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Progress in quantitative technique of circulating cell free DNA and its role in cancer diagnosis and prognosis. Cancer Genet 2019; 239:75-84. [PMID: 31639530 DOI: 10.1016/j.cancergen.2019.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/24/2019] [Accepted: 10/09/2019] [Indexed: 01/21/2023]
Abstract
The interest in the potential application value of circulating cell free DNA (ccfDNA) has increased rapidly in recent years, as numerous researchers have demonstrated that the change of its level in the blood is associated with many diseases. Its potential role in cancer management is of particular concern. In comparison with traditional invasive tissue biopsy, quantitative analysis of ccfDNA level for the detection of cancer is advantageous due to the non-invasiveness of blood collection. Moreover, its clinical significance in prognosis prediction and dynamic monitoring of disease progression in cancer patients is equally worthy of attention. At the same time, quantitative detection of ccfDNA is being improved to pursue higher sensitivity due to its low concentration in the blood sample. In this review, we will summarize the progress in quantitative technology of ccfDNA and describe the possible relationship between ccfDNA level and cancer diagnosis and prognosis prediction.
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Khummuang S, Lee HG, Joo SS, Park JW, Choi JY, Oh JH, Kim KH, Youn HH, Kim M, Cho BW. Comparison for immunophysiological responses of Jeju and Thoroughbred horses after exercise. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:424-435. [PMID: 31480163 PMCID: PMC7054627 DOI: 10.5713/ajas.19.0260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/12/2019] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The study was conducted to investigate variations in the immunophysiological responses to exercise-induced stress in Jeju and Thoroughbred horses. METHODS Blood samples were collected from the jugular veins of adult Jeju (n = 5) and Thoroughbred (n = 5) horses before and after 30 min of exercise. The hematological, biochemical, and immunological profiles of the blood samples were analyzed. Blood smears were stained and observed under a microscope. The concentration of cell-free (cf) DNA in the plasma was determined using real time polymerase chain reaction (PCR). Peripheral blood mononuclear cells (PBMCs) and polymorphonuclear cells were separated using Polymorphprep, and the expression of various stress-related and chemokine receptor genes was measured using reverse transcriptase (RT) and real-time PCR. RESULTS After exercise, Jeju and Thoroughbred horses displayed stress responses with significantly increased rectal temperatures, cortisol levels, and muscle catabolism-associated metabolites. Red blood cell indices were significantly higher in Thoroughbred horses than in Jeju horses after exercise. In addition, exercise-induced stress triggered the formation of neutrophil extracellular traps (NETs) and reduced platelet counts in Jeju horses but not in Thoroughbred horses. Heat shock protein 72 and heat shock protein family A (Hsp70) member 6 expression is rapidly modulated in response to exercise-induced stress in the PBMCs of Jeju horses. The expression of CXC chemokine receptor 4 in PBMCs was higher in Thoroughbred horses than in Jeju horses after exercise. CONCLUSION In summary, the different immunophysiological responses of Jeju and Thoroughbred horses explain the differences in the physiological and anatomical properties of the two breeds. The physiology of Thoroughbred horses makes them suitable for racing as they are less sensitive to exercise-induced stress compared to that of Jeju horses. This study provides a basis for investigating the link between exercise-induced stresses and the physiological alteration of horses. Hence, our findings show that some of assessed parameters could be used to determine the endurance performance of horses.
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Affiliation(s)
- Saichit Khummuang
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Hyo Gun Lee
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Sang Seok Joo
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Jeong-Woong Park
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Jae-Young Choi
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Jin Hyeog Oh
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Kyoung Hwan Kim
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Hyun-Hee Youn
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Myunghoo Kim
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Byung-Wook Cho
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
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Bronkhorst AJ, Ungerer V, Holdenrieder S. Comparison of methods for the quantification of cell-free DNA isolated from cell culture supernatant. Tumour Biol 2019; 41:1010428319866369. [DOI: 10.1177/1010428319866369] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Gaining a better understanding of the biological properties of cell-free DNA constitutes an important step in the development of clinically meaningful cell-free DNA–based tests. Since the in vivo characterization of cell-free DNA is complicated by the immense heterogeneity of blood samples, an increasing number of in vitro cell culture experiments, which offer a greater level of control, are being conducted. However, cell culture studies are currently faced with three notable caveats. First, the concentration of cell-free DNA in vitro is relatively low. Second, the median amount and size of cell-free DNA in culture medium varies greatly between cell types. Third, the amount and size of cell-free DNA in the culture medium of a single cell line fluctuates over time. Although these are interesting findings, it can also be a great source of experimental confusion and emphasizes the importance of method optimization and standardization. Therefore, in this study, we compared five commonly used cell-free DNA quantification methods, including quantitative polymerase chain reaction, Qubit Double-Stranded DNA High Sensitivity assay, Quant-iT PicoGreen Assay, Bioanalyzer High Sensitivity DNA assay, and NanoDrop Onec. Analysis of the resulting data, along with an interpretation of theoretical values (i.e. the theoretical detection and quantification limits of the respective methods), enables the calculation of optimal conditions for several important preanalytical steps pertaining to each quantification method and different cell types, including the (1) time-point at which culture medium should be collected for cell-free DNA extraction, (2) amount of cell culture supernatant from which to isolate cell-free DNA, (3) volume of elution buffer, and (4) volume of cell-free DNA sample to use for quantification.
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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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Circulating, Cell-Free DNA for Monitoring Player Load in Professional Football. Int J Sports Physiol Perform 2019; 14:718-726. [PMID: 30427238 DOI: 10.1123/ijspp.2018-0756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Purpose: Player monitoring in elite sport settings is becoming increasingly important. Questionnaire-based methods and biomarkers such as circulating, cell-free DNA (cfDNA) are suggested for load monitoring. cfDNA concentrations were shown to increase depending on total distance covered in football and were associated with overtraining in weight lifters. Thus, the objective of this study was to examine whether cfDNA is feasible as a monitoring tool in elite football players. Methods: Capillary blood samples from 22 male elite football players were collected over 4 mo of a regular season. Sampling was conducted the day before, 1 day after, or several days after regular-season games and/or training. In addition, each player filled in a visual analogue scale (VAS) questionnaire including the items "general perceived exertion," "muscular fatigue," and "mental fatigue." Performance during training and games was tracked by the Catapult system and with the OPTA system, respectively. Results: cfDNA values were significantly elevated in players the day after regular-season games (1.4-fold; P = .0004) in line with the scores of the VAS. Both parameters showed significantly higher values during midweek-game weeks. cfDNA concentrations correlated with training data, and VAS was correlated with the tracking of the season games. However, cfDNA and VAS did not correlate with each other. Conclusions: cfDNA concentrations at rest and VAS scores are influenced by previous load in professional football players. Future studies will reveal whether cfDNA might serve as a practically applicable marker for player load in football players.
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Eskandari M, Manoochehrabadi S, Pashaiefar H, Zaimy MA, Ahmadvand M. Clinical significance of cell-free DNA as a prognostic biomarker in patients with diffuse large B-cell lymphoma. Blood Res 2019; 54:114-119. [PMID: 31309089 PMCID: PMC6614089 DOI: 10.5045/br.2019.54.2.114] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/03/2019] [Accepted: 01/07/2019] [Indexed: 12/22/2022] Open
Abstract
Background Cell-free DNA (cfDNA) has the potential to serve as a non-invasive prognostic biomarker in some types of neoplasia. The investigation of plasma concentration of cfDNA may reveal its use as a valuable biomarker for risk stratification of diffuse large B-cell lymphoma (DLBCL). The present prognostic value of plasma cfDNA has not been widely confirmed in DLBCL subjects. Here, we evaluated cfDNA plasma concentration and assessed its potential prognostic value as an early DLBCL diagnostic tool. Methods cfDNA concentrations in plasma samples from 40 patients with DLBCL during diagnosis and of 38 normal controls were determined with quantitative polymerase chain reaction (qPCR) for the multi-locus L1PA2 gene. Results Statistically significant elevation in plasma cfDNA concentrations was observed in patients with DLBCL as compared to that in normal controls (P<0.05). A cutoff point of 2.071 ng/mL provided 82.5% sensitivity and 62.8% specificity and allowed successful discrimination of patients with DLBCL from normal controls (area under the curve=0.777; P=0.00003). Furthermore, patients with DLBCL showing higher concentrations of cfDNA had shorter overall survival (median, 9 mo; P=0.022) than those with lower cfDNA levels. In addition, elevated cfDNA concentration was significantly associated with age, B-symptoms, International Prognostic Index (IPI) score, and different stages of disease (all P<0.05). Conclusion Quantification of cfDNA with qPCR at the time of diagnosis may allow identification of patients with high cfDNA concentration, which correlates with aggressive clinical outcomes and adverse prognosis.
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Affiliation(s)
- Mahsa Eskandari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Saba Manoochehrabadi
- Medical Genetics, Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Pashaiefar
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Cell Therapy and Hematopoietic Stem Cell Transplantation Research Center, Hematologic Malignancies Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Zaimy
- Department of Medical Genetics, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Mohammad Ahmadvand
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Cell Therapy and Hematopoietic Stem Cell Transplantation Research Center, Hematologic Malignancies Research Center, Tehran University of Medical Sciences, Tehran, Iran
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Brahmer A, Neuberger E, Esch-Heisser L, Haller N, Jorgensen MM, Baek R, Möbius W, Simon P, Krämer-Albers EM. Platelets, endothelial cells and leukocytes contribute to the exercise-triggered release of extracellular vesicles into the circulation. J Extracell Vesicles 2019; 8:1615820. [PMID: 31191831 PMCID: PMC6542154 DOI: 10.1080/20013078.2019.1615820] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/05/2019] [Accepted: 05/03/2019] [Indexed: 12/18/2022] Open
Abstract
Physical activity initiates a wide range of multi-systemic adaptations that promote mental and physical health. Recent work demonstrated that exercise triggers the release of extracellular vesicles (EVs) into the circulation, possibly contributing to exercise-associated adaptive systemic signalling. Circulating EVs comprise a heterogeneous collection of different EV-subclasses released from various cell types. So far, a comprehensive picture of the parental and target cell types, EV-subpopulation diversity and functional properties of EVs released during exercise (ExerVs) is lacking. Here, we performed a detailed EV-phenotyping analysis to explore the cellular origin and potential subtypes of ExerVs. Healthy male athletes were subjected to an incremental cycling test until exhaustion and blood was drawn before, during, and immediately after the test. Analysis of total blood plasma by EV Array suggested endothelial and leukocyte characteristics of ExerVs. We further purified ExerVs from plasma by size exclusion chromatography as well as CD9-, CD63- or CD81-immunobead isolation to examine ExerV-subclass dynamics. EV-marker analysis demonstrated increasing EV-levels during cycling exercise, with highest levels at peak exercise in all EV-subclasses analysed. Phenotyping of ExerVs using a multiplexed flow-cytometry platform revealed a pattern of cell surface markers associated with ExerVs and identified lymphocytes (CD4, CD8), monocytes (CD14), platelets (CD41, CD42, CD62P), endothelial cells (CD105, CD146) and antigen presenting cells (MHC-II) as ExerV-parental cells. We conclude that multiple cell types associated with the circulatory system contribute to a pool of heterogeneous ExerVs, which may be involved in exercise-related signalling mechanisms and tissue crosstalk.
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Affiliation(s)
- Alexandra Brahmer
- Institute of Developmental Biology and Neurobiology, Biology of Extracellular Vesicles, University of Mainz, Mainz, Germany
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Mainz, Germany
| | - Elmo Neuberger
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Mainz, Germany
| | - Leona Esch-Heisser
- Institute of Developmental Biology and Neurobiology, Biology of Extracellular Vesicles, University of Mainz, Mainz, Germany
| | - Nils Haller
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Mainz, Germany
| | - Malene Moeller Jorgensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
- Part of Extracellular Vesicle Research Center Denmark (EVsearch.dk), Aalborg, Denmark
| | - Rikke Baek
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
- Part of Extracellular Vesicle Research Center Denmark (EVsearch.dk), Aalborg, Denmark
| | - Wiebke Möbius
- Department of Neurogenetics, Electron Microscopy Core Unit, Max Planck Institute of Experimental Medicine, Göttingen, Germany
- Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Mainz, Germany
| | - Eva-Maria Krämer-Albers
- Institute of Developmental Biology and Neurobiology, Biology of Extracellular Vesicles, University of Mainz, Mainz, Germany
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Reduced deoxyribonuclease enzyme activity in response to high postinjury mitochondrial DNA concentration provides a therapeutic target for Systemic Inflammatory Response Syndrome. J Trauma Acute Care Surg 2019; 85:354-358. [PMID: 30080781 DOI: 10.1097/ta.0000000000001919] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Cell-free mitochondrial DNA (mtDNA) is proinflammatory and has been detected in high concentrations in trauma patients' plasma. Deoxyribonuclease (DNAse) is the free plasma enzyme responsible for the digestion of extracellular DNA. The relationship between mtDNA and DNAse after major trauma is unknown. We hypothesized that DNAse activity would be elevated after injury and trauma surgery and would be associated with high concentrations of extracellular DNA. METHODS Two-year prospective study was performed on 103 consecutive trauma patients (male, 81%; age, 38 years [interquartile range, 30-59 years]; injury severity score, 18 [interquartile range, 12-26 years]) who underwent standardized major orthopedic trauma surgical interventions. Blood was collected at five perioperative time points (preoperative, postoperative, 7 hours, 24 hours, and 3 days postoperatively). Healthy control subjects (n = 20) were also sampled. Cell-free mtDNA and nuclear DNA (nDNA) were measured using quantitative polymerase chain reaction. Deoxyribonuclease was also assayed in the same plasma samples. RESULTS Increased levels of mtDNA (from preoperative 163 ± 86 ng/mL to 3 days 282 ± 201 ng/mL, p < 0.0001) and nDNA (from preoperative 28 ± 20 ng/mL to 3 days 37 ± 27 ng/mL, p < 0.05) were present in trauma patients at all perioperative time points compared with healthy controls (mtDNA: 4 ± 2 ng/mL; nDNA: 10 ± 5 ng/mL). Deoxyribonuclease activity was lower in the trauma cohort (from preoperative 0.06 ± 0.04U/mL to 3 days 0.08 ± 0.04U/mL, p < 0.0001) compared with healthy controls (DNAse: 0.17 ± 0.03U/mL). There was no correlation between DNAse and perioperative DNA concentrations. Elevated mtDNA (but not nDNA) correlated with the development of systemic inflammatory response syndrome (SIRS) (p = 0.026) but not multiple organ failure. CONCLUSIONS The significant perioperative elevation in plasma-free mtDNA concentration is associated with the development of SIRS. The fact that increased cell-free DNA concentrations present with significantly lower than healthy control DNAse activity suggests a potential therapeutic opportunity with DNAse administration to modulate postinjury severe SIRS. LEVEL OF EVIDENCE Prognostic/Epidemiological, level II.
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Kustanovich A, Schwartz R, Peretz T, Grinshpun A. Life and death of circulating cell-free DNA. Cancer Biol Ther 2019; 20:1057-1067. [PMID: 30990132 PMCID: PMC6606043 DOI: 10.1080/15384047.2019.1598759] [Citation(s) in RCA: 305] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/24/2019] [Accepted: 03/12/2019] [Indexed: 12/18/2022] Open
Abstract
Tumor-specific, circulating cell-free DNA in liquid biopsies is a promising source of biomarkers for minimally invasive serial monitoring of treatment responses in cancer management. We will review the current understanding of the origin of circulating cell-free DNA and different forms of DNA release (including various types of cell death and active secretion processes) and clearance routes. The dynamics of extracellular DNA in blood during therapy and the role of circulating DNA in pathophysiological processes (tumor-associated inflammation, NETosis, and pre-metastatic niche development) provide insights into the mechanisms that contribute to tumor development and metastases formation. Better knowledge of circulating tumor-specific cell-free DNA could facilitate the development of new therapeutic and diagnostic options for cancer management.
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Affiliation(s)
- Anatoli Kustanovich
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ruth Schwartz
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tamar Peretz
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Albert Grinshpun
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Johansson G, Andersson D, Filges S, Li J, Muth A, Godfrey TE, Ståhlberg A. Considerations and quality controls when analyzing cell-free tumor DNA. BIOMOLECULAR DETECTION AND QUANTIFICATION 2019; 17:100078. [PMID: 30906693 PMCID: PMC6416156 DOI: 10.1016/j.bdq.2018.12.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/05/2018] [Accepted: 12/19/2018] [Indexed: 12/18/2022]
Abstract
Circulating cell-free tumor DNA (ctDNA) is a promising biomarker in cancer. Ultrasensitive technologies enable detection of low (< 0.1%) mutant allele frequencies, a pre-requisite to fully utilize the potential of ctDNA in cancer diagnostics. In addition, the entire liquid biopsy workflow needs to be carefully optimized to enable reliable ctDNA analysis. Here, we discuss important considerations for ctDNA detection in plasma. We show how each experimental step can easily be evaluated using simple quantitative PCR assays, including detection of cellular DNA contamination and PCR inhibition. Furthermore, ctDNA assay performance is also demonstrated to be affected by both DNA fragmentation and target sequence. Finally, we show that quantitative PCR is useful to estimate the required sequencing depth and to monitor DNA losses throughout the workflow. The use of quality control assays enables the development of robust and standardized workflows that facilitate the implementation of ctDNA analysis into clinical routine.
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Affiliation(s)
- Gustav Johansson
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 1F, 413 90, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
- Respiratory Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Daniel Andersson
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 1F, 413 90, Gothenburg, Sweden
| | - Stefan Filges
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 1F, 413 90, Gothenburg, Sweden
| | - Junrui Li
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 1F, 413 90, Gothenburg, Sweden
| | - Andreas Muth
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Tony E. Godfrey
- Department of Surgery, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Anders Ståhlberg
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 1F, 413 90, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
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Bronkhorst AJ, Ungerer V, Holdenrieder S. The emerging role of cell-free DNA as a molecular marker for cancer management. BIOMOLECULAR DETECTION AND QUANTIFICATION 2019; 17:100087. [PMID: 30923679 PMCID: PMC6425120 DOI: 10.1016/j.bdq.2019.100087] [Citation(s) in RCA: 317] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/26/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023]
Abstract
An increasing number of studies demonstrate the potential use of cell-free DNA (cfDNA) as a surrogate marker for multiple indications in cancer, including diagnosis, prognosis, and monitoring. However, harnessing the full potential of cfDNA requires (i) the optimization and standardization of preanalytical steps, (ii) refinement of current analysis strategies, and, perhaps most importantly, (iii) significant improvements in our understanding of its origin, physical properties, and dynamics in circulation. The latter knowledge is crucial for interpreting the associations between changes in the baseline characteristics of cfDNA and the clinical manifestations of cancer. In this review we explore recent advancements and highlight the current gaps in our knowledge concerning each point of contact between cfDNA analysis and the different stages of cancer management.
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Affiliation(s)
| | | | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße. 36, D-80636, Munich, Germany
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Becker C, Schmidt S, Neuberger EWI, Kirsch P, Simon P, Dettweiler U. Children's Cortisol and Cell-Free DNA Trajectories in Relation to Sedentary Behavior and Physical Activity in School: A Pilot Study. Front Public Health 2019; 7:26. [PMID: 30873396 PMCID: PMC6400867 DOI: 10.3389/fpubh.2019.00026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 01/31/2019] [Indexed: 11/25/2022] Open
Abstract
The worldwide prevalence of mental disorders in children and adolescents increased constantly. Additionally, the recommended amount of physical activity (PA) is not achieved by this age group. These circumstances are associated with negative impacts on their health status in later life and can lead to public health issues. The exposure to natural green environments (NGE) seems to be beneficial for human health. The compulsory school system offers great opportunities to reach every child with suitable health-related contents and interventions at an early stage. The concept of Education Outside the Classroom (EOtC) uses NGE and sets focus on PA. Therefore, EOtC might be a beneficial educational intervention to promote students health. The association between biological stress markers and sedentary behavior (SB) plus PA is insufficiently evaluated in school settings. This exploratory study aims to evaluate the association between students' cortisol, plus circulating cell-free deoxyribonucleic acid (cfDNA) levels, and their SB, light PA (LPA), and moderate-to-vigorous PA (MVPA). We assessed data from an EOtC program (intervention group [IG], n = 37; control group [CG], n = 11) in three seasons (fall/spring/summer) in outdoor lessons (IG) in a NGE and normal indoor lessons (CG). SB and PA were evaluated by accelerometry, and cortisol and cfDNA levels by saliva samples. Fitted Bayesian hierarchical linear models evaluated the association between cortisol and cfDNA, and compositional SB/LPA/MVPA. A steady decline of cortisol in the IG is associated with relatively high levels of LPA (posterior mean = −0.728; credible interval [CRI 95%]: −1.268; −0.190). SB and MVPA tended to exhibit a similar effect in the CG. A high amount of cfDNA is positively associated with a relatively high amount of SB in the IG (posterior mean, 1.285; CRI: 0.390; 2.191), the same association is likely for LPA and MVPA in both groups. To conclude, LPA seems to support a healthy cortisol decrease in children during outdoor lessons in NGEs. Associations between cfDNA and SB/PA need to be evaluated in further research. This study facilitates the formulation of straightforward and directed hypotheses for further research with a focus on the potential health promotion of EOtC.
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Affiliation(s)
- Christoph Becker
- Department of Sport and Health Sciences, Technical University of Munich, Munich, Germany
| | - Sebastian Schmidt
- Faculty of Social Science, Media and Sport, Johannes Gutenberg University, Mainz, Germany
| | - Elmo W I Neuberger
- Faculty of Social Science, Media and Sport, Johannes Gutenberg University, Mainz, Germany
| | - Peter Kirsch
- Department of Clinical Psychology, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Perikles Simon
- Faculty of Social Science, Media and Sport, Johannes Gutenberg University, Mainz, Germany
| | - Ulrich Dettweiler
- Department of Cultural Studies and Languages, Faculty of Arts and Education, University of Stavanger, Stavanger, Norway
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Zhang J, Li J, Saucier JB, Feng Y, Jiang Y, Sinson J, McCombs AK, Schmitt ES, Peacock S, Chen S, Dai H, Ge X, Wang G, Shaw CA, Mei H, Breman A, Xia F, Yang Y, Purgason A, Pourpak A, Chen Z, Wang X, Wang Y, Kulkarni S, Choy KW, Wapner RJ, Van den Veyver IB, Beaudet A, Parmar S, Wong LJ, Eng CM. Non-invasive prenatal sequencing for multiple Mendelian monogenic disorders using circulating cell-free fetal DNA. Nat Med 2019; 25:439-447. [PMID: 30692697 DOI: 10.1038/s41591-018-0334-x] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 12/17/2018] [Indexed: 02/02/2023]
Abstract
Current non-invasive prenatal screening is targeted toward the detection of chromosomal abnormalities in the fetus1,2. However, screening for many dominant monogenic disorders associated with de novo mutations is not available, despite their relatively high incidence3. Here we report on the development and validation of, and early clinical experience with, a new approach for non-invasive prenatal sequencing for a panel of causative genes for frequent dominant monogenic diseases. Cell-free DNA (cfDNA) extracted from maternal plasma was barcoded, enriched, and then analyzed by next-generation sequencing (NGS) for targeted regions. Low-level fetal variants were identified by a statistical analysis adjusted for NGS read count and fetal fraction. Pathogenic or likely pathogenic variants were confirmed by a secondary amplicon-based test on cfDNA. Clinical tests were performed on 422 pregnancies with or without abnormal ultrasound findings or family history. Follow-up studies on cases with available outcome results confirmed 20 true-positive, 127 true-negative, zero false-positive, and zero-false negative results. The initial clinical study demonstrated that this non-invasive test can provide valuable molecular information for the detection of a wide spectrum of dominant monogenic diseases, complementing current screening for aneuploidies or carrier screening for recessive disorders.
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Affiliation(s)
- Jinglan Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | | | | | | | | | | | - Anne K McCombs
- Office of Clinical Research, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xiaoyan Ge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Statistics, Rice University, Houston, TX, USA
| | - Hui Mei
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Amy Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Zhao Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yue Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shashikant Kulkarni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Arthur Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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63
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Manueldas S, Benterud T, Rueegg CS, Garberg HT, Huun MU, Pankratov L, Åsegg-Atneosen M, Solberg R, Escobar J, Saugstad OD, Baumbusch LO. Temporal patterns of circulating cell-free DNA (cfDNA) in a newborn piglet model of perinatal asphyxia. PLoS One 2018; 13:e0206601. [PMID: 30475817 PMCID: PMC6261042 DOI: 10.1371/journal.pone.0206601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 10/16/2018] [Indexed: 12/18/2022] Open
Abstract
Perinatal asphyxia is a severe medical condition resulting from oxygen deficiency (hypoxia) at the time of birth, causing worldwide approximately 680,000 newborn deaths every year. Better prediction of severity of damages including early biomarkers is highly demanded. Elevated levels of circulating cell-free DNA (cfDNA) in blood have been reported for a range of different diseases and conditions, including cancer and prematurity. The objective of this study was to validate methods for assessing cfDNA in blood and cerebrospinal fluid (CSF) and to explore temporal variations in a piglet model of neonatal hypoxia-reoxygenation. Different cfDNA extraction methods in combination with cfDNA detection systems were tested, including a fluorescent assay using SYBR Gold and a qRT-PCR-based technique. Newborn piglets (n = 55) were exposed to hypoxia-reoxygenation, hypoxia-reoxygenation and hypothermia, or were part of the sham-operated control group. Blood was sampled at baseline and at post-intervention, further at 30, 270, and 570 minutes after the end of hypoxia. Applying the fluorescent method, cfDNA concentration in piglets exposed to hypoxia (n = 32) increased from 36.8±27.6 ng/ml prior to hypoxia to a peak level of 61.5±54.9 ng/ml after the intervention and deceased to 32.3±19.1 ng/ml at 570 minutes of reoxygenation, whereas the group of sham-operated control animals (n = 11) revealed a balanced cfDNA profile. Animals exposed to hypoxia and additionally treated with hypothermia (n = 12) expressed a cfDNA concentration of 54.4±16.9 ng/ml at baseline, 39.2±26.9 ng/ml at the end of hypoxia, and of 41.1±34.2 ng/ml at 570 minutes post-intervention. Concentrations of cfDNA in the CSF of piglets exposed to hypoxia revealed at post-intervention higher levels in comparison to the controls. However, these observations were only tendencies and not significant. In a first methodological proof-of-principle study exploring cfDNA using a piglet model of hypoxia-reoxygenation variations in the temporal patterns suggest that cfDNA might be an early indicator for damages caused by perinatal asphyxia.
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Affiliation(s)
- Sophia Manueldas
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Torkil Benterud
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Corina Silvia Rueegg
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Håvard Tetlie Garberg
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Marianne Ullestad Huun
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Leonid Pankratov
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Monica Åsegg-Atneosen
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Rønnaug Solberg
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Department of Pediatrics, Vestfold Hospital Trust, Tønsberg, Norway
| | - Javier Escobar
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Ola Didrik Saugstad
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Lars Oliver Baumbusch
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
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64
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Gyanchandani R, Kvam E, Heller R, Finehout E, Smith N, Kota K, Nelson JR, Griffin W, Puhalla S, Brufsky AM, Davidson NE, Lee AV. Whole genome amplification of cell-free DNA enables detection of circulating tumor DNA mutations from fingerstick capillary blood. Sci Rep 2018; 8:17313. [PMID: 30470782 PMCID: PMC6251935 DOI: 10.1038/s41598-018-35470-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/01/2018] [Indexed: 12/25/2022] Open
Abstract
The ability to measure mutations in plasma cell-free DNA (cfDNA) has the potential to revolutionize cancer surveillance and treatment by enabling longitudinal monitoring not possible with solid tumor biopsies. However, obtaining sufficient quantities of cfDNA remains a challenge for assay development and clinical translation; consequently, large volumes of venous blood are typically required. Here, we test proof-of-concept for using smaller volumes via fingerstick collection. Matched venous and fingerstick blood were obtained from seven patients with metastatic breast cancer. Fingerstick blood was separated at point-of-care using a novel paper-based concept to isolate plasma centrifuge-free. Patient cfDNA was then analyzed with or without a new method for whole genome amplification via rolling-circle amplification (WG-RCA). We identified somatic mutations by targeted sequencing and compared the concordance of mutation detection from venous and amplified capillary samples by droplet-digital PCR. Patient mutations were detected with 100% concordance after WG-RCA, although in some samples, allele frequencies showed greater variation likely due to differential amplification or primer inaccessibility. These pilot findings provide physiological evidence that circulating tumor DNA is accessible by fingerstick and sustains presence/absence of mutation detection after whole-genome amplification. Further refinement may enable simpler and less-invasive methods for longitudinal or theranostic surveillance of metastatic cancer.
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Affiliation(s)
- Rekha Gyanchandani
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA.,Western Oncolytics, 265 William Pitt Way, Pittsburgh, PA, 15238, USA
| | - Erik Kvam
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA.
| | - Ryan Heller
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA.,QIAGEN, 100 Cummings Center, Beverly, MA, 01915, USA
| | - Erin Finehout
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA.,Terumo BCT, 10811 Collins Ave, Lakewood, CO, 80215, USA
| | - Nicholas Smith
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Karthik Kota
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - John R Nelson
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA
| | - Weston Griffin
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA
| | - Shannon Puhalla
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Adam M Brufsky
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Nancy E Davidson
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA.,Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA, 98109, USA
| | - Adrian V Lee
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA.
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65
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Malbec R, Cacheux J, Cordelier P, Leichlé T, Joseph P, Bancaud A. Microfluidics for minute DNA sample analysis: open challenges for genetic testing of cell-free circulating DNA in blood plasma. MICRO AND NANO ENGINEERING 2018. [DOI: 10.1016/j.mne.2018.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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66
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Fettke H, Kwan EM, Azad AA. Cell-free DNA in cancer: current insights. Cell Oncol (Dordr) 2018; 42:13-28. [PMID: 30367445 DOI: 10.1007/s13402-018-0413-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The field of liquid biopsies in oncology is rapidly expanding, with the application of cell-free circulating tumour DNA (ctDNA) showing promise in this era of precision medicine. Compared with traditional clinical and radiographic tumour monitoring methods, the analysis of ctDNA provides a minimally-invasive and technically feasible approach to assess temporal and spatial molecular evolutions of the tumour landscape. The constantly advancing technological platforms available for ctDNA extraction and analysis allow greater analytical sensitivities than ever before. The potential translational impact of ctDNA as a blood-based biomarker for the identification, characterization and monitoring of cancer has been demonstrated in numerous proof-of-concept studies, with ctDNA analysis beginning to be applied clinically across multiple facets of oncology. CONCLUSIONS In this review we discuss the biology, recent advancements, technical considerations and clinical implications of ctDNA in the context of cancer, and highlight important challenges and future directions for the integration of ctDNA into standardised patient care.
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Affiliation(s)
- Heidi Fettke
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.
| | - Edmond M Kwan
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.,Department of Medical Oncology, Monash Health, Melbourne, Australia
| | - Arun A Azad
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.,Department of Medical Oncology, Monash Health, Melbourne, Australia
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67
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Huo Q, Zhou M, Cooper DKC, Dai Y, Xie N, Mou L. Circulating miRNA or circulating DNA-Potential biomarkers for organ transplant rejection. Xenotransplantation 2018. [DOI: 10.1111/xen.12444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Qin Huo
- College of Life Science and Oceanography; Shenzhen University; Shenzhen Guangdong China
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center; Institute of Translational Medicine; Shenzhen Second People's Hospital; First Affiliated Hospital of Shenzhen University; Shenzhen Guangdong China
| | - Ming Zhou
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center; Institute of Translational Medicine; Shenzhen Second People's Hospital; First Affiliated Hospital of Shenzhen University; Shenzhen Guangdong China
| | - David K. C. Cooper
- Xenotransplantation Program; Department of Surgery; The University of Alabama at Birmingham; Birmingham Alabama
| | - Yifan Dai
- Jiangsu Key Laboratory of Xenotransplantation; Nanjing Medical University; Nanjing Jiangsu China
| | - Ni Xie
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center; Institute of Translational Medicine; Shenzhen Second People's Hospital; First Affiliated Hospital of Shenzhen University; Shenzhen Guangdong China
| | - Lisha Mou
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center; Institute of Translational Medicine; Shenzhen Second People's Hospital; First Affiliated Hospital of Shenzhen University; Shenzhen Guangdong China
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68
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Zhao Y, Li Y, Chen P, Li S, Luo J, Xia H. Performance comparison of blood collection tubes as liquid biopsy storage system for minimizing cfDNA contamination from genomic DNA. J Clin Lab Anal 2018; 33:e22670. [PMID: 30191594 DOI: 10.1002/jcla.22670] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/03/2018] [Accepted: 08/14/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The ratio of target cfDNA in total plasma is low. The abundant gDNA background resulting from blood cell lysis caused by improper operation has become a major obstacle to accurately measure cfDNA. In this study, we investigated the storage capacity of three blood cell collection tubes (BCTs) in the prevention of genomic DNA contamination caused by white blood cell rupture and evaluated their performance when they were utilized combining with highly sensitive mutation detection technology. METHODS Blood samples were drawn from six healthy blood donors and stored in three types of BCTs (BD K2 -EDTA tube, Roche tube, and Streck tube). Plasma samples were isolated at specific time points (day 0, day 3, day 7, and day 14) for content analysis. RESULTS Roche BCT was more capable for preventing cfDNA contamination caused by white blood cell disruption within 14 days, comparing with BD K2 -EDTA tube and Streck tube. Severe white blood cell lysis and gDNA contamination were found in the BD tube. The impacts of Roche and Streck tubes on the quantity and complexity of next-generation sequencing (NGS) libraries did not differ significantly within 3 days, satisfying most of our daily demands. In addition, the rupture of WBC was not synchronized with hemolysis in BCTs. CONCLUSION This study showed that capacities of blood collection tubes differed considerably in preservation of blood samples. Therefore, suitable blood collection devices should be selected to minimize gDNA contamination and to standardize blood samples processing for achieving more accurate and reliable clinical analysis of cfDNA.
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Affiliation(s)
- Yunlong Zhao
- Department of Cardiothoracic Surgery, First Affiliated Hospital of PLA General Hospital, Beijing, China
| | - Yingjie Li
- Department of Cardiothoracic Surgery, First Affiliated Hospital of PLA General Hospital, Beijing, China
| | - Ping Chen
- Department of Cardiothoracic Surgery, First Affiliated Hospital of PLA General Hospital, Beijing, China
| | - Shaojun Li
- Department of Cardiothoracic Surgery, First Affiliated Hospital of PLA General Hospital, Beijing, China
| | - Jian Luo
- Burning Rock Biotech, Guangzhou, China
| | - Hui Xia
- Department of Cardiothoracic Surgery, First Affiliated Hospital of PLA General Hospital, Beijing, China
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69
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Finotti A, Allegretti M, Gasparello J, Giacomini P, Spandidos DA, Spoto G, Gambari R. Liquid biopsy and PCR-free ultrasensitive detection systems in oncology (Review). Int J Oncol 2018; 53:1395-1434. [PMID: 30085333 PMCID: PMC6086621 DOI: 10.3892/ijo.2018.4516] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/31/2018] [Indexed: 02/07/2023] Open
Abstract
In oncology, liquid biopsy is used in the detection of next-generation analytes, such as tumor cells, cell-free nucleic acids and exosomes in peripheral blood and other body fluids from cancer patients. It is considered one of the most advanced non-invasive diagnostic systems to enable clinically relevant actions and implement precision medicine. Medical actions include, but are not limited to, early diagnosis, staging, prognosis, anticipation (lead time) and the prediction of therapy responses, as well as follow-up. Historically, the applications of liquid biopsy in cancer have focused on circulating tumor cells (CTCs). More recently, this analysis has been extended to circulating free DNA (cfDNA) and microRNAs (miRNAs or miRs) associated with cancer, with potential applications for development into multi-marker diagnostic, prognostic and therapeutic signatures. Liquid biopsies avoid some key limitations of conventional tumor tissue biopsies, including invasive tumor sampling, under-representation of tumor heterogeneity and poor description of clonal evolution during metastatic dissemination, strongly reducing the need for multiple sampling. On the other hand, this approach suffers from important drawbacks, i.e., the fragmentation of cfDNA, the instability of RNA, the low concentrations of certain analytes in body fluids and the confounding presence of normal, as well as aberrant DNAs and RNAs. For these reasons, the analysis of cfDNA has been mostly focused on mutations arising in, and pathognomonicity of, tumor DNA, while the analysis of cfRNA has been mostly focused on miRNA patterns strongly associated with neoplastic transformation/progression. This review lists some major applicative areas, briefly addresses how technology is bypassing liquid biopsy limitations, and places a particular emphasis on novel, PCR-free platforms. The ongoing collaborative efforts of major international consortia are reviewed. In addition to basic and applied research, we will consider technological transfer, including patents, patent applications and available information on clinical trials aimed at verifying the potential of liquid biopsy in cancer.
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Affiliation(s)
- Alessia Finotti
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
| | - Matteo Allegretti
- Oncogenomics and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
| | - Patrizio Giacomini
- Oncogenomics and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Crete, Greece
| | - Giuseppe Spoto
- Department of Chemistry, Catania University, 95125 Catania, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
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70
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Gorgannezhad L, Umer M, Islam MN, Nguyen NT, Shiddiky MJA. Circulating tumor DNA and liquid biopsy: opportunities, challenges, and recent advances in detection technologies. LAB ON A CHIP 2018; 18:1174-1196. [PMID: 29569666 DOI: 10.1039/c8lc00100f] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Cell-free DNA (cfDNA) refers to short fragments of acellular nucleic acids detectable in almost all body fluids, including blood, and is involved in various physiological and pathological phenomena such as immunity, coagulation, aging, and cancer. In cancer patients, a fraction of hematogenous cfDNA originates from tumors, termed circulating tumor DNA (ctDNA), and may carry the same mutations and genetic alterations as those of a primary tumor. Thus, ctDNA potentially provides an opportunity for noninvasive assessment of cancer. Recent advances in ctDNA analysis methods will potentially lead to the development of a liquid biopsy tool for the diagnosis, prognosis, therapy response monitoring, and tracking the rise of new mutant sub-clones in cancer patients. Over the past few decades, cancer-specific mutations in ctDNA have been detected using a variety of untargeted methods such as digital karyotyping, personalized analysis of rearranged ends (PARE), whole-genome sequencing of ctDNA, and targeted approaches such as conventional and digital PCR-based methods and deep sequencing-based technologies. More recently, several chip-based electrochemical sensors have been developed for the analysis of ctDNA in patient samples. This paper aims to comprehensively review the diagnostic, prognostic, and predictive potential of ctDNA as a minimally invasive liquid biopsy for cancer patients. We also present an overview of current advances in the analytical sensitivity and accuracy of ctDNA analysis methods as well as biological and technical challenges, which need to be resolved for the integration of ctDNA analysis into routine clinical practice.
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Affiliation(s)
- Lena Gorgannezhad
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad Umer
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Md Nazmul Islam
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
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71
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Thurairajah K, Briggs GD, Balogh ZJ. The source of cell-free mitochondrial DNA in trauma and potential therapeutic strategies. Eur J Trauma Emerg Surg 2018; 44:325-334. [PMID: 29633007 PMCID: PMC6002458 DOI: 10.1007/s00068-018-0954-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/03/2018] [Indexed: 01/04/2023]
Abstract
Mitochondria play a key role in the pathophysiology of post-injury inflammation. Cell-free mitochondrial DNA (cf-mtDNA) is now understood to catalyse sterile inflammation after trauma. Observations in trauma cohorts have identified high cf-mtDNA in patients with systemic inflammatory response syndrome and multiple organ failure as well as following major surgery. The source of cf-mtDNA can be various cells affected by mechanical and hypoxic injury (passive mechanism) or induced by inflammatory mechanisms (active mechanism). Multiple forms of cf-mtDNA exist; mtDNA fragments, mtDNA in microparticles/vesicles and cell-free mitochondria. Trauma to cells that are rich in mitochondria are believed to release more cf-mtDNA. This review describes the current understanding of the mechanisms of cf-mtDNA release, its systemic effects and the potential therapeutic implications related to its modification. Although current understanding is insufficient to change trauma management, focussed research goals have been identified to pave the way for monitoring and manipulation of cf-mtDNA release and effects in trauma.
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Affiliation(s)
- Kabilan Thurairajah
- Department of Traumatology, John Hunter Hospital and University of Newcastle, Newcastle, NSW, Australia
| | - Gabrielle Daisy Briggs
- Department of Traumatology, John Hunter Hospital and University of Newcastle, Newcastle, NSW, Australia
| | - Zsolt Janos Balogh
- Department of Traumatology, John Hunter Hospital and University of Newcastle, Newcastle, NSW, Australia.
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72
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Rodda AE, Parker BJ, Spencer A, Corrie SR. Extending Circulating Tumor DNA Analysis to Ultralow Abundance Mutations: Techniques and Challenges. ACS Sens 2018; 3:540-560. [PMID: 29441780 DOI: 10.1021/acssensors.7b00953] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid biopsies that analyze circulating tumor DNA (ctDNA) hold great promise in the guidance of clinical treatment for various cancers. However, the innate characteristics of ctDNA make it a difficult target: ctDNA is highly fragmented, and found at very low concentrations, both in absolute terms and relative to wildtype species. Clinically relevant target sequences often differ from the wildtype species by a single DNA base pair. These characteristics make analyzing mutant ctDNA a uniquely difficult process. Despite this, techniques have recently emerged for analyzing ctDNA, and have been used in pilot studies that showed promising results. These techniques each have various drawbacks, either in their analytical capabilities or in practical considerations, which restrict their application to many clinical situations. Many of the most promising potential applications of ctDNA require assay characteristics that are not currently available, and new techniques with these properties could have benefits in companion diagnostics, monitoring response to treatment and early detection. Here we review the current state of the art in ctDNA detection, with critical comparison of the analytical techniques themselves. We also examine the improvements required to expand ctDNA diagnostics to more advanced applications and discuss the most likely pathways for these improvements.
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Affiliation(s)
| | | | - Andrew Spencer
- Myeloma Research Group, Australian Center for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
- Malignant Haematology & Stem Cell Transplantation Service, Alfred Hospital, Melbourne, Victoria 3004, Australia
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73
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Vrba L, Futscher BW. A suite of DNA methylation markers that can detect most common human cancers. Epigenetics 2018; 13:61-72. [PMID: 29212414 DOI: 10.1080/15592294.2017.1412907] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cancer-specific DNA methylation from the tumor derived fraction of cell free DNA found in blood samples could be used for minimally invasive detection and monitoring of cancer. The knowledge of marker regions with cancer-specific DNA methylation is necessary to the success of such a process. We analyzed the largest cancer DNA methylation dataset available-TCGA Illumina HumanMethylation450 data with over 8,500 tumors-in order to find cancer-specific DNA methylation markers for most common human cancers. First, we identified differentially methylated regions for individual cancer types and those were further filtered against data from normal tissues to obtain marker regions with cancer-specific methylation, resulting in a total of 1,250 hypermethylated and 584 hypomethylated marker CpGs. From hypermethylated markers, optimal sets of six markers for each TCGA cancer type were chosen that could identify most tumors with high specificity and sensitivity [area under the curve (AUC): 0.969-1.000] and a universal 12 marker set that can detect tumors of all 33 TCGA cancer types (AUC >0.84). In addition to hundreds of new DNA methylation markers, our approach also identified markers that are in current clinical use, SEPT9 and GSTP1, indicating the validity of our approach and a significant potential utility for the newly discovered markers. The hypermethylated markers are linked to polycomb associated loci and a significant fraction of the discovered markers is within noncoding RNA genes; one of the best markers is MIR129-2. Future clinical testing of herein discovered markers will confirm new markers that will improve minimally invasive diagnosis and monitoring for multiple cancers.
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Affiliation(s)
- Lukas Vrba
- a The University of Arizona Cancer Center , Tucson , AZ 85724 , USA
| | - Bernard W Futscher
- a The University of Arizona Cancer Center , Tucson , AZ 85724 , USA.,b Department of Pharmacology & Toxicology, College of Pharmacy , The University of Arizona , Tucson , AZ 85724 , USA
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74
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Haller N, Helmig S, Taenny P, Petry J, Schmidt S, Simon P. Circulating, cell-free DNA as a marker for exercise load in intermittent sports. PLoS One 2018; 13:e0191915. [PMID: 29370268 PMCID: PMC5784997 DOI: 10.1371/journal.pone.0191915] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 12/20/2017] [Indexed: 12/21/2022] Open
Abstract
Background Attempts to establish a biomarker reflecting individual player load in intermittent sports such as football have failed so far. Increases in circulating DNA (cfDNA) have been demonstrated in various endurance sports settings. While it has been proposed that cfDNA could be a suitable marker for player load in intermittent sports, the effects on cfDNA of repeated sprinting as an essential feature in intermittent sports are unknown. For the first time, we assessed both alterations of cfDNA due to repeated maximal sprints and due to a professional football game. Methods Nine participants were subjected to a standardised sprint training session with cross-over design of five maximal sprints of 40 meters with either “short” (1 minute) or “long” pauses (5 minutes). Capillary cfDNA and lactate were measured after every sprint and venous cfDNA before and after each series of sprints. Moreover, capillary cfDNA and lactate values were taken in 23 professional football players before and after incremental exercise testing, during the course of a training week at rest (baseline) and in all 17 enrolled players following a season game. Results Lactate and venous cfDNA increased more pronounced during “short” compared to “long” (1.4-fold, p = 0.032 and 1.7-fold, p = 0.016) and cfDNA correlated significantly with lactate (r = 0.69; p<0.001). Incremental exercise testing increased cfDNA 7.0-fold (p<0.001). The season game increased cfDNA 22.7-fold (p<0.0001), while lactate showed a 2.0-fold (p = 0.09) increase compared to baseline. Fold-changes in cfDNA correlated with distance covered during game (spearman’s r = 0.87, p = 0.0012), while no correlation between lactate and the tracking data could be found. Discussion We show for the first time that cfDNA could be an objective marker for distance covered in elite intermittent sports. In contrast to the potential of more established blood-based markers like IL-6, CK, or CRP, cfDNA shows by far the strongest fold-change and a high correlation with a particular load related aspect in professional football.
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Affiliation(s)
- Nils Haller
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Susanne Helmig
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Pascal Taenny
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Julian Petry
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Sebastian Schmidt
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
- * E-mail:
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Mariner PD, Korst A, Karimpour-Fard A, Stauffer BL, Miyamoto SD, Sucharov CC. Improved Detection of Circulating miRNAs in Serum and Plasma Following Rapid Heat/Freeze Cycling. Microrna 2018; 7:138-147. [PMID: 29658445 PMCID: PMC6198569 DOI: 10.2174/2211536607666180416152112] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 01/31/2018] [Accepted: 04/10/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND The measurement of circulating miRNAs has proven to be a powerful biomarker tool for several disease processes. Current protocols for the detection of miRNAs usually involve an RNA extraction step, requiring a substantial volume of patient serum or plasma to obtain sufficient input material. OBJECTIVE Here, we describe a novel methodology that allows detection of a large number of miRNAs from a small volume of serum or plasma without the need for RNA extraction. METHODS Three μl of serum or plasma was subjected to three cycles of high and low temperatures (heat/freeze cycles) followed by miRNA arrays. RESULTS Our results indicate that miRNA detection following this process is highly reproducible when comparing multiple samples from the same subject. Moreover, this protocol increases the reproducibility of miRNA detection in samples that were previously subjected to multiple freeze-thaw cycles. Importantly, the detection of miRNAs from serum vs. plasma following heat/freeze cycling are highly comparable, indicating that this heat/freeze process effectively eliminates differences in detection between serum and plasma samples that have been reported using other sample preparation methodologies. CONCLUSION We propose that this method is a potent alternative to current RNA extraction protocols, substantially reducing the amount of sample necessary for miRNA detection while simultaneously improving miRNA detection and reproducibility.
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Affiliation(s)
| | | | | | | | | | - Carmen C. Sucharov
- Address correspondence to this author at the Department of Medicine, Division of Cardiology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, USA; Tel: 303 724 5409; Fax: 303 724 5450; E-mail:
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76
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Whale AS, Fernandez-Gonzalez A, Gutteridge A, Devonshire AS. Control Materials and Digital PCR Methods for Evaluation of Circulating Cell-Free DNA Extractions from Plasma. Methods Mol Biol 2018; 1768:45-65. [PMID: 29717437 DOI: 10.1007/978-1-4939-7778-9_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Cell-free DNA is an accessible source of genetic material found naturally in plasma that could be used in many diagnostic applications. Translation of cfDNA analysis methods from research laboratories into the clinic would benefit from controls for monitoring the efficiency of patient sample purification and for quality control of the whole workflow from extraction through to analysis. Here we describe two types of control materials that can be "spiked" into plasma samples to monitor and evaluate different aspects of the workflow. The first control material is an internal control that enables evaluation of extraction efficiency, fragment size bias, and sample inhibition. The second control material serves as a parallel quality control material for measurement of specific genetic targets such as tumor mutations.
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77
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Lee H, Choi M, Hwang SH, Cho Y. A Versatile Nanowire Platform for Highly Efficient Isolation and Direct PCR-free Colorimetric Detection of Human Papillomavirus DNA from Unprocessed Urine. Am J Cancer Res 2018; 8:399-409. [PMID: 29290816 PMCID: PMC5743556 DOI: 10.7150/thno.21696] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 08/09/2017] [Indexed: 11/05/2022] Open
Abstract
Purpose: As human papillomavirus (HPV) is primarily responsible for the development of cervical cancer, significant efforts have been devoted to develop novel strategies for detecting and identifying HPV DNA in urine. The analysis of target DNA sequences in urine offers a potential alternative to conventional methods as a non-invasive clinical screening and diagnostic assessment tool for the detection of HPV. However, the lack of efficient approaches to isolate and directly detect HPV DNA in urine has restricted its potential clinical use. In this study, we demonstrated a novel approach of using polyethylenimine-conjugated magnetic polypyrrole nanowires (PEI-mPpy NWs) for the extraction, identification, and PCR-free colorimetric detection of high-risk strains of HPV DNA sequences, particularly HPV-16 and HPV-18, in urine specimens of cervical cancer patients. Materials and Methods: We fabricated and characterized polyethylenimine-conjugated magnetic nanowires (PEI/mPpy NWs). PEI/mPpy NWs-based HPV DNA isolation and detection strategy appears to be a cost-effective and practical technology with greater sensitivity and accuracy than other urine-based methods. Results: The analytical and clinical performance of PEI-mPpy NWs was evaluated and compared with those of cervical swabs, demonstrating a superior type-specific concordance rate of 100% between urine and cervical swabs, even when using a small volume of urine (300 µL). Conclusion: We envision that PEI-mPpy NWs provide substantive evidence for clinical diagnosis and management of HPV-associated disease with their excellent performance in the recovery and detection of HPV DNA from minimal amounts of urine samples.
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78
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Volckmar AL, Sültmann H, Riediger A, Fioretos T, Schirmacher P, Endris V, Stenzinger A, Dietz S. A field guide for cancer diagnostics using cell-free DNA: From principles to practice and clinical applications. Genes Chromosomes Cancer 2017; 57:123-139. [DOI: 10.1002/gcc.22517] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 12/16/2022] Open
Affiliation(s)
- Anna-Lena Volckmar
- Institute of Pathology, University Hospital Heidelberg; Heidelberg Germany
| | - Holger Sültmann
- Division of Cancer Genome Research; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK); Heidelberg Germany
| | - Anja Riediger
- Division of Cancer Genome Research; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK); Heidelberg Germany
| | - Thoas Fioretos
- Department of Clinical Genetics; Lund University; Lund Sweden
- Department of Clinical Genetics; University and Regional Laboratories; Region Skåne Lund Sweden
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg; Heidelberg Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg; Heidelberg Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg; Heidelberg Germany
- German Cancer Consortium (DKTK), Partner Site Heidelberg, and German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Steffen Dietz
- Division of Cancer Genome Research; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK); Heidelberg Germany
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Sefrioui D, Beaussire L, Perdrix A, Clatot F, Michel P, Frebourg T, Di Fiore F, Sarafan-Vasseur N. Direct circulating tumor DNA detection from unpurified plasma using a digital PCR platform. Clin Biochem 2017. [DOI: 10.1016/j.clinbiochem.2017.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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80
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Economopoulou P, Kotsantis I, Kyrodimos E, Lianidou E, Psyrri A. Liquid biopsy: An emerging prognostic and predictive tool in Head and Neck Squamous Cell Carcinoma (HNSCC). Focus on Circulating Tumor Cells (CTCs). Oral Oncol 2017; 74:83-89. [DOI: 10.1016/j.oraloncology.2017.09.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 09/07/2017] [Accepted: 09/14/2017] [Indexed: 01/17/2023]
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81
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Tug S, Tross AK, Hegen P, Neuberger EWI, Helmig S, Schöllhorn W, Simon P. Acute effects of strength exercises and effects of regular strength training on cell free DNA concentrations in blood plasma. PLoS One 2017; 12:e0184668. [PMID: 28910365 PMCID: PMC5599009 DOI: 10.1371/journal.pone.0184668] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/28/2017] [Indexed: 01/05/2023] Open
Abstract
Creatine kinase (CK) is a marker for muscle cell damage with limited potential as marker for training load in strength training. Recent exercise studies identified cell free DNA (cfDNA) as a marker for aseptic inflammation and cell damage. Here we overserved in a pilot study the acute effects during strength exercise and chronic effects of regular strength training on cfDNA concentrations over a period of four weeks in three training groups applying conservation training (CT) at 60% of the 1 repetition maximum, high intensity-low repetition training (HT) at 90% of the 1 repetition maximum and differential training (DT) at 60% of the 1 repetition maximum. EDTA-plasma samples were collected before every training session, and on the first and last training day repeatedly after every set of exercises. CfDNA increased significantly by 1.62-fold (mean (±SD) before first exercise: 8.31 (2.84) ng/ml, after last exercise 13.48 (4.12) ng/ml) across all groups within a single training session (p<0.001). The increase was 1.77-fold higher (mean (±SD) before first exercise: 12.23 (6.29) ng/ml, after last exercise 17.73 (11.24) ng/ml) in HT compared to CT (mean (±SD) before first exercise: 6.79 (1.28) ng/ml, after last exercise 10.05 (2.89) ng/ml) (p = 0.01). DNA size analysis suggested predominant release of short, mononucleosomal DNA-fragments in the acute exercise setting, while we detected an increase of mostly longer, polynucleosomal cfDNA-fragments at rest before the training session only at day two with a subsequent return to baseline (p<0.001). In contrast, training procedures did not cause any alterations in CK. Our results suggest that during strength exercise short-fragmented cfDNA is released, reflecting a fast, aseptic inflammatory response, while elevation of longer fragments at baseline on day two seemed to reflect mild cellular damage due to a novel training regime. We critically discuss the implications of our findings for future evaluations of cfDNA as a marker for training load in strength training.
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Affiliation(s)
- Suzan Tug
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Anna-Katharina Tross
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Patrick Hegen
- Institute for Training and Movement Science, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Elmo Wanja Immanuel Neuberger
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Susanne Helmig
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Wolfgang Schöllhorn
- Institute for Training and Movement Science, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Perikles Simon
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
- * E-mail:
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82
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Karami F, Noori Daloii MR, Hantooshzadeh S, Modarressi MH. Comparing the Efficiency of Three Protocols in Isolation of Cell Free Fetal DNA From Maternal Blood. J Family Reprod Health 2017; 11:146-151. [PMID: 30018651 PMCID: PMC6045694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
Objective: Recent advances in non-invasive prenatal diagnosis (NIPD) through cell free fetal DNA (cffDNA) has highlighted cffDNA purification as a critical initial step. Herein, we aimed to compare the efficiency of one proposed protocol with two commercial kits for isolation of cffDNA. Materials and methods: cffDNA was isolated from whole blood of 50 normal pregnancies using one proposed manual protocol compared with QIAamp DNA Blood Mini and Bioneer Kits. Methylated DNA immunoprecipitation real time polymerase chain reaction (MeDIP-Real time PCR) was performed to quantify three fetal specific sequences. Results: Maximum cffDNA quantity was obtained by suggested protocol (248.79 ± 14.07 ng/µl) and the best quality was achieved by Bioneer Kit (OD ratio: 260/280 nm/nm: 1.69 ± 0.09, 260/230 nm/nm: 1.15 ± 0.13) (p < 0.001). Enrichment of fetal specific sequences was significantly higher when proposed protocol was used to isolate cffDNA (p = 0.01). Conclusion: Inhibitory effect of NaI on nucleases and double digestion of DNA associated proteins may be the main reasons behind the superiority of suggested protocol. Significantly higher amplification of fetal specific sequences in suggested protocol would be a strong evidence on recovery of small fetal fragments as demonstrated with its maximum total DNA quantity and amplification in different PCR reactions.
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Affiliation(s)
- Fatemeh Karami
- Departement of Medical Genetics, Applied Biophotonics Research Center, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Seddigheh Hantooshzadeh
- Vali-e-Asr Reproductive Health Research Center, School of Medicine, Tehran University of Medical Sciences, Iran
| | - Mohammad Hossein Modarressi
- Departement of Medical Genetics, Science and Research Branch, Islamic Azad University, Tehran, Iran; Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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83
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Ehlert T, Tug S, Brahmer A, Neef V, Heid F, Werner C, Jansen-Winkeln B, Kneist W, Lang H, Gockel I, Simon P. Establishing PNB-qPCR for quantifying minimal ctDNA concentrations during tumour resection. Sci Rep 2017; 7:8876. [PMID: 28827745 PMCID: PMC5566323 DOI: 10.1038/s41598-017-09137-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 07/20/2017] [Indexed: 12/15/2022] Open
Abstract
The analysis of blood plasma or serum as a non-invasive alternative to tissue biopsies is a much-pursued goal in cancer research. Various methods and approaches have been presented to determine a patient’s tumour status, chances of survival, and response to therapy from serum or plasma samples. We established PNB-qPCR (Pooled, Nested, WT-Blocking qPCR), a highly specific nested qPCR with various modifications to detect and quantify minute amounts of circulating tumour DNA (ctDNA) from very limited blood plasma samples. PNB-qPCR is a nested qPCR technique combining ARMS primers, blocking primers, LNA probes, and pooling of multiple first round products for sensitive quantification of the seven most frequent point mutations in KRAS exon 2. Using this approach, we were able to characterize ctDNA and total cell-free DNA (cfDNA) kinetics by selective amplification of KRAS mutated DNA fragments in the blood plasma over the course of tumour resection and the surrounding days. Whereas total cfDNA concentrations increased over the surgical and regenerative process, ctDNA levels showed a different scheme, rising only directly after tumour resection and about three days after the surgery. For the first time, we present insights into the impact of surgery on the release of ctDNA and total cfDNA.
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Affiliation(s)
- T Ehlert
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Faculty of Social Science, Media and Sport, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - S Tug
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Faculty of Social Science, Media and Sport, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - A Brahmer
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Faculty of Social Science, Media and Sport, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - V Neef
- Department of Anaesthesiology, University Medical Centre Mainz, Mainz, Germany
| | - F Heid
- Department of Anaesthesiology, University Medical Centre Mainz, Mainz, Germany
| | - C Werner
- Department of Anaesthesiology, University Medical Centre Mainz, Mainz, Germany
| | - B Jansen-Winkeln
- Department of General, Visceral and Transplant Surgery, University Medical Centre, Mainz, Germany.,Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Medical Centre of Leipzig, Leipzig, Germany
| | - W Kneist
- Department of General, Visceral and Transplant Surgery, University Medical Centre, Mainz, Germany
| | - H Lang
- Department of General, Visceral and Transplant Surgery, University Medical Centre, Mainz, Germany
| | - I Gockel
- Department of General, Visceral and Transplant Surgery, University Medical Centre, Mainz, Germany.,Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Medical Centre of Leipzig, Leipzig, Germany
| | - P Simon
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Faculty of Social Science, Media and Sport, Johannes Gutenberg-University Mainz, Mainz, Germany.
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84
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Karlas T, Weise L, Kuhn S, Krenzien F, Mehdorn M, Petroff D, Linder N, Schaudinn A, Busse H, Keim V, Pratschke J, Wiegand J, Splith K, Schmelzle M. Correlation of cell-free DNA plasma concentration with severity of non-alcoholic fatty liver disease. J Transl Med 2017; 15:106. [PMID: 28521774 PMCID: PMC5437653 DOI: 10.1186/s12967-017-1208-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/04/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The assessment of fibrosis and inflammatory activity is essential to identify patients with non-alcoholic fatty liver disease (NAFLD) at risk for progressive disease. Serum markers and ultrasound-based methods can replace liver biopsy for fibrosis staging, whereas non-invasive characterization of inflammatory activity remains a clinical challenge. Cell-free DNA (cfDNA) is a novel non-invasive biomarker for assessing cellular inflammation and cell death, which has not been evaluated in NAFLD. METHODS Patients and healthy controls from two previous studies were included. NAFLD disease activity and severity were non-invasively characterized by liver stiffness measurement (transient elastography, TE) including steatosis assessment with controlled attenuation parameter (CAP), single-proton magnetic resonance spectroscopy (1H-MRS) for determination of hepatic fat fraction, aminotransferases and serum ferritin. cfDNA levels (90 and 222 bp fragments) were analyzed using quantitative real-time PCR. RESULTS Fifty-eight NAFLD patients (age 62 ± 11 years, BMI 28.2 ± 3.5 kg/m2) and 13 healthy controls (age 38 ± 12 years, BMI 22.4 ± 2.1 kg/m2) were included. 90 bp cfDNA levels were significantly higher in NAFLD patients compared to healthy controls: 3.7 (1.3-23.1) vs. 2.9 (1.4-4.1) ng/mL (p = 0.014). In the NAFLD cohort, circulating cfDNA correlated significantly with disease activity and severity, especially in patients with elevated liver stiffness (n = 13, 22%) compared to cases with TE values ≤7 kPa: cf90 bp 6.05 (2.41-23.13) vs. 3.16 (1.29-7.31) ng/mL (p < 0.001), and cf222 bp 14.41 (9.27-22.90) vs. 11.32 (6.05-18.28) ng/mL (p = 0.0041). CONCLUSIONS Cell-free DNA plasma concentration correlates with established non-invasive markers of NAFLD activity and severity. Therefore, cfDNA should be further evaluated as biomarker for identifying patients at risk for progressive NAFLD.
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Affiliation(s)
- Thomas Karlas
- 0000 0000 8517 9062grid.411339.dDepartment of Medicine, Neurology and Dermatology, Division of Gastroenterology and Rheumatology, University Hospital Leipzig, Leipzig, Germany
- 0000 0001 2230 9752grid.9647.cIFB Adiposity Diseases, Leipzig University Medical Center, Leipzig, Germany
| | - Lara Weise
- 0000 0001 2230 9752grid.9647.cMedical Faculty, Leipzig University, Leipzig, Germany
| | - Stephanie Kuhn
- 0000 0004 0492 3830grid.7492.8Department Environmental Immunology, Helmholtz Centre for Environmental Research GmbH-UFZ, Leipzig, Germany
| | - Felix Krenzien
- 0000 0001 2218 4662grid.6363.0Department of Surgery, Campus Virchow-Klinikum, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Mehdorn
- 0000 0000 8517 9062grid.411339.dDepartment of Visceral-, Transplantation-, Thoracic- and Vascular Surgery, University Hospital Leipzig, Leipzig, Germany
| | - David Petroff
- 0000 0001 2230 9752grid.9647.cClinical Trial Centre, Leipzig University, Leipzig, Germany
| | - Nicolas Linder
- 0000 0000 8517 9062grid.411339.dDepartment of Diagnostic and Interventional Radiology, University Hospital Leipzig, Leipzig, Germany
| | - Alexander Schaudinn
- 0000 0000 8517 9062grid.411339.dDepartment of Diagnostic and Interventional Radiology, University Hospital Leipzig, Leipzig, Germany
| | - Harald Busse
- 0000 0000 8517 9062grid.411339.dDepartment of Diagnostic and Interventional Radiology, University Hospital Leipzig, Leipzig, Germany
| | - Volker Keim
- 0000 0000 8517 9062grid.411339.dDepartment of Medicine, Neurology and Dermatology, Division of Gastroenterology and Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Johann Pratschke
- 0000 0001 2218 4662grid.6363.0Department of Surgery, Campus Virchow-Klinikum, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes Wiegand
- 0000 0000 8517 9062grid.411339.dDepartment of Medicine, Neurology and Dermatology, Division of Gastroenterology and Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Katrin Splith
- 0000 0001 2218 4662grid.6363.0Department of Surgery, Campus Virchow-Klinikum, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Moritz Schmelzle
- 0000 0001 2218 4662grid.6363.0Department of Surgery, Campus Virchow-Klinikum, Charité-Universitätsmedizin Berlin, Berlin, Germany
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85
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Extraction of cell-free DNA from urine, using polylysine-coated silica particles. Anal Bioanal Chem 2017; 409:4021-4025. [DOI: 10.1007/s00216-017-0345-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/16/2017] [Accepted: 03/28/2017] [Indexed: 10/19/2022]
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86
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Wan JCM, Massie C, Garcia-Corbacho J, Mouliere F, Brenton JD, Caldas C, Pacey S, Baird R, Rosenfeld N. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer 2017; 17:223-238. [PMID: 28233803 DOI: 10.1038/nrc.2017.7] [Citation(s) in RCA: 1537] [Impact Index Per Article: 219.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Improvements in genomic and molecular methods are expanding the range of potential applications for circulating tumour DNA (ctDNA), both in a research setting and as a 'liquid biopsy' for cancer management. Proof-of-principle studies have demonstrated the translational potential of ctDNA for prognostication, molecular profiling and monitoring. The field is now in an exciting transitional period in which ctDNA analysis is beginning to be applied clinically, although there is still much to learn about the biology of cell-free DNA. This is an opportune time to appraise potential approaches to ctDNA analysis, and to consider their applications in personalized oncology and in cancer research.
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Affiliation(s)
- Jonathan C M Wan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
| | - Charles Massie
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
| | - Javier Garcia-Corbacho
- Clinical Trials Unit, Clinic Institute of Haematological and Oncological Diseases, Hospital Clinic de Barcelona, IDIBAPs, Carrer de Villarroel, 170 Barcelona 08036, Spain
| | - Florent Mouliere
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
| | - James D Brenton
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Simon Pacey
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Richard Baird
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
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87
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Letendre JA, Goggs R. Measurement of plasma cell-free DNA concentrations in dogs with sepsis, trauma, and neoplasia. J Vet Emerg Crit Care (San Antonio) 2017; 27:307-314. [PMID: 28295988 DOI: 10.1111/vec.12592] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/04/2015] [Accepted: 11/08/2015] [Indexed: 01/02/2023]
Abstract
OBJECTIVES To determine if cell-free DNA (cfDNA) was identifiable in canine plasma, to evaluate 3 techniques for the measurement of plasma cfDNA concentrations in dogs presented to an emergency service, and to compare the plasma cfDNA concentrations of healthy dogs to those with sepsis, trauma, and neoplasia. DESIGN Retrospective study of banked canine plasma samples collected between May 2014 and December 2014. SETTING Dogs presented to the emergency service of a university veterinary teaching hospital. ANIMALS Plasma cfDNA was measured on residual plasma samples obtained from 15 dogs with sepsis, 15 dogs with moderate-severe trauma, 15 dogs diagnosed with a sarcoma. Plasma cfDNA was also measured in 15 healthy dogs. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Assay linearity, repeatability, and reproducibility were evaluated. Quantification of cfDNA was performed in duplicate on diluted citrated plasma and following DNA purification using 2 fluorescence assays (SYBR-Gold; Quant-iT) and by ultraviolet absorbance spectroscopy. Fluorescence intensities (FIs) were converted to cfDNA concentrations using standard curves. Median FI values and cfDNA concentrations were compared to healthy controls using the Kruskal-Wallis test, with adjustment for multiple comparisons. Alpha was set at 0.05. Both assays had excellent linearity, and acceptable repeatability and reproducibility. Compared to controls, plasma cfDNA concentrations were significantly increased in dogs with sepsis or moderate-severe trauma with both assays (P ≤ 0.003). Dogs with neoplasia had significantly increased cfDNA concentrations with the Quant-iT assay only (P = 0.003). When measurements were performed on purified DNA, only dogs with moderate-severe trauma had significantly increased cfDNA concentrations (P < 0.001; SYBR-Gold assay). CONCLUSIONS cfDNA can be readily identified in canine plasma using 2 fluorescence assays. DNA extraction offers no advantage over direct measurement. Compared to healthy controls, dogs with sepsis or moderate-severe trauma have significantly increased plasma cfDNA concentrations.
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Affiliation(s)
- Jo-Annie Letendre
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853
| | - Robert Goggs
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853
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88
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Lu JL, Liang ZY. Circulating free DNA in the era of precision oncology: Pre- and post-analytical concerns. Chronic Dis Transl Med 2016; 2:223-230. [PMID: 29063046 PMCID: PMC5643833 DOI: 10.1016/j.cdtm.2016.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Indexed: 02/06/2023] Open
Abstract
Cancer treatment has entered the era of precision medicine, where knowledge of a patient's genetic profile is used to facilitate early diagnosis, drug selection, prognosis, prediction of drug responsiveness, the onset of secondary resistance, and relapse. Circulating free DNA (cfDNA) has emerged as an ideal source of genetic information for cancer patients, and numerous studies have explored its validity in various clinical applications. However, clinical implementation of cfDNA-based tests has been slow. In this review, we addressed some of the pre- and post-analytical issues regarding cfDNA tests. First, we summarized the characteristics of cfDNA and reviewed the methods used to identify tumor-derived cfDNA from the pool of total cfDNA. Second, we described the procedures used to extract cfDNA, which have a great impact on representativeness and yield. Finally, we discussed our thoughts on the validation of cfDNA-based tests and the reporting of test results amid drastic limitations.
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Affiliation(s)
| | - Zhi-Yong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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89
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A Comparison of Cell-Free DNA Isolation Kits: Isolation and Quantification of Cell-Free DNA in Plasma. J Mol Diagn 2016; 19:162-168. [PMID: 27865784 DOI: 10.1016/j.jmoldx.2016.09.009] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/02/2016] [Accepted: 09/16/2016] [Indexed: 12/13/2022] Open
Abstract
The analysis of cell-free DNA (cfDNA) as a sensitive biomarker for cancer diagnosis and monitoring has resulted in a need for efficient and standardized cfDNA isolation. In this study, we compared the isolation efficiency of the QIAamp circulating nucleic acid kit (QIA) with four other cfDNA isolation kits: the PME free-circulating DNA Extraction Kit (PME), the Maxwell RSC ccfDNA Plasma Kit (RSC), the EpiQuick Circulating Cell-Free DNA Isolation Kit (EQ), and two consecutive versions of the NEXTprep-Mag cfDNA Isolation Kit (NpMV1/2). cfDNA was isolated from 10 plasma samples, of which five contained KRAS mutated cell-free tumor DNA (ctDNA). Digital droplet PCR was used to quantify the total cfDNA concentration as well as the KRAS mutated ctDNA fraction. cfDNA integrity was assessed with real-time quantitative PCR. The QIA and the RSC kits displayed similar isolation efficiencies of both KRAS mutated ctDNA and nonmutated cfDNA, whereas the yield generated by the PME and NpMV2 kits was significantly lower. Real-time quantitative PCR indicated the presence of digital droplet PCR inhibiting agents in the eluates of the NpMV1 and EQ kits. To conclude, this study presents two highly efficient isolation kits for cfDNA isolation, of which the RSC kit has the advantage of a fully automated protocol over the labor-intensive QIA kit.
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90
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Betsou F, Bulla A, Cho SY, Clements J, Chuaqui R, Coppola D, De Souza Y, De Wilde A, Grizzle W, Guadagni F, Gunter E, Heil S, Hodgkinson V, Kessler J, Kiehntopf M, Kim HS, Koppandi I, Shea K, Singh R, Sobel M, Somiari S, Spyropoulos D, Stone M, Tybring G, Valyi-Nagy K, Van den Eynden G, Wadhwa L. Assays for Qualification and Quality Stratification of Clinical Biospecimens Used in Research: A Technical Report from the ISBER Biospecimen Science Working Group. Biopreserv Biobank 2016; 14:398-409. [PMID: 27046294 PMCID: PMC5896556 DOI: 10.1089/bio.2016.0018] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
This technical report presents quality control (QC) assays that can be performed in order to qualify clinical biospecimens that have been biobanked for use in research. Some QC assays are specific to a disease area. Some QC assays are specific to a particular downstream analytical platform. When such a qualification is not possible, QC assays are presented that can be performed to stratify clinical biospecimens according to their biomolecular quality.
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Affiliation(s)
- Fay Betsou
- Integrated BioBank of Luxemburg (IBBL), Luxembourg, Luxembourg
| | - Alexandre Bulla
- Biotheque-SML, Division of Genetics and Laboratory Medicine (DMGL), University Hospital of Geneva, Geneva, Switzerland
| | - Sang Yun Cho
- National Biobank of Korea, Cheongju, South Korea
| | - Judith Clements
- Australian Prostate Cancer Bioresource/Queensland University of Technology, Brisbane, Australia
| | - Rodrigo Chuaqui
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis (DCTD), National Cancer Institute, Rockville, Maryland
| | - Domenico Coppola
- Moffitt Cancer Center, Department of Anatomic Pathology, University of South Florida, Tampa, Florida
| | - Yvonne De Souza
- University of California, San Francisco, AIDS Specimen Bank, San Francisco, California
| | | | | | | | | | - Stacey Heil
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Verity Hodgkinson
- Cancer Research Division, Cancer Council NSW, Woolloomooloo, Australia
| | | | | | - Hee Sung Kim
- Department of Pathology, Chung-Ang University College of Medicine, Dongjak-gu, South Korea
| | | | | | - Rajeev Singh
- Houston Methodist Research Institute, Biorepository, Houston, Texas
| | - Marc Sobel
- American Society for Investigative Pathology, Bethesda, Maryland
| | - Stella Somiari
- Biobank and Biospecimen Science Research, Windber Research Institute, Windber, Pennsylvania
| | - Demetri Spyropoulos
- Department of Pathology and Laboratory Medicine, Children's Research Institute, Medical University of South Carolina, Charleston, South Carolina
| | - Mars Stone
- Blood Systems Research Institute, San Francisco, California
| | | | - Klara Valyi-Nagy
- University of Illinois Biorepository, Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
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91
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Lee H, Jeon S, Seo JS, Goh SH, Han JY, Cho Y. A novel strategy for highly efficient isolation and analysis of circulating tumor-specific cell-free DNA from lung cancer patients using a reusable conducting polymer nanostructure. Biomaterials 2016; 101:251-7. [DOI: 10.1016/j.biomaterials.2016.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/01/2016] [Accepted: 06/02/2016] [Indexed: 01/05/2023]
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92
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Vu BT, Tan Le D, Van Pham P. Liquid biopsies: tumour diagnosis and treatment monitoring. BIOMEDICAL RESEARCH AND THERAPY 2016. [DOI: 10.7603/s40730-016-0035-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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93
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Alanio A, Sturny-Leclère A, Benabou M, Guigue N, Bretagne S. Variation in copy number of the 28S rDNA of Aspergillus fumigatus measured by droplet digital PCR and analog quantitative real-time PCR. J Microbiol Methods 2016; 127:160-163. [DOI: 10.1016/j.mimet.2016.06.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 06/11/2016] [Accepted: 06/13/2016] [Indexed: 10/21/2022]
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94
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Sorber L, Zwaenepoel K, Deschoolmeester V, Van Schil PEY, Van Meerbeeck J, Lardon F, Rolfo C, Pauwels P. Circulating cell-free nucleic acids and platelets as a liquid biopsy in the provision of personalized therapy for lung cancer patients. Lung Cancer 2016; 107:100-107. [PMID: 27180141 DOI: 10.1016/j.lungcan.2016.04.026] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/29/2016] [Accepted: 04/30/2016] [Indexed: 12/12/2022]
Abstract
Lung cancer is the predominant cause of cancer-related mortality in the world. The majority of patients present with locally advanced or metastatic non-small-cell lung cancer (NSCLC). Treatment for NSCLC is evolving from the use of cytotoxic chemotherapy to personalized treatment based on molecular alterations. Unfortunately, the quality of the available tumor biopsy and/or cytology material is not always adequate to perform the necessary molecular testing, which has prompted the search for alternatives. This review examines the use of circulating cell-free nucleic acids (cfNA), consisting of both circulating cell-free (tumoral) DNA (cfDNA-ctDNA) and RNA (cfRNA), as a liquid biopsy in lung cancer. The development of sensitive and accurate techniques such as Next-Generation Sequencing (NGS); Beads, Emulsion, Amplification, and Magnetics (BEAMing); and Digital PCR (dPCR), have made it possible to detect the specific genetic alterations (e.g. EGFR mutations, MET amplifications, and ALK and ROS1 translocations) for which targeted therapies are already available. Moreover, the ability to detect and quantify these tumor mutations has enabled the follow-up of tumor dynamics in real time. Liquid biopsy offers opportunities to detect resistance mechanisms, such as the EGFR T790M mutation in the case of EGFR TKI use, at an early stage. Several studies have already established the predictive and prognostic value of measuring ctNA concentration in the blood. To conclude, using ctNA analysis as a liquid biopsy has many advantages and allows for a variety of clinical and investigational applications.
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Affiliation(s)
- L Sorber
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium.
| | - K Zwaenepoel
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
| | - V Deschoolmeester
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
| | - P E Y Van Schil
- Department of Thoracic and Vascular Surgery, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
| | - J Van Meerbeeck
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; Department of Thoracic Oncology/MOCA, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
| | - F Lardon
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - C Rolfo
- Oncology & Phase I Unit-Early Clinical Trials, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
| | - P Pauwels
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
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95
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Song J, Liu C, Bais S, Mauk MG, Bau HH, Greenberg RM. Molecular Detection of Schistosome Infections with a Disposable Microfluidic Cassette. PLoS Negl Trop Dis 2015; 9:e0004318. [PMID: 26720725 PMCID: PMC4700990 DOI: 10.1371/journal.pntd.0004318] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 12/01/2015] [Indexed: 12/23/2022] Open
Abstract
Parasitic helminths such as schistosomes, as well as filarial and soil-transmitted nematodes, are estimated to infect at least a billion people worldwide, with devastating impacts on human health and economic development. Diagnosis and monitoring of infection dynamics and efficacy of treatment depend almost entirely on methods that are inaccurate, labor-intensive, and unreliable. These shortcomings are amplified and take on added significance in mass drug administration programs, where measures of effectiveness depend on accurate monitoring of treatment success (or failure), changes in disease transmission rates, and emergence of possible drug resistance. Here, we adapt isothermal molecular assays such as loop-mediated isothermal amplification (LAMP) to a simple, hand-held, custom-made field-ready microfluidic device that allows sensitive and specific detection of schistosome cell-free nucleic acids in serum and plasma (separated with a point-of-care plasma separator) from Schistosoma mansoni-infected mice. Cell-free S. mansoni DNA was detected with our device without prior extraction from blood. Our chip exhibits high sensitivity (~2 x 10(-17) g/μL), with a positive signal for S. mansoni DNA detectable as early as one week post infection, several weeks before parasite egg production commences. These results indicate that incorporation of isothermal amplification strategies with our chips could represent a strategy for rapid, simple, low-cost diagnosis of both pre-patent and chronic schistosome infections as well as potential monitoring of treatment efficacy.
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Affiliation(s)
- Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Changchun Liu
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Swarna Bais
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael G. Mauk
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Haim H. Bau
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Robert M. Greenberg
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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96
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Identification of Predictive Early Biomarkers for Sterile-SIRS after Cardiovascular Surgery. PLoS One 2015; 10:e0135527. [PMID: 26263001 PMCID: PMC4532358 DOI: 10.1371/journal.pone.0135527] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 07/22/2015] [Indexed: 12/21/2022] Open
Abstract
Systemic inflammatory response syndrome (SIRS) is a common complication after cardiovascular surgery that in severe cases can lead to multiple organ dysfunction syndrome and even death. We therefore set out to identify reliable early biomarkers for SIRS in a prospective small patient study for timely intervention. 21 Patients scheduled for planned cardiovascular surgery were recruited in the study, monitored for signs of SIRS and blood samples were taken to investigate biomarkers at pre-assigned time points: day of admission, start of surgery, end of surgery, days 1, 2, 3, 5 and 8 post surgery. Stored plasma and cryopreserved blood samples were analyzed for cytokine expression (IL1β, IL2, IL6, IL8, IL10, TNFα, IFNγ), other pro-inflammatory markers (sCD163, sTREM-1, ESM-1) and response to endotoxin. Acute phase proteins CRP, PCT and pro-inflammatory cytokines IL6 and IL8 were significantly increased (p<0.001) at the end of surgery in all patients but could not distinguish between groups. Normalization of samples revealed significant increases in IL1β changes (p<0.05) and decreased responses to endotoxin (p<0.01) in the SIRS group at the end of surgery. Soluble TREM-1 plasma concentrations were significantly increased in patients with SIRS (p<0.01). This small scale patient study could show that common sepsis markers PCT, CRP, IL6 and TNFα had low predictive value for early diagnosis of SIRS after cardiovascular surgery. A combination of normalized IL1β plasma levels, responses to endotoxin and soluble TREM-1 plasma concentrations at the end of surgery are predictive markers of SIRS development in this small scale study and could act as an indicator for starting early therapeutic interventions.
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97
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Mouliere F, Rosenfeld N. Circulating tumor-derived DNA is shorter than somatic DNA in plasma. Proc Natl Acad Sci U S A 2015; 112:3178-9. [PMID: 25733911 PMCID: PMC4371901 DOI: 10.1073/pnas.1501321112] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Florent Mouliere
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
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98
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Abstract
Abstract
BACKGROUND
Targeted therapies have markedly changed the treatment of cancer over the past 10 years. However, almost all tumors acquire resistance to systemic treatment as a result of tumor heterogeneity, clonal evolution, and selection. Although genotyping is the most currently used method for categorizing tumors for clinical decisions, tumor tissues provide only a snapshot, or are often difficult to obtain. To overcome these issues, methods are needed for a rapid, cost-effective, and noninvasive identification of biomarkers at various time points during the course of disease. Because cell-free circulating tumor DNA (ctDNA) is a potential surrogate for the entire tumor genome, the use of ctDNA as a liquid biopsy may help to obtain the genetic follow-up data that are urgently needed.
CONTENT
This review includes recent studies exploring the diagnostic, prognostic, and predictive potential of ctDNA as a liquid biopsy in cancer. In addition, it covers biological and technical aspects, including recent advances in the analytical sensitivity and accuracy of DNA analysis as well as hurdles that have to be overcome before implementation into clinical routine.
SUMMARY
Although the analysis of ctDNA is a promising area, and despite all efforts to develop suitable tools for a comprehensive analysis of tumor genomes from plasma DNA, the liquid biopsy is not yet routinely used as a clinical application. Harmonization of preanalytical and analytical procedures is needed to provide clinical standards to validate the liquid biopsy as a clinical biomarker in well-designed and sufficiently powered multicenter studies.
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Affiliation(s)
- Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Peter Ulz
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jochen B Geigl
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
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99
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Karlsson K, Sahlin E, Iwarsson E, Westgren M, Nordenskjöld M, Linnarsson S. Amplification-free sequencing of cell-free DNA for prenatal non-invasive diagnosis of chromosomal aberrations. Genomics 2014; 105:150-8. [PMID: 25543032 DOI: 10.1016/j.ygeno.2014.12.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 12/10/2014] [Accepted: 12/16/2014] [Indexed: 11/15/2022]
Abstract
Cell-free DNA has been used for fetal rhesus factor and sex determination, fetal aneuploidy screening, cancer diagnostics and monitoring, and other applications. However current methods of using cell free DNA require amplification, which leads to allelic dropout and bias especially when starting with small amounts of DNA. Here we describe an amplification-free method for sequencing of cell-free DNA, even from low levels of starting material. We evaluated this method in the context of prenatal diagnosis of fetal aneuploidy and compared it with a PCR-based library preparation method as well as a recently described method using unique molecular identifiers (UMI). All methods performed well, however coverage was increased by the amplification-free method and GC-induced bias was reduced by both the amplification-free method and the UMI method. Future diagnostic applications including whole genome sequencing of cell-free DNA will benefit from amplification-free sequencing.
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Affiliation(s)
- Kasper Karlsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 1, SE-171 77 Stockholm, Sweden
| | - Ellika Sahlin
- Clinical Genetics Unit, Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital Solna, 17176 Stockholm, Sweden
| | - Erik Iwarsson
- Clinical Genetics Unit, Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital Solna, 17176 Stockholm, Sweden
| | - Magnus Westgren
- Karolinska Institutet, Department of Obstet Gynecol, Division of Clinical Science, Intervention and Technology, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Clinical Genetics Unit, Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital Solna, 17176 Stockholm, Sweden
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 1, SE-171 77 Stockholm, Sweden.
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100
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Lin Y, Wang X, Jin H. EGFR-TKI resistance in NSCLC patients: mechanisms and strategies. Am J Cancer Res 2014; 4:411-435. [PMID: 25232485 PMCID: PMC4163608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 08/16/2014] [Indexed: 06/03/2023] Open
Abstract
The epidermal growth factor receptor (EGFR) is a kind of receptor tyrosine kinase (RTK) that plays a critical role in the initiation and development of malignant tumors via modulating downstream signaling pathways. In non-small cell lung cancer (NSCLC), the activating mutations located in the tyrosine kinase domains of EGFR have been demonstrated in multiple researches as the "Achilles' heel" of this deadly disease since they could be well-targeted by epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs). However, it's still too early to celebrate since the first-generation EGFR-TKIs such as gefitinib and erlotinib have only achieved limited clinical benefits and acquired resistance to this kind of drugs occurred inevitably in almost all the NSCLC patients. In order to make the most of EGFR-TKIs and develop more effective regimens for the NSCLC patients, researchers majoring in different aspects start a battle against EGFR-TKI resistance. Challenging as it is, we still progress stably and step firmly toward the final victory. This review will summarize the major mechanisms of acquired resistance to EGFR-TKIs, and then discuss the development of rationally designed molecular target drugs in accordance with each mechanism, in the hope of shedding light on the great achievements we have obtained and tough obstacles we have to overcome in the battle against this deadly disease.
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Affiliation(s)
- Yuxin Lin
- Department of Medical Oncology, Sir Runrun Shaw Hospital, Medical School of Zhejiang University Hangzhou, China
| | - Xian Wang
- Department of Medical Oncology, Sir Runrun Shaw Hospital, Medical School of Zhejiang University Hangzhou, China
| | - Hongchuan Jin
- Department of Medical Oncology, Sir Runrun Shaw Hospital, Medical School of Zhejiang University Hangzhou, China
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