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Chu AA, Gao HX, Wu TT, Zhang Z. Survival outcomes correlate with the level of cell-free circulating DNA in ST-elevation myocardial infarction. JOURNAL OF RESEARCH IN MEDICAL SCIENCES : THE OFFICIAL JOURNAL OF ISFAHAN UNIVERSITY OF MEDICAL SCIENCES 2024; 29:8. [PMID: 38524748 PMCID: PMC10956566 DOI: 10.4103/jrms.jrms_335_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/04/2023] [Accepted: 10/03/2023] [Indexed: 03/26/2024]
Abstract
Background Myocardial infarction (MI) can lead to higher cellular damage, making cell-free DNA (cfDNA) a potential biomarker for assessing disease severity. The aim of this study is to evaluate survival predictions using cfDNA measurements and assess its correlation with MI. Materials and Methods A direct fluorescence assay was employed to measure cfDNA content in the blood samples of participants. The inclusion criteria included patients who gave informed consent, suffering from ST-elevation myocardial infraction (STEMI) based on established diagnostic criteria (joint ESC/ACC guidelines), between the age of 18 and 80 years old, and had elevated troponin biomarker levels. The study included 150 patients diagnosed with STEMI and 50 healthy volunteers as controls. Serial monitoring of patients was conducted to track their postdisease status. The rate of change of cfDNA was calculated and daily measurements for 7 days were recorded. Results Mean levels of cfDNA were found to be 5.93 times higher in patients with STEMI compared to healthy controls, providing clear evidence of a clinical correlation between cfDNA and STEMI. Patients were further categorized based on their survival status within a 90-day period. The study observed a strong predictive relationship between the rate of change of cfDNA during daily measurements and survival outcomes. To assess its predictive capability, a receiver operating characteristics (ROC) curve analysis was performed. The ROC analysis identified an optimal cutoff value of 2.50 for cfDNA, with a sensitivity of 81.5% and specificity of 74.0% in predicting disease outcomes. Conclusion This study demonstrates a robust association between cfDNA and STEMI, indicating that cfDNA levels can be a valuable early prognostic factor for patients. Serial measurements of cfDNA during early disease onset hold promise as an effective approach for predicting survival outcomes in MI patients.
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Affiliation(s)
- Ai-Ai Chu
- Heart Center, The First Affiliated Hospital, Lanzhou University, Lanzhou, China
- Department of Cardiology, Gansu Provincial People’s Hospital, Lanzhou, China
| | - Han-Xiang Gao
- Heart Center, The First Affiliated Hospital, Lanzhou University, Lanzhou, China
| | - Ting-Ting Wu
- Heart Center, The First Affiliated Hospital, Lanzhou University, Lanzhou, China
| | - Zheng Zhang
- Heart Center, The First Affiliated Hospital, Lanzhou University, Lanzhou, China
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2
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Tan E, Liu D, Perry L, Zhu J, Cid-Serra X, Deane A, Yeo C, Ajani A. Cell-free DNA as a potential biomarker for acute myocardial infarction: A systematic review and meta-analysis. IJC HEART & VASCULATURE 2023; 47:101246. [PMID: 37560328 PMCID: PMC10407200 DOI: 10.1016/j.ijcha.2023.101246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Tissue necrosis releases cell-free deoxyribonucleic acid (cfDNA), leading to rapid increases in plasma concentration with clearance independent of kidney function. AIM To explore the diagnostic role of cfDNA in acute myocardial infarction (AMI). METHODS This systematic review and meta-analysis included studies of cfDNA in patients with AMI and a comparator group without AMI. The quality assessment of diagnostic accuracy studies-2 (QUADAS-2) tool was used, with AMI determined from the criteria of the original study. Standardised mean differences (SMD) were obtained using a random-effects inverse variance model. Heterogeneity was reported as I2. Pooled sensitivity and specificity were computed using a bivariate model. The area under the curve (AUC) was estimated from a hierarchical summary receiver operating characteristics curve. RESULTS Seventeen studies were identified involving 1804 patients (n = 819 in the AMI group, n = 985 in the comparator group). Circulating cfDNA concentrations were greater in the AMI group (SMD 3.47 (95%CI: 2.54-4.41, p < 0.001)). The studies were of variable methodological quality with substantial heterogeneity (I2 = 98%, p < 0.001), possibly due to the differences in cfDNA quantification methodologies (Chi2 25.16, p < 0.001, I2 = 92%). Diagnostic accuracy was determined using six studies (n = 804), which yielded a sensitivity of 87% (95%CI: 72%-95%) and specificity of 96% (95%CI: 92%-98%). The AUC was 0.96 (95%CI: 0.93-0.98). Two studies reported a relationship between peak cfDNA and peak troponin. No studies reported data for patients with pre-existing kidney impairment. CONCLUSION Plasma cfDNA appears to be a reliable biomarker of myocardial injury. Inferences from existing results are limited owing to methodology heterogeneity.
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Affiliation(s)
- Elinor Tan
- Department of Intensive Care Unit, The Royal Melbourne Hospital, Melbourne, Australia
| | - Daniel Liu
- Department of Anesthesiology, The Royal Melbourne Hospital, Melbourne, Australia
| | - Luke Perry
- Department of Anesthesiology, The Royal Melbourne Hospital, Melbourne, Australia
| | - John Zhu
- Department of General Medicine, The Royal Melbourne Hospital, Melbourne, Australia
| | - Ximena Cid-Serra
- Department of General Medicine, The Royal Melbourne Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
| | - Adam Deane
- Department of Intensive Care Unit, The Royal Melbourne Hospital, Melbourne, Australia
| | - Colin Yeo
- Department of Cardiology, Changi General Hospital, Singapore
| | - Andrew Ajani
- Department of Cardiology, The Royal Melbourne Hospital, Melbourne, Australia
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3
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Cuadrat RRC, Kratzer A, Arnal HG, Rathgeber A, Wreczycka K, Blume A, Gündüz IB, Ebenal V, Mauno T, Osberg B, Moobed M, Hartung J, Jakobs K, Seppelt C, Meteva D, Haghikia A, Leistner D, Landmesser U, Akalin A. Cardiovascular disease biomarkers derived from circulating cell-free DNA methylation. NAR Genom Bioinform 2023; 5:lqad061. [PMID: 37388821 PMCID: PMC10304763 DOI: 10.1093/nargab/lqad061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023] Open
Abstract
Acute coronary syndrome (ACS) remains a major cause of worldwide mortality. The syndrome occurs when blood flow to the heart muscle is decreased or blocked, causing muscle tissues to die or malfunction. There are three main types of ACS: Non-ST-elevation myocardial infarction, ST-elevation myocardial infarction, and unstable angina. The treatment depends on the type of ACS, and this is decided by a combination of clinical findings, such as electrocardiogram and plasma biomarkers. Circulating cell-free DNA (ccfDNA) is proposed as an additional marker for ACS since the damaged tissues can release DNA to the bloodstream. We used ccfDNA methylation profiles for differentiating between the ACS types and provided computational tools to repeat similar analysis for other diseases. We leveraged cell type specificity of DNA methylation to deconvolute the ccfDNA cell types of origin and to find methylation-based biomarkers that stratify patients. We identified hundreds of methylation markers associated with ACS types and validated them in an independent cohort. Many such markers were associated with genes involved in cardiovascular conditions and inflammation. ccfDNA methylation showed promise as a non-invasive diagnostic for acute coronary events. These methods are not limited to acute events, and may be used for chronic cardiovascular diseases as well.
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Affiliation(s)
| | | | | | - Anja C Rathgeber
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Katarzyna Wreczycka
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Alexander Blume
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Irem B Gündüz
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Veronika Ebenal
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Tiina Mauno
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Brendan Osberg
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Minoo Moobed
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Johannes Hartung
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Kai Jakobs
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Claudio Seppelt
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Universitätsklinikum Frankfurt am Main, Medizinische Klinik 3, Klinik für Kardiologie und Angiologie, Germany
| | - Denitsa Meteva
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Arash Haghikia
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - David M Leistner
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Universitätsklinikum Frankfurt am Main, Medizinische Klinik 3, Klinik für Kardiologie und Angiologie, Germany
| | - Ulf Landmesser
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Altuna Akalin
- To whom correspondence should be addressed. Tel: +49 30 94 060 42 71; Fax: +49 30 94 060 49 341;
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4
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Fisher IF, Shemer R, Dor Y. Epigenetic liquid biopsies: a novel putative biomarker in immunology and inflammation. Trends Immunol 2023; 44:356-364. [PMID: 37012121 DOI: 10.1016/j.it.2023.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
Immune and inflammatory processes occurring within tissues are often undetectable by blood cell counts, standard circulating biomarkers, or imaging, representing an unmet biomedical need. Here, we outline recent advances indicating that liquid biopsies can broadly inform human immune system dynamics. Nucleosome-size fragments of cell-free DNA (cfDNA) released from dying cells into blood contain rich epigenetic information such as methylation, fragmentation, and histone mark patterns. This information allows to infer the cfDNA cell of origin, as well as pre-cell death gene expression patterns. We propose that the analysis of epigenetic features of immune cell-derived cfDNA can shed light on immune cell turnover dynamics in healthy people, and inform the study and diagnosis of cancer, local inflammation, infectious or autoimmune diseases, as well as responses to vaccination.
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5
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Lower Circulating Cell-Free Mitochondrial DNA Is Associated with Heart Failure in Type 2 Diabetes Mellitus Patients. CARDIOGENETICS 2023. [DOI: 10.3390/cardiogenetics13010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Cell-free nuclear (cf-nDNA) and mitochondrial (cf-mDNA) DNA are released from damaged cells in type 2 diabetes mellitus (T2DM) patients, contributing to adverse cardiac remodeling, vascular dysfunction, and inflammation. The purpose of this study was to correlate the presence and type of cf-DNAs with HF in T2DM patients. A total of 612 T2DM patients were prescreened by using a local database, and 240 patients (120 non-HF and 120 HF individuals) were ultimately selected. The collection of medical information, including both echocardiography and Doppler imagery, as well as the assessment of biochemistry parameters and the circulating biomarkers, were performed at baseline. The N-terminal brain natriuretic pro-peptide (NT-proBNP) and cf-nDNA/cf-mtDNA levels were measured via an ELISA kit and real-time quantitative PCR tests, respectively. We found that HF patients possessed significantly higher levels of cf-nDNA (9.9 ± 2.5 μmol/L vs. 5.4 ± 2.7 μmol/L; p = 0.04) and lower cf-mtDNA (15.7 ± 3.3 μmol/L vs. 30.4 ± 4.8 μmol/L; p = 0.001) than those without HF. The multivariate log regression showed that the discriminative potency of cf-nDNA >7.6 μmol/L (OR = 1.07; 95% CI = 1.03–1.12; p = 0.01) was higher that the NT-proBNP (odds ratio [OR] = 1.10; 95% confidence interval [CI] = 1.04–1.19; p = 0.001) for HF. In conclusion, we independently established that elevated levels of cf-nDNA, originating from NT-proBNP, were associated with HF in T2DM patients.
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6
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Abstract
Cardiovascular disease (CVD) remains the major cause of morbidity and mortality globally. Accumulating evidence indicates that coronary heart disease (CHD) contributes to the majority of cardiovascular deaths. With the development of precision medicine, the diagnosis and treatment of coronary heart disease are becoming more refined and individualized. Molecular diagnosis technology and individualized treatment are gradually applied to the clinical diagnosis and treatment of CHD. It is great significance to seek sensitive biological indicators to help early diagnosis and improve prognosis of CHD. Liquid biopsy is a minimally invasive technique, which is widely used to detect molecular biomarkers of tumors without invasive biopsy. Compared with the field of oncology, it is not easy to get the diseased tissue in CVD, especially CHD. Therefore, the idea of "fluid biopsy" is very attractive, and its progress may provide new and useful noninvasive indicators for CHD. By analyzing circulating cells or their products in blood, saliva, and urine samples, we can investigate the molecular changes that occur in each patient at a specific point in time, thus continuously monitoring the evolution of CHD. For example, the assessment of cell-free DNA (cfDNA) levels may help predict the severity of acute myocardial infarction and diagnose heart transplant rejection. Moreover, the unmethylated FAM101A gene may specifically track the cfDNA derived from cardiomyocyte death, which provides a powerful diagnostic biomarker for apoptosis during ischemia. In addition, the changes of plasma circulating miR-92 levels may predict the occurrence of acute coronary syndrome (ACS) onset in patients with diabetes. Liquid biopsy can reflect the disease state through patients' body fluids and may noninvasively provide dynamic and rich molecular information related to CHD. It has great application potential in early warning and auxiliary diagnosis, real-time monitoring of curative effect, medication guidance and exploration of drug resistance mechanism, prognosis judgment, and risk classification of CHD. This chapter will review the latest progress of liquid biopsy in accurate diagnosis and treatment of CHD, meanwhile explore the application status and clinical prospect of liquid biopsy in CHD, in order to improve the importance of precision medicine and personalized treatment in this field.
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Affiliation(s)
- Wenyan Zhu
- Chongqing Engineering Research Center of Pharmaceutical Sciences, Chongqing Medical and Pharmaceutical College, Chongqing, China
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Xiang Li
- Department of Cardiology, the First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
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7
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Xu X, Wu Y, Xu S, Yin Y, Ageno W, De Stefano V, Zhao Q, Qi X. Clinical significance of neutrophil extracellular traps biomarkers in thrombosis. Thromb J 2022; 20:63. [PMID: 36224604 PMCID: PMC9555260 DOI: 10.1186/s12959-022-00421-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/25/2022] [Indexed: 11/10/2022] Open
Abstract
Neutrophil extracellular traps (NETs) may be associated with the development of thrombosis. Experimental studies have confirmed the presence of NETs in thrombi specimens and potential role of NETs in the mechanisms of thrombosis. Clinical studies also have demonstrated significant changes in the levels of serum or plasma NETs biomarkers, such as citrullinated histones, myeloperoxidase, neutrophil elastase, nucleosomes, DNA, and their complexes in patients with thrombosis. This paper aims to comprehensively review the currently available evidence regarding the change in the levels of NETs biomarkers in patients with thrombosis, summarize the role of NETs and its biomarkers in the development and prognostic assessment of venous thromboembolism, coronary artery diseases, ischemic stroke, cancer-associated thromboembolism, and coronavirus disease 2019-associated thromboembolism, explore the potential therapeutic implications of NETs, and further discuss the shortcomings of existing NETs biomarkers in serum and plasma and their detection methods.
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Affiliation(s)
- Xiangbo Xu
- Department of Gastroenterology, General Hospital of Northern Theater Command (the Teaching School of Shenyang Pharmaceutical University), Shenyang, China.,Department of Life Science and Biochemistry, Shenyang Pharmaceutical University, Shenyang, China.,Department of Pharmacy, General Hospital of Northern Theater Command (the Teaching School of Shenyang Pharmaceutical University), Shenyang, China
| | - Yuting Wu
- Department of Life Science and Biochemistry, Shenyang Pharmaceutical University, Shenyang, China.,Department of Pharmacy, General Hospital of Northern Theater Command (the Teaching School of Shenyang Pharmaceutical University), Shenyang, China
| | - Shixue Xu
- Department of Gastroenterology, General Hospital of Northern Theater Command (the Teaching School of Shenyang Pharmaceutical University), Shenyang, China
| | - Yue Yin
- Department of Gastroenterology, General Hospital of Northern Theater Command (the Teaching School of Shenyang Pharmaceutical University), Shenyang, China
| | - Walter Ageno
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Valerio De Stefano
- Department of Radiological and Hematological Sciences, Catholic University, Fondazione Policlinico A. Gemelli IRCCS, Section of Hematology, Rome, Italy
| | - Qingchun Zhao
- Department of Life Science and Biochemistry, Shenyang Pharmaceutical University, Shenyang, China. .,Department of Pharmacy, General Hospital of Northern Theater Command (the Teaching School of Shenyang Pharmaceutical University), Shenyang, China.
| | - Xingshun Qi
- Department of Gastroenterology, General Hospital of Northern Theater Command (the Teaching School of Shenyang Pharmaceutical University), Shenyang, China. .,Department of Life Science and Biochemistry, Shenyang Pharmaceutical University, Shenyang, China.
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8
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Kananen L, Hurme M, Bürkle A, Moreno-Villanueva M, Bernhardt J, Debacq-Chainiaux F, Grubeck-Loebenstein B, Malavolta M, Basso A, Piacenza F, Collino S, Gonos ES, Sikora E, Gradinaru D, Jansen EHJM, Dollé MET, Salmon M, Stuetz W, Weber D, Grune T, Breusing N, Simm A, Capri M, Franceschi C, Slagboom E, Talbot D, Libert C, Raitanen J, Koskinen S, Härkänen T, Stenholm S, Ala-Korpela M, Lehtimäki T, Raitakari OT, Ukkola O, Kähönen M, Jylhä M, Jylhävä J. Circulating cell-free DNA in health and disease - the relationship to health behaviours, ageing phenotypes and metabolomics. GeroScience 2022; 45:85-103. [PMID: 35864375 PMCID: PMC9886738 DOI: 10.1007/s11357-022-00590-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/06/2022] [Indexed: 02/03/2023] Open
Abstract
Circulating cell-free DNA (cf-DNA) has emerged as a promising biomarker of ageing, tissue damage and cellular stress. However, less is known about health behaviours, ageing phenotypes and metabolic processes that lead to elevated cf-DNA levels. We sought to analyse the relationship of circulating cf-DNA level to age, sex, smoking, physical activity, vegetable consumption, ageing phenotypes (physical functioning, the number of diseases, frailty) and an extensive panel of biomarkers including blood and urine metabolites and inflammatory markers in three human cohorts (N = 5385; 17-82 years). The relationships were assessed using correlation statistics, and linear and penalised regressions (the Lasso), also stratified by sex.cf-DNA levels were significantly higher in men than in women, and especially in middle-aged men and women who smoke, and in older more frail individuals. Correlation statistics of biomarker data showed that cf-DNA level was higher with elevated inflammation (C-reactive protein, interleukin-6), and higher levels of homocysteine, and proportion of red blood cells and lower levels of ascorbic acid. Inflammation (C-reactive protein, glycoprotein acetylation), amino acids (isoleucine, leucine, tyrosine), and ketogenesis (3-hydroxybutyrate) were included in the cf-DNA level-related biomarker profiles in at least two of the cohorts.In conclusion, circulating cf-DNA level is different by sex, and related to health behaviour, health decline and metabolic processes common in health and disease. These results can inform future studies where epidemiological and biological pathways of cf-DNA are to be analysed in details, and for studies evaluating cf-DNA as a potential clinical marker.
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Affiliation(s)
- Laura Kananen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden. .,Faculty of Social Sciences (Health Sciences), and Gerontology Research Center, Tampere University, Tampere, Finland. .,Faculty of Medicine and Health Technology, and Gerontology Research Center, Tampere University, Tampere, Finland.
| | - Mikko Hurme
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, and Gerontology Research Center, Tampere University, Tampere, Finland
| | - Alexander Bürkle
- grid.9811.10000 0001 0658 7699Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - Maria Moreno-Villanueva
- grid.9811.10000 0001 0658 7699Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | | | - Florence Debacq-Chainiaux
- grid.6520.10000 0001 2242 8479URBC-Narilis, University of Namur, Rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Beatrix Grubeck-Loebenstein
- grid.5771.40000 0001 2151 8122Research Institute for Biomedical Aging Research, University of Innsbruck, Rennweg, 10, 6020 Innsbruck, Austria
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - Andrea Basso
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - Sebastiano Collino
- grid.5333.60000000121839049Nestlé Research, Nestlé Institute of Health Sciences, EPFL Innovation Park, 1015 Lausanne, Switzerland
| | - Efstathios S. Gonos
- grid.22459.380000 0001 2232 6894Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Ewa Sikora
- grid.419305.a0000 0001 1943 2944Laboratory of the Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur street, 02-093 Warsaw, Poland
| | - Daniela Gradinaru
- grid.8194.40000 0000 9828 7548Department of Biochemistry, Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Eugene H. J. M. Jansen
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Centre for Health Protection, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - Martijn E. T. Dollé
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Centre for Health Protection, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - Michel Salmon
- grid.425994.7Straticell, Science Park Crealys, Rue Jean Sonet 10, 5032 Les Isnes, Belgium
| | - Wolfgang Stuetz
- grid.9464.f0000 0001 2290 1502Institute of Nutritional Sciences (140), University of Hohenheim, 70593 Stuttgart, Germany
| | - Daniela Weber
- grid.418213.d0000 0004 0390 0098Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany
| | - Tilman Grune
- grid.418213.d0000 0004 0390 0098Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany ,grid.10420.370000 0001 2286 1424Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria ,grid.9464.f0000 0001 2290 1502Institute of Nutritional Medicine (180), University of Hohenheim, 70593 Stuttgart, Germany
| | - Nicolle Breusing
- grid.9464.f0000 0001 2290 1502Institute of Nutritional Medicine (180), University of Hohenheim, 70593 Stuttgart, Germany
| | - Andreas Simm
- grid.461820.90000 0004 0390 1701Department of Cardiothoracic Surgery, University Hospital Halle, Ernst-Grube Str. 40, 06120 Halle (Saale), Germany
| | - Miriam Capri
- grid.6292.f0000 0004 1757 1758DIMES- Department of Experimental, Diagnostic and Specialty Medicine,
Interdepartmental Center “Alma Mater Research Institute On Global Challenges and Climate Change (Alma Climate)”,
Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Claudio Franceschi
- grid.6292.f0000 0004 1757 1758DIMES- Department of Experimental, Diagnostic and Specialty Medicine,
Interdepartmental Center “Alma Mater Research Institute On Global Challenges and Climate Change (Alma Climate)”,
Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Eline Slagboom
- grid.10419.3d0000000089452978Section of Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Duncan Talbot
- Unilever Science and Technology, Beauty and Personal Care, Sharnbrook, UK
| | - Claude Libert
- grid.11486.3a0000000104788040Center for Inflammation Research, VIB, Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jani Raitanen
- grid.502801.e0000 0001 2314 6254Faculty of Social Sciences (Health Sciences), and Gerontology Research Center, Tampere University, Tampere, Finland
| | - Seppo Koskinen
- grid.14758.3f0000 0001 1013 0499National Institute for Health and Welfare, Helsinki, Finland
| | - Tommi Härkänen
- grid.14758.3f0000 0001 1013 0499National Institute for Health and Welfare, Helsinki, Finland
| | - Sari Stenholm
- grid.1374.10000 0001 2097 1371Department of Public Health, University of Turku and Turku University Hospital, Turku, Finland ,grid.1374.10000 0001 2097 1371Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Mika Ala-Korpela
- grid.10858.340000 0001 0941 4873Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland ,grid.10858.340000 0001 0941 4873Center for Life Course Health Research, University of Oulu, Oulu, Finland ,grid.9668.10000 0001 0726 2490NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Terho Lehtimäki
- grid.502801.e0000 0001 2314 6254Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Cardiovascular Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland ,grid.511163.10000 0004 0518 4910Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Olli T. Raitakari
- grid.1374.10000 0001 2097 1371Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland ,grid.1374.10000 0001 2097 1371Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland ,grid.410552.70000 0004 0628 215XDepartment of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Olavi Ukkola
- grid.10858.340000 0001 0941 4873Research Unit of Internal Medicine, Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Mika Kähönen
- grid.502801.e0000 0001 2314 6254Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Cardiovascular Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland ,grid.412330.70000 0004 0628 2985Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Marja Jylhä
- grid.502801.e0000 0001 2314 6254Faculty of Social Sciences (Health Sciences), and Gerontology Research Center, Tampere University, Tampere, Finland
| | - Juulia Jylhävä
- grid.4714.60000 0004 1937 0626Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden ,grid.502801.e0000 0001 2314 6254Faculty of Social Sciences (Health Sciences), and Gerontology Research Center, Tampere University, Tampere, Finland
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9
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Ren J, Jiang L, Liu X, Liao Y, Zhao X, Tang F, Yu H, Shao Y, Wang J, Wen L, Song L. Heart-specific DNA methylation analysis in plasma for the investigation of myocardial damage. J Transl Med 2022; 20:36. [PMID: 35062960 PMCID: PMC8780310 DOI: 10.1186/s12967-022-03234-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background Circulating cell-free DNA (cfDNA) can be released when myocardial damage occurs. Methods Here, we used the methylated CpG tandem amplification and sequencing (MCTA-seq) method for analyzing dynamic changes in heart-derived DNA in plasma samples from myocardial infarction (MI) patients. Results We identified six CGCGCGG loci showing heart-specific hypermethylation patterns. MCTA-seq deconvolution analysis combining these loci detected heart-released cfDNA in MI patients at hospital admission, and showed that the prominently elevated total cfDNA level after percutaneous coronary intervention (PCI) was derived from both the heart and white blood cells. Furthermore, for the top marker CORO6, we developed a digital droplet PCR (ddPCR) assay that clearly detected heart damage signals in cfDNA of MI patients at hospital admission. Conclusions Our study provides insights into MI pathologies and developed a new ddPCR assay for detecting myocardial damage in clinical applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03234-9.
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Affiliation(s)
- Jie Ren
- Biomedical Pioneering Innovation Center, School of Life Sciences, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, 100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Lin Jiang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100871, China.,National Clinical Research Center for Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100871, China
| | - Xiaomeng Liu
- Biomedical Pioneering Innovation Center, School of Life Sciences, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China.,Radiation Oncology Key Laboratory of Sichuan Province, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuhan Liao
- Biomedical Pioneering Innovation Center, School of Life Sciences, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, 100871, China
| | - Xueyan Zhao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100871, China.,National Clinical Research Center for Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100871, China
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, 100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Huimin Yu
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yibing Shao
- Department of Cardiology, Qingdao Municipal Hospital, Qingdao, Shandong, China
| | - Jizheng Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100871, China. .,National Clinical Research Center for Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100871, China.
| | - Lu Wen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China. .,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, 100871, China.
| | - Lei Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100871, China. .,National Clinical Research Center for Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100871, China.
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10
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Schneider L, Usherwood T, Tripathi A. A microfluidic platform for high-purity cell free DNA extraction from plasma for non-invasive prenatal testing. Prenat Diagn 2022; 42:240-253. [PMID: 35032044 DOI: 10.1002/pd.6092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/22/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Increase the yield and purity of cell-free DNA (cfDNA) extracted from plasma for non-invasive prenatal testing (NIPT) as inefficiencies in this extraction and purification can dramatically affect the sensitivity and specificity of the test. METHODS This work integrates cfDNA extraction from plasma with a microfluidic chip platform by combining magnetic bead-based extraction and electroosmotic flow on the microfluidic chip. Various wash buffers and voltage conditions were simulated using COMSOL Multiphysics Modeling and tested experimentally. RESULTS When performing the first wash step of this assay on the microfluidic chip with 300 V applied across the channel there was a six-fold increase in the A260 /A230 ratio showing a significant improvement (p value 0.0005) in the purity of the extracted sample all while maintaining a yield of 68.19%. These values are critical as a high yield results in more sample to analyze and an increase in A260 /A230 ratio corresponds to a decrease in salt contaminants such as guanidinium thiocyanate which can interfere with downstream processes during DNA library preparation and potentially hinder the NIPT screening results. CONCLUSIONS This technique has the potential to improve NIPT outcomes and other clinically relevant workflows that use cfDNA as an analyte such as cancer detection.
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Affiliation(s)
- Lindsay Schneider
- Center for Biomedical Engineering, Brown University, Providence, Rhode Island, USA
| | - Thomas Usherwood
- Center for Biomedical Engineering, Brown University, Providence, Rhode Island, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, Brown University, Providence, Rhode Island, USA
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11
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Sun HW, Dai SJ, Kong HR, Fan JX, Yang FY, Dai JQ, Jin YP, Yu GZ, Chen BC, Shi KQ. Accurate prediction of acute pancreatitis severity based on genome-wide cell free DNA methylation profiles. Clin Epigenetics 2021; 13:223. [PMID: 34915915 PMCID: PMC8680202 DOI: 10.1186/s13148-021-01217-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 12/12/2021] [Indexed: 01/15/2023] Open
Abstract
Background Patients with severe acute pancreatitis (SAP) have a high mortality, thus early diagnosis and interventions are critical for improving survival. However, conventional tests are limited in acute pancreatitis (AP) stratification. We aimed to assess AP severity by integrating the informative clinical measurements with cell free DNA (cfDNA) methylation markers. Methods One hundred and seventy-five blood samples were collected from 61 AP patients at multiple time points, plus 24 samples from healthy individuals. Genome-wide cfDNA methylation profiles of all samples were characterized with reduced representative bisulfite sequencing. Clinical blood tests covering 93 biomarkers were performed on AP patients within 24 h. SAP predication models were built based on cfDNA methylation and conventional blood biomarkers separately and in combination. Results We identified 565 and 59 cfDNA methylation markers informative for acute pancreatitis and its severity. These markers were used to develop prediction models for AP and SAP with area under the receiver operating characteristic of 0.92 and 0.81, respectively. Twelve blood biomarkers were systematically screened for a predictor of SAP with a sensitivity of 87.5% for SAP, and a specificity of 100% in mild acute pancreatitis, significantly higher than existing blood tests. An expanded model integrating 12 conventional blood biomarkers with 59 cfDNA methylation markers further improved the SAP prediction sensitivity to 92.2%. Conclusions These findings have demonstrated that accurate prediction of SAP by the integration of conventional and novel blood molecular markers, paving the way for early and effective SAP intervention through a non-invasive rapid diagnostic test. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01217-z.
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Affiliation(s)
- Hong-Wei Sun
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Sheng-Jie Dai
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hong-Ru Kong
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jie-Xiang Fan
- Translational Medicine Laboratory, Key Laboratory of Intelligent Critical Care and Life Support Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, No. 1 FanHai West Road, OuHai, Wenzhou, 325000, China
| | - Fang-Yuan Yang
- Translational Medicine Laboratory, Key Laboratory of Intelligent Critical Care and Life Support Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, No. 1 FanHai West Road, OuHai, Wenzhou, 325000, China
| | - Ju-Qing Dai
- Translational Medicine Laboratory, Key Laboratory of Intelligent Critical Care and Life Support Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, No. 1 FanHai West Road, OuHai, Wenzhou, 325000, China
| | - Yue-Peng Jin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Guan-Zhen Yu
- Translational Medicine Laboratory, Key Laboratory of Intelligent Critical Care and Life Support Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, No. 1 FanHai West Road, OuHai, Wenzhou, 325000, China
| | - Bi-Cheng Chen
- Translational Medicine Laboratory, Key Laboratory of Intelligent Critical Care and Life Support Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, No. 1 FanHai West Road, OuHai, Wenzhou, 325000, China
| | - Ke-Qing Shi
- Translational Medicine Laboratory, Key Laboratory of Intelligent Critical Care and Life Support Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, No. 1 FanHai West Road, OuHai, Wenzhou, 325000, China. .,Key Laboratory of Intelligent Critical Care and Life Support Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
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12
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Dhawan UK, Bhattacharya P, Narayanan S, Manickam V, Aggarwal A, Subramanian M. Hypercholesterolemia Impairs Clearance of Neutrophil Extracellular Traps and Promotes Inflammation and Atherosclerotic Plaque Progression. Arterioscler Thromb Vasc Biol 2021; 41:2598-2615. [PMID: 34348488 PMCID: PMC8454501 DOI: 10.1161/atvbaha.120.316389] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/26/2021] [Indexed: 01/02/2023]
Abstract
Objective: Hypercholesterolemia-induced NETosis and accumulation of neutrophil extracellular traps (NETs) in the atherosclerotic lesion exacerbates inflammation and is causally implicated in plaque progression. We investigated whether hypercholesterolemia additionally impairs the clearance of NETs mediated by endonucleases such as DNase1 and DNase1L3 and its implication in advanced atherosclerotic plaque progression. Approach and Results: Using a mouse model, we demonstrate that an experimental increase in the systemic level of NETs leads to a rapid increase in serum DNase activity, which is critical for the prompt clearance of NETs and achieving inflammation resolution. Importantly, hypercholesterolemic mice demonstrate an impairment in this critical NET-induced DNase response with consequent delay in the clearance of NETs and defective inflammation resolution. Administration of tauroursodeoxycholic acid, a chemical chaperone that relieves endoplasmic reticulum stress, rescued the hypercholesterolemia-induced impairment in the NET-induced DNase response suggesting a causal role for endoplasmic reticulum stress in this phenomenon. Correction of the defective DNase response with exogenous supplementation of DNase1 in Apoe-/- mice with advanced atherosclerosis resulted in a decrease in plaque NET content and significant plaque remodeling with decreased area of plaque necrosis and increased collagen content. From a translational standpoint, we demonstrate that humans with hypercholesterolemia have elevated systemic extracellular DNA levels and decreased plasma DNase activity. Conclusions: These data suggest that hypercholesterolemia impairs the NET-induced DNase response resulting in defective clearance and accumulation of NETs in the atherosclerotic plaque. Therefore, strategies aimed at rescuing this defect could be of potential therapeutic benefit in promoting inflammation resolution and atherosclerotic plaque stabilization.
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Affiliation(s)
- Umesh Kumar Dhawan
- Centre for Biochemical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom (U.K.D., M.S.)
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India (U.K.D., P.B., S.N., V.M., A.A., M.S.)
| | - Purbasha Bhattacharya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India (U.K.D., P.B., S.N., V.M., A.A., M.S.)
- Academy of Scientific and Innovative Research, Ghaziabad, India (P.B., A.A.)
| | - Sriram Narayanan
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India (U.K.D., P.B., S.N., V.M., A.A., M.S.)
| | - Vijayprakash Manickam
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India (U.K.D., P.B., S.N., V.M., A.A., M.S.)
| | - Ayush Aggarwal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India (U.K.D., P.B., S.N., V.M., A.A., M.S.)
- Academy of Scientific and Innovative Research, Ghaziabad, India (P.B., A.A.)
| | - Manikandan Subramanian
- Centre for Biochemical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom (U.K.D., M.S.)
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India (U.K.D., P.B., S.N., V.M., A.A., M.S.)
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13
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Einbinder Y, Shnaider A, Ghanayem K, Basok A, Rogachev B, Lior Y, Haviv YS, Cohen-Hagai K, Nacasch N, Rozenberg I, Benchetrit S, Zitman-Gal T, Douvdevani A. Elevated Circulating Cell-Free DNA in Hemodialysis-Treated Patients Is Associated with Increased Mortality. Am J Nephrol 2020; 51:852-860. [PMID: 33105130 DOI: 10.1159/000510771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/06/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Predicting the mortality risk of patients un-dergoing hemodialysis (HD) is challenging. Cell-free DNA (cfDNA) is released into circulation from dying cells, and its elevation is predictive of unfavorable outcome. In a pilot study, we found post-HD cfDNA level to be a predictor of all-cause mortality. Thus, the aim of this study was to confirm the prognostic power of cfDNA in a larger prospective cohort study conducted at 2 medical centers. METHODS CfDNA levels were measured by a rapid fluorometric assay on sera obtained before and after 1 HD session. One hundred fifty-three patients were followed up to 46 months for mortality during which time 47 patients died. We compared the predictive value of cfDNA to age, comorbidities, and standard blood tests. RESULTS Examining standard blood tests, only post-HD cfDNA levels were elevated in the non-survivor group compared to survivors (959 vs. 803 ng/mL, p = 0.04). Pre- and post-HD cfDNA levels correlated with age and diabetes. Patients with elevated cfDNA (>850 ng/mL) showed lower survival than those with normal levels. A Cox proportional hazard regression model demonstrated a significant hazard ratio of 1.92 for post-HD cfDNA levels. Logistic regression models showed that post-HD cfDNA was a significant predictor of mortality at 1-3 years with odd ratios of 4.61, 4.36, and 6.22, respectively. CONCLUSIONS Post-HD cfDNA level was superior to standard blood tests and could serve as a biomarker to assist in decision-making for HD-treated patients.
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Affiliation(s)
- Yael Einbinder
- Department of Nephrology and Hypertension, Meir Medical Center, Kfar Saba, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alla Shnaider
- Department of Nephrology, Soroka University Medical Center and Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Khaled Ghanayem
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anna Basok
- Department of Nephrology, Soroka University Medical Center and Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Boris Rogachev
- Department of Nephrology, Soroka University Medical Center and Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yotam Lior
- Department of Clinical Biochemistry and Pharmacology, Soroka University Medical Center and Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Clinical Research Center, Soroka University Medical Center and Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yosef Shmuel Haviv
- Department of Nephrology, Soroka University Medical Center and Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Keren Cohen-Hagai
- Department of Nephrology and Hypertension, Meir Medical Center, Kfar Saba, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Naomi Nacasch
- Department of Nephrology and Hypertension, Meir Medical Center, Kfar Saba, Israel
| | - Ilan Rozenberg
- Department of Nephrology and Hypertension, Meir Medical Center, Kfar Saba, Israel
| | - Sydney Benchetrit
- Department of Nephrology and Hypertension, Meir Medical Center, Kfar Saba, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tali Zitman-Gal
- Department of Nephrology and Hypertension, Meir Medical Center, Kfar Saba, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amos Douvdevani
- Department of Nephrology, Soroka University Medical Center and Ben-Gurion University of the Negev, Beer-Sheva, Israel,
- Department of Clinical Biochemistry and Pharmacology, Soroka University Medical Center and Ben-Gurion University of the Negev, Beer-Sheva, Israel,
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14
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Circulating cell-free DNA level predicts all-cause mortality independent of other predictors in the Health 2000 survey. Sci Rep 2020; 10:13809. [PMID: 32796872 PMCID: PMC7427793 DOI: 10.1038/s41598-020-70526-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/10/2020] [Indexed: 12/22/2022] Open
Abstract
Increased levels of circulating cell-free DNA (cf-DNA) are associated with and predict poor health outcomes. However, its predictive ability for mortality in population-based samples remains understudied. We analysed the capability of cf-DNA to predict all-cause mortality and assessed whether it adds predictive value on top of the other risk factors in the Health 2000 survey (n = 1,257, 46–76 years of age, 15-years-follow-up, 18% deceased). When analysed in a multivariate model with the other factors that independently predicted mortality in the sample (age, gender, self-rated health, smoking and plasma levels of glucose and adiponectin), increases in cf-DNA levels were associated with increased risk of mortality (hazard ratio [HR] for 0.1 µg increase in cf-DNA: 1.017, 95% confidence interval [CI] 1.008–1.026, p = 0.0003). Inclusion of cf-DNA in the model improved the model fit and discrimination. Stratifying the analysis by cardiovascular disease (CVD) status indicated that cf-DNA predicted mortality equally well in individuals with (HR 1.018, 95% CI 1.008–1.026, p = 0.002) and without (HR 1.018, 95% CI 1.001–1.035, p = 0.033) CVD. In conclusion, our study indicates that cf-DNA level predicts mortality in middle-aged and older individuals, also among those with established CVD, and adds significant value to mortality prediction. Our results thus underscore the role of cf-DNA as a viable marker of health.
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15
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Double-Stranded DNA and NETs Components in Relation to Clinical Outcome After ST-Elevation Myocardial Infarction. Sci Rep 2020; 10:5007. [PMID: 32193509 PMCID: PMC7081350 DOI: 10.1038/s41598-020-61971-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/03/2020] [Indexed: 12/14/2022] Open
Abstract
Neutrophil extracellular traps (NETs) have been implicated in atherothrombosis; however, their potential role as markers of risk is unclear. We investigated whether circulating NETs-related components associated with clinical outcome and hypercoagulability in ST-elevation myocardial infarction (STEMI). In this observational cohort study, STEMI patients admitted for PCI (n = 956) were followed for median 4.6 years, recording 190 events (reinfarction, unscheduled revascularization, stroke, heart failure hospitalization, or death). Serum drawn median 18 hours post-PCI was used to quantify double-stranded DNA (dsDNA) and the more specific NETs markers myeloperoxidase-DNA and citrullinated histone 3. Levels of the NETs markers did not differ significantly between groups with/without a primary composite endpoint. However, patients who died (n = 76) had higher dsDNA compared to survivors (p < 0.001). Above-median dsDNA was associated with an increased number of deaths (54 vs. 22, p < 0.001). dsDNA in the upper quartiles (Q) was associated with increased mortality (Q3 vs. Q1 + 2 adjusted HR: 1.89 [95% CI 1.03 to 3.49], p = 0.041 and Q4 vs. Q1 + 2 adjusted HR: 2.28 [95% CI 1.19 to 4.36], p = 0.013). dsDNA was weakly correlated with D-dimer (rs = 0.17, p < 0.001). dsDNA levels associated with increased all-cause mortality, yet weakly with hypercoagulability in STEMI patients. The prognostic significance of potentially NETs-related markers requires further exploration.
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16
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Plasma Concentrations of Extracellular DNA in Acute Kidney Injury. Diagnostics (Basel) 2020; 10:diagnostics10030152. [PMID: 32168933 PMCID: PMC7151483 DOI: 10.3390/diagnostics10030152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/02/2020] [Accepted: 03/09/2020] [Indexed: 12/18/2022] Open
Abstract
Current diagnostic methods of acute kidney injury (AKI) have limited sensitivity and specificity. Tissue injury has been linked to an increase in the concentrations of extracellular DNA (ecDNA) in plasma. A rapid turnover of ecDNA in the circulation makes it a potential marker with high sensitivity. This study aimed to analyze the concentration of ecDNA in plasma in animal models of AKI. Three different fractions of ecDNA were measured—total ecDNA was assessed fluorometrically, while nuclear ecDNA (ncDNA) and mitochondrial DNA (mtDNA) were analyzed using quantitative real-time PCR. AKI was induced using four different murine models of AKI-bilateral ureteral obstruction (BUO), glycerol-induced AKI (GLY), ischemia–reperfusion injury (IRI) and bilateral nephrectomy (BNx). Total ecDNA was significantly higher in BUO (p < 0.05) and GLY (p < 0.05) compared to the respective control groups. ncDNA was significantly higher in BUO (p < 0.05) compared to SHAM. No significant differences in the concentrations of mtDNA were found between the groups. The plasma concentrations of different fractions of ecDNA are dependent on the mechanism of induction of AKI and warrant further investigation as potential surrogate markers of AKI.
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17
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Li X, Hu R, Luo T, Peng C, Gong L, Hu J, Yang S, Li Q. Serum cell-free DNA and progression of diabetic kidney disease: a prospective study. BMJ Open Diabetes Res Care 2020; 8:8/1/e001078. [PMID: 32152147 PMCID: PMC7064129 DOI: 10.1136/bmjdrc-2019-001078] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/15/2020] [Accepted: 02/04/2020] [Indexed: 12/24/2022] Open
Abstract
AIMS Cell-free DNA (cfDNA) is associated with diabetes and cardiovascular diseases. Our study was to evaluate whether serum cfDNA could predict the progression of diabetic kidney disease (DKD). METHODS In this prospective study, a total of 160 patients with DKD were enrolled, and the kidney function was followed up by measurement of estimated glomerular filtration rate (eGFR) and urinary albumin-creatinine ratio (UACR) for three consecutive years. At baseline, concentrations of serum cfDNA were measured. DKD progression was defined as two-continuous decrease in eGFR and changes of UACR from less than 300 mg/g at baseline to higher than 300 mg/g at last follow-up. Regression models were used to analyze associations of serum cfDNA with the DKD progression. RESULTS In total, 131 patients finished all the follow-up visits. At the end of the study, 64 patients showed decreased eGFR and 29 patients had changes of UACR from less than 300 mg/g at baseline to higher than 300 mg/g at follow-up. At baseline, the progression group had higher serum cfDNA levels than the non-progression group (960.49 (816.53, 1073.65) ng/mL vs 824.51 (701.34, 987.06) ng/mL, p=0.014). Serum cfDNA levels were significantly negatively associated with the 1.5-year eGFR change (r=-0.219 p=0.009) and 3-year eGFR change (r=-0.181, p=0.043). Multivariate logistic analyses showed that after adjustment of age, gender, body mass index, fast plasma glucose, smoking, triglycerides, total cholesterol, duration of diabetes, systolic blood pressure, diabetic retinopathy, eGFR, high sensitivity C-reactive protein, angiotensin receptor blocker/ACE inhibitor usage, with the increase of one SD of serum cfDNA levels, the risk of DKD progression increased by 2.4 times (OR, 2.46; 95% CI 1.84 to 4.89). CONCLUSION Serum cfDNA is closely associated with DKD, and it might be a predictor of DKD progression in patients with type 2 diabetes.
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Affiliation(s)
- Xuan Li
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, Chongqing, China
| | - RenZhi Hu
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, Chongqing, China
| | - Ting Luo
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, Chongqing, China
| | - Chuan Peng
- The Chongqing Key Laboratory of Translational Medicine in Major Metabolic Diseases, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lilin Gong
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, Chongqing, China
| | - Jinbo Hu
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, Chongqing, China
| | - Shumin Yang
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, Chongqing, China
| | - Qifu Li
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, Chongqing, China
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18
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Cell free DNA as a diagnostic and prognostic marker for cardiovascular diseases. Clin Chim Acta 2020; 503:145-150. [PMID: 31978408 DOI: 10.1016/j.cca.2020.01.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 12/14/2022]
Abstract
Release of cell free DNA (cfDNA) from damaged or dead cells routinely occurs in normal physiology. Recently, cfDNA has emerged as an essential biomarker in cardiovascular disease (CVD) of potential prognostic and diagnostic significance. Within the last decade, significant research efforts have been devoted to uncovering the mechanisms mediating cfDNA release and its outcome-predicting ability. The current review focuses on the pathways for cfDNA release in myocardial infarction, heart failure and hypertension, and discusses implementation of cfDNA monitoring to assess the overall development of these disease states and predict future complications.
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19
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Shi J, Zhang R, Li J, Zhang R. Size profile of cell-free DNA: A beacon guiding the practice and innovation of clinical testing. Theranostics 2020; 10:4737-4748. [PMID: 32308746 PMCID: PMC7163439 DOI: 10.7150/thno.42565] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/06/2020] [Indexed: 12/25/2022] Open
Abstract
Cell-free DNA (cfDNA) has pioneered the development of noninvasive prenatal testing and liquid biopsy, its emerging applications include organ transplantation, autoimmune diseases, and many other disorders; size profile of cfDNA is a crucial biological property and is essential for its clinical applications. Therefore, a thorough mastery of the characteristic and potential applications of cfDNA size profile is needed. Methods: Based on the recent researches, we summarized the size profile of cfDNA in pregnant women, tumor patients, transplant recipients and systemic lupus erythematosus (SLE) patients to explore the common features. We also concluded the applications of size profile in pre-analytical phases, analytical phases for novel assays, and preparation of quality control materials (QCMs). Results: The size profile of cfDNA shared common features in different populations, and was distributed as a "ladder" pattern with a dominant peak at ~166 bp. However, cfDNA entailed slightly discrepant characteristics due to specific tissues of origin. The dominant peaks of fetal and maternal cfDNA fragments in pregnant women were at 143 bp and 166 bp, respectively. The plasma cfDNA in tumor patients, transplant recipients, and SLE patients had a peak of around 166 bp. In pre-analytical phases, size profile served as a vital indicator to judge the eligibility of specimens, thus ensuring the successful implementation of assays. More importantly, the size profile had the potential to enrich short fragments, calculate fetal fraction, detect fetal abnormalities, predict tumor progress in analytical phase and to guide the preparation of QCMs. Conclusions: Our finding summarized the characteristics and potential applications of cfDNA size profile, providing clinical researchers with novel assays by the extensive application of cfDNA.
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Affiliation(s)
- Jiping Shi
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Runling Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
- ✉ Corresponding author: Rui Zhang, Ph.D, Mailing address: National Center for Clinical Laboratories, Beijing Hospital, No.1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China. Tel: 86-10-58115053; Fax: 86-10-65212064; E-mail:
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20
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Pathophysiology of ctDNA Release into the Circulation and Its Characteristics: What Is Important for Clinical Applications. Recent Results Cancer Res 2020; 215:163-180. [PMID: 31605229 DOI: 10.1007/978-3-030-26439-0_9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The clinical implications of being able to accurately detect tumor-derived DNA in the circulation, termed circulating tumor DNA (ctDNA), could be enormous. Already, a plethora of clinical applications is under validation that include detection of minimal residual disease and predicting recurrence, monitoring response and resistance to treatment, identifying targets for therapies, and early detection. ctDNA is only a fraction of the total cell-free DNA (cfDNA) which confounds its detection and sometimes conceals its properties. To use ctDNA as a cancer biomarker with confidence, we need to understand its nature. Its characteristics, including size, half-life, and amount, are critical for the development of tests for its detection and discrimination from the rest of the cfDNA. Technological advances have enabled the detection and quantification of individual fragments of cfDNA, which is pivotal for clinical applications. Understanding the causes, the source of and the mechanisms of release of ctDNA are important for the interpretation of test results. Despite the many advances in understanding the nature and biology of ctDNA, we do not yet have a clear appreciation of the processes that govern its presence and levels in the circulation. ctDNA is not detectable in the blood of every cancer patient, and there is not a directly proportional relationship to tumor type, size, or stage. It is not clear if the lack of correlation with these specific clinical parameters is strictly due to technical or biological challenges. Better understanding of the pathophysiology of ctDNA is therefore important for the improvement of clinical applications and interpretation of their results.
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21
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Urabe F, Kosaka N, Ito K, Kimura T, Egawa S, Ochiya T. Extracellular vesicles as biomarkers and therapeutic targets for cancer. Am J Physiol Cell Physiol 2019; 318:C29-C39. [PMID: 31693397 DOI: 10.1152/ajpcell.00280.2019] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Extracellular vesicles (EVs) are small lipid membrane vesicles that are secreted from almost all kinds of cells into the extracellular space. EVs are widely accepted to be involved in various cellular processes; in particular, EVs derived from cancer cells have been reported to play important roles in modifying the tumor microenvironment and promoting tumor progression. In addition, EVs derived from cancer cells encapsulate various kinds of tumor-specific molecules, such as proteins and RNAs, which contribute to cancer malignancy. Therefore, the unveiling of the precise mechanism of intercellular communication via EVs in cancer patients will provide a novel strategy for cancer treatment. Furthermore, a focus on the contents of EVs could promote the use of EVs in body fluids as clinically useful diagnostic and prognostic biomarkers. In this review, we summarize the current research knowledge on EVs as biomarkers and therapeutic targets and discuss their potential clinical applications.
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Affiliation(s)
- Fumihiko Urabe
- Department of Molecular and Cellular Medicine, Tokyo Medical University, Tokyo, Japan.,Department of Urology, The Jikei University School of Medicine, Tokyo, Japan
| | - Nobuyoshi Kosaka
- Department of Molecular and Cellular Medicine, Tokyo Medical University, Tokyo, Japan
| | - Kagenori Ito
- Department of Urology, The Jikei University School of Medicine, Tokyo, Japan
| | - Takahiro Kimura
- Department of Urology, The Jikei University School of Medicine, Tokyo, Japan
| | - Shin Egawa
- Department of Urology, The Jikei University School of Medicine, Tokyo, Japan
| | - Takahiro Ochiya
- Department of Molecular and Cellular Medicine, Tokyo Medical University, Tokyo, Japan
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22
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Chang CC, Chiu PF, Wu CL, Kuo CL, Huang CS, Liu CS, Huang CH. Urinary cell-free mitochondrial and nuclear deoxyribonucleic acid correlates with the prognosis of chronic kidney diseases. BMC Nephrol 2019; 20:391. [PMID: 31660901 PMCID: PMC6816217 DOI: 10.1186/s12882-019-1549-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/04/2019] [Indexed: 01/16/2023] Open
Abstract
Introduction Cell-free deoxyribonucleic acid DNA (cf-DNA) in urine is promising due to the advantage of urine as an easily obtained and non-invasive sample source over tissue and blood. In clinical practice, it is important to identify non-invasive biomarkers of chronic kidney disease (CKD) in monitoring and surveillance of disease progression. Information is limited, however, regarding the relationship between urine and plasma cf-DNA and the renal outcome in CKD patients. Methods One hundred and thirty-one CKD patients were enrolled between January 2016 and September 2018. Baseline urine and plasma cell-free mitochondrial DNA (cf-mtDNA) and cell-free nuclear DNA (cf-nDNA) were isolated using quantitative real-time PCR. Estimated glomerular filtration rate (eGFR) measurement was performed at baseline and 6-month follow-up. Favorable renal outcome was defined as eGFR at 6 months minus baseline eGFR> = 0. Receiver operator characteristics (ROC) curve analysis was performed to assess different samples of cf-DNA to predict favorable renal outcomes at 6 months. A multivariate linear regression model was used to evaluate independent associations between possible predictors and different samples of cf-DNA. Results Patients with an advanced stage of CKD has significantly low plasma cf-nDNA and high plasma neutrophil gelatinase-associated lipocalin (NGAL) levels. Low urine cf-mtDNA, cf-nDNA levels and low plasma NGAL were significantly correlated with favorable renal outcomes at 6 months. The urine albumin-creatinine ratio (ACR) or urine protein-creatinine ratio (PCR) level is a robust predictor of cf-mtDNA and cf-nDNA in CKD patients. Baseline urine levels of cf-mtDNA and cf-nDNA could predict renal outcomes at 6 months. Conclusions Urinary cf-mtDNA and cf-nDNA may provide novel prognostic biomarkers for renal outcome in CKD patients. The levels of plasma cf-nDNA and plasma NGAL are significantly correlated with the severity of CKD. Electronic supplementary material The online version of this article (10.1186/s12882-019-1549-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chia-Chu Chang
- Department of Internal Medicine, Kuang Tien General Hospital, Taichung, Taiwan.,Department of Nutrition, Hungkuang University, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Ping-Fang Chiu
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Nephrology Division, Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan.,Vascular & Genomic Research Center, Changhua Christian Hospital, Changhua, Taiwan.,Center of General Education Tunghai University, Taichung, Taiwan
| | - Chia-Lin Wu
- Nephrology Division, Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan.,Internal Medicine Research Center, Changhua Christian Hospital, Changhua, Taiwan
| | - Cheng-Ling Kuo
- Vascular & Genomic Research Center, Changhua Christian Hospital, Changhua, Taiwan
| | - Ching-Shan Huang
- Vascular & Genomic Research Center, Changhua Christian Hospital, Changhua, Taiwan
| | - Chin-San Liu
- Vascular & Genomic Research Center, Changhua Christian Hospital, Changhua, Taiwan.,Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
| | - Ching-Hui Huang
- Vascular & Genomic Research Center, Changhua Christian Hospital, Changhua, Taiwan. .,Department of Cardiology, Changhua Christian Hospital, Changhua, Taiwan. .,Institute of Statistics and Information Science, National Changhua University of Education, Changhua, Taiwan. .,School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Department of Beauty Science and Graduate Institute of Beauty Science Technology, Chienkuo Technology University, Changhua, Taiwan.
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23
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Zachariah MA, Oliveira-Costa JP, Carter BS, Stott SL, Nahed BV. Blood-based biomarkers for the diagnosis and monitoring of gliomas. Neuro Oncol 2019; 20:1155-1161. [PMID: 29746665 DOI: 10.1093/neuonc/noy074] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Monitoring patient response to treatment is challenging for most cancers, but it is particularly difficult in glioblastoma multiform, the most common and aggressive form of malignant brain tumor. These tumors exhibit a high degree of heterogeneity which may not be reflected in a biopsy. To determine if the current standard of care is effective, glioma patients are monitored using MRI or CT scans, an effective but sometimes misleading approach due to the phenomenon of pseudoprogression. As such, there is incredible need for a minimally invasive "liquid biopsy" to assist in molecularly characterizing the tumors while also aiding in the identification of true progression in glioblastoma. This review details the status and potential impact for circulating tumor cells, extracellular vesicles, ctDNA, and ctRNA, putative circulating biomarkers found in the blood in glioblastoma patients. As mutation-based therapy becomes more prevalent in gliomas, blood-based analyses may offer a non-invasive method of identifying mutations. The ability to obtain serial "liquid biopsies" will provide unique opportunities to study the evolution of tumors and mechanisms of treatment resistance and monitor for mutational changes in response to therapy.
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Affiliation(s)
- Marcus A Zachariah
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Joao Paulo Oliveira-Costa
- Department of Medicine, Center for Cancer Research for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Shannon L Stott
- Department of Medicine, Center for Cancer Research for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Brian V Nahed
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
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24
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Liu J, Yang D, Wang X, Zhu Z, Wang T, Ma A, Liu P. Neutrophil extracellular traps and dsDNA predict outcomes among patients with ST-elevation myocardial infarction. Sci Rep 2019; 9:11599. [PMID: 31406121 PMCID: PMC6690880 DOI: 10.1038/s41598-019-47853-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/25/2019] [Indexed: 02/02/2023] Open
Abstract
Neutrophil extracellular traps (NETs) which have a potential role in noninfectious diseases, may play an important role in patients with acute coronary syndrome. The goal of this study was to investigate the association of NETs and in-hospital major adverse cardiac events among patients with ST-segment elevation myocardial infarction (STEMI). Using immunofluorescence staining, ELISA, and fluorescent enzyme standard instrument, we assessed NETs and NETs-related factors. Multivariate analyses were performed after univariate analyses to investigate which variables were independently associated with major adverse cardiac events. Compared with peripheral arteries, we observed neutrophils obtained from infarct-related artery (IRA) releasing NETs. The dsDNA levels, NET-specific marker myeloperoxidase/deoxyribonucleic acid (MPO/DNA) complexes and NETs-related factor tissue factor were significantly higher in coronary plasma samples. Multivariate analysis that white cell counts and coronary dsDNA were independently associated with in-hospital major adverse cardiac events. ROC curve for coronary dsDNA showed sensitivity of 78.0% and specificity of 53% for the cut-off value of 0.39ug/ml. Conclusion, these results provide evidences indicating NETs were associated with STIM, and occurrence of adverse cardiac events.
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Affiliation(s)
- Jing Liu
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China
| | - Dandan Yang
- Cardiovascular Department, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Xiqiang Wang
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China
| | - Zhonghai Zhu
- Department of Epidemiology and biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, P.R. China
| | - Tingzhong Wang
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China.,Key Laboratory of Molecular Cardiology, Shaanxi Province, P.R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, P.R. China
| | - Aiqun Ma
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China.,Key Laboratory of Molecular Cardiology, Shaanxi Province, P.R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, P.R. China
| | - Ping Liu
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P.R. China. .,Key Laboratory of Molecular Cardiology, Shaanxi Province, P.R. China. .,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, P.R. China.
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25
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Lu YT, Delijani K, Mecum A, Goldkorn A. Current status of liquid biopsies for the detection and management of prostate cancer. Cancer Manag Res 2019; 11:5271-5291. [PMID: 31239778 PMCID: PMC6559244 DOI: 10.2147/cmar.s170380] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/18/2019] [Indexed: 12/14/2022] Open
Abstract
In recent years, new therapeutic options have become available for prostate cancer (PC) patients, generating an urgent need for better biomarkers to guide the choice of therapy and monitor treatment response. Liquid biopsies, including circulating tumor cells (CTCs), circulating nucleic acids, and exosomes, have been developed as minimally invasive assays allowing oncologists to monitor PC patients with real-time cellular or molecular information. While CTC counts remain the most extensively validated prognostic biomarker to monitor treatment response, recent advances demonstrate that CTC morphology and androgen receptor characterization can provide additional information to guide the choice of treatment. Characterization of cell-free DNA (cfDNA) is another rapidly emerging field with novel technologies capable of monitoring the evolution of treatment relevant alterations such as those in DNA damage repair genes for poly (ADP-ribose) polymerase (PARP) inhibition. In addition, several new liquid biopsy fields are emerging, including the characterization of heterogeneity, CTC RNA sequencing, the culture and xenografting of CTCs, and the characterization of extracellular vesicles (EVs) and circulating microRNAs. This review describes the clinical utilization of liquid biopsies in the management of PC patients and emerging liquid biopsy technologies with the potential to advance personalized cancer therapy.
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Affiliation(s)
- Yi-Tsung Lu
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Kevin Delijani
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Andrew Mecum
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Amir Goldkorn
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
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26
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González-Billalabeitia E, Conteduca V, Wetterskog D, Jayaram A, Attard G. Circulating tumor DNA in advanced prostate cancer: transitioning from discovery to a clinically implemented test. Prostate Cancer Prostatic Dis 2019; 22:195-205. [PMID: 30413805 PMCID: PMC6398580 DOI: 10.1038/s41391-018-0098-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 08/21/2018] [Accepted: 09/08/2018] [Indexed: 12/13/2022]
Abstract
The genomic landscape of metastatic castration-resistant prostate cancer (mCRPC) differs from that of the primary tumor and is dynamic during tumor progression. The real-time and repeated characterization of this process via conventional solid tumor biopsies is challenging. Alternatively, circulating cell-free DNA (cfDNA) containing circulating tumor DNA (ctDNA) can be obtained from patient plasma using minimally disruptive blood draws and is amenable to sequential analysis. ctDNA has high overlap with the genomic sequences of biopsies from metastases and has the advantage of being representative of multiple metastases. The availability of techniques with high sensitivity and specificity, such as next-generation sequencing (NGS) and digital PCR, has greatly contributed to the development of the cfDNA field and enabled the detection of genomic alterations at low ctDNA fractions. In mCRPC, a number of clinically relevant genomic alterations have been tracked in ctDNA, including androgen receptor (AR) aberrations, which have been shown to be associated with an adverse outcome to novel antiandrogen therapies, and alterations in homologous recombination repair (HRR) genes, which have been associated with a response to PARP inhibitors. Several clinical applications have been proposed for cfDNA analysis, including its use as a prognostic tool, as a predictive biomarker, to monitor tumor response and to identify novel mechanisms of resistance. To date, the cfDNA analysis has provided interesting results, but there is an urgent need for these findings to be confirmed in prospective clinical trials.
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Affiliation(s)
- Enrique González-Billalabeitia
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, IMIB-Universidad de Murcia, Murcia, 30008, Spain.
- Universidad Católica San Antonio de Murcia (UCAM), Murcia, 30107, Spain.
| | - Vincenza Conteduca
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST), IRCCS, Meldola, 47014, Italy
- Research Department of Oncology, University College London Cancer Institute, London, UK
| | - Daniel Wetterskog
- Research Department of Oncology, University College London Cancer Institute, London, UK
| | - Anuradha Jayaram
- Research Department of Oncology, University College London Cancer Institute, London, UK
| | - Gerhardt Attard
- Research Department of Oncology, University College London Cancer Institute, London, UK.
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27
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Detection of Minimal Residual Disease Using ctDNA in Lung Cancer: Current Evidence and Future Directions. J Thorac Oncol 2019; 14:16-24. [DOI: 10.1016/j.jtho.2018.09.022] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 09/21/2018] [Indexed: 01/06/2023]
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28
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Lappas M, Georgiou HM, Willcox JC, Permezel M, Shub A, Maynard CL, Joglekar MV, Hardikar AA. Postpartum Circulating Cell-Free Insulin DNA Levels Are Higher in Women with Previous Gestational Diabetes Mellitus Who Develop Type 2 Diabetes in Later Life. J Diabetes Res 2019; 2019:3264184. [PMID: 31428654 PMCID: PMC6681610 DOI: 10.1155/2019/3264184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/04/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Women with previous gestational diabetes mellitus (GDM) have evidence of postpartum β-cell dysfunction, which increases their risk of developing type 2 diabetes (T2DM) later in life. Elevated levels of circulating cell-free preproinsulin (INS) DNA correlate with dying β-cells in both mice and humans. The aim of this study was to determine if cell-free circulating INS DNA levels are higher in women with previous GDM who develop T2DM. METHODS We used droplet digital (dd) PCR to measure the levels of cell-free circulating methylated and unmethylated INS DNA in plasma from 97 women with normal glucose tolerance (NGT), 12 weeks following an index GDM pregnancy. Women were assessed for up to 10 years for the development of T2DM. RESULTS In the follow-up period, 22% of women developed T2DM. Compared with NGT women, total cell-free INS DNA levels were significantly higher in women who developed T2DM (P = 0.02). There was no difference in cell-free circulating unmethylated and methylated INS DNA levels between NGT women and women who developed T2DM (P = 0.09 and P = 0.07, respectively). CONCLUSIONS In women with a previous index GDM pregnancy, postpartum levels of cell-free circulating INS DNA are significantly higher in those women who later developed T2DM.
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Affiliation(s)
- Martha Lappas
- Obstetrics, Nutrition and Endocrinology Group, Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Heidelberg, Victoria, Australia
| | - Harry M. Georgiou
- Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Heidelberg, Victoria, Australia
| | - Jane C. Willcox
- School of Allied Health, College of Science, Health and Engineering, La Trobe University, Bundoora, Victoria, Australia
| | - Michael Permezel
- Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Heidelberg, Victoria, Australia
| | - Alexis Shub
- Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Heidelberg, Victoria, Australia
| | - Cody-Lee Maynard
- Islet Biology and Diabetes Group, NHMRC Clinical Trials Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Mugdha V. Joglekar
- Islet Biology and Diabetes Group, NHMRC Clinical Trials Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Anandwardhan A. Hardikar
- Islet Biology and Diabetes Group, NHMRC Clinical Trials Centre, The University of Sydney, Camperdown, NSW, Australia
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Jung M, Dodsworth M, Thum T. Inflammatory cells and their non-coding RNAs as targets for treating myocardial infarction. Basic Res Cardiol 2018; 114:4. [PMID: 30523422 PMCID: PMC6290728 DOI: 10.1007/s00395-018-0712-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 11/29/2018] [Indexed: 12/22/2022]
Abstract
Myocardial infarction triggers infiltration of several types of immune cells that coordinate both innate and adaptive immune responses. These play a dual role in post-infarction cardiac remodeling by initiating and resolving inflammatory processes, which needs to occur in a timely and well-orchestrated way to ensure a reestablishment of normalized cardiac functions. Thus, therapeutic modulation of immune responses might have benefits for infarct patients. While such strategies have shown great potential in treating cancer, applications in the post-infarction context have been disappointing. One challenge has been the complexity and plasticity of immune cells and their functions in cardiac regulation and healing. The types appear in patterns that are temporally and spatially distinct, while influencing each other and the surrounding tissue. A comprehensive understanding of the immune cell repertoire and their regulatory functions following infarction is sorely needed. Processes of cardiac remodeling trigger additional genetic changes that may also play critical roles in the aftermath of cardiovascular disease. Some of these changes involve non-coding RNAs that play crucial roles in the regulation of immune cells and may, therefore, be of therapeutic interest. This review summarizes what is currently known about the functions of immune cells and non-coding RNAs during post-infarction wound healing. We address some of the challenges that remain and describe novel therapeutic approaches under development that are based on regulating immune responses through non-coding RNAs in the aftermath of the disease.
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Affiliation(s)
- Mira Jung
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Michael Dodsworth
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
- National Heart and Lung Institute, Imperial College London, London, UK.
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Characteristics, properties, and potential applications of circulating cell-free dna in clinical diagnostics: a focus on transplantation. J Immunol Methods 2018; 463:27-38. [DOI: 10.1016/j.jim.2018.09.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 09/19/2018] [Accepted: 09/24/2018] [Indexed: 12/18/2022]
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Tian Y, Charles EJ, Yan Z, Wu D, French BA, Kron IL, Yang Z. The myocardial infarct-exacerbating effect of cell-free DNA is mediated by the high-mobility group box 1-receptor for advanced glycation end products-Toll-like receptor 9 pathway. J Thorac Cardiovasc Surg 2018; 157:2256-2269.e3. [PMID: 30401529 DOI: 10.1016/j.jtcvs.2018.09.043] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 08/13/2018] [Accepted: 09/12/2018] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Damage-associated molecular patterns, such as high-mobility group box 1 (HMGB1) and cell-free DNA (cfDNA), play critical roles in mediating ischemia-reperfusion injury (IRI). HMGB1 activates RAGE to exacerbate IRI, but the mechanism underlying cfDNA-induced myocardial IRI remains unknown. We hypothesized that the infarct-exacerbating effect of cfDNA is mediated by HMGB1 and receptor for advanced glycation end products (RAGE). METHODS C57BL/6 wild type mice, RAGE knockout (KO), and Toll-like receptor 9 KO mice underwent 20- or 40-minute occlusions of the left coronary artery followed by up to 60 minutes of reperfusion. Cardiac coronary perfusate was acquired from ischemic hearts without reperfusion. Exogenous mitochondrial DNA was acquired from livers of normal C57BL/6 mice. Myocardial infarct size (IS) was reported as percent risk region, as measured by 2,3,5-triphenyltetrazolium chloride and Phthalo blue (Heucotech, Fairless Hill, Pa) staining. cfDNA levels were measured by Sytox Green assay (Thermo Fisher Scientific, Waltham, Mass) and/or spectrophotometer. RESULTS Free HMGB1 and cfDNA levels were increased in the ischemic myocardium during prolonged ischemia and subsequently in the plasma during reperfusion. In C57BL/6 mice undergoing 40'/60' IRI, deoxyribonuclease I, or anti-HMGB1 monoclonal antibody reduced IS by approximately half to 29.0% ± 5.2% and 24.3% ± 3.5% (P < .05 vs control 54.3% ± 3.4%). However, combined treatment with deoxyribonuclease I + anti-HMGB1 monoclonal antibody did not further attenuate IS (29.3% ± 4.9%). In C57BL/6 mice undergoing 20'/60' IRI, injection of 40'/5' plasma upon reperfusion increased IS by more than 3-fold (to 19.9 ± 4.3; P < .05). This IS exacerbation was abolished by pretreating the plasma with deoxyribonuclease I or by depleting the HMGB1 by immunoprecipitation, or by splenectomy. The infarct-exacerbating effect also disappeared in RAGE KO mice and Toll-like receptor 9 KO mice. Injection of 40'/0' coronary perfusate upon reperfusion similarly increased IS. The levels of HMGB1 and cfDNA were significantly elevated in the 40'/0' coronary perfusate and 40'/reperfusion (min) plasma but not in those with 10' ischemia. In C57BL/6 mice without IRI, 40'/5' plasma significantly increased the interleukin-1β protein and messenger RNA expression in the spleen by 30 minutes after injection. Intravenous bolus injection of recombinant HMGB1 (0.1 μg/g) or mitochondrial DNA (0.5 μg/g) 5 minutes before reperfusion did not exacerbate IS (P = not significant vs control). However, combined administration of recombinant HMGB1 + mitochondrial DNA significantly increased IS (P < .05 vs individual treated groups) and this infarct-exacerbating effect disappeared in RAGE KO mice and splenectomized C57BL/6 mice. The accumulation of cfDNA in the spleen after combined recombinant HMGB1 + mitochondrial DNA treatment was significantly more elevated in C57BL/6 mice than in RAGE KO mice. CONCLUSIONS Both HMGB1 and cfDNA are released from the heart upon reperfusion after prolonged ischemia and both contribute importantly and interdependently to post-IRI by a common RAGE-Toll-like receptor 9-dependent mechanism. Depleting either of these 2 damage-associated molecular patterns suffices to significantly reduce IS by approximately 50%.
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Affiliation(s)
- Yikui Tian
- Department of Surgery, University of Virginia, Charlottesville, Va; Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Eric J Charles
- Department of Surgery, University of Virginia, Charlottesville, Va
| | - Zhen Yan
- Department of Cardiovascular Medicine, University of Virginia, Charlottesville, Va
| | - Di Wu
- Department of Surgery, University of Virginia, Charlottesville, Va
| | - Brent A French
- Department of Cardiovascular Medicine, University of Virginia, Charlottesville, Va; Department of Biomedical Engineering, University of Virginia, Charlottesville, Va
| | - Irving L Kron
- Department of Surgery, University of Virginia, Charlottesville, Va
| | - Zequan Yang
- Department of Surgery, University of Virginia, Charlottesville, Va; Department of Biomedical Engineering, University of Virginia, Charlottesville, Va.
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Xie J, Yang J, Hu P. Correlations of Circulating Cell-Free DNA With Clinical Manifestations in Acute Myocardial Infarction. Am J Med Sci 2018; 356:121-129. [PMID: 30219153 DOI: 10.1016/j.amjms.2018.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 01/05/2023]
Abstract
BACKGROUND The objective of the study was to examine the potential use of circulating cell free DNA (cfDNA) in acute myocardial infarction (AMI) patients and correlate it with clinical features. Serial monitoring was conducted to assess any associations to disease. METHODS Quantification of cfDNA was performed on 130 cardiovascular disease (CVD) patients as well as 30 healthy volunteers. Serial samplings were conducted using PicoGreen dsDNA assay. Of the 130 patients with CVD, 100 had an AMI and measurements were taken during treatment. Short and medium intervals serial sampling of patients' blood were undertaken. RESULTS The results were highly correlative of CVD disease status. The mean concentration of cfDNA in patients with AMI was 5 folds higher during the onset of disease compared with healthy volunteers. The cfDNA content was also higher than other patients with CVD. Interestingly, short term monitoring of patients with AMI showed distinct trends that highlighted the severity of the disease and linked to complication events. Medium term monitoring showed 2 distinctive groups with 1 that had their cfDNA returned to basal levels and the other with persistently elevated cfDNA levels. CONCLUSIONS Measuring cfDNA in patients with CVD offers an alternative approach to monitor the disease and has potential clinical applications to identify high-risk individuals.
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Affiliation(s)
- Jin Xie
- Department of Cardiology, Jingzhou Central Hospital, the Second Clinical Medical College, Yangtze University, Jingzhou, Hubei Sheng, China
| | - Jiawei Yang
- Department of Cardiology, Jingzhou Central Hospital, the Second Clinical Medical College, Yangtze University, Jingzhou, Hubei Sheng, China
| | - Pei Hu
- Department of Cardiology, Jingzhou Central Hospital, the Second Clinical Medical College, Yangtze University, Jingzhou, Hubei Sheng, China.
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Khakoo S, Georgiou A, Gerlinger M, Cunningham D, Starling N. Circulating tumour DNA, a promising biomarker for the management of colorectal cancer. Crit Rev Oncol Hematol 2018; 122:72-82. [PMID: 29458792 DOI: 10.1016/j.critrevonc.2017.12.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/18/2017] [Accepted: 12/06/2017] [Indexed: 02/08/2023] Open
Abstract
Circulating cell free tumour DNA (ctDNA) maintains the same genomic alterations that are present in the corresponding tumour, thereby allowing for quantitative and qualitative real-time evaluation in body fluids as an alternative to onerous repeat biopsies. Improvements in the sensitivity of techniques used to identify ctDNA has led to a surge of research investigating its role in the detection of: early disease, relapse, response to therapy and emerging drug resistance mechanisms. Following curative surgery, ctDNA detection is a promising marker of minimal residual disease and could better select patients for adjuvant chemotherapy. Longitudinal monitoring could help identify early relapse. In metastatic disease, ctDNA can predict response to chemotherapy prior to evidence of disease progression on imaging and investigate novel primary and acquired resistance mechanisms to targeted therapies. More experience in detecting, analysing and interpreting ctDNA within prospective trials, will better define its role for implementation into routine clinical practice.
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Affiliation(s)
- Shelize Khakoo
- Department of Medicine, Royal Marsden Hospital, London and Surrey, United Kingdom
| | - Alexandros Georgiou
- Department of Medicine, Royal Marsden Hospital, London and Surrey, United Kingdom; Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Marco Gerlinger
- Department of Medicine, Royal Marsden Hospital, London and Surrey, United Kingdom; Centre of Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - David Cunningham
- Department of Medicine, Royal Marsden Hospital, London and Surrey, United Kingdom
| | - Naureen Starling
- Department of Medicine, Royal Marsden Hospital, London and Surrey, United Kingdom.
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Tang JH, Chia D. Liquid Biopsies in the Screening of Oncogenic Mutations in NSCLC and its Application in Targeted Therapy. Crit Rev Oncog 2018; 20:357-71. [PMID: 27279235 DOI: 10.1615/critrevoncog.v20.i5-6.90] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Non-small cell lung cancer (NSCLC) still dominates cancer-related deaths in America. Despite this, new discoveries and advancements in technology are helping with the detection and treatment of NSCLC. The discovery of circulating tumor DNA in blood and other biofluids is essential for the creation of a DNA biomarker. Limitations in technology and sequencing have stunted assay development, but with recent advancements in the next-generation sequencing, droplet digital PCR, and EFIRM, the detection of mutations in biofluids has become possible with reasonable sensitivity and specificity. These methods have been applied to the detection of mutations in NSCLC by measuring the levels of circulating tumor DNA. ALK fusion genes along with mutations in EGFR and KRAS have been shown to correlate to tumor size and metastasis. These methods allow for noninvasive, affordable, and efficient diagnoses of oncogenic mutations that overcome the issues of traditional biopsies. These issues include tumor heterogeneity and early detection of cancers with asymptomatic early stages. Early detection and treatment remain the best way to ensure survival. This review aims to describe these new technologies along with their application in mutation detection in NSCLC in order to proactively utilize targeted anticancer therapy.
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Affiliation(s)
- Jason H Tang
- Department of Pathology, UCLA David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - David Chia
- Department of Pathology, UCLA David Geffen School of Medicine at UCLA, Los Angeles, CA
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Cell-free DNA: the role in pathophysiology and as a biomarker in kidney diseases. Expert Rev Mol Med 2018; 20:e1. [PMID: 29343314 DOI: 10.1017/erm.2017.12] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell-free DNA (cfDNA) is present in various body fluids and originates mostly from blood cells. In specific conditions, circulating cfDNA might be derived from tumours, donor organs after transplantation or from the foetus during pregnancy. The analysis of cfDNA is mainly used for genetic analyses of the source tissue -tumour, foetus or for the early detection of graft rejection. It might serve also as a nonspecific biomarker of tissue damage in critical care medicine. In kidney diseases, cfDNA increases during haemodialysis and indicates cell damage. In patients with renal cell carcinoma, cfDNA in plasma and its integrity is studied for monitoring of tumour growth, the effects of chemotherapy and for prognosis. Urinary cfDNA is highly fragmented, but the technical hurdles can now be overcome and urinary cfDNA is being evaluated as a potential biomarker of renal injury and urinary tract tumours. Beyond its diagnostic application, cfDNA might also be involved in the pathogenesis of diseases affecting the kidneys as shown for systemic lupus, sepsis and some pregnancy-related pathologies. Recent data suggest that increased cfDNA is associated with acute kidney injury. In this review, we discuss the biological characteristics, sources of cfDNA, its potential use as a biomarker as well as its role in the pathogenesis of renal and urinary diseases.
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Abstract
Head and neck cancer (HNC) includes a diverse range of malignancies arising commonly from mucosal epithelia of the upper aerodigestive tract. Head and neck squamous cell carcinoma (HNSCC), the most common form of HNC, develops in the oral cavity, pharynx, and larynx and is associated with tobacco exposure, alcohol abuse, and infection with oncogenic viruses. Despite global advances in cancer care, HNSCC often presents with advanced disease and is associated with poor 5-year survival of ~50%. Genotyping tumor tissue to guide clinical decision-making is becoming commonplace in modern oncology, but in the management of HNSCC, tissue biopsies with cytopathology or histopathology remain the mainstay for diagnosis. Furthermore, conventional biopsies are temporally and spatially limited, often providing a brief snapshot of a single region of a heterogeneous tumor. In the absence of a useful biomarker, both primary and recurrent HNSCCs are diagnosed with conventional imaging and clinical examination. As a result, many patients are diagnosed with advanced disease. Tumor DNA is an emerging biomarker in HNSCC. DNA fragments are constantly being shed from tumors and metastatic lesions, and can therefore be detected in blood and other bodily fluids. Utilizing next-generation sequencing techniques, these tumor DNA can be characterized and quantified. This can serve as a minimally invasive liquid biopsy allowing for specific tumor profiling, dynamic tumor burden monitoring, and active surveillance for disease recurrences. In HNSCC, analysis of tumor DNA has the potential to enhance tumor profiling, aid in determining patient prognosis, and guide treatment decisions.
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Affiliation(s)
- Joseph A Bellairs
- Pritzker School of Medicine, University of Chicago, 5841 S. Maryland Avenue, MC 1035, Chicago, IL, 60637, USA
| | - Rifat Hasina
- Section of Otolaryngology-Head and Neck Surgery, University of Chicago Medicine, Chicago, IL, USA
| | - Nishant Agrawal
- Pritzker School of Medicine, University of Chicago, 5841 S. Maryland Avenue, MC 1035, Chicago, IL, 60637, USA.
- Section of Otolaryngology-Head and Neck Surgery, University of Chicago Medicine, Chicago, IL, USA.
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Nakagomi H, Hirotsu Y, Amemiya K, Nakada H, Inoue M, Mochizuki H, Oyama T, Omata M. Rapid Changes in Circulating Tumor DNA in Serially Sampled Plasma During Treatment of Breast Cancer: A Case Report. AMERICAN JOURNAL OF CASE REPORTS 2017; 18:26-32. [PMID: 28065930 PMCID: PMC5240877 DOI: 10.12659/ajcr.901295] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Patient: Female, 45 Final Diagnosis: Breast cancer Symptoms: Breast tumor Medication: — Clinical Procedure: Analysis of circulating tumor DNA Specialty: Oncology
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Affiliation(s)
- Hiroshi Nakagomi
- Department of Surgery, Yamanashi Prefectural Central Hospital, Kofu, Yamanashi, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, Kofu, Yamanashi, Japan
| | - Kenji Amemiya
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, Kofu, Yamanashi, Japan
| | - Haruka Nakada
- Department of Surgery, Yamanashi Prefectural Central Hospital, Kofu, Yamanashi, Japan
| | - Masayuki Inoue
- Department of Surgery, Yamanashi Prefectural Central Hospital, Kofu, Yamanashi, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, Kofu, Yamanashi, Japan
| | - Toshio Oyama
- Department of Pathology, Yamanashi Prefectural Central Hospital, Kofu, Yamanashi, Japan
| | - Masao Omata
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, Kofu, Yamanashi, Japan.,University of Tokyo, Tokyo, Japan
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Perakis S, Auer M, Belic J, Heitzer E. Advances in Circulating Tumor DNA Analysis. Adv Clin Chem 2017; 80:73-153. [PMID: 28431643 DOI: 10.1016/bs.acc.2016.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The analysis of cell-free circulating tumor DNA (ctDNA) is a very promising tool and might revolutionize cancer care with respect to early detection, identification of minimal residual disease, assessment of treatment response, and monitoring tumor evolution. ctDNA analysis, often referred to as "liquid biopsy" offers what tissue biopsies cannot-a continuous monitoring of tumor-specific changes during the entire course of the disease. Owing to technological improvements, efforts for the establishment of preanalytical and analytical benchmark, and the inclusion of ctDNA analyses in clinical trial, an actual clinical implementation has come within easy reach. In this chapter, recent advances of the analysis of ctDNA are summarized starting from the discovery of cell-free DNA, to methodological approaches and the clinical applicability.
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Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Martina Auer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria.
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The Time Course of Markers of Neutrophil Extracellular Traps in Patients Undergoing Revascularisation for Acute Myocardial Infarction or Stable Angina Pectoris. Mediators Inflamm 2016; 2016:2182358. [PMID: 28074081 PMCID: PMC5198181 DOI: 10.1155/2016/2182358] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/05/2016] [Accepted: 11/15/2016] [Indexed: 01/13/2023] Open
Abstract
Background and Aims. Neutrophil extracellular traps (NETs) have been identified in acute myocardial infarction. We assessed the time profile and association with infarct size for NETs markers in ST-elevation myocardial infarction (STEMI) and stable angina pectoris (AP). Methods. In 20 patients with STEMI and 10 with AP undergoing percutaneous coronary intervention (PCI), blood samples were collected before PCI (only AP group) and after 3 and 12 hours, days 1, 3, 5, 7, and 14 for measurement of NETs markers. Results. Double-stranded deoxyribonucleic acid (dsDNA) and nucleosome levels were higher in STEMI than AP until day 3 and 12 hours (p < 0.03, all). DsDNA declined after day 5 in both groups (p < 0.04, all), while nucleosomes declined until day 3 only in the AP group (p < 0.05, all). DsDNA correlated with peak troponin T and creatine kinase MB (CKMB) at day 5 (r = 0.48, p = 0.03, both) and with MRI-measured infarct size at days 5 and 7 (r = 0.61, p = 0.01 and r = 0.52, p = 0.04, resp.), while nucleosomes correlated with infarct size at day 5 (r = 0.58, p = 0.02). Conclusions. High levels of NETs markers were observed in STEMI shortly after revascularisation and were partly associated with infarct size. The decline thereafter in both groups indicates a role for NETs in both acute and chronic atherothrombosis.
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Lippi G, Sanchis-Gomar F, Cervellin G. Cell-free DNA for diagnosing myocardial infarction: not ready for prime time. Clin Chem Lab Med 2016; 53:1895-901. [PMID: 25883207 DOI: 10.1515/cclm-2015-0252] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 03/26/2015] [Indexed: 11/15/2022]
Abstract
A modest amount of cell-free DNA is constantly present in human blood, originating from programmed cell death, apoptosis and rupture of blood cells or pathogens. Acute or chronic cell injury contributes to enhance the pool of circulating nucleic acids, so that their assessment may be regarded as an appealing perspective for diagnosing myocardial ischemia. We performed a search in Medline, Web of Science and Scopus to identify clinical studies that investigated the concentration of cell-free DNA in patients with myocardial ischemia. Overall, eight case-control studies could be detected and reviewed. Although the concentration of cell-free DNA was found to be higher in the diseased than in the healthy population, the scenario was inconclusive due to the fact that the overall number of subjects studied was modest, the populations were unclearly defined, cases and controls were not adequately matched, the methodology for measuring the reference cardiac biomarkers was inadequately described, and the diagnostic performance of cell-free DNA was not benchmarked against highly sensitive troponin immunoassays. Several biological and technical hurdles were also identified in cell-free DNA testing, including the lack of specificity and unsuitable kinetics for early diagnosis of myocardial ischemia, the long turnaround time and low throughput, the need for specialized instrumentation and dedicated personnel, the lack of standardization or harmonization of analytical techniques, the incremental costs and the high vulnerability to preanalytical variables. Hence it seems reasonable to conclude that the analysis of cell-free DNA is not ready for prime time in diagnostics of myocardial ischemia.
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Neueste technologische Entwicklungen für die Analyse von zirkulierender Tumor-DNA. MED GENET-BERLIN 2016. [DOI: 10.1007/s11825-016-0089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Zusammenfassung
Die Analyse von zirkulierender Tumor-DNA, zusammen mit der Analyse von zirkulierenden Tumorzellen auch oft Liquid Biopsy genannt, ist ein sich rasch entwickelndes Feld in der medizinischen Forschung. Obwohl es von der Entdeckung der zellfreien DNA bis hin zur Erkenntnis, dass sie sich als Biomarker eignet, Jahrzehnte gedauert hat, wurde der klinische Nutzen der ctDNA hinsichtlich der Überwachung des Therapieansprechens, der Identifizierung von Resistenzmechanismen und neu aufkommenden Therapiezielen sowie der Detektion von minimaler Resterkrankung mittlerweile in unzähligen Studien bewiesen.
Aufgrund der hohen Variabilität, mit der ctDNA in der Zirkulation vorkommt, sowie der starken Fragmentierung, stellt die ctDNA aber einen schwierigen Analyten dar. In den letzten Jahren haben erhebliche technologische Fortschritte dazu beigetragen, dass eine Routineanwendung der ctDNA-Analysen tatsächlich realisierbar wird, sofern eine Reihe von regulatorischen Hürden überwunden wird.
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Parsons HA, Beaver JA, Park BH. Circulating Plasma Tumor DNA. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 882:259-76. [PMID: 26987539 DOI: 10.1007/978-3-319-22909-6_11] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Circulating cell-free DNA (ccfDNA)--first identified in 1947--is "naked" DNA that is free-floating in the blood, and derived from both normal and diseased cells. In the 1970s, scientists observed that patients with cancer had elevated levels of ccfDNA as compared to their healthy, cancer-free counterparts. The maternal fetal medicine community first developed techniques to identify the small fraction of fetal-derived ccfDNA for diagnostic purposes. Similarly, due to the presence of tumor-specific (somatic) variations in all cancers, the fraction of circulating cell-free plasma tumor DNA (ptDNA) in the larger pool of ccfDNA derived from normal cells can serve as extremely specific blood-based biomarkers for a patient's cancer. In theory this "liquid biopsy" can provide a real-time assessment of molecular tumor genotype (qualitative) and existing tumor burden (quantitative). Historically, the major limitation for ptDNA as a biomarker has been related to a low detection rate; however, current and developing techniques have improved sensitivity dramatically. In this chapter, we discuss these methods, including digital polymerase chain reaction and various approaches to tagged next-generation sequencing.
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Affiliation(s)
- Heather A Parsons
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Bunting and Blaustein Building, 1650 Orleans Street, Room 151, 21287, Baltimore, MD, USA
| | - Julia A Beaver
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Bunting and Blaustein Building, 1650 Orleans Street, Room 151, 21287, Baltimore, MD, USA
| | - Ben H Park
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Bunting and Blaustein Building, 1650 Orleans Street, Room 151, 21287, Baltimore, MD, USA.
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Levy B, Hu ZI, Cordova KN, Close S, Lee K, Becker D. Clinical Utility of Liquid Diagnostic Platforms in Non-Small Cell Lung Cancer. Oncologist 2016; 21:1121-30. [PMID: 27388233 DOI: 10.1634/theoncologist.2016-0082] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/27/2016] [Indexed: 11/17/2022] Open
Abstract
UNLABELLED : A firmer understanding of the genomic landscape of lung cancer has recently led to targeted, therapeutic advances in non-small cell lung cancer. Historically, the reference standard for the diagnosis and genetic interrogation for advanced-stage patients has been tissue acquisition via computed tomography-guided core or fine needle aspiration biopsy. However, this process can frequently put the patient at risk and remains complicated by sample availability and tumor heterogeneity. In addition, the time required to complete the diagnostic assays can negatively affect clinical care. Technological advances in recent years have led to the development of blood-based diagnostics or "liquid biopsies" with great potential to quickly diagnose and genotype lung cancer using a minimally invasive technique. Recent studies have suggested that molecular alterations identified in cell-free DNA (cfDNA) or circulating tumor DNA can serve as an accurate molecular proxy of tumor biology and reliably predict the response to tyrosine kinase therapy. In addition, several trials have demonstrated the high accuracy of microRNA (miRNA) platforms in discerning cancerous versus benign nodules in high-risk, screened patients. Despite the promise of these platforms, issues remain, including varying sensitivities and specificities between competing platforms and a lack of standardization of techniques and downstream processing. In the present report, the clinical applications of liquid biopsy technologies, including circulating tumor cells, proteomics, miRNA, and cfDNA for NSCLC, are reviewed and insight is provided into the diagnostic and therapeutic implications and challenges of these platforms. IMPLICATIONS FOR PRACTICE Although tumor biopsies remain the reference standard for the diagnosis and genotyping of non-small cell lung cancer, they remain fraught with logistical complexities that can delay treatment decisions and affect clinical care. Liquid diagnostic platforms, including cell-free DNA, proteomic signatures, RNA (mRNA and microRNA), and circulating tumor cells, have the potential to overcome many of these barriers, including rapid and accurate identification of de novo and resistant genetic alterations, real-time monitoring of treatment responses, prognosis of outcomes, and identification of minimal residual disease. The present report provides insights into new liquid diagnostic platforms in non-small cell lung cancer and discusses the promise and challenges of their current and future clinical use.
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Affiliation(s)
- Benjamin Levy
- Icahn School of Medicine, Mount Sinai Health System, New York, New York, USA
| | - Zishuo I Hu
- Icahn School of Medicine, Mount Sinai Health System, New York, New York, USA
| | | | | | - Karen Lee
- Icahn School of Medicine, Mount Sinai Health System, New York, New York, USA
| | - Daniel Becker
- Veterans Affairs Hospital, New York University, New York, New York, USA
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Jiang P, Lo YD. The Long and Short of Circulating Cell-Free DNA and the Ins and Outs of Molecular Diagnostics. Trends Genet 2016; 32:360-371. [DOI: 10.1016/j.tig.2016.03.009] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/30/2016] [Indexed: 12/25/2022]
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Identification of tissue-specific cell death using methylation patterns of circulating DNA. Proc Natl Acad Sci U S A 2016; 113:E1826-34. [PMID: 26976580 DOI: 10.1073/pnas.1519286113] [Citation(s) in RCA: 398] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Minimally invasive detection of cell death could prove an invaluable resource in many physiologic and pathologic situations. Cell-free circulating DNA (cfDNA) released from dying cells is emerging as a diagnostic tool for monitoring cancer dynamics and graft failure. However, existing methods rely on differences in DNA sequences in source tissues, so that cell death cannot be identified in tissues with a normal genome. We developed a method of detecting tissue-specific cell death in humans based on tissue-specific methylation patterns in cfDNA. We interrogated tissue-specific methylome databases to identify cell type-specific DNA methylation signatures and developed a method to detect these signatures in mixed DNA samples. We isolated cfDNA from plasma or serum of donors, treated the cfDNA with bisulfite, PCR-amplified the cfDNA, and sequenced it to quantify cfDNA carrying the methylation markers of the cell type of interest. Pancreatic β-cell DNA was identified in the circulation of patients with recently diagnosed type-1 diabetes and islet-graft recipients; oligodendrocyte DNA was identified in patients with relapsing multiple sclerosis; neuronal/glial DNA was identified in patients after traumatic brain injury or cardiac arrest; and exocrine pancreas DNA was identified in patients with pancreatic cancer or pancreatitis. This proof-of-concept study demonstrates that the tissue origins of cfDNA and thus the rate of death of specific cell types can be determined in humans. The approach can be adapted to identify cfDNA derived from any cell type in the body, offering a minimally invasive window for diagnosing and monitoring a broad spectrum of human pathologies as well as providing a better understanding of normal tissue dynamics.
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Bakir M, Engin A, Kuskucu MA, Bakir S, Gündag O, Midilli K. Relationship of plasma cell-free DNA level with mortality and prognosis in patients with Crimean-Congo hemorrhagic fever. J Med Virol 2016; 88:1152-8. [PMID: 26680021 DOI: 10.1002/jmv.24446] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2015] [Indexed: 11/09/2022]
Abstract
Crimean-Congo hemorrhagic fever (CCHF) is a viral infection. Circulating plasma cell-free DNA (pcf-DNA) is a novel marker indicating cellular damage. So far, the role of pcf-DNA did not investigate in CCHF patients. In the current study, pcf-DNA levels were investigated in CCHF patients with different clinical severity grades to explore the relationship between circulating pcf-DNA level, virus load, and disease severity. Seventy-two patients were categorized as mild, intermediate, and severe based on severity grading scores. The pcf-DNA level was obtained from all participants on admission and from the survivors on the day of the discharge. The controls consisted of 31 healthy. Although the pcf-DNA level at admission was higher in patients than in the controls, the difference was not statistically significant (P = 0.291). However, at admission and in the convalescent period, the difference between pcf-DNA levels in mild, intermediate, and severe patient groups was significant. The pcf-DNA level in severe patients was higher than in the others. Furthermore, compared to survivors, non-survivors had higher pcf-DNA levels at admission (P = 0.001). A direct relationship was found between the pcf-DNA level and the viral load on the day of discharge in surviving patients. ROC curve analysis identified a pcf-DNA level of 0.42 as the optimal cut-off for prediction of mortality. The positive predictive value, negative predictive value, specificity, and sensitivity for predicting mortality was 100%, 72%, 100%, and 79%, respectively. In summary, our findings revealed that pcf-DNA levels may be used as a biomarker in predicting CHHF prognosis.
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Affiliation(s)
- Mehmet Bakir
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Aynur Engin
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Mert Ahmet Kuskucu
- Department of Microbiology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Sevtap Bakir
- Department of Biochemistry, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Omür Gündag
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Kenan Midilli
- Department of Microbiology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
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Dietrich D. Current status and future perspectives of circulating cell-free DNA methylation in clinical diagnostics. ACTA ACUST UNITED AC 2016. [DOI: 10.1515/labmed-2016-0039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Abstract:Aberrant DNA methylation is a hallmark of malignancies and can be detected in circulating cell-free DNA (ccfDNA) in bodily fluids, i.e. blood plasma, serum and urine. The availability of technologies that allow for an accurate and sensitive quantification of ccfDNA DNA methylation enables the precise monitoring of dynamic pathologic processes and pharmacodynamics. Recently, the first ccfDNA methylation biomarker
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Brisuda A, Pazourkova E, Soukup V, Horinek A, Hrbáček J, Capoun O, Svobodova I, Pospisilova S, Korabecna M, Mares J, Hanuš T, Babjuk M. Urinary Cell-Free DNA Quantification as Non-Invasive Biomarker in Patients with Bladder Cancer. Urol Int 2015; 96:25-31. [PMID: 26338254 DOI: 10.1159/000438828] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 07/16/2015] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Concentration of urinary cell-free DNA (ucfDNA) belongs to potential bladder cancer markers, but the reported results are inconsistent due to the use of various non-standardised methodologies. The aim of the study was to standardise the methodology for ucfDNA quantification as a potential non-invasive tumour biomarker. MATERIAL AND METHODS In total, 66 patients and 34 controls were enrolled into the study. Volumes of each urine portion (V) were recorded and ucfDNA concentrations (c) were measured using real-time PCR. Total amounts (TA) of ucfDNA were calculated and compared between patients and controls. Diagnostic accuracy of the TA of ucfDNA was determined. RESULTS The calculation of TA of ucfDNA in the second urine portion was the most appropriate approach to ucfDNA quantification, as there was logarithmic dependence between the volume and the concentration of a urine portion (p = 0.0001). Using this methodology, we were able to discriminate between bladder cancer patients and subjects without bladder tumours (p = 0.0002) with area under the ROC curve of 0.725. Positive and negative predictive value of the test was 90 and 45%, respectively. CONCLUSION Quantification of ucf DNA according to our modified method could provide a potential non-invasive biomarker for diagnosis of patients with bladder cancer.
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Affiliation(s)
- Antonin Brisuda
- Department of Urology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
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Patel KM, Tsui DWY. The translational potential of circulating tumour DNA in oncology. Clin Biochem 2015; 48:957-61. [PMID: 25889059 DOI: 10.1016/j.clinbiochem.2015.04.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 02/05/2023]
Abstract
The recent understanding of tumour heterogeneity and cancer evolution in response to therapy has raised questions about the value of historical or single site biopsies for guiding treatment decisions. The ability of ctDNA analysis to reveal de novo mutations (i.e., without prior knowledge), allows monitoring of clonal heterogeneity without the need for multiple tumour biopsies. Additionally, ctDNA monitoring of such heterogeneity and novel mutation detection will allow clinicians to detect resistant mechanisms early and tailor treatment therapies accordingly. If ctDNA can be used to detect low volume cancerous states, it will have important applications in treatment stratification post-surgery/radical radiotherapy and may have a role in patient screening. Mutant cfDNA can also be detected in other bodily fluids that are easily accessible and may aid detection of rare mutant alleles in certain cancer types. This article outlines recent advances in these areas.
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Affiliation(s)
- K M Patel
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; Department of Academic Urology, University of Cambridge Hospitals, Box 243, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - D W Y Tsui
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
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Lou X, Hou Y, Liang D, Peng L, Chen H, Ma S, Zhang L. A novel Alu-based real-time PCR method for the quantitative detection of plasma circulating cell-free DNA: sensitivity and specificity for the diagnosis of myocardial infarction. Int J Mol Med 2014; 35:72-80. [PMID: 25374065 PMCID: PMC4249756 DOI: 10.3892/ijmm.2014.1991] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 10/20/2014] [Indexed: 01/09/2023] Open
Abstract
In the present study, we aimed to develop and validate a rapid and sensitive, Alu-based real-time PCR method for the detection of circulating cell-free DNA (cfDNA). This method targeted repetitive elements of the Alu reduplicative elements in the human genome, followed by signal amplification using fluorescence quantification. Standard Alu-puc57 vectors were constructed and 5 pairs of specific primers were designed. Valuation was conducted concerning linearity, variation and recovery. We found 5 linear responses (R1–5=0.998–0.999). The average intra- and inter-assay coefficients of variance were 12.98 and 10.75%, respectively. The recovery was 82.33–114.01%, with a mean recovery index of 101.26%. This Alu-based assay was reliable, accurate and sensitive for the quantitative detection of cfDNA. Plasma from normal controls and patients with myocardial infarction (MI) were analyzed, and the baseline levels of cfDNA were higher in the MI group. The area under the receiver operating characteristic (ROC) curve for Alu1, Alu2, Alu3, Alu4, Alu5 and Alu (Alu1 + Alu2 + Alu3 + Alu4 + Alu5) was 0.887, 0.758, 0.857, 0.940, 0.968 and 0.933, respectively. The optimal cut-off value for Alu1, Alu2, Alu3, Alu4, Alu5 and Alu to predict MI was 3.71, 1.93, 0.22, 3.73, 6.13 and 6.40 log copies/ml. We demonstrate that this new method is a reliable, accurate and sensitive method for the quantitative detection of cfDNA and that it is useful for studying the regulation of cfDNA in certain pathological conditions. Alu4, Alu5 and Alu showed better sensitivity and specificity for the diagnosis of MI compared with cardiac troponin I (cTnI), creatine kinase MB (CK-MB) isoenzyme and lactate dehydrogenase (LDH). Alu5 had the best prognostic ability.
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Affiliation(s)
- Xiaoli Lou
- Department of Central Laboratory, Songjiang Hospital Affiliated First People's Hospital, Shanghai Jiao Tong University, Shanghai 201600, P.R. China
| | - Yanqiang Hou
- Department of Central Laboratory, Songjiang Hospital Affiliated First People's Hospital, Shanghai Jiao Tong University, Shanghai 201600, P.R. China
| | - Dongyu Liang
- Department of Central Laboratory, Songjiang Hospital Affiliated First People's Hospital, Shanghai Jiao Tong University, Shanghai 201600, P.R. China
| | - Liang Peng
- Department of Central Laboratory, Songjiang Hospital Affiliated First People's Hospital, Shanghai Jiao Tong University, Shanghai 201600, P.R. China
| | - Hongwei Chen
- Department of Central Laboratory, Songjiang Hospital Affiliated First People's Hospital, Shanghai Jiao Tong University, Shanghai 201600, P.R. China
| | - Shanyuan Ma
- Department of Central Laboratory, Songjiang Hospital Affiliated First People's Hospital, Shanghai Jiao Tong University, Shanghai 201600, P.R. China
| | - Lurong Zhang
- Department of Radiation Oncology, Shands Cancer Center, University of Florida, Gainesville, FL 32610, USA
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