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Lee S, Kang S, Heo J, Hong Y, Vu TH, Truong AD, Lillehoj HS, Hong YH. MicroRNA expression profiling in the lungs of genetically different Ri chicken lines against the highly pathogenic avian influenza H5N1 virus. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2023; 65:838-855. [PMID: 37970505 PMCID: PMC10640957 DOI: 10.5187/jast.2022.e127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/09/2022] [Accepted: 12/23/2022] [Indexed: 11/17/2023]
Abstract
The highly pathogenic avian influenza (HPAI) virus triggers infectious diseases, resulting in pulmonary damage and high mortality in domestic poultry worldwide. This study aimed to analyze miRNA expression profiles after infection with the HPAI H5N1 virus in resistant and susceptible lines of Ri chickens.For this purpose, resistant and susceptible lines of Vietnamese Ri chicken were used based on the A/G allele of Mx and BF2 genes. These genes are responsible for innate antiviral activity and were selected to determine differentially expressed (DE) miRNAs in HPAI-infected chicken lines using small RNA sequencing. A total of 44 miRNAs were DE after 3 days of infection with the H5N1 virus. Computational program analysis indicated the candidate target genes for DE miRNAs to possess significant functions related to cytokines, chemokines, MAPK signaling pathway, ErBb signaling pathway, and Wnt signaling pathway. Several DE miRNA-mRNA matches were suggested to play crucial roles in mediating immune functions against viral evasion. These results revealed the potential regulatory roles of miRNAs in the immune response of the two Ri chicken lines against HPAI H5N1 virus infection in the lungs.
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Affiliation(s)
- Sooyeon Lee
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Suyeon Kang
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Jubi Heo
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Yeojin Hong
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Thi Hao Vu
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Anh Duc Truong
- Department of Biochemistry and Immunology,
National Institute of Veterinary Research, Hanoi 100000, Viet
Nam
| | - Hyun S Lillehoj
- Animal Biosciences and Biotechnology
Laboratory, Agricultural Research Services, United States Department of
Agriculture, Beltsville, MD 20705, USA
| | - Yeong Ho Hong
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
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2
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Wang L, Western D, Timsina J, Repaci C, Song WM, Norton J, Kohlfeld P, Budde J, Climer S, Butt OH, Jacobson D, Garvin M, Templeton AR, Campagna S, O’Halloran J, Presti R, Goss CW, Mudd PA, Ances BM, Zhang B, Sung YJ, Cruchaga C. Plasma proteomics of SARS-CoV-2 infection and severity reveals impact on Alzheimer's and coronary disease pathways. iScience 2023; 26:106408. [PMID: 36974157 PMCID: PMC10010831 DOI: 10.1016/j.isci.2023.106408] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/21/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Identification of proteins dysregulated by COVID-19 infection is critically important for better understanding of its pathophysiology, building prognostic models, and identifying new targets. Plasma proteomic profiling of 4,301 proteins was performed in two independent datasets and tested for the association for three COVID-19 outcomes (infection, ventilation, and death). We identified 1,449 proteins consistently associated in both datasets with any of these three outcomes. We subsequently created highly accurate models that distinctively predict infection, ventilation, and death. These proteins were enriched in specific biological processes including cytokine signaling, Alzheimer's disease, and coronary artery disease. Mendelian randomization and gene network analyses identified eight causal proteins and 141 highly connected hub proteins including 35 with known drug targets. Our findings provide distinctive prognostic biomarkers for two severe COVID-19 outcomes, reveal their relationship to Alzheimer's disease and coronary artery disease, and identify potential therapeutic targets for COVID-19 outcomes.
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Affiliation(s)
- Lihua Wang
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel Western
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Charlie Repaci
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Pat Kohlfeld
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Sharlee Climer
- Department of Computer Science, University of Missouri-St. Louis, St. Louis, MO, USA
| | - Omar H. Butt
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michael Garvin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Alan R. Templeton
- Department of Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Shawn Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Jane O’Halloran
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel Presti
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Charles W. Goss
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Philip A. Mudd
- Department of Emergency Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Beau M. Ances
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St Louis, MO, USA
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3
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Rashid MU, Glover KKM, Lao Y, Spicer V, Coombs KM. Temporal proteomic analyses of human lung cells distinguish high pathogenicity influenza viruses and coronaviruses from low pathogenicity viruses. Front Microbiol 2022; 13:994512. [PMID: 36299731 PMCID: PMC9589293 DOI: 10.3389/fmicb.2022.994512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/23/2022] [Indexed: 11/29/2022] Open
Abstract
Newly re-emerging viruses are of significant global concern. In late 2019, a new coronavirus, SARS-CoV-2, emerged in China and soon spread worldwide, causing the COVID-19 pandemic, which to date has caused >6 M deaths. There has been a wealth of studies on this new virus since its emergence. The coronaviruses consist of many animal and human pathogens, with some of the human coronavirus, such as strain OC43, normally causing only mild cold-like symptoms. Viruses usurp host cellular processes to successfully replicate. We used tandem mass tag mass spectrometry-based proteomic analyses of human lung MRC-5 cells infected with OC43 for various periods of time to delineate virus-induced host cell alterations. Numerous proteins involved in lipid metabolism, molecular transport, small molecule biochemistry, cell death and survival, humoral immune response, and inflammatory response were dysregulated. Comparison of our findings to previous studies that examined a range of differentially pathogenic influenza A viruses (IAV), and to SARS-CoV-2 data, revealed that proteins involved in the cell cycle, cytokine signaling, DNA replication, and anti-inflammatory responses were generally similarly affected by virtually all tested IAV and CoV. However, proteins involved in necrosis, protein metabolism, ECM regulation, and signal transduction were generally different. In addition, the more pathogenic CoV and IAV activated Rb-dependent repression of E2F-mediated transcription, whereas less pathogenic influenza and coronaviruses either inhibited or had no effect on this pathway.
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Affiliation(s)
- Mahamud-ur Rashid
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Kathleen K. M. Glover
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Ying Lao
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Victor Spicer
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Kevin M. Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
- Children’s Hospital Research Institute of Manitoba, John Buhler Research Center, Winnipeg, MB, Canada
- *Correspondence: Kevin M. Coombs,
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4
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Wang L, Western D, Timsina J, Repaci C, Song WM, Norton J, Kohlfeld P, Budde J, Climer S, Butt OH, Jacobson D, Garvin M, Templeton AR, Campagna S, O’Halloran J, Presti R, Goss CW, Mudd PA, Ances BM, Zhang B, Sung YJ, Cruchaga C. Plasma proteomics of SARS-CoV-2 infection and severity reveals impact on Alzheimer and coronary disease pathways. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.07.25.22278025. [PMID: 35923315 PMCID: PMC9347279 DOI: 10.1101/2022.07.25.22278025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Identification of the plasma proteomic changes of Coronavirus disease 2019 (COVID-19) is essential to understanding the pathophysiology of the disease and developing predictive models and novel therapeutics. We performed plasma deep proteomic profiling from 332 COVID-19 patients and 150 controls and pursued replication in an independent cohort (297 cases and 76 controls) to find potential biomarkers and causal proteins for three COVID-19 outcomes (infection, ventilation, and death). We identified and replicated 1,449 proteins associated with any of the three outcomes (841 for infection, 833 for ventilation, and 253 for death) that can be query on a web portal ( https://covid.proteomics.wustl.edu/ ). Using those proteins and machine learning approached we created and validated specific prediction models for ventilation (AUC>0.91), death (AUC>0.95) and either outcome (AUC>0.80). These proteins were also enriched in specific biological processes, including immune and cytokine signaling (FDR ≤ 3.72×10 -14 ), Alzheimer's disease (FDR ≤ 5.46×10 -10 ) and coronary artery disease (FDR ≤ 4.64×10 -2 ). Mendelian randomization using pQTL as instrumental variants nominated BCAT2 and GOLM1 as a causal proteins for COVID-19. Causal gene network analyses identified 141 highly connected key proteins, of which 35 have known drug targets with FDA-approved compounds. Our findings provide distinctive prognostic biomarkers for two severe COVID-19 outcomes (ventilation and death), reveal their relationship to Alzheimer's disease and coronary artery disease, and identify potential therapeutic targets for COVID-19 outcomes.
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Affiliation(s)
- Lihua Wang
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Dan Western
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Charlie Repaci
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Pat Kohlfeld
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Sharlee Climer
- Department of Computer Science, University of Missouri-St. Louis, St. Louis, MO, USA
| | - Omar H. Butt
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michael Garvin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Alan R Templeton
- Department of Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Shawn Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Jane O’Halloran
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel Presti
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Charles W. Goss
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Philip A. Mudd
- Department of Emergency Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Beau M. Ances
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St Louis, MO, USA
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5
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Chen X, Li Z, Wang S, Tong G, Chen K, Zhao Y. Proteomic Analysis Reveals Zinc-finger CCHC-type Containing Protein 3 as a Factor Inhibiting Virus Infection by Promoting Innate Signaling. Virus Res 2022; 319:198876. [PMID: 35872280 PMCID: PMC9347187 DOI: 10.1016/j.virusres.2022.198876] [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: 04/15/2022] [Revised: 06/24/2022] [Accepted: 07/21/2022] [Indexed: 12/09/2022]
Abstract
Influenza a virus exploits host machinery to benefit its replication in host cells. Knowledge of host factors reveals the complicated interaction and provides potential targets for antiviral treatment. Here, instead of the traditional proteomic analysis, we employed a 4D label free proteomic method to identify cellular factors in A549 cells treated with avian H9N2 virus. We observed that 425 proteins were upregulated and 502 proteins were downregulated. Western blotting and quantitative real-time PCR results showed that the zinc-finger CCHC-type containing protein 3 (ZCCHC3) levels were markedly induced by H9N2 infection. Transient expression assay showed that ZCCHC3 expression decreased NP protein levels and viral titers, whereas knockdown of ZCCHC3 enhanced viral growth. Specifically, ZCCHC3 promoted the expression of IFN-β, leading to the increased transcription of IFN downstream antiviral factors. Surprisingly, viral NS1 protein was able to antagonize the antiviral effect of ZCCHC3 by downregulating IFN-β. Eventually, we observed that chicken finger CCCH-type containing protein 3, named ZC3H3, could also suppress the replication of H9N2 virus and the coronavirus-infectious bronchitis virus (IBV) in DF-1 cells. Together, our results showed the cellular proteomic response to H9N2 infection and identified ZCCHC3 as a novel antiviral factor against H9N2 infection, contributing to the understanding of host-virus interaction.
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Affiliation(s)
- Xiaoyong Chen
- Institute of Animal Science, Wenzhou Academy of Agricultural Sciences, Zhejiang, People's Republic of China; Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China.
| | - Ziwei Li
- Institute of Animal Science, Wenzhou Academy of Agricultural Sciences, Zhejiang, People's Republic of China
| | - Shuaiwei Wang
- Institute of Animal Science, Wenzhou Academy of Agricultural Sciences, Zhejiang, People's Republic of China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Keyuan Chen
- Union Hospital, Fujian Medical University, Fuzhou, People's Republic of China
| | - Yan Zhao
- Institute of Animal Science, Wenzhou Academy of Agricultural Sciences, Zhejiang, People's Republic of China.
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6
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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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7
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Yang Y, Zhang Y, Yang C, Fang F, Wang Y, Chang H, Chen Z, Chen P. Differential mitochondrial proteomic analysis of A549 cells infected with avian influenza virus subtypes H5 and H9. Virol J 2021; 18:39. [PMID: 33602268 PMCID: PMC7891018 DOI: 10.1186/s12985-021-01512-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/08/2021] [Indexed: 01/14/2023] Open
Abstract
Background Both the highly pathogenic avian influenza (HPAI) H5N1 and low pathogenic avian influenza (LPAI) H9N2 viruses have been reported to cross species barriers to infect humans. H5N1 viruses can cause severe damage and are associated with a high mortality rate, but H9N2 viruses do not cause such outcomes. Our purpose was to use proteomics technology to study the differential expression of mitochondrial-related proteins related to H5N1 and H9N2 virus infections.
Methods According to the determined viral infection titer, A549 cells were infected with 1 multiplicity of infection virus, and the mitochondria were extracted after 24 h of incubation. The protein from lysed mitochondria was analyzed by the BCA method to determine the protein concentration, as well as SDS-PAGE (preliminary analysis), two-dimensional gel electrophoresis, and mass spectrometry. Differential protein spots were selected, and Western blotting was performed to verify the proteomics results. The identified proteins were subjected to GO analysis for subcellular localization, KEGG analysis for functional classification and signaling pathways assessment, and STRING analysis for functional protein association network construction. Results In the 2-D gel electrophoresis analysis, 227 protein spots were detected in the H5N1-infected group, and 169 protein spots were detected in the H9N2-infected group. Protein spots were further subjected to mass spectrometry identification and removal of redundancy, and 32 differentially expressed proteins were identified. Compared with the H9N2 group, the H5N1-infected group had 16 upregulated mitochondrial proteins and 16 downregulated proteins. The differential expression of 70-kDa heat shock protein analogs, short-chain enoyl-CoA hydratase, malate dehydrogenase, and ATP synthase was verified by Western blot, and the results were consistent with the proteomics findings. Functional analysis indicated that these differentially expressed proteins were primarily involved in apoptosis and metabolism. Conclusions Compared with their expression in the H9N2 group, the differential expression of eight mitochondrial proteins in the H5N1 group led to host T cell activation, antigen presentation, stress response, ATP synthesis and cell apoptosis reduction, leading to higher pathogenicity of H5N1 than H9N2. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01512-4.
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Affiliation(s)
- Yuting Yang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Yun Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Changcheng Yang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Fang Fang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Ying Wang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Haiyan Chang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Ze Chen
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China. .,Shanghai Institute of Biological Products, Shanghai, 200052, China.
| | - Ping Chen
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China.
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8
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Abdollahi H, Rezaei-Tavirani M, Ghalyanchilangeroudi A, Maghsoudloo H, Hashemzadeh M, Hosseini H, Barin A. Coronavirus: proteomics analysis of chicken kidney tissue infected with variant 2 (IS-1494)-like avian infectious bronchitis virus. Arch Virol 2020; 166:101-113. [PMID: 33083914 PMCID: PMC7574675 DOI: 10.1007/s00705-020-04845-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 08/03/2020] [Indexed: 11/28/2022]
Abstract
Avian infectious bronchitis virus is one of the most important gammacoronaviruses, which causes a highly contagious disease. In this study, we investigated changes in the proteome of kidney tissue of specific-pathogen-free (SPF) chickens that were infected with an isolate of the nephrotropic variant 2 genotype (IS/1494/06) of avian coronavirus. Twenty 1-day-old SPF White Leghorn chickens were randomly divided into two groups, each comprising 10 chickens, which were kept in separate positive-pressure isolators. Chickens in group A served as a virus-free control group up to the end of the experiment, whereas chickens in group B were inoculated with 0.1 ml of 104.5 EID50 of the IBV/chicken/Iran/UTIVO-C/2014 isolate of IBV, and kidney tissue samples were collected at 2 and 7 days post-inoculation (dpi) from both groups. Sequencing of five protein spots at 2 dpi and 22 spots at 7 dpi that showed differential expression by two-dimensional electrophoresis (2DE) along with fold change greater than 2 was done by MS-MALDI/TOF/TOF. Furthermore, the corresponding protein-protein interaction (PPI) networks at 2 and 7 dpi were identified to develop a detailed understanding of the mechanism of molecular pathogenesis. Topological graph analysis of this undirected PPI network revealed the effect of 10 genes in the 2 dpi PPI network and nine genes in the 7 dpi PPI network during virus pathogenesis. Proteins that were found by 2DE analysis and MS/TOF-TOF mass spectrometry to be down- or upregulated were subjected to PPI network analysis to identify interactions with other cellular components. The results show that cellular metabolism was altered due to viral infection. Additionally, multifunctional heat shock proteins with a significant role in host cell survival may be employed circuitously by the virus to reach its target. The data from this study suggest that the process of pathogenesis that occurs during avian coronavirus infection involves the regulation of vital cellular processes and the gradual disruption of critical cellular functions.
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Affiliation(s)
- Hamed Abdollahi
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,National Reference Laboratory, Diagnosis & Applied Studies Center, Iran Veterinary Organization, Tehran, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arash Ghalyanchilangeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Hossein Maghsoudloo
- National Reference Laboratory, Diagnosis & Applied Studies Center, Iran Veterinary Organization, Tehran, Iran
| | | | - Hossein Hosseini
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Karaj Islamic Azad University, Alborz, Iran
| | - Abbas Barin
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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9
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Yasmin AR, Omar AR, Farhanah MI, Hiscox AJ, Yeap SK. Quantitative Proteomics Analysis Revealed Compromised Chicken Dendritic Cells Function at Early Stage of Very Virulent Infectious Bursal Disease Virus Infection. Avian Dis 2020; 63:275-288. [PMID: 31251527 DOI: 10.1637/11936-072418-reg.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/19/2018] [Indexed: 11/05/2022]
Abstract
Chicken dendritic cells (DCs) have been demonstrated to be susceptible to infectious bursal disease virus (IBDV), a causative agent of acute and immunosuppressed disease in young chicks known as infectious bursal disease. Further functional characterization of IBDV-infected DCs of chickens is required to provide a better understanding on the influence of the virus on chicken bone marrow-derived dendritic cells (BM-DCs) following very virulent (vv) IBDV infection. Membrane proteins of BM-DCs were extracted and the proteins were further denatured and reduced before performing labeling with isobaric tags for relative and absolute quantitation. The differential expression protein profiles were identified and quantified using liquid chromatography coupled with tandem mass spectrometry, and later validated using flow cytometry and real-time reverse transcriptase PCR. The analysis has identified 134 differentially regulated proteins from a total of 283 proteins (cutoff values of ≤0.67, ≥1.5, and ProtScore >1.3 at 95% confidence interval), which produced high-yield membrane fractions. The entry of vvIBDV into the plasma membrane of BM-DCs was observed at 3 hr postinfection by the disruption of several important protein molecule functions, namely apoptosis, RNA/DNA/protein synthesis, and transport and cellular organization, without the activation of proteins associated with signaling. At the later stage of infection, vvIBDV induced expression of several proteins, namely CD200 receptor 1-A, integrin alpha-5, HSP-90, cathepsin, lysosomal-associated membrane protein, and Ras-related proteins, which play crucial roles in signaling, apoptosis, stress response, and antigen processing as well as in secretion of danger-associated proteins. These findings collectively indicated that the chicken DCs are expressing various receptors regarded as potential targets for pathogen interaction during viral infection. Therefore, fundamental study of the interaction of DCs and IBDV will provide valuable information in understanding the role of professional antigen-presenting cells in chickens and their molecular interactions during IBDV infection and vaccination.
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Affiliation(s)
- A R Yasmin
- Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,Department of Veterinary Laboratory Diagnosis, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia,
| | - A R Omar
- Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - M I Farhanah
- Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - A J Hiscox
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L3 5RF, United Kingdom
| | - S K Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia
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10
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Asim M, Sarath Babu V, Qin Z, Zhao L, Su J, Li J, Tu J, Kou H, Lin L. Inhibition of Cyclophilin A on the replication of red spotted grouper nervous necrosis virus associates with multiple pro-inflammatory factors. FISH & SHELLFISH IMMUNOLOGY 2019; 92:172-180. [PMID: 31176008 PMCID: PMC7111709 DOI: 10.1016/j.fsi.2019.05.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/28/2019] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Cyclophilin A (CypA) is a ubiquitously expressed cellular protein and involves in diverse pathological conditions, including infection and inflammation. CypA acts as a key factor in the replication of several viruses. However, little is known about the role of CypA in the replication of the red-spotted grouper nervous necrosis virus (RGNNV). In the present report, grouper CypA (GF-CypA) was cloned from the grouper fin cell line (GF-1) derived from orange-spotted grouper (Epinephelus coioides). Sequence analysis found that GF-CypA open reading frame (ORF) of 495 bp encodes a polypeptide of 164 amino acids residues with a molecular weight of 17.4 kDa. The deduced amino acid sequence shared highly conserved regions with CypA of other animal species, showing that GF-CypA is a new member of Cyclophilin A family. We observed that GF-CypA was up-regulated in the GF-1 cells infected with RGNNV. Additionally, overexpression of CypA could significantly inhibit the replication of RGNNV in GF-1 cells. By contrast, when the GF-CypA was knock-downed by siRNA in GF-1 cells, the replication of RGNNV was enhanced. Furthermore, the expressions of pro-inflammatory factors, such as TNF-2, TNF-α, IL-1b, and ISG-15, were increased in GF-CypA transfected GF-1 cells challenged with RGNNV, indicating that GF-CypA might be involved in the regulation of the host pro-inflammatory factors. Altogether, we conclude that GF-CypA plays a vital role in the inhibitory effect of RGNNV replication that might be modulating the cytokines secretion in GF-1 cells during RGNNV infection. These results will shed new light on the function of CypA in the replication of RGNNV and will pave a new way for the prevention of the infection of RGNNV in fish.
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Affiliation(s)
- Muhammad Asim
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - V Sarath Babu
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Zhendong Qin
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Lijuan Zhao
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Jianguo Su
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jun Li
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China; School of Biological Sciences, Lake Superior State University, Sault Ste. Marie, MI, 49783, USA
| | - Jiagang Tu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hongyan Kou
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China.
| | - Li Lin
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China.
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11
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Valdés A, Zhao H, Pettersson U, Lind SB. Time-resolved proteomics of adenovirus infected cells. PLoS One 2018; 13:e0204522. [PMID: 30252905 PMCID: PMC6155545 DOI: 10.1371/journal.pone.0204522] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/10/2018] [Indexed: 12/30/2022] Open
Abstract
Viral infections cause large problems in the world and deeper understanding of the disease mechanisms is needed. Here we present an analytical strategy to investigate the host cell protein changes during human adenovirus type 2 (HAdV-C2 or Ad2) infection of lung fibroblasts by stable isotope labelling of amino acids in cell culture (SILAC) and nanoLC-MS/MS. This work focuses on early phase of infection (6 and 12 h post-infection (hpi)) but the data is combined with previously published late phase (24 and 36 hpi) proteomics data to produce a time series covering the complete infection. As many as 2169 proteins were quantitatively monitored from 6 to 36 hpi, while some proteins were time-specific. After applying different filter criteria, 2027 and 2150 proteins were quantified at 6 and 12 hpi and among them, 431 and 544 were significantly altered at the two time points. Pathway analysis showed that the De novo purine and pyrimidine biosynthesis, Glycolysis and Cytoskeletal regulation by Rho GTPase pathways were activated early during infection while inactivation of the Integrin signalling pathway started between 6 and 12 hpi. Moreover, upstream regulator analysis predicted MYC to be activated with time of infection and protein and RNA data for genes controlled by this transcription factor showed good correlation, which validated the use of protein data for this prediction. Among the identified phosphorylation sites, a group related to glycolysis and cytoskeletal reorganization were up-regulated during infection. The results show specific aspects on how the host cell proteins, the final products in the genetic information flow, are influenced by Ad2 infection, which would be overlooked if only knowledge derived from mRNA data is considered.
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Affiliation(s)
- Alberto Valdés
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Hongxing Zhao
- The Beijer Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden
| | - Ulf Pettersson
- The Beijer Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden
| | - Sara Bergström Lind
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
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12
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Zhang C, Meng J. Identification of differentially expressed proteins in Ostrinia furnacalis adults after exposure to ultraviolet A. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:25071-25079. [PMID: 29936613 DOI: 10.1007/s11356-018-2580-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/18/2018] [Indexed: 06/08/2023]
Abstract
Ultraviolet A (UVA), the major component of solar UV irradiation, is an important environmental factor inducing damage to insects including cell death, photoreceptor damage, and oxidative stress. In order to improve understanding of the adaptation mechanisms of insect after UVA exposure, a comparative proteomic analysis was carried out to reveal differential protein expression in Ostrinia furnacalis. Three-day-old adults were treated with UVA for 1 h. Total proteins of control and UVA-treated insects were examined using two-dimensional electrophoresis (2-DE). 2-DE analysis demonstrated that 19 proteins were increased and 18 proteins were decreased significantly in O. furnacalis after UVA exposure, respectively. Thirty differentially expressed proteins were successfully identified by mass spectrometry. The identified proteins were involved in diverse biological processes, such as signal transduction, transport processing, cellular stress, metabolisms, and cytoskeleton organization. Our results reveal that the response patterns of O. furnacalis to UVA irradiation are complex and provide novel insights into the adaptation response to UVA irradiation stress.
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Affiliation(s)
- Changyu Zhang
- Guizhou Key Laboratory for Plant Pest Management of Mountain Region, College of Agriculture, Guizhou University, Guiyang, China.
| | - Jianyu Meng
- Guizhou Tobacco Science Research Institute, Guiyang, China
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13
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Bhowmick R, Derakhshan T, Liang Y, Ritchey J, Liu L, Gappa-Fahlenkamp H. A Three-Dimensional Human Tissue-Engineered Lung Model to Study Influenza A Infection. Tissue Eng Part A 2018; 24:1468-1480. [PMID: 29732955 DOI: 10.1089/ten.tea.2017.0449] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Influenza A virus (IAV) claims ∼250,000-500,000 lives annually worldwide. Currently, there are a few in vitro models available to study IAV immunopathology. Monolayer cultures of cell lines and primary lung cells (two-dimensional [2D] cell culture) is the most commonly used tool, however, this system does not have the in vivo-like structure of the lung and immune responses to IAV as it lacks the three-dimensional (3D) tissue structure. To recapitulate the lung physiology in vitro, a system that contains multiple cell types within a 3D environment that allows cell movement and interaction would provide a critical tool. In this study, as a first step in designing a 3D-Human Tissue-Engineered Lung Model (3D-HTLM), we describe the 3D culture of primary human small airway epithelial cells (HSAEpCs) and determined the immunophenotype of this system in response to IAV infections. We constructed a 3D chitosan-collagen scaffold and cultured HSAEpCs on these scaffolds at air-liquid interface (ALI). These 3D cultures were compared with 2D-cultured HSAEpCs for viability, morphology, marker protein expression, and cell differentiation. Results showed that the 3D-cultured HSAEpCs at ALI yielded maximum viable cells and morphologically resembled the in vivo lower airway epithelium. There were also significant increases in aquaporin-5 and cytokeratin-14 expression for HSAEpCs cultured in 3D compared to 2D. The 3D culture system was used to study the infection of HSAEpCs with two major IAV strains, H1N1 and H3N2. The HSAEpCs showed distinct changes in marker protein expression, both at mRNA and protein levels, and the release of proinflammatory cytokines. This study is the first step in the development of the 3D-HTLM, which will have wide applicability in studying pulmonary pathophysiology and therapeutics development.
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Affiliation(s)
- Rudra Bhowmick
- 1 School of Chemical Engineering, Oklahoma State University , Stillwater, Oklahoma
| | - Tahereh Derakhshan
- 1 School of Chemical Engineering, Oklahoma State University , Stillwater, Oklahoma
| | - Yurong Liang
- 2 Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University , Stillwater, Oklahoma
| | - Jerry Ritchey
- 3 Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University , Stillwater, Oklahoma
| | - Lin Liu
- 2 Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University , Stillwater, Oklahoma
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14
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Chen H, Shi P, Fan F, Tu M, Xu Z, Xu X, Du M. Complementation of UPLC-Q-TOF-MS and CESI-Q-TOF-MS on identification and determination of peptides from bovine lactoferrin. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1084:150-157. [DOI: 10.1016/j.jchromb.2018.03.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/05/2018] [Accepted: 03/10/2018] [Indexed: 12/27/2022]
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15
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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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16
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Liu W, Li J, Zheng W, Shang Y, Zhao Z, Wang S, Bi Y, Zhang S, Xu C, Duan Z, Zhang L, Wang YL, Jiang Z, Liu W, Sun L. Cyclophilin A-regulated ubiquitination is critical for RIG-I-mediated antiviral immune responses. eLife 2017; 6:e24425. [PMID: 28594325 PMCID: PMC5484619 DOI: 10.7554/elife.24425] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 06/07/2017] [Indexed: 12/20/2022] Open
Abstract
RIG-I is a key cytosolic pattern recognition receptor that interacts with MAVS to induce type I interferons (IFNs) against RNA virus infection. In this study, we found that cyclophilin A (CypA), a peptidyl-prolyl cis/trans isomerase, functioned as a critical positive regulator of RIG-I-mediated antiviral immune responses. Deficiency of CypA impaired RIG-I-mediated type I IFN production and promoted viral replication in human cells and mice. Upon Sendai virus infection, CypA increased the interaction between RIG-I and its E3 ubiquitin ligase TRIM25, leading to enhanced TRIM25-mediated K63-linked ubiquitination of RIG-I that facilitated recruitment of RIG-I to MAVS. In addition, CypA and TRIM25 competitively interacted with MAVS, thereby inhibiting TRIM25-induced K48-linked ubiquitination of MAVS. Taken together, our findings reveal an essential role of CypA in boosting RIG-I-mediated antiviral immune responses by controlling the ubiquitination of RIG-I and MAVS.
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Affiliation(s)
- Wei Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Weinan Zheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yingli Shang
- College of Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Zhendong Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuang Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chongfeng Xu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ziyuan Duan
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lianfeng Zhang
- Key Laboratory of Human Disease Comparative Medicine, Ministry of Health, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medical Center, Peking Union Medical College, Beijing, China
| | - Yue L Wang
- Department of Pathology, University of Chicago, Chicago, United States
| | - Zhengfan Jiang
- The Education Ministry Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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17
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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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18
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Biron D, Nedelkov D, Missé D, Holzmuller P. Proteomics and Host–Pathogen Interactions. GENETICS AND EVOLUTION OF INFECTIOUS DISEASES 2017. [PMCID: PMC7149668 DOI: 10.1016/b978-0-12-799942-5.00011-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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19
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Yu G, Liang W, Liu J, Meng D, Wei L, Chai T, Cai Y. Proteomic Analysis of Differential Expression of Cellular Proteins in Response to Avian H9N2 Virus Infection of A549 Cells. Front Microbiol 2016; 7:1962. [PMID: 28018302 PMCID: PMC5156691 DOI: 10.3389/fmicb.2016.01962] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 11/23/2016] [Indexed: 01/11/2023] Open
Abstract
In this study, differentially expressed proteins in A549 cells (human lung adenocarcinoma epithelial cell line) infected with H9N2 avian influenza virus (AIV) were investigated by two-dimensional electrophoresis (2-DE). Sixteen different spots between the groups (ratio > 2, p < 0.05) were identified with mass spectrometry identification. Proteins located in the downstream of the NF-κB and IFN transcription factor pathways were identified, e.g., ISG15. Actin and keratin were also identified, suggesting that the cytoskeleton may plays an important role in the AIV infection of mammalian cells. These findings could provide insights into the interaction between host and influenza viruses and might provide valuable information for clarifying the pathogenesis of viral infections as well.
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Affiliation(s)
- Guanliu Yu
- College of Veterinary Medicine, Shandong Agricultural University, Sino-German Cooperative Research Centre for Zoonosis of Animal Origin Shandong Province Tai'an, China
| | - Wei Liang
- College of Veterinary Medicine, Shandong Agricultural University, Sino-German Cooperative Research Centre for Zoonosis of Animal Origin Shandong Province Tai'an, China
| | - Jiyuan Liu
- College of Veterinary Medicine, Shandong Agricultural University, Sino-German Cooperative Research Centre for Zoonosis of Animal Origin Shandong Province Tai'an, China
| | - Dan Meng
- College of Veterinary Medicine, Shandong Agricultural University, Sino-German Cooperative Research Centre for Zoonosis of Animal Origin Shandong Province Tai'an, China
| | - Liangmeng Wei
- College of Veterinary Medicine, Shandong Agricultural University, Sino-German Cooperative Research Centre for Zoonosis of Animal Origin Shandong Province Tai'an, China
| | - Tongjie Chai
- College of Veterinary Medicine, Shandong Agricultural University, Sino-German Cooperative Research Centre for Zoonosis of Animal Origin Shandong Province Tai'an, China
| | - Yumei Cai
- College of Veterinary Medicine, Shandong Agricultural University, Sino-German Cooperative Research Centre for Zoonosis of Animal Origin Shandong Province Tai'an, China
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20
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Differential expression and characterization of cypermethrin-degrading potential proteins in Bacillus thuringiensis strain, SG4. 3 Biotech 2016; 6:225. [PMID: 28330297 PMCID: PMC5071268 DOI: 10.1007/s13205-016-0541-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 10/03/2016] [Indexed: 12/29/2022] Open
Abstract
A cypermethrin-degrading bacterium (SG4) was isolated from the pesticide-contaminated soil in the agricultural field of the crop research centre of the University, and characterized as Bacillus thuringiensis strain, SG4. The bacterium degraded 78.9 % of cypermethrin (50 ppm) in 15 days when grown in a minimal medium. To understand the functional proteins of cypermethrin degradation in Bacillus thuringiensis strain SG4, a comparative proteomic analysis was performed in the presence/absence of cypermethrin after 5 days of incubation in minimal medium. More than 450 spots corresponding to different proteins were recorded by 2D electrophoresis. We report expression of 223 and 250 unique proteins under normal and induced conditions (cypermethrin stress), respectively. Identified proteins were categorized into different functional groups on the basis of their biological functions, viz., catabolic enzymes, translational and stress proteins, etc. Characterization of cypermethrin-specific proteins in a bacterial strain will help in biodegradation practices in situ.
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21
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Söderholm S, Fu Y, Gaelings L, Belanov S, Yetukuri L, Berlinkov M, Cheltsov AV, Anders S, Aittokallio T, Nyman TA, Matikainen S, Kainov DE. Multi-Omics Studies towards Novel Modulators of Influenza A Virus-Host Interaction. Viruses 2016; 8:v8100269. [PMID: 27690086 PMCID: PMC5086605 DOI: 10.3390/v8100269] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 09/13/2016] [Accepted: 09/22/2016] [Indexed: 12/20/2022] Open
Abstract
Human influenza A viruses (IAVs) cause global pandemics and epidemics. These viruses evolve rapidly, making current treatment options ineffective. To identify novel modulators of IAV–host interactions, we re-analyzed our recent transcriptomics, metabolomics, proteomics, phosphoproteomics, and genomics/virtual ligand screening data. We identified 713 potential modulators targeting 199 cellular and two viral proteins. Anti-influenza activity for 48 of them has been reported previously, whereas the antiviral efficacy of the 665 remains unknown. Studying anti-influenza efficacy and immuno/neuro-modulating properties of these compounds and their combinations as well as potential viral and host resistance to them may lead to the discovery of novel modulators of IAV–host interactions, which might be more effective than the currently available anti-influenza therapeutics.
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Affiliation(s)
- Sandra Söderholm
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland.
- Finnish Institute of Occupational Health, Helsinki 00250, Finland.
| | - Yu Fu
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Lana Gaelings
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Sergey Belanov
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Laxman Yetukuri
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Mikhail Berlinkov
- Institute of Mathematics and Computer Science, Ural Federal University, Yekaterinburg 620083, Russia.
| | - Anton V Cheltsov
- Q-Mol L.L.C. in Silico Pharmaceuticals, San Diego, CA 92037, USA.
| | - Simon Anders
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
- Department of Mathematics and Statistics, University of Turku, Turku 20014, Finland.
| | | | - Sampsa Matikainen
- Finnish Institute of Occupational Health, Helsinki 00250, Finland.
- Department of Rheumatology, Helsinki University Hospital, University of Helsinki, Helsinki 00015, Finland.
| | - Denis E Kainov
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
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22
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Chemical Modifications of Peptides and Proteins with Low Concentration Formaldehyde Studied by Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60949-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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23
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PENG QS, LI GP, SUN WC, YANG JB, QUAN GH, LIU N. Analysis of ISG15-Modified Proteins from A549 Cells in Response to Influenza Virus Infection by Liquid Chromatography-Tandem Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60936-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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Voigt EA, Swick A, Yin J. Rapid induction and persistence of paracrine-induced cellular antiviral states arrest viral infection spread in A549 cells. Virology 2016; 496:59-66. [PMID: 27254596 DOI: 10.1016/j.virol.2016.05.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/20/2016] [Accepted: 05/23/2016] [Indexed: 12/31/2022]
Abstract
The virus/host interaction is a complex interplay between pro- and anti-viral factors that ultimately determines the spread or halt of virus infections in tissues. This interplay develops over multiple rounds of infection. The purpose of this study was to determine how cellular-level processes combine to impact the spatial spread of infection. We measured the kinetics of virus replication (VSV), antiviral paracrine signal upregulation and secretion, spatial spread of virus and paracrine antiviral signaling, and inhibition of virus production in antiviral-exposed A549 human lung epithelial cells. We found that initially infected cells released antiviral signals 4-to-7h following production of virus. However, the subsequent rapid dissemination of signal and fast induction of a robust and persistent antiviral state ultimately led to a suppression of infection spread. This work shows how cellular responses to infection and activation of antiviral responses can integrate to ultimately control infection spread across host cell populations.
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Affiliation(s)
- Emily A Voigt
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Adam Swick
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - John Yin
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
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25
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Marion T, Elbahesh H, Thomas PG, DeVincenzo JP, Webby R, Schughart K. Respiratory Mucosal Proteome Quantification in Human Influenza Infections. PLoS One 2016; 11:e0153674. [PMID: 27088501 PMCID: PMC4835085 DOI: 10.1371/journal.pone.0153674] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/01/2016] [Indexed: 01/08/2023] Open
Abstract
Respiratory influenza virus infections represent a serious threat to human health. Underlying medical conditions and genetic make-up predispose some influenza patients to more severe forms of disease. To date, only a few studies have been performed in patients to correlate a selected group of cytokines and chemokines with influenza infection. Therefore, we evaluated the potential of a novel multiplex micro-proteomics technology, SOMAscan, to quantify proteins in the respiratory mucosa of influenza A and B infected individuals. The analysis included but was not limited to quantification of cytokines and chemokines detected in previous studies. SOMAscan quantified more than 1,000 secreted proteins in small nasal wash volumes from infected and healthy individuals. Our results illustrate the utility of micro-proteomic technology for analysis of proteins in small volumes of respiratory mucosal samples. Furthermore, when we compared nasal wash samples from influenza-infected patients with viral load ≥ 28 and increased IL-6 and CXCL10 to healthy controls, we identified 162 differentially-expressed proteins between the two groups. This number greatly exceeds the number of DEPs identified in previous studies in human influenza patients. Most of the identified proteins were associated with the host immune response to infection, and changes in protein levels of 151 of the DEPs were significantly correlated with viral load. Most important, SOMAscan identified differentially expressed proteins heretofore not associated with respiratory influenza infection in humans. Our study is the first report for the use of SOMAscan to screen nasal secretions. It establishes a precedent for micro-proteomic quantification of proteins that reflect ongoing response to respiratory infection.
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Affiliation(s)
- Tony Marion
- University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, United States of America
| | - Husni Elbahesh
- University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, United States of America
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, United States of America
| | - John P. DeVincenzo
- University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, United States of America
- University of Tennessee Health Science Center, Department of Pediatrics, Memphis, United States of America
- Children’s Foundation Research Center at Le Bonheur Children’s Hospital, Memphis, United States of America
| | - Richard Webby
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, United States of America
| | - Klaus Schughart
- University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, United States of America
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
- University of Veterinary Medicine Hannover, Hannover, Germany
- * E-mail:
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26
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Du J, Xing S, Tian Z, Gao S, Xie J, Chang H, Liu G, Luo J, Yin H. Proteomic analysis of sheep primary testicular cells infected with bluetongue virus. Proteomics 2016; 16:1499-514. [PMID: 26989863 PMCID: PMC7168089 DOI: 10.1002/pmic.201500275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 01/03/2016] [Accepted: 03/11/2016] [Indexed: 01/06/2023]
Abstract
Bluetongue virus (BTV) causes a non‐contagious, arthropod‐transmitted disease in wild and domestic ruminants, such as sheep. In this study, we used iTRAQ labeling coupled with LC‐MS/MS for quantitative identification of differentially expressed proteins in BTV‐infected sheep testicular (ST) cells. Relative quantitative data were obtained for 4455 proteins in BTV‐ and mock‐infected ST cells, among which 101 and 479 proteins were differentially expressed at 24 and 48 h post‐infection, respectively, indicating further proteomic changes during the later stages of infection. Ten corresponding genes of differentially expressed proteins were validated via real‐time RT‐PCR. Expression levels of three representative proteins, eIF4a1, STAT1 and HSP27, were further confirmed via western blot analysis. Bioinformatics analysis disclosed that the differentially expressed proteins are primarily involved in biological processes related to innate immune response, signal transduction, nucleocytoplasmic transport, transcription and apoptosis. Several upregulated proteins were associated with the RIG‐I‐like receptor signaling pathway and endocytosis. To our knowledge, this study represents the first attempt to investigate proteome‐wide dysregulation in BTV‐infected cells with the aid of quantitative proteomics. Our collective results not only enhance understanding of the host response to BTV infection but also highlight multiple potential targets for the development of antiviral agents.
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Affiliation(s)
- Junzheng Du
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Shanshan Xing
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Zhancheng Tian
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Shandian Gao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Junren Xie
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Huiyun Chang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, P. R. China
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27
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Shen S, Li J, Hilchey S, Shen X, Tu C, Qiu X, Ng A, Ghaemmaghami S, Wu H, Zand MS, Qu J. Ion-Current-Based Temporal Proteomic Profiling of Influenza-A-Virus-Infected Mouse Lungs Revealed Underlying Mechanisms of Altered Integrity of the Lung Microvascular Barrier. J Proteome Res 2016; 15:540-53. [PMID: 26650791 DOI: 10.1021/acs.jproteome.5b00927] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Investigation of influenza-A-virus (IAV)-infected lung proteomes will greatly promote our understanding on the virus-host crosstalk. Using a detergent-cocktail extraction and digestion procedure and a reproducible ion-current-based method, we performed the first comprehensive temporal analysis of mouse IAV infection. Mouse lung tissues at three time points post-inoculation were compared with controls (n = 4/group), and >1600 proteins were quantified without missing value in any animal. Significantly changed proteins were identified at 4 days (n = 144), 7 days (n = 695), and 10 days (n = 396) after infection, with low false altered protein rates (1.73-8.39%). Functional annotation revealed several key biological processes involved in the systemic host responses. Intriguingly, decreased levels of several cell junction proteins as well as increased levels of tissue metalloproteinase MMP9 were observed, reflecting the IAV-induced structural breakdown of lung epithelial barrier. Supporting evidence of MMP9 activation came from immunoassays examining the abundance and phosphorylation states of all MAPKs and several relevant molecules. Importantly, IAV-induced MMP gelatinase expression was suggested to be specific to MMP9, and p38 MAPK may contribute predominantly to MMP9 elevation. These findings help to resolve the long-lasting debate regarding the signaling pathways of IAV-induced MMP9 expression and shed light on the molecular mechanisms underlying pulmonary capillary-alveolar leak syndrome that can occur during influenza infection.
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Affiliation(s)
- Shichen Shen
- New York State Center of Excellence in Bioinformatics & Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States.,Jacobs School of Medicine and Biomedical Sciences, SUNY at Buffalo , South Campus, Buffalo, New York 14214, United States
| | - Jun Li
- Department of Pharmaceutical Sciences, SUNY at Buffalo , South Campus, Buffalo, New York 14214, United States.,New York State Center of Excellence in Bioinformatics & Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Shannon Hilchey
- Division of Nephrology, University of Rochester Medical Center , 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Xiaomeng Shen
- New York State Center of Excellence in Bioinformatics & Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States.,Jacobs School of Medicine and Biomedical Sciences, SUNY at Buffalo , South Campus, Buffalo, New York 14214, United States
| | - Chengjian Tu
- Department of Pharmaceutical Sciences, SUNY at Buffalo , South Campus, Buffalo, New York 14214, United States.,New York State Center of Excellence in Bioinformatics & Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester , 265 Crittenden Boulevard, Rochester, New York 14642, United States
| | - Andrew Ng
- Jacobs School of Medicine and Biomedical Sciences, SUNY at Buffalo , South Campus, Buffalo, New York 14214, United States
| | - Sina Ghaemmaghami
- Department of Biology, University of Rochester , 402 Hutchison Hall, Rochester, New York 14627, United States
| | - Hulin Wu
- Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston , 1200 Pressler Street, Houston, Texas 77030, United States
| | - Martin S Zand
- Division of Nephrology, University of Rochester Medical Center , 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, SUNY at Buffalo , South Campus, Buffalo, New York 14214, United States.,New York State Center of Excellence in Bioinformatics & Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States
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28
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Proteomics Analysis of Cellular Proteins Co-Immunoprecipitated with Nucleoprotein of Influenza A Virus (H7N9). Int J Mol Sci 2015; 16:25982-98. [PMID: 26528969 PMCID: PMC4661793 DOI: 10.3390/ijms161125934] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/13/2015] [Accepted: 10/22/2015] [Indexed: 01/18/2023] Open
Abstract
Avian influenza A viruses are serious veterinary pathogens that normally circulate among avian populations, causing substantial economic impacts. Some strains of avian influenza A viruses, such as H5N1, H9N2, and recently reported H7N9, have been occasionally found to adapt to humans from other species. In order to replicate efficiently in the new host, influenza viruses have to interact with a variety of host factors. In the present study, H7N9 nucleoprotein was transfected into human HEK293T cells, followed by immunoprecipitated and analyzed by proteomics approaches. A series of host proteins co-immunoprecipitated were identified with high confidence, some of which were found to be acetylated at their lysine residues. Bioinformatics analysis revealed that spliceosome might be the most relevant pathway involved in host response to nucleoprotein expression, increasing our emerging knowledge of host proteins that might be involved in influenza virus replication activities.
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29
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Sun Y, Hu B, Fan C, Jia L, Zhang Y, Du A, Zheng X, Zhou J. iTRAQ-based quantitative subcellular proteomic analysis of Avibirnavirus-infected cells. Electrophoresis 2015; 36:1596-611. [PMID: 25929241 PMCID: PMC7163642 DOI: 10.1002/elps.201500014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/22/2015] [Accepted: 03/25/2015] [Indexed: 11/19/2022]
Abstract
Infectious bursal disease virus (IBDV) enters the host cells via endocytic pathway to achieve viral replication in the cytoplasm. Here, we performed LC-MS/MS coupled with isobaric tags for relative and absolute quantification labeling of differentially abundant proteins of IBDV-infected cells using a subcellular fractionation strategy. We show that the viral infection regulates the abundance and/or subcellular localization of 3211 proteins during early infection. In total, 23 cellular proteins in the cytoplasmic proteome and 34 in the nuclear proteome were significantly altered after virus infection. These differentially abundant proteins are involved in such biological processes as immune response, signal transduction, RNA processing, macromolecular biosynthesis, energy metabolism, virus binding, and cellular apoptosis. Moreover, transcriptional profiles of the 25 genes corresponding to the identified proteins were analyzed by quantitative real-time RT-PCR. Ingenuity Pathway Analysis clustered the differentially abundant proteins primarily into the mTOR pathway, PI3K/Akt pathway, and interferon-β signaling cascades. Confocal microscopy showed colocalization of the viral protein VP3 with host proteins heterogeneous nuclear ribonucleoprotein H1, nuclear factor 45, apoptosis inhibitor 5, nuclear protein localization protein 4 and DEAD-box RNA helicase 42 during the virus infection. Together, these identified subcellular constituents provide important information for understanding host-IBDV interactions and underlying mechanisms of IBDV infection and pathogenesis.
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Affiliation(s)
- Yanting Sun
- Key Laboratory of Animal Virology of Ministry of AgricultureZhejiang UniversityHangzhouP. R. China
| | - Boli Hu
- College of Veterinary MedicineNanjing Agricultural UniversityNanjingP. R. China
| | - Chengfei Fan
- Key Laboratory of Animal Virology of Ministry of AgricultureZhejiang UniversityHangzhouP. R. China
| | - Lu Jia
- Key Laboratory of Animal Virology of Ministry of AgricultureZhejiang UniversityHangzhouP. R. China
| | - Yina Zhang
- Key Laboratory of Animal Virology of Ministry of AgricultureZhejiang UniversityHangzhouP. R. China
| | - Aifang Du
- Key Laboratory of Animal Virology of Ministry of AgricultureZhejiang UniversityHangzhouP. R. China
| | - Xiaojuan Zheng
- Key Laboratory of Animal Virology of Ministry of AgricultureZhejiang UniversityHangzhouP. R. China
- State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated Hospital, Zhejiang UniversityHangzhouP. R. China
| | - Jiyong Zhou
- Key Laboratory of Animal Virology of Ministry of AgricultureZhejiang UniversityHangzhouP. R. China
- College of Veterinary MedicineNanjing Agricultural UniversityNanjingP. R. China
- State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated Hospital, Zhejiang UniversityHangzhouP. R. China
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30
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Comparative Study of Three Methods of Sample Preparation for Proteomics Research. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1016/s1872-2040(15)60828-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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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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32
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Qi W, Tian J, Su S, Huang L, Li H, Liao M. Identification of potential virulence determinants associated H9N2 avian influenza virus PB2 E627K mutation by comparative proteomics. Proteomics 2015; 15:1512-24. [PMID: 25641917 DOI: 10.1002/pmic.201400309] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 12/03/2014] [Accepted: 01/13/2015] [Indexed: 12/14/2022]
Abstract
Some highly pathogenic H5N1, H7N9, and H10N8 isolated from China carried six internal genes from H9N2 avian influenza viruses (AIV) and the key amino acids at 627 in PB2 of these viruses had mutated to K. To investigate the mechanism of increased pathogenicity for H9N2 AIV PB2 627K, we analyzed the difference in mouse lung proteins expression response to PB2 K627E. By iTRAQ method, we found that the mutated K627E contributed to a set of differentially expressed lung proteins, including five upregulated proteins and nine downregulated proteins at 12 h postinfection; ten upregulated proteins and 25 downregulated proteins at 72 h postinfection. These proteins were chiefly involved within the cytoskeleton and motor proteins, antiviral proteins, regulation of glucocorticoids signal-associated proteins, pro- and anti-inflammatory proteins. Alteration of moesin, FKBP4, Hsp70, ezrin, and pulmonary surfactant protein A (sp-A) may play important roles in increasing virulence and decreasing lungs antiviral response. Further, three upregulated proteins (moesin, ezrin, and sp-A) caused by PB2 K627E were also confirmed in A549 cells. Moreover, overexpression of sp-A in A549 inhibited virus replication and downregulation promoted virus replication. In this study, sp-A as a potential virulence determinant associated H9N2 AIV PB2 E627K mutation was identified using comparative proteomics.
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Affiliation(s)
- Wenbao Qi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, P. R. China
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Qinghong S, Shen G, Lina S, Yueming Z, Xiaoou L, Jianlin W, Chengyan H, Hongjun L, Haifeng Z. Comparative proteomics analysis of differential proteins in respond to doxorubicin resistance in myelogenous leukemia cell lines. Proteome Sci 2015; 13:1. [PMID: 25628518 PMCID: PMC4307195 DOI: 10.1186/s12953-014-0057-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/15/2014] [Indexed: 01/14/2023] Open
Abstract
Background Chemoresistance remains a significant challenge in chronic myelogenous leukemia (CML) management, which is one of the most critical prognostic factors. Elucidation the molecular mechanisms underlying the resistance to chemoresistance may lead to better clinical outcomes. Results In order to identify potential protein targets involved in the drug-resistant phenotype of leukemia, especially the chronic myelogenous leukemia (CML), we used a high-resolution “ultra-zoom” 2DE-based proteomics approach to characterize global protein expression patterns in doxorubicin-resistant myelogenous leukemia cells compared with parental control cells. Ultra-high resolution of 2DE was achieved by using a series of slightly overlapping narrow-range IPG strips during isoelectric focusing (IEF) separation. A total number of 44 proteins with altered abundances were detected and identified by MALDI-TOF or LC-MS/MS. Among these proteins, enolase, aldolase, HSP70 and sorcin were up-regulated in doxorubicin-resistant myelogenous leukemia cell line, whereas HSP27 was down-regulated. Some of the results have been validated by Western blotting. Both enolase and aldolase were first reported to be involved in chemoresistance, suggesting that process of glycolysis in doxorubicin-resistant myelogenous leukemia cells was accelerated to some extent to provide more energy to survive chemical stress. Possible roles of most of the identified proteins in development of chemoresistance in myelogenous leukemia cells were fully discussed. The results presented here could provide clues to further study for elucidating the mechanisms underlying drug resistance in leukemia. Conclusions As a whole, under the chemical stress, the doxorubicin-resistant myelogenous leukemia cells may employ various protective strategies to survive. These include: (i) pumping the cytotoxic drug out of the cells by P-glycoprotein, (ii) increased storage of fermentable fuel, (iii) sophisticated cellular protection by molecular chaperones, (iv) improved handling of intracellular calcium, (v) increased glucose utilization via increased rates of glycolysis. In the present study, proteomic analysis of leukemia cells and their drug resistant variants revealed multiple alterations in protein expression. Our results indicate that the development of drug resistance in doxorubicin-resistant myelogenous leukemia cells is a complex phenomenon undergoing several mechanisms. Electronic supplementary material The online version of this article (doi:10.1186/s12953-014-0057-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shi Qinghong
- Jilin University China-Japan Union Hospital, Changchun, 130033 China
| | - Gao Shen
- Jilin University China-Japan Union Hospital, Changchun, 130033 China
| | - Song Lina
- Jilin University China-Japan Union Hospital, Changchun, 130033 China
| | - Zhao Yueming
- Jilin University China-Japan Union Hospital, Changchun, 130033 China ; Tumor Hospital of Jilin Province, Changchun, 130021 China
| | - Li Xiaoou
- Tumor Hospital of Jilin Province, Changchun, 130021 China
| | - Wu Jianlin
- State Key Laboratory for Quality Research in Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau, China
| | - He Chengyan
- Jilin University China-Japan Union Hospital, Changchun, 130033 China
| | - Li Hongjun
- Jilin University China-Japan Union Hospital, Changchun, 130033 China
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Mass spectrometric analysis revealing phosphorylation modifications of periostin. Chem Res Chin Univ 2014. [DOI: 10.1007/s40242-014-4317-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Meng J, Zhang C, Chen X, Cao Y, Shang S. Differential protein expression in the susceptible and resistant Myzus persicae (Sulzer) to imidacloprid. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2014; 115:1-8. [PMID: 25307459 DOI: 10.1016/j.pestbp.2014.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 09/03/2014] [Accepted: 09/03/2014] [Indexed: 06/04/2023]
Abstract
Myzus persicae, a serious economic agricultural pest, has developed resistance to imidacloprid (IMI), which was widely used to control this aphid worldwide. To gain a better understanding of the mechanisms of IMI resistance in M. persicae, we carried out a comparative proteomic analysis. Total proteins of the IMI-susceptible and resistant strains were extracted and separated by two-dimensional gel electrophoresis. More than 1300 protein spots were reproducibly detected, including 14 that were more abundant and 14 less abundant. Mass spectrometry analysis and database searching helped us to identify 25 differentially abundant proteins. The identified proteins were categorized into several functional groups including signal transduction, RNA processing, protein processing, transport processing, stress response, metabolisms, and cytoskeleton structure, etc. This study is the first analysis of differentially expressed proteins in IMI-susceptible and resistant M. Persicae, and gives new insights into the mechanisms of IMI resistance in M. persicae.
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Affiliation(s)
- JianYu Meng
- Guizhou Tobacco Science Research Institute, Guiyang 550081, China
| | - ChangYu Zhang
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - XingJiang Chen
- Guizhou Tobacco Science Research Institute, Guiyang 550081, China
| | - Yi Cao
- Guizhou Tobacco Science Research Institute, Guiyang 550081, China
| | - ShengHua Shang
- Guizhou Tobacco Science Research Institute, Guiyang 550081, China.
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Deng X, Cong Y, Yin R, Yang G, Ding C, Yu S, Liu X, Wang C, Ding Z. Proteomic analysis of chicken peripheral blood mononuclear cells after infection by Newcastle disease virus. J Vet Sci 2014; 15:511-7. [PMID: 25234324 PMCID: PMC4269593 DOI: 10.4142/jvs.2014.15.4.511] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 07/18/2014] [Indexed: 11/20/2022] Open
Abstract
Characteristic clinical manifestations of Newcastle disease include leukopenia and immunosuppression. Peripheral blood mononuclear cells (PBMCs) are the main targets of Newcastle disease virus (NDV) infection. To survey changes in proteomic expression in chicken PBMCs following NDV infection, PBMC proteins from 30 chickens were separated using two- dimensional electrophoresis (2-DE) and subjected to mass spectrometry analysis. Quantitative intensity analysis showed that the expression of 78 proteins increased more than two-fold. Thirty-five proteins exhibited consistent changes in expression and 13 were identified as unique proteins by matrix assisted laser desorption ionization-time of flight mass spectrometer/mass spectrometer including three that were down-regulated and 10 that were up-regulated. These proteins were sorted into five groups based on function: macromolecular biosynthesis, cytoskeleton organization, metabolism, stress responses, and signal transduction. Furthermore, Western blot analysis confirmed the down-regulation of integrin-linked kinase expression and up-regulation of lamin A production. These data provide insight into the in vivo response of target cells to NDV infection at the molecular level. Additionally, results from this study have helped elucidate the molecular pathogenesis of NDV and may facilitate the development of new antiviral therapies as well as innovative diagnostic methods.
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Affiliation(s)
- Xiaoyu Deng
- Laboratory of Infectious Diseases, College of Veterinary Medicine, Jilin University, Changchun 130062, China
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Fusion-related host proteins are actively regulated by NA during influenza infection as revealed by quantitative proteomics analysis. PLoS One 2014; 9:e105947. [PMID: 25153908 PMCID: PMC4143309 DOI: 10.1371/journal.pone.0105947] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 07/28/2014] [Indexed: 12/31/2022] Open
Abstract
Three recombinant influenza A viruses with different neuraminidases (NAs) in the background of A/PR/8/34 (PR8), named rPR8-H5N1NA, rPR8-H9N2NA, and rPR8-H1N1NA, derived from H5N1, H9N2, H1N1 (swine) viruses, respectively, were constructed. We performed a quantitative proteomics analysis to investigate differential protein expression in Madin-Darby canine kidney (MDCK) cells infected with recombinant and wild-type influenza viruses to determine whether NA replacement would alter host cell gene expression. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-TOF MS) and two-dimensional gel electrophoresis (2-DE), we identified 12 up-regulated and 49 down-regulated protein spots, including cytoskeletal proteins, molecular biosynthesis proteins, ubiquitin-proteasome pathway proteins, and heat shock proteins. The most significant changes in infected cells were observed for molecular biosynthesis proteins. We found more differentially expressed protein spots in cells infected with rPR8-H5N1NA or rPR8-H9N2NA viruses than cells infected with wild-type virus. Many of those proteins are postulated to be involved in cell-cell fusion, but the full mechanism remains to be explored. Meanwhile, our data demonstrate that the wild-type virus has evolutionary advantages over recombinant viruses.
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Boyanova D, Nilla S, Klau GW, Dandekar T, Müller T, Dittrich M. Functional module search in protein networks based on semantic similarity improves the analysis of proteomics data. Mol Cell Proteomics 2014; 13:1877-89. [PMID: 24807868 DOI: 10.1074/mcp.m113.032839] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The continuously evolving field of proteomics produces increasing amounts of data while improving the quality of protein identifications. Albeit quantitative measurements are becoming more popular, many proteomic studies are still based on non-quantitative methods for protein identification. These studies result in potentially large sets of identified proteins, where the biological interpretation of proteins can be challenging. Systems biology develops innovative network-based methods, which allow an integrated analysis of these data. Here we present a novel approach, which combines prior knowledge of protein-protein interactions (PPI) with proteomics data using functional similarity measurements of interacting proteins. This integrated network analysis exactly identifies network modules with a maximal consistent functional similarity reflecting biological processes of the investigated cells. We validated our approach on small (H9N2 virus-infected gastric cells) and large (blood constituents) proteomic data sets. Using this novel algorithm, we identified characteristic functional modules in virus-infected cells, comprising key signaling proteins (e.g. the stress-related kinase RAF1) and demonstrate that this method allows a module-based functional characterization of cell types. Analysis of a large proteome data set of blood constituents resulted in clear separation of blood cells according to their developmental origin. A detailed investigation of the T-cell proteome further illustrates how the algorithm partitions large networks into functional subnetworks each representing specific cellular functions. These results demonstrate that the integrated network approach not only allows a detailed analysis of proteome networks but also yields a functional decomposition of complex proteomic data sets and thereby provides deeper insights into the underlying cellular processes of the investigated system.
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Affiliation(s)
- Desislava Boyanova
- From the ‡Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Santosh Nilla
- From the ‡Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Gunnar W Klau
- §Life Sciences, Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098 XG Amsterdam, The Netherlands
| | - Thomas Dandekar
- From the ‡Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Tobias Müller
- From the ‡Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Marcus Dittrich
- From the ‡Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany;
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Sun J, Han Z, Shao Y, Cao Z, Kong X, Liu S. Comparative proteome analysis of tracheal tissues in response to infectious bronchitis coronavirus, Newcastle disease virus, and avian influenza virus H9 subtype virus infection. Proteomics 2014; 14:1403-23. [PMID: 24610701 PMCID: PMC7167649 DOI: 10.1002/pmic.201300404] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 02/16/2014] [Accepted: 03/04/2014] [Indexed: 01/29/2023]
Abstract
Infectious bronchitis coronavirus (IBV), Newcastle disease virus (NDV), and avian influenza virus (AIV) H9 subtype are major pathogens of chickens causing serious respiratory tract disease and heavy economic losses. To better understand the replication features of these viruses in their target organs and molecular pathogenesis of these different viruses, comparative proteomic analysis was performed to investigate the proteome changes of primary target organ during IBV, NDV, and AIV H9 infections, using 2D‐DIGE followed MALDI‐TOF/TOF‐MS. In total, 44, 39, 41, 48, and 38 proteins were identified in the tracheal tissues of the chickens inoculated with IBV (ck/CH/LDL/97I, H120), NDV (La Sota), and AIV H9, and between ck/CH/LDL/97I and H120, respectively. Bioinformatics analysis showed that IBV, NDV, and AIV H9 induced similar core host responses involved in biosynthetic, catabolic, metabolic, signal transduction, transport, cytoskeleton organization, macromolecular complex assembly, cell death, response to stress, and immune system process. Comparative analysis of host response induced by different viruses indicated differences in protein expression changes induced by IBV, NDV, and AIV H9 may be responsible for the specific pathogenesis of these different viruses. Our result reveals specific host response to IBV, NDV, and AIVH9 infections and provides insights into the distinct pathogenic mechanisms of these avian respiratory viruses.
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Affiliation(s)
- Junfeng Sun
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, P. R. China
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Wu H, Song W, Gao X, Liu N, Wang P, Chen H, Cai Z. Proteomics study of N-acetylcysteine response in H1N1-infected cells by using mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:741-749. [PMID: 24573805 DOI: 10.1002/rcm.6840] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 01/12/2014] [Accepted: 01/13/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE The pathology of A/Puerto Rico/8/1934 (H1N1) infection associated with the interaction of virus and its host cells is not clear. N-Acetylcysteine (NAC) is an antioxidant as well as a premier antitoxin and immune support substance. A high dose of NAC was recently reported for a therapy of H1N1 (2009) influenza pneumonia. METHODS NAC was used as a small-molecule organic probe to investigate the protein expression of human lung carcinoma cell line (A549) infected by influenza virus A/Puerto Rico/8/1934 (H1N1). Differential proteins were identified from MALDI-TOF MS and Q-TOF MS/MS analyses. RESULTS The obtained results showed that NAC kept cells away from apoptosis. Virus-infected cells were arrested in G0/G1 phase. The lowest cell population of G0/G1 phase was detected when the cells were treated by 10 mM NAC for one day. Application of MS-based proteomics allowed the identification of the differential proteins. Software analysis showed that four proteins had close relationship. CONCLUSIONS The results indicated that NAC as a small-molecule probe might effect the protein expression of A549 cells infected by the H1N1 virus.
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Affiliation(s)
- Hanzhi Wu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
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Zhou YJ, Zhu JP, Zhou T, Cheng Q, Yu LX, Wang YX, Yang S, Jiang YF, Tong W, Gao F, Yu H, Li GX, Tong GZ. Identification of differentially expressed proteins in porcine alveolar macrophages infected with virulent/attenuated strains of porcine reproductive and respiratory syndrome virus. PLoS One 2014; 9:e85767. [PMID: 24465692 PMCID: PMC3897507 DOI: 10.1371/journal.pone.0085767] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 12/06/2013] [Indexed: 12/15/2022] Open
Abstract
The highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) is still a serious threat to the swine industry. However, the pathogenic mechanism of HP-PRRSV remains unclear. We infected host porcine alveolar macrophages (PAMs) with the virulent HuN4 strain and the attenuated HuN4-F112 strain and then utilized fluorescent two-dimensional difference gel electrophoresis (2D-DIGE) to screen for intracellular proteins that were differentially expressed in host cells infected with the two strains. There were 153 proteins with significant different expression (P<0.01) observed, 42 of which were subjected to mass spectrometry, and 24 proteins were identified. PAM cells infected with the virulent strain showed upregulated expression of pyruvate kinase M2 (PKM2), heat shock protein beta-1 (HSPB1), and proteasome subunit alpha type 6 (PSMA6), which were downregulated in cells infected with the attenuated strain. The upregulation of PKM2 provides sufficient energy for viral replication, and the upregulation of HSPB1 inhibits host cell apoptosis and therefore facilitates mass replication of the virulent strain, while the upregulation of PSMA6 facilitates the evasion of immune surveillance by the virus. Studying on those molecules mentioned above may be able to help us to understand some unrevealed details of HP-PRRSV infection, and then help us to decrease its threat to the swine industry in the future.
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Affiliation(s)
- Yan-Jun Zhou
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, CAAS, Shanghai, China
| | - Jian-Ping Zhu
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, CAAS, Shanghai, China
| | - Tao Zhou
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Qun Cheng
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, CAAS, Shanghai, China
| | - Ling-Xue Yu
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, CAAS, Shanghai, China
| | - Ya-Xin Wang
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, CAAS, Shanghai, China
| | - Shen Yang
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, CAAS, Shanghai, China
| | - Yi-Feng Jiang
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, CAAS, Shanghai, China
| | - Wu Tong
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, CAAS, Shanghai, China
| | - Fei Gao
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, CAAS, Shanghai, China
| | - Hai Yu
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, CAAS, Shanghai, China
| | - Guo-Xin Li
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, CAAS, Shanghai, China
| | - Guang-Zhi Tong
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, CAAS, Shanghai, China
- * E-mail:
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Cyclophilin A: a key player for human disease. Cell Death Dis 2013; 4:e888. [PMID: 24176846 PMCID: PMC3920964 DOI: 10.1038/cddis.2013.410] [Citation(s) in RCA: 310] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/10/2013] [Accepted: 09/11/2013] [Indexed: 01/23/2023]
Abstract
Cyclophilin A (CyPA) is a ubiquitously distributed protein belonging to the immunophilin family. CyPA has peptidyl prolyl cis-trans isomerase (PPIase) activity, which regulates protein folding and trafficking. Although CyPA was initially believed to function primarily as an intracellular protein, recent studies have revealed that it can be secreted by cells in response to inflammatory stimuli. Current research in animal models and humans has provided compelling evidences supporting the critical function of CyPA in several human diseases. This review discusses recently available data about CyPA in cardiovascular diseases, viral infections, neurodegeneration, cancer, rheumatoid arthritis, sepsis, asthma, periodontitis and aging. It is believed that further elucidations of the role of CyPA will provide a better understanding of the molecular mechanisms underlying these diseases and will help develop novel pharmacological therapies.
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Wu X, Wang S, Yu Y, Zhang J, Sun Z, Yan Y, Zhou J. Subcellular proteomic analysis of human host cells infected with H3N2 swine influenza virus. Proteomics 2013; 13:3309-26. [PMID: 24115376 DOI: 10.1002/pmic.201300180] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 08/25/2013] [Accepted: 08/28/2013] [Indexed: 11/10/2022]
Abstract
Cross-species transmissions of swine influenza viruses (SIVs) raise great public health concerns. In this study, subcellular proteomic profiles of human A549 cells inoculated with H3N2 subtype SIV were used to characterize dynamic cellular responses to infection. By 2DE and MS, 27 differentially expressed (13 upregulated, 14 downregulated) cytoplasmic proteins and 20 differentially expressed (13 upregulated, 7 downregulated) nuclear proteins were identified. Gene ontology analysis suggested that these differentially expressed proteins were mainly involved in cell death, stress response, lipid metabolism, cell signaling, and RNA PTMs. Moreover, 25 corresponding genes of the differentially expressed proteins were quantitated by real time RT-PCR to examine the transcriptional profiles between mock- and virus-infected A549 cells. Western blot analysis confirmed that changes in abundance of identified cellular proteins heterogeneous nuclear ribonucleoprotein (hnRNP) U, hnRNP C, ALDH1A1, tryptophanyl-tRNA synthetase, IFI35, and HSPB1 in H3N2 SIV-infected cells were consistent with results of 2DE analysis. By confocal microscopy, nucleus-to-cytoplasm translocation of hnRNP C and colocalization between the viral nonstructural protein 1 and hnRNP C as well as N-myc (and STAT) interactor were observed upon infection. Ingenuity Pathway Analysis revealed that cellular proteins altered during infection were grouped mainly into NFκB and interferon signaling networks. Collectively, these identified subcellular constituents provide an important framework for understanding host/SIV interactions and underlying mechanisms of SIV cross-species infection and pathogenesis.
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Affiliation(s)
- Xiaopeng Wu
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, P. R. China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University, Hangzhou, P. R. China
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Zhao H, Yang J, Li K, Ding X, Lin R, Ma Y, Liu J, Zhong Z, Qian X, Bo X, Zhou Z, Wang S. Proteomic analysis at the subcellular level for host targets against influenza A virus (H1N1). Antiviral Res 2013; 100:673-87. [PMID: 24161511 DOI: 10.1016/j.antiviral.2013.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 01/28/2023]
Abstract
Influenza viruses (IVs) trigger a series of intracellular signaling events and induce complex cellular responses from the infected host cell. Accumulating evidence suggests that host cell proteins play an essential role in viral propagation and represent novel antiviral therapeutic targets. Subcellular proteomic technology provides a method for understanding regional differences at the protein level. The present study, which utilized subcellular proteomic technology, aimed to identify host cell proteins involved in influenza virus (HIN1) infection. Two-dimensional gel electrophoresis (2-DE) combined with mass spectrum (MS) was performed on protein extracts from the nuclei, cytoplasm, and mitochondria of infected and control human lung epithelial cells (A549). In total, 112 differentially expressed protein molecules were identified; 80 protein spots were successfully validated using MS. The differential expression of ISG15, MIF, PDCD5, and UCHL1 was confirmed by western blot. Furthermore, antisense oligodeoxyribonucleotide (ODN) targeting ISG15, MIF, PDCD5, and UCHL1 significantly mitigated HIN1 propagation, cytopathic effects, vRNA by RT-qPCR, and rescued cell viability in A549 cells. Taken together, the differentially expressed proteins identified in this study might provide novel targets for anti-influenza drug development.
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Affiliation(s)
- Haibao Zhao
- Beijing Institute of Radiation Medicine, Beijing 100850, PR China
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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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Zhang J, Hu YH, Xiao ZZ, Sun L. Megalocytivirus-induced proteins of turbot (Scophthalmus maximus): identification and antiviral potential. J Proteomics 2013; 91:430-43. [PMID: 23933595 DOI: 10.1016/j.jprot.2013.07.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/24/2013] [Accepted: 07/30/2013] [Indexed: 11/19/2022]
Abstract
UNLABELLED Megalocytivirus is an important fish pathogen with a broad host range that includes turbot. In this study, proteomic analysis was conducted to examine turbot proteins modulated in expression by megalocytivirus infection. Thirty five proteins from spleen were identified to be differentially expressed at 2days post-viral infection (dpi) and 7dpi. Three upregulated proteins, i.e. heat shock protein 70 (Hsp70), Mx protein, and natural killer enhancing factor (NKEF), were further analyzed for potential antiviral effect. For this purpose, turbot were administered separately with the plasmids pHsp70, pMx, and pNKEF, which express Hsp70, Mx, and NKEF respectively, before megalocytivirus infection. Viral dissemination and propagation in spleen were subsequently determined. The results showed that the viral loads in fish administered with pNKEF were significantly reduced. To examine the potential of Hsp70, Mx, and NKEF as immunological adjuvant, turbot were immunized with a DNA vaccine in the presence of pHsp70, pMx, or pNKEF. Subsequent analysis showed that the presence of pNKEF and pHsp70, but not pMx, significantly reduced viral infection and enhanced fish survival. Taken together, these results indicate that NKEF exhibits antiviral property against megalocytivirus, and that both NKEF and Hsp70 may be used in DNA vaccine-based control of megalocytivirus infection. BIOLOGICAL SIGNIFICANCE This study provides the first proteomic picture of turbot in response to megalocytivirus infection. We demonstrated that megalocytivirus infection modulates the expression of turbot proteins associated with various cellular functions, and that one of the upregulated proteins, NKEF, exhibits antiviral effect when overexpressed in vivo, while another upregulated protein, Hsp70, exhibits adjuvant effect when co-immunized with a DNA vaccine. These results add molecular insights into turbot immune response induced by megalocytivirus and provide candidate proteins with application potentials in the control of megalocytivirus-associated disease.
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Affiliation(s)
- Jian Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China
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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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Liu X, Zhao Z, Liu W. Insights into the roles of cyclophilin A during influenza virus infection. Viruses 2013; 5:182-91. [PMID: 23322171 PMCID: PMC3564116 DOI: 10.3390/v5010182] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 12/22/2012] [Accepted: 01/09/2013] [Indexed: 01/31/2023] Open
Abstract
Cyclophilin A (CypA) is the main member of the immunophilin superfamily that has peptidyl-prolyl cis-trans isomerase activity. CypA participates in protein folding, cell signaling, inflammation and tumorigenesis. Further, CypA plays critical roles in the replication of several viruses. Upon influenza virus infection, CypA inhibits viral replication by interacting with the M1 protein. In addition, CypA is incorporated into the influenza virus virions. Finally, Cyclosporin A (CsA), the main inhibitor of CypA, inhibits influenza virus replication through CypA-dependent and -independent pathways. This review briefly summarizes recent advances in understanding the roles of CypA during influenza virus infection.
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Affiliation(s)
- Xiaoling Liu
- Center for Molecular Virology, Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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Wu Y, Peng C, Xu L, Zheng X, Liao M, Yan Y, Jin Y, Zhou J. Proteome dynamics in primary target organ of infectious bursal disease virus. Proteomics 2012; 12:1844-59. [PMID: 22623289 DOI: 10.1002/pmic.201100479] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Viruses induce dramatic changes in target tissue during pathogenesis, including host cellular responses that either limit or support the pathogen. The infectious bursal disease virus (IBDV) targets primarily the bursa of Fabricius (BF) of chickens, causing severe immunodeficiency. Here, we characterized the cellular proteome changes of the BF caused by IBDV replication in vivo using 2DE followed MALDI-TOF MS identification. Comparative analysis of multiple 2DE gels revealed that the majority of protein expression changes appeared between 24 and 96 h after IBDV infection. MS identified 54 altered cell proteins, 12 of which were notably upregulated by IBDV infection. Meanwhile, the other 42 cellular proteins were considerably suppressed by IBDV infection and are involved in protein degradation, energy metabolism, stress response, host macromolecular biosynthesis, and transport process. The upregulation of β-actin and downregulation of dynamin during IBDV infection were also confirmed by Western blot and immunofluorescence analysis. These altered protein expressions provide a response profile of chicken BF to virulent IBDV infection. Further functional study on these altered proteins may lead to better understanding of pathogenic mechanisms of virulent IBDV infection and to new potential therapeutic targets.
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Affiliation(s)
- Yongping Wu
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, P. R. China
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50
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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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