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Casini F, Valentino MS, Lorenzo MG, Caiazzo R, Coppola C, David D, Di Tonno R, Giacomet V. Use of transcriptomics for diagnosis of infections and sepsis in children: A narrative review. Acta Paediatr 2024; 113:670-676. [PMID: 38243675 DOI: 10.1111/apa.17119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
AIM The aim of this review was to summarise the most recent evidence about the use of omics-based techniques as an instrument for a more rapid and accurate characterisation of respiratory tract infections, neurological infections and sepsis in paediatrics. METHODS We performed a narrative review using PubMed and a set of inclusion criteria: English language articles, clinical trials, meta-analysis and reviews including only paediatric population inherited to this topic in the last 15 years. RESULTS The examined studies suggest that host gene expression signatures are an effective method to characterise the different types of infections, to distinguish infection from colonisation and, in some cases, to assess the severity of the disease in children. CONCLUSIONS 'Omics-based techniques' may help to define the aetiology of infections in paediatrics, representing a useful tool to choose the most appropriate therapies and limit antibiotic resistance.
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Affiliation(s)
- Francesca Casini
- Pediatric Department, "Vittore Buzzi" Children's Hospital, Milan, Italy
| | - Maria Sole Valentino
- Pediatric Infectious Disease Unit, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Marc Garcia Lorenzo
- Pediatric Infectious Disease Unit, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Roberta Caiazzo
- Pediatric Infectious Disease Unit, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Crescenzo Coppola
- Pediatric Infectious Disease Unit, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Daniela David
- Pediatric Infectious Disease Unit, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Raffaella Di Tonno
- Pediatric Infectious Disease Unit, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Vania Giacomet
- Pediatric Infectious Disease Unit, Luigi Sacco Hospital, University of Milan, Milan, Italy
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2
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Müller S, Kröger C, Schultze JL, Aschenbrenner AC. Whole blood stimulation as a tool for studying the human immune system. Eur J Immunol 2024; 54:e2350519. [PMID: 38103010 DOI: 10.1002/eji.202350519] [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: 06/01/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
The human immune system is best accessible via tissues and organs not requiring major surgical intervention, such as blood. In many circumstances, circulating immune cells correlate with an individual's health state and give insight into physiological and pathophysiological processes. Stimulating whole blood ex vivo is a powerful tool to investigate immune responses. In the context of clinical research, the applications of whole blood stimulation include host immunity, disease characterization, diagnosis, treatment, and drug development. Here, we summarize different setups and readouts of whole blood assays and discuss applications for preclinical research and clinical practice. Finally, we propose combining whole blood stimulation with high-throughput technologies, such as single-cell RNA-sequencing, to comprehensively analyze the human immune system for the identification of biomarkers, therapeutic interventions as well as companion diagnostics.
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Affiliation(s)
- Sophie Müller
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Genomics & Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Charlotte Kröger
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
- Genomics & Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
- Genomics & Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE and University of Bonn, Bonn, Germany
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
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3
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Kalchev Y, Murdjeva M. Current methods for microbiological diagnosis of acute central nervous system infections. Folia Med (Plovdiv) 2022; 64:709-715. [PMID: 36876544 DOI: 10.3897/folmed.64.e72257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/04/2021] [Indexed: 11/06/2022] Open
Abstract
The incidence of infections affecting the central nervous system has increased in recent years, making neuroinfections a current global health problem. The central nervous system is quite well protected from the external and internal environments, although it is susceptible to infection by a wide variety of pathogens. The etiological diversity further complicates the management of such infections because it is important to identify correctly the specific cause in order to choose the most appropriate antimicrobial therapy. Diagnosis is made not only based on clinical and epidemiological data but also on the results of clinical laboratory and microbiological examination of cerebrospinal fluid. This article aims to review current microbiological methods in the diagnosis of acute central nervous system infections and help healthcare providers to recognize their advantages and limitations in order to manage their patients appropriately.
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4
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Ha MK, Bartholomeus E, Van Os L, Dandelooy J, Leysen J, Aerts O, Siozopoulou V, De Smet E, Gielen J, Guerti K, De Maeseneer M, Herregods N, Lechkar B, Wittoek R, Geens E, Claes L, Zaqout M, Dewals W, Lemay A, Tuerlinckx D, Weynants D, Vanlede K, van Berlaer G, Raes M, Verhelst H, Boiy T, Van Damme P, Jansen AC, Meuwissen M, Sabato V, Van Camp G, Suls A, Werff ten Bosch JVD, Dehoorne J, Joos R, Laukens K, Meysman P, Ogunjimi B. Blood transcriptomics to facilitate diagnosis and stratification in pediatric rheumatic diseases - a proof of concept study. Pediatr Rheumatol Online J 2022; 20:91. [PMID: 36253751 PMCID: PMC9575227 DOI: 10.1186/s12969-022-00747-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/24/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Transcriptome profiling of blood cells is an efficient tool to study the gene expression signatures of rheumatic diseases. This study aims to improve the early diagnosis of pediatric rheumatic diseases by investigating patients' blood gene expression and applying machine learning on the transcriptome data to develop predictive models. METHODS RNA sequencing was performed on whole blood collected from children with rheumatic diseases. Random Forest classification models were developed based on the transcriptome data of 48 rheumatic patients, 46 children with viral infection, and 35 controls to classify different disease groups. The performance of these classifiers was evaluated by leave-one-out cross-validation. Analyses of differentially expressed genes (DEG), gene ontology (GO), and interferon-stimulated gene (ISG) score were also conducted. RESULTS Our first classifier could differentiate pediatric rheumatic patients from controls and infection cases with high area-under-the-curve (AUC) values (AUC = 0.8 ± 0.1 and 0.7 ± 0.1, respectively). Three other classifiers could distinguish chronic recurrent multifocal osteomyelitis (CRMO), juvenile idiopathic arthritis (JIA), and interferonopathies (IFN) from control and infection cases with AUC ≥ 0.8. DEG and GO analyses reveal that the pathophysiology of CRMO, IFN, and JIA involves innate immune responses including myeloid leukocyte and granulocyte activation, neutrophil activation and degranulation. IFN is specifically mediated by antibacterial and antifungal defense responses, CRMO by cellular response to cytokine, and JIA by cellular response to chemical stimulus. IFN patients particularly had the highest mean ISG score among all disease groups. CONCLUSION Our data show that blood transcriptomics combined with machine learning is a promising diagnostic tool for pediatric rheumatic diseases and may assist physicians in making data-driven and patient-specific decisions in clinical practice.
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Affiliation(s)
- My Kieu Ha
- Center for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium. .,Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium. .,Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium.
| | - Esther Bartholomeus
- grid.5284.b0000 0001 0790 3681Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium ,grid.5284.b0000 0001 0790 3681Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium ,grid.411414.50000 0004 0626 3418Center of Medical Genetics, University of Antwerp, Antwerp University Hospital, Edegem, Belgium
| | - Luc Van Os
- grid.411414.50000 0004 0626 3418Ophthalmology Department, Antwerp University Hospital, Edegem, Belgium
| | - Julie Dandelooy
- grid.411414.50000 0004 0626 3418Dermatology Department, Antwerp University Hospital, Edegem, Belgium
| | - Julie Leysen
- grid.411414.50000 0004 0626 3418Dermatology Department, Antwerp University Hospital, Edegem, Belgium ,grid.5284.b0000 0001 0790 3681Department of Translational Research in Immunology and Inflammation, University of Antwerp, Wilrijk, Belgium
| | - Olivier Aerts
- grid.411414.50000 0004 0626 3418Dermatology Department, Antwerp University Hospital, Edegem, Belgium ,grid.5284.b0000 0001 0790 3681Department of Translational Research in Immunology and Inflammation, University of Antwerp, Wilrijk, Belgium
| | - Vasiliki Siozopoulou
- grid.411414.50000 0004 0626 3418Pathology Department, Antwerp University Hospital, Edegem, Belgium
| | - Eline De Smet
- grid.411414.50000 0004 0626 3418Radiology Department, Antwerp University Hospital, Edegem, Belgium
| | - Jan Gielen
- grid.411414.50000 0004 0626 3418Radiology Department, Antwerp University Hospital, Edegem, Belgium ,grid.5284.b0000 0001 0790 3681Department of Molecular – Morphology – Microscopy, University of Antwerp, Wilrijk, Belgium
| | - Khadija Guerti
- grid.411414.50000 0004 0626 3418Clinical Biology Department, Antwerp University Hospital, Edegem, Belgium
| | | | - Nele Herregods
- grid.410566.00000 0004 0626 3303Radiology Department, Ghent University Hospital, Ghent, Belgium
| | - Bouchra Lechkar
- grid.411414.50000 0004 0626 3418Department of Immunology, Allergology, and Rheumatology, Antwerp University Hospital, Edegem, Belgium
| | - Ruth Wittoek
- grid.410566.00000 0004 0626 3303Rheumatology Department, Ghent University Hospital, Ghent, Belgium ,grid.411414.50000 0004 0626 3418Rheumatology Department, Antwerp Hospital Network, Antwerp, Belgium
| | - Elke Geens
- grid.411414.50000 0004 0626 3418Rheumatology Department, Antwerp Hospital Network, Antwerp, Belgium
| | - Laura Claes
- grid.411414.50000 0004 0626 3418Pediatric Neurology Unit, Antwerp University Hospital, Edegem, Belgium
| | - Mahmoud Zaqout
- grid.411414.50000 0004 0626 3418Pediatric Cardiology Department, Antwerp University Hospital, Edegem, Belgium ,grid.411414.50000 0004 0626 3418Pediatric Cardiology Department, Antwerp Hospital Network, Antwerp, Belgium
| | - Wendy Dewals
- grid.411414.50000 0004 0626 3418Pediatric Cardiology Department, Antwerp University Hospital, Edegem, Belgium
| | - Annelies Lemay
- Department of Pediatrics, Turnhout General Hospital, Turnhout, Belgium
| | - David Tuerlinckx
- grid.7942.80000 0001 2294 713XDepartment of Pediatrics, Catholic University of Louvain, Louvain-la-Neuve, Belgium ,grid.6520.10000 0001 2242 8479Department of Pediatrics, Namur University Hospital Center, Site Dinant, Dinant, Belgium
| | - David Weynants
- grid.6520.10000 0001 2242 8479Department of Pediatrics, Namur University Hospital Center, Site Sainte-Elisabeth, Namur, Belgium
| | - Koen Vanlede
- Department of Pediatrics, Nikolaas General Hospital, Sint-Niklaas, Belgium
| | - Gerlant van Berlaer
- Department of Emergency Medicine/Pediatric Care, Brussels University Hospital, Jette, Belgium
| | - Marc Raes
- grid.414977.80000 0004 0578 1096Department of Pediatrics, Jessa Hospital, Hasselt, Belgium
| | - Helene Verhelst
- grid.410566.00000 0004 0626 3303Department of Pediatric Neurology, Ghent University Hospital, Ghent, Belgium
| | - Tine Boiy
- grid.411414.50000 0004 0626 3418Department of Pediatric Rheumatology, Antwerp University Hospital, Edegem, Belgium
| | - Pierre Van Damme
- grid.5284.b0000 0001 0790 3681Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium ,grid.5284.b0000 0001 0790 3681Center for the Evaluation of Vaccine, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Anna C. Jansen
- grid.411414.50000 0004 0626 3418Pediatric Neurology Unit, Antwerp University Hospital, Edegem, Belgium
| | - Marije Meuwissen
- grid.5284.b0000 0001 0790 3681Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Vito Sabato
- grid.411414.50000 0004 0626 3418Department of Immunology, Allergology, and Rheumatology, Antwerp University Hospital, Edegem, Belgium ,Antwerp Center for Pediatric Rheumatology and Autoinflammatory Diseases, Antwerp, Belgium
| | - Guy Van Camp
- grid.411414.50000 0004 0626 3418Center of Medical Genetics, University of Antwerp, Antwerp University Hospital, Edegem, Belgium
| | - Arvid Suls
- grid.5284.b0000 0001 0790 3681Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| | | | - Joke Dehoorne
- grid.410566.00000 0004 0626 3303Department of Pediatric Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - Rik Joos
- grid.411414.50000 0004 0626 3418Rheumatology Department, Antwerp Hospital Network, Antwerp, Belgium ,grid.411414.50000 0004 0626 3418Department of Pediatric Rheumatology, Antwerp University Hospital, Edegem, Belgium ,Antwerp Center for Pediatric Rheumatology and Autoinflammatory Diseases, Antwerp, Belgium ,grid.410566.00000 0004 0626 3303Department of Pediatric Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - Kris Laukens
- grid.5284.b0000 0001 0790 3681Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium ,grid.5284.b0000 0001 0790 3681ADREM Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium ,grid.5284.b0000 0001 0790 3681Biomedical Informatics Research Network Antwerp, University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- grid.5284.b0000 0001 0790 3681Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium ,grid.5284.b0000 0001 0790 3681ADREM Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium ,grid.5284.b0000 0001 0790 3681Biomedical Informatics Research Network Antwerp, University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- Center for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium. .,Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium. .,Rheumatology Department, Antwerp Hospital Network, Antwerp, Belgium. .,Department of Pediatric Rheumatology, Antwerp University Hospital, Edegem, Belgium. .,Antwerp Center for Pediatric Rheumatology and Autoinflammatory Diseases, Antwerp, Belgium. .,Department of Pediatric Rheumatology, Brussels University Hospital, Jette, Belgium.
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5
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Kelly E, Whelan SO, Harriss E, Murphy S, Pollard AJ, O' Connor D. Systematic review of host genomic biomarkers of invasive bacterial disease: Distinguishing bacterial from non-bacterial causes of acute febrile illness. EBioMedicine 2022; 81:104110. [PMID: 35792524 PMCID: PMC9256842 DOI: 10.1016/j.ebiom.2022.104110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 12/03/2022] Open
Abstract
Background Infectious diseases play a significant role in the global burden of disease. The gold standard for the diagnosis of bacterial infection, bacterial culture, can lead to diagnostic delays and inappropriate antibiotic use. The advent of high- throughput technologies has led to the discovery of host-based genomic biomarkers of infection, capable of differentiating bacterial from other causes of infection, but few have achieved validation for use in a clinical setting. Methods A systematic review was performed. PubMed/Ovid Medline, Ovid Embase and Scopus databases were searched for relevant studies from inception up to 30/03/2022 with forward and backward citation searching of key references. Studies assessing the diagnostic performance of human host genomic biomarkers of bacterial infection were included. Study selection and assessment of quality were conducted by two independent reviewers. A meta-analysis was undertaken using a diagnostic random-effects model. The review was registered with PROSPERO (ID: CRD42021208462). Findings Seventy-two studies evaluating the performance of 116 biomarkers in 16,216 patients were included. Forty-six studies examined TB-specific biomarker performance and twenty-four studies assessed biomarker performance in a paediatric population. The results of pooled sensitivity, specificity, negative and positive likelihood ratio, and diagnostic odds ratio of genomic biomarkers of bacterial infection were 0.80 (95% CI 0.78 to 0.82), 0.86 (95% CI 0.84 to 0.88), 0.18 (95% CI 0.16 to 0.21), 5.5 (95% CI 4.9 to 6.3), 30.1 (95% CI 24 to 37), respectively. Significant between-study heterogeneity (I2 77%) was present. Interpretation Host derived genomic biomarkers show significant potential for clinical use as diagnostic tests of bacterial infection however, further validation and attention to test platform is warranted before clinical implementation can be achieved. Funding No funding received.
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Affiliation(s)
- Eimear Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford. UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Seán Olann Whelan
- Department of Clinical Microbiology, Galway University Hospital, Galway, Ireland
| | - Eli Harriss
- Bodleian Health Care Libraries, University of Oxford
| | - Sarah Murphy
- Department of Paediatrics, Cork University Maternity Hospital, Wilton, Cork, Ireland
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford. UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel O' Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford. UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
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6
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Artificial Intelligence in Differential Diagnostics of Meningitis: A Nationwide Study. Diagnostics (Basel) 2021; 11:diagnostics11040602. [PMID: 33800653 PMCID: PMC8065596 DOI: 10.3390/diagnostics11040602] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 11/17/2022] Open
Abstract
Differential diagnosis between bacterial and viral meningitis is crucial. In our study, to differentiate bacterial vs. viral meningitis, three machine learning (ML) algorithms (multiple logistic regression (MLR), random forest (RF), and naïve-Bayes (NB)) were applied for the two age groups (0-14 and >14 years) of patients with meningitis by both conventional (culture) and molecular (PCR) methods. Cerebrospinal fluid (CSF) neutrophils, CSF lymphocytes, neutrophil-to-lymphocyte ratio (NLR), blood albumin, blood C-reactive protein (CRP), glucose, blood soluble urokinase-type plasminogen activator receptor (suPAR), and CSF lymphocytes-to-blood CRP ratio (LCR) were used as predictors for the ML algorithms. The performance of the ML algorithms was evaluated through a cross-validation procedure, and optimal predictions of the type of meningitis were above 95% for viral and 78% for bacterial meningitis. Overall, MLR and RF yielded the best performance when using CSF neutrophils, CSF lymphocytes, NLR, albumin, glucose, gender, and CRP. Also, our results reconfirm the high diagnostic accuracy of NLR in the differential diagnosis between bacterial and viral meningitis.
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7
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Aschenbrenner AC, Mouktaroudi M, Krämer B, Oestreich M, Antonakos N, Nuesch-Germano M, Gkizeli K, Bonaguro L, Reusch N, Baßler K, Saridaki M, Knoll R, Pecht T, Kapellos TS, Doulou S, Kröger C, Herbert M, Holsten L, Horne A, Gemünd ID, Rovina N, Agrawal S, Dahm K, van Uelft M, Drews A, Lenkeit L, Bruse N, Gerretsen J, Gierlich J, Becker M, Händler K, Kraut M, Theis H, Mengiste S, De Domenico E, Schulte-Schrepping J, Seep L, Raabe J, Hoffmeister C, ToVinh M, Keitel V, Rieke G, Talevi V, Skowasch D, Aziz NA, Pickkers P, van de Veerdonk FL, Netea MG, Schultze JL, Kox M, Breteler MMB, Nattermann J, Koutsoukou A, Giamarellos-Bourboulis EJ, Ulas T. Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. Genome Med 2021; 13:7. [PMID: 33441124 DOI: 10.1101/2020.07.07.20148395] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/18/2020] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 pandemic is currently leading to increasing numbers of COVID-19 patients all over the world. Clinical presentations range from asymptomatic, mild respiratory tract infection, to severe cases with acute respiratory distress syndrome, respiratory failure, and death. Reports on a dysregulated immune system in the severe cases call for a better characterization and understanding of the changes in the immune system. METHODS In order to dissect COVID-19-driven immune host responses, we performed RNA-seq of whole blood cell transcriptomes and granulocyte preparations from mild and severe COVID-19 patients and analyzed the data using a combination of conventional and data-driven co-expression analysis. Additionally, publicly available data was used to show the distinction from COVID-19 to other diseases. Reverse drug target prediction was used to identify known or novel drug candidates based on finding from data-driven findings. RESULTS Here, we profiled whole blood transcriptomes of 39 COVID-19 patients and 10 control donors enabling a data-driven stratification based on molecular phenotype. Neutrophil activation-associated signatures were prominently enriched in severe patient groups, which was corroborated in whole blood transcriptomes from an independent second cohort of 30 as well as in granulocyte samples from a third cohort of 16 COVID-19 patients (44 samples). Comparison of COVID-19 blood transcriptomes with those of a collection of over 3100 samples derived from 12 different viral infections, inflammatory diseases, and independent control samples revealed highly specific transcriptome signatures for COVID-19. Further, stratified transcriptomes predicted patient subgroup-specific drug candidates targeting the dysregulated systemic immune response of the host. CONCLUSIONS Our study provides novel insights in the distinct molecular subgroups or phenotypes that are not simply explained by clinical parameters. We show that whole blood transcriptomes are extremely informative for COVID-19 since they capture granulocytes which are major drivers of disease severity.
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Affiliation(s)
- Anna C Aschenbrenner
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maria Mouktaroudi
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Benjamin Krämer
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Marie Oestreich
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nikolaos Antonakos
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Melanie Nuesch-Germano
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Konstantina Gkizeli
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Lorenzo Bonaguro
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nico Reusch
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Kevin Baßler
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Maria Saridaki
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Rainer Knoll
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Tal Pecht
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Theodore S Kapellos
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Sarandia Doulou
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Charlotte Kröger
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Miriam Herbert
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Lisa Holsten
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Arik Horne
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Ioanna D Gemünd
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nikoletta Rovina
- 1st Department of Pulmonary Medicine and Intensive Care Unit, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Shobhit Agrawal
- West German Genome Center (WGGC), University of Bonn, Bonn, Germany
| | - Kilian Dahm
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Martina van Uelft
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Anna Drews
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Lena Lenkeit
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Niklas Bruse
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jelle Gerretsen
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jannik Gierlich
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Matthias Becker
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Kristian Händler
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Michael Kraut
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Heidi Theis
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Simachew Mengiste
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Elena De Domenico
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Lea Seep
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jan Raabe
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | | | - Michael ToVinh
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Verena Keitel
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gereon Rieke
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Valentina Talevi
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Dirk Skowasch
- Department of Internal Medicine II, Section of Pneumology, University Hospital of Bonn (UKB), Bonn, Germany
| | - N Ahmad Aziz
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Peter Pickkers
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frank L van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Immunology & Metabolism, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Matthijs Kox
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Monique M B Breteler
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Jacob Nattermann
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
- German Center for Infection Research (DZIF), Bonn, Germany
| | - Antonia Koutsoukou
- 1st Department of Pulmonary Medicine and Intensive Care Unit, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | | | - Thomas Ulas
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.
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8
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Aschenbrenner AC, Mouktaroudi M, Krämer B, Oestreich M, Antonakos N, Nuesch-Germano M, Gkizeli K, Bonaguro L, Reusch N, Baßler K, Saridaki M, Knoll R, Pecht T, Kapellos TS, Doulou S, Kröger C, Herbert M, Holsten L, Horne A, Gemünd ID, Rovina N, Agrawal S, Dahm K, van Uelft M, Drews A, Lenkeit L, Bruse N, Gerretsen J, Gierlich J, Becker M, Händler K, Kraut M, Theis H, Mengiste S, De Domenico E, Schulte-Schrepping J, Seep L, Raabe J, Hoffmeister C, ToVinh M, Keitel V, Rieke G, Talevi V, Skowasch D, Aziz NA, Pickkers P, van de Veerdonk FL, Netea MG, Schultze JL, Kox M, Breteler MMB, Nattermann J, Koutsoukou A, Giamarellos-Bourboulis EJ, Ulas T. Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. Genome Med 2021; 13:7. [PMID: 33441124 PMCID: PMC7805430 DOI: 10.1186/s13073-020-00823-5] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/18/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 pandemic is currently leading to increasing numbers of COVID-19 patients all over the world. Clinical presentations range from asymptomatic, mild respiratory tract infection, to severe cases with acute respiratory distress syndrome, respiratory failure, and death. Reports on a dysregulated immune system in the severe cases call for a better characterization and understanding of the changes in the immune system. METHODS In order to dissect COVID-19-driven immune host responses, we performed RNA-seq of whole blood cell transcriptomes and granulocyte preparations from mild and severe COVID-19 patients and analyzed the data using a combination of conventional and data-driven co-expression analysis. Additionally, publicly available data was used to show the distinction from COVID-19 to other diseases. Reverse drug target prediction was used to identify known or novel drug candidates based on finding from data-driven findings. RESULTS Here, we profiled whole blood transcriptomes of 39 COVID-19 patients and 10 control donors enabling a data-driven stratification based on molecular phenotype. Neutrophil activation-associated signatures were prominently enriched in severe patient groups, which was corroborated in whole blood transcriptomes from an independent second cohort of 30 as well as in granulocyte samples from a third cohort of 16 COVID-19 patients (44 samples). Comparison of COVID-19 blood transcriptomes with those of a collection of over 3100 samples derived from 12 different viral infections, inflammatory diseases, and independent control samples revealed highly specific transcriptome signatures for COVID-19. Further, stratified transcriptomes predicted patient subgroup-specific drug candidates targeting the dysregulated systemic immune response of the host. CONCLUSIONS Our study provides novel insights in the distinct molecular subgroups or phenotypes that are not simply explained by clinical parameters. We show that whole blood transcriptomes are extremely informative for COVID-19 since they capture granulocytes which are major drivers of disease severity.
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Affiliation(s)
- Anna C Aschenbrenner
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maria Mouktaroudi
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Benjamin Krämer
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Marie Oestreich
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nikolaos Antonakos
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Melanie Nuesch-Germano
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Konstantina Gkizeli
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Lorenzo Bonaguro
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nico Reusch
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Kevin Baßler
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Maria Saridaki
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Rainer Knoll
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Tal Pecht
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Theodore S Kapellos
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Sarandia Doulou
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Charlotte Kröger
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Miriam Herbert
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Lisa Holsten
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Arik Horne
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Ioanna D Gemünd
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nikoletta Rovina
- 1st Department of Pulmonary Medicine and Intensive Care Unit, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Shobhit Agrawal
- West German Genome Center (WGGC), University of Bonn, Bonn, Germany
| | - Kilian Dahm
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Martina van Uelft
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Anna Drews
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Lena Lenkeit
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Niklas Bruse
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jelle Gerretsen
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jannik Gierlich
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Matthias Becker
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Kristian Händler
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Michael Kraut
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Heidi Theis
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Simachew Mengiste
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Elena De Domenico
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Lea Seep
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jan Raabe
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | | | - Michael ToVinh
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Verena Keitel
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gereon Rieke
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Valentina Talevi
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Dirk Skowasch
- Department of Internal Medicine II, Section of Pneumology, University Hospital of Bonn (UKB), Bonn, Germany
| | - N Ahmad Aziz
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Peter Pickkers
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frank L van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Immunology & Metabolism, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Matthijs Kox
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Monique M B Breteler
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Jacob Nattermann
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
- German Center for Infection Research (DZIF), Bonn, Germany
| | - Antonia Koutsoukou
- 1st Department of Pulmonary Medicine and Intensive Care Unit, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | | | - Thomas Ulas
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.
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9
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Poma AM, Genoni A, Broccolo F, Denaro M, Pugliese A, Basolo F, Toniolo A. Immune Transcriptome of Cells Infected with Enterovirus Strains Obtained from Cases of Type 1 Diabetes. Microorganisms 2020; 8:microorganisms8071031. [PMID: 32664675 PMCID: PMC7409211 DOI: 10.3390/microorganisms8071031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
Enterovirus (EV) infection of insulin-producing pancreatic beta cells is associated with type 1 diabetes (T1D), but little is known about the mechanisms that lead the virus to cause a persistent infection and, possibly, to induce beta cell autoimmunity. A cell line susceptible to most enterovirus types was infected with EV isolates from cases of T1D and, for comparison, with a replication-competent strain of coxsackievirus B3. The transcription of immune-related genes and secretion of cytokines was evaluated in infected vs. uninfected cells. Acutely infected cells showed the preserved transcription of type I interferon (IFN) pathways and the enhanced transcription/secretion of IL6, IL8, LIF, MCP1, and TGFB1. On the other hand, infection by defective EV strains obtained from diabetic subjects suppressed IFN pathways and the transcription of most cytokines, while enhancing the expression of IL8, IL18, IL32, and MCP1. IL18 and IL32 are known for their pathogenic role in autoimmune diabetes. Thus, the cytokine profile of AV3 cells infected by diabetes-derived EV strains closely matches that observed in patients at the early stages of T1D. The concordance of our results with clinically verified information reinforces the hypothesis that the immune changes observed in type 1 diabetic patients are due to a hardly noticeable virus infection.
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Affiliation(s)
- Anello Marcello Poma
- Department of Surgical, Medical, Molecular Pathology and Clinical Area, University of Pisa, 56126 Pisa, Italy; (M.D.); (F.B.)
- Correspondence:
| | - Angelo Genoni
- Medical Microbiology, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy; (A.G.); (A.T.)
| | - Francesco Broccolo
- Medical Microbiology, Department of Medical Sciences, University Milano Bicocca, 20126 Milano, Italy;
| | - Maria Denaro
- Department of Surgical, Medical, Molecular Pathology and Clinical Area, University of Pisa, 56126 Pisa, Italy; (M.D.); (F.B.)
| | - Alberto Pugliese
- Diabetes Research Institute, University of Miami, Miami, FL 33136, USA;
| | - Fulvio Basolo
- Department of Surgical, Medical, Molecular Pathology and Clinical Area, University of Pisa, 56126 Pisa, Italy; (M.D.); (F.B.)
| | - Antonio Toniolo
- Medical Microbiology, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy; (A.G.); (A.T.)
- Global Virus Network, 21100 Varese, Italy
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