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Ye Y, Fan H, Li Q, Zhang Z, Miao P, Zhu J, Liu J, Zhang J, Liao M. Differential proteome response to H5N1 highly pathogenic avian influenza (HPAI) viruses infection in duck. Front Immunol 2022; 13:965454. [PMID: 36059479 PMCID: PMC9438030 DOI: 10.3389/fimmu.2022.965454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Ducks and wild aquatic birds are the natural reservoirs of avian influenza viruses. However, the host proteome response that causes disease in vivo by the H5N1 HPAI virus is still unclear. This study presented a comprehensive analysis of the proteome response in Muscovy duck lung tissue during 3 days of infection with either a highly virulent DK383 or an avirulent DK212. An unbiased strategy- isobaric tags for relative and absolute quantitation (iTRAQ) in conjunction with high-performance liquid chromatography with tandem mass spectrometry (HPLC-MS/MS) was utilized to investigate the infection mechanism. Pathways derived from analysis of 292 significantly altered proteins may contribute to the high pathogenic nature and disease progression of H5N1 viruses. Global proteome profiles indicated improved correlation with the virus titers and gene expression patterns between the two strains of the H5N1 virus. DK383 replicated more efficiently and induced a stronger response specific to severe disease. While proteins involved in the immune response of neutrophils were increased markedly by DK383, DK212 evoked a distinct response characterized by an increase in proteins involved in the maturation of dendritic cells, adhesion of phagocytes, and immune response of macrophages. The differentially activated Akt/mTOR/p70S6K pathway might involve in the host response to H5N1 viruses. Therefore, systematically integrated with datasets from primary genomic and virus titer results, proteomic analyses may help reveal the potential pathogenesis.
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Affiliation(s)
- Yu Ye
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- College of Animal Technology and Science, Jiangxi Agricultural University, Nanchang, China
| | - Huiying Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
| | - Qi Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonoses Control and Prevention of Guangdong, Guangzhou, China
| | - Zhen Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Control and Prevention of Guangdong Higher Education Institutes, Guangzhou, China
| | - Peisi Miao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Jiangsu Coinnovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Jun Zhu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Jie Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonoses Control and Prevention of Guangdong, Guangzhou, China
- Key Laboratory of Control and Prevention of Guangdong Higher Education Institutes, Guangzhou, China
| | - Jie Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- Key Laboratory of Zoonoses Control and Prevention of Guangdong, Guangzhou, China
- Key Laboratory of Control and Prevention of Guangdong Higher Education Institutes, Guangzhou, China
- *Correspondence: Ming Liao,
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2
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Vijayakumar P, Raut AA, Chingtham S, Murugkar HV, Kulkarni DD, Sood R, Singh VP, Mishra A. Proteomic analysis of differential expression of lung proteins in response to highly pathogenic avian influenza virus infection in chickens. Arch Virol 2021; 167:141-152. [PMID: 34786609 DOI: 10.1007/s00705-021-05287-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/16/2021] [Indexed: 12/21/2022]
Abstract
Elucidation of the molecular pathogenesis underlying virus-host interactions is important for the development of new diagnostic and therapeutic strategies against highly pathogenic avian influenza (HPAI) virus infection in chickens. However, the pathogenesis of HPAI virus in chickens is not completely understood. To identify the intracellular signaling pathways and critical host proteins associated with influenza pathogenesis, we analyzed the lung proteome of a chicken infected with HPAI H5N1 virus (A/duck/India/02CA10/2011/Agartala). Mass spectrometry data sets were searched against the chicken UniProt reference database. At the local false discovery rate level of 5%, a total of 3313 proteins with the presence of at least one unique peptide were identified in the chicken lung proteome datasets. Differential expression analysis of these proteins showed that 247 and 1754 proteins were downregulated at 12 h and 48 h postinfection, respectively. We observed expression of proteins of the predominant signaling pathways, including Toll-like receptors (TLRs), retinoic acid-inducible gene I-like receptors (RLRs), NOD-like receptors (NLRs), and JAK-STAT signaling. Activation of these pathways is associated with the cytokine storm effect and thus may be the cause of the severity of HPAI H5N1 infection in chickens. We also observed the expression of myeloid differentiation primary response protein (MyD88), inhibitor of nuclear factor kappa B kinase subunit beta (IKBKB), interleukin 1 receptor associated kinase 4 (IRAK4), RELA proto-oncogene NF-κB subunit (RELA), and mitochondrial antiviral signaling protein (MAVS), which are involved in critical signaling pathways, as well as other, less-commonly identified proteins such as hepatocyte nuclear factor 4 alpha (HNF4A), ELAV-like RNA binding protein 1 (ELAVL1), fibronectin 1 (FN1), COP9 signalosome subunit 5 (COPS5), cullin 1 (CUL1), breast cancer type 1 susceptibility protein (BRCA1), and the FYN proto-oncogene Src family tyrosine kinase (FYN) as main hub proteins that might play important roles in influenza pathogenesis in chickens. In summary, we identified the signaling pathways and the proteomic determinants associated with disease pathogenesis in chickens infected with HPAI H5N1 virus.
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Affiliation(s)
- Periyasamy Vijayakumar
- Pathogenomics Laboratory, ICAR-National Institute of High-Security Animal Diseases, OIE Reference lab for Avian Influenza, Bhopal, 462021, Madhya Pradesh, India.,Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Orathanadu, 614625, Tamil Nadu, India
| | - Ashwin Ashok Raut
- Pathogenomics Laboratory, ICAR-National Institute of High-Security Animal Diseases, OIE Reference lab for Avian Influenza, Bhopal, 462021, Madhya Pradesh, India
| | - Santhalembi Chingtham
- Pathogenomics Laboratory, ICAR-National Institute of High-Security Animal Diseases, OIE Reference lab for Avian Influenza, Bhopal, 462021, Madhya Pradesh, India
| | - Harshad V Murugkar
- ICAR -National Institute of High-Security Animal Diseases, OIE Reference lab for Avian Influenza, Bhopal, 462021, Madhya Pradesh, India
| | - Diwakar D Kulkarni
- ICAR -National Institute of High-Security Animal Diseases, OIE Reference lab for Avian Influenza, Bhopal, 462021, Madhya Pradesh, India
| | - Richa Sood
- ICAR -National Institute of High-Security Animal Diseases, OIE Reference lab for Avian Influenza, Bhopal, 462021, Madhya Pradesh, India
| | - Vijendra Pal Singh
- ICAR -National Institute of High-Security Animal Diseases, OIE Reference lab for Avian Influenza, Bhopal, 462021, Madhya Pradesh, India
| | - Anamika Mishra
- Pathogenomics Laboratory, ICAR-National Institute of High-Security Animal Diseases, OIE Reference lab for Avian Influenza, Bhopal, 462021, Madhya Pradesh, India.
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3
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Bucsan AN, Mehra S, Khader SA, Kaushal D. The current state of animal models and genomic approaches towards identifying and validating molecular determinants of Mycobacterium tuberculosis infection and tuberculosis disease. Pathog Dis 2020; 77:5543892. [PMID: 31381766 PMCID: PMC6687098 DOI: 10.1093/femspd/ftz037] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 07/25/2019] [Indexed: 12/31/2022] Open
Abstract
Animal models are important in understanding both the pathogenesis of and immunity to tuberculosis (TB). Unfortunately, we are beginning to understand that no animal model perfectly recapitulates the human TB syndrome, which encompasses numerous different stages. Furthermore, Mycobacterium tuberculosis infection is a very heterogeneous event at both the levels of pathogenesis and immunity. This review seeks to establish the current understanding of TB pathogenesis and immunity, as validated in the animal models of TB in active use today. We especially focus on the use of modern genomic approaches in these models to determine the mechanism and the role of specific molecular pathways. Animal models have significantly enhanced our understanding of TB. Incorporation of contemporary technologies such as single cell transcriptomics, high-parameter flow cytometric immune profiling, proteomics, proteomic flow cytometry and immunocytometry into the animal models in use will further enhance our understanding of TB and facilitate the development of treatment and vaccination strategies.
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Affiliation(s)
- Allison N Bucsan
- Tulane Center for Tuberculosis Research, Covington, LA, USA.,Tulane National Primate Research Center, Covington, LA, USA
| | - Smriti Mehra
- Tulane National Primate Research Center, Covington, LA, USA
| | | | - Deepak Kaushal
- Tulane Center for Tuberculosis Research, Covington, LA, USA.,Tulane National Primate Research Center, Covington, LA, USA.,Southwest National Primate Research Center, San Antonio, TX, USA.,Texas Biomedical Research Institute, San Antonio, TX, USA
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4
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Casadei E, Salinas I. Comparative models for human nasal infections and immunity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 92:212-222. [PMID: 30513304 PMCID: PMC7102639 DOI: 10.1016/j.dci.2018.11.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 05/09/2023]
Abstract
The human olfactory system is a mucosal surface and a major portal of entry for respiratory and neurotropic pathogens into the body. Understanding how the human nasopharynx-associated lymphoid tissue (NALT) halts the progression of pathogens into the lower respiratory tract or the central nervous system is key for developing effective cures. Although traditionally mice have been used as the gold-standard model for the study of human nasal diseases, mouse models present important caveats due to major anatomical and functional differences of the human and murine olfactory system and NALT. We summarize the NALT anatomy of different animal groups that have thus far been used to study host-pathogen interactions at the olfactory mucosa and to test nasal vaccines. The goal of this review is to highlight the strengths and limitations of each animal model of nasal immunity and to identify the areas of research that require further investigation to advance human health.
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Affiliation(s)
- Elisa Casadei
- University of New Mexico, Department of Biology, Center for Evolutionary and Theoretical Immunology (CETI), Albuquerque, NM, USA.
| | - Irene Salinas
- University of New Mexico, Department of Biology, Center for Evolutionary and Theoretical Immunology (CETI), Albuquerque, NM, USA
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5
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Sanada T, Yasui F, Honda T, Kayesh MEH, Takano JI, Shiogama Y, Yasutomi Y, Tsukiyama-Kohara K, Kohara M. Avian H5N1 influenza virus infection causes severe pneumonia in the Northern tree shrew (Tupaia belangeri). Virology 2019; 529:101-110. [PMID: 30684692 DOI: 10.1016/j.virol.2019.01.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/14/2019] [Accepted: 01/14/2019] [Indexed: 01/07/2023]
Abstract
Avian-origin influenza viruses like H5N1 and H7N9 often cause severe symptoms with high mortality in humans. Animal models are useful for clarification of the mechanisms of pathogenicity of these infections. In this study, to expand the potential utility of the Northern tree shrew (Tupaia belangeri) for influenza virus infection, we assessed the pathogenicity of H5N1 and H7N9 avian influenza viruses in tupaia. Infectious virus was detected continuously from nasal, oral, tracheal, and conjunctival swab samples in the animals infected with these viruses. H5N1 influenza virus infection of tupaia caused severe diffuse pneumonia with fever and weight loss. In contrast, H7N9 influenza virus infection caused focal pneumonia. The severity of pneumonia was correlated with proinflammatory cytokine transcript levels. These results indicated that tupaia can be another suitable animal model for avian influenza virus research.
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Affiliation(s)
- Takahiro Sanada
- Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Fumihiko Yasui
- Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
| | - Tomoko Honda
- Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Mohammad Enamul Hoque Kayesh
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima-city, Kagoshima 890-0065, Japan
| | - Jun-Ichiro Takano
- Laboratory of Immunoregulation and Vaccine Research, Tsukuba Primate Research Center, National Institute of Biomedical Innovation, Health and Nutrition, 1-1 Hachimandai, Tsukuba, Ibaraki 305-0843, Japan
| | - Yumiko Shiogama
- Laboratory of Immunoregulation and Vaccine Research, Tsukuba Primate Research Center, National Institute of Biomedical Innovation, Health and Nutrition, 1-1 Hachimandai, Tsukuba, Ibaraki 305-0843, Japan
| | - Yasuhiro Yasutomi
- Laboratory of Immunoregulation and Vaccine Research, Tsukuba Primate Research Center, National Institute of Biomedical Innovation, Health and Nutrition, 1-1 Hachimandai, Tsukuba, Ibaraki 305-0843, Japan
| | - Kyoko Tsukiyama-Kohara
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima-city, Kagoshima 890-0065, Japan
| | - Michinori Kohara
- Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
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6
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Bortz E, Wu TT, Patel P, Whitelegge JP, Sun R. Proteomics of Bronchoalveolar Lavage Fluid Reveals a Lung Oxidative Stress Response in Murine Herpesvirus-68 Infection. Viruses 2018; 10:v10120670. [PMID: 30486363 PMCID: PMC6316452 DOI: 10.3390/v10120670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 11/15/2018] [Accepted: 11/20/2018] [Indexed: 12/25/2022] Open
Abstract
Murine herpesvirus-68 (MHV-68) productively infects mouse lungs, exhibiting a complex pathology characteristic of both acute viral infections and chronic respiratory diseases. We sought to discover proteins differentially expressed in bronchoalveolar lavage (BAL) from mice infected with MHV-68. Mice were infected intranasally with MHV-68. After nine days, as the lytic phase of infection resolved, differential BAL proteins were identified by two-dimensional (2D) electrophoresis and mass spectrometry. Of 23 unique proteins, acute phase proteins, vitamin A transport, and oxidative stress response factors Pdx6 and EC-SOD (Sod3) were enriched. Correspondingly, iNOS2 was induced in lung tissue by seven days post-infection. Oxidative stress was partly a direct result of MHV-68 infection, as reactive oxygen species (ROS) were induced in cultured murine NIH3T3 fibroblasts and human lung A549 cells infected with MHV-68. Finally, mice infected with a recombinant MHV-68 co-expressing inflammatory cytokine murine interleukin 6 (IL6) showed exacerbated oxidative stress and soluble type I collagen characteristic of tissue recovery. Thus, oxidative stress appears to be a salient feature of MHV-68 pathogenesis, in part caused by lytic replication of the virus and IL6. Proteins and small molecules in lung oxidative stress networks therefore may provide new therapeutic targets to ameliorate respiratory virus infections.
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Affiliation(s)
- Eric Bortz
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA.
| | - Ting-Ting Wu
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
| | - Parthive Patel
- Center for Molecular Biology and German Cancer Research Center (DKFZ), University of Heidelberg (ZMBH), 69120 Heidelberg, Germany.
| | - Julian P Whitelegge
- The Pasarow Mass Spectrometry Laboratory & the Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
| | - Ren Sun
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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7
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Abstract
Viruses utilize a number of host factors in order to carry out their replication cycles. Influenza A virus (IAV) and human respiratory syncytial virus (RSV) both infect the tissues of the respiratory tract, and as such we hypothesize that they might require similar host factors. Several published genome-wide screens have identified putative IAV host factors; however, there is significant discordance between their hits. In order to build on this work, we integrated a variety of "OMICS" data sources using two complementary network analyses, yielding 51 genes enriched for both IAV and RSV replication. We designed a targeted small interfering RNA (siRNA)-based assay to screen these genes against IAV under robust conditions and identified 13 genes supported by two IAV subtypes in both primary and transformed human lung cells. One of these hits, RNA binding motif 14 (RBM14), was validated as a required host factor and furthermore was shown to relocalize to the nucleolus upon IAV infection but not with other viruses. Additionally, the IAV NS1 protein is both necessary and sufficient for RBM14 relocalization, and relocalization also requires the double-stranded RNA (dsRNA) binding capacity of NS1. This work reports the discovery of a new host requirement for IAV replication and exposes a novel example of interplay between IAV NS1 and the host protein, RBM14.IMPORTANCE Influenza A virus (IAV) and respiratory syncytial virus (RSV) present major global disease burdens. There are high economic costs associated with morbidity as well as significant mortality rates, especially in developing countries, in children, and in the elderly. There are currently limited therapeutic options for these viruses, which underscores the need for novel research into virus biology that may lead to the discovery of new therapeutic approaches. This work extends existing research into host factors involved in virus replication and explores the interaction between IAV and one such host factor, RBM14. Further study to fully characterize this interaction may elucidate novel mechanisms used by the virus during its replication cycle and open new avenues for understanding virus biology.
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8
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Belser JA, Maines TR, Tumpey TM. Importance of 1918 virus reconstruction to current assessments of pandemic risk. Virology 2018; 524:45-55. [PMID: 30142572 PMCID: PMC9036538 DOI: 10.1016/j.virol.2018.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/25/2018] [Accepted: 08/09/2018] [Indexed: 01/13/2023]
Abstract
Reconstruction of the 1918 influenza virus has facilitated considerable advancements in our understanding of this extraordinary pandemic virus. However, the benefits of virus reconstruction are not limited to this one strain. Here, we provide an overview of laboratory studies which have evaluated the reconstructed 1918 virus, and highlight key discoveries about determinants of virulence and transmissibility associated with this virus in mammals. We further discuss recent and current pandemic threats from avian and swine reservoirs, and provide specific examples of how reconstruction of the 1918 pandemic virus has improved our ability to contextualize research employing novel and emerging strains. As influenza viruses continue to evolve and pose a threat to human health, studying past pandemic viruses is key to future preparedness efforts.
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Affiliation(s)
- Jessica A Belser
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Taronna R Maines
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Terrence M Tumpey
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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9
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Zhang K, Xu WW, Zhang Z, Liu J, Li J, Sun L, Sun W, Jiao P, Sang X, Ren Z, Yu Z, Li Y, Feng N, Wang T, Wang H, Yang S, Zhao Y, Zhang X, Wilker PR, Liu W, Liao M, Chen H, Gao Y, Xia X. The innate immunity of guinea pigs against highly pathogenic avian influenza virus infection. Oncotarget 2018; 8:30422-30437. [PMID: 28418930 PMCID: PMC5444753 DOI: 10.18632/oncotarget.16503] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 02/27/2017] [Indexed: 12/20/2022] Open
Abstract
H5N1 avian influenza viruses are a major pandemic concern. In contrast to the highly virulent phenotype of H5N1 in humans and many animal models, guinea pigs do not typically display signs of severe disease in response to H5N1 virus infection. Here, proteomic and transcriptional profiling were applied to identify host factors that account for the observed attenuation of A/Tiger/Harbin/01/2002 (H5N1) virulence in guinea pigs. RIG-I and numerous interferon stimulated genes were among host proteins with altered expression in guinea pig lungs during H5N1 infection. Overexpression of RIG-I or the RIG-I adaptor protein MAVS in guinea pig cell lines inhibited H5N1 replication. Endogenous GBP-1 expression was required for RIG-I mediated inhibition of viral replication upstream of the activity of MAVS. Furthermore, we show that guinea pig complement is involved in viral clearance, the regulation of inflammation, and cellular apoptosis during influenza virus infection of guinea pigs. This work uncovers features of the guinea pig innate immune response to influenza that may render guinea pigs resistant to highly pathogenic influenza viruses.
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Affiliation(s)
- Kun Zhang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China.,Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, 23298, USA
| | - Wei Wei Xu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Zhaowei Zhang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Jing Liu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Lijuan Sun
- Department of Influenza Vaccine, Changchun Institute of Biological Product, Changchun, 130062, PR China
| | - Weiyang Sun
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Peirong Jiao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Xiaoyu Sang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Zhiguang Ren
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Zhijun Yu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Yuanguo Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Na Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Tiecheng Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Hualei Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Songtao Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Yongkun Zhao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Xuemei Zhang
- Department of Influenza Vaccine, Changchun Institute of Biological Product, Changchun, 130062, PR China
| | - Peter R Wilker
- Department of Microbiology, University of Wisconsin La Crosse, La Crosse, Wisconsin, 54601, USA
| | - WenJun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, PR China
| | - Yuwei Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
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10
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Mindaye ST, Ilyushina NA, Fantoni G, Alterman MA, Donnelly RP, Eichelberger MC. Impact of Influenza A Virus Infection on the Proteomes of Human Bronchoepithelial Cells from Different Donors. J Proteome Res 2017; 16:3287-3297. [DOI: 10.1021/acs.jproteome.7b00286] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Samuel T. Mindaye
- Division
of Viral Products, OVRR, CBER, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Natalia A. Ilyushina
- Division
of Biotechnology Research and Review II, CDER, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Giovanna Fantoni
- Division
of Viral Products, OVRR, CBER, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Michail A. Alterman
- Division
of Cellular and Gene Therapies, OTAT, CBER, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Raymond P. Donnelly
- Division
of Biotechnology Research and Review II, CDER, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Maryna C. Eichelberger
- Division
of Viral Products, OVRR, CBER, Food and Drug Administration, Silver Spring, Maryland 20993, United States
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11
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Influenza-Omics and the Host Response: Recent Advances and Future Prospects. Pathogens 2017; 6:pathogens6020025. [PMID: 28604586 PMCID: PMC5488659 DOI: 10.3390/pathogens6020025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/07/2017] [Accepted: 06/08/2017] [Indexed: 12/23/2022] Open
Abstract
Influenza A viruses (IAV) continually evolve and have the capacity to cause global pandemics. Because IAV represents an ongoing threat, identifying novel therapies and host innate immune factors that contribute to IAV pathogenesis is of considerable interest. This review summarizes the relevant literature as it relates to global host responses to influenza infection at both the proteome and transcriptome level. The various-omics infection systems that include but are not limited to ferrets, mice, pigs, and even the controlled infection of humans are reviewed. Discussion focuses on recent advances, remaining challenges, and knowledge gaps as it relates to influenza-omics infection outcomes.
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12
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Mishra A, Vijayakumar P, Raut AA. Emerging avian influenza infections: Current understanding of innate immune response and molecular pathogenesis. Int Rev Immunol 2017; 36:89-107. [PMID: 28272907 DOI: 10.1080/08830185.2017.1291640] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The highly pathogenic avian influenza viruses (HPAIVs) cause severe disease in gallinaceous poultry species, domestic ducks, various aquatic and terrestrial wild bird species as well as humans. The outcome of the disease is determined by complex interactions of multiple components of the host, the virus, and the environment. While the host-innate immune response plays an important role for clearance of infection, excessive inflammatory immune response (cytokine storm) may contribute to morbidity and mortality of the host. Therefore, innate immunity response in avian influenza infection has two distinct roles. However, the viral pathogenic mechanism varies widely in different avian species, which are not completely understood. In this review, we summarized the current understanding and gaps in host-pathogen interaction of avian influenza infection in birds. In first part of this article, we summarized influenza viral pathogenesis of gallinaceous and non-gallinaceous avian species. Then we discussed innate immune response against influenza infection, cytokine storm, differential host immune responses against different pathotypes, and response in different avian species. Finally, we reviewed the systems biology approach to study host-pathogen interaction in avian species for better characterization of molecular pathogenesis of the disease. Wild aquatic birds act as natural reservoir of AIVs. Better understanding of host-pathogen interaction in natural reservoir is fundamental to understand the properties of AIV infection and development of improved vaccine and therapeutic strategies against influenza.
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Affiliation(s)
- Anamika Mishra
- a Pathogenomics Laboratory , OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases , Bhopal , Madhya Pradesh , India
| | - Periyasamy Vijayakumar
- a Pathogenomics Laboratory , OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases , Bhopal , Madhya Pradesh , India
| | - Ashwin Ashok Raut
- a Pathogenomics Laboratory , OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases , Bhopal , Madhya Pradesh , India
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13
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Heazlewood JL, Schrimpf SP, Becher D, Riedel K, Tholey A, Bendixen E. Multi-Organism Proteomes (iMOP): Advancing our Understanding of Human Biology. Proteomics 2016; 15:2885-94. [PMID: 26331910 DOI: 10.1002/pmic.201570153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Joshua L Heazlewood
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria, 3010, Australia.,Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94702, USA
| | - Sabine P Schrimpf
- Institute of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland
| | - Dörte Becher
- Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Greifswald, Germany
| | - Katrin Riedel
- Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Greifswald, Germany
| | - Andreas Tholey
- Systematische Proteomforschung & Bioanalytik, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Emøke Bendixen
- Department of Molecular Biology and Genetics, University of Aarhus, Denmark
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14
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A Systems Biology Approach to the Coordination of Defensive and Offensive Molecular Mechanisms in the Innate and Adaptive Host-Pathogen Interaction Networks. PLoS One 2016; 11:e0149303. [PMID: 26881892 PMCID: PMC4755559 DOI: 10.1371/journal.pone.0149303] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/29/2016] [Indexed: 11/19/2022] Open
Abstract
Infected zebrafish coordinates defensive and offensive molecular mechanisms in response to Candida albicans infections, and invasive C. albicans coordinates corresponding molecular mechanisms to interact with the host. However, knowledge of the ensuing infection-activated signaling networks in both host and pathogen and their interspecific crosstalk during the innate and adaptive phases of the infection processes remains incomplete. In the present study, dynamic network modeling, protein interaction databases, and dual transcriptome data from zebrafish and C. albicans during infection were used to infer infection-activated host-pathogen dynamic interaction networks. The consideration of host-pathogen dynamic interaction systems as innate and adaptive loops and subsequent comparisons of inferred innate and adaptive networks indicated previously unrecognized crosstalk between known pathways and suggested roles of immunological memory in the coordination of host defensive and offensive molecular mechanisms to achieve specific and powerful defense against pathogens. Moreover, pathogens enhance intraspecific crosstalk and abrogate host apoptosis to accommodate enhanced host defense mechanisms during the adaptive phase. Accordingly, links between physiological phenomena and changes in the coordination of defensive and offensive molecular mechanisms highlight the importance of host-pathogen molecular interaction networks, and consequent inferences of the host-pathogen relationship could be translated into biomedical applications.
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15
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Tripathi S, Garcia-Sastre A. Antiviral innate immunity through the lens of systems biology. Virus Res 2015; 218:10-7. [PMID: 26657882 DOI: 10.1016/j.virusres.2015.11.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/30/2015] [Indexed: 12/25/2022]
Abstract
Cellular innate immunity poses the first hurdle against invading viruses in their attempt to establish infection. This antiviral response is manifested with the detection of viral components by the host cell, followed by transduction of antiviral signals, transcription and translation of antiviral effectors and leads to the establishment of an antiviral state. These events occur in a rather branched and interconnected sequence than a linear path. Traditionally, these processes were studied in the context of a single virus and a host component. However, with the advent of rapid and affordable OMICS technologies it has become feasible to address such questions on a global scale. In the discipline of Systems Biology', extensive omics datasets are assimilated using computational tools and mathematical models to acquire deeper understanding of complex biological processes. In this review we have catalogued and discussed the application of Systems Biology approaches in dissecting the antiviral innate immune responses.
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Affiliation(s)
- Shashank Tripathi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, NY, USA
| | - Adolfo Garcia-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, NY, USA.
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16
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Kebaabetswe LP, Haick AK, Gritsenko MA, Fillmore TL, Chu RK, Purvine SO, Webb-Robertson BJ, Matzke MM, Smith RD, Waters KM, Metz TO, Miura TA. Proteomic analysis reveals down-regulation of surfactant protein B in murine type II pneumocytes infected with influenza A virus. Virology 2015; 483:96-107. [PMID: 25965799 DOI: 10.1016/j.virol.2015.03.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 01/13/2015] [Accepted: 03/18/2015] [Indexed: 11/29/2022]
Abstract
Infection of type II alveolar epithelial (ATII) cells by influenza A viruses (IAV) correlates with severe respiratory disease in humans and mice. To understand pathogenic mechanisms during IAV infection of ATII cells, murine ATII cells were cultured to maintain a differentiated phenotype, infected with IAV-PR8, which causes severe lung pathology in mice, and proteomics analyses were performed using liquid chromatography-mass spectrometry. PR8 infection increased levels of proteins involved in interferon signaling, antigen presentation, and cytoskeleton regulation. Proteins involved in mitochondrial membrane permeability, energy metabolism, and chromatin formation had reduced levels in PR8-infected cells. Phenotypic markers of ATII cells in vivo were identified, confirming the differentiation status of the cultures. Surfactant protein B had decreased levels in PR8-infected cells, which was confirmed by immunoblotting and immunofluorescence assays. Analysis of ATII cell protein profiles will elucidate cellular processes in IAV pathogenesis, which may provide insight into potential therapies to modulate disease severity.
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Affiliation(s)
- Lemme P Kebaabetswe
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Anoria K Haick
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Thomas L Fillmore
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Bobbie-Jo Webb-Robertson
- Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Melissa M Matzke
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, 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
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Tanya A Miura
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
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17
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The use of nonhuman primates in research on seasonal, pandemic and avian influenza, 1893-2014. Antiviral Res 2015; 117:75-98. [PMID: 25746173 DOI: 10.1016/j.antiviral.2015.02.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 02/19/2015] [Accepted: 02/26/2015] [Indexed: 11/22/2022]
Abstract
Attempts to reproduce the features of human influenza in laboratory animals date from the early 1890s, when Richard Pfeiffer inoculated apes with bacteria recovered from influenza patients and produced a mild respiratory illness. Numerous studies employing nonhuman primates (NHPs) were performed during the 1918 pandemic and the following decade. Most used bacterial preparations to infect animals, but some sought a filterable agent for the disease. Since the viral etiology of influenza was established in the early 1930s, studies in NHPs have been supplemented by a much larger number of experiments in mice, ferrets and human volunteers. However, the emergence of a novel swine-origin H1N1 influenza virus in 1976 and the highly pathogenic H5N1 avian influenza virus in 1997 stimulated an increase in NHP research, because these agents are difficult to study in naturally infected patients and cannot be administered to human volunteers. In this paper, we review the published literature on the use of NHPs in influenza research from 1893 through the end of 2014. The first section summarizes observational studies of naturally occurring influenza-like syndromes in wild and captive primates, including serologic investigations. The second provides a chronological account of experimental infections of NHPs, beginning with Pfeiffer's study and covering all published research on seasonal and pandemic influenza viruses, including vaccine and antiviral drug testing. The third section reviews experimental infections of NHPs with avian influenza viruses that have caused disease in humans since 1997. The paper concludes with suggestions for further studies to more clearly define and optimize the role of NHPs as experimental animals for influenza research.
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18
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Abstract
Systems-level analysis of biological processes strives to comprehensively and quantitatively evaluate the interactions between the relevant molecular components over time, thereby enabling development of models that can be employed to ultimately predict behavior. Rapid development in measurement technologies (omics), when combined with the accessible nature of the cellular constituents themselves, is allowing the field of innate immunity to take significant strides toward this lofty goal. In this review, we survey exciting results derived from systems biology analyses of the immune system, ranging from gene regulatory networks to influenza pathogenesis and systems vaccinology.
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19
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Palermo RE, Tisoncik-Go J, Korth MJ, Katze MG. Old world monkeys and new age science: the evolution of nonhuman primate systems virology. ILAR J 2014; 54:166-80. [PMID: 24174440 DOI: 10.1093/ilar/ilt039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nonhuman primate (NHP) biomedical models are critical to our understanding of human health and disease, yet we are still in the early stages of developing sufficient tools to support primate genomic research that allow us to better understand the basis of phenotypic traits in NHP models of disease. A mere 7 years ago, the limited NHP transcriptome profiling that was being performed was done using complementary DNA arrays based on human genome sequences, and the lack of NHP genomic information and immunologic reagents precluded the use of NHPs in functional genomic studies. Since then, significant strides have been made in developing genomics capabilities for NHP research, from the rhesus macaque genome sequencing project to the construction of the first macaque-specific high-density oligonucleotide microarray, paving the way for further resource development and additional primate sequencing projects. Complete published draft genome sequences are now available for the chimpanzee ( Chimpanzee Sequencing Analysis Consortium 2005), bonobo ( Prufer et al. 2012), gorilla ( Scally et al. 2012), and baboon ( Ensembl.org 2013), along with the recently completed draft genomes for the cynomolgus macaque and Chinese rhesus macaque. Against this backdrop of both expanding sequence data and the early application of sequence-derived DNA microarrays tools, we will contextualize the development of these community resources and their application to infectious disease research through a literature review of NHP models of acquired immune deficiency syndrome and models of respiratory virus infection. In particular, we will review the use of -omics approaches in studies of simian immunodeficiency virus and respiratory virus pathogenesis and vaccine development, emphasizing the acute and innate responses and the relationship of these to the course of disease and to the evolution of adaptive immunity.
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20
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Systems biology and systems genetics - novel innovative approaches to study host-pathogen interactions during influenza infection. Curr Opin Virol 2014; 6:47-54. [PMID: 24769047 DOI: 10.1016/j.coviro.2014.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/04/2014] [Accepted: 03/14/2014] [Indexed: 11/19/2022]
Abstract
Influenza represents a serious threat to public health with thousands of deaths each year. A deeper understanding of the host-pathogen interactions is urgently needed to evaluate individual and population risks for severe influenza disease and to identify new therapeutic targets. Here, we review recent progress in large scale omics technologies, systems genetics as well as new mathematical and computational developments that are now in place to apply a systems biology approach for a comprehensive description of the multidimensional host response to influenza infection. In addition, we describe how results from experimental animal models can be translated to humans, and we discuss some of the future challenges ahead.
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21
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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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22
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Human systems immunology: hypothesis-based modeling and unbiased data-driven approaches. Semin Immunol 2013; 25:193-200. [PMID: 23375135 PMCID: PMC3836867 DOI: 10.1016/j.smim.2012.11.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/08/2012] [Indexed: 11/23/2022]
Abstract
Systems immunology is an emerging paradigm that aims at a more systematic and quantitative understanding of the immune system. Two major approaches have been utilized to date in this field: unbiased data-driven modeling to comprehensively identify molecular and cellular components of a system and their interactions; and hypothesis-based quantitative modeling to understand the operating principles of a system by extracting a minimal set of variables and rules underlying them. In this review, we describe applications of the two approaches to the study of viral infections and autoimmune diseases in humans, and discuss possible ways by which these two approaches can synergize when applied to human immunology.
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23
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Kordyukova LV, Serebryakova MV. Mass spectrometric approaches to study enveloped viruses: new possibilities for structural biology and prophylactic medicine. BIOCHEMISTRY (MOSCOW) 2013; 77:830-42. [PMID: 22860905 PMCID: PMC7087845 DOI: 10.1134/s0006297912080044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
This review considers principles of the use of mass spectrometry for the study of biological macromolecules. Some examples of protein identification, virion proteomics, testing vaccine preparations, and strain surveillance are represented. Possibilities of structural characterization of viral proteins and their posttranslational modifications are shown. The authors’ studies by MALDI-MS on S-acylation of glycoproteins from various families of enveloped viruses and on oligomerization of the influenza virus hemagglutinin transmembrane domains are summarized.
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Affiliation(s)
- L V Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia.
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24
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Kroeker AL, Ezzati P, Coombs KM, Halayko AJ. Influenza A Infection of Primary Human Airway Epithelial Cells Up-Regulates Proteins Related to Purine Metabolism and Ubiquitin-Related Signaling. J Proteome Res 2013; 12:3139-51. [DOI: 10.1021/pr400464p] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Andrea L. Kroeker
- Department of Physiology, Faculty
of Medicine, University of Manitoba, Winnipeg
R3E 0J9, Canada
- Manitoba
Institute of Child
Health, Room 641 John Buhler Research Center, University of Manitoba, Winnipeg R3E 3P4, Canada
- Manitoba Center for Proteomics
and Systems Biology, Room 799 John Buhler Research Centre, University of Manitoba, Winnipeg R3E 3P4, Canada
| | - Peyman Ezzati
- Manitoba Center for Proteomics
and Systems Biology, Room 799 John Buhler Research Centre, University of Manitoba, Winnipeg R3E 3P4, Canada
| | - Kevin M. Coombs
- Department of Physiology, Faculty
of Medicine, University of Manitoba, Winnipeg
R3E 0J9, Canada
- Manitoba
Institute of Child
Health, Room 641 John Buhler Research Center, University of Manitoba, Winnipeg R3E 3P4, Canada
- Manitoba Center for Proteomics
and Systems Biology, Room 799 John Buhler Research Centre, University of Manitoba, Winnipeg R3E 3P4, Canada
- Department of Medical Microbiology,
Faculty of Medicine, University of Manitoba, Winnipeg R3E 0J9, Canada
| | - Andrew J. Halayko
- Department of Physiology, Faculty
of Medicine, University of Manitoba, Winnipeg
R3E 0J9, Canada
- Manitoba
Institute of Child
Health, Room 641 John Buhler Research Center, University of Manitoba, Winnipeg R3E 3P4, Canada
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25
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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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26
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Zhao D, Liang L, Li Y, Liu L, Guan Y, Jiang Y, Chen H. Proteomic analysis of the lungs of mice infected with different pathotypes of H5N1 avian influenza viruses. Proteomics 2012; 12:1970-82. [PMID: 22623221 DOI: 10.1002/pmic.201100619] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The virulence of influenza virus is determined by viral and host factors. Data on the genetic basis of the virulence of H5N1 influenza viruses have increased over the past decade; however, the contributions of host factors to the outcomes of H5N1 infection remain largely unknown. Here, we tested two chicken H5N1 viruses in mice and found that A/chicken/VN1214/2007 was nonlethal in mice and only replicated in the lung, whereas A/chicken/VN1180/2006 was highly lethal and replicated systemically in mice. To investigate the host response against these two different virus infections, we performed proteomic analysis by using 2D DIGE on the lung tissues of mice collected on days 1 and 3 postinoculation with different viruses or PBS as a control. Thirty-nine differentially expressed (DE) proteins related to "immune and stimulus response," "macromolecular biosynthesis and metabolism," and "cellular component and cytoskeleton" were identified in the virus-inoculated groups. Moreover, 13 DE proteins were identified between the two virus-inoculated groups, implying that these proteins may play important roles in the different outcomes of infection with these two viruses. Our data provide important information regarding the host response to mild and lethal H5N1 influenza virus infection.
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Affiliation(s)
- Dongming Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
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27
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Kroeker AL, Ezzati P, Halayko AJ, Coombs KM. Response of primary human airway epithelial cells to influenza infection: a quantitative proteomic study. J Proteome Res 2012; 11:4132-46. [PMID: 22694362 PMCID: PMC3411195 DOI: 10.1021/pr300239r] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
Influenza A virus exerts a large health burden during
both yearly epidemics and global pandemics. However, designing effective
vaccine and treatment options has proven difficult since the virus
evolves rapidly. Therefore, it may be beneficial to identify host proteins associated with viral infection and replication
to establish potential new antiviral targets. We have previously measured
host protein responses in continuously cultured A549 cells infected
with mouse-adapted virus strain A/PR/8/34(H1N1; PR8). We here identify
and measure host proteins differentially regulated in more relevant
primary human bronchial airway epithelial (HBAE) cells. A total of
3740 cytosolic HBAE proteins were identified by 2D LC–MS/MS,
of which 52 were up-regulated ≥2-fold and 41 were down-regulated ≥2-fold
after PR8 infection. Up-regulated HBAE proteins clustered primarily
into interferon signaling, other host defense processes, and molecular
transport, whereas down-regulated proteins were associated with cell
death signaling pathways, cell adhesion and motility, and lipid metabolism.
Comparison to influenza-infected A549 cells indicated some common
influenza-induced host cell alterations, including defense response,
molecular transport proteins, and cell adhesion. However, HBAE-specific
alterations consisted of interferon and cell death signaling. These
data point to important differences between influenza replication
in continuous and primary cell lines and/or alveolar and bronchial
epithelial cells.
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Affiliation(s)
- Andrea L Kroeker
- Manitoba Institute of Child Health, John Buhler Research Center, Department of Physiology, University of Manitoba, Winnipeg, Canada R3E 3P4
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28
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Brown JN, Ortiz GM, Angel TE, Jacobs JM, Gritsenko M, Chan EY, Purdy DE, Murnane RD, Larsen K, Palermo RE, Shukla AK, Clauss TR, Katze MG, McCune JM, Smith RD. Morphine produces immunosuppressive effects in nonhuman primates at the proteomic and cellular levels. Mol Cell Proteomics 2012; 11:605-18. [PMID: 22580588 DOI: 10.1074/mcp.m111.016121] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Morphine has long been known to have immunosuppressive properties in vivo, but the molecular and immunologic changes induced by it are incompletely understood. To explore how these changes interact with lentiviral infections in vivo, animals from two nonhuman primate species (African green monkeys and pigtailed macaques) were provided morphine and studied using a systems biology approach. Biological specimens were obtained from multiple sources (e.g. lymph node, colon, cerebrospinal fluid, and peripheral blood) before and after the administration of morphine (titrated up to a maximum dose of 5 mg/kg over a period of 20 days). Cellular immune, plasma cytokine, and proteome changes were measured and morphine-induced changes in these parameters were assessed on an interorgan, interindividual, and interspecies basis. In both species, morphine was associated with decreased levels of Ki-67(+) T-cell activation but with only minimal changes in overall T-cell counts, neutrophil counts, and NK cell counts. Although changes in T-cell maturation were observed, these varied across the various tissue/fluid compartments studied. Proteomic analysis revealed a morphine-induced suppressive effect in lymph nodes, with decreased abundance of protein mediators involved in the functional categories of energy metabolism, signaling, and maintenance of cell structure. These findings have direct relevance for understanding the impact of heroin addiction and the opioids used to treat addiction as well as on the potential interplay between opioid abuse and the immunological response to an infective agent.
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Affiliation(s)
- Joseph N Brown
- Biological Sciences Division, Pacific Northwest National Laboratories, Richland, Washington 99352, USA
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29
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Baskin C. The role and contributions of systems biology to the non-human primate model of influenza pathogenesis and vaccinology. Curr Top Microbiol Immunol 2012; 363:69-85. [PMID: 22890718 DOI: 10.1007/82_2012_248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nonhuman primates have proven to be valuable models in the study of seasonal and highly pathogenic influenza virus infections, prophylaxis, and therapy. Due to their close genetic relationship to humans, these animals share anatomic, postural, physiological, and immune features with us of key importance when it comes to progression and mitigation of respiratory infections. Their lower susceptibility to natural influenza infection even presents an advantage in the laboratory setting because of the need for immunologically naïve animals, and since nonhuman primates are relatively genetically diverse within one species, their study provides an essential complement to the body of knowledge acquired with inbred animal models. However, ethical and cost considerations typically result in smaller experiments and a need to look at additional levels of biological information in order to maximize insights gained from these studies. Systems biology is a powerful tool for this purpose, because it provides a much needed wide angle view of complex interactions taking places in organisms which are more than the sum of their parts. This chapter will describe the extent to which functional genomics and proteomics have successfully integrated with other, more traditional tools in the areas of clinical presentation, pathology, and immunology during influenza infections in nonhuman primates. It will also describe the unique contributions systems biology has made to our understanding of host-virus interactions, as well as response to vaccination and antiviral therapy.
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Affiliation(s)
- Carole Baskin
- Science Foundation Arizona, 400 East Van Buren Street, Phoenix, AZ, 85004, USA.
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Comparative proteome analyses of host protein expression in response to Enterovirus 71 and Coxsackievirus A16 infections. J Proteomics 2011; 74:2018-24. [PMID: 21621020 DOI: 10.1016/j.jprot.2011.05.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Revised: 04/25/2011] [Accepted: 05/10/2011] [Indexed: 11/21/2022]
Abstract
Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) are the main etiological agents of Hand, Foot and Mouth Disease (HFMD), a common disease among children and had caused several outbreaks in the Asia-Pacific region. Although being genetically close to each other, EV71 infection can cause serious and fatal neurological complications like encephalitis, myocarditis, acute flaccid paralysis (AFP) and aseptic meningitis, but not in CA16 infections. In this study, the cellular response of host cells infected with EV71 and CA16 was characterized and compared by 2-dimensional proteome analyses. A total of 16 proteins were identified to be differentially expressed in EV71 and CA16-infected host cells. Desmin and HSP27, both indirectly regulate the contraction of muscle cells, were significantly downregulated as a result of EV71 infection, suggesting a link to acute flaccid paralysis. The ability of EV71 to evade host immune system may be due to the downregulation of MHC-I synthesis proteins like protein disulfide isomerase A3 and calreticulin. Proteins such as nucleophosmin, nuclear ribonucleoprotein C, and eukaryotic translation initiation factor 2 were all downregulated significantly, suggesting the rapid shutting down of host translation machinery by EV71. These findings provide insight into the nature of high virulent EV71 infection as compared to CA16.
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Abstract
The recent H1N1 pandemic that emerged in 2009 has illustrated how swiftly a new influenza virus can circulate the globe. Here we explain the origins of the 2009 pandemic virus, and other twentieth century pandemics. We also consider the impact of the 2009 pandemic in the human population and the use of vaccines and antiviral drugs. Thankfully this outbreak was much less severe than that associated with Spanish flu in 1918. We describe the viral factors that affect virulence of influenza and speculate on the future course of this virus in humans and animals.
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Affiliation(s)
- Nigel Curtis
- Royal Children's Hosp., Dept. Paediatrics, University of Melbourne, Parkville, 3052 Victoria Australia
| | - Adam Finn
- Institute of Child Life and Health, UBHT Education Centre, University of Bristol, Upper Maudlin Street, Bristol, BS2 8AE United Kingdom
| | - Andrew J. Pollard
- University of Oxford, Level 4,John Radcliffe Hospital, Oxford, OX3 9DU United Kingdom
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