto Nacional de Câncer (INCA-HCIII), Rio de Janeiro, Brazil
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Ungerer V, Bronkhorst AJ, Holdenrieder S. Preanalytical variables that affect the outcome of cell-free DNA measurements. Crit Rev Clin Lab Sci 2020; 57:484-507. [DOI: 10.1080/10408363.2020.1750558] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Abel J. Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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Wan Z, Peng X, Ma L, Tian Q, Wu S, Li J, Ling J, Lv W, Ding B, Tan J, Zhang Z. Targeted Sequencing of Genomic Repeat Regions Detects Circulating Cell-free Echinococcus DNA. PLoS Negl Trop Dis 2020; 14:e0008147. [PMID: 32155159 PMCID: PMC7083330 DOI: 10.1371/journal.pntd.0008147] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 03/20/2020] [Accepted: 02/18/2020] [Indexed: 11/20/2022] Open
Abstract
Background Echinococcosis is a chronic zoonosis caused by tapeworms of the genus Echinococcus. Treatment of the disease is often expensive and complicated, sometimes requiring extensive surgery. Ultrasonographic imaging is currently the main technique for diagnosis, while immunological analysis provides additional information. Confirmation still needs pathological analysis. However, these diagnostic techniques generally detect infection in late stages of the disease. An accurate, early and non-invasive molecular diagnostic method is still unavailable. Methodology/Principal findings We sequenced the cell-free DNA (cfDNA) from plasma of echinococcosis patients and confirmed the presence of Echinococcus DNA. To improve detection sensitivity, we developed a method based on targeted next-generation sequencing of repeat regions. Simulation experiments demonstrate that the targeted sequencing is sensitive enough to detect as little as 0.1% of an Echinococcus genome in 1 mL of plasma. Results obtained using patient plasma shows that the Area Under the Curve (AUC) of the method is 0.862, with a detection sensitivity of 62.50% and specificity of 100%, corresponding to a Youden-index of 0.625. Conclusions/Significance This study provides evidence that hydatid cysts release cfDNA fragments into patient plasma. Using the repeat region targeted sequencing method, highly specific detection of Echinococcus infection was achieved. This study paves a new avenue for potential non-invasive screening and diagnosis of echinococcosis. Echinococcosis is a severe chronic parasitic disease caused by tapeworms of the genus Echinococcus. According to the World Health Organization, there are more than 1 million people living with echinococcosis worldwide. For decades, little progress has been made to develop a molecular diagnosis and specific treatment for the disease. Although imaging and immunological detection are used for diagnosis, these technologies are either only effective for late stages of the disease or hardly conclusive. The detection of cell-free DNA has been a powerful tool for precise diagnosis. In this study, we showed the presence of Echinococcus-derived cell-free DNA in plasma of echinococcosis patients. We further established an assay to detect parasite DNA in blood samples based on amplification of Echinococcus specific repeat regions followed by targeted next-generation sequencing. This technique provides a new method for potential extensive screening and precision diagnosis of echinococcosis with high specificity.
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Affiliation(s)
- Zhengqing Wan
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Xiaoqing Peng
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Lu Ma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Qingshan Tian
- Center for Prevention and Treatment of Echinococcosis, Qinghai Provincial People's Hospital, Xining, Qinghai, China
| | - Shizheng Wu
- Department of Neurology, Qinghai Provincial People's Hospital, Xining, Qinghai, China
| | - Junqi Li
- Sunrain Biotechnology Corporation, Changsha, Hunan, China
| | - Jie Ling
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
| | - Weigang Lv
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Binrong Ding
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Jieqiong Tan
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Zhuohua Zhang
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
- Department of Neurosciences, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- * E-mail:
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Perspectives of the Application of Liquid Biopsy in Colorectal Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6843180. [PMID: 32258135 PMCID: PMC7085834 DOI: 10.1155/2020/6843180] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is one of the most common gastrointestinal tumors and the second leading cause of cancer death worldwide. Since traditional biopsies are invasive and do not reflect tumor heterogeneity or monitor the dynamic progression of tumors, there is an urgent need for new noninvasive methods that can supplement and improve the current management strategies of CRC. Blood-based liquid biopsies are a promising noninvasive biomarker that can detect disease early, assist in staging, monitor treatment responses, and predict relapse and metastasis. Over time, an increasing number of experiments have indicated the clinical utility of liquid biopsies in CRC. In this review, we mainly focus on the development of circulating tumor cells and circulating tumor DNA as key components of liquid biopsies in CRC and introduce the potential of exosomal microRNAs as emerging liquid biopsy markers in clinical application for CRC.
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Bronkhorst AJ, Ungerer V, Holdenrieder S. Early detection of cancer using circulating tumor DNA: biological, physiological and analytical considerations. Crit Rev Clin Lab Sci 2019:1-17. [PMID: 31865831 DOI: 10.1080/10408363.2019.1700902] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Early diagnosis of cancer improves the efficacy of curative therapies. However, due to the difficulties involved in distinguishing between small early-stage tumors and normal biological variation, early detection of cancer is an extremely challenging task and there are currently no clinically validated biomarkers for a pan-cancer screening test. It is thus of particular significance that increasing evidence indicates the potential of circulating tumor DNA (ctDNA) molecules, which are fragmented segments of DNA shed from tumor cells into adjacent body fluids and the circulatory system, to serve as molecular markers for early cancer detection and thereby allow early intervention and improvement of therapeutic and survival outcomes. This is possible because ctDNA molecules bear cancer-specific fragmentation patterns, nucleosome depletion motifs, and genetic and epigenetic alterations, as distinct from plasma DNA originating from non-cancerous tissues/cells. Compared to traditional biomarkers, ctDNA analysis therefore presents the distinctive advantage of detecting tumor-specific alterations. However, based on a thorough survey of the literature, theoretical and empirical evidence suggests that current ctDNA analysis strategies, which are mainly based on DNA mutation detection, do not demonstrate the necessary diagnostic sensitivity and specificity that is required for broad clinical implementation in a screening context. Therefore, in this review we explain the biological, physiological, and analytical challenges toward the development of clinically meaningful ctDNA tests. In addition, we explore some approaches that can be implemented in order to increase the sensitivity and specificity of ctDNA assays.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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Stawski R, Walczak K, Perdas E, Wlodarczyk A, Sarniak A, Kosielski P, Meissner P, Budlewski T, Padula G, Nowak D. Decreased integrity of exercise-induced plasma cell free nuclear DNA - negative association with the increased oxidants production by circulating phagocytes. Sci Rep 2019; 9:15970. [PMID: 31685910 PMCID: PMC6828751 DOI: 10.1038/s41598-019-52409-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/12/2019] [Indexed: 12/21/2022] Open
Abstract
Strenuous exercise increases circulating cell free DNA (cfDNA) and stimulates blood phagocytes to generate reactive oxygen species (ROS) which may induce DNA strand breaks. We tested whether: (A) elevated cfDNA in response to three repeated bouts of exhaustive exercise has decreased integrity; (B) each bout of exercise increases luminol enhanced whole blood chemiluminescence (LBCL) as a measure of ROS production by polymorphonuclear leukocytes. Eleven men performed three treadmill exercise tests to exhaustion separated by 72 hours of resting. Pre- and post-exercise concentrations and integrity of cf nuclear and mitochondrial DNA (cf n-DNA, cf mt-DNA) and resting (r) and fMLP (n-formyl-methionyl-leucyl-phenylalanine)-stimulated LBCL were determined. Each bout increased concentrations of cf n-DNA by more than 10-times which was accompanied by about 2-times elevated post-exercise rLBCL and fMLP-LBCL. Post-exercise cf n-DNA integrity (integrity index, I229/97) decreased after the first (0.59 ± 0.19 vs. 0.48 ± 0.18) and second (0.53 ± 0.14 vs. 0.44 ± 0.17) bout of exercise. There were negative correlations between I229/97 and rLBCL (ƍ = –0.37), and I229/97 and fMLP-LBCL (ƍ = –0.40) – analysis of pooled pre- and post-exercise data (n = 66). cf mt- DNA integrity (I218/78) did not alter in response to exercise. This suggests an involvement of phagocyte ROS in cf n-DNA strand breaks in response to exhaustive exercise.
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Affiliation(s)
- Robert Stawski
- Department of Clinical Physiology, Medical University of Lodz, Lodz, Poland
| | - Konrad Walczak
- Department of Internal Medicine and Nephrodiabetology, Medical University of Lodz, Lodz, Poland
| | - Ewelina Perdas
- Department of Cardiovascular Physiology, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Anna Wlodarczyk
- Department of Sleep Medicine and Metabolic Disorders, Medical University of Lodz, Lodz, Poland
| | - Agata Sarniak
- Department of General Physiology, Medical University of Lodz, Lodz, Poland
| | - Piotr Kosielski
- Academic Laboratory of Movement and Human Physical Performance, Medical University of Lodz, Lodz, Poland
| | - Pawel Meissner
- Academic Laboratory of Movement and Human Physical Performance, Medical University of Lodz, Lodz, Poland
| | - Tomasz Budlewski
- Department of Rheumatology, Medical University of Lodz, University Hospital name of the Military Medical Academy-Central Hospital Veterans of Lodz Ul. Pieniny 30, 92-115, Łódź, Poland
| | - Gianluca Padula
- Academic Laboratory of Movement and Human Physical Performance, Medical University of Lodz, Lodz, Poland
| | - Dariusz Nowak
- Department of Clinical Physiology, Medical University of Lodz, Lodz, Poland.
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van der Pol Y, Mouliere F. Toward the Early Detection of Cancer by Decoding the Epigenetic and Environmental Fingerprints of Cell-Free DNA. Cancer Cell 2019; 36:350-368. [PMID: 31614115 DOI: 10.1016/j.ccell.2019.09.003] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/18/2019] [Accepted: 09/06/2019] [Indexed: 12/15/2022]
Abstract
Widespread adaptation of liquid biopsy for the early detection of cancer has yet to reach clinical utility. Circulating tumor DNA is commonly detected though the presence of genetic alterations, but only a minor fraction of tumor-derived cell-free DNA (cfDNA) fragments exhibit mutations. The cellular processes occurring in cancer development mark the chromatin. These epigenetic marks are reflected by modifications in the cfDNA methylation, fragment size, and structure. In this review, we describe how going beyond DNA sequence information alone, by analyzing cfDNA epigenetic and immune signatures, boosts the potential of liquid biopsy for the early detection of cancer.
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Affiliation(s)
- Ymke van der Pol
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
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Wang HC, Lin YT, Hsu SY, Tsai NW, Lai YR, Su BYJ, Kung CT, Lu CH. Serial plasma DNA levels as predictors of outcome in patients with acute traumatic cervical spinal cord injury. J Transl Med 2019; 17:329. [PMID: 31570098 PMCID: PMC6771086 DOI: 10.1186/s12967-019-2084-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 09/23/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Acute traumatic cervical spinal cord injury (SCI) is a leading cause of disability in adolescents and young adults worldwide. Evidence from previous studies suggests that circulating cell-free DNA is associated with severity following acute injury. The present study determined whether plasma DNA levels in acute cervical SCI are predictive of outcome. METHODS In present study, serial plasma nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) levels were obtained from 44 patients with acute traumatic cervical SCI at five time points from day 1 to day 180 post-injury. Control blood samples were obtained from 66 volunteers. RESULTS Data showed a significant increase in plasma nDNA and mtDNA concentrations at admission in SCI patients compared to the control group. Plasma nDNA levels at admission, but not plasma mtDNA levels, were significantly associated with the Japanese Orthopaedic Association (JOA) score and Injury Severity Score in patients with acute traumatic cervical SCI. In patients with non-excellent outcomes, plasma nDNA increased significantly at days 1, 14 and 30 post-injury. Furthermore, its level at day 14 was independently associated with outcome. Higher plasma nDNA levels at the chosen cutoff point (> 45.6 ng/ml) predicted poorer outcome with a sensitivity of 78.9% and a specificity of 78.4%. CONCLUSIONS These results indicate JOA score performance and plasma nDNA levels reflect the severity of spinal cord injury. Therefore, the plasma nDNA assays can be considered as potential neuropathological markers in patients with acute traumatic cervical SCI.
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Affiliation(s)
- Hung-Chen Wang
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yu-Tsai Lin
- Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Shih-Yuan Hsu
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Nai-Wen Tsai
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta Pei Road, Niao Sung Dist., Kaohsiung, Taiwan
| | - Yun-Ru Lai
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta Pei Road, Niao Sung Dist., Kaohsiung, Taiwan
| | - Ben Yu-Jih Su
- Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chia-Te Kung
- Department of Emergency Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Cheng-Hsien Lu
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta Pei Road, Niao Sung Dist., Kaohsiung, Taiwan. .,Department of Biological Science, National Sun Yat-Sen University, Kaohsiung, Taiwan. .,Department of Neurology, Xiamen Chang Gung Memorial Hospital, Xiamen, Fujian, China.
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Alborelli I, Generali D, Jermann P, Cappelletti MR, Ferrero G, Scaggiante B, Bortul M, Zanconati F, Nicolet S, Haegele J, Bubendorf L, Aceto N, Scaltriti M, Mucci G, Quagliata L, Novelli G. Cell-free DNA analysis in healthy individuals by next-generation sequencing: a proof of concept and technical validation study. Cell Death Dis 2019; 10:534. [PMID: 31296838 PMCID: PMC6624284 DOI: 10.1038/s41419-019-1770-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 02/08/2023]
Abstract
Pre-symptomatic screening of genetic alterations might help identify subpopulations of individuals that could enter into early access prevention programs. Since liquid biopsy is minimally invasive it can be used for longitudinal studies in healthy volunteers to monitor events of progression from normal tissue to pre-cancerous and cancerous condition. Yet, cell-free DNA (cfDNA) analysis in healthy individuals comes with substantial challenges such as the lack of large cohort studies addressing the impact of mutations in healthy individuals or the low abundance of cfDNA in plasma. In this study, we aimed to investigate the technical feasibility of cfDNA analysis in a collection of 114 clinically healthy individuals. We first addressed the impact of pre-analytical factors such as cfDNA yield and quality on sequencing performance and compared healthy to cancer donor samples. We then confirmed the validity of our testing strategy by evaluating the mutational status concordance in matched tissue and plasma specimens collected from cancer patients. Finally, we screened our group of healthy donors for genetic alterations, comparing individuals who did not develop any tumor to patients who developed either a benign neoplasm or cancer during 1-10 years of follow-up time. To conclude, we have established a rapid and reliable liquid biopsy workflow that allowed us to study genomic alterations with a limit of detection as low as 0.08% of variant allelic frequency in healthy individuals. We detected pathogenic cancer mutations in four healthy donors that later developed a benign neoplasm or invasive breast cancer up to 10 years after blood collection. Even though larger prospective studies are needed to address the specificity and sensitivity of liquid biopsy as a clinical tool for early cancer detection, systematic screening of healthy individuals will help understanding early events of tumor formation.
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Affiliation(s)
- Ilaria Alborelli
- Institute of Pathology, University Hospital Basel, 4031, Basel, Switzerland.
| | - Daniele Generali
- Breast Cancer Unit and Translational Research Unit, ASST Cremona, Viale Concordia 1, 26100, Cremona, Italy
- Department of Medical Surgery and Health Sciences, University of Trieste, 34129, Trieste, Italy
| | - Philip Jermann
- Institute of Pathology, University Hospital Basel, 4031, Basel, Switzerland
| | - Maria Rosa Cappelletti
- Breast Cancer Unit and Translational Research Unit, ASST Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Giuseppina Ferrero
- Breast Cancer Unit and Translational Research Unit, ASST Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Bruna Scaggiante
- Department of Life Sciences, University of Trieste, Via Giorgeri, 1, 34127, Trieste, Italy
| | - Marina Bortul
- Department of Medical Surgery and Health Sciences, University of Trieste, 34129, Trieste, Italy
| | - Fabrizio Zanconati
- Department of Medical Surgery and Health Sciences, University of Trieste, 34129, Trieste, Italy
| | - Stefan Nicolet
- Institute of Pathology, University Hospital Basel, 4031, Basel, Switzerland
| | - Jasmin Haegele
- Institute of Pathology, University Hospital Basel, 4031, Basel, Switzerland
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Lukas Bubendorf
- Institute of Pathology, University Hospital Basel, 4031, Basel, Switzerland
| | - Nicola Aceto
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel, 4058, Basel, Switzerland
| | - Maurizio Scaltriti
- Human Oncology & Pathogenesis Program (HOPP), Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, 10065, New York, NY, USA
| | - Giuseppe Mucci
- Bioscience Institute, Via Rovereta 42, Falciano, 47891, San Marino, Italy
| | - Luca Quagliata
- Institute of Pathology, University Hospital Basel, 4031, Basel, Switzerland
- Thermo Fisher Scientific, 6300, Zug, Switzerland
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
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