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Savino F, Dini M, Clemente A, Calvi C, Pau A, Galliano I, Gambarino S, Bergallo M. Nasopharyngeal and Peripheral Blood Type II Interferon Signature Evaluation in Infants during Respiratory Syncytial Virus Infection. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:259. [PMID: 38399546 PMCID: PMC10890591 DOI: 10.3390/medicina60020259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
Background and Objectives: In this study, we applied one-step real time rt-PCR technology type II INF signature to blood and nasopharyngeal (NPS) swabs of acute early recovery children < 1 years hospitalized for bronchiolitis with laboratory-confirmed RSV infection. Materials and Methods: A prospective observational case-control study was conducted in 2021-2022. The study took place in Children Hospital "Regina Margherita", Torino Italy. The study included 66 infants, of which 30 patients were hospitalized for bronchiolitis due to RSV infection and 36 age-matched controls. Inclusion criteria included a positive RSV test for infants with bronchiolitis. We collected peripheral blood and nasopharyngeal swabs for relative quantification of type II Interferon signature by One-Step Multiplex PCR real time. Results: IFN levels were downregulated in the peripheral blood of bronchiolitis patients; these data were not confirmed in the nasopharyngeal swab. There was no correlation between NPS and the type II IFN score in peripheral blood. Conclusions: our study shows for the first time that type II IFN score was significant reduced in peripheral blood of infants with bronchiolitis by RSV compared to age-matched healthy controls; in the NPS swab this resulted downregulation was not statistically significant and the type II IFN score in the NPS swab can be used as marker of resolution of infection or improvement of clinical conditions.
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Affiliation(s)
- Francesco Savino
- Early Infancy Special Care Unit, Regina Margherita Children Hospital, A.O.U. Città della Salute e della Scienza di Torino, 10126 Torino, Italy;
| | - Maddalena Dini
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- BioMole srl, Via Quarello 15/A, 10135 Turin, Italy
| | - Anna Clemente
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
| | - Cristina Calvi
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children’s Hospital, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Anna Pau
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
| | - Ilaria Galliano
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children’s Hospital, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Stefano Gambarino
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- BioMole srl, Via Quarello 15/A, 10135 Turin, Italy
| | - Massimiliano Bergallo
- Paediatric Laboratory, Department of Public Health and Pediatric Sciences, Medical School, University of Turin, 10136 Turin, Italy; (M.D.); (A.C.); (C.C.); (A.P.); (I.G.)
- BioMole srl, Via Quarello 15/A, 10135 Turin, Italy
- Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children’s Hospital, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
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2
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Macchia I, La Sorsa V, Urbani F, Moretti S, Antonucci C, Afferni C, Schiavoni G. Eosinophils as potential biomarkers in respiratory viral infections. Front Immunol 2023; 14:1170035. [PMID: 37483591 PMCID: PMC10358847 DOI: 10.3389/fimmu.2023.1170035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/30/2023] [Indexed: 07/25/2023] Open
Abstract
Eosinophils are bone marrow-derived granulocytes that, under homeostatic conditions, account for as much as 1-3% of peripheral blood leukocytes. During inflammation, eosinophils can rapidly expand and infiltrate inflamed tissues, guided by cytokines and alarmins (such as IL-33), adhesion molecules and chemokines. Eosinophils play a prominent role in allergic asthma and parasitic infections. Nonetheless, they participate in the immune response against respiratory viruses such as respiratory syncytial virus and influenza. Notably, respiratory viruses are associated with asthma exacerbation. Eosinophils release several molecules endowed with antiviral activity, including cationic proteins, RNases and reactive oxygen and nitrogen species. On the other hand, eosinophils release several cytokines involved in homeostasis maintenance and Th2-related inflammation. In the context of SARS-CoV-2 infection, emerging evidence indicates that eosinophils can represent possible blood-based biomarkers for diagnosis, prognosis, and severity prediction of disease. In particular, eosinopenia seems to be an indicator of severity among patients with COVID-19, whereas an increased eosinophil count is associated with a better prognosis, including a lower incidence of complications and mortality. In the present review, we provide an overview of the role and plasticity of eosinophils focusing on various respiratory viral infections and in the context of viral and allergic disease comorbidities. We will discuss the potential utility of eosinophils as prognostic/predictive immune biomarkers in emerging respiratory viral diseases, particularly COVID-19. Finally, we will revisit some of the relevant methods and tools that have contributed to the advances in the dissection of various eosinophil subsets in different pathological settings for future biomarker definition.
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Affiliation(s)
- Iole Macchia
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Valentina La Sorsa
- Research Coordination and Support Service, Istituto Superiore di Sanità, Rome, Italy
| | - Francesca Urbani
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Sonia Moretti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, Rome, Italy
| | - Caterina Antonucci
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Claudia Afferni
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Giovanna Schiavoni
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
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3
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Nicolas De Lamballerie C, Pizzorno A, Dubois J, Padey B, Julien T, Traversier A, Carbonneau J, Orcel E, Lina B, Hamelin ME, Roche M, Textoris J, Boivin G, Legras-Lachuer C, Terrier O, Rosa-Calatrava M. Human Respiratory Syncytial Virus-Induced Immune Signature of Infection Revealed by Transcriptome Analysis of Clinical Pediatric Nasopharyngeal Swab Samples. J Infect Dis 2020; 223:1052-1061. [PMID: 32726438 DOI: 10.1093/infdis/jiaa468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/24/2020] [Indexed: 11/12/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) constitutes one the main causes of respiratory infection in neonates and infants worldwide. Transcriptome analysis of clinical samples using high-throughput technologies remains an important tool to better understand virus-host complex interactions in the real-life setting but also to identify new diagnosis/prognosis markers or therapeutics targets. A major challenge when exploiting clinical samples such as nasal swabs, washes, or bronchoalveolar lavages is the poor quantity and integrity of nucleic acids. In this study, we applied a tailored transcriptomics workflow to exploit nasal wash samples from children who tested positive for HRSV. Our analysis revealed a characteristic immune signature as a direct reflection of HRSV pathogenesis and highlighted putative biomarkers of interest such as IP-10, TMEM190, MCEMP1, and TIMM23.
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Affiliation(s)
- Claire Nicolas De Lamballerie
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France.,Viroscan3D SAS, Lyon, France
| | - Andrés Pizzorno
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Julia Dubois
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Blandine Padey
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Thomas Julien
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France.,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Aurélien Traversier
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Julie Carbonneau
- Research Center in Infectious Diseases, Centre Hospitalier Universitaire de Quebec and Laval University, Quebec City, Quebec, Canada
| | | | - Bruno Lina
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Marie-Eve Hamelin
- Research Center in Infectious Diseases, Centre Hospitalier Universitaire de Quebec and Laval University, Quebec City, Quebec, Canada
| | | | - Julien Textoris
- Pathophysiology of Injury-Induced Immunosuppression, Hospices Civils de Lyon, bioMérieux, Université Claude Bernard Lyon 1, Hôpital Edouard Herriot, Lyon, France
| | - Guy Boivin
- Research Center in Infectious Diseases, Centre Hospitalier Universitaire de Quebec and Laval University, Quebec City, Quebec, Canada
| | - Catherine Legras-Lachuer
- Viroscan3D SAS, Lyon, France.,Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, France
| | - Olivier Terrier
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Manuel Rosa-Calatrava
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France.,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
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4
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Raeven RHM, van Riet E, Meiring HD, Metz B, Kersten GFA. Systems vaccinology and big data in the vaccine development chain. Immunology 2018; 156:33-46. [PMID: 30317555 PMCID: PMC6283655 DOI: 10.1111/imm.13012] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/03/2018] [Indexed: 02/06/2023] Open
Abstract
Systems vaccinology has proven a fascinating development in the last decade. Where traditionally vaccine development has been dominated by trial and error, systems vaccinology is a tool that provides novel and comprehensive understanding if properly used. Data sets retrieved from systems‐based studies endorse rational design and effective development of safe and efficacious vaccines. In this review we first describe different omics‐techniques that form the pillars of systems vaccinology. In the second part, the application of systems vaccinology in the different stages of vaccine development is described. Overall, this review shows that systems vaccinology has become an important tool anywhere in the vaccine development chain.
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Affiliation(s)
- René H M Raeven
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands
| | - Elly van Riet
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands
| | - Hugo D Meiring
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands
| | - Bernard Metz
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands
| | - Gideon F A Kersten
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands.,Leiden Academic Center for Drug Research, Division of Biotherapeutics, Leiden University, Leiden, The Netherlands
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5
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Pennings JLA, Mariman R, Hodemaekers HM, Reemers SSN, Janssen R, Guichelaar T. Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance. Sci Rep 2018; 8:16653. [PMID: 30413794 PMCID: PMC6226529 DOI: 10.1038/s41598-018-35180-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/30/2018] [Indexed: 12/25/2022] Open
Abstract
Aging poses an increased risk of severe infection by respiratory syncytial virus (RSV). The many different biological pathways comprising the response to infection in lungs that are influenced by aging are complex and remain to be defined more thoroughly. Towards finding new directions in research on aging, we aimed to define biological pathways in the acute response to RSV that are affected in the lungs by aging. We therefore profiled the full transcriptome of lung tissue of mice prior to and during RSV infection both at young and old age. In the absence of RSV, we found aging to downregulate genes that are involved in constitution of the extracellular matrix. Moreover, uninfected old mice showed elevated expression of pathways that resemble injury, metabolic aberrations, and disorders mediated by functions of the immune system that were induced at young age only by an exogenous trigger like RSV. Furthermore, infection by RSV mounted stronger activation of anti-viral type-I interferon pathways at old age. Despite such exaggerated anti-viral responses, old mice showed reduced control of virus. Altogether, our findings emphasize important roles in aging-related susceptibility to respiratory disease for extracellular matrix dysfunctions and dysregulated immune activation in lungs.
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Affiliation(s)
- Jeroen L A Pennings
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Rob Mariman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Hennie M Hodemaekers
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Sylvia S N Reemers
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,MSD Animal Health, Boxmeer, The Netherlands
| | - Riny Janssen
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Teun Guichelaar
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
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6
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Do LAH, Pellet J, van Doorn HR, Tran AT, Nguyen BH, Tran TTL, Tran QH, Vo QB, Tran Dac NA, Trinh HN, Nguyen TTH, Le Binh BT, Nguyen HMK, Nguyen MT, Thai QT, Vo TV, Ngo NQM, Dang TKH, Cao NH, Tran TV, Ho LV, De Meulder B, Auffray C, Hofstra JJ, Farrar J, Bryant JE, de Jong M, Hibberd ML. Host Transcription Profile in Nasal Epithelium and Whole Blood of Hospitalized Children Under 2 Years of Age With Respiratory Syncytial Virus Infection. J Infect Dis 2017; 217:134-146. [PMID: 29029245 PMCID: PMC5853303 DOI: 10.1093/infdis/jix519] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/18/2017] [Accepted: 09/25/2017] [Indexed: 12/29/2022] Open
Abstract
Background Most insights into the cascade of immune events after acute respiratory syncytial virus (RSV) infection have been obtained from animal experiments or in vitro models. Methods In this study, we investigated host gene expression profiles in nasopharyngeal (NP) swabs and whole blood samples during natural RSV and rhinovirus (hRV) infection (acute versus early recovery phase) in 83 hospitalized patients <2 years old with lower respiratory tract infections. Results Respiratory syncytial virus infection induced strong and persistent innate immune responses including interferon signaling and pathways related to chemokine/cytokine signaling in both compartments. Interferon-α/β, NOTCH1 signaling pathways and potential biomarkers HIST1H4E, IL7R, ISG15 in NP samples, or BCL6, HIST2H2AC, CCNA1 in blood are leading pathways and hub genes that were associated with both RSV load and severity. The observed RSV-induced gene expression patterns did not differ significantly in NP swab and blood specimens. In contrast, hRV infection did not as strongly induce expression of innate immunity pathways, and significant differences were observed between NP swab and blood specimens. Conclusions We conclude that RSV induced strong and persistent innate immune responses and that RSV severity may be related to development of T follicular helper cells and antiviral inflammatory sequelae derived from high activation of BCL6.
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Affiliation(s)
- Lien Anh Ha Do
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Johann Pellet
- Murdoch Children’s Research Institute, Melbourne, Australia
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | | | | | | | | | - Quoc Bao Vo
- Children Hospital 2, Ho Chi Minh City, Vietnam
| | | | | | | | | | | | | | | | - Thanh Vu Vo
- Children Hospital 1, Ho Chi Minh City, Vietnam
| | | | | | | | | | - Lu Viet Ho
- Children Hospital 2, Ho Chi Minh City, Vietnam
| | | | - Charles Auffray
- European Institute for Systems Biology and Medicine, Lyon, France
| | - Jorrit-Jan Hofstra
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, The Netherlands
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Menno de Jong
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, The Netherlands
| | - Martin L Hibberd
- Genome Institute of Singapore
- London School of Hygiene & Tropical Medicine, United Kingdom
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7
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Levitz R, Gao Y, Dozmorov I, Song R, Wakeland EK, Kahn JS. Distinct patterns of innate immune activation by clinical isolates of respiratory syncytial virus. PLoS One 2017; 12:e0184318. [PMID: 28877226 PMCID: PMC5587315 DOI: 10.1371/journal.pone.0184318] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/22/2017] [Indexed: 11/25/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a major respiratory pathogen of infants and young children. Multiple strains of both subgroup A and B viruses circulate during each seasonal epidemic. Genetic heterogeneity among RSV genomes, in large part due to the error prone RNA-dependent, RNA polymerase, could mediate variations in pathogenicity. We evaluated clinical strains of RSV for their ability to induce the innate immune response. Subgroup B viruses were used to infect human pulmonary epithelial cells (A549) and primary monocyte-derived human macrophages (MDM) from a variety of donors. Secretions of IL-6 and CCL5 (RANTES) from infected cells were measured following infection. Host and viral transcriptome expression were assessed using RNA-SEQ technology and the genomic sequences of several clinical isolates were determined. There were dramatic differences in the induction of IL-6 and CCL5 in both A549 cells and MDM infected with a variety of clinical isolates of RSV. Transcriptome analyses revealed that the pattern of innate immune activation in MDM was virus-specific and host-specific. Specifically, viruses that induced high levels of secreted IL-6 and CCL5 tended to induce cellular innate immune pathways whereas viruses that induced relatively low level of IL-6 or CCL5 did not induce or suppressed innate immune gene expression. Activation of the host innate immune response mapped to variations in the RSV G gene and the M2-1 gene. Viral transcriptome data indicated that there was a gradient of transcription across the RSV genome though in some strains, RSV G was the expressed in the highest amounts at late times post-infection. Clinical strains of RSV differ in cytokine/chemokine induction and in induction and suppression of host genes expression suggesting that these viruses may have inherent differences in virulence potential. Identification of the genetic elements responsible for these differences may lead to novel approaches to antiviral agents and vaccines.
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Affiliation(s)
- Ruth Levitz
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yajing Gao
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Igor Dozmorov
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Ran Song
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Edward K. Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jeffrey S. Kahn
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
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8
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McDonald JU, Kaforou M, Clare S, Hale C, Ivanova M, Huntley D, Dorner M, Wright VJ, Levin M, Martinon-Torres F, Herberg JA, Tregoning JS. A Simple Screening Approach To Prioritize Genes for Functional Analysis Identifies a Role for Interferon Regulatory Factor 7 in the Control of Respiratory Syncytial Virus Disease. mSystems 2016; 1:e00051-16. [PMID: 27822537 PMCID: PMC5069771 DOI: 10.1128/msystems.00051-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 05/26/2016] [Indexed: 12/21/2022] Open
Abstract
Greater understanding of the functions of host gene products in response to infection is required. While many of these genes enable pathogen clearance, some enhance pathogen growth or contribute to disease symptoms. Many studies have profiled transcriptomic and proteomic responses to infection, generating large data sets, but selecting targets for further study is challenging. Here we propose a novel data-mining approach combining multiple heterogeneous data sets to prioritize genes for further study by using respiratory syncytial virus (RSV) infection as a model pathogen with a significant health care impact. The assumption was that the more frequently a gene is detected across multiple studies, the more important its role is. A literature search was performed to find data sets of genes and proteins that change after RSV infection. The data sets were standardized, collated into a single database, and then panned to determine which genes occurred in multiple data sets, generating a candidate gene list. This candidate gene list was validated by using both a clinical cohort and in vitro screening. We identified several genes that were frequently expressed following RSV infection with no assigned function in RSV control, including IFI27, IFIT3, IFI44L, GBP1, OAS3, IFI44, and IRF7. Drilling down into the function of these genes, we demonstrate a role in disease for the gene for interferon regulatory factor 7, which was highly ranked on the list, but not for IRF1, which was not. Thus, we have developed and validated an approach for collating published data sets into a manageable list of candidates, identifying novel targets for future analysis. IMPORTANCE Making the most of "big data" is one of the core challenges of current biology. There is a large array of heterogeneous data sets of host gene responses to infection, but these data sets do not inform us about gene function and require specialized skill sets and training for their utilization. Here we describe an approach that combines and simplifies these data sets, distilling this information into a single list of genes commonly upregulated in response to infection with RSV as a model pathogen. Many of the genes on the list have unknown functions in RSV disease. We validated the gene list with new clinical, in vitro, and in vivo data. This approach allows the rapid selection of genes of interest for further, more-detailed studies, thus reducing time and costs. Furthermore, the approach is simple to use and widely applicable to a range of diseases.
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Affiliation(s)
- Jacqueline U. McDonald
- Mucosal Infection and Immunity Group, Section of Virology, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatrics, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - Simon Clare
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Christine Hale
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Maria Ivanova
- Mucosal Infection and Immunity Group, Section of Virology, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - Derek Huntley
- Imperial College Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, United Kingdom
| | - Marcus Dorner
- Molecular Virology, Section of Virology, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - Victoria J. Wright
- Section of Paediatrics, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - Michael Levin
- Section of Paediatrics, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - Federico Martinon-Torres
- Department of Paediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Jethro A. Herberg
- Section of Paediatrics, Imperial College London, St. Mary’s Campus, London, United Kingdom
| | - John S. Tregoning
- Mucosal Infection and Immunity Group, Section of Virology, Imperial College London, St. Mary’s Campus, London, United Kingdom
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9
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Eosinophil-Derived Neurotoxin (EDN/RNase 2) and the Mouse Eosinophil-Associated RNases (mEars): Expanding Roles in Promoting Host Defense. Int J Mol Sci 2015; 16:15442-55. [PMID: 26184157 PMCID: PMC4519907 DOI: 10.3390/ijms160715442] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 06/18/2015] [Accepted: 06/30/2015] [Indexed: 12/30/2022] Open
Abstract
The eosinophil-derived neurotoxin (EDN/RNase2) and its divergent orthologs, the mouse eosinophil-associated RNases (mEars), are prominent secretory proteins of eosinophilic leukocytes and are all members of the larger family of RNase A-type ribonucleases. While EDN has broad antiviral activity, targeting RNA viruses via mechanisms that may require enzymatic activity, more recent studies have elucidated how these RNases may generate host defense via roles in promoting leukocyte activation, maturation, and chemotaxis. This review provides an update on recent discoveries, and highlights the versatility of this family in promoting innate immunity.
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10
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Lee Y, Kim YJ, Jung YJ, Kim KH, Kwon YM, Kim SI, Kang SM. Systems biology from virus to humans. J Anal Sci Technol 2015; 6:3. [PMID: 26269748 PMCID: PMC4527316 DOI: 10.1186/s40543-015-0047-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/15/2015] [Indexed: 12/19/2022] Open
Abstract
Natural infection and then recovery are considered to be the most effective means for hosts to build protective immunity. Thus, mimicking natural infection of pathogens, many live attenuated vaccines such as influenza virus, and yellow fever vaccine 17D were developed and have been successfully used to induce protective immunity. However, humans fail to generate long-term protective immunity to some pathogens after natural infection such as influenza virus, respiratory syncytial virus (RSV), and human immunodeficiency virus (HIV) even if they survive initial infections. Many vaccines are suboptimal since much mortality is still occurring, which is exampled by influenza and tuberculosis. It is critically important to increase our understanding on protein components of pathogens and vaccines as well as cellular and host responses to infections and vaccinations. Here, we highlight recent advances in gene transcripts and protein analysis results in the systems biology to enhance our understanding of viral pathogens, vaccines, and host cell responses.
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Affiliation(s)
- Youri Lee
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Yu-Jin Kim
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Yu-Jin Jung
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Ki-Hye Kim
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Young-Man Kwon
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
| | - Seung Il Kim
- Division of Life Science, Korea Basic Science Institute, Daejeon, 305-333 South Korea
| | - Sang-Moo Kang
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303 USA
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Abstract
Innate immune cells, particularly macrophages and epithelial cells, play a key role in multiple layers of immune responses. Alarmins and pro-inflammatory cytokines from the IL (interleukin)-1 and TNF (tumour necrosis factor) families initiate the cascade of events by inducing chemokine release from bystander cells and by the up-regulation of adhesion molecules required for transendothelial trafficking of immune cells. Furthermore, innate cytokines produced by dendritic cells, macrophages, epithelial cells and innate lymphoid cells seem to play a critical role in polarization of helper T-cell cytokine profiles into specific subsets of Th1/Th2/Th17 effector cells or regulatory T-cells. Lastly, the innate immune system down-regulates effector mechanisms and restores homoeostasis in injured tissue via cytokines from the IL-10 and TGF (transforming growth factor) families mainly released from macrophages, preferentially the M2 subset, which have a capacity to induce regulatory T-cells, inhibit the production of pro-inflammatory cytokines and induce healing of the tissue by regulating extracellular matrix protein deposition and angiogenesis. Cytokines produced by innate immune cells represent an attractive target for therapeutic intervention, and multiple molecules are currently being tested clinically in patients with inflammatory bowel disease, rheumatoid arthritis, systemic diseases, autoinflammatory syndromes, fibrosing processes or malignancies. In addition to the already widely used blockers of TNFα and the tested inhibitors of IL-1 and IL-6, multiple therapeutic molecules are currently in clinical trials targeting TNF-related molecules [APRIL (a proliferation-inducing ligand) and BAFF (B-cell-activating factor belonging to the TNF family)], chemokine receptors, IL-17, TGFβ and other cytokines.
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Everitt AR, Clare S, McDonald JU, Kane L, Harcourt K, Ahras M, Lall A, Hale C, Rodgers A, Young DB, Haque A, Billker O, Tregoning JS, Dougan G, Kellam P. Defining the range of pathogens susceptible to Ifitm3 restriction using a knockout mouse model. PLoS One 2013; 8:e80723. [PMID: 24278312 PMCID: PMC3836756 DOI: 10.1371/journal.pone.0080723] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/16/2013] [Indexed: 12/22/2022] Open
Abstract
The interferon-inducible transmembrane (IFITM) family of proteins has been shown to restrict a broad range of viruses in vitro and in vivo by halting progress through the late endosomal pathway. Further, single nucleotide polymorphisms (SNPs) in its sequence have been linked with risk of developing severe influenza virus infections in humans. The number of viruses restricted by this host protein has continued to grow since it was first demonstrated as playing an antiviral role; all of which enter cells via the endosomal pathway. We therefore sought to test the limits of antimicrobial restriction by Ifitm3 using a knockout mouse model. We showed that Ifitm3 does not impact on the restriction or pathogenesis of bacterial (Salmonella typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis) or protozoan (Plasmodium berghei) pathogens, despite in vitro evidence. However, Ifitm3 is capable of restricting respiratory syncytial virus (RSV) in vivo either through directly restricting RSV cell infection, or by exerting a previously uncharacterised function controlling disease pathogenesis. This represents the first demonstration of a virus that enters directly through the plasma membrane, without the need for the endosomal pathway, being restricted by the IFITM family; therefore further defining the role of these antiviral proteins.
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Affiliation(s)
- Aaron R. Everitt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- * E-mail:
| | - Simon Clare
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Jacqueline U. McDonald
- Mucosal Infection and Immunity Group, Section of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
| | - Leanne Kane
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Katherine Harcourt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Malika Ahras
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Amar Lall
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Christine Hale
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Angela Rodgers
- Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Douglas B. Young
- Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Ashraful Haque
- Malaria Immunology Laboratory, Queensland Institute of Medical Research and The Australian Centre for Vaccine Development, Herston, Brisbane, Queensland, Australia
| | - Oliver Billker
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - John S. Tregoning
- Mucosal Infection and Immunity Group, Section of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Infection, University College London, London, United Kingdom
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Mejias A, Dimo B, Suarez NM, Garcia C, Suarez-Arrabal MC, Jartti T, Blankenship D, Jordan-Villegas A, Ardura MI, Xu Z, Banchereau J, Chaussabel D, Ramilo O. Whole blood gene expression profiles to assess pathogenesis and disease severity in infants with respiratory syncytial virus infection. PLoS Med 2013; 10:e1001549. [PMID: 24265599 PMCID: PMC3825655 DOI: 10.1371/journal.pmed.1001549] [Citation(s) in RCA: 237] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 09/30/2013] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is the leading cause of viral lower respiratory tract infection (LRTI) and hospitalization in infants. Mostly because of the incomplete understanding of the disease pathogenesis, there is no licensed vaccine, and treatment remains symptomatic. We analyzed whole blood transcriptional profiles to characterize the global host immune response to acute RSV LRTI in infants, to characterize its specificity compared with influenza and human rhinovirus (HRV) LRTI, and to identify biomarkers that can objectively assess RSV disease severity. METHODS AND FINDINGS This was a prospective observational study over six respiratory seasons including a cohort of infants hospitalized with RSV (n = 135), HRV (n = 30), and influenza (n = 16) LRTI, and healthy age- and sex-matched controls (n = 39). A specific RSV transcriptional profile was identified in whole blood (training cohort, n = 45 infants; Dallas, Texas, US) and validated in three different cohorts (test cohort, n = 46, Dallas, Texas, US; validation cohort A, n = 16, Turku, Finland; validation cohort B, n = 28, Columbus, Ohio, US) with high sensitivity (94% [95% CI 87%-98%]) and specificity (98% [95% CI 88%-99%]). It classified infants with RSV LRTI versus HRV or influenza LRTI with 95% accuracy. The immune dysregulation induced by RSV (overexpression of neutrophil, inflammation, and interferon genes, and suppression of T and B cell genes) persisted beyond the acute disease, and immune dysregulation was greatly impaired in younger infants (<6 mo). We identified a genomic score that significantly correlated with outcomes of care including a clinical disease severity score and, more importantly, length of hospitalization and duration of supplemental O2. CONCLUSIONS Blood RNA profiles of infants with RSV LRTI allow specific diagnosis, better understanding of disease pathogenesis, and assessment of disease severity. This study opens new avenues for biomarker discovery and identification of potential therapeutic or preventive targets, and demonstrates that large microarray datasets can be translated into a biologically meaningful context and applied to the clinical setting. Please see later in the article for the Editors' Summary.
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Affiliation(s)
- Asuncion Mejias
- Division of Pediatric Infectious Disease, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- * E-mail: (AM); (OR)
| | - Blerta Dimo
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Nicolas M. Suarez
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Carla Garcia
- Division of Pediatric Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - M. Carmen Suarez-Arrabal
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Tuomas Jartti
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Derek Blankenship
- Department of Statistics, Baylor Research Institute, Dallas, Texas, United States of America
| | - Alejandro Jordan-Villegas
- Division of Pediatric Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Monica I. Ardura
- Division of Pediatric Infectious Disease, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Zhaohui Xu
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, Texas, United States of America
| | - Jacques Banchereau
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, Texas, United States of America
| | - Damien Chaussabel
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, Texas, United States of America
- Benaroya Research Institute, Seattle, Washington, United States of America
| | - Octavio Ramilo
- Division of Pediatric Infectious Disease, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- * E-mail: (AM); (OR)
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14
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Tripp RA, Mejias A, Ramilo O. Host gene expression and respiratory syncytial virus infection. Curr Top Microbiol Immunol 2013; 372:193-209. [PMID: 24362691 DOI: 10.1007/978-3-642-38919-1_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Advances in RNA interference (RNAi) and transcription studies have facilitated the application of systematic cell-based loss- or gain-of-function and cell response screening that enable genome-wide analysis of cell factors involved in viral replication and disease. Application of both experimental and computational biology approaches have led to crucial insights into virus infection, its life cycle, and host gene targets for disease intervention. A better understanding of the spatial and temporal host gene interactions during viral infection has enabled insights into mechanisms by which viral proteins co-opt host cell function, and host regulatory mechanisms that influence disease and treatment outcome. In this chapter, approaches to host gene discovery and transcriptome profiling for respiratory syncytial virus (RSV) are discussed in the context of biological relevance for disease intervention in the clinical setting and vaccine development.
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Affiliation(s)
- Ralph A Tripp
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA,
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16
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McGillivary G, Jordan ZB, Peeples ME, Bakaletz LO. Replication of respiratory syncytial virus is inhibited by the host defense molecule viperin. J Innate Immun 2012; 5:60-71. [PMID: 23018837 DOI: 10.1159/000342473] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 08/07/2012] [Indexed: 01/12/2023] Open
Abstract
Respiratory syncytial virus (RSV) is an important viral pathogen of otitis media, bronchiolitis, and pneumonia. As infection of the upper airways is a precondition for the development of these diseases, understanding RSV pathogenesis and the host response induced by RSV in this niche may enable the development of novel therapeutic strategies against this virus. We have used a microarray approach and showed that expression of the gene that encodes the antiviral protein viperin was significantly upregulated in the chinchilla nasopharynx up to 1 week after RSV challenge. Overexpression of human viperin in vitro diminished the ability of RSV to infect HeLa or A549 cells. Furthermore, transduction of the chinchilla airways with a recombinant adeno-associated virus vector that encodes viperin resulted in reduced titers of RSV in the nasopharyngeal lavage fluid. Collectively, these data indicated that viperin plays a significant role in the innate immune defense against RSV.
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Affiliation(s)
- Glen McGillivary
- Center for Microbial Pathogenesis, The Research Institute, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio 43205-2696, USA
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Hussell T, Godlee A, Salek-Ardakani S, Snelgrove RJ. Respiratory viral infections: knowledge based therapeutics. Curr Opin Immunol 2012; 24:438-43. [PMID: 22770666 DOI: 10.1016/j.coi.2012.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 05/15/2012] [Accepted: 06/06/2012] [Indexed: 12/13/2022]
Abstract
Lung viral infections continue to kill millions of people worldwide. Virus-specific properties, replication kinetics and longevity affect the subsequent vigour of innate and adaptive immunity, which contribute to clinical manifestations. The point at which lung innate immunity activates is different between individuals and is determined by age, genetics, underlying conditions and infection history. On resolution of virus-induced lung disease an 'altered state of homeostasis' exists that in turn affects the next antigenic challenge. The last two years has produced a plethora of studies on the resolution of inflammatory lung disease; highlighting potential for immune modulation. In the future a more precise etiological diagnosis, combined with a knowledge of co-morbidities and an immune signature will lead to the development of more specifically targeted therapeutics.
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Affiliation(s)
- Tracy Hussell
- Imperial College London, Leukocyte Biology Section, National Heart and Lung Institute, London SW7 2AZ, UK.
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