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Li W, Lin Y, Wang X, Yang H, Ding Y, Chen Z, He Z, Zhang J, Zhao L, Jiao P. Chicken UFL1 Restricts Avian Influenza Virus Replication by Disrupting the Viral Polymerase Complex and Facilitating Type I IFN Production. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1479-1492. [PMID: 38477617 DOI: 10.4049/jimmunol.2300613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024]
Abstract
During avian influenza virus (AIV) infection, host defensive proteins promote antiviral innate immunity or antagonize viral components to limit viral replication. UFM1-specific ligase 1 (UFL1) is involved in regulating innate immunity and DNA virus replication in mammals, but the molecular mechanism by which chicken (ch)UFL1 regulates AIV replication is unclear. In this study, we first identified chUFL1 as a negative regulator of AIV replication by enhancing innate immunity and disrupting the assembly of the viral polymerase complex. Mechanistically, chUFL1 interacted with chicken stimulator of IFN genes (chSTING) and contributed to chSTING dimerization and the formation of the STING-TBK1-IRF7 complex. We further demonstrated that chUFL1 promoted K63-linked polyubiquitination of chSTING at K308 to facilitate chSTING-mediated type I IFN production independent of UFMylation. Additionally, chUFL1 expression was upregulated in response to AIV infection. Importantly, chUFL1 also interacted with the AIV PA protein to inhibit viral polymerase activity. Furthermore, chUFL1 impeded the nuclear import of the AIV PA protein and the assembly of the viral polymerase complex to suppress AIV replication. Collectively, these findings demonstrate that chUFL1 restricts AIV replication by disrupting the viral polymerase complex and facilitating type I IFN production, which provides new insights into the regulation of AIV replication in chickens.
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Affiliation(s)
- Weiqiang Li
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, Guangzhou, China
| | - Yu Lin
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Xiyi Wang
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Huixing Yang
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Yangbao Ding
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Zuxian Chen
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Zhuoliang He
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Junsheng Zhang
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Luxiang Zhao
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Peirong Jiao
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, Guangzhou, China
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2
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Melton A, Doyle-Meyers LA, Blair RV, Midkiff C, Melton HJ, Russell-Lodrigue K, Aye PP, Schiro F, Fahlberg M, Szeltner D, Spencer S, Beddingfield BJ, Goff K, Golden N, Penney T, Picou B, Hensley K, Chandler KE, Plante JA, Plante KS, Weaver SC, Roy CJ, Hoxie JA, Gao H, Montefiori DC, Mankowski JL, Bohm RP, Rappaport J, Maness NJ. The pigtail macaque (Macaca nemestrina) model of COVID-19 reproduces diverse clinical outcomes and reveals new and complex signatures of disease. PLoS Pathog 2021; 17:e1010162. [PMID: 34929014 PMCID: PMC8722729 DOI: 10.1371/journal.ppat.1010162] [Citation(s) in RCA: 8] [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: 09/06/2021] [Revised: 01/03/2022] [Accepted: 12/01/2021] [Indexed: 01/08/2023] Open
Abstract
The novel coronavirus SARS-CoV-2, the causative agent of COVID-19 disease, has killed over five million people worldwide as of December 2021 with infections rising again due to the emergence of highly transmissible variants. Animal models that faithfully recapitulate human disease are critical for assessing SARS-CoV-2 viral and immune dynamics, for understanding mechanisms of disease, and for testing vaccines and therapeutics. Pigtail macaques (PTM, Macaca nemestrina) demonstrate a rapid and severe disease course when infected with simian immunodeficiency virus (SIV), including the development of severe cardiovascular symptoms that are pertinent to COVID-19 manifestations in humans. We thus proposed this species may likewise exhibit severe COVID-19 disease upon infection with SARS-CoV-2. Here, we extensively studied a cohort of SARS-CoV-2-infected PTM euthanized either 6- or 21-days after respiratory viral challenge. We show that PTM demonstrate largely mild-to-moderate COVID-19 disease. Pulmonary infiltrates were dominated by T cells, including CD4+ T cells that upregulate CD8 and express cytotoxic molecules, as well as virus-targeting T cells that were predominantly CD4+. We also noted increases in inflammatory and coagulation markers in blood, pulmonary pathologic lesions, and the development of neutralizing antibodies. Together, our data demonstrate that SARS-CoV-2 infection of PTM recapitulates important features of COVID-19 and reveals new immune and viral dynamics and thus may serve as a useful animal model for studying pathogenesis and testing vaccines and therapeutics.
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Affiliation(s)
- Alexandra Melton
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Biomedical Science Training Program, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Lara A. Doyle-Meyers
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Robert V. Blair
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Cecily Midkiff
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Hunter J. Melton
- Florida State University, Department of Statistics, Tallahassee, Florida, United States of America
| | - Kasi Russell-Lodrigue
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Pyone P. Aye
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Faith Schiro
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Marissa Fahlberg
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Dawn Szeltner
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Skye Spencer
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | | | - Kelly Goff
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Nadia Golden
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Toni Penney
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Breanna Picou
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Krystle Hensley
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Kristin E. Chandler
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Jessica A. Plante
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kenneth S. Plante
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Scott C. Weaver
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Chad J. Roy
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - James A. Hoxie
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hongmei Gao
- Duke University Medical Center, Duke Human Vaccine Institute, Durham, North Carolina, United States of America
| | - David C. Montefiori
- Duke University Medical Center, Duke Human Vaccine Institute, Durham, North Carolina, United States of America
| | - Joseph L. Mankowski
- Department of Molecular and Comparative Pathobiology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Rudolf P. Bohm
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Jay Rappaport
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Nicholas J. Maness
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
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3
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Differential proteomic analysis of respiratory samples from patients suffering from influenza. Virusdisease 2016; 27:226-233. [PMID: 28466033 DOI: 10.1007/s13337-016-0332-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/20/2016] [Indexed: 02/03/2023] Open
Abstract
The exact molecular pathways involved in the pathogenesis of influenza are yet unclear. In the present study we investigated the upper respiratory proteome in influenza patients. 200 nasal and throat swab samples were collected from patients suffering from acute respiratory illness. These samples were confirmed for influenza pandemic A/H1N1/2009 and influenza type B using qRT-PCR. 10 similar swabs were collected from healthy individuals and were used as controls. Proteins were extracted from the cell pellets and were subjected to 2-D gel electrophoresis. The differentially expressed proteins were identified using MALDI-TOF. Identified proteins were classified into different functional groups based on functions reported in the databases. 25 % of these proteins were involved in cytoskeletal formation, whereas 14 % were involved in signal transduction. Proteins involved in anti-viral responses, Ca-signaling, transport, and tumor suppression constituted 10 % each, where as 5 % of proteins each belong to Nicotinic acetylcholine receptor, Protein Synthesis and anti-bacterial proteins. 10 % of the proteins have not been described previously. This is the first report on respiratory proteome profile in Influenza patients. The study emphasizes the role of such profiling studies using multiple platforms for bio-marker discoveries, especially non-invasive diagnostic marker in Influenza and other infectious diseases.
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Abstract
The preceding chapters describe essential aspects of viral pathogenesis, including virus–cell interactions; viral spread within a host; and intrinsic, innate, and adaptive immune responses. This chapter extends the theme and addresses diverse patterns of viral infections that are determined by both the virus and the host. Thus, virulence or susceptibility depends upon the specific virus–host combination. This is particularly true in the case of persistent infections, which involve a delicate balance between virus and host. We will focus first on virus virulence and host susceptibility, and then turn to the complex variables that govern persistent infections. Chapters 4–6, on innate, adaptive, and aberrant immunity, and Chapters 11–15, on systems biology approaches, also provide important insights into the patterns of infection.
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5
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Thangavel RR, Bouvier NM. Animal models for influenza virus pathogenesis, transmission, and immunology. J Immunol Methods 2014; 410:60-79. [PMID: 24709389 PMCID: PMC4163064 DOI: 10.1016/j.jim.2014.03.023] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/22/2014] [Accepted: 03/24/2014] [Indexed: 12/24/2022]
Abstract
In humans, infection with an influenza A or B virus manifests typically as an acute and self-limited upper respiratory tract illness characterized by fever, cough, sore throat, and malaise. However, influenza can present along a broad spectrum of disease, ranging from sub-clinical or even asymptomatic infection to a severe primary viral pneumonia requiring advanced medical supportive care. Disease severity depends upon the virulence of the influenza virus strain and the immune competence and previous influenza exposures of the patient. Animal models are used in influenza research not only to elucidate the viral and host factors that affect influenza disease outcomes in and spread among susceptible hosts, but also to evaluate interventions designed to prevent or reduce influenza morbidity and mortality in man. This review will focus on the three animal models currently used most frequently in influenza virus research - mice, ferrets, and guinea pigs - and discuss the advantages and disadvantages of each.
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Affiliation(s)
- Rajagowthamee R Thangavel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Nicole M Bouvier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA.
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6
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Terrier O, Textoris J, Carron C, Marcel V, Bourdon JC, Rosa-Calatrava M. Host microRNA molecular signatures associated with human H1N1 and H3N2 influenza A viruses reveal an unanticipated antiviral activity for miR-146a. J Gen Virol 2013; 94:985-995. [PMID: 23343627 DOI: 10.1099/vir.0.049528-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
While post-transcriptional regulation of gene expression by microRNAs (miRNAs) has been shown to be involved in influenza virus replication cycle, only a few studies have further investigated this aspect in a human cellular model infected with human influenza viruses. In this study, we performed miRNA global profiling in human lung epithelial cells (A549) infected by two different subtypes of human influenza A viruses (H1N1 and H3N2). We identified a common miRNA signature in response to infection by the two different strains, highlighting a pool of five miRNAs commonly deregulated, which are known to be involved in the innate immune response or apoptosis. Among the five miRNA hits, the only upregulated miRNA in response to influenza infection corresponded to miR-146a. Based on a previously published gene expression dataset, we extracted inversely correlated miR-146a target genes and determined their first-level interactants. This functional analysis revealed eight distinct biological processes strongly associated with these interactants: Toll-like receptor pathway, innate immune response, cytokine production and apoptosis. To better understand the biological significance of miR-146a upregulation, using a reporter assay and a specific anti-miR-146a inhibitor, we confirmed that infection increased the endogenous miR-146a promoter activity and that inhibition of miR-146a significantly increased viral propagation. Altogether, our results suggest a functional role of miR-146a in the outcome of influenza infection, at the crossroads of several biological processes.
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Affiliation(s)
- Olivier Terrier
- Laboratoire de Virologie et Pathologie Humaine VirPath, Equipe VirCell, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Julien Textoris
- Laboratoire d'Immunologie, UMR CNRS 7278, INSERM U1095, Faculté de Médecine Timone, Marseille, France
| | - Coralie Carron
- Laboratoire de Virologie et Pathologie Humaine VirPath, Equipe VirCell, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Virginie Marcel
- Division of Medical Sciences, Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital, Dundee, Scotland, UK
| | - Jean-Christophe Bourdon
- Division of Medical Sciences, Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital, Dundee, Scotland, UK
| | - Manuel Rosa-Calatrava
- Laboratoire de Virologie et Pathologie Humaine VirPath, Equipe VirCell, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
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7
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Korth MJ, Tchitchek N, Benecke AG, Katze MG. Systems approaches to influenza-virus host interactions and the pathogenesis of highly virulent and pandemic viruses. Semin Immunol 2012; 25:228-39. [PMID: 23218769 PMCID: PMC3596458 DOI: 10.1016/j.smim.2012.11.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 11/08/2012] [Indexed: 12/14/2022]
Abstract
Influenza virus research has recently undergone a shift from a virus-centric perspective to one that embraces the full spectrum of virus-host interactions and cellular signaling events that determine disease outcome. This change has been brought about by the increasing use and expanding scope of high-throughput molecular profiling and computational biology, which together fuel discovery in systems biology. In this review, we show how these approaches have revealed an uncontrolled inflammatory response as a contributor to the extreme virulence of the 1918 pandemic and avian H5N1 viruses, and how this response differs from that induced by the 2009 H1N1 viruses responsible for the most recent influenza pandemic. We also discuss how new animal models, such as the Collaborative Cross mouse systems genetics platform, are key to the necessary systematic investigation of the impact of host genetics on infection outcome, how genome-wide RNAi screens have identified hundreds of cellular factors involved in viral replication, and how systems biology approaches are making possible the rational design of new drugs and vaccines against an ever-evolving respiratory virus.
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Affiliation(s)
- Marcus J Korth
- Department of Microbiology, School of Medicine, and Washington National Primate Research Center, University of Washington, Seattle, WA 98195-8070, USA
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8
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Liu L, Zhou J, Wang Y, Mason RJ, Funk CJ, Du Y. Proteome alterations in primary human alveolar macrophages in response to influenza A virus infection. J Proteome Res 2012; 11:4091-101. [PMID: 22709384 DOI: 10.1021/pr3001332] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To obtain a global picture of how alveolar macrophages respond to influenza A virus (IAV) infection, we used a quantitative proteomics method to systematically examine protein expression in the IAV-infected primary human alveolar macrophages. Of the 1214 proteins identified, 43 were significantly up-regulated and 63 significantly down-regulated at >95% confidence. The expression of an array of interferon (IFN)-induced proteins was significantly increased in the IAV-infected macrophages. The protein with the greatest expression increase was ISG15, an IFN-induced protein that has been shown to play an important role in antiviral defense. Concomitantly, quantitative real-time PCR analysis revealed that the gene expression of type I IFNs increased substantially following virus infection. Our results are consistent with the notion that type I IFNs play a vital role in the response of human alveolar macrophages to IAV infection. In addition to the IFN-mediated responses, inflammatory response, apoptosis, and redox state rebalancing appeared also to be major pathways that were affected by IAV infection. Furthermore, our data suggest that alveolar macrophages may play a crucial role in regenerating alveolar epithelium during IAV infection.
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Affiliation(s)
- Lin Liu
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
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9
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Gaajetaan GR, Bruggeman CA, Stassen FR. The type I interferon response during viral infections: a "SWOT" analysis. Rev Med Virol 2011; 22:122-37. [PMID: 21971992 PMCID: PMC7169250 DOI: 10.1002/rmv.713] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 08/26/2011] [Accepted: 08/31/2011] [Indexed: 12/24/2022]
Abstract
The type I interferon (IFN) response is a strong and crucial moderator for the control of viral infections. The strength of this system is illustrated by the fact that, despite some temporary discomfort like a common cold or diarrhea, most viral infections will not cause major harm to the healthy immunocompetent host. To achieve this, the immune system is equipped with a wide array of pattern recognition receptors and the subsequent coordinated type I IFN response orchestrated by plasmacytoid dendritic cells (pDCs) and conventional dendritic cells (cDCs). The production of type I IFN subtypes by dendritic cells (DCs), but also other cells is crucial for the execution of many antiviral processes. Despite this coordinated response, morbidity and mortality are still common in viral disease due to the ability of viruses to exploit the weaknesses of the immune system. Viruses successfully evade immunity and infection can result in aberrant immune responses. However, these weaknesses also open opportunities for improvement via clinical interventions as can be seen in current vaccination and antiviral treatment programs. The application of IFNs, Toll-like receptor ligands, DCs, and antiviral proteins is now being investigated to further limit viral infections. Unfortunately, a common threat during stimulation of immunity is the possible initiation or aggravation of autoimmunity. Also the translation from animal models to the human situation remains difficult. With a Strengths-Weaknesses-Opportunities-Threats ("SWOT") analysis, we discuss the interaction between host and virus as well as (future) therapeutic options, related to the type I IFN system.
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Affiliation(s)
- Giel R Gaajetaan
- Department of Medical Microbiology, Maastricht University Medical Center, The Netherlands
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10
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Zhang L, Zhang X, Ma Q, Ma F, Zhou H. Transcriptomics and proteomics in the study of H1N1 2009. GENOMICS PROTEOMICS & BIOINFORMATICS 2011; 8:139-44. [PMID: 20970742 PMCID: PMC5054133 DOI: 10.1016/s1672-0229(10)60016-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Influenza A virus (H1N1) 2009, a new swine-origin influenza A virus, has been spread worldwidely and caused great public fear. High-throughput transcriptomics and proteomics methods are now being used to identify H1N1 and H1N1-host interaction. This article reviews recent transcriptomics and proteomics research in H1N1 diagnosis, treatment, and H1N1 virus-host interaction, to offer some help for further understanding the infection mechanism and controlling H1N1 transmission.
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Affiliation(s)
- Lijun Zhang
- Department of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410078, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- Corresponding authors.
| | - Xiaojun Zhang
- Department of Neurosurgery, Fuzhou General Hospital, Fuzhou 350025, China
| | - Qing Ma
- School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, NY 14260, USA
| | - Fang Ma
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Honghao Zhou
- Department of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410078, China
- Corresponding authors.
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11
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Macaque proteome response to highly pathogenic avian influenza and 1918 reassortant influenza virus infections. J Virol 2010; 84:12058-68. [PMID: 20844032 DOI: 10.1128/jvi.01129-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The host proteome response and molecular mechanisms that drive disease in vivo during infection by a human isolate of the highly pathogenic avian influenza virus (HPAI) and 1918 pandemic influenza virus remain poorly understood. This study presents a comprehensive characterization of the proteome response in cynomolgus macaque (Macaca fascicularis) lung tissue over 7 days of infection with HPAI (the most virulent), a reassortant virus containing 1918 hemagglutinin and neuraminidase surface proteins (intermediate virulence), or a human seasonal strain (least virulent). A high-sensitivity two-dimensional liquid chromatography-tandem mass spectroscopy strategy and functional network analysis were implemented to gain insight into response pathways activated in macaques during influenza virus infection. A macaque protein database was assembled and used in the identification of 35,239 unique peptide sequences corresponding to approximately 4,259 proteins. Quantitative analysis identified an increase in expression of 400 proteins during viral infection. The abundance levels of a subset of these 400 proteins produced strong correlations with disease progression observed in the macaques, distinguishing a "core" response to viral infection from a "high" response specific to severe disease. Proteome expression profiles revealed distinct temporal response kinetics between viral strains, with HPAI inducing the most rapid response. While proteins involved in the immune response, metabolism, and transport were increased rapidly in the lung by HPAI, the other viruses produced a delayed response, characterized by an increase in proteins involved in oxidative phosphorylation, RNA processing, and translation. Proteomic results were integrated with previous genomic and pathological analysis to characterize the dynamic nature of the influenza virus infection process.
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12
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Herfst S, van den Brand JMA, Schrauwen EJA, de Wit E, Munster VJ, van Amerongen G, Linster M, Zaaraoui F, van Ijcken WFJ, Rimmelzwaan GF, Osterhaus ADME, Fouchier RAM, Andeweg AC, Kuiken T. Pandemic 2009 H1N1 influenza virus causes diffuse alveolar damage in cynomolgus macaques. Vet Pathol 2010; 47:1040-7. [PMID: 20647595 DOI: 10.1177/0300985810374836] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The pathogenesis of lower respiratory tract disease from the pandemic 2009 H1N1 (H1N1v) influenza A virus is poorly understood. Therefore, either H1N1v virus or a seasonal human H1N1 influenza A virus was inoculated into cynomolgus macaques as a nonhuman primate model of influenza pneumonia, and virological, pathological, and microarray analyses were performed. Macaques in the H1N1v group had virus-associated diffuse alveolar damage involving both type I and type II alveolar epithelial cells and affecting an average of 16% of the lung area. In comparison, macaques in the seasonal H1N1 group had milder pulmonary lesions. H1N1v virus tended to be reisolated from more locations in the respiratory tract and at higher titers than seasonal H1N1 virus. In contrast, differential expression of messenger RNA transcripts between H1N1v and seasonal H1N1 groups did not show significant differences. The most upregulated genes in H1N1v lung samples with lesions belonged to the innate immune response and proinflammatory pathways and correlated with histopathological results. Our results demonstrate that the H1N1v virus infects alveolar epithelial cells and causes diffuse alveolar damage in a nonhuman primate model. Its higher pathogenicity compared with a seasonal H1N1 virus may be explained in part by higher replication in the lower respiratory tract.
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Affiliation(s)
- S Herfst
- Department of Virology, Erasmus Medical Center Rotterdam, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
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13
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Bodewes R, Rimmelzwaan GF, Osterhaus ADME. Animal models for the preclinical evaluation of candidate influenza vaccines. Expert Rev Vaccines 2010; 9:59-72. [PMID: 20021306 DOI: 10.1586/erv.09.148] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
At present, new influenza A (H1N1)2009 viruses of swine origin are responsible for the first influenza pandemic of the 21st Century. In addition, highly pathogenic avian influenza A/H5N1 viruses continue to cause outbreaks in poultry and, after zoonotic transmission, cause an ever-increasing number of human cases, of which 59% have a fatal clinical outcome. It is also feared that these viruses adapt to replication in humans and become transmissible from human to human. The development of effective vaccines against epidemic and (potentially) pandemic viruses is therefore considered a priority. In this review, we discuss animal models that are used for the preclinical evaluation of novel candidate influenza vaccines. In most cases, a tier of multiple animal models is used before the evaluation of vaccine candidates in clinical trials is considered. Commonly, vaccines are tested for safety and efficacy in mice, ferrets and/or macaques. The use of each of these species has its advantages and limitations, which are addressed here.
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Affiliation(s)
- Rogier Bodewes
- Department of Virology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
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McDonald SM, Matthijnssens J, McAllen JK, Hine E, Overton L, Wang S, Lemey P, Zeller M, Van Ranst M, Spiro DJ, Patton JT. Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations. PLoS Pathog 2009; 5:e1000634. [PMID: 19851457 PMCID: PMC2760143 DOI: 10.1371/journal.ppat.1000634] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 09/25/2009] [Indexed: 01/08/2023] Open
Abstract
Group A human rotaviruses (RVs) are a major cause of severe gastroenteritis in infants and young children. Yet, aside from the genes encoding serotype antigens (VP7; G-type and VP4; P-type), little is known about the genetic make-up of emerging and endemic human RV strains. To gain insight into the diversity and evolution of RVs circulating at a single location over a period of time, we sequenced the eleven-segmented, double-stranded RNA genomes of fifty-one G3P[8] strains collected from 1974 to 1991 at Children's Hospital National Medical Center, Washington, D. C. During this period, G1P[8] strains typically dominated, comprising on average 56% of RV infections each year in hospitalized children. A notable exception was in the 1976 and 1991 winter seasons when the incidence of G1P[8] infections decreased dramatically, a trend that correlated with a significant increase in G3P[8] infections. Our sequence analysis indicates that the 1976 season was characterized by the presence of several genetically distinct, co-circulating clades of G3P[8] viruses, which contained minor but significant differences in their encoded proteins. These 1976 lineages did not readily exchange gene segments with each other, but instead remained stable over the course of the season. In contrast, the 1991 season contained a single major clade, whose genome constellation was similar to one of the 1976 clades. The 1991 clade may have gained a fitness advantage after reassorting with as of yet unidentified RV strain(s). This study reveals for the first time that genetically distinct RV clades of the same G/P-type can co-circulate and cause disease. The findings from this study also suggest that, although gene segment exchange occurs, most reassortant strains are replaced over time by lineages with preferred genome constellations. Elucidation of the selective pressures that favor maintenance of RVs with certain sets of genes may be necessary to anticipate future vaccine needs.
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Affiliation(s)
- Sarah M. McDonald
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jelle Matthijnssens
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, K.U. Leuven, Leuven, Belgium
| | - John K. McAllen
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Erin Hine
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Larry Overton
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Shiliang Wang
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Philippe Lemey
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, K.U. Leuven, Leuven, Belgium
| | - Mark Zeller
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, K.U. Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, K.U. Leuven, Leuven, Belgium
| | - David J. Spiro
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - John T. Patton
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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15
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Vester D, Rapp E, Gade D, Genzel Y, Reichl U. Quantitative analysis of cellular proteome alterations in human influenza A virus-infected mammalian cell lines. Proteomics 2009; 9:3316-27. [PMID: 19504497 DOI: 10.1002/pmic.200800893] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the last years virus-host cell interactions were investigated in numerous studies. Viral strategies for evasion of innate immune response, inhibition of cellular protein synthesis and permission of viral RNA and protein production were disclosed. With quantitative proteome technology, comprehensive studies concerning the impact of viruses on the cellular machinery of their host cells at protein level are possible. Therefore, 2-D DIGE and nanoHPLC-nanoESI-MS/MS analysis were used to qualitatively and quantitatively determine the dynamic cellular proteome responses of two mammalian cell lines to human influenza A virus infection. A cell line used for vaccine production (MDCK) was compared with a human lung carcinoma cell line (A549) as a reference model. Analyzing 2-D gels of the proteomes of uninfected and influenza-infected host cells, 16 quantitatively altered protein spots (at least +/-1.7-fold change in relative abundance, p<0.001) were identified for both cell lines. Most significant changes were found for keratins, major components of the cytoskeleton system, and for Mx proteins, interferon-induced key components of the host cell defense. Time series analysis of infection processes allowed the identification of further proteins that are described to be involved in protein synthesis, signal transduction and apoptosis events. Most likely, these proteins are required for supporting functions during influenza viral life cycle or host cell stress response. Quantitative proteome-wide profiling of virus infection can provide insights into complexity and dynamics of virus-host cell interactions and may accelerate antiviral research and support optimization of vaccine manufacturing processes.
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Affiliation(s)
- Diana Vester
- Bioprocess Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.
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16
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Kash JC. Applications of high-throughput genomics to antiviral research: evasion of antiviral responses and activation of inflammation during fulminant RNA virus infection. Antiviral Res 2009; 83:10-20. [PMID: 19375457 PMCID: PMC3457704 DOI: 10.1016/j.antiviral.2009.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 04/01/2009] [Accepted: 04/09/2009] [Indexed: 12/18/2022]
Abstract
Host responses can contribute to the severity of viral infection, through the failure of innate antiviral mechanisms to recognize and restrict the pathogen, the development of intense systemic inflammation leading to circulatory failure or through tissue injury resulting from overly exuberant cell-mediated immune responses. High-throughput genomics methods are now being used to identify the biochemical pathways underlying ineffective or damaging host responses in a number of acute and chronic viral infections. This article reviews recent gene expression studies of 1918 H1N1 influenza and Ebola hemorrhagic fever in cell culture and animal models, focusing on how genomics experiments can be used to increase our understanding of the mechanisms that permit those viruses to cause rapidly overwhelming infection. Particular attention is paid to how evasion of type I IFN responses in infected cells might contribute to over-activation of inflammatory responses. Reviewing recent research and describing how future studies might be tailored to understand the relationship between the infected cell and its environment, this article discusses how the rapidly growing field of high-throughput genomics can contribute to a more complete understanding of severe, acute viral infections and identify novel targets for therapeutic intervention.
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Affiliation(s)
- John C Kash
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892-3203, USA.
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van der Laan JW, Herberts C, Lambkin-Williams R, Boyers A, Mann AJ, Oxford J. Animal models in influenza vaccine testing. Expert Rev Vaccines 2008; 7:783-93. [PMID: 18665776 DOI: 10.1586/14760584.7.6.783] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The threat of a pandemic outbreak of influenza A H5N1 and H2N2 has brought attention to the development of new vaccines. Regulatory authorities require companies to provide data proving the effectiveness of vaccines, which cannot, however, be based on real efficacy data in humans. A weight-of-evidence approach may be used, based on evidence of protection in an appropriate animal model and the satisfaction of the surrogate end points in the clinical situation. In this review, we will discuss various animal species that can be infected with influenza. The main animals used for testing vaccines destined for human use are laboratory mice and ferrets and, to a lesser extent, macaques. We will focus particularly on these species.
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Affiliation(s)
- Jan Willem van der Laan
- Section on Safety of Medicines and Teratology, Centre for Biological Medicines and Medical Technology, National Institute for Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, The Netherlands.
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Abstract
By providing a global and integrated view of the host response to infection, functional genomic and systems-biology approaches are contributing to our understanding of RNA virus–host interactions. One area in which these approaches are being put to particularly good use is in shedding new light on the components of innate antiviral defence mechanisms and the viral strategies used to regulate or overcome them. Genomic analyses have helped to reveal virus-specific differences in the way that viral recognition through pathogen-recognition receptors (PRRs) initiates intracellular signalling cascades. Whereas influenza virus appears to signal primarily through retinoic-acid-inducible gene I (RIG-I), West Nile virus signals through both RIG-I and melanoma differentiation-associated gene 5 (MDA5). Both viruses induce the expression of interferon (IFN)-regulatory factor 3 (IRF3) target genes and IFN-stimulated genes (ISGs). Genomic analyses have provided a comprehensive view of the transcriptional programmes that are induced by Toll-like receptor (TLR) activation. One transcriptional profile is universally activated by all TLRs and a second profile is specific to TLR3 and TLR4. Nuclear factor-κB (NF-κB) is the key regulator of the universal response, which occurs early after TLR stimulation, and the IFN-stimulated response element (ISRE) is the key component of the TLR3/TLR4 response, which is induced after the NF-κB response. Some highly virulent viruses, such as Ebola virus and rabies virus, are successful at inhibiting ISG expression, resulting in the marked suppression of genes in key innate antiviral pathways, including those mediated by IRF3. There seems to be a correlation between the antagonism of the IFN response and virulence. Genomic analyses of the host response to the reconstructed 1918 pandemic influenza virus have revealed similarities and differences to contemporary influenza virus infection. Contemporary and 1918 influenza viruses each trigger an innate immune response that includes the expression of NF-κB and IRF3 target genes, and both viruses trigger a robust cytokine response that attracts immune-cell infiltration to infected tissues. Unlike contemporary virus strains, in which the early response to infection is resolved, the innate immune response triggered by the 1918 influenza virus is characterized by a strong and sustained induction that is associated with massive tissue damage and death. Global gene-expression profiling has revealed that many effective, attenuated live-virus vaccines transiently induce a stronger type I IFN response than the cognate pathogen, and therefore implicates modulation of this response as an important strategy in rational vaccine design.
By providing a global view of the host response to infection, functional genomic approaches are proving useful in deciphering complex virus–host interactions. Here, the authors reveal how such approaches are being used to better understand viral triggering and regulation of host innate immune responses. Although often encoding fewer than a dozen genes, RNA viruses can overcome host antiviral responses and wreak havoc on the cells they infect. Some manage to evade host antiviral defences, whereas others elicit an aberrant or disproportional immune response. Both scenarios can result in the disruption of intracellular signalling pathways and significant pathology in the host. Systems-biology approaches are increasingly being used to study the processes of viral triggering and regulation of host immune responses. By providing a global and integrated view of cellular events, these approaches are beginning to unravel some of the complexities of virus–host interactions and provide new insights into how RNA viruses cause disease.
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Sugrue RJ, Tan BH, Yeo DSY, Sutejo R. Antiviral Drugs for the Control of Pandemic Influenza Virus. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2008. [DOI: 10.47102/annals-acadmedsg.v37n6p518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the advent of an influenza virus pandemic it is likely that the administration of antiviral drugs will be an important first line of defence against the virus. The drugs currently in use are effective against seasonal influenza virus infection, and some cases have been used in the treatment of patients infected with the avian H5N1 influenza virus. However, it is becoming clear that the emergence of drug-resistant viruses will potentially be a major problem in the future efforts to control influenza virus infection. In addition, during a new pandemic, sufficient quantities of these agents will need to be distributed to many different parts of the world, possibly at short notice. In this review we provide an overview of some of the drugs that are currently available for the treatment and prevention of influenza virus infection. In addition, basic research on influenza virus is providing a much better understanding of the biology of the virus, which is offering the possibility of new anti-influenza virus drugs. We therefore also review some new antiviral strategies that are being reported in the scientific literature, which may form the basis of the next generation of antiviral strategies during a future influenza virus pandemic.
Key words: Antiviral, Amantadine, Pandemic influenza virus, Oseltamivir, siRNA
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Baas T, Taubenberger JK, Chong PY, Chui P, Katze MG. SARS-CoV virus-host interactions and comparative etiologies of acute respiratory distress syndrome as determined by transcriptional and cytokine profiling of formalin-fixed paraffin-embedded tissues. J Interferon Cytokine Res 2006; 26:309-17. [PMID: 16689659 PMCID: PMC4496958 DOI: 10.1089/jir.2006.26.309] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
These studies attempt to understand more fully the host response and pathogenesis associated with severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) by monitoring gene expression using formalin-fixed paraffin-embedded (FFPE) pulmonary autopsy tissues. These tissues were from patients in different hospitals in Singapore who were diagnosed with various microbial infections, including SARS-CoV, that caused acute respiratory distress syndrome (ARDS). Global expression patterns showed limited correlation between end-stage ARDS and the initiating pathogen, but when focusing on a subset of genes implicated in pulmonary pathogenesis, molecular signatures of pulmonary disease were obtained and appeared to be influenced by preexisting pulmonary complications and also bacterial components of infection. Many factors detected during pulmonary damage and repair, such as extracellular matrix (ECM) components, transforming growth factor (TGF) enhancers, acute-phase proteins, and antioxidants, were included in the molecular profiles of these ARDS lung tissues. In addition, differential expression of cytokines within these pulmonary tissues were observed, including notable genes involved in the interferon (IFN) pathway, such as Stat1, IFN regulatory factor-1 (IRF-1), interleukin-6 (IL-6), IL-8, and IL-18, that are often characterized as elevated in ARDS patients.
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Affiliation(s)
- Tracey Baas
- Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 98195
| | - Jeffery K. Taubenberger
- Division of Molecular Pathology, Department of Cellular Pathology and Genetics, Armed Forces Institute of Pathology (AFIP), Washington, DC 20306
| | - Pek Yoon Chong
- Department of Pathology and Laboratory Medicine, Mount Elizabeth Hospital, Singapore
| | - Paul Chui
- The Center for Forensic Medicine, Health Science Authority, Singapore
| | - Michael G. Katze
- Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 98195
- Washington National Primate Research Center, University of Washington, Seattle, WA 98195
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