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Nusshag C, Schreiber P, Uhrig J, Zeier M, Krautkrämer E. In-cell Western assay to quantify infection with pathogenic orthohantavirus Puumala virus in replication kinetics and antiviral drug testing. Virus Res 2023; 337:199230. [PMID: 37777116 PMCID: PMC10590686 DOI: 10.1016/j.virusres.2023.199230] [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: 08/25/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Hemorrhagic fever with renal syndrome (HFRS) represents a serious zoonotic disease caused by orthohantaviruses in Eurasia. A specific antiviral therapy is not available. HFRS is characterized by acute kidney injury (AKI) with often massive proteinuria. Infection of kidney cells may contribute to the clinical picture. However, orthohantaviral replication in kidney cells is not well characterized. Therefore, we aimed to perform a reliable high-throughput assay that allows the quantification of infection rates and testing of antiviral compounds in different cell types. We quantified relative infection rates of Eurasian pathogenic Puumala virus (PUUV) by staining of nucleocapsid protein (N protein) in an in-cell Western (ICW) assay. Vero E6 cells, derived from the African green monkey and commonly used in viral cell culture studies, and the human podocyte cell line CIHP (conditionally immortalized human podocytes) were used to test the ICW assay for replication kinetics and antiviral drug testing. Quantification of infection by ICW revealed reliable results for both cell types, as shown by their correlation with immunofluorescence quantification results by counting infected cells. Evaluation of antiviral efficacy of ribavirin by ICW assay revealed differences in the toxicity (TC) and inhibitory concentrations (IC) between Vero E6 cells and podocytes. IC5O of ribavirin in podocytes is about 12-fold lower than in Vero E6 cells. In summary, ICW assay together with relevant human target cells represents an important tool for the study of hantaviral replication and drug testing.
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Affiliation(s)
- Christian Nusshag
- Department of Nephrology, University of Heidelberg, Im Neuenheimer Feld 162, Heidelberg 69120, Germany
| | - Pamela Schreiber
- Department of Nephrology, University of Heidelberg, Im Neuenheimer Feld 162, Heidelberg 69120, Germany
| | - Josephine Uhrig
- Department of Nephrology, University of Heidelberg, Im Neuenheimer Feld 162, Heidelberg 69120, Germany
| | - Martin Zeier
- Department of Nephrology, University of Heidelberg, Im Neuenheimer Feld 162, Heidelberg 69120, Germany
| | - Ellen Krautkrämer
- Department of Nephrology, University of Heidelberg, Im Neuenheimer Feld 162, Heidelberg 69120, Germany.
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2
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Olesen AS, Lohse L, Johnston CM, Rasmussen TB, Bøtner A, Belsham GJ. Increased Presence of Circulating Cell-Free, Fragmented, Host DNA in Pigs Infected with Virulent African Swine Fever Virus. Viruses 2023; 15:2133. [PMID: 37896910 PMCID: PMC10612093 DOI: 10.3390/v15102133] [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: 09/18/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
African swine fever virus (ASFV) causes severe hemorrhagic disease in domestic pigs and wild boar, often with high case fatality rates. The virus replicates in the circulating cells of the monocyte-macrophage lineage and within lymphoid tissues. The infection leads to high fever and a variety of clinical signs. In this study, it was observed that ASFV infection in pigs resulted in a >1000-fold increase in the level of circulating cell-free DNA (cfDNA), derived from the nuclei of host cells in the serum. This change occurred in parallel with the increase in circulating ASFV DNA. In addition, elevated levels (about 30-fold higher) of host mitochondrial DNA (mtDNA) were detected in the serum from ASFV-infected pigs. For comparison, the release of the cellular enzyme, lactate dehydrogenase (LDH), a commonly used marker of cellular damage, was also found to be elevated during ASFV infection, but later and less consistently. The sera from pigs infected with classical swine fever virus (CSFV), which causes a clinically similar disease to ASFV, were also tested but, surprisingly, this infection did not result in the release of cfDNA, mtDNA, or LDH. It was concluded that the level of cfDNA in the serum is a sensitive host marker of virulent ASFV infection.
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Affiliation(s)
- Ann Sofie Olesen
- Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen, Denmark; (L.L.); (C.M.J.); (T.B.R.)
| | - Louise Lohse
- Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen, Denmark; (L.L.); (C.M.J.); (T.B.R.)
| | - Camille Melissa Johnston
- Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen, Denmark; (L.L.); (C.M.J.); (T.B.R.)
| | - Thomas Bruun Rasmussen
- Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen, Denmark; (L.L.); (C.M.J.); (T.B.R.)
| | - Anette Bøtner
- Section for Veterinary Clinical Microbiology, Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg, Denmark;
| | - Graham J. Belsham
- Section for Veterinary Clinical Microbiology, Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg, Denmark;
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3
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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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4
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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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5
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Guo ZW, Liu Q, Yang X, Cai GX, Han BW, Huang LM, Li CX, Liang ZK, Zhai XM, Lin L, Li K, Zhang M, Liu TC, Pan RL, Wu YS, Yang XX. Noninvasive prediction of axillary lymph node status in breast cancer using promoter profiling of circulating cell-free DNA. J Transl Med 2022; 20:557. [PMID: 36463222 PMCID: PMC9719247 DOI: 10.1186/s12967-022-03724-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/24/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Lymph node metastasis (LNM) is one of the most important factors affecting the prognosis of breast cancer. The accurate evaluation of lymph node status is useful to predict the outcomes of patients and guide the choice of cancer treatment. However, there is still lack of a low-cost non-invasive method to assess the status of axillary lymph node (ALN). Gene expression signature has been used to assess lymph node metastasis status of breast cancer. In addition, nucleosome footprint of cell-free DNA (cfDNA) carries gene expression information of its original tissues, so it may be used to evaluate the axillary lymph node status in breast cancer. METHODS In this study, we found that the cfDNA nucleosome footprints between the ALN-positive patients and ALN-negative patients showed different patterns by implementing whole-genome sequencing (WGS) to detect 15 ALN-positive and 15 ALN-negative patients. In order to further evaluate its potential for assessing ALN status, we developed a classifier with multiple machine learning models by using 330 WGS data of cfDNA from 162 ALN-positive and 168 ALN-negative samples to distinguish these two types of patients. RESULTS We found that the promoter profiling between the ALN-positive patients and ALN-negative patients showed distinct patterns. In addition, we observed 1071 genes with differential promoter coverage and their functions were closely related to tumorigenesis. We found that the predictive classifier based on promoter profiling with a support vector machine model, named PPCNM, produced the largest area under the curve of 0.897 (95% confidence interval 0.86-0.93). CONCLUSIONS These results indicate that promoter profiling can be used to distinguish ALN-positive patients from ALN-negative patients, which may be helpful to guide the choice of cancer treatment.
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Affiliation(s)
- Zhi-Wei Guo
- grid.284723.80000 0000 8877 7471Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1838 N. Guangzhou Ave, Guangzhou, 510515 China ,grid.413432.30000 0004 1798 5993Guangzhou First People’s Hospital, The Second Affiliated Hospital of South China University of Technology, Guangzhou, 510180 People’s Republic of China
| | - Qing Liu
- grid.452881.20000 0004 0604 5998Department of Breast Surgery, The First People’s Hospital of Foshan, 81 N. North Lingnan Avenue, Foshan, China
| | - Xu Yang
- grid.284723.80000 0000 8877 7471Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1838 N. Guangzhou Ave, Guangzhou, 510515 China
| | - Geng-Xi Cai
- grid.452881.20000 0004 0604 5998Department of Breast Surgery, The First People’s Hospital of Foshan, 81 N. North Lingnan Avenue, Foshan, China ,grid.12981.330000 0001 2360 039XSun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 China
| | - Bo-Wei Han
- grid.284723.80000 0000 8877 7471Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1838 N. Guangzhou Ave, Guangzhou, 510515 China
| | - Li-Min Huang
- grid.284723.80000 0000 8877 7471Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1838 N. Guangzhou Ave, Guangzhou, 510515 China
| | - Chun-Xi Li
- grid.284723.80000 0000 8877 7471Department of Respiratory and Critical Care Medicine, Chronic Airways Diseases Laboratory, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 China
| | - Zhi-Kun Liang
- grid.284723.80000 0000 8877 7471Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1838 N. Guangzhou Ave, Guangzhou, 510515 China
| | - Xiang-Ming Zhai
- grid.284723.80000 0000 8877 7471Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1838 N. Guangzhou Ave, Guangzhou, 510515 China
| | - Li Lin
- grid.284723.80000 0000 8877 7471Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1838 N. Guangzhou Ave, Guangzhou, 510515 China
| | - Kun Li
- Guangzhou XGene Co., Ltd. High-Tech Development Zone, Guangzhou, 510665 People’s Republic of China
| | - Min Zhang
- grid.284723.80000 0000 8877 7471Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1838 N. Guangzhou Ave, Guangzhou, 510515 China
| | - Tian-Cai Liu
- grid.284723.80000 0000 8877 7471Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1838 N. Guangzhou Ave, Guangzhou, 510515 China
| | - Rui-lin Pan
- grid.452881.20000 0004 0604 5998Department of Breast Surgery, The First People’s Hospital of Foshan, 81 N. North Lingnan Avenue, Foshan, China
| | - Ying-Song Wu
- grid.284723.80000 0000 8877 7471Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1838 N. Guangzhou Ave, Guangzhou, 510515 China
| | - Xue-Xi Yang
- grid.284723.80000 0000 8877 7471Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1838 N. Guangzhou Ave, Guangzhou, 510515 China
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6
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Wang M, Zhang C, Ma Y, Tang K, Zhang X, Jia X, Hu H, Zhuang R, Jin B, Zhang Y, Zhang Y. Anti-platelet factor 4/heparin antibodies in patients with Hantaan virus infection. Res Pract Thromb Haemost 2022; 6:e12813. [PMID: 36246479 PMCID: PMC9548412 DOI: 10.1002/rth2.12813] [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: 01/01/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background Hemorrhagic fever with renal syndrome (HFRS) induced by Hantaan virus infection and heparin‐induced thrombocytopenia (HIT) are associated with symptoms such as thrombocytopenia and thrombosis. However, related molecules, such as anti–platelet factor 4 (PF4)/heparin antibodies, in patients with HFRS have not been evaluated. Objectives To test plasma levels of anti‐PF4/heparin antibodies and study the possible role of these antibodies in HFRS pathogenesis. Methods Indirect ELISA was used to determine plasma levels of anti‐PF4/heparin antibodies in 75 patients with HFRS and 20 normal controls. The 4Ts (thrombocytopenia, timing of platelet count fall, thrombosis or other sequelae, and other causes of thrombocytopenia) scoring system was used to determine the probability of HIT occurrence. A PF4‐enhanced platelet activation assay was used to detect the pathological effects of anti‐PF4/heparin antibodies. The laboratory/clinical features and viral load of all the patients were also assessed. Results Of the 75 patients with HFRS enrolled in this study, 69 had thrombocytopenia. Platelet count was negatively correlated with Hantaan viral load. Moreover, the optical density (OD) values of plasma antibodies against PF4/heparin in normal controls were less than 0.65, 4 patients tested strongly positive for anti‐PF4/heparin antibodies (OD values, 1.51–3.87), 21 patients were weakly positive (OD values, 0.66–0.74), and 50 patients were negative (OD values, 0.16–0.65). Moreover, all 4 patients who tested strongly positive for anti‐PF4/heparin antibodies showed a low probability of HIT (4Ts score of 3 or less) and had negative results in the PF4‐enhanced platelet activation assay. Conclusions Hantaan virus infection produces nonpathogenic antibodies against PF4/heparin; however, the generation mechanism of these antibodies requires further study.
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Affiliation(s)
- Meng Wang
- Department of ImmunologyBasic Medicine SchoolAir Force Medical UniversityXi'anChina,Department of ImmunologyMedicine SchoolYanan UniversityYananChina
| | - Chun‐mei Zhang
- Department of ImmunologyBasic Medicine SchoolAir Force Medical UniversityXi'anChina
| | - Ying Ma
- Department of ImmunologyBasic Medicine SchoolAir Force Medical UniversityXi'anChina
| | - Kang Tang
- Department of ImmunologyBasic Medicine SchoolAir Force Medical UniversityXi'anChina
| | - Xi‐yue Zhang
- Department of ImmunologyBasic Medicine SchoolAir Force Medical UniversityXi'anChina,Department of Pathogenic BiologyMedicine SchoolYanan UniversityYananChina
| | - Xiao‐zhou Jia
- Department of Infectious DiseaseXi'an Eighth HospitalXi'anChina
| | - Hai‐feng Hu
- Department of Infectious DiseaseTangdu Hospital of Air Force Medical UniversityXi'anChina
| | - Ran Zhuang
- Department of ImmunologyBasic Medicine SchoolAir Force Medical UniversityXi'anChina
| | - Bo‐quan Jin
- Department of ImmunologyBasic Medicine SchoolAir Force Medical UniversityXi'anChina
| | - Yu‐si Zhang
- Department of ImmunologyBasic Medicine SchoolAir Force Medical UniversityXi'anChina
| | - Yun Zhang
- Department of ImmunologyBasic Medicine SchoolAir Force Medical UniversityXi'anChina
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Kim PJ, Olymbios M, Siu A, Wever Pinzon O, Adler E, Liang N, Swenerton R, Sternberg J, Kaur N, Ahmed E, Chen YA, Fehringer G, Demko ZP, Billings PR, Stehlik J. A novel donor-derived cell-free DNA assay for the detection of acute rejection in heart transplantation. J Heart Lung Transplant 2022; 41:919-927. [PMID: 35577713 PMCID: PMC9670834 DOI: 10.1016/j.healun.2022.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/06/2022] [Accepted: 04/04/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Endomyocardial biopsy (EMB), the reference surveillance test for acute rejection (AR) in heart transplant (HTx) recipients, is invasive, costly, and shows significant interobserver variability. Recent studies indicate that donor-derived cell-free DNA (dd-cfDNA), obtained non-invasively from blood, is associated with AR and could reduce the frequency of EMB surveillance. The aim of this study was to examine the performance characteristics of a novel test for detecting AR in adult HTx recipients. METHODS Plasma samples with contemporaneous EMBs were obtained from HTx recipients. A clinically available SNP-based massively multiplexed-PCR dd-cfDNA assay was used to measure dd-cfDNA fraction. dd-cfDNA fractions were compared with EMB-defined rejection status and test performance was assessed by constructing ROC curves and calculating accuracy measures. RESULTS A total of 811 samples from 223 patients with dd-cfDNA testing and contemporaneous EMB were eligible for the study. dd-cfDNA fraction was significantly higher in AR (median 0.58%, IQR, 0.13%-1.68%) compared to non-AR (median 0.04%, IQR, 0.01%-0.11%, pc < 0.001). ROC analysis produced an area under the curve (AUC-ROC) of 0.86 (95% CI, 0.77-0.96). Defining samples with dd-cfDNA fraction ≥0.15% as AR yielded 78.5% sensitivity (95% CI, 60.7%-96.3%) and 76.9% specificity (95% CI, 71.1%-82.7%). Positive and negative predictive values were 25.1% (95% CI, 18.8%-31.5%) and 97.3% (95% CI, 95.1%-99.5%) respectively, calculated using the cohort AR prevalence of 9.0% (95% CI, 5.3%-12.8%) with adjustment for repeat samples. CONCLUSIONS This novel dd-cfDNA test detects AR in HTx recipients with good accuracy and holds promise as a noninvasive test for AR in HTx recipients.
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Affiliation(s)
- Paul J Kim
- UC San Diego Health, San Diego, California
| | | | - Alfonso Siu
- Division of Cardiovascular Medicine, University of Utah School of Medicine, Salt Lake City, Utah
| | - Omar Wever Pinzon
- Division of Cardiovascular Medicine, University of Utah School of Medicine, Salt Lake City, Utah
| | - Eric Adler
- UC San Diego Health, San Diego, California
| | | | | | | | | | | | | | | | | | | | - Josef Stehlik
- Division of Cardiovascular Medicine, University of Utah School of Medicine, Salt Lake City, Utah.
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8
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Yang Y, Li M, Ma Y, Ye W, Si Y, Zheng X, Liu H, Cheng L, Zhang L, Zhang H, Zhang X, Lei Y, Shen L, Zhang F, Ma H. LncRNA NEAT1 Potentiates SREBP2 Activity to Promote Inflammatory Macrophage Activation and Limit Hantaan Virus Propagation. Front Microbiol 2022; 13:849020. [PMID: 35495674 PMCID: PMC9044491 DOI: 10.3389/fmicb.2022.849020] [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: 01/05/2022] [Accepted: 03/10/2022] [Indexed: 11/17/2022] Open
Abstract
As the global prototypical zoonotic hantavirus, Hantaan virus (HTNV) is prevalent in Asia and is the leading causative agent of severe hemorrhagic fever with renal syndrome (HFRS), which has profound morbidity and mortality. Macrophages are crucial components of the host innate immune system and serve as the first line of defense against HTNV infection. Previous studies indicated that the viral replication efficiency in macrophages determines hantavirus pathogenicity, but it remains unknown which factor manipulates the macrophage activation pattern and the virus-host interaction process. Here, we performed the transcriptomic analysis of HTNV-infected mouse bone marrow-derived macrophages and identified the long noncoding RNA (lncRNA) nuclear enriched abundant transcript 1 (NEAT1), especially the isoform NEAT1-2, as one of the lncRNAs that is differentially expressed at the early phase. Based on coculture experiments, we revealed that silencing NEAT1-2 hinders inflammatory macrophage activation and facilitates HTNV propagation, while enhancing NEAT1-2 transcription effectively restrains viral replication. Furthermore, sterol response element binding factor-2 (SREBP2), which controls the cholesterol metabolism process, was found to stimulate macrophages by promoting the production of multiple inflammatory cytokines upon HTNV infection. NEAT1-2 could potentiate SREBP2 activity by upregulating Srebf1 expression and interacting with SREBP2, thus stimulating inflammatory macrophages and limiting HTNV propagation. More importantly, we demonstrated that the NEAT1-2 expression level in patient monocytes was negatively correlated with viral load and HFRS disease progression. Our results identified a function and mechanism of action for the lncRNA NEAT1 in heightening SREBP2-mediated macrophage activation to restrain hantaviral propagation and revealed the association of NEAT1 with HFRS severity.
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Affiliation(s)
- Yongheng Yang
- College of Life Sciences, Northwest University, Xi'an, China.,Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Mengyun Li
- College of Life Sciences, Northwest University, Xi'an, China.,Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Yongtao Ma
- Department of Emergency, Children's Hospital of Kaifeng City, Kaifeng, China
| | - Wei Ye
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Yue Si
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Xuyang Zheng
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China.,Department of Infectious Diseases, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - He Liu
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Linfeng Cheng
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Liang Zhang
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Hui Zhang
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Xijing Zhang
- Department of Anesthesiology and Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Yingfeng Lei
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Lixin Shen
- College of Life Sciences, Northwest University, Xi'an, China
| | - Fanglin Zhang
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Hongwei Ma
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China.,Department of Anesthesiology and Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
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Clinical and Immunological Predictors of Hemorrhagic Fever with Renal Syndrome Outcome during the Early Phase. Viruses 2022; 14:v14030595. [PMID: 35337004 PMCID: PMC8954228 DOI: 10.3390/v14030595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 11/16/2022] Open
Abstract
The ability to accurately predict the early progression of hemorrhagic fever with renal syndrome (HFRS) is crucial for reducing morbidity and mortality rates in severely affected patients. However, the utility of biomarkers for predicting clinical outcomes remains elusive in HFRS. The aims of the current study were to analyze the serum levels of immune function-related proteins and identify novel biomarkers that may help ascertain clinical outcomes of HFRS. Enzyme-linked immunosorbent assay, Luminex, and bioanalyzer assays were used to quantitatively detect 15 biomarkers in 49 serum samples of 26 patients with HFRS. High hemoglobin (HGB) and low urine output (UO) levels were identified as potential biomarkers associated with the acute HFRS. The serum soluble urokinase plasminogen activator receptor (suPAR) and C-X-C motif chemokine ligand 10 (CXCL10) values increased in the early phase of diseases. Elevated suPAR, interleukin-10 (IL-10), CXCL10, and decreased transforming growth factor-beta 3 (TGF-β3) were representative predictors of the disease severity. Upregulation of the HGB showed a significant correlation with high levels of suPAR and CXCL10. Reduced UO positively correlated with increased suPAR, CXCL10, and TGF-β2, and decreased vascular endothelial growth factor and TGF-β3. The changing HGB and UO criteria, high suPAR, IL-10, CXCL10, and low TGF-β3 of HFRS raise significant awareness for physicians regarding prospective biomarkers for monitoring early warning signs of HFRS. This study provides critical insights into the clinical and immunological biomarkers for disease severity and progression in patients with HFRS to identify early predictions of fatal outcomes.
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10
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Kasi PM, Fehringer G, Taniguchi H, Starling N, Nakamura Y, Kotani D, Powles T, Li BT, Pusztai L, Aushev VN, Kalashnikova E, Sharma S, Malhotra M, Demko ZP, Aleshin A, Rodriguez A, Billings PR, Grothey A, Taieb J, Cunningham D, Yoshino T, Kopetz S. Impact of Circulating Tumor DNA-Based Detection of Molecular Residual Disease on the Conduct and Design of Clinical Trials for Solid Tumors. JCO Precis Oncol 2022; 6:e2100181. [PMID: 35263168 PMCID: PMC8926064 DOI: 10.1200/po.21.00181] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Earlier detection of cancer recurrence using circulating tumor DNA (ctDNA) to detect molecular residual disease (MRD) has the potential to dramatically affect cancer management. We review evidence supporting the use of ctDNA as a biomarker for detection of MRD and highlight the potential impact that ctDNA testing could have on the conduct of clinical trials.
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Affiliation(s)
- Pashtoon M Kasi
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA
| | | | - Hiroya Taniguchi
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Naureen Starling
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Daisuke Kotani
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Thomas Powles
- Barts Cancer Institute, Queen Mary University of London ECMC, Barts Health, London, United Kingdom
| | - Bob T Li
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY
| | - Lajos Pusztai
- Yale Cancer Center, Yale School of Medicine, New Haven, CT
| | | | | | | | | | | | | | | | | | - Axel Grothey
- West Cancer Center and Research Institute, Germantown, TN
| | - Julien Taieb
- Georges Pompidou European Hospital, SIRIC-CARPEM, Université de Paris, Paris, France
| | - David Cunningham
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
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11
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Jr JOR, Yoo J, Desai A, Brossart K, McCormick S, Malashevich AK, Bloom MS, Fehringer G, White R, Billings PR, Tabriziani H, Demko ZP, Gauthier P, Akkina SK, David-Neto E. Association between total cell free DNA and SARS-CoV-2 in Kidney Transplant Patients: A Preliminary Study. Transplant Proc 2022; 54:1446-1454. [PMID: 35618524 PMCID: PMC8920956 DOI: 10.1016/j.transproceed.2022.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022]
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12
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Severity Biomarkers in Puumala Hantavirus Infection. Viruses 2021; 14:v14010045. [PMID: 35062248 PMCID: PMC8778356 DOI: 10.3390/v14010045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
Annually, over 10,000 cases of hemorrhagic fever with renal syndrome (HFRS) are diagnosed in Europe. Puumala hantavirus (PUUV) causes most of the European HFRS cases. PUUV causes usually a relatively mild disease, which is rarely fatal. However, the severity of the infection varies greatly, and factors affecting the severity are mostly unrevealed. Host genes are known to have an effect. The typical clinical features in PUUV infection include acute kidney injury, thrombocytopenia, and increased vascular permeability. The primary target of hantavirus is the endothelium of the vessels of different organs. Although PUUV does not cause direct cytopathology of the endothelial cells, remarkable changes in both the barrier function of the endothelium and the function of the infected endothelial cells occur. Host immune or inflammatory mechanisms are probably important in the development of the capillary leakage. Several immunoinflammatory biomarkers have been studied in the context of assessing the severity of HFRS caused by PUUV. Most of them are not used in clinical practice, but the increasing knowledge about the biomarkers has elucidated the pathogenesis of PUUV infection.
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13
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Extremely High Cell-free DNA Levels Observed in Renal Allograft Patient With SARS-CoV-2 Infection. Transplant Direct 2021; 7:e691. [PMID: 33912658 PMCID: PMC8078311 DOI: 10.1097/txd.0000000000001145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/10/2021] [Accepted: 02/13/2021] [Indexed: 11/27/2022] Open
Abstract
Beyond its widely recognized morbidity and mortality, coronavirus disease 2019 poses an additional health risk to renal allograft recipients. Detection and measurement of donor-derived cell-free DNA (dd-cfDNA), expressed as a fraction of the total cell-free DNA (cfDNA), has emerged as a noninvasive biomarker for allograft rejection. Here, we present a case report of a patient who was infected with severe acute respiratory syndrome coronavirus 2, 11 mo post-kidney transplant. The patient was serially monitored using an analytically and clinically validated massively multiplex PCR-based dd-cfDNA assay to assess allograft injury and risk for rejection. Over the course of infection, low dd-cfDNA fractions were observed (below the 1% cutoff) and were accompanied by unusually highly elevated levels of total cfDNA, which gradually declined as the infection resolved. The case study highlights the variability in total cfDNA levels during and after viral infection, and the need to consider both total and dd-cfDNA levels when clinically interpreting the results for allograft rejection. Furthermore, the study highlights the importance of serial testing, wherein an interplay between total cfDNA and dd-cfDNA can inform the optimization of a patient's immunosuppressive treatment regimen in response to infection.
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14
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Guo Z, Yang F, Zhang J, Zhang Z, Li K, Tian Q, Hou H, Xu C, Lu Q, Ren Z, Yang X, Lv Z, Wang K, Yang X, Wu Y, Yang X. Whole-Genome Promoter Profiling of Plasma DNA Exhibits Diagnostic Value for Placenta-Origin Pregnancy Complications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1901819. [PMID: 32274292 PMCID: PMC7141029 DOI: 10.1002/advs.201901819] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 02/03/2020] [Indexed: 06/06/2023]
Abstract
Placenta-origin pregnancy complications, including preeclampsia (PE), gestational diabetes mellitus (GDM), fetal growth restriction (FGR), and macrosomia (MA) are common occurrences in pregnancy, resulting in significant morbidity and mortality for both mother and fetus. However, despite their frequency, there are no reliable methods for the early diagnosis of these complications. Since cfDNA is mainly derived from placental trophoblasts and maternal hematopoietic cells, it might have information for gene expression which can be used for disease prediction. Here, low coverage whole-genome sequencing on plasma DNA from 2,199 pregnancies is performed based on retrospective cohorts of 3,200 pregnant women. Read depth in the promoter regions is examined to define read-depth distribution patterns of promoters for pregnancy complications and controls. Using machine learning methods, classifiers for predicting pregnancy complications are developed. Using these classifiers, complications are successfully predicted with an accuracy of 80.3%, 78.9%, 72.1%, and 83.0% for MA, FGR, GDM, and PE, respectively. The findings suggest that promoter profiling of cfDNA may be used as a biological biomarker for predicting pregnancy complications at early gestational age.
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Affiliation(s)
- Zhiwei Guo
- Institute of Antibody EngineeringSchool of Laboratory Medicine and BiotechnologySouthern Medical UniversityGuangzhou510515China
| | - Fang Yang
- Department of Obstetrics and GynecologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Jun Zhang
- Department of ObstetricsThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510630China
| | - Zhigang Zhang
- Department of PathologyCangzhou People's HospitalCangzhou061000China
| | - Kun Li
- Institute of Antibody EngineeringSchool of Laboratory Medicine and BiotechnologySouthern Medical UniversityGuangzhou510515China
| | - Qi Tian
- Department of ObstetricsThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510630China
| | - Hongying Hou
- Department of ObstetricsThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510630China
| | - Cailing Xu
- Department of Obstetrics and GynecologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Qianwen Lu
- Department of Obstetrics and GynecologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Zhonglu Ren
- Department of Obstetrics and GynecologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Xiaoxue Yang
- Department of Obstetrics and GynecologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Zenglu Lv
- Department of PathologyCangzhou People's HospitalCangzhou061000China
| | - Ke Wang
- Department of Obstetrics and GynecologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Xinping Yang
- Department of Obstetrics and GynecologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Yingsong Wu
- Institute of Antibody EngineeringSchool of Laboratory Medicine and BiotechnologySouthern Medical UniversityGuangzhou510515China
| | - Xuexi Yang
- Institute of Antibody EngineeringSchool of Laboratory Medicine and BiotechnologySouthern Medical UniversityGuangzhou510515China
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15
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Seminal cell-free DNA levels measured by PicoGreen fluorochrome are associated with sperm fertility criteria. ZYGOTE 2017; 25:111-119. [PMID: 28264730 DOI: 10.1017/s0967199416000307] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Previous investigations suggested that elevated cell-free DNA (cfDNA) can indicate non-healthy states. However, the potential association between cfDNA seminal plasma levels and fertility sperm parameters has not yet been determined. Therefore, the present study evaluated the association between seminal cfDNA levels and sperm fertility criteria to determine the use of seminal cfDNA quantification. An in vivo protocol quantified cfDNA levels of semen samples obtained from 163 male patients using fluorescent PicoGreen dye staining. To confirm if semen cfDNA quantification is realistic, an in vitro complementary test was performed using three or four semen samples. The fresh sperm samples were exposed to paraquat that generates high levels of superoxide anion causing oxidative stress and cell mortality. The results showed significant association between dsDNA levels and several sperm fertility parameters, such as low viability and alterations of motility and morphology. The in vitro analysis confirmed the association between dsDNA levels and sperm viability. Together, these results suggest that dsDNA levels could be an important biomarker to test sperm fertility.
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16
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Khaiboullina SF, Morzunov SP, St Jeor SC, Rizvanov AA, Lombardi VC. Hantavirus Infection Suppresses Thrombospondin-1 Expression in Cultured Endothelial Cells in a Strain-Specific Manner. Front Microbiol 2016; 7:1077. [PMID: 27486439 PMCID: PMC4950404 DOI: 10.3389/fmicb.2016.01077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 06/27/2016] [Indexed: 11/13/2022] Open
Abstract
Hantavirus infection is associated with two frequently fatal diseases in humans: Hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS). The pathogenesis of hantavirus infection is complex and not fully understood; however, it is believed to involve virus-induced hyperinflammatory immune responses. Thrombospondin-1 (THBS1) is a large homotrimeric protein that plays a putative role in regulating blood homeostasis. Hyperresponsiveness to inflammatory stimuli has also been associated with defects in the THBS1 gene. Our data suggest that hantavirus infection of human umbilical cord vein endothelial cells (HUVEC) suppress the accumulation of THBS1 in the extracellular matrix. Additionally, this suppression is dependent on virus replication, implying a direct mechanism of action. Our data also imply that the pathogenic Andes and Hantaan strains inhibit THBS1 expression while the non-pathogenic Prospect Hill strain showed little inhibition. These observations suggest that a dysregulation of THBS1 may contribute to the pathogenesis of hantavirus infection.
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Affiliation(s)
- Svetlana F Khaiboullina
- Nevada Center for Biomedical ResearchReno, NV, USA; Department of Genetics, Institute of Fundamental Medicine and Biology, Kazan Federal UniversityKazan, Russia
| | - Sergey P Morzunov
- Nevada State Public Health Laboratory, University of Nevada, Reno School of Medicine Reno, NV, USA
| | - Stephen C St Jeor
- Department of Immunology and Microbiology, University of Nevada, Reno School of Medicine Reno, NV, USA
| | - Albert A Rizvanov
- Department of Genetics, Institute of Fundamental Medicine and Biology, Kazan Federal University Kazan, Russia
| | - Vincent C Lombardi
- Nevada Center for Biomedical ResearchReno, NV, USA; Department of Biochemistry and Molecular Biology, University of NevadaReno, NV, USA
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17
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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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18
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Jeong DW, Moon JY, Choi YW, Moon H, Kim K, Lee YH, Kim SY, Kim YG, Jeong KH, Lee SH. Effect of blood pressure and glycemic control on the plasma cell-free DNA in hemodialysis patients. Kidney Res Clin Pract 2015; 34:201-6. [PMID: 26779422 PMCID: PMC4688578 DOI: 10.1016/j.krcp.2015.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 09/01/2015] [Accepted: 09/21/2015] [Indexed: 12/21/2022] Open
Abstract
Background The plasma levels of cell-free DNA (cfDNA) are known to be elevated under inflammatory or apoptotic conditions. Increased cfDNA levels have been reported in hemodialysis (HD) patients. The aim of this study was to investigate the clinical significance of cfDNA in HD patients. Methods A total of 95 patients on HD were enrolled. We measured their predialysis cfDNA levels using real-time EIF2C1 gene sequence amplification and analyzed its association with certain clinical parameters. Results The mean plasma cfDNA level in the HD patients was 3,884 ± 407 GE/mL, and the mean plasma cfDNA level in the control group was 1,420 ± 121 GE/mL (P < 0.05). Diabetic patients showed higher plasma cfDNA levels compared with nondiabetic patients (P < 0.01). Patients with cardiovascular complications also showed higher plasma cfDNA levels compared with those without cardiovascular complication (P < 0.05). In univariable analysis, the cfDNA level was associated with 3-month mean systolic blood pressure (SBP), white blood cell, serum albumin, creatinine (Cr), normalized protein catabolic rate in HD patients. In diabetic patients, it was significantly correlated with SBP, hemoglobin A1c, and serum albumin. In multivariate analysis, SBP was the independent determinant for the cfDNA level. In diabetic patients, cfDNA level was independently associated with hemoglobin A1c and SBP. Conclusions In patients with HD, cfDNA is elevated in diabetic patients and patients with cardiovascular diseases. Uncontrolled hypertension and poor glycemic control are independent determinants for the elevated cfDNA. Our data suggest that cfDNA might be a marker of vascular injury rather than proinflammatory condition in HD patients.
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Affiliation(s)
- Da Wun Jeong
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Ju-Young Moon
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Young-Wook Choi
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Haena Moon
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Kipyo Kim
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Yu-Ho Lee
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Se-Yeun Kim
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Yang-Gyun Kim
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Kyung-Hwan Jeong
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Sang-Ho Lee
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Korea
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19
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Lewis JM, Heineck DP, Heller MJ. Detecting cancer biomarkers in blood: challenges for new molecular diagnostic and point-of-care tests using cell-free nucleic acids. Expert Rev Mol Diagn 2015; 15:1187-200. [PMID: 26189641 DOI: 10.1586/14737159.2015.1069709] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
As we move into the era of individualized cancer treatment, the need for more sophisticated cancer diagnostics has emerged. Cell-free (cf) nucleic acids (cf-DNA, cf-RNA) and other cellular nanoparticulates are now considered important and selective biomarkers. There is great hope that blood-borne cf-nucleic acids can be used for 'liquid biopsies', replacing more invasive tissue biopsies to analyze cancer mutations and monitor therapy. Conventional techniques for cf-nucleic acid biomarker isolation from blood are generally time-consuming, complicated and expensive. They require relatively large blood samples, which must be processed to serum or plasma before isolation of biomarkers can proceed. Such cumbersome sample preparation also limits the widespread use of powerful, downstream genomic analyses, including PCR and DNA sequencing. These limitations also preclude rapid, point-of-care diagnostic applications. Thus, new technologies that allow rapid isolation of biomarkers directly from blood will permit seamless sample-to-answer solutions that enable next-generation point-of-care molecular diagnostics.
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Affiliation(s)
- Jean M Lewis
- a 1 Department of Nanoengineering, University of California - San Diego, SME Building, 9500 Gilman Dr., La Jolla, CA 92093-0448, USA
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20
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Release of bulk cell free DNA during physical exercise occurs independent of extracellular vesicles. Eur J Appl Physiol 2015; 115:2271-80. [DOI: 10.1007/s00421-015-3207-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 06/23/2015] [Indexed: 12/18/2022]
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21
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Yang WE, Woods CW, Tsalik EL. Host-Based Diagnostics for Detection and Prognosis of Infectious Diseases. J Microbiol Methods 2015. [DOI: 10.1016/bs.mim.2015.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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