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Stumpff JP, Kim SY, McFadden MI, Nishida A, Shirazi R, Steuerman Y, Gat-Viks I, Forero A, Nair MG, Morrison J. Pleural macrophages translocate to the lung during infection to promote improved influenza outcomes. Proc Natl Acad Sci U S A 2023; 120:e2300474120. [PMID: 38100417 PMCID: PMC10743374 DOI: 10.1073/pnas.2300474120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 10/30/2023] [Indexed: 12/17/2023] Open
Abstract
Seasonal influenza results in 3 to 5 million cases of severe disease and 250,000 to 500,000 deaths annually. Macrophages have been implicated in both the resolution and progression of the disease, but the drivers of these outcomes are poorly understood. We probed mouse lung transcriptomic datasets using the Digital Cell Quantifier algorithm to predict immune cell subsets that correlated with mild or severe influenza A virus (IAV) infection outcomes. We identified a unique lung macrophage population that transcriptionally resembled small serosal cavity macrophages and whose presence correlated with mild disease. Until now, the study of serosal macrophage translocation in the context of viral infections has been neglected. Here, we show that pleural macrophages (PMs) migrate from the pleural cavity to the lung after infection with IAV. We found that the depletion of PMs increased morbidity and pulmonary inflammation. There were increased proinflammatory cytokines in the pleural cavity and an influx of neutrophils within the lung. Our results show that PMs are recruited to the lung during IAV infection and contribute to recovery from influenza. This study expands our knowledge of PM plasticity and identifies a source of lung macrophages independent of monocyte recruitment and local proliferation.
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Affiliation(s)
- James P. Stumpff
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA92521
| | - Sang Yong Kim
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA92521
| | - Matthew I. McFadden
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH43210
| | - Andrew Nishida
- Department of Microbiology, University of Washington, Seattle, WA98109
| | - Roksana Shirazi
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA92521
| | - Yael Steuerman
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv6997801, Israel
| | - Irit Gat-Viks
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv6997801, Israel
| | - Adriana Forero
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH43210
| | - Meera G. Nair
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA92521
| | - Juliet Morrison
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA92521
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2
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Huo C, Tang Y, Li X, Han D, Gu Q, Su R, Liu Y, Reiter RJ, Liu G, Hu Y, Yang H. Melatonin alleviates lung injury in H1N1-infected mice by mast cell inactivation and cytokine storm suppression. PLoS Pathog 2023; 19:e1011406. [PMID: 37200384 DOI: 10.1371/journal.ppat.1011406] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/07/2023] [Indexed: 05/20/2023] Open
Abstract
Influenza A virus (IAV) H1N1 infection is a constant threat to human health and it remains so due to the lack of an effective treatment. Since melatonin is a potent antioxidant and anti-inflammatory molecule with anti-viral action, in the present study we used melatonin to protect against H1N1 infection under in vitro and in vivo conditions. The death rate of the H1N1-infected mice was negatively associated with the nose and lung tissue local melatonin levels but not with serum melatonin concentrations. The H1N1-infected AANAT-/- melatonin-deficient mice had a significantly higher death rate than that of the WT mice and melatonin administration significantly reduced the death rate. All evidence confirmed the protective effects of melatonin against H1N1 infection. Further study identified that the mast cells were the primary targets of melatonin action, i.e., melatonin suppresses the mast cell activation caused by H1N1 infection. The molecular mechanisms involved melatonin down-regulation of gene expression for the HIF-1 pathway and inhibition of proinflammatory cytokine release from mast cells; this resulted in a reduction in the migration and activation of the macrophages and neutrophils in the lung tissue. This pathway was mediated by melatonin receptor 2 (MT2) since the MT2 specific antagonist 4P-PDOT significantly blocked the effects of melatonin on mast cell activation. Via targeting mast cells, melatonin suppressed apoptosis of alveolar epithelial cells and the lung injury caused by H1N1 infection. The findings provide a novel mechanism to protect against the H1N1-induced pulmonary injury, which may better facilitate the progress of new strategies to fight H1N1 infection or other IAV viral infections.
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Affiliation(s)
- Caiyun Huo
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yuling Tang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xinsen Li
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Deping Han
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qingyue Gu
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ruijing Su
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yunjie Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Russel J Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, Long School of Medicine, San Antonio, Texas, United States of America
| | - Guoshi Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yanxin Hu
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Hanchun Yang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Li M, He Q, Chen L. Identifying Hub Genes and miRNA-mRNA Regulatory Networks in Mice Infected with H1N1 Influenza Virus. DISEASE MARKERS 2023; 2023:2291051. [PMID: 37228892 PMCID: PMC10205411 DOI: 10.1155/2023/2291051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 05/27/2023]
Abstract
H1N1 influenza virus is a major factor in seasonal influenza outbreaks. After the body is infected with the influenza virus, the expression of certain mRNAs, including miRNAs, could be affected. However, the association between these mRNAs and miRNAs remains unclear. This study is aimed at identifying differentially expressed genes (DEGs) and miRNAs (DEmiRs) caused by H1N1 influenza virus infection and constructing a miRNA-mRNA regulatory network. Nine GSE datasets were downloaded from the Gene Expression Omnibus database, of which seven were mRNA data and two were miRNA data. The limma package in R language package was used to analyze array data, and edgeR package was used to analyze high-throughput sequencing data. At the same time, the genes related to H1N1 infection were further screened by WGCNA analysis. DEGs were subjected to Gene Ontology and KEGG pathway enrichment analyses by DAVID database, while the STRING database predicted the protein-protein interaction (PPI) network. The correspondence between miRNA and target mRNA was analyzed by the miRWalk database. Cytoscape software was used to output PPI results, identify hub genes, and construct a miRNA-mRNA regulatory network. 114 DEGs and 37 candidate DEmiRs were identified for subsequent analysis. These DEGs were significantly enriched in response to the virus, cytokine activity, and symbiont-containing vacuole membrane. According to KEGG analysis, DEGs were enriched in PD-L1 expression and PD-1 checkpoint pathway. The key point Cd274 (PD-L1) was highly expressed in the H1N1-infected group. Finally, a potential miRNA-mRNA regulatory network (containing 8 candidate DEmiRs and 69 candidate DEGs) and a PPI network were constructed. After that, three hub genes were identified: Ifit3, Stat2, and Irf7. These hub genes and Cd274 were validated by another independent high-throughput dataset and were highly expressed pattern. This study will help researchers gain insights into the intrinsic effects of H1N1 influenza virus infection on the host and suggest a novel association of H1N1 virus with the host immune system.
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Affiliation(s)
- Mingyang Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, Yunnan, China
| | - Qizhi He
- School of Basic Medical Science, Changsha Medical University, Changsha, Hunan, China
| | - Lingli Chen
- Hunan University of Chinese Medicine, Changsha, Hunan, China
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4
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Gopalakrishnan A, Joseph J, Shirey KA, Keegan AD, Boukhvalova MS, Vogel SN, Blanco JCG. Protection against influenza-induced Acute Lung Injury (ALI) by enhanced induction of M2a macrophages: possible role of PPARγ/RXR ligands in IL-4-induced M2a macrophage differentiation. Front Immunol 2022; 13:968336. [PMID: 36052067 PMCID: PMC9424652 DOI: 10.3389/fimmu.2022.968336] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Many respiratory viruses cause lung damage that may evolve into acute lung injury (ALI), a cytokine storm, acute respiratory distress syndrome, and ultimately, death. Peroxisome proliferator activated receptor gamma (PPARγ), a member of the nuclear hormone receptor (NHR) family of transcription factors, regulates transcription by forming heterodimers with another NHR family member, Retinoid X Receptor (RXR). Each component of the heterodimer binds specific ligands that modify transcriptional capacity of the entire heterodimer by recruiting different co-activators/co-repressors. However, the role of PPARγ/RXR ligands in the context of influenza infection is not well understood. PPARγ is associated with macrophage differentiation to an anti-inflammatory M2 state. We show that mice lacking the IL-4Rα receptor, required for M2a macrophage differentiation, are more susceptible to mouse-adapted influenza (A/PR/8/34; "PR8")-induced lethality. Mice lacking Ptgs2, that encodes COX-2, a key proinflammatory M1 macrophage mediator, are more resistant. Blocking the receptor for COX-2-induced Prostaglandin E2 (PGE2) was also protective. Treatment with pioglitazone (PGZ), a PPARγ ligand, increased survival from PR8 infection, decreased M1 macrophage gene expression, and increased PPARγ mRNA in lungs. Conversely, conditional knockout mice expressing PPARγ-deficient macrophages were significantly more sensitive to PR8-induced lethality. These findings were extended in cotton rats: PGZ blunted lung inflammation and M1 cytokine gene expression after challenge with non-adapted human influenza. To study mechanisms by which PPARγ/RXR transcription factors induce canonical M2a genes, WT mouse macrophages were treated with IL-4 in the absence or presence of rosiglitazone (RGZ; PPARγ ligand), LG100754 (LG; RXR ligand), or both. IL-4 dose-dependently induced M2a genes Arg1, Mrc1, Chil3, and Retnla. Treatment of macrophages with IL-4 and RGZ and/or LG differentially affected induction of Arg1 and Mrc1 vs. Chil3 and Retnla gene expression. In PPARγ-deficient macrophages, IL-4 alone failed to induce Arg1 and Mrc1 gene expression; however, concurrent treatment with LG or RGZ + LG enhanced IL-4-induced Arg1 and Mrc1 expression, but to a lower level than in WT macrophages, findings confirmed in the murine alveolar macrophage cell line, MH-S. These findings support a model in which PPARγ/RXR heterodimers control IL-4-induced M2a differentiation, and suggest that PPARγ/RXR agonists should be considered as important tools for clinical intervention against influenza-induced ALI.
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Affiliation(s)
- Archana Gopalakrishnan
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, MD, United States
| | - John Joseph
- Sigmovir Biosystems, Inc., Rockville, MD, United States
| | - Kari Ann Shirey
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, MD, United States
| | - Achsah D. Keegan
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, MD, United States
- Center for Vascular and Inflammatory Diseases, University of Maryland, School of Medicine, Baltimore, MD, United States
| | | | - Stefanie N. Vogel
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, MD, United States
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5
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Deng NH, Zhou ZX, Liu HT, Tian Z, Wu ZF, Liu XY, Xiong WH, Wang Z, Jiang ZS. TRIMs: Generalists Regulating the NLRP3 Inflammasome Signaling Pathway. DNA Cell Biol 2022; 41:262-275. [PMID: 35180350 PMCID: PMC8972007 DOI: 10.1089/dna.2021.0943] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Inflammation is a double-edged sword. The moderate inflammatory response is a fundamental defense mechanism produced by the body's resistance to dangerous stimuli and a repair process of the body itself. Increasing studies have confirmed that the overactivation of the inflammasome is involved in the occurrence and development of inflammatory diseases. Strictly controlling the overactivation of the inflammasome and preventing excessive inflammatory response have always been the research focus on inflammatory diseases. However, the endogenous regulatory mechanism of inflammasome is not completely clear. The tripartite motif (TRIM) protein is one of the members of E3 ligases in the process of ubiquitination. The universality and importance of the functions of TRIM members are recognized, including the regulation of inflammatory response. This article will focus on research on the relationship between TRIMs and NLRP3 Inflammasome, which may help us make some references for future related research and the discovery of treatment methods.
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Affiliation(s)
- Nian-Hua Deng
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Hengyang Medical School, University of South China, Hengyang City, PR China
| | - Zhi-Xiang Zhou
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Hengyang Medical School, University of South China, Hengyang City, PR China
| | - Hui-Ting Liu
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Hengyang Medical School, University of South China, Hengyang City, PR China
| | - Zhen Tian
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Hengyang Medical School, University of South China, Hengyang City, PR China
| | - Ze-Fan Wu
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Hengyang Medical School, University of South China, Hengyang City, PR China
| | - Xi-Yan Liu
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Hengyang Medical School, University of South China, Hengyang City, PR China
| | - Wen-Hao Xiong
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Hengyang Medical School, University of South China, Hengyang City, PR China
| | - Zuo Wang
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Hengyang Medical School, University of South China, Hengyang City, PR China
| | - Zhi-Sheng Jiang
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Hengyang Medical School, University of South China, Hengyang City, PR China.,Address correspondence to: Zhi-Sheng Jiang, PhD, Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Hengyang Medical School, University of South China, Hengyang City, Hunan Province 421001, PR China
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6
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Heterogeneity of Early Host Response to Infection with Four Low-Pathogenic H7 Viruses with a Different Evolutionary History in the Field. Viruses 2021; 13:v13112323. [PMID: 34835129 PMCID: PMC8620788 DOI: 10.3390/v13112323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Once low-pathogenic avian influenza viruses (LPAIVs) of the H5 and H7 subtypes from wild birds enter into poultry species, there is the possibility of them mutating into highly pathogenic avian influenza viruses (HPAIVs), resulting in severe epizootics with up to 100% mortality. This mutation from a LPAIV to HPAIV strain is the main cause of an AIV’s major economic impact on poultry production. Although AIVs are inextricably linked to their hosts in their evolutionary history, the contribution of host-related factors in the emergence of HPAI viruses has only been marginally explored so far. In this study, transcriptomic sequencing of tracheal tissue from chickens infected with four distinct LP H7 viruses, characterized by a different history of pathogenicity evolution in the field, was implemented. Despite the inoculation of a normalized infectious dose of viruses belonging to the same subtype (H7) and pathotype (LPAI), the use of animals of the same age, sex and species as well as the identification of a comparable viral load in the target samples, the analyses revealed a heterogeneity in the gene expression profile in response to infection with each of the H7 viruses administered.
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7
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Nudelman I, Kudrin D, Nudelman G, Deshpande R, Hartmann BM, Kleinstein SH, Myers CL, Sealfon SC, Zaslavsky E. Comparing Host Module Activation Patterns and Temporal Dynamics in Infection by Influenza H1N1 Viruses. Front Immunol 2021; 12:691758. [PMID: 34335598 PMCID: PMC8317020 DOI: 10.3389/fimmu.2021.691758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Influenza is a serious global health threat that shows varying pathogenicity among different virus strains. Understanding similarities and differences among activated functional pathways in the host responses can help elucidate therapeutic targets responsible for pathogenesis. To compare the types and timing of functional modules activated in host cells by four influenza viruses of varying pathogenicity, we developed a new DYNAmic MOdule (DYNAMO) method that addresses the need to compare functional module utilization over time. This integrative approach overlays whole genome time series expression data onto an immune-specific functional network, and extracts conserved modules exhibiting either different temporal patterns or overall transcriptional activity. We identified a common core response to influenza virus infection that is temporally shifted for different viruses. We also identified differentially regulated functional modules that reveal unique elements of responses to different virus strains. Our work highlights the usefulness of combining time series gene expression data with a functional interaction map to capture temporal dynamics of the same cellular pathways under different conditions. Our results help elucidate conservation of the immune response both globally and at a granular level, and provide mechanistic insight into the differences in the host response to infection by influenza strains of varying pathogenicity.
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Affiliation(s)
- Irina Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Division of General Internal Medicine, New York University Langone Medical Centre, New York, NY, United States
| | - Daniil Kudrin
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Raamesh Deshpande
- Department of Computer Science and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN, United States
| | - Boris M Hartmann
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Steven H Kleinstein
- Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN, United States.,Program in Biomedical Informatics and Computational Biology, University of Minnesota - Twin Cities, Minneapolis, MN, United States
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, NY, United States
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8
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Kosyreva A, Dzhalilova D, Lokhonina A, Vishnyakova P, Fatkhudinov T. The Role of Macrophages in the Pathogenesis of SARS-CoV-2-Associated Acute Respiratory Distress Syndrome. Front Immunol 2021; 12:682871. [PMID: 34040616 PMCID: PMC8141811 DOI: 10.3389/fimmu.2021.682871] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/22/2021] [Indexed: 12/11/2022] Open
Abstract
Macrophages are cells that mediate both innate and adaptive immunity reactions, playing a major role in both physiological and pathological processes. Systemic SARS-CoV-2-associated complications include acute respiratory distress syndrome (ARDS), disseminated intravascular coagulation syndrome, edema, and pneumonia. These are predominantly effects of massive macrophage activation that collectively can be defined as macrophage activation syndrome. In this review we focus on the role of macrophages in COVID-19, as pathogenesis of the new coronavirus infection, especially in cases complicated by ARDS, largely depends on macrophage phenotypes and functionalities. We describe participation of monocytes, monocyte-derived and resident lung macrophages in SARS-CoV-2-associated ARDS and discuss possible utility of cell therapies for its treatment, notably the use of reprogrammed macrophages with stable pro- or anti-inflammatory phenotypes.
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Affiliation(s)
- Anna Kosyreva
- Department of Neuromorphology, Science Research Institute of Human Morphology, Moscow, Russia
- Histology Department, Peoples Friendship University of Russia (RUDN University), Moscow, Russia
| | - Dzhuliia Dzhalilova
- Department of Immunomorphology of Inflammation, Science Research Institute of Human Morphology, Moscow, Russia
| | - Anastasia Lokhonina
- Histology Department, Peoples Friendship University of Russia (RUDN University), Moscow, Russia
- Department of Regenerative Medicine, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named After Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, Moscow, Russia
| | - Polina Vishnyakova
- Histology Department, Peoples Friendship University of Russia (RUDN University), Moscow, Russia
- Department of Regenerative Medicine, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named After Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, Moscow, Russia
| | - Timur Fatkhudinov
- Histology Department, Peoples Friendship University of Russia (RUDN University), Moscow, Russia
- Department of Growth and Development, Science Research Institute of Human Morphology, Moscow, Russia
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9
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Hang Y, Tan L, Chen Q, Liu Q, Jin Y. E3 ubiquitin ligase TRIM24 deficiency promotes NLRP3/caspase-1/IL-1β-mediated pyroptosis in endometriosis. Cell Biol Int 2021; 45:1561-1570. [PMID: 33724611 DOI: 10.1002/cbin.11592] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 02/10/2021] [Accepted: 03/14/2021] [Indexed: 12/11/2022]
Abstract
Endometriosis is an inflammation-dependent disease that shares similarities with malignant tumors including attachment and infiltration. Tripartite motif-containing 24 (TRIM24) has been illustrated in inflammatory responses and gynecological tumors, and Nod-like receptor protein 3 (NLRP3) inflammasome has been implicated in endometriosis. However, the involvement of TRIM24 and the role of NLRP3/caspase-1/interleukin-1β (IL-1β)-mediated pyroptosis in endometriosis remain obscure. In this study, we originally detected the decreased expression of TRIM24 in the ectopic endometrium of endometriosis compared with the normal endometrium. Then we measured the promoted protein expression of pyroptotic biomarkers (NLRP3, procaspase-1, caspase-1, pro-IL-1β, and IL-1β) using Western blot analysis and the stimulated secretion of IL-1β and IL-18 by enzyme-linked immunosorbent assay in ectopic human endometrial stromal cells (hESC) compared with normal hESC. TRIM24-small-interfering RNA (siTRIM24) was used to silence TRIM24, whereas TRIM24-pcDNA3.1 was used for overexpressing TRIM24. The migration of hESC was determined by a Transwell migration assay. Coimmunoprecipitation and ubiquitination analyses were conducted to explore the interaction between TRIM24 and NLRP3. Subsequently, we found that TRIM24 negatively regulated NLRP3/caspase-1/IL-1β-mediated pyroptosis and cell migration of hESC, and CY-09, the specific inhibitor of NLRP3, could reverse the promoted pyroptosis and cell migration induced by siTRIM24. Furthermore, TRIM24 interacted with NLRP3 and the upregulation of TRIM24 facilitated the ubiquitination of NLRP3 in ectopic hESC. Our findings suggest that TRIM24 may participate in the progression of endometriosis through the NLRP3/caspase-1/IL-1β-mediated pyroptotic pathway via ubiquitination of NLRP3, which reveals the significant molecular mechanism underlying endometriosis.
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Affiliation(s)
- Yuanyuan Hang
- Department of Traditional Chinese Medicine, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Li Tan
- Department of Gynecology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qiong Chen
- Department of Traditional Chinese Medicine, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qiaoli Liu
- Department of Traditional Chinese Medicine, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuli Jin
- Department of Gynecology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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10
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di Bari I, Franzin R, Picerno A, Stasi A, Cimmarusti MT, Di Chiano M, Curci C, Pontrelli P, Chironna M, Castellano G, Gallone A, Sabbà C, Gesualdo L, Sallustio F. Severe acute respiratory syndrome coronavirus 2 may exploit human transcription factors involved in retinoic acid and interferon-mediated response: a hypothesis supported by an in silico analysis. New Microbes New Infect 2021; 41:100853. [PMID: 33680474 PMCID: PMC7912353 DOI: 10.1016/j.nmni.2021.100853] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023] Open
Abstract
The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19), resulting in acute respiratory disease, is a worldwide emergency. Because recently it has been found that SARS-CoV is dependent on host transcription factors (TF) to express the viral genes, efforts are required to understand the molecular interplay between virus and host response. By bioinformatic analysis, we investigated human TF that can bind the SARS-CoV-2 sequence and can be involved in viral transcription. In particular, we analysed the key role of TF involved in interferon (IFN) response. We found that several TF could be induced by the IFN antiviral response, specifically some induced by IFN-stimulated gene factor 3 (ISGF3) and by unphosphorylated ISGF3, which were found to promote the transcription of several viral open reading frame. Moreover, we found 22 TF binding sites present only in the sequence of virus infecting humans but not bat coronavirus RaTG13. The 22 TF are involved in IFN, retinoic acid signalling and regulation of transcription by RNA polymerase II, thus facilitating its own replication cycle. This mechanism, by competition, may steal the human TF involved in these processes, explaining SARS-CoV-2's disruption of IFN-I signalling in host cells and the mechanism of the SARS retinoic acid depletion syndrome leading to the cytokine storm. We identified three TF binding sites present exclusively in the Brazilian SARS-CoV-2 P.1 variant that may explain the higher severity of the respiratory syndrome. These data shed light on SARS-CoV-2 dependence from the host transcription machinery associated with IFN response and strengthen our knowledge of the virus's transcription and replicative activity, thus paving the way for new targets for drug design and therapeutic approaches.
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Affiliation(s)
- I di Bari
- Department of Emergency and Organ Transplantation, University of Bari 'Aldo Moro', Bari, Italy
| | - R Franzin
- Department of Emergency and Organ Transplantation, University of Bari 'Aldo Moro', Bari, Italy
| | - A Picerno
- Department of Emergency and Organ Transplantation, University of Bari 'Aldo Moro', Bari, Italy
| | - A Stasi
- Department of Emergency and Organ Transplantation, University of Bari 'Aldo Moro', Bari, Italy
| | - M T Cimmarusti
- Department of Emergency and Organ Transplantation, University of Bari 'Aldo Moro', Bari, Italy
| | - M Di Chiano
- Department of Emergency and Organ Transplantation, University of Bari 'Aldo Moro', Bari, Italy
| | - C Curci
- Department of Emergency and Organ Transplantation, University of Bari 'Aldo Moro', Bari, Italy.,Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari 'Aldo Moro', Bari, Italy
| | - P Pontrelli
- Department of Emergency and Organ Transplantation, University of Bari 'Aldo Moro', Bari, Italy
| | - M Chironna
- Department of Biomedical Sciences and Human Oncology- Hygiene Section, University of Bari, Bari, Italy
| | - G Castellano
- Department of Medical and Surgical Science, University of Foggia, Foggia, Italy
| | - A Gallone
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari 'Aldo Moro', Bari, Italy
| | - C Sabbà
- Department of Interdisciplinary Medicine, University of Bari 'Aldo Moro', Bari, Italy
| | - L Gesualdo
- Department of Emergency and Organ Transplantation, University of Bari 'Aldo Moro', Bari, Italy
| | - F Sallustio
- Department of Interdisciplinary Medicine, University of Bari 'Aldo Moro', Bari, Italy
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11
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Murphy-Schafer AR, Paust S. Divergent Mast Cell Responses Modulate Antiviral Immunity During Influenza Virus Infection. Front Cell Infect Microbiol 2021; 11:580679. [PMID: 33680987 PMCID: PMC7935524 DOI: 10.3389/fcimb.2021.580679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022] Open
Abstract
Influenza A virus (IAV) is a respiratory pathogen that infects millions of people each year. Both seasonal and pandemic strains of IAV are capable of causing severe respiratory disease with a high risk of respiratory failure and opportunistic secondary infection. A strong inflammatory cytokine response is a hallmark of severe IAV infection. The widespread tissue damage and edema in the lung during severe influenza is largely attributed to an overexuberant production of inflammatory cytokines and cell killing by resident and infiltrating leukocytes. Mast cells (MCs) are a sentinel hematopoietic cell type situated at mucosal sites, including the lung. Poised to react immediately upon detecting infection, MCs produce a vast array of immune modulating molecules, including inflammatory cytokines, chemokines, and proteases. As such, MCs have been implicated as a source of the immunopathology observed in severe influenza. However, a growing body of evidence indicates that MCs play an essential role not only in inducing an inflammatory response but in suppressing inflammation as well. MC-derived immune suppressive cytokines are essential to the resolution of a number of viral infections and other immune insults. Absence of MCs prolongs infection, exacerbates tissue damage, and contributes to dissemination of the pathogen to other tissues. Production of cytokines such as IL-10 and IL-6 by MCs is essential for mitigating the inflammation and tissue damage caused by innate and adaptive immune cells alike. The two opposing functions of MCs—one pro-inflammatory and one anti-inflammatory—distinguish MCs as master regulators of immunity at the site of infection. Amongst the first cells to respond to infection or injury, MCs persist for the duration of the infection, modulating the recruitment, activation, and eventual suppression of other immune cells. In this review, we will discuss the immune modulatory roles of MCs over the course of viral infection and propose that the immune suppressive mediators produced by MCs are vital to minimizing immunopathology during influenza infection.
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Affiliation(s)
- Ashleigh R Murphy-Schafer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Silke Paust
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
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12
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Wang G, Liu D, Hu J, Gu M, Wang X, He D, Zhang L, Li J, Zheng X, Zeng Z, Liu H, Hu S, Peng D, Jiao X, Liu X. Mutations during the adaptation of H7N9 avian influenza virus to mice lungs enhance human-like sialic acid binding activity and virulence in mice. Vet Microbiol 2021; 254:109000. [PMID: 33515926 DOI: 10.1016/j.vetmic.2021.109000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/18/2021] [Indexed: 01/18/2023]
Abstract
The first avian H7N9 influenza outbreak in spring of 2013 emerged in an unprecedented transmission from infected poultry to humans in the Yangtze delta area, eastern China, posing a dual challenge to public health and poultry industry. However, the mechanism for how avian H7N9 influenza virus adapts to mammalian hosts has not been clearly understood. Here, to identify adaptive changes that confer enhanced virulence of H7N9 virus in mammals, we generated a mouse-adapted H7N9 variant virus (S8) by serial lung-to-lung passages of the wild-type SDL124 virus in mice and compared their phenotype in vivo and in vitro. Sequence analysis showed that the two viruses differed by 27 amino acids distributed among six genes, containing changes in PB2 (E627K, D701N) and HA (Q226L) genes. The 50% mouse lethal dose (MLD50) of S8 reduced about 500 folds, to be moderately pathogenic to mice when compared to that of low pathogenic wild-type SDL124. Moreover, S8 replicated efficiently in mouse lungs and displayed expanded tissue tropism, and induced a greater degree of pulmonary edema and higher level of inflammatory cell infiltration in bronchoalveolar lavage fluids than SDL124 did. Interestingly, the mouse adapted S8 virus obtained strong affinity for human-like (SAα-2,6 Gal) receptor during the adaptation in mice. Correspondingly, compared with SDL124 virus, S8 virus showed higher replication efficiency in mammalian cells, whereas lower replication ability in avian cells. Taken together, these findings suggest that these mutations synergistically elevate the ability of H7N9 virus to disseminate to multiple organs and subsequently enhance the virulence of H7N9 virus in mammalian hosts.
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Affiliation(s)
- Guoqing Wang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China
| | - Dong Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China
| | - Jiao Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China
| | - Min Gu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China
| | - Xiaoquan Wang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China
| | - Dongchang He
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China
| | - Lei Zhang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China
| | - Jun Li
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China
| | - Xinxin Zheng
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China
| | - Zixiong Zeng
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China
| | - Huimou Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China
| | - Shunlin Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China
| | - Daxin Peng
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China
| | - Xinan Jiao
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China.
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13
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Desterke C, Turhan AG, Bennaceur-Griscelli A, Griscelli F. PPARγ Cistrome Repression during Activation of Lung Monocyte-Macrophages in Severe COVID-19. iScience 2020; 23:101611. [PMID: 33015591 PMCID: PMC7518203 DOI: 10.1016/j.isci.2020.101611] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/06/2020] [Accepted: 09/22/2020] [Indexed: 12/19/2022] Open
Abstract
The molecular mechanisms of cytokine storm in patients with severe COVID-19 infections are poorly understood. To uncover these events, we performed transcriptome analyses of lung biopsies from patients with COVID-19, revealing a gene enrichment pattern similar to that of PPARγ-knockout macrophages. Single-cell gene expression analysis of bronchoalveolar lavage fluids revealed a characteristic trajectory of PPARγ-related disturbance in the CD14+/CD16+ cells. We identified a correlation with the disease severity and the reduced expression of several members of the PPARγ complex such as EP300, RXRA, RARA, SUMO1, NR3C1, and CCDC88A. ChIP-seq analyses confirmed repression of the PPARγ-RXRA-NR3C1 cistrome in COVID-19 lung samples. Further analysis of protein-protein networks highlighted an interaction between the PPARγ-associated protein SUMO1 and a nucleoprotein of the SARS virus. Overall, these results demonstrate for the first time the involvement of the PPARγ complex in severe COVID-19 lung disease and suggest strongly its role in the major monocyte/macrophage-mediated inflammatory storm.
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Affiliation(s)
- Christophe Desterke
- INSERM UA9- University Paris-Saclay, Institut André Lwoff, Bâtiment A CNRS, 7 rue Guy Moquet, 94800 Villejuif, France
| | - Ali G Turhan
- INSERM UA9- University Paris-Saclay, Institut André Lwoff, Bâtiment A CNRS, 7 rue Guy Moquet, 94800 Villejuif, France.,ESTeam Paris Sud, INGESTEM National IPSC Infrastructure, University Paris-Saclay, 94800 Villejuif, France.,Division of Hematology, APHP-Paris Saclay University Hospitals, Le Kremlin Bicêtre 94275, Villejuif 94800, France.,University Paris Saclay, Faculty of Medicine, Le Kremlin Bicêtre 94275, France
| | - Annelise Bennaceur-Griscelli
- INSERM UA9- University Paris-Saclay, Institut André Lwoff, Bâtiment A CNRS, 7 rue Guy Moquet, 94800 Villejuif, France.,ESTeam Paris Sud, INGESTEM National IPSC Infrastructure, University Paris-Saclay, 94800 Villejuif, France.,Division of Hematology, APHP-Paris Saclay University Hospitals, Le Kremlin Bicêtre 94275, Villejuif 94800, France.,University Paris Saclay, Faculty of Medicine, Le Kremlin Bicêtre 94275, France
| | - Frank Griscelli
- INSERM UA9- University Paris-Saclay, Institut André Lwoff, Bâtiment A CNRS, 7 rue Guy Moquet, 94800 Villejuif, France.,ESTeam Paris Sud, INGESTEM National IPSC Infrastructure, University Paris-Saclay, 94800 Villejuif, France.,University of Paris, Faculty Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France.,Gustave-Roussy Cancer Institute, Department of Biopathology, 94800 Villejuif, France
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14
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Development of Novel Anti-influenza Thiazolides with Relatively Broad-Spectrum Antiviral Potentials. Antimicrob Agents Chemother 2020; 64:AAC.00222-20. [PMID: 32312780 DOI: 10.1128/aac.00222-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/14/2020] [Indexed: 12/31/2022] Open
Abstract
Seasonal and pandemic influenza causes 650,000 deaths annually in the world. The emergence of drug resistance to specific anti-influenza virus drugs such as oseltamivir and baloxavir marboxil highlights the urgency of novel anti-influenza chemical entity discovery. In this study, we report a series of novel thiazolides derived from an FDA-approved drug, nitazoxanide, with antiviral activity against influenza and a broad range of viruses. The preferred candidates 4a and 4d showed significantly enhanced anti-influenza virus potentials, with 10-fold improvement compared to results with nitazoxanide, and were effective against a variety of influenza virus subtypes including oseltamivir-resistant strains. Notably, the combination using compounds 4a/4d and oseltamivir carboxylate or zanamivir displayed synergistic antiviral effects against oseltamivir-resistant strains. Mode-of-action analysis demonstrated that compounds 4a/4d acted at the late phase of the viral infection cycle through inhibiting viral RNA transcription and replication. Further experiments showed that treatment with compounds 4a/4d significantly inhibited influenza virus infection in human lung organoids, suggesting the druggability of the novel thiazolides. In-depth transcriptome analysis revealed a series of upregulated cellular genes that may contribute to the antiviral activities of 4a/4d. Together, the results of our study indicated the direction to optimize nitazoxanide as an anti-influenza drug and discovered two candidates with novel structures, compounds 4a/4d, that have relatively broad-spectrum antiviral potentials.
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15
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Wu H, Zhang S, Huo C, Zou S, Lian Z, Hu Y. iTRAQ-based proteomic and bioinformatic characterization of human mast cells upon infection by the influenza A virus strains H1N1 and H5N1. FEBS Lett 2019; 593:2612-2627. [PMID: 31271652 DOI: 10.1002/1873-3468.13523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/26/2019] [Accepted: 06/19/2019] [Indexed: 12/12/2022]
Abstract
Mast cells can support the replication of influenza A virus, although how this occurs is poorly understood. In the present study, using quantitative MS, we analyzed the proteome of human mast cells infected with different influenza A virus strains at 12 h post-infection. Forty-one differentially expressed proteins were identified in human mast cells upon infection by the virulent H5N1 (A/Chicken/Henan/1/04) virus compared to the seasonal H1N1 (A/WSN/33) virus. Bioinformatic analyses confirmed that H1N1 significantly regulates the RNA degradation pathway via up-regulation of CCR4-NOT transcription complex subunit 4, whereas apoptosis could be suppressed by H5N1 via down-regulation of the tumor protein p53 signaling pathway with P ≤ 0.05 at 12 h post-infection. The hypoxia-inducible factor-1 signaling pathway of human mast cells is more susceptible to infection by H5N1 than by H1N1 virus.
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Affiliation(s)
- Hongping Wu
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shouping Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
| | - Caiyun Huo
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shumei Zou
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, China
| | - Zhengxing Lian
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yanxin Hu
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
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16
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Predicting Host Immune Cell Dynamics and Key Disease-Associated Genes Using Tissue Transcriptional Profiles. Processes (Basel) 2019. [DOI: 10.3390/pr7050301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Motivation: Immune cell dynamics is a critical factor of disease-associated pathology (immunopathology) that also impacts the levels of mRNAs in diseased tissue. Deconvolution algorithms attempt to infer cell quantities in a tissue/organ sample based on gene expression profiles and are often evaluated using artificial, non-complex samples. Their accuracy on estimating cell counts given temporal tissue gene expression data remains not well characterized and has never been characterized when using diseased lung. Further, how to remove the effects of cell migration on transcript counts to improve discovery of disease factors is an open question. Results: Four cell count inference (i.e., deconvolution) tools are evaluated using microarray data from influenza-infected lung sampled at several time points post-infection. The analysis finds that inferred cell quantities are accurate only for select cell types and there is a tendency for algorithms to have a good relative fit (R 2 ) but a poor absolute fit (normalized mean squared error; NMSE), which suggests systemic biases exist. Nonetheless, using cell fraction estimates to adjust gene expression data, we show that genes associated with influenza virus replication and increased infection pathology are more likely to be identified as significant than when applying traditional statistical tests.
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17
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Ashwin H, Seifert K, Forrester S, Brown N, MacDonald S, James S, Lagos D, Timmis J, Mottram JC, Croft SL, Kaye PM. Tissue and host species-specific transcriptional changes in models of experimental visceral leishmaniasis. Wellcome Open Res 2019; 3:135. [PMID: 30542664 PMCID: PMC6248268 DOI: 10.12688/wellcomeopenres.14867.2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2018] [Indexed: 12/19/2022] Open
Abstract
Background: Human visceral leishmaniasis, caused by infection with Leishmania donovani or L. infantum, is a potentially fatal disease affecting 50,000-90,000 people yearly in 75 disease endemic countries, with more than 20,000 deaths reported. Experimental models of infection play a major role in understanding parasite biology, host-pathogen interaction, disease pathogenesis, and parasite transmission. In addition, they have an essential role in the identification and pre-clinical evaluation of new drugs and vaccines. However, our understanding of these models remains fragmentary. Although the immune response to Leishmania donovani infection in mice has been extensively characterized, transcriptomic analysis capturing the tissue-specific evolution of disease has yet to be reported. Methods: We provide an analysis of the transcriptome of spleen, liver and peripheral blood of BALB/c mice infected with L. donovani. Where possible, we compare our data in murine experimental visceral leishmaniasis with transcriptomic data in the public domain obtained from the study of L. donovani-infected hamsters and patients with human visceral leishmaniasis. Digitised whole slide images showing the histopathology in spleen and liver are made available via a dedicated website, www.leishpathnet.org. Results: Our analysis confirms marked tissue-specific alterations in the transcriptome of infected mice over time and identifies previously unrecognized parallels and differences between murine, hamster and human responses to infection. We show commonality of interferon-regulated genes whilst confirming a greater activation of type 2 immune pathways in infected hamsters compared to mice. Cytokine genes and genes encoding immune checkpoints were markedly tissue specific and dynamic in their expression, and pathways focused on non-immune cells reflected tissue specific immunopathology. Our data also addresses the value of measuring peripheral blood transcriptomics as a potential window into underlying systemic disease. Conclusions: Our transcriptomic data, coupled with histopathologic analysis of the tissue response, provide an additional resource to underpin future mechanistic studies and to guide clinical research.
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Affiliation(s)
- Helen Ashwin
- Centre for Immunology and Infection, University of York, York, YO10 5DD, UK
| | - Karin Seifert
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Sarah Forrester
- Centre for Immunology and Infection, University of York, York, YO10 5DD, UK
| | - Najmeeyah Brown
- Centre for Immunology and Infection, University of York, York, YO10 5DD, UK
| | - Sandy MacDonald
- Bioscience Technology Facility, Deptartment of Biology, University of York, York, YO10 5DD, UK
| | - Sally James
- Bioscience Technology Facility, Deptartment of Biology, University of York, York, YO10 5DD, UK
| | - Dimitris Lagos
- Centre for Immunology and Infection, University of York, York, YO10 5DD, UK
| | - Jon Timmis
- Dept of Electronic Engineering, University of York, York, YO10 5DD, UK
| | - Jeremy C Mottram
- Centre for Immunology and Infection, University of York, York, YO10 5DD, UK
| | - Simon L. Croft
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Paul M. Kaye
- Centre for Immunology and Infection, University of York, York, YO10 5DD, UK
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18
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Mast cells as protectors of health. J Allergy Clin Immunol 2018; 144:S4-S18. [PMID: 30468774 DOI: 10.1016/j.jaci.2018.10.054] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/16/2018] [Accepted: 10/05/2018] [Indexed: 12/20/2022]
Abstract
Mast cells (MCs), which are well known for their effector functions in TH2-skewed allergic and also autoimmune inflammation, have become increasingly acknowledged for their role in protection of health. It is now clear that they are also key modulators of immune responses at interface organs, such as the skin or gut. MCs can prime tissues for adequate inflammatory responses and cooperate with dendritic cells in T-cell activation. They also regulate harmful immune responses in trauma and help to successfully orchestrate pregnancy. This review focuses on the beneficial effects of MCs on tissue homeostasis and elimination of toxins or venoms. MCs can enhance pathogen clearance in many bacterial, viral, and parasitic infections, such as through Toll-like receptor 2-triggered degranulation, secretion of antimicrobial cathelicidins, neutrophil recruitment, or provision of extracellular DNA traps. The role of MCs in tumors is more ambiguous; however, encouraging new findings show they can change the tumor microenvironment toward antitumor immunity when adequately triggered. Uterine tissue remodeling by α-chymase (mast cell protease [MCP] 5) is crucial for successful embryo implantation. MCP-4 and the tryptase MCP-6 emerge to be protective in central nervous system trauma by reducing inflammatory damage and excessive scar formation, thereby protecting axon growth. Last but not least, proteases, such as carboxypeptidase A, released by FcεRI-activated MCs detoxify an increasing number of venoms and endogenous toxins. A better understanding of the plasticity of MCs will help improve these advantageous effects and hint at ways to cut down detrimental MC actions.
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Ashwin H, Seifert K, Forrester S, Brown N, MacDonald S, James S, Lagos D, Timmis J, Mottram JC, Croft SL, Kaye PM. Tissue and host species-specific transcriptional changes in models of experimental visceral leishmaniasis. Wellcome Open Res 2018; 3:135. [PMID: 30542664 PMCID: PMC6248268 DOI: 10.12688/wellcomeopenres.14867.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2018] [Indexed: 11/08/2023] Open
Abstract
Background: Human visceral leishmaniasis, caused by infection with Leishmania donovani or L. infantum, is a potentially fatal disease affecting 50,000-90,000 people yearly in 75 disease endemic countries, with more than 20,000 deaths reported. Experimental models of infection play a major role in understanding parasite biology, host-pathogen interaction, disease pathogenesis, and parasite transmission. In addition, they have an essential role in the identification and pre-clinical evaluation of new drugs and vaccines. However, our understanding of these models remains fragmentary. Although the immune response to Leishmania donovani infection in mice has been extensively characterized, transcriptomic analysis capturing the tissue-specific evolution of disease has yet to be reported. Methods: We provide an analysis of the transcriptome of spleen, liver and peripheral blood of BALB/c mice infected with L. donovani. Where possible, we compare our data in murine experimental visceral leishmaniasis with transcriptomic data in the public domain obtained from the study of L. donovani-infected hamsters and patients with human visceral leishmaniasis. Digitised whole slide images showing the histopathology in spleen and liver are made available via a dedicated website, www.leishpathnet.org. Results: Our analysis confirms marked tissue-specific alterations in the transcriptome of infected mice over time and identifies previously unrecognized parallels and differences between murine, hamster and human responses to infection. We show commonality of interferon-regulated genes whilst confirming a greater activation of type 2 immune pathways in infected hamsters compared to mice. Cytokine genes and genes encoding immune checkpoints were markedly tissue specific and dynamic in their expression, and pathways focused on non-immune cells reflected tissue specific immunopathology. Our data also addresses the value of measuring peripheral blood transcriptomics as a potential window into underlying systemic disease. Conclusions: Our transcriptomic data, coupled with histopathologic analysis of the tissue response, provide an additional resource to underpin future mechanistic studies and to guide clinical research.
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Affiliation(s)
- Helen Ashwin
- Centre for Immunology and Infection, University of York, York, YO10 5DD, UK
| | - Karin Seifert
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Sarah Forrester
- Centre for Immunology and Infection, University of York, York, YO10 5DD, UK
| | - Najmeeyah Brown
- Centre for Immunology and Infection, University of York, York, YO10 5DD, UK
| | - Sandy MacDonald
- Bioscience Technology Facility, Deptartment of Biology, University of York, York, YO10 5DD, UK
| | - Sally James
- Bioscience Technology Facility, Deptartment of Biology, University of York, York, YO10 5DD, UK
| | - Dimitris Lagos
- Centre for Immunology and Infection, University of York, York, YO10 5DD, UK
| | - Jon Timmis
- Dept of Electronic Engineering, University of York, York, YO10 5DD, UK
| | - Jeremy C Mottram
- Centre for Immunology and Infection, University of York, York, YO10 5DD, UK
| | - Simon L. Croft
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Paul M. Kaye
- Centre for Immunology and Infection, University of York, York, YO10 5DD, UK
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20
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Halstead ES, Umstead TM, Davies ML, Kawasawa YI, Silveyra P, Howyrlak J, Yang L, Guo W, Hu S, Hewage EK, Chroneos ZC. GM-CSF overexpression after influenza a virus infection prevents mortality and moderates M1-like airway monocyte/macrophage polarization. Respir Res 2018; 19:3. [PMID: 29304863 PMCID: PMC5756339 DOI: 10.1186/s12931-017-0708-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/18/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Influenza A viruses cause life-threatening pneumonia and lung injury in the lower respiratory tract. Application of high GM-CSF levels prior to infection has been shown to reduce morbidity and mortality from pathogenic influenza infection in mice, but the mechanisms of protection and treatment efficacy have not been established. METHODS Mice were infected intranasally with influenza A virus (PR8 strain). Supra-physiologic levels of GM-CSF were induced in the airways using the double transgenic GM-CSF (DTGM) or littermate control mice starting on 3 days post-infection (dpi). Assessment of respiratory mechanical parameters was performed using the flexiVent rodent ventilator. RNA sequence analysis was performed on FACS-sorted airway macrophage subsets at 8 dpi. RESULTS Supra-physiologic levels of GM-CSF conferred a survival benefit, arrested the deterioration of lung mechanics, and reduced the abundance of protein exudates in bronchoalveolar (BAL) fluid to near baseline levels. Transcriptome analysis, and subsequent validation ELISA assays, revealed that excess GM-CSF re-directs macrophages from an "M1-like" to a more "M2-like" activation state as revealed by alterations in the ratios of CXCL9 and CCL17 in BAL fluid, respectively. Ingenuity pathway analysis predicted that GM-CSF surplus during IAV infection elicits expression of anti-inflammatory mediators and moderates M1 macrophage pro-inflammatory signaling by Type II interferon (IFN-γ). CONCLUSIONS Our data indicate that application of high levels of GM-CSF in the lung after influenza A virus infection alters pathogenic "M1-like" macrophage inflammation. These results indicate a possible therapeutic strategy for respiratory virus-associated pneumonia and acute lung injury.
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Affiliation(s)
- E. Scott Halstead
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Todd M. Umstead
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Michael L. Davies
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Yuka Imamura Kawasawa
- Departments of Pharmacology & Biochemistry and Molecular Biology, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Patricia Silveyra
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Judie Howyrlak
- Departments of Medicine and Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Linlin Yang
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Weichao Guo
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Sanmei Hu
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Eranda Kurundu Hewage
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Zissis C. Chroneos
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA USA
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21
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Huang F, Chen J, Zhang J, Tan L, Lu G, Luo Y, Pan T, Liang J, Li Q, Luo B, Zhang H, Lu G. Identification of a novel compound targeting the nuclear export of influenza A virus nucleoprotein. J Cell Mol Med 2017; 22:1826-1839. [PMID: 29193684 PMCID: PMC5824420 DOI: 10.1111/jcmm.13467] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/23/2017] [Indexed: 12/25/2022] Open
Abstract
Although antiviral drugs are available for the treatment of influenza infection, it is an urgent requirement to develop new antiviral drugs regarding the emergence of drug‐resistant viruses. The nucleoprotein (NP) is conserved among all influenza A viruses (IAVs) and has no cellular equivalent. Therefore, NP is an ideal target for the development of new IAV inhibitors. In this study, we identified a novel anti‐influenza compound, ZBMD‐1, from a library of 20,000 compounds using cell‐based influenza A infection assays. We found that ZBMD‐1 inhibited the replication of H1N1 and H3N2 influenza A virus strains in vitro, with an IC50 ranging from 0.41–1.14 μM. Furthermore, ZBMD‐1 inhibited the polymerase activity and specifically impaired the nuclear export of NP. Further investigation indicated that ZBMD‐1 binds to the nuclear export signal 3 (NES3) domain and the dimer interface of the NP pocket. ZBMD‐1 also protected mice that were challenged with lethal doses of A/PR/8/1934 (H1N1) virus, effectively relieving lung histopathology changes, as well as strongly inhibiting the expression of pro‐inflammatory cytokines/chemokines, without inducing toxicity effects in mice. These results suggest that ZBMD‐1 is a promising anti‐influenza compound which can be further investigated as a useful strategy against IAVs in the future.
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Affiliation(s)
- Feng Huang
- Department of Respiration, Affiliated Guangzhou Women and Children's Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.,Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jingliang Chen
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Junsong Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Likai Tan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Gui Lu
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yongjie Luo
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ting Pan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Juanran Liang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Qianwen Li
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Baohong Luo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Gen Lu
- Department of Respiration, Affiliated Guangzhou Women and Children's Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
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22
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Almansa R, Martínez-Orellana P, Rico L, Iglesias V, Ortega A, Vidaña B, Martínez J, Expósito A, Montoya M, Bermejo-Martin JF. Pulmonary transcriptomic responses indicate a dual role of inflammation in pneumonia development and viral clearance during 2009 pandemic influenza infection. PeerJ 2017; 5:e3915. [PMID: 29038764 PMCID: PMC5640978 DOI: 10.7717/peerj.3915] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/21/2017] [Indexed: 12/22/2022] Open
Abstract
Background The interaction between influenza virus and the host response to infection clearly plays an important role in determining the outcome of infection. While much is known on the participation of inflammation on the pathogenesis of severe A (H1N1) pandemic 09-influenza virus, its role in the course of non-fatal pneumonia has not been fully addressed. Methods A systems biology approach was used to define gene expression profiles, histology and viral dynamics in the lungs of healthy immune-competent mice with pneumonia caused by a human influenza A (H1N1) pdm09 virus, which successfully resolved the infection. Results Viral infection activated a marked pro-inflammatory response at the lung level paralleling the emergence of histological changes. Cellular immune response and cytokine signaling were the two signaling pathway categories more representative of our analysis. This transcriptome response was associated to viral clearance, and its resolution was accompanied by resolution of histopathology. Discussion These findings suggest a dual role of pulmonary inflammation in viral clearance and development of pneumonia during non-fatal infection caused by the 2009 pandemic influenza virus. Understanding the dynamics of the host’s transcriptomic and virological changes over the course of the infection caused by A (H1N1) pdm09 virus may help identifying the immune response profiles associated with an effective response against influenza virus.
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Affiliation(s)
- Raquel Almansa
- Laboratory of Biomedical Research in Sepsis (BIOSEPSIS), Hospital Clínico Universitario de Valladolid, Instituto de Estudios de Ciencias de la Salud de Castilla y León (IECSCYL), Valladolid, Spain
| | - Pamela Martínez-Orellana
- Centre de Recerca en Sanitat Animal (CReSA), Universitat Autónoma de Barcelona, IRTA, Barcelona, Spain
| | - Lucía Rico
- Laboratory of Biomedical Research in Sepsis (BIOSEPSIS), Hospital Clínico Universitario de Valladolid, Instituto de Estudios de Ciencias de la Salud de Castilla y León (IECSCYL), Valladolid, Spain
| | - Verónica Iglesias
- Laboratory of Biomedical Research in Sepsis (BIOSEPSIS), Hospital Clínico Universitario de Valladolid, Instituto de Estudios de Ciencias de la Salud de Castilla y León (IECSCYL), Valladolid, Spain
| | - Alicia Ortega
- Laboratory of Biomedical Research in Sepsis (BIOSEPSIS), Hospital Clínico Universitario de Valladolid, Instituto de Estudios de Ciencias de la Salud de Castilla y León (IECSCYL), Valladolid, Spain
| | - Beatriz Vidaña
- Department of Pathology, Animal and Plant Health Agency (APHA), Surrey, UK
| | - Jorge Martínez
- Centre de Recerca en Sanitat Animal (CReSA), Universitat Autónoma de Barcelona, IRTA, Barcelona, Spain.,Departament de Sanitat i d'Anatomia Animals, Universitat Autónoma de Barcelona, Barcelona, Spain
| | - Ana Expósito
- Laboratory of Biomedical Research in Sepsis (BIOSEPSIS), Hospital Clínico Universitario de Valladolid, Instituto de Estudios de Ciencias de la Salud de Castilla y León (IECSCYL), Valladolid, Spain
| | - María Montoya
- Centre de Recerca en Sanitat Animal (CReSA), Universitat Autónoma de Barcelona, IRTA, Barcelona, Spain.,African Swine Fever Virus Immunology Group, The Pirbright Institute, Surrey, UK
| | - Jesús F Bermejo-Martin
- Laboratory of Biomedical Research in Sepsis (BIOSEPSIS), Hospital Clínico Universitario de Valladolid, Instituto de Estudios de Ciencias de la Salud de Castilla y León (IECSCYL), Valladolid, Spain
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23
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Cole SL, Dunning J, Kok WL, Benam KH, Benlahrech A, Repapi E, Martinez FO, Drumright L, Powell TJ, Bennett M, Elderfield R, Thomas C, Dong T, McCauley J, Liew FY, Taylor S, Zambon M, Barclay W, Cerundolo V, Openshaw PJ, McMichael AJ, Ho LP. M1-like monocytes are a major immunological determinant of severity in previously healthy adults with life-threatening influenza. JCI Insight 2017; 2:e91868. [PMID: 28405622 PMCID: PMC5374077 DOI: 10.1172/jci.insight.91868] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In each influenza season, a distinct group of young, otherwise healthy individuals with no risk factors succumbs to life-threatening infection. To better understand the cause for this, we analyzed a broad range of immune responses in blood from a unique cohort of patients, comprising previously healthy individuals hospitalized with and without respiratory failure during one influenza season, and infected with one specific influenza A strain. This analysis was compared with similarly hospitalized influenza patients with known risk factors (total of n = 60 patients recruited). We found a sustained increase in a specific subset of proinflammatory monocytes, with high TNF-α expression and an M1-like phenotype (independent of viral titers), in these previously healthy patients with severe disease. The relationship between M1-like monocytes and immunopathology was strengthened using murine models of influenza, in which severe infection generated using different models (including the high-pathogenicity H5N1 strain) was also accompanied by high levels of circulating M1-like monocytes. Additionally, a raised M1/M2 macrophage ratio in the lungs was observed. These studies identify a specific subtype of monocytes as a modifiable immunological determinant of disease severity in this subgroup of severely ill, previously healthy patients, offering potential novel therapeutic avenues. In a cohort of influenza patients, previously healthy and young patients who succumbed to life-threatening disease were defined by high levels of circulating M1-like, TNF-αhi monocytes.
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Affiliation(s)
- Suzanne L Cole
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Jake Dunning
- National Heart and Lung Division, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Wai Ling Kok
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Kambez Hajipouran Benam
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Adel Benlahrech
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Emmanouela Repapi
- Computational Biology Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Fernando O Martinez
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Lydia Drumright
- National Heart and Lung Division, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Timothy J Powell
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Ruth Elderfield
- Section of Virology, Faculty of Medicine, Wright Fleming Institute, Imperial College London, London, United Kingdom
| | - Catherine Thomas
- National Infection Service, Public Health England, Colindale, London, United Kingdom
| | | | - Tao Dong
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Foo Y Liew
- Division of Immunology, Infection and Inflammation, University of Glasgow, Glasgow, United Kingdom.,School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Stephen Taylor
- Computational Biology Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Maria Zambon
- National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Wendy Barclay
- Section of Virology, Faculty of Medicine, Wright Fleming Institute, Imperial College London, London, United Kingdom
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter J Openshaw
- National Heart and Lung Division, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Andrew J McMichael
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ling-Pei Ho
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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24
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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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25
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Abstract
Metabolism refers to the chemical reactions that occur in living cells, and the reactants and products of these reactions compose the metabolome. The lipidome is comprised by hydrophobic metabolites and includes several broad classes of structurally diverse molecules. Lipids supplied by the host cell are required for many viral processes, and many if not all viruses have evolved mechanisms to perturb host metabolism to promote viral replication. This chapter provides background and a framework for examining the role of lipid metabolites in viral processes and rational attempts to target host metabolism as an antiviral strategy.
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26
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Husain M, Kyjovska ZO, Bourdon-Lacombe J, Saber AT, Jensen KA, Jacobsen NR, Williams A, Wallin H, Halappanavar S, Vogel U, Yauk CL. Carbon black nanoparticles induce biphasic gene expression changes associated with inflammatory responses in the lungs of C57BL/6 mice following a single intratracheal instillation. Toxicol Appl Pharmacol 2015; 289:573-88. [PMID: 26551751 PMCID: PMC7103116 DOI: 10.1016/j.taap.2015.11.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 11/05/2015] [Accepted: 11/05/2015] [Indexed: 01/08/2023]
Abstract
Inhalation of carbon black nanoparticles (CBNPs) causes pulmonary inflammation; however, time course data to evaluate the detailed evolution of lung inflammatory responses are lacking. Here we establish a time-series of lung inflammatory response to CBNPs. Female C57BL/6 mice were intratracheally instilled with 162 μg CBNPs alongside vehicle controls. Lung tissues were examined 3h, and 1, 2, 3, 4, 5, 14, and 42 days (d) post-exposure. Global gene expression and pulmonary inflammation were assessed. DNA damage was evaluated in bronchoalveolar lavage (BAL) cells and lung tissue using the comet assay. Increased neutrophil influx was observed at all time-points. DNA strand breaks were increased in BAL cells 3h post-exposure, and in lung tissues 2-5d post-exposure. Approximately 2600 genes were differentially expressed (± 1.5 fold; p ≤ 0.05) across all time-points in the lungs of exposed mice. Altered transcript levels were associated with immune-inflammatory response and acute phase response pathways, consistent with the BAL profiles and expression changes found in common respiratory infectious diseases. Genes involved in DNA repair, apoptosis, cell cycle regulation, and muscle contraction were also differentially expressed. Gene expression changes associated with inflammatory response followed a biphasic pattern, with initial changes at 3h post-exposure declining to base-levels by 3d, increasing again at 14 d, and then persisting to 42 d post-exposure. Thus, this single CBNP exposure that was equivalent to nine 8-h working days at the current Danish occupational exposure limit induced biphasic inflammatory response in gene expression that lasted until 42 d post-exposure, raising concern over the chronic effects of CBNP exposure.
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Affiliation(s)
- Mainul Husain
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada.
| | - Zdenka O Kyjovska
- National Research Centre for the Working Environment, Copenhagen, Denmark.
| | - Julie Bourdon-Lacombe
- Water and Air Quality Bureau, Safe Environments Directorate, HECSB, Health Canada, Ottawa, ON, Canada.
| | - Anne T Saber
- National Research Centre for the Working Environment, Copenhagen, Denmark.
| | - Keld A Jensen
- National Research Centre for the Working Environment, Copenhagen, Denmark.
| | - Nicklas R Jacobsen
- National Research Centre for the Working Environment, Copenhagen, Denmark.
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada.
| | - Håkan Wallin
- National Research Centre for the Working Environment, Copenhagen, Denmark; Institute of Public Health, University of Copenhagen, Denmark.
| | - Sabina Halappanavar
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada.
| | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark; Institute of Micro- and Nanotechnology, Technical University of Denmark, Lyngby, Denmark.
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada.
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27
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The 1918 Influenza Virus PB2 Protein Enhances Virulence through the Disruption of Inflammatory and Wnt-Mediated Signaling in Mice. J Virol 2015; 90:2240-53. [PMID: 26656717 DOI: 10.1128/jvi.02974-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 12/01/2015] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED The 1918-1919 influenza pandemic remains the single greatest infectious disease outbreak in the past century. Mouse and nonhuman primate infection models have shown that the 1918 virus induces overly aggressive innate and proinflammatory responses. To understand the response to viral infection and the role of individual 1918 genes on the host response to the 1918 virus, we examined reassortant avian viruses nearly identical to the pandemic 1918 virus (1918-like avian virus) carrying either the 1918 hemagglutinin (HA) or PB2 gene. In mice, both genes enhanced 1918-like avian virus replication, but only the mammalian host adaptation of the 1918-like avian virus through reassortment of the 1918 PB2 led to increased lethality. Through the combination of viral genetics and host transcriptional profiling, we provide a multidimensional view of the molecular mechanisms by which the 1918 PB2 gene drives viral pathogenicity. We demonstrate that 1918 PB2 enhances immune and inflammatory responses concomitant with increased cellular infiltration in the lung. We also show for the first time, that 1918 PB2 expression results in the repression of both canonical and noncanonical Wnt signaling pathways, which are crucial for inflammation-mediated lung regeneration and repair. Finally, we utilize regulatory enrichment and network analysis to define the molecular regulators of inflammation, epithelial regeneration, and lung immunopathology that are dysregulated during influenza virus infection. Taken together, our data suggest that while both HA and PB2 are important for viral replication, only 1918 PB2 exacerbates lung damage in mice infected with a reassortant 1918-like avian virus. IMPORTANCE As viral pathogenesis is determined in part by the host response, understanding the key host molecular driver(s) of virus-mediated disease, in relation to individual viral genes, is a promising approach to host-oriented drug efforts in preventing disease. Previous studies have demonstrated the importance of host adaptive genes, HA and PB2, in mediating disease although the mechanisms by which they do so are still poorly understood. Here, we combine viral genetics and host transcriptional profiling to show that although both 1918 HA and 1918 PB2 are important mediators of efficient viral replication, only 1918 PB2 impacts the pathogenicity of an avian influenza virus sharing high homology to the 1918 pandemic influenza virus. We demonstrate that 1918 PB2 enhances deleterious inflammatory responses and the inhibition of regeneration and repair functions coordinated by Wnt signaling in the lungs of infected mice, thereby promoting virus-associated disease.
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28
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Graham AC, Temple RM, Obar JJ. Mast cells and influenza a virus: association with allergic responses and beyond. Front Immunol 2015; 6:238. [PMID: 26042121 PMCID: PMC4435071 DOI: 10.3389/fimmu.2015.00238] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/01/2015] [Indexed: 12/07/2022] Open
Abstract
Influenza A virus (IAV) is a widespread infectious agent commonly found in mammalian and avian species. In humans, IAV is a respiratory pathogen that causes seasonal infections associated with significant morbidity in young and elderly populations, and has a large economic impact. Moreover, IAV has the potential to cause both zoonotic spillover infection and global pandemics, which have significantly greater morbidity and mortality across all ages. The pathology associated with these pandemic and spillover infections appear to be the result of an excessive inflammatory response leading to severe lung damage, which likely predisposes the lungs for secondary bacterial infections. The lung is protected from pathogens by alveolar epithelial cells, endothelial cells, tissue resident alveolar macrophages, dendritic cells, and mast cells. The importance of mast cells during bacterial and parasitic infections has been extensively studied; yet, the role of these hematopoietic cells during viral infections is only beginning to emerge. Recently, it has been shown that mast cells can be directly activated in response to IAV, releasing mediators such histamine, proteases, leukotrienes, inflammatory cytokines, and antiviral chemokines, which participate in the excessive inflammatory and pathological response observed during IAV infections. In this review, we will examine the relationship between mast cells and IAV, and discuss the role of mast cells as a potential drug target during highly pathological IAV infections. Finally, we proposed an emerging role for mast cells in other viral infections associated with significant host pathology.
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Affiliation(s)
- Amy C Graham
- Department of Microbiology and Immunology, Montana State University , Bozeman, MT , USA
| | - Rachel M Temple
- Department of Microbiology and Immunology, Montana State University , Bozeman, MT , USA
| | - Joshua J Obar
- Department of Microbiology and Immunology, Montana State University , Bozeman, MT , USA
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29
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Kamal RP, Katz JM, York IA. Molecular determinants of influenza virus pathogenesis in mice. Curr Top Microbiol Immunol 2015; 385:243-74. [PMID: 25038937 DOI: 10.1007/82_2014_388] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mice are widely used for studying influenza virus pathogenesis and immunology because of their low cost, the wide availability of mouse-specific reagents, and the large number of mouse strains available, including knockout and transgenic strains. However, mice do not fully recapitulate the signs of influenza infection of humans: transmission of influenza between mice is much less efficient than in humans, and influenza viruses often require adaptation before they are able to efficiently replicate in mice. In the process of mouse adaptation, influenza viruses acquire mutations that enhance their ability to attach to mouse cells, replicate within the cells, and suppress immunity, among other functions. Many such mouse-adaptive mutations have been identified, covering all 8 genomic segments of the virus. Identification and analysis of these mutations have provided insight into the molecular determinants of influenza virulence and pathogenesis, not only in mice but also in humans and other species. In particular, several mouse-adaptive mutations of avian influenza viruses have proved to be general mammalian-adaptive changes that are potential markers of pre-pandemic viruses. As well as evaluating influenza pathogenesis, mice have also been used as models for evaluation of novel vaccines and anti-viral therapies. Mice can be a useful animal model for studying influenza biology as long as differences between human and mice infections are taken into account.
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Affiliation(s)
- Ram P Kamal
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA,
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30
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Sethi G, Kwon Y, Burkhalter RJ, Pathak HB, Madan R, McHugh S, Atay S, Murthy S, Tawfik OW, Godwin AK. PTN signaling: Components and mechanistic insights in human ovarian cancer. Mol Carcinog 2014; 54:1772-85. [PMID: 25418856 DOI: 10.1002/mc.22249] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 09/30/2014] [Accepted: 10/10/2014] [Indexed: 12/13/2022]
Abstract
Molecular vulnerabilities represent promising candidates for the development of targeted therapies that hold the promise to overcome the challenges encountered with non-targeted chemotherapy for the treatment of ovarian cancer. Through a synthetic lethality screen, we previously identified pleiotrophin (PTN) as a molecular vulnerability in ovarian cancer and showed that siRNA-mediated PTN knockdown induced apoptotic cell death in epithelial ovarian cancer (EOC) cells. Although, it is well known that PTN elicits its pro-tumorigenic effects through its receptor, protein tyrosine phosphatase receptor Z1 (PTPRZ1), little is known about the potential importance of this pathway in the pathogenesis of ovarian cancer. In this study, we show that PTN is expressed, produced, and secreted in a panel of EOC cell lines. PTN levels in serous ovarian tumor tissues are on average 3.5-fold higher relative to normal tissue and PTN is detectable in serum samples of patients with EOC. PTPRZ1 is also expressed and produced by EOC cells and is found to be up-regulated in serous ovarian tumor tissue relative to normal ovarian surface epithelial tissue (P < 0.05). Gene silencing of PTPRZ1 in EOC cell lines using siRNA-mediated knockdown shows that PTPRZ1 is essential for viability and results in significant apoptosis with no effect on the cell cycle phase distribution. In order to determine how PTN mediates survival, we silenced the gene using siRNA mediated knockdown and performed expression profiling of 36 survival-related genes. Through computational mapping of the differentially expressed genes, members of the MAPK (mitogen-activated protein kinase) family were found to be likely effectors of PTN signaling in EOC cells. Our results provide the first experimental evidence that PTN and its signaling components may be of significance in the pathogenesis of epithelial ovarian cancer and provide a rationale for clinical evaluation of MAPK inhibitors in PTN and/or PTPRZ1 expressing ovarian tumors.
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Affiliation(s)
- Geetika Sethi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas.,Department of Biochemistry, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Youngjoo Kwon
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Rebecca J Burkhalter
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Harsh B Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas.,University of Kansas Cancer Center, Kansas City, Kansas
| | - Rashna Madan
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Sarah McHugh
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Safinur Atay
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Smruthi Murthy
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Ossama W Tawfik
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas.,University of Kansas Cancer Center, Kansas City, Kansas
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31
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Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A, Bolles M, Carter V, Chang J, Clauss TRW, Dash P, Diercks AH, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kaiser SM, Kelly S, Law GL, Li C, Li J, Long C, Luna ML, Matzke M, McDermott J, Menachery V, Metz TO, Mitchell H, Monroe ME, Navarro G, Neumann G, Podyminogin RL, Purvine SO, Rosenberger CM, Sanders CJ, Schepmoes AA, Shukla AK, Sims A, Sova P, Tam VC, Tchitchek N, Thomas PG, Tilton SC, Totura A, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Aderem A, Katze MG, Scheuermann RH. A comprehensive collection of systems biology data characterizing the host response to viral infection. Sci Data 2014; 1:140033. [PMID: 25977790 PMCID: PMC4410982 DOI: 10.1038/sdata.2014.33] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 08/15/2014] [Indexed: 12/13/2022] Open
Abstract
The Systems Biology for Infectious Diseases Research program was established by
the U.S. National Institute of Allergy and Infectious Diseases to investigate
host-pathogen interactions at a systems level. This program generated 47
transcriptomic and proteomic datasets from 30 studies that investigate
in vivo and in vitro host responses to
viral infections. Human pathogens in the Orthomyxoviridae and
Coronaviridae families, especially pandemic H1N1 and avian
H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus
(SARS-CoV), were investigated. Study validation was demonstrated via
experimental quality control measures and meta-analysis of independent
experiments performed under similar conditions. Primary assay results are
archived at the GEO and PeptideAtlas public repositories, while processed
statistical results together with standardized metadata are publically available
at the Influenza Research Database (www.fludb.org) and the Virus Pathogen
Resource (www.viprbrc.org). By comparing data from mutant versus wild-type
virus and host strains, RNA versus protein differential expression, and
infection with genetically similar strains, these data can be used to further
investigate genetic and physiological determinants of host responses to viral
infection.
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Affiliation(s)
| | | | - Sanjeev Kumar
- Northrop Grumman Information Systems, Health IT , Rockville, MD 20850, USA
| | - Edward B Klem
- Northrop Grumman Information Systems, Health IT , Rockville, MD 20850, USA
| | - Sudhakar Agnihothram
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | | | - Armand Bankhead
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA ; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health Sciences University , Portland, Oregon 97239-3098, USA
| | - Meagen Bolles
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Victoria Carter
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Jean Chang
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Therese R W Clauss
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Pradyot Dash
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Alan H Diercks
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Amie J Eisfeld
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Amy Ellis
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Shufang Fan
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7264, USA
| | - Lisa E Gralinski
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Richard R Green
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Masato Hatta
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Robert A Heegel
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jon M Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Sophia Jeng
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA
| | - Laurence Josset
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Shari M Kaiser
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Sara Kelly
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - G Lynn Law
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Chengjun Li
- Division of Animal influenza, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Harbin, Heilongjiang Province 150001, China
| | - Jiangning Li
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Casey Long
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Maria L Luna
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Melissa Matzke
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jason McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Vineet Menachery
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Hugh Mitchell
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Garnet Navarro
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Gabriele Neumann
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | | | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, WA 99354, USA
| | | | - Catherine J Sanders
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Anil K Shukla
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Amy Sims
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Pavel Sova
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Vincent C Tam
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Nicolas Tchitchek
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Susan C Tilton
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Allison Totura
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Jing Wang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | | | - Ji Wen
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jeffrey M Weiss
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Feng Yang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Qibin Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Shannon McWeeney
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA ; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health Sciences University , Portland, Oregon 97239-3098, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Yoshihiro Kawaoka
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA ; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Alan Aderem
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Michael G Katze
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA ; Washington National Primate Research Center, University of Washington , Seattle, WA 98195, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute , La Jolla, CA 92037, USA ; Department of Pathology, University of California , San Diego, CA 92093, USA
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32
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Liu ZP, Wu H, Zhu J, Miao H. Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection. BMC Bioinformatics 2014; 15:336. [PMID: 25281301 PMCID: PMC4287445 DOI: 10.1186/1471-2105-15-336] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/23/2014] [Indexed: 12/13/2022] Open
Abstract
Background Respiratory epithelial cells are the primary target of influenza virus infection in human. However, the molecular mechanisms of airway epithelial cell responses to viral infection are not fully understood. Revealing genome-wide transcriptional and post-transcriptional regulatory relationships can further advance our understanding of this problem, which motivates the development of novel and more efficient computational methods to simultaneously infer the transcriptional and post-transcriptional regulatory networks. Results Here we propose a novel framework named SITPR to investigate the interactions among transcription factors (TFs), microRNAs (miRNAs) and target genes. Briefly, a background regulatory network on a genome-wide scale (~23,000 nodes and ~370,000 potential interactions) is constructed from curated knowledge and algorithm predictions, to which the identification of transcriptional and post-transcriptional regulatory relationships is anchored. To reduce the dimension of the associated computing problem down to an affordable size, several topological and data-based approaches are used. Furthermore, we propose the constrained LASSO formulation and combine it with the dynamic Bayesian network (DBN) model to identify the activated regulatory relationships from time-course expression data. Our simulation studies on networks of different sizes suggest that the proposed framework can effectively determine the genuine regulations among TFs, miRNAs and target genes; also, we compare SITPR with several selected state-of-the-art algorithms to further evaluate its performance. By applying the SITPR framework to mRNA and miRNA expression data generated from human lung epithelial A549 cells in response to A/Mexico/InDRE4487/2009 (H1N1) virus infection, we are able to detect the activated transcriptional and post-transcriptional regulatory relationships as well as the significant regulatory motifs. Conclusion Compared with other representative state-of-the-art algorithms, the proposed SITPR framework can more effectively identify the activated transcriptional and post-transcriptional regulations simultaneously from a given background network. The idea of SITPR is generally applicable to the analysis of gene regulatory networks in human cells. The results obtained for human respiratory epithelial cells suggest the importance of the transcriptional, post-transcriptional regulations as well as their synergies in the innate immune responses against IAV infection. Electronic supplementary material The online version of this article (doi:10.1186/1471-2105-15-336) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Jian Zhu
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY 14642, USA.
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33
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Perwitasari O, Johnson S, Yan X, Howerth E, Shacham S, Landesman Y, Baloglu E, McCauley D, Tamir S, Tompkins SM, Tripp RA. Verdinexor, a novel selective inhibitor of nuclear export, reduces influenza a virus replication in vitro and in vivo. J Virol 2014; 88:10228-43. [PMID: 24965445 PMCID: PMC4136318 DOI: 10.1128/jvi.01774-14] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Influenza is a global health concern, causing death, morbidity, and economic losses. Chemotherapeutics that target influenza virus are available; however, rapid emergence of drug-resistant strains is common. Therapeutic targeting of host proteins hijacked by influenza virus to facilitate replication is an antiviral strategy to reduce the development of drug resistance. Nuclear export of influenza virus ribonucleoprotein (vRNP) from infected cells has been shown to be mediated by exportin 1 (XPO1) interaction with viral nuclear export protein tethered to vRNP. RNA interference screening has identified XPO1 as a host proinfluenza factor where XPO1 silencing results in reduced influenza virus replication. The Streptomyces metabolite XPO1 inhibitor leptomycin B (LMB) has been shown to limit influenza virus replication in vitro; however, LMB is toxic in vivo, which makes it unsuitable for therapeutic use. In this study, we tested the anti-influenza virus activity of a new class of orally available small-molecule selective inhibitors of nuclear export, specifically, the XPO1 antagonist KPT-335 (verdinexor). Verdinexor was shown to potently and selectively inhibit vRNP export and effectively inhibited the replication of various influenza virus A and B strains in vitro, including pandemic H1N1 virus, highly pathogenic H5N1 avian influenza virus, and the recently emerged H7N9 strain. In vivo, prophylactic and therapeutic administration of verdinexor protected mice against disease pathology following a challenge with influenza virus A/California/04/09 or A/Philippines/2/82-X79, as well as reduced lung viral loads and proinflammatory cytokine expression, while having minimal toxicity. These studies show that verdinexor acts as a novel anti-influenza virus therapeutic agent. IMPORTANCE Antiviral drugs represent important means of influenza virus control. However, substantial resistance to currently approved influenza therapeutic drugs has developed. New antiviral approaches are required to address drug resistance and reduce the burden of influenza virus-related disease. This study addressed critical preclinical studies for the development of verdinexor (KPT-335) as a novel antiviral drug. Verdinexor blocks progeny influenza virus genome nuclear export, thus effectively inhibiting virus replication. Verdinexor was found to limit the replication of various strains of influenza A and B viruses, including a pandemic H1N1 influenza virus strain, a highly pathogenic H5N1 avian influenza virus strain, and a recently emerging H7N9 influenza virus strain. Importantly, oral verdinexor treatments, given prophylactically or therapeutically, were efficacious in limiting lung virus burdens in influenza virus-infected mice, in addition to limiting lung proinflammatory cytokine expression, pathology, and death. Thus, this study demonstrated that verdinexor is efficacious against influenza virus infection in vitro and in vivo.
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Affiliation(s)
- Olivia Perwitasari
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Scott Johnson
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Xiuzhen Yan
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Elizabeth Howerth
- Department of Pathology, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Sharon Shacham
- Karyopharm Therapeutics, Inc., Natick, Massachusetts, USA
| | | | - Erkan Baloglu
- Karyopharm Therapeutics, Inc., Natick, Massachusetts, USA
| | | | - Sharon Tamir
- Karyopharm Therapeutics, Inc., Natick, Massachusetts, USA
| | - S Mark Tompkins
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Ralph A Tripp
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
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34
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H7N9 and other pathogenic avian influenza viruses elicit a three-pronged transcriptomic signature that is reminiscent of 1918 influenza virus and is associated with lethal outcome in mice. J Virol 2014; 88:10556-68. [PMID: 24991006 DOI: 10.1128/jvi.00570-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED Modulating the host response is a promising approach to treating influenza, caused by a virus whose pathogenesis is determined in part by the reaction it elicits within the host. Though the pathogenicity of emerging H7N9 influenza virus in several animal models has been reported, these studies have not included a detailed characterization of the host response following infection. Therefore, we characterized the transcriptomic response of BALB/c mice infected with H7N9 (A/Anhui/01/2013) virus and compared it to the responses induced by H5N1 (A/Vietnam/1203/2004), H7N7 (A/Netherlands/219/2003), and pandemic 2009 H1N1 (A/Mexico/4482/2009) influenza viruses. We found that responses to the H7 subtype viruses were intermediate to those elicited by H5N1 and pdm09H1N1 early in infection but that they evolved to resemble the H5N1 response as infection progressed. H5N1, H7N7, and H7N9 viruses were pathogenic in mice, and this pathogenicity correlated with increased transcription of cytokine response genes and decreased transcription of lipid metabolism and coagulation signaling genes. This three-pronged transcriptomic signature was observed in mice infected with pathogenic H1N1 strains such as the 1918 virus, indicating that it may be predictive of pathogenicity across multiple influenza virus strains. Finally, we used host transcriptomic profiling to computationally predict drugs that reverse the host response to H7N9 infection, and we identified six FDA-approved drugs that could potentially be repurposed to treat H7N9 and other pathogenic influenza viruses. IMPORTANCE Emerging avian influenza viruses are of global concern because the human population is immunologically naive to them. Current influenza drugs target viral molecules, but the high mutation rate of influenza viruses eventually leads to the development of antiviral resistance. As the host evolves far more slowly than the virus, and influenza pathogenesis is determined in part by the host response, targeting the host response is a promising approach to treating influenza. Here we characterize the host transcriptomic response to emerging H7N9 influenza virus and compare it with the responses to H7N7, H5N1, and pdm09H1N1. All three avian viruses were pathogenic in mice and elicited a transcriptomic signature that also occurs in response to the legendary 1918 influenza virus. Our work identifies host responses that could be targeted to treat severe H7N9 influenza and identifies six FDA-approved drugs that could potentially be repurposed as H7N9 influenza therapeutics.
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35
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Josset L, Tchitchek N, Gralinski LE, Ferris MT, Eisfeld AJ, Green RR, Thomas MJ, Tisoncik-Go J, Schroth GP, Kawaoka Y, Pardo-Manuel de Villena F, Baric RS, Heise MT, Peng X, Katze MG. Annotation of long non-coding RNAs expressed in collaborative cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts. RNA Biol 2014; 11:875-90. [PMID: 24922324 PMCID: PMC4179962 DOI: 10.4161/rna.29442] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/28/2014] [Accepted: 06/03/2014] [Indexed: 11/19/2022] Open
Abstract
The outcome of respiratory virus infection is determined by a complex interplay of viral and host factors. Some potentially important host factors for the antiviral response, whose functions remain largely unexplored, are long non-coding RNAs (lncRNAs). Here we systematically inferred the regulatory functions of host lncRNAs in response to influenza A virus and severe acute respiratory syndrome coronavirus (SARS-CoV) based on their similarity in expression with genes of known function. We performed total RNA-Seq on viral-infected lungs from eight mouse strains, yielding a large data set of transcriptional responses. Overall 5,329 lncRNAs were differentially expressed after infection. Most of the lncRNAs were co-expressed with coding genes in modules enriched in genes associated with lung homeostasis pathways or immune response processes. Each lncRNA was further individually annotated using a rank-based method, enabling us to associate 5,295 lncRNAs to at least one gene set and to predict their potential cis effects. We validated the lncRNAs predicted to be interferon-stimulated by profiling mouse responses after interferon-α treatment. Altogether, these results provide a broad categorization of potential lncRNA functions and identify subsets of lncRNAs with likely key roles in respiratory virus pathogenesis. These data are fully accessible through the MOuse NOn-Code Lung interactive database (MONOCLdb).
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Affiliation(s)
- Laurence Josset
- Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
| | - Nicolas Tchitchek
- Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
| | - Lisa E Gralinski
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
- Department of Epidemiology; University of North Carolina-Chapel Hill; Chapel Hill, NC USA
| | - Martin T Ferris
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
- Department of Genetics; University of North Carolina-Chapel Hill; Chapel Hill, NC USA
| | - Amie J Eisfeld
- Department of Pathobiological Sciences; Influenza Research Institute; University of Wisconsin-Madison; Madison, WI USA
| | - Richard R Green
- Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
| | - Matthew J Thomas
- Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
| | - Jennifer Tisoncik-Go
- Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
| | | | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences; Influenza Research Institute; University of Wisconsin-Madison; Madison, WI USA
| | | | - Ralph S Baric
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
- Department of Epidemiology; University of North Carolina-Chapel Hill; Chapel Hill, NC USA
| | - Mark T Heise
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
- Department of Genetics; University of North Carolina-Chapel Hill; Chapel Hill, NC USA
| | - Xinxia Peng
- Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
| | - Michael G Katze
- Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA
- Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA
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Liu Q, Chen H, Huang J, Chen Y, Gu M, Wang X, Hu S, Liu X, Liu X. A nonpathogenic duck-origin H9N2 influenza A virus adapts to high pathogenicity in mice. Arch Virol 2014; 159:2243-52. [PMID: 24696271 DOI: 10.1007/s00705-014-2062-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/19/2014] [Indexed: 11/26/2022]
Abstract
H9N2 influenza viruses continue to circulate in wild birds and poultry in Eurasian countries and have repeatedly infected mammals, including pigs and humans, posing a significant threat to public health. To understand the adaptation of H9N2 influenza viruses to mammals, we serially passaged a nonpathogenic duck-origin H9N2 influenza virus, A/duck/Jiangsu/1/2008 (DK1), in mouse lungs. Increased virulence was detectable after five sequential passages, and a highly pathogenic mouse-adapted strain (DK1-MA) with a 50% mouse lethal dose of 10(2.37) 50% egg infectious dose was obtained after 18 passages. DK1-MA grew faster and reached significantly higher titers than DK1 in mouse lungs and could sporadically spread to other organs. Moreover, DK1-MA induced a greater magnitude of pulmonary edema and higher levels of inflammatory cellular infiltration in bronchoalveolar lavage fluids than DK1 did. Genomic sequence alignment revealed eight amino acid substitutions (HA-L80F, HA-N193D, NA-A27T, PB2-F404L, PA-D3V, PA-S225R, NP-V105M, M1-A166V) in six viral proteins of DK1-MA compared with DK1 virus. Except for HA-L80F, the other seven substitutions were all located in known functional regions involved in interaction of viral proteins or interaction between the virus and host factors. Taken together, our results suggest that multiple amino acid substitutions may be involved in the adaptation of H9N2 avian influenza virus to mice, resulting in lethal infection, enhanced viral replication, severe pulmonary edema, and excessive inflammatory cellular infiltration in lungs. These observations provide helpful insights into the pathogenic potential of H9N2 avian influenza viruses that could pose threats to human health in the future.
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Affiliation(s)
- Qingtao Liu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
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Altboum Z, Steuerman Y, David E, Barnett-Itzhaki Z, Valadarsky L, Keren-Shaul H, Meningher T, Mendelson E, Mandelboim M, Gat-Viks I, Amit I. Digital cell quantification identifies global immune cell dynamics during influenza infection. Mol Syst Biol 2014; 10:720. [PMID: 24586061 PMCID: PMC4023392 DOI: 10.1002/msb.134947] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Hundreds of immune cell types work in coordination to maintain tissue homeostasis. Upon infection, dramatic changes occur with the localization, migration, and proliferation of the immune cells to first alert the body of the danger, confine it to limit spreading, and finally extinguish the threat and bring the tissue back to homeostasis. Since current technologies can follow the dynamics of only a limited number of cell types, we have yet to grasp the full complexity of global in vivo cell dynamics in normal developmental processes and disease. Here, we devise a computational method, digital cell quantification (DCQ), which combines genome‐wide gene expression data with an immune cell compendium to infer in vivo changes in the quantities of 213 immune cell subpopulations. DCQ was applied to study global immune cell dynamics in mice lungs at ten time points during 7 days of flu infection. We find dramatic changes in quantities of 70 immune cell types, including various innate, adaptive, and progenitor immune cells. We focus on the previously unreported dynamics of four immune dendritic cell subtypes and suggest a specific role for CD103+CD11b−DCs in early stages of disease and CD8+pDC in late stages of flu infection.
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Affiliation(s)
- Zeev Altboum
- Department of Immunology, Weizmann Institute, Rehovot, Israel
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TRIM24 promotes glioma progression and enhances chemoresistance through activation of the PI3K/Akt signaling pathway. Oncogene 2014; 34:600-10. [PMID: 24469053 DOI: 10.1038/onc.2013.593] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 10/14/2013] [Accepted: 12/18/2013] [Indexed: 12/14/2022]
Abstract
The tripartite motif protein TRIM24 (tripartite motif-containing 24) has been found to play distinct roles in tumor development and progression, according to different tumor contexts. However, it remains elusive whether TRIM24 plays a role in malignant gliomas that are the most common and deadly primary brain tumors in adults. We report here that TRIM24 expression is positively correlated with glioma malignancy and is negatively associated with prognosis of patients with newly diagnosed glioblastoma, which is the most malignant form of gliomas but displays highly heterogeneous clinical outcome. The multivariate Cox regression analysis demonstrates the independent predictive value of TRIM24 expression level for overall and progression-free survival. Knockdown of TRIM24 suppresses cell proliferation, cell cycle progression, clone formation and in vivo tumor development, whereas overexpression of TRIM24 promotes cell growth. Chromatin immunoprecipitation, real-time reverse transcription-PCR and mutation analyses demonstrate that TRIM24 binds to the PIK3CA promoter via its PHD-Bromo domain to activate the transcription of PIK3CA gene, thus enhancing phosphatidylinositide 3-kinase (PI3K)/Akt signaling. The pan-PI3K inhibitor LY294002 and small interfering RNA targeting PIK3CA both abrogate the growth-promoting effect of TRIM24. Moreover, TRIM24 regulates the expression of DNA repair enzyme O(6)-methylguanine-DNA methyltransferase (MGMT) through PI3K/Akt/nuclear factor-κB signaling transduction and enhances resistance to temozolomide, the standard chemotherapeutic agent for glioblastoma. Finally, glioblastoma patients with low TRIM24 expression benefit from chemotherapy, whereas those with high TRIM24 expression do not have such benefit. Our results suggest that TRIM24 might serve as a potential prognostic marker and therapeutic target for the management of malignant gliomas.
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Josset L, Tisoncik-Go J, Katze MG. Moving H5N1 studies into the era of systems biology. Virus Res 2013; 178:151-67. [PMID: 23499671 PMCID: PMC3834220 DOI: 10.1016/j.virusres.2013.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 02/24/2013] [Indexed: 12/20/2022]
Abstract
The dynamics of H5N1 influenza virus pathogenesis are multifaceted and can be seen as an emergent property that cannot be comprehended without looking at the system as a whole. In past years, most of the high-throughput studies on H5N1-host interactions have focused on the host transcriptomic response, at the cellular or the lung tissue level. These studies pointed out that the dynamics and magnitude of the innate immune response and immune cell infiltration is critical to H5N1 pathogenesis. However, viral-host interactions are multidimensional and advances in technologies are creating new possibilities to systematically measure additional levels of 'omic data (e.g. proteomic, metabolomic, and RNA profiling) at each temporal and spatial scale (from the single cell to the organism) of the host response. Natural host genetic variation represents another dimension of the host response that determines pathogenesis. Systems biology models of H5N1 disease aim at understanding and predicting pathogenesis through integration of these different dimensions by using intensive computational modeling. In this review, we describe the importance of 'omic studies for providing a more comprehensive view of infection and mathematical models that are being developed to integrate these data. This review provides a roadmap for what needs to be done in the future and what computational strategies should be used to build a global model of H5N1 pathogenesis. It is time for systems biology of H5N1 pathogenesis to take center stage as the field moves toward a more comprehensive view of virus-host interactions.
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Affiliation(s)
- Laurence Josset
- Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 98195, United States
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40
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Quantitative modeling of virus evolutionary dynamics and adaptation in serial passages using empirically inferred fitness landscapes. J Virol 2013; 88:1039-50. [PMID: 24198414 DOI: 10.1128/jvi.02958-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We describe a stochastic virus evolution model representing genomic diversification and within-host selection during experimental serial passages under cell culture or live-host conditions. The model incorporates realistic descriptions of the virus genotypes in nucleotide and amino acid sequence spaces, as well as their diversification from error-prone replications. It quantitatively considers factors such as target cell number, bottleneck size, passage period, infection and cell death rates, and the replication rate of different genotypes, allowing for systematic examinations of how their changes affect the evolutionary dynamics of viruses during passages. The relative probability for a viral population to achieve adaptation under a new host environment, quantified by the rate with which a target sequence frequency rises above 50%, was found to be most sensitive to factors related to sequence structure (distance from the wild type to the target) and selection strength (host cell number and bottleneck size). For parameter values representative of RNA viruses, the likelihood of observing adaptations during passages became negligible as the required number of mutations rose above two amino acid sites. We modeled the specific adaptation process of influenza A H5N1 viruses in mammalian hosts by simulating the evolutionary dynamics of H5 strains under the fitness landscape inferred from multiple sequence alignments of H3 proteins. In light of comparisons with experimental findings, we observed that the evolutionary dynamics of adaptation is strongly affected not only by the tendency toward increasing fitness values but also by the accessibility of pathways between genotypes constrained by the genetic code.
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Insights into the increasing virulence of the swine-origin pandemic H1N1/2009 influenza virus. Sci Rep 2013; 3:1601. [PMID: 23549303 PMCID: PMC3615340 DOI: 10.1038/srep01601] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 03/19/2013] [Indexed: 12/26/2022] Open
Abstract
Pandemic H1N1/2009 viruses have been stabilized in swine herds, and some strains display higher pathogenicity than the human-origin isolates. In this study, high-throughput RNA sequencing (RNA-seq) is applied to explore the systemic transcriptome responses of the mouse lungs infected by swine (Jia6/10) and human (LN/09) H1N1/2009 viruses. The transcriptome data show that Jia6/10 activates stronger virus-sensing signals, such as the toll-like receptor, RIG-I like receptor and NOD-like receptor signalings, as well as a stronger NF-κB and JAK-STAT singals, which play significant roles in inducing innate immunity. Most cytokines and interferon-stimulated genes show higher expression lever in Jia/06 infected groups. Meanwhile, virus Jia6/10 activates stronger production of reactive oxygen species, which might further promote higher mutation rate of the virus genome. Collectively, our data reveal that the swine-origin pandemic H1N1/2009 virus elicits a stronger innate immune reaction and pro-oxidation stimulation, which might relate closely to the increasing pathogenicity.
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Treating influenza with statins and other immunomodulatory agents. Antiviral Res 2013; 99:417-35. [PMID: 23831494 DOI: 10.1016/j.antiviral.2013.06.018] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 06/19/2013] [Accepted: 06/25/2013] [Indexed: 12/28/2022]
Abstract
Statins not only reduce levels of LDL-cholesterol, they counteract the inflammatory changes associated with acute coronary syndrome and improve survival. Similarly, in patients hospitalized with laboratory-confirmed seasonal influenza, statin treatment is associated with a 41% reduction in 30-day mortality. Most patients of any age who are at increased risk of influenza mortality have chronic low-grade inflammation characteristic of metabolic syndrome. Moreover, differences in the immune responses of children and adults seem responsible for the low mortality in children and high mortality in adults seen in the 1918 influenza pandemic and in other acute infectious and non-infectious conditions. These differences probably reflect human evolutionary development. Thus the host response to influenza seems to be the major determinant of outcome. Outpatient statins are associated with reductions in hospitalizations and deaths due to sepsis and pneumonia. Inpatient statins are also associated with reductions in short-term pneumonia mortality. Other immunomodulatory agents--ACE inhibitors (ACEIs), angiotensin receptor blockers (ARBs), PPARγ and PPARα agonists (glitazones and fibrates) and AMPK agonists (metformin)--also reduce mortality in patients with pneumonia (ACEIs, ARBs) or in mouse models of influenza (PPAR and AMPK agonists). In experimental studies, treatment has not increased virus replication. Thus effective management of influenza may not always require targeting the virus with vaccines or antiviral agents. Clinical investigators, not systems biologists, have been the first to suggest that immunomodulatory agents might be used to treat influenza patients, but randomized controlled trials will be needed to provide convincing evidence that they work. To guide the choice of which agent(s) to study, we need new types of laboratory research in animal models and clinical and epidemiological research in patients with critical illness. These studies will have crucial implications for global public health. During the 2009 H1N1 influenza pandemic, timely and affordable supplies of vaccines and antiviral agents were unavailable to more than 90% of the world's people. In contrast, statins and other immunomodulatory agents are currently produced as inexpensive generics, global supplies are huge, and they would be available to treat patients in any country with a basic health care system on the first pandemic day. Treatment with statins and other immunomodulatory agents represents a new approach to reducing mortality caused by seasonal and pandemic influenza.
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Graham AC, Hilmer KM, Zickovich JM, Obar JJ. Inflammatory response of mast cells during influenza A virus infection is mediated by active infection and RIG-I signaling. THE JOURNAL OF IMMUNOLOGY 2013; 190:4676-84. [PMID: 23526820 DOI: 10.4049/jimmunol.1202096] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Influenza A virus (IAV) is a major respiratory pathogen of both humans and animals. The lung is protected from pathogens by alveolar epithelial cells, tissue-resident alveolar macrophages, dendritic cells, and mast cells. The role of alveolar epithelial cells, endothelial cells, and alveolar macrophages during IAV infection has been studied previously. In this study, we address the role of mast cells during IAV infection. Respiratory infection with A/WSN/33 causes significant disease and immunopathology in C57BL/6 mice but not in B6.Cg-Kit(W-sh) mice, which lack mast cells. During in vitro coculture, A/WSN/33 caused mast cells to release histamine, secrete cytokines and chemokines, and produce leukotrienes. Moreover, when mast cells were infected with IAV, the virus did not replicate within mast cells. Importantly, human H1N1, H3N2, and influenza B virus isolates also could activate mast cells in vitro. Mast cell production of cytokines and chemokines occurs in a RIG-I/MAVS-dependent mechanism; in contrast, histamine production occurred through a RIG-I/MAVS-independent mechanism. Our data highlight that, following IAV infection, the response of mast cells is controlled by multiple receptors. In conclusion, we identified a unique inflammatory cascade activated during IAV infection that could potentially be targeted to limit morbidity following IAV infection.
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Affiliation(s)
- Amy C Graham
- Department of Immunology and Infectious Diseases, Montana State University, Bozeman, MT 59718, USA
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Phenotypic differences in virulence and immune response in closely related clinical isolates of influenza A 2009 H1N1 pandemic viruses in mice. PLoS One 2013; 8:e56602. [PMID: 23441208 PMCID: PMC3575477 DOI: 10.1371/journal.pone.0056602] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/14/2013] [Indexed: 01/07/2023] Open
Abstract
To capture the possible genotypic and phenotypic differences of the 2009 influenza A virus H1N1 pandemic (H1N1pdm) strains circulating in adult hospitalized patients, we isolated and sequenced nine H1N1pdm viruses from patients hospitalized during 2009–2010 with severe influenza pneumonia in Kentucky. Each viral isolate was characterized in mice along with two additional H1N1 pandemic strains and one seasonal strain to assess replication and virulence. All isolates showed similar levels of replication in nasal turbinates and lung, but varied in their ability to cause morbidity. Further differences were identified in cytokine and chemokine responses. IL-6 and KC were expressed early in mice infected with strains associated with higher virulence. Strains that showed lower pathogenicity in mice had greater IFNγ, MIG, and IL-10 responses. A principal component analysis (PCA) of the cytokine and chemokine profiles revealed 4 immune response phenotypes that correlated with the severity of disease. A/KY/180/10, which showed the greatest virulence with a rapid onset of disease progression, was compared in additional studies with A/KY/136/09, which showed low virulence in mice. Analyses comparing a low (KY/136) versus a high (KY/180) virulent isolate showed a significant difference in the kinetics of infection within the lower respiratory tract and immune responses. Notably by 4 DPI, virus titers within the lung, bronchoalveolar lavage fluid (BALf), and cells within the BAL (BALc) revealed that the KY/136 replicated in BALc, while KY/180 replication persisted in lungs and BALc. In summary, our studies suggest four phenotypic groups based on immune responses that result in different virulence outcomes in H1N1pdm isolates with a high degree of genetic similarity. In vitro studies with two of these isolates suggested that the more virulent isolate, KY/180, replicates productively in macrophages and this may be a key determinant in tipping the response toward a more severe disease progression.
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The PA-gene-mediated lethal dissemination and excessive innate immune response contribute to the high virulence of H5N1 avian influenza virus in mice. J Virol 2012; 87:2660-72. [PMID: 23255810 DOI: 10.1128/jvi.02891-12] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Highly pathogenic H5N1 influenza A virus remains a substantial threat to public health. To understand the molecular basis and host mechanism for the high virulence of H5N1 viruses in mammals, we compared two H5N1 isolates which have similar genetic backgrounds but greatly differ in their virulence in mice. A/Chicken/Jiangsu/k0402/2010 (CK10) is highly pathogenic, whereas A/Goose/Jiangsu/k0403/2010 (GS10) is nonpathogenic. We first showed that CK10 elicited a more potent innate immune response than did GS10 in mouse lungs by increasing the number and expression levels of activated genes. We then generated a series of reassortants between the two viruses and evaluated their virulence in mice. Inclusion of the CK10 PA gene in the GS10 background resulted in a dramatic increase in virulence. Conversely, expression of the GS10 PA gene in the CK10 background significantly attenuated the virulence. These results demonstrated that the PA gene mainly determines the pathogenicity discrepancy between CK10 and GS10 in mice. We further determined that arginine (R) at position 353 of the PA gene contributes to the high virulence of CK10 in mice. The reciprocal substitution at position 353 in PA or the exchange of the entire PA gene largely caused the transfer of viral phenotypes, including virus replication, polymerase activity, and manipulation of the innate response, between CK10 and GS10. We therefore defined a novel molecular marker associated with the high virulence of H5N1 influenza viruses, providing further insights into the pathogenesis of H5N1 viruses in mammals.
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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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Go JT, Belisle SE, Tchitchek N, Tumpey TM, Ma W, Richt JA, Safronetz D, Feldmann H, Katze MG. 2009 pandemic H1N1 influenza virus elicits similar clinical course but differential host transcriptional response in mouse, macaque, and swine infection models. BMC Genomics 2012; 13:627. [PMID: 23153050 PMCID: PMC3532173 DOI: 10.1186/1471-2164-13-627] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Accepted: 11/04/2012] [Indexed: 12/24/2022] Open
Abstract
Background The 2009 pandemic H1N1 influenza virus emerged in swine and quickly became a major global health threat. In mouse, non human primate, and swine infection models, the pH1N1 virus efficiently replicates in the lung and induces pro-inflammatory host responses; however, whether similar or different cellular pathways were impacted by pH1N1 virus across independent infection models remains to be further defined. To address this we have performed a comparative transcriptomic analysis of acute phase responses to a single pH1N1 influenza virus, A/California/04/2009 (CA04), in the lung of mice, macaques and swine. Results Despite similarities in the clinical course, we observed differences in inflammatory molecules elicited, and the kinetics of their gene expression changes across all three species. We found genes associated with the retinoid X receptor (RXR) signaling pathway known to control pro-inflammatory and metabolic processes that were differentially regulated during infection in each species, though the heterodimeric RXR partner, pathway associated signaling molecules, and gene expression patterns varied among the three species. Conclusions By comparing transcriptional changes in the context of clinical and virological measures, we identified differences in the host transcriptional response to pH1N1 virus across independent models of acute infection. Antiviral resistance and the emergence of new influenza viruses have placed more focus on developing drugs that target the immune system. Underlying overt clinical disease are molecular events that suggest therapeutic targets identified in one host may not be appropriate in another.
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Affiliation(s)
- Jennifer T Go
- Department of Microbiology, University of Washington, Seattle, 98195, USA.
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