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Erdem H, Balkan İİ, Karaali R, Ürkmez S, Mete B, Aygün G, Saltoğlu N, Tabak ÖF, Kuşkucu MA. Cell free DNA as a new prognostic biomarker for COVID-19, A prospective cohort study. Diagn Microbiol Infect Dis 2024; 110:116367. [PMID: 38896890 DOI: 10.1016/j.diagmicrobio.2024.116367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 05/02/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024]
Abstract
Predicting the need of hospitalization and intensive care in COVID-19 patients has been challenging with current diagnostic tests since the beginning of the pandemic. We aimed to test cell free DNA (cfDNA) as a novel biomarker for COVID-19 disease severity and mortality. cfDNA concentration was quantified by RT-PCR based test. One hundred and sixty-eight patients(85 outpatients, 61 inpatients,22 ICU) included the study. Mean initial plasma cfDNA levels were significantly different (p < 0.01) in outpatients (1.190,66 ng/ml), inpatients (8.258,10 ng/ml) and ICU patients (84.806,87 ng/ml). ROC analysis showed with 95 % specificity that patients with initial cfDNA concentrations ≥6.389 ng/ml need to be hospitalized and those ≥26.104 ng/ml require ICU referral. cfDNA concentration was correlated with neutrophil/lymphocyte ratio, lymphocyte level, CRP, AST, LDH, CK, fibrinogen, ferritin and D-dimer. Plasma cfDNA levels on admission, well correlating with disease severity and mortality in COVID-19 that found as a useful biomarker.
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Affiliation(s)
- Hazal Erdem
- Kars Harakani State Hospital, Infectious Diseases and Clinical Microbiology; Istanbul University-Cerrahpasa, Cerrahpasa School of Medicine, Infectious Diseases and Clinical Microbiology.
| | - İlker İnanç Balkan
- Istanbul University-Cerrahpasa, Cerrahpasa School of Medicine, Infectious Diseases and Clinical Microbiology
| | - Rıdvan Karaali
- Istanbul University-Cerrahpasa, Cerrahpasa School of Medicine, Infectious Diseases and Clinical Microbiology
| | - Seval Ürkmez
- Istanbul University-Cerrahpasa, Cerrahpasa School of Medicine, Anesthesiology and Reanimation
| | - Birgül Mete
- Istanbul University-Cerrahpasa, Cerrahpasa School of Medicine, Infectious Diseases and Clinical Microbiology
| | - Gökhan Aygün
- Istanbul University-Cerrahpasa, Cerrahpasa School of Medicine, Infectious Diseases and Clinical Microbiology; Istanbul University-Cerrahpasa, Cerrahpasa School of Medicine, Medical Microbiology
| | - Neşe Saltoğlu
- Istanbul University-Cerrahpasa, Cerrahpasa School of Medicine, Infectious Diseases and Clinical Microbiology
| | - Ömer Fehmi Tabak
- Istanbul University-Cerrahpasa, Cerrahpasa School of Medicine, Infectious Diseases and Clinical Microbiology
| | - Mert Ahmet Kuşkucu
- Istanbul University-Cerrahpasa, Cerrahpasa School of Medicine, Medical Microbiology; Koc University, School of Medicine, Medical Microbiology; Koç University İşbank Center for Infectious Diseases (KUISCID)
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Harutyunyan T, Sargsyan A, Kalashyan L, Igityan H, Grigoryan B, Davtyan H, Aroutiounian R, Liehr T, Hovhannisyan G. Changes in Telomere Length in Leukocytes and Leukemic Cells after Ultrashort Electron Beam Radiation. Int J Mol Sci 2024; 25:6709. [PMID: 38928414 PMCID: PMC11203595 DOI: 10.3390/ijms25126709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Application of laser-generated electron beams in radiotherapy is a recent development. Accordingly, mechanisms of biological response to radiation damage need to be investigated. In this study, telomere length (TL) as endpoint of genetic damage was analyzed in human blood cells (leukocytes) and K562 leukemic cells irradiated with laser-generated ultrashort electron beam. Metaphases and interphases were analyzed in quantitative fluorescence in situ hybridization (Q-FISH) to assess TL. TLs were shortened compared to non-irradiated controls in both settings (metaphase and interphase) after irradiation with 0.5, 1.5, and 3.0 Gy in blood leukocytes. Radiation also caused a significant TL shortening detectable in the interphase of K562 cells. Overall, a negative correlation between TL and radiation doses was observed in normal and leukemic cells in a dose-dependent manner. K562 cells were more sensitive than normal blood cells to increasing doses of ultrashort electron beam radiation. As telomere shortening leads to genome instability and cell death, the results obtained confirm the suitability of this biomarker for assessing genotoxic effects of accelerated electrons for their further use in radiation therapy. Observed differences in TL shortening between normal and K562 cells provide an opportunity for further development of optimal radiation parameters to reduce side effects in normal cells during radiotherapy.
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Affiliation(s)
- Tigran Harutyunyan
- Laboratory of General and Molecular Genetics, Research Institute of Biology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (T.H.); (A.S.); (L.K.); (H.I.); (R.A.); (G.H.)
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia
| | - Anzhela Sargsyan
- Laboratory of General and Molecular Genetics, Research Institute of Biology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (T.H.); (A.S.); (L.K.); (H.I.); (R.A.); (G.H.)
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia
| | - Lily Kalashyan
- Laboratory of General and Molecular Genetics, Research Institute of Biology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (T.H.); (A.S.); (L.K.); (H.I.); (R.A.); (G.H.)
| | - Hovhannes Igityan
- Laboratory of General and Molecular Genetics, Research Institute of Biology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (T.H.); (A.S.); (L.K.); (H.I.); (R.A.); (G.H.)
| | - Bagrat Grigoryan
- CANDLE Synchrotron Research Institute, Acharyan 31, Yerevan 0040, Armenia; (B.G.); (H.D.)
| | - Hakob Davtyan
- CANDLE Synchrotron Research Institute, Acharyan 31, Yerevan 0040, Armenia; (B.G.); (H.D.)
| | - Rouben Aroutiounian
- Laboratory of General and Molecular Genetics, Research Institute of Biology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (T.H.); (A.S.); (L.K.); (H.I.); (R.A.); (G.H.)
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany
| | - Galina Hovhannisyan
- Laboratory of General and Molecular Genetics, Research Institute of Biology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (T.H.); (A.S.); (L.K.); (H.I.); (R.A.); (G.H.)
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia
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Heil M. Self-DNA driven inflammation in COVID-19 and after mRNA-based vaccination: lessons for non-COVID-19 pathologies. Front Immunol 2024; 14:1259879. [PMID: 38439942 PMCID: PMC10910434 DOI: 10.3389/fimmu.2023.1259879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/26/2023] [Indexed: 03/06/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic triggered an unprecedented concentration of economic and research efforts to generate knowledge at unequalled speed on deregulated interferon type I signalling and nuclear factor kappa light chain enhancer in B-cells (NF-κB)-driven interleukin (IL)-1β, IL-6, IL-18 secretion causing cytokine storms. The translation of the knowledge on how the resulting systemic inflammation can lead to life-threatening complications into novel treatments and vaccine technologies is underway. Nevertheless, previously existing knowledge on the role of cytoplasmatic or circulating self-DNA as a pro-inflammatory damage-associated molecular pattern (DAMP) was largely ignored. Pathologies reported 'de novo' for patients infected with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV)-2 to be outcomes of self-DNA-driven inflammation in fact had been linked earlier to self-DNA in different contexts, e.g., the infection with Human Immunodeficiency Virus (HIV)-1, sterile inflammation, and autoimmune diseases. I highlight particularly how synergies with other DAMPs can render immunogenic properties to normally non-immunogenic extracellular self-DNA, and I discuss the shared features of the gp41 unit of the HIV-1 envelope protein and the SARS-CoV 2 Spike protein that enable HIV-1 and SARS-CoV-2 to interact with cell or nuclear membranes, trigger syncytia formation, inflict damage to their host's DNA, and trigger inflammation - likely for their own benefit. These similarities motivate speculations that similar mechanisms to those driven by gp41 can explain how inflammatory self-DNA contributes to some of most frequent adverse events after vaccination with the BNT162b2 mRNA (Pfizer/BioNTech) or the mRNA-1273 (Moderna) vaccine, i.e., myocarditis, herpes zoster, rheumatoid arthritis, autoimmune nephritis or hepatitis, new-onset systemic lupus erythematosus, and flare-ups of psoriasis or lupus. The hope is to motivate a wider application of the lessons learned from the experiences with COVID-19 and the new mRNA vaccines to combat future non-COVID-19 diseases.
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Affiliation(s)
- Martin Heil
- Departamento de Ingeniería Genética, Laboratorio de Ecología de Plantas, Centro de Investigación y de Estudios Avanzados (CINVESTAV)-Unidad Irapuato, Irapuato, Mexico
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Bhansali D, Akinade T, Li T, Zhong Y, Liu F, Huang H, Tu Z, Devey EA, Zhu Y, Jensen DD, Leong KW. Comparative Analysis of Nucleic Acid-Binding Polymers as Potential Anti-Inflammatory Nanocarriers. Pharmaceutics 2023; 16:10. [PMID: 38276488 PMCID: PMC10819575 DOI: 10.3390/pharmaceutics16010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Conventionally, nanocarriers are used to regulate the controlled release of therapeutic payloads. Increasingly, they can also be designed to have an intrinsic therapeutic effect. For example, a positively charged nanocarrier can bind damage-associated molecular patterns, inhibiting toll-like receptor (TLR) pathway activation and thus modulating inflammation. These nucleic acid-binding nanomaterials (NABNs), which scavenge pro-inflammatory stimuli, exist in diverse forms, ranging from soluble polymers to nanoparticles and 2D nanosheets. Unlike conventional drugs that primarily address inflammation symptoms, these NABPs target the upstream inflammation initiation pathway by removing the agonists responsible for inflammation. Many NABNs have demonstrated effectiveness in murine models of inflammatory diseases. However, these scavengers have not been systematically studied and compared within a single setting. Herein, we screen a subset of the most potent NABNs to define their relative efficiency in scavenging cell-free nucleic acids and inhibiting various TLR pathways. This study helps interpret existing in vivo results and provides insights into the future design of anti-inflammatory nanocarriers.
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Affiliation(s)
- Divya Bhansali
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; (D.B.)
| | - Tolulope Akinade
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; (D.B.)
| | - Tianyu Li
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; (D.B.)
| | - Yiling Zhong
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; (D.B.)
| | - Feng Liu
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; (D.B.)
| | - Hanyao Huang
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; (D.B.)
| | - Zhaoxu Tu
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; (D.B.)
| | - Elsie A. Devey
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; (D.B.)
| | - Yuefei Zhu
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; (D.B.)
| | - Dane D. Jensen
- Translational Research Center, College of Dentistry, New York University, New York, NY 10010, USA;
- Pain Research Center, New York University, New York, NY 10010, USA
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; (D.B.)
- Department of Systems Biology, Columbia University, New York, NY 10027, USA
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Hoeter K, Neuberger E, Fischer S, Herbst M, Juškevičiūtė E, Enders K, Rossmann H, Sprinzl MF, Simon P, Bodenstein M, Schaefer M. Evidence for the utility of cfDNA plasma concentrations to predict disease severity in COVID-19: a retrospective pilot study. PeerJ 2023; 11:e16072. [PMID: 37744227 PMCID: PMC10512938 DOI: 10.7717/peerj.16072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 08/20/2023] [Indexed: 09/26/2023] Open
Abstract
Background COVID-19 is a worldwide pandemic caused by the highly infective SARS-CoV-2. There is a need for biomarkers not only for overall prognosis but also for predicting the response to treatments and thus for improvements in the clinical management of patients with COVID-19. Circulating cell-free DNA (cfDNA) has emerged as a promising biomarker in the assessment of various pathological conditions. The aim of this retrospective and observational pilot study was to investigate the range of cfDNA plasma concentrations in hospitalized COVID-19 patients during the first wave of SARS-CoV-2 infection, to relate them to established inflammatory parameters as a correlative biomarker for disease severity, and to compare them with plasma levels in a healthy control group. Methods Lithium-Heparin plasma samples were obtained from COVID-19 patients (n = 21) during hospitalization in the University Medical Centre of Mainz, Germany between March and June 2020, and the cfDNA concentrations were determined by quantitative PCR yielding amplicons of long interspersed nuclear elements (LINE-1). The cfDNA levels were compared with those of an uninfected control group (n = 19). Results Plasma cfDNA levels in COVID-19 patients ranged from 247.5 to 6,346.25 ng/ml and the mean concentration was 1,831 ± 1,388 ng/ml (± standard deviation), which was significantly different from the levels of the uninfected control group (p < 0.001). Regarding clinical complications, the highest correlation was found between cfDNA levels and the myositis (p = 0.049). In addition, cfDNA levels correlated with the "WHO clinical progression scale". D-Dimer and C-reactive protein (CRP) were the clinical laboratory parameters with the highest correlations with cfDNA levels. Conclusion The results of this observational pilot study show a wide range in cfDNA plasma concentrations in patients with COVID-19 during the first wave of infection and confirm that cfDNA plasma concentrations serve as a predictive biomarker of disease severity in COVID-19.
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Affiliation(s)
- Katharina Hoeter
- Department of Anaesthesiology, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Elmo Neuberger
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Susanne Fischer
- Department of Anaesthesiology, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Manuel Herbst
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Ema Juškevičiūtė
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes-Gutenberg Universität Mainz, Mainz, Germany
- Institute of Sport Science and Innovations, Lithuanian Sports University, Kaunas, Lithuania
| | - Kira Enders
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Heidi Rossmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Martin F. Sprinzl
- Department of Internal Medicine I, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Perikles Simon
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Marc Bodenstein
- Department of Anaesthesiology, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Michael Schaefer
- Department of Anaesthesiology, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
- Focus Program Translational Neurosciences (FTN), Johannes Gutenberg-University, Mainz, Germany
- Research Center for Immunotherapy, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
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Hovhannisyan G, Harutyunyan T, Aroutiounian R, Liehr T. The Diagnostic, Prognostic, and Therapeutic Potential of Cell-Free DNA with a Special Focus on COVID-19 and Other Viral Infections. Int J Mol Sci 2023; 24:14163. [PMID: 37762464 PMCID: PMC10532175 DOI: 10.3390/ijms241814163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Cell-free DNA (cfDNA) in human blood serum, urine, and other body fluids recently became a commonly used diagnostic marker associated with various pathologies. This is because cfDNA enables a much higher sensitivity than standard biochemical parameters. The presence of and/or increased level of cfDNA has been reported for various diseases, including viral infections, including COVID-19. Here, we review cfDNA in general, how it has been identified, where it can derive from, its molecular features, and mechanisms of release and clearance. General suitability of cfDNA for diagnostic questions, possible shortcomings and future directions are discussed, with a special focus on coronavirus infection.
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Affiliation(s)
- Galina Hovhannisyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (G.H.); (T.H.); (R.A.)
| | - Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (G.H.); (T.H.); (R.A.)
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (G.H.); (T.H.); (R.A.)
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, 07747 Jena, Germany
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