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Tang HT, Nörz D, Grunwald M, Giersch K, Pfefferle S, Fischer N, Aepfelbacher M, Rohde H, Lütgehetmann M. Analytical and clinical validation of a novel, laboratory-developed, modular multiplex-PCR panel for fully automated high-throughput detection of 16 respiratory viruses. J Clin Virol 2024; 173:105693. [PMID: 38820916 DOI: 10.1016/j.jcv.2024.105693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
BACKGROUND Viral respiratory Infections pose a health risk, especially to vulnerable patient populations. Effective testing programs can detect and differentiate these infections at an early stage, which is particularly important for high-risk clinical departments. The objective of this study was to develop and validate a multiplex PCR-panel for 16 different respiratory viruses on a fully-automated high-throughput platform. METHODS Three multiplex-PCR assays were designed to run on the cobas5800/6800/8800 systems, consolidating 16 viral targets: RESP1: SARS-CoV-2, influenza-A/B, RSV; RESP2: hMPV, hBoV, hAdV, rhino-/ENV; RESP3: HPIV-1-4, hCoV-229E, hCoV-NL63, hCoV-OC43, hCoV-HKU1. Analytic performance was evaluated using digital-PCR based standards and international reference material. Clinical performance was determined by comparing results from clinical samples with reference assays. RESULTS Analytical sensitivity (i.e. lower limit of detection (LoD), 95 % probability of detection) was determined as follows: SARS-CoV-2: 29.3 IU/ml, influenza-A: 179.9 cp/ml, influenza-B: 333.9 cp/ml and RSV: 283.1 cp/ml. LoDs of other pathogens ranged between 9.4 cp/ml (hCoV-NL63) and 21,419 cp/ml (HPIV-2). Linearity was verified over 4-7 log-steps with pooled standard differentials (SD) ranging between 0.18-0.70ct. Inter-/intra-run variability (precision) was assessed for all targets over 3 days. SDs ranged between 0.13-0.74ct. Positive agreement in clinical samples was 99.4 % and 95 % for SARS-CoV-2 and influenza-A respectively. Other targets were in the 80-100 % range. Negative agreement varied between 96.3-100 %. DISCUSSION Lab-developed tests are a key factor for effective clinical diagnostics. The multiplex panel presented in this study demonstrated high performance and provides an easily scalable high-throughput solution for respiratory virus testing, e.g. for testing in high-risk patient populations.
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Affiliation(s)
- Hui Ting Tang
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Dominik Nörz
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Moritz Grunwald
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Katja Giersch
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Susanne Pfefferle
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Nicole Fischer
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Martin Aepfelbacher
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Holger Rohde
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Marc Lütgehetmann
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany.
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2
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Xia C, Wang T, Hahm B. Triggering Degradation of Host Cellular Proteins for Robust Propagation of Influenza Viruses. Int J Mol Sci 2024; 25:4677. [PMID: 38731896 PMCID: PMC11083682 DOI: 10.3390/ijms25094677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Following infection, influenza viruses strive to establish a new host cellular environment optimized for efficient viral replication and propagation. Influenza viruses use or hijack numerous host factors and machinery not only to fulfill their own replication process but also to constantly evade the host's antiviral and immune response. For this purpose, influenza viruses appear to have formulated diverse strategies to manipulate the host proteins or signaling pathways. One of the most effective tactics is to specifically induce the degradation of the cellular proteins that are detrimental to the virus life cycle. Here, we summarize the cellular factors that are deemed to have been purposefully degraded by influenza virus infection. The focus is laid on the mechanisms for the protein ubiquitination and degradation in association with facilitated viral amplification. The fate of influenza viral infection of hosts is heavily reliant on the outcomes of the interplay between the virus and the host antiviral immunity. Understanding the processes of how influenza viruses instigate the protein destruction pathways could provide a foundation for the development of advanced therapeutics to target host proteins and conquer influenza.
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Affiliation(s)
- Chuan Xia
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Ting Wang
- Department of Bioengineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China;
| | - Bumsuk Hahm
- Departments of Surgery & Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212, USA
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3
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Fanshawe TR, Tonner S, Turner PJ, Cogdale J, Glogowska M, de Lusignan S, Okusi C, Perera R, Sebastianpillai P, Williams A, Zambon M, Nicholson BD, Hobbs FDR, Hayward GN. Diagnostic accuracy of a point-of-care antigen test for SARS-CoV-2 and influenza in a primary care population (RAPTOR-C19). Clin Microbiol Infect 2024; 30:380-386. [PMID: 38103638 DOI: 10.1016/j.cmi.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/20/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
OBJECTIVES Limited evidence exists for the diagnostic performance of point-of-care tests for SARS-CoV-2 and influenza in community healthcare. We carried out a prospective diagnostic accuracy study of the LumiraDx™ SARS-CoV-2 and influenza A or B assay in primary care. METHODS Total of 913 adults and children with symptoms of current SARS-CoV-2 infection were recruited from 18 UK primary care practices during a period when Omicron was the predominant COVID variant of concern (June 2022 to December 2022). Trained health care staff performed the index test, with diagnostic accuracy parameters estimated for SARS-CoV-2 and influenza against real-time reverse-transcription PCR (rtRT-PCR). RESULTS 151/887 participants were SARS-CoV-2 rtRT-PCR positive, 109 positive for Influenza A, 6 for Influenza B. Index test sensitivity for SARS-CoV-2 was 80.8% (122 of the 151, 95% CI, 73.6-86.7%) and specificity 98.9% (728 of the 736, 95% CI, 97.9-99.5%). For influenza A, sensitivity was 61.5% (67 of the 109, 95% CI, 51.7-70.6%) and specificity 99.4% (771 of the 776, 95% CI, 98.5-99.8%). Sensitivity to detect SARS-CoV-2 and influenza dropped sharply at rtRT-PCR cycle thresholds (Ct) > 30. DISCUSSIONS The LumiraDx™ SARS-CoV-2 and influenza A/B assay had moderate sensitivity for SARS-CoV-2 in symptomatic patients in primary care, with lower performance with high rtRT-PCR Ct. Negative results in this patient group cannot definitively rule out SARS-CoV-2 or influenza.
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Affiliation(s)
- Thomas R Fanshawe
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK.
| | - Sharon Tonner
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Philip J Turner
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Jade Cogdale
- Virus Reference Department, Respiratory Virus Unit, UK Health Security Agency, UK
| | - Margaret Glogowska
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Simon de Lusignan
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Cecilia Okusi
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Rafael Perera
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Praveen Sebastianpillai
- Immunization and Vaccine Preventable Diseases Division and Public Health Programmes, UK Health Security Agency, UK
| | - Alice Williams
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Maria Zambon
- Influenza and Respiratory Virology and Polio Reference Service, UK Health Security Agency, UK; NIHR Health Protection Research Unit, Imperial College London, UK
| | - Brian D Nicholson
- Virus Reference Department, Respiratory Virus Unit, UK Health Security Agency, UK
| | - F D Richard Hobbs
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; Virus Reference Department, Respiratory Virus Unit, UK Health Security Agency, UK
| | - Gail N Hayward
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; Virus Reference Department, Respiratory Virus Unit, UK Health Security Agency, UK
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4
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Trick AY, Chen F, Chen L, Lee P, Hasnain AC, Mostafa HH, Carroll KC, Wang T. Point-of-Care Platform for Rapid Multiplexed Detection of SARS-CoV-2 Variants and Respiratory Pathogens. ADVANCED MATERIALS TECHNOLOGIES 2022; 7:2101013. [PMID: 35441089 PMCID: PMC9011450 DOI: 10.1002/admt.202101013] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/20/2021] [Indexed: 05/25/2023]
Abstract
The rise of highly transmissible SARS-CoV-2 variants brings new challenges and concerns with vaccine efficacy, diagnostic sensitivity, and public health responses to end the pandemic. Widespread detection of variants is critical to inform policy decisions to mitigate further spread, and postpandemic multiplexed screening of respiratory viruses will be necessary to properly manage patients presenting with similar respiratory symptoms. In this work, a portable, magnetofluidic cartridge platform for automated polymerase chain reaction testing in <30 min is developed. Cartridges are designed for multiplexed detection of SARS-CoV-2 with either identification of variant mutations or screening for Influenza A and B. Moreover, the platform can perform identification of B.1.1.7 and B.1.351 variants and the multiplexed SARS-CoV-2/Influenza assay using archived clinical nasopharyngeal swab eluates and saliva samples. This work illustrates a path toward affordable and immediate testing with potential to aid surveillance of viral variants and inform patient treatment.
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Affiliation(s)
- Alexander Y. Trick
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
| | - Fan‐En Chen
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
| | - Liben Chen
- Department of Mechanical EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
| | - Pei‐Wei Lee
- Department of Mechanical EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
| | | | - Heba H. Mostafa
- Division of Medical MicrobiologyDepartment of PathologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Karen C. Carroll
- Division of Medical MicrobiologyDepartment of PathologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Tza‐Huei Wang
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
- Department of Mechanical EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
- Institute for NanoBiotechnologyJohns Hopkins UniversityBaltimoreMD21218USA
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5
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How Influenza A Virus NS1 Deals with the Ubiquitin System to Evade Innate Immunity. Viruses 2021; 13:v13112309. [PMID: 34835115 PMCID: PMC8619935 DOI: 10.3390/v13112309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/14/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022] Open
Abstract
Ubiquitination is a post-translational modification regulating critical cellular processes such as protein degradation, trafficking and signaling pathways, including activation of the innate immune response. Therefore, viruses, and particularly influenza A virus (IAV), have evolved different mechanisms to counteract this system to perform proper infection. Among IAV proteins, the non-structural protein NS1 is shown to be one of the main virulence factors involved in these viral hijackings. NS1 is notably able to inhibit the host's antiviral response through the perturbation of ubiquitination in different ways, as discussed in this review.
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6
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Δ133p53β isoform pro-invasive activity is regulated through an aggregation-dependent mechanism in cancer cells. Nat Commun 2021; 12:5463. [PMID: 34526502 PMCID: PMC8443592 DOI: 10.1038/s41467-021-25550-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 08/04/2021] [Indexed: 11/09/2022] Open
Abstract
The p53 isoform, Δ133p53β, is critical in promoting cancer. Here we report that Δ133p53β activity is regulated through an aggregation-dependent mechanism. Δ133p53β aggregates were observed in cancer cells and tumour biopsies. The Δ133p53β aggregation depends on association with interacting partners including p63 family members or the CCT chaperone complex. Depletion of the CCT complex promotes accumulation of Δ133p53β aggregates and loss of Δ133p53β dependent cancer cell invasion. In contrast, association with p63 family members recruits Δ133p53β from aggregates increasing its intracellular mobility. Our study reveals novel mechanisms of cancer progression for p53 isoforms which are regulated through sequestration in aggregates and recruitment upon association with specific partners like p63 isoforms or CCT chaperone complex, that critically influence cancer cell features like EMT, migration and invasion.
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7
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Kwan PKW, Cross GB, Naftalin CM, Ahidjo BA, Mok CK, Fanusi F, Permata Sari I, Chia SC, Kumar SK, Alagha R, Tham SM, Archuleta S, Sessions OM, Hibberd ML, Paton NI. A blood RNA transcriptome signature for COVID-19. BMC Med Genomics 2021; 14:155. [PMID: 34116667 PMCID: PMC8193593 DOI: 10.1186/s12920-021-01006-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/04/2021] [Indexed: 12/13/2022] Open
Abstract
Background COVID-19 is a respiratory viral infection with unique features including a more chronic course and systemic disease manifestations including multiple organ involvement; and there are differences in disease severity between ethnic groups. The immunological basis for disease has not been fully characterised. Analysis of whole-blood RNA expression may provide valuable information on disease pathogenesis.
Methods We studied 45 patients with confirmed COVID-19 infection within 10 days from onset of illness and a control group of 19 asymptomatic healthy volunteers with no known exposure to COVID-19 in the previous 14 days. Relevant demographic and clinical information was collected and a blood sample was drawn from all participants for whole-blood RNA sequencing. We evaluated differentially-expressed genes in COVID-19 patients (log2 fold change ≥ 1 versus healthy controls; false-discovery rate < 0.05) and associated protein pathways and compared these to published whole-blood signatures for respiratory syncytial virus (RSV) and influenza. We developed a disease score reflecting the overall magnitude of expression of internally-validated genes and assessed the relationship between the disease score and clinical disease parameters. Results We found 135 differentially-expressed genes in the patients with COVID-19 (median age 35 years; 82% male; 36% Chinese, 53% South Asian ethnicity). Of the 117 induced genes, 14 were found in datasets from RSV and 40 from influenza; 95 genes were unique to COVID-19. Protein pathways were mostly generic responses to viral infections, including apoptosis by P53-associated pathway, but also included some unique pathways such as viral carcinogenesis. There were no major qualitative differences in pathways between ethnic groups. The composite gene-expression score was correlated with the time from onset of symptoms and nasal swab qPCR CT values (both p < 0.01) but was not related to participant age, gender, ethnicity or the presence or absence of chest X-ray abnormalities (all p > 0.05). Conclusions The whole-blood transcriptome of COVID-19 has overall similarity with other respiratory infections but there are some unique pathways that merit further exploration to determine clinical relevance. The approach to a disease score may be of value, but needs further validation in a population with a greater range of disease severity. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01006-w.
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Affiliation(s)
- Philip Kam Weng Kwan
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Gail B Cross
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore.,Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Claire M Naftalin
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Bintou A Ahidjo
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore.,Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Chee Keng Mok
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore.,Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Felic Fanusi
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Intan Permata Sari
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Siok Ching Chia
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Shoban Krishna Kumar
- Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Rawan Alagha
- Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Sai Meng Tham
- Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Sophia Archuleta
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore.,Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - October M Sessions
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Martin L Hibberd
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore.,London School of Hygiene and Tropical Medicine, London, UK
| | - Nicholas I Paton
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore. .,Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore. .,London School of Hygiene and Tropical Medicine, London, UK. .,Infectious Diseases Translational Research Programme, National University of Singapore, Singapore, Singapore. .,Infectious Diseases Translational Research Programme and Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block Level 10, 1E Kent Ridge Road, Singapore, 119228, Singapore.
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8
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Trick AY, Chen FE, Chen L, Lee PW, Hasnain AC, Mostafa HH, Carroll KC, Wang TH. Magnetofluidic platform for rapid multiplexed screening of SARS-CoV-2 variants and respiratory pathogens. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.10.21256995. [PMID: 34013284 PMCID: PMC8132258 DOI: 10.1101/2021.05.10.21256995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The rise of highly transmissible SARS-CoV-2 variants brings new challenges and concerns with vaccine efficacy, diagnostic sensitivity, and public health responses in the fight to end the pandemic. Widespread detection of variant strains will be critical to inform policy decisions to mitigate further spread, and post-pandemic multiplexed screening of respiratory viruses will be necessary to properly manage patients presenting with similar respiratory symptoms. In this work, we have developed a portable, magnetofluidic cartridge platform for automated PCR testing in <30 min. Cartridges were designed for multiplexed detection of SARS-CoV-2 with either distinctive variant mutations or with Influenza A and B. The platform demonstrated a limit of detection down to 2 copies/µL SARS-CoV-2 RNA with successful identification of B.1.1.7 and B.1.351 variants. The multiplexed SARS-CoV-2/Flu assay was validated using archived clinical nasopharyngeal swab eluates ( n = 116) with an overall sensitivity/specificity of 98.1%/95.2%, 85.7%/100%, 100%/98.2%, respectively, for SARS-CoV-2, Influenza A, and Influenza B. Further testing with saliva ( n = 14) demonstrated successful detection of all SARS-CoV-2 positive samples with no false-positives.
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Affiliation(s)
- Alexander Y Trick
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Liben Chen
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Pei-Wei Lee
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alexander C Hasnain
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBiotechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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9
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Nörz D, Hoffmann A, Aepfelbacher M, Pfefferle S, Lütgehetmann M. Clinical evaluation of a fully automated, laboratory-developed multiplex RT-PCR assay integrating dual-target SARS-CoV-2 and influenza A/B detection on a high-throughput platform. J Med Microbiol 2021; 70. [PMID: 33404401 PMCID: PMC8131019 DOI: 10.1099/jmm.0.001295] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Introduction. Laboratories worldwide are facing high demand for molecular testing during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, which might be further aggravated by the upcoming influenza season in the northern hemisphere.Gap Statement. Given that the symptoms of influenza are largely indistinguishable from those of coronavirus disease 2019 (COVID-19), both SARS-CoV-2 and the influenza viruses require concurrent testing by RT-PCR in patients presenting with symptoms of respiratory tract infection.Aim. We adapted and evaluated a laboratory-developed multiplex RT-PCR assay for simultaneous detection of SARS-CoV-2 (dual target), influenza A and influenza B (SC2/InflA/InflB-UCT) on a fully automated high-throughput system (cobas6800).Methodology. Analytical performance was assessed by serial dilution of quantified reference material and cell culture stocks in transport medium, including pretreatment for chemical inactivation. For clinical evaluation, residual portions of 164 predetermined patient samples containing SARS-CoV-2 (n=52), influenza A (n=43) or influenza B (n=19), as well as a set of negative samples, were subjected to the novel multiplex assay.Results. The assay demonstrated comparable analytical performance to currently available commercial tests, with limits of detection of 94.9 cp ml-1 for SARS-CoV-2, 14.6 cp ml-1 for influenza A and 422.3 cp ml-1 for influenza B. Clinical evaluation showed excellent agreement with the comparator assays (sensitivity of 98.1, 97.7 and 100 % for Sars-CoV-2 and influenza A and B, respectively).Conclusion. The SC2/InflA/InflB-UCT allows for efficient high-throughput testing for all three pathogens and thus provides streamlined diagnostics while conserving resources during the influenza season.
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Affiliation(s)
- Dominik Nörz
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Armin Hoffmann
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Martin Aepfelbacher
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Susanne Pfefferle
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Marc Lütgehetmann
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
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10
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Sajuthi SP, DeFord P, Li Y, Jackson ND, Montgomery MT, Everman JL, Rios CL, Pruesse E, Nolin JD, Plender EG, Wechsler ME, Mak ACY, Eng C, Salazar S, Medina V, Wohlford EM, Huntsman S, Nickerson DA, Germer S, Zody MC, Abecasis G, Kang HM, Rice KM, Kumar R, Oh S, Rodriguez-Santana J, Burchard EG, Seibold MA. Type 2 and interferon inflammation regulate SARS-CoV-2 entry factor expression in the airway epithelium. Nat Commun 2020; 11:5139. [PMID: 33046696 PMCID: PMC7550582 DOI: 10.1038/s41467-020-18781-2] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/08/2020] [Indexed: 11/08/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2, an emerging virus that utilizes host proteins ACE2 and TMPRSS2 as entry factors. Understanding the factors affecting the pattern and levels of expression of these genes is important for deeper understanding of SARS-CoV-2 tropism and pathogenesis. Here we explore the role of genetics and co-expression networks in regulating these genes in the airway, through the analysis of nasal airway transcriptome data from 695 children. We identify expression quantitative trait loci for both ACE2 and TMPRSS2, that vary in frequency across world populations. We find TMPRSS2 is part of a mucus secretory network, highly upregulated by type 2 (T2) inflammation through the action of interleukin-13, and that the interferon response to respiratory viruses highly upregulates ACE2 expression. IL-13 and virus infection mediated effects on ACE2 expression were also observed at the protein level in the airway epithelium. Finally, we define airway responses to common coronavirus infections in children, finding that these infections generate host responses similar to other viral species, including upregulation of IL6 and ACE2. Our results reveal possible mechanisms influencing SARS-CoV-2 infectivity and COVID-19 clinical outcomes.
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Grants
- R01 ES015794 NIEHS NIH HHS
- R01 HL120393 NHLBI NIH HHS
- HL128439 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL141992 NHLBI NIH HHS
- UM1 HG008901 NHGRI NIH HHS
- R01 HL141845 NHLBI NIH HHS
- HL107202 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- HHSN268201800001C NHLBI NIH HHS
- U01 HG009080 NHGRI NIH HHS
- HL138626 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL117626 NHLBI NIH HHS
- HL135156 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- HL132821 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P01 HL107202 NHLBI NIH HHS
- K01 HL140218 NHLBI NIH HHS
- U01 HL120393 NHLBI NIH HHS
- HL117004 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL135156 NHLBI NIH HHS
- T32 GM007546 NIGMS NIH HHS
- MD010443 U.S. Department of Health & Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)
- R01 HL128439 NHLBI NIH HHS
- R01 HL117004 NHLBI NIH HHS
- P60 MD006902 NIMHD NIH HHS
- HHSN268201600032C NHLBI NIH HHS
- U24 HG008956 NHGRI NIH HHS
- P01 HL132821 NHLBI NIH HHS
- R01 MD010443 NIMHD NIH HHS
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Affiliation(s)
- Satria P Sajuthi
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Peter DeFord
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Yingchun Li
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Nathan D Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Michael T Montgomery
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Jamie L Everman
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Cydney L Rios
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Elmar Pruesse
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - James D Nolin
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Elizabeth G Plender
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | | | - Angel C Y Mak
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sandra Salazar
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Vivian Medina
- Centro de Neumología Pediátrica, San Juan, Puerto Rico
| | - Eric M Wohlford
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Division of Pediatric Allergy and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Northwest Genomics Center, Seattle, WA, USA
- Brotman Baty Institute, Seattle, WA, USA
| | | | | | - Gonçalo Abecasis
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Hyun Min Kang
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Rajesh Kumar
- Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University, Chicago, IL, USA
| | - Sam Oh
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.
- Department of Pediatrics, National Jewish Health, Denver, CO, USA.
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado-AMC, Aurora, CO, USA.
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11
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Jang WS, Lim DH, Nam J, Mihn DC, Sung HW, Lim CS, Kim J. Development of a multiplex isothermal amplification molecular diagnosis method for on-site diagnosis of influenza. PLoS One 2020; 15:e0238615. [PMID: 32915821 PMCID: PMC7485819 DOI: 10.1371/journal.pone.0238615] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/20/2020] [Indexed: 01/30/2023] Open
Abstract
Influenza, which is an acute respiratory disease caused by the influenza virus, represents a worldwide public health and economic problem owing to the significant morbidity and mortality caused by its seasonal epidemics and pandemics. Sensitive and convenient methodologies for the detection of influenza viruses are important for clinical care and infection control as well as epidemiological investigations. Here, we developed a multiplex reverse transcription loop-mediated isothermal amplification (RT-LAMP) with quencher/fluorescence oligonucleotides connected by a 5' backward loop (LF or LB) primer for the detection of two subtypes of influenza viruses: Influenza A (A/H1 and A/H3) and influenza B. The detection limits of the multiplex RT-LAMP assay were 103 copies and 102 copies of RNA for influenza A and influenza B, respectively. The sensitivities of the multiplex influenza A/B/IC RT-LAMP assay were 94.62% and 97.50% for influenza A and influenza B clinical samples, respectively. The specificities of the multiplex influenza A/B/IC RT-LAMP assay were 100% for influenza A, influenza B, and healthy clinical samples. In addition, the multiplex influenza A/B/IC RT-LAMP assay had no cross-reactivity with other respiratory viruses.
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Affiliation(s)
- Woong Sik Jang
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Da Hye Lim
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jeonghun Nam
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Do-CiC Mihn
- Department of Diagnostic Immunology, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Haan Woo Sung
- Department of Veterinary Microbiology, College of Veterinary Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jeeyong Kim
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
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12
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Nilsson K, Abdurahman S, Schwartz S. Influenza virus natural sequence heterogeneity in segment 8 affects interactions with cellular RNA-binding proteins and splicing efficiency. Virology 2020; 549:39-50. [PMID: 32829114 DOI: 10.1016/j.virol.2020.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 11/18/2022]
Abstract
Segment 8 mRNAs of influenza virus A/Brevig Misson/1918/1 (H1N1) are poorly spliced compared to segment 8 mRNAs of influenza virus A/Netherlands/178/95 (H3N2). Using oligonucleotide-mediated protein pull down with oligos spanning the entire length of segment 8 of either influenza virus H1N1 or influenza virus H3N2 we identified cellular RNA binding proteins that interacted with oligonucleotides derived from either H1N1 or H3N2 sequences. When the identified hot spots for RNA binding proteins in H1N1 segment 8 mRNAs were replaced by H3N2 sequences, splicing efficiency increased significantly. Replacing as few as three nucleotides of the H1N1 mRNA with sequences from H3N2 mRNA, enhanced splicing of the H1N1 mRNAs. Cellular proteins U2AF65 and HuR interacted preferentially with the 3'-splice site of H3N2 and overexpression of HuR reduced the levels of unspliced H1N1 mRNAs, suggesting that U2AF65 and HuR contribute to control of influenza virus mRNA splicing.
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MESH Headings
- A549 Cells
- Alternative Splicing
- ELAV-Like Protein 1/genetics
- ELAV-Like Protein 1/metabolism
- Genetic Variation
- HeLa Cells
- Host-Pathogen Interactions/genetics
- Humans
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/metabolism
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/metabolism
- Oligonucleotides/chemistry
- Oligonucleotides/metabolism
- Plasmids/chemistry
- Plasmids/metabolism
- Protein Binding
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Splicing Factor U2AF/genetics
- Splicing Factor U2AF/metabolism
- Transfection
- Viral Nonstructural Proteins/genetics
- Viral Nonstructural Proteins/metabolism
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Affiliation(s)
- Kersti Nilsson
- Department of Laboratory Medicine, BMC-B13, Lund University, 221 84, Lund, Sweden
| | - Samir Abdurahman
- Department of Science and Technology, Örebro University, 701 82, Örebro, Sweden
| | - Stefan Schwartz
- Department of Laboratory Medicine, BMC-B13, Lund University, 221 84, Lund, Sweden.
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13
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Sajuthi SP, DeFord P, Jackson ND, Montgomery MT, Everman JL, Rios CL, Pruesse E, Nolin JD, Plender EG, Wechsler ME, Mak ACY, Eng C, Salazar S, Medina V, Wohlford EM, Huntsman S, Nickerson DA, Germer S, Zody MC, Abecasis G, Kang HM, Rice KM, Kumar R, Oh S, Rodriguez-Santana J, Burchard EG, Seibold MA. Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.09.034454. [PMID: 32511326 PMCID: PMC7239056 DOI: 10.1101/2020.04.09.034454] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Coronavirus disease 2019 (COVID-19) outcomes vary from asymptomatic infection to death. This disparity may reflect different airway levels of the SARS-CoV-2 receptor, ACE2, and the spike protein activator, TMPRSS2. Here we explore the role of genetics and co-expression networks in regulating these genes in the airway, through the analysis of nasal airway transcriptome data from 695 children. We identify expression quantitative trait loci (eQTL) for both ACE2 and TMPRSS2, that vary in frequency across world populations. Importantly, we find TMPRSS2 is part of a mucus secretory network, highly upregulated by T2 inflammation through the action of interleukin-13, and that interferon response to respiratory viruses highly upregulates ACE2 expression. Finally, we define airway responses to coronavirus infections in children, finding that these infections upregulate IL6 while also stimulating a more pronounced cytotoxic immune response relative to other respiratory viruses. Our results reveal mechanisms likely influencing SARS-CoV-2 infectivity and COVID-19 clinical outcomes.
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Affiliation(s)
- Satria P. Sajuthi
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - Peter DeFord
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - Nathan D. Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - Michael T. Montgomery
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - Jamie L. Everman
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - Cydney L. Rios
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - Elmar Pruesse
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - James D. Nolin
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | - Elizabeth G. Plender
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
| | | | - Angel CY Mak
- Department of Medicine, Therapeutic Sciences University of California San Francisco, San Francisco, CA
| | - Celeste Eng
- Department of Medicine, Therapeutic Sciences University of California San Francisco, San Francisco, CA
| | - Sandra Salazar
- Department of Medicine, Therapeutic Sciences University of California San Francisco, San Francisco, CA
| | - Vivian Medina
- Centro de Neumología Pediátrica, San Juan, Puerto Rico
| | - Eric M. Wohlford
- Department of Medicine, Therapeutic Sciences University of California San Francisco, San Francisco, CA
- Division of Pediatric Allergy and Immunology, Therapeutic Sciences University of California San Francisco, San Francisco, CA
| | - Scott Huntsman
- Department of Medicine, Therapeutic Sciences University of California San Francisco, San Francisco, CA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Northwest Genomics Center, Seattle, WA, USA
- Brotman Baty Institute, Seattle, WA, USA
| | | | | | - Gonçalo Abecasis
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Hyun Min Kang
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Kenneth M. Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Rajesh Kumar
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, III
| | - Sam Oh
- Department of Medicine, Therapeutic Sciences University of California San Francisco, San Francisco, CA
| | | | - Esteban G. Burchard
- Department of Medicine, Therapeutic Sciences University of California San Francisco, San Francisco, CA
- Department of Bioengineering and Therapeutic Sciences University of California San Francisco, San Francisco, CA
| | - Max A. Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206 USA
- Department of Pediatrics, National Jewish Health, Denver, CO, 80206 USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado-AMC, Aurora, CO, 80045 USA
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14
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Dubois J, Rosa-Calatrava M, Terrier O. Un mécanisme inédit de détournement viro-induit de p53 dans le contexte de l’infection par les virus influenza. Med Sci (Paris) 2020; 36:106-108. [DOI: 10.1051/medsci/2020004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Characterization of cellular transcriptomic signatures induced by different respiratory viruses in human reconstituted airway epithelia. Sci Rep 2019; 9:11493. [PMID: 31391513 PMCID: PMC6685967 DOI: 10.1038/s41598-019-48013-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/29/2019] [Indexed: 11/17/2022] Open
Abstract
Acute respiratory infections, a large part being of viral origin, constitute a major public health issue. To propose alternative and/or new therapeutic approaches, it is necessary to increase our knowledge about the interactions between respiratory viruses and their primary cellular targets using the most biologically relevant experimental models. In this study, we used RNAseq to characterize and compare the transcriptomic signature of infection induced by different major respiratory viruses (Influenza viruses, hRSV and hMPV) in a model of reconstituted human airway epithelia. Our results confirm the importance of several cellular pathways commonly or specifically induced by these respiratory viruses, such as the innate immune response or antiviral defense. A very interesting common feature revealed by the global virogenomic signature shared between hRSV, hMPV and influenza viruses is the global downregulation of cilium-related gene expression, in good agreement with experimental evaluation of mucociliary clearance. Beyond providing new information about respiratory virus/host interactions, our study also underlines the interest of using biologically relevant experimental models to study human respiratory viruses.
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16
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Wu H, Zhang S, Huo C, Zou S, Lian Z, Hu Y. iTRAQ-based proteomic and bioinformatic characterization of human mast cells upon infection by the influenza A virus strains H1N1 and H5N1. FEBS Lett 2019; 593:2612-2627. [PMID: 31271652 DOI: 10.1002/1873-3468.13523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/26/2019] [Accepted: 06/19/2019] [Indexed: 12/12/2022]
Abstract
Mast cells can support the replication of influenza A virus, although how this occurs is poorly understood. In the present study, using quantitative MS, we analyzed the proteome of human mast cells infected with different influenza A virus strains at 12 h post-infection. Forty-one differentially expressed proteins were identified in human mast cells upon infection by the virulent H5N1 (A/Chicken/Henan/1/04) virus compared to the seasonal H1N1 (A/WSN/33) virus. Bioinformatic analyses confirmed that H1N1 significantly regulates the RNA degradation pathway via up-regulation of CCR4-NOT transcription complex subunit 4, whereas apoptosis could be suppressed by H5N1 via down-regulation of the tumor protein p53 signaling pathway with P ≤ 0.05 at 12 h post-infection. The hypoxia-inducible factor-1 signaling pathway of human mast cells is more susceptible to infection by H5N1 than by H1N1 virus.
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Affiliation(s)
- Hongping Wu
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shouping Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
| | - Caiyun Huo
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shumei Zou
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, China
| | - Zhengxing Lian
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yanxin Hu
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
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17
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The Nonstructural NS1 Protein of Influenza Viruses Modulates TP53 Splicing through Host Factor CPSF4. J Virol 2019; 93:JVI.02168-18. [PMID: 30651364 DOI: 10.1128/jvi.02168-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/04/2019] [Indexed: 12/14/2022] Open
Abstract
Influenza A viruses (IAV) are known to modulate and "hijack" several cellular host mechanisms, including gene splicing and RNA maturation machineries. These modulations alter host cellular responses and enable an optimal expression of viral products throughout infection. The interplay between the host protein p53 and IAV, in particular through the viral nonstructural protein NS1, has been shown to be supportive for IAV replication. However, it remains unknown whether alternatively spliced isoforms of p53, known to modulate p53 transcriptional activity, are affected by IAV infection and contribute to IAV replication. Using a TP53 minigene, which mimics intron 9 alternative splicing, we have shown here that the NS1 protein of IAV changes the expression pattern of p53 isoforms. Our results demonstrate that CPSF4 (cellular protein cleavage and polyadenylation specificity factor 4) independently and the interaction between NS1 and CPSF4 modulate the alternative splicing of TP53 transcripts, which may result in the differential activation of p53-responsive genes. Finally, we report that CPSF4 and most likely beta and gamma spliced p53 isoforms affect both viral replication and IAV-associated type I interferon secretion. All together, our data show that cellular p53 and CPSF4 factors, both interacting with viral NS1, have a crucial role during IAV replication that allows IAV to interact with and alter the expression of alternatively spliced p53 isoforms in order to regulate the cellular innate response, especially via type I interferon secretion, and perform efficient viral replication.IMPORTANCE Influenza A viruses (IAV) constitute a major public health issue, causing illness and death in high-risk populations during seasonal epidemics or pandemics. IAV are known to modulate cellular pathways to promote their replication and avoid immune restriction via the targeting of several cellular proteins. One of these proteins, p53, is a master regulator involved in a large panel of biological processes, including cell cycle arrest, apoptosis, or senescence. This "cellular gatekeeper" is also involved in the control of viral infections, and viruses have developed a wide diversity of mechanisms to modulate/hijack p53 functions to achieve an optimal replication in their hosts. Our group and others have previously shown that p53 activity is finely modulated by different multilevel mechanisms during IAV infection. Here, we characterized IAV nonstructural protein NS1 and the cellular factor CPSF4 as major partners involved in the IAV-induced modulation of the TP53 alternative splicing that was associated with a strong modulation of p53 activity and notably the p53-mediated antiviral response.
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18
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Kim JW, Lee CY, Nguyen TT, Kim IH, Kwon HJ, Kim JH. An optimized molecular method for detection of influenza A virus using improved generic primers and concentration of the viral genomic RNA and nucleoprotein complex. J Vet Diagn Invest 2019; 31:175-183. [PMID: 30795722 DOI: 10.1177/1040638719830760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
For reported primer sets used to detect influenza A viruses (IAVs), we verified the nucleotide identities with 9,103 complete sequences of matrix (M) genes. At best, only 93.2% and 85.3% of the sequences had a 100% match with reported forward and reverse primers, respectively. Therefore, we designed new degenerate forward and reverse primers with 100% identity to 94.4% and 96.2% of compared genes, respectively, and the primer set was used with SYBR-based reverse-transcription real-time PCR (SYBR-RT-rtPCR) for lower detection limits. The sensitivity of SYBR-RT-rtPCR with the new primers was 10-fold higher than that with a conventional method in ~2.37% of all M genes in the database used in our study. We successfully increased the sensitivity of SYBR-RT-rtPCR by concentrating the viral ribonucleoprotein (RNP) using immunomagnetic beads and Triton X-100. The improved generic primer set and RNP concentration method may be useful for sensitive detection of IAVs.
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Affiliation(s)
- Ji-Woon Kim
- Laboratory of Avian Diseases (J-W Kim, Lee, Nguyen, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Department of Farm Animal Medicine (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Farm Animal Clinical Training and Research Center, Institutes of Green Bio Science and Technology (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Research Institute for Veterinary Science (Kwon, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Cheongju, Republic of Korea (I-H Kim)
| | - Chung-Young Lee
- Laboratory of Avian Diseases (J-W Kim, Lee, Nguyen, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Department of Farm Animal Medicine (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Farm Animal Clinical Training and Research Center, Institutes of Green Bio Science and Technology (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Research Institute for Veterinary Science (Kwon, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Cheongju, Republic of Korea (I-H Kim)
| | - Thanh Trung Nguyen
- Laboratory of Avian Diseases (J-W Kim, Lee, Nguyen, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Department of Farm Animal Medicine (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Farm Animal Clinical Training and Research Center, Institutes of Green Bio Science and Technology (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Research Institute for Veterinary Science (Kwon, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Cheongju, Republic of Korea (I-H Kim)
| | - Il-Hwan Kim
- Laboratory of Avian Diseases (J-W Kim, Lee, Nguyen, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Department of Farm Animal Medicine (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Farm Animal Clinical Training and Research Center, Institutes of Green Bio Science and Technology (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Research Institute for Veterinary Science (Kwon, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Cheongju, Republic of Korea (I-H Kim)
| | - Hyuk-Joon Kwon
- Laboratory of Avian Diseases (J-W Kim, Lee, Nguyen, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Department of Farm Animal Medicine (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Farm Animal Clinical Training and Research Center, Institutes of Green Bio Science and Technology (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Research Institute for Veterinary Science (Kwon, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Cheongju, Republic of Korea (I-H Kim)
| | - Jae-Hong Kim
- Laboratory of Avian Diseases (J-W Kim, Lee, Nguyen, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Department of Farm Animal Medicine (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Farm Animal Clinical Training and Research Center, Institutes of Green Bio Science and Technology (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Research Institute for Veterinary Science (Kwon, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Cheongju, Republic of Korea (I-H Kim)
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19
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De Vlugt C, Sikora D, Pelchat M. Insight into Influenza: A Virus Cap-Snatching. Viruses 2018; 10:v10110641. [PMID: 30453478 PMCID: PMC6266781 DOI: 10.3390/v10110641] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/12/2018] [Accepted: 11/15/2018] [Indexed: 12/27/2022] Open
Abstract
The influenza A virus (IAV) genome consists of eight single-stranded RNA segments. Each segment is associated with a protein complex, with the 3′ and 5′ ends bound to the RNA-dependent RNA polymerase (RdRp) and the remainder associated with the viral nucleoprotein. During transcription of viral mRNA, this ribonucleoprotein complex steals short, 5′-capped transcripts produced by the cellular DNA dependent RNA polymerase II (RNAPII) and uses them to prime transcription of viral mRNA. Here, we review the current knowledge on the process of IAV cap-snatching and suggest a requirement for RNAPII promoter-proximal pausing for efficient IAV mRNA transcription.
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Affiliation(s)
- Corey De Vlugt
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - Dorota Sikora
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - Martin Pelchat
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
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20
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Machado D, Pizzorno A, Hoffmann J, Traversier A, Endtz H, Lina B, Rosa-Calatrava M, Paranhos-Baccala G, Terrier O. Role of p53/NF-κB functional balance in respiratory syncytial virus-induced inflammation response. J Gen Virol 2018; 99:489-500. [PMID: 29504924 DOI: 10.1099/jgv.0.001040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The interplay between respiratory syncytial virus (RSV) and the p53 pathway has only been reported in a limited number of studies, yet the underlying abrogation mechanisms of p53 activity during the time course of infection, possibly involving viral proteins, remained unclear. Here, we demonstrate that RSV infection impairs global p53 transcriptional activity, notably via its proteasome-dependent degradation at late stages of infection. We also demonstrate that NS1 and NS2 contribute to the abrogation of p53 activity, and used different experimental strategies (e.g. siRNA, small molecules) to underline the antiviral contribution of p53 in the context of RSV infection. Notably, our study highlights a strong RSV-induced disequilibrium of the p53/NF-κB functional balance, which appears to contribute to the up-regulation of the expression of several proinflammatory cytokines and chemokines.
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Affiliation(s)
- Daniela Machado
- Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France.,Virologie et Pathologie Humaine - VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Andrés Pizzorno
- Virologie et Pathologie Humaine - VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Jonathan Hoffmann
- Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Aurélien Traversier
- Virologie et Pathologie Humaine - VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Hubert Endtz
- Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Bruno Lina
- Virologie et Pathologie Humaine - VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France.,Hospices Civils de Lyon, Centre National de Référence des Virus Influenza France Sud, Laboratoire de Virologie, Groupement Hospitalier Nord, Lyon, France
| | - Manuel Rosa-Calatrava
- Virologie et Pathologie Humaine - VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Gláucia Paranhos-Baccala
- Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France.,Present address: Center of Excellence for Tropical Infectious Diseases, Medical Diagnostic Discovery Department (MD3) bioMérieux, Brazil
| | - Olivier Terrier
- Virologie et Pathologie Humaine - VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
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21
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Pizzorno A, Dubois J, Machado D, Cartet G, Traversier A, Julien T, Lina B, Bourdon JC, Rosa-Calatrava M, Terrier O. Influenza A viruses alter the stability and antiviral contribution of host E3-ubiquitin ligase Mdm2 during the time-course of infection. Sci Rep 2018; 8:3746. [PMID: 29487367 PMCID: PMC5829072 DOI: 10.1038/s41598-018-22139-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/19/2018] [Indexed: 11/09/2022] Open
Abstract
The interplay between influenza A viruses (IAV) and the p53 pathway has been reported in several studies, highlighting the antiviral contribution of p53. Here, we investigated the impact of IAV on the E3-ubiquitin ligase Mdm2, a major regulator of p53, and observed that IAV targets Mdm2, notably via its non-structural protein (NS1), therefore altering Mdm2 stability, p53/Mdm2 interaction and regulatory loop during the time-course of infection. This study also highlights a new antiviral facet of Mdm2 possibly increasing the list of its many p53-independent functions. Altogether, our work contributes to better understand the mechanisms underlining the complex interactions between IAV and the p53 pathway, for which both NS1 and Mdm2 arise as key players.
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Affiliation(s)
- Andrés Pizzorno
- Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, CNRS UMR5308, France
| | - Julia Dubois
- Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, CNRS UMR5308, France
| | - Daniela Machado
- Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, CNRS UMR5308, France
- Laboratoire des Pathogènes Emergents, Fondation Mérieux. CIRI, UCBL1- INSERM U1111, ENS Lyon, CNRS UMR5308, Lyon, France
| | - Gaëlle Cartet
- Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, CNRS UMR5308, France
| | - Aurelien Traversier
- Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, CNRS UMR5308, France
| | - Thomas Julien
- Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, CNRS UMR5308, France
| | - Bruno Lina
- Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, CNRS UMR5308, France
- Laboratoire de Virologie, Centre National de Référence des virus Influenza, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France
| | - Jean-Christophe Bourdon
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Manuel Rosa-Calatrava
- Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, CNRS UMR5308, France
| | - Olivier Terrier
- Virologie et Pathologie Humaine-VirPath team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, CNRS UMR5308, France.
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22
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Sikora D, Rocheleau L, Brown EG, Pelchat M. Influenza A virus cap-snatches host RNAs based on their abundance early after infection. Virology 2017. [PMID: 28646652 DOI: 10.1016/j.virol.2017.06.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The influenza A virus RNA polymerase cleaves the 5' ends of host RNAs and uses these RNA fragments as primers for viral mRNA synthesis. We performed deep sequencing of the 5' host-derived ends of the eight viral mRNAs of influenza A/Puerto Rico/8/1934 (H1N1) virus in infected A549 cells, and compared the population to those of A/Hong Kong/1/1968 (H3N2) and A/WSN/1933 (H1N1). In the three strains, the viral RNAs target different populations of host RNAs. Host RNAs are cap-snatched based on their abundance, and we found that RNAs encoding proteins involved in metabolism are overrepresented in the cap-snatched populations. Because this overrepresentation could be a reflection of the host response early after infection, and thus of the increased availability of these transcripts, our results suggest that host RNAs are cap-snatched mainly based on their abundance without preferential targeting.
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Affiliation(s)
- Dorota Sikora
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Lynda Rocheleau
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Earl G Brown
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
| | - Martin Pelchat
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5.
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23
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Gao Z, Hu J, Liang Y, Yang Q, Yan K, Liu D, Wang X, Gu M, Liu X, Hu S, Hu Z, Liu H, Liu W, Chen S, Peng D, Jiao XA, Liu X. Generation and Comprehensive Analysis of Host Cell Interactome of the PA Protein of the Highly Pathogenic H5N1 Avian Influenza Virus in Mammalian Cells. Front Microbiol 2017; 8:739. [PMID: 28503168 PMCID: PMC5408021 DOI: 10.3389/fmicb.2017.00739] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/10/2017] [Indexed: 12/26/2022] Open
Abstract
Accumulating data have identified the important roles of PA protein in replication and pathogenicity of influenza A virus (IAV). Identification of host factors that interact with the PA protein may accelerate our understanding of IAV pathogenesis. In this study, using immunoprecipitation assay combined with liquid chromatography-tandem mass spectrometry, we identified 278 human cellular proteins that might interact with PA of H5N1 IAV. Gene Ontology annotation revealed that the identified proteins are highly associated with viral translation and replication. Further KEGG pathway analysis of the interactome profile highlighted cellular pathways associated with translation, infectious disease, and signal transduction. In addition, Diseases and Functions analysis suggested that these cellular proteins are highly related with Organismal Injury and Abnormalities and Cell Death and Survival. Moreover, two cellular proteins (nucleolin and eukaryotic translation elongation factor 1-alpha 1) identified both in this study and others were further validated to interact with PA using co-immunoprecipitation and co-localization assays. Therefore, this study presented the interactome data of H5N1 IAV PA protein in human cells which may provide novel cellular target proteins for elucidating the potential molecular functions of PA in regulating the lifecycle of IAV in human cells.
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Affiliation(s)
- Zhao Gao
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Jiao Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Yanyan Liang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Qian Yang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Kun Yan
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Dong Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Xiaoquan Wang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Min Gu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Xiaowen Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Shunlin Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Zenglei Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Huimou Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Wenbo Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Sujuan Chen
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Daxin Peng
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
| | - Xin-An Jiao
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou UniversityYangzhou, China
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou UniversityYangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Jiangsu Key Laboratory of Zoonosis, Yangzhou UniversityYangzhou, China
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24
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Olivos DJ, Mayo LD. Emerging Non-Canonical Functions and Regulation by p53: p53 and Stemness. Int J Mol Sci 2016; 17:ijms17121982. [PMID: 27898034 PMCID: PMC5187782 DOI: 10.3390/ijms17121982] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/10/2016] [Accepted: 11/15/2016] [Indexed: 01/15/2023] Open
Abstract
Since its discovery nearly 40 years ago, p53 has ascended to the forefront of investigated genes and proteins across diverse research disciplines and is recognized most exclusively for its role in cancer as a tumor suppressor. Levine and Oren (2009) reviewed the evolution of p53 detailing the significant discoveries of each decade since its first report in 1979. In this review, we will highlight the emerging non-canonical functions and regulation of p53 in stem cells. We will focus on general themes shared among p53's functions in non-malignant stem cells and cancer stem-like cells (CSCs) and the influence of p53 on the microenvironment and CSC niche. We will also examine p53 gain of function (GOF) roles in stemness. Mutant p53 (mutp53) GOFs that lead to survival, drug resistance and colonization are reviewed in the context of the acquisition of advantageous transformation processes, such as differentiation and dedifferentiation, epithelial-to-mesenchymal transition (EMT) and stem cell senescence and quiescence. Finally, we will conclude with therapeutic strategies that restore wild-type p53 (wtp53) function in cancer and CSCs, including RING finger E3 ligases and CSC maintenance. The mechanisms by which wtp53 and mutp53 influence stemness in non-malignant stem cells and CSCs or tumor-initiating cells (TICs) are poorly understood thus far. Further elucidation of p53's effects on stemness could lead to novel therapeutic strategies in cancer research.
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Affiliation(s)
- David J Olivos
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
- Department of Pediatrics, Herman B Wells Center for Pediatrics Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Lindsey D Mayo
- Department of Pediatrics, Herman B Wells Center for Pediatrics Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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25
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Abstract
It is poorly understood how a single protein, p53, can be responsive to so many stress signals and orchestrates very diverse cell responses to maintain/restore cell/tissue functions. The uncovering that TP53 gene physiologically expresses, in a tissue-dependent manner, several p53 splice variants (isoforms) provides an explanation to its pleiotropic biological activities. Here, we summarize a decade of research on p53 isoforms. The clinical studies and the diverse cellular and animal models of p53 isoforms (zebrafish, Drosophila, and mouse) lead us to realize that a p53-mediated cell response is, in fact, the sum of the intrinsic activities of the coexpressed p53 isoforms and that unbalancing expression of different p53 isoforms leads to cancer, premature aging, (neuro)degenerative diseases, inflammation, embryo malformations, or defects in tissue regeneration. Cracking the p53 isoforms' code is, thus, a necessary step to improve cancer treatment. It also opens new exciting perspectives in tissue regeneration.
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Affiliation(s)
- Sebastien M Joruiz
- Dundee Cancer Centre, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, United Kingdom
| | - Jean-Christophe Bourdon
- Dundee Cancer Centre, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, United Kingdom
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26
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Terrier O, Carron C, De Chassey B, Dubois J, Traversier A, Julien T, Cartet G, Proust A, Hacot S, Ressnikoff D, Lotteau V, Lina B, Diaz JJ, Moules V, Rosa-Calatrava M. Nucleolin interacts with influenza A nucleoprotein and contributes to viral ribonucleoprotein complexes nuclear trafficking and efficient influenza viral replication. Sci Rep 2016; 6:29006. [PMID: 27373907 PMCID: PMC4931502 DOI: 10.1038/srep29006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 06/09/2016] [Indexed: 01/18/2023] Open
Abstract
Influenza viruses replicate their single-stranded RNA genomes in the nucleus of infected cells and these replicated genomes (vRNPs) are then exported from the nucleus to the cytoplasm and plasma membrane before budding. To achieve this export, influenza viruses hijack the host cell export machinery. However, the complete mechanisms underlying this hijacking remain not fully understood. We have previously shown that influenza viruses induce a marked alteration of the nucleus during the time-course of infection and notably in the nucleolar compartment. In this study, we discovered that a major nucleolar component, called nucleolin, is required for an efficient export of vRNPs and viral replication. We have notably shown that nucleolin interacts with the viral nucleoprotein (NP) that mainly constitutes vRNPs. Our results suggest that this interaction could allow vRNPs to "catch" the host cell export machinery, a necessary step for viral replication.
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Affiliation(s)
- Olivier Terrier
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Coralie Carron
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Benoît De Chassey
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Julia Dubois
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Aurélien Traversier
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Thomas Julien
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Lyon 1, Lyon, France
| | - Gaëlle Cartet
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Anaïs Proust
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Lyon 1, Lyon, France
| | - Sabine Hacot
- Centre de Recherche en Cancérologie de Lyon, UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, Lyon, France and Université de Lyon, Lyon, France
| | - Denis Ressnikoff
- CIQLE, Centre d’imagerie quantitative Lyon-Est, Université Claude Bernard Lyon 1, Lyon, France
| | - Vincent Lotteau
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Bruno Lina
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Hospices Civils de Lyon, Laboratory of Virology, Lyon, France
| | - Jean-Jacques Diaz
- Centre de Recherche en Cancérologie de Lyon, UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, Lyon, France and Université de Lyon, Lyon, France
| | - Vincent Moules
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Lyon 1, Lyon, France
| | - Manuel Rosa-Calatrava
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Lyon 1, Lyon, France
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27
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Poissy J, Terrier O, Lina B, Textoris J, Rosa-Calatrava M. [Modulation of transcriptomic signature of the infected host: a new therapeutic strategy for the management of severe viral infections? Example of the flu]. ACTA ACUST UNITED AC 2016; 25:53-61. [PMID: 32288744 PMCID: PMC7117810 DOI: 10.1007/s13546-016-1188-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/08/2016] [Indexed: 11/13/2022]
Abstract
Ces dernières décennies ont été marquées par l’émergence ou la réémergence de virus responsables d’épidémies ou de pandémies plus ou moins sévères. Les stratégies préventives sont prises à défaut, et l’arsenal antiviral curatif est limité d’autant plus que les résistances virales peuvent apparaître rapidement. Par ailleurs, le développement de nouvelles molécules nécessite un délai incompatible avec la réponse rapide nécessaire lors d’une épidémie d’envergure ou d’une pandémie. C’est la raison pour laquelle de nouvelles approches thérapeutiques sont nécessaires. Un concept novateur est le repositionnement de molécules déjà sur le marché en exploitant leur capacité à inverser la réponse transcriptomique cellulaire de l’hôte infecté. En identifiant des molécules qui visent l’hôte et non le virus, cette stratégie permet d’avoir un large spectre d’action et d’être potentiellement actif sur de nouveaux variants. La mise en place de cette stratégie nécessite de caractériser les réponses cellulaires spécifiques de l’infection virale d’intérêt, de cribler in silico des molécules candidates, de les tester sur modèles cellulaires et animaux, avant d’envisager des essais cliniques chez l’homme. Nous présenterons cette démarche en prenant pour exemple l’infection grippale.
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Affiliation(s)
- J Poissy
- Université de médecine de Lille, F-59000 Lille, France.,2Pôle de réanimation, hôpital Salengro-CHRU de Lille, rue Emile-Laine, F-59037 Lille cedex, France
| | - O Terrier
- 3Laboratoire de virologie et pathologie humaine VirPath, université Claude-Bernard-Lyon-I (UCBL1), hospices civils de Lyon (HCL), International Center for Infectiology Research, Inserm (CIRI), U1111, CNRS, UMR5308, École normale supérieure de Lyon, faculté de médecine RTH Laennec, rue Guillaume-Paradin, F-69372 Lyon cedex 08, France
| | - B Lina
- 3Laboratoire de virologie et pathologie humaine VirPath, université Claude-Bernard-Lyon-I (UCBL1), hospices civils de Lyon (HCL), International Center for Infectiology Research, Inserm (CIRI), U1111, CNRS, UMR5308, École normale supérieure de Lyon, faculté de médecine RTH Laennec, rue Guillaume-Paradin, F-69372 Lyon cedex 08, France.,4Centre national de référence des virus influenza, CBPE, hospices civils de Lyon et Virpath, université Claude-Bernard-Lyon, F-69622 Villeurbanne cedex, France
| | - J Textoris
- 5Service d'anesthésie et de réanimation, hospices civils de Lyon, hôpital Édouard-Herriot, 5, place d'Arsonval, F-69437 Lyon cedex 03, France.,6Pathophysiology of Injury-Induced Immunosuppression (PI3), EA mixte hospices civils de Lyon, bioMérieux, université Claude-Bernard-Lyon-I (UCBL1), hôpital Édouard-Herriot, 5, place d'Arsonval, F-69437 Lyon cedex 03, France
| | - M Rosa-Calatrava
- 3Laboratoire de virologie et pathologie humaine VirPath, université Claude-Bernard-Lyon-I (UCBL1), hospices civils de Lyon (HCL), International Center for Infectiology Research, Inserm (CIRI), U1111, CNRS, UMR5308, École normale supérieure de Lyon, faculté de médecine RTH Laennec, rue Guillaume-Paradin, F-69372 Lyon cedex 08, France
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28
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Identification of suitable reference gene in goat peripheral blood mononuclear cells (PBMCs) infected with peste des petits ruminants virus (PPRV). Livest Sci 2015. [DOI: 10.1016/j.livsci.2015.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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29
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Yan W, Wei J, Deng X, Shi Z, Zhu Z, Shao D, Li B, Wang S, Tong G, Ma Z. Transcriptional analysis of immune-related gene expression in p53-deficient mice with increased susceptibility to influenza A virus infection. BMC Med Genomics 2015; 8:52. [PMID: 26282854 PMCID: PMC4539693 DOI: 10.1186/s12920-015-0127-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 08/06/2015] [Indexed: 11/18/2022] Open
Abstract
Background p53 is a tumor suppressor that contributes to the host immune response against viral infections in addition to its well-established protective role against cancer development. In response to influenza A virus (IAV) infection, p53 is activated and plays an essential role in inhibiting IAV replication. As a transcription factor, p53 regulates the expression of a range of downstream responsive genes either directly or indirectly in response to viral infection. We compared the expression profiles of immune-related genes between IAV-infected wild-type p53 (p53WT) and p53-deficient (p53KO) mice to gain an insight into the basis of p53-mediated antiviral response. Methods p53KO and p53WT mice were infected with influenza A/Puerto Rico/8/1934 (PR8) strain. Clinical symptoms and body weight changes were monitored daily. Lung specimens of IAV-infected mice were collected for analysis of virus titers and gene expression profiles. The difference in immune-related gene expression levels between IAV-infected p53KO and p53WT mice was comparatively determined using microarray analysis and confirmed by quantitative real-time reverse transcription polymerase chain reaction. Results p53KO mice showed an increased susceptibility to IAV infection compared to p53WT mice. Microarray analysis of gene expression profiles in the lungs of IAV-infected mice indicated that the increased susceptibility was associated with significantly changed expression levels in a range of immune-related genes in IAV-infected p53KO mice. A significantly attenuated expression of Ifng (encoding interferon (IFN)-gamma), Irf7 (encoding IFN regulator factor 7), and antiviral genes, such as Mx2 and Eif2ak2 (encoding PKR), were observed in IAV-infected p53KO mice, suggesting an impaired IFN-mediated immune response against IAV infection in the absence of p53. In addition, dysregulated expression levels of proinflammatory cytokines and chemokines, such as Ccl2 (encoding MCP-1), Cxcl9, Cxcl10 (encoding IP-10), and Tnf, were detected in IAV-infected p53KO mice during early IAV infection, reflecting an aberrant inflammatory response. Conclusion Lack of p53 resulted in the impaired expression of genes involved in IFN signaling and the dysregulated expression of cytokine and chemokine genes in IAV-infected mice, suggesting an essential role of p53 in the regulation of antiviral and inflammatory responses during IAV infection. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0127-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenjun Yan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, No. 518, Ziyue Road, Shanghai,, 200241, PR China.
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, No. 518, Ziyue Road, Shanghai,, 200241, PR China.
| | - Xufang Deng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, No. 518, Ziyue Road, Shanghai,, 200241, PR China.
| | - Zixue Shi
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, No. 518, Ziyue Road, Shanghai,, 200241, PR China.
| | - Zixiang Zhu
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China.
| | - Donghua Shao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, No. 518, Ziyue Road, Shanghai,, 200241, PR China.
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, No. 518, Ziyue Road, Shanghai,, 200241, PR China.
| | - Shaohui Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, No. 518, Ziyue Road, Shanghai,, 200241, PR China.
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, No. 518, Ziyue Road, Shanghai,, 200241, PR China.
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, No. 518, Ziyue Road, Shanghai,, 200241, PR China.
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Arsic N, Gadea G, Lagerqvist EL, Busson M, Cahuzac N, Brock C, Hollande F, Gire V, Pannequin J, Roux P. The p53 isoform Δ133p53β promotes cancer stem cell potential. Stem Cell Reports 2015; 4:531-40. [PMID: 25754205 PMCID: PMC4400643 DOI: 10.1016/j.stemcr.2015.02.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 02/03/2015] [Accepted: 02/03/2015] [Indexed: 11/18/2022] Open
Abstract
Cancer stem cells (CSC) are responsible for cancer chemoresistance and metastasis formation. Here we report that Δ133p53β, a TP53 splice variant, enhanced cancer cell stemness in MCF-7 breast cancer cells, while its depletion reduced it. Δ133p53β stimulated the expression of the key pluripotency factors SOX2, OCT3/4, and NANOG. Similarly, in highly metastatic breast cancer cells, aggressiveness was coupled with enhanced CSC potential and Δ133p53β expression. Like in MCF-7 cells, SOX2, OCT3/4, and NANOG expression were positively regulated by Δ133p53β in these cells. Finally, treatment of MCF-7 cells with etoposide, a cytotoxic anti-cancer drug, increased CSC formation and SOX2, OCT3/4, and NANOG expression via Δ133p53, thus potentially increasing the risk of cancer recurrence. Our findings show that Δ133p53β supports CSC potential. Moreover, they indicate that the TP53 gene, which is considered a major tumor suppressor gene, also acts as an oncogene via the Δ133p53β isoform. The Δ133p53β isoform promotes stemness of breast cancer cells The Δ133p53β isoform regulates SOX2, OCT3/4, and NANOG expression, but not C-MYC Etoposide promotes cancer cell stemness through Δ133p53β induction Δ133p53β expression, like p53 mutations, promotes cancer cell stemness
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Affiliation(s)
- Nikola Arsic
- Centre National de la Recherche Scientifique, UMR 5237, Centre de Recherche en Biochimie Macromoléculaire, Université Montpellier, 1919 route de Mende, 34293 Montpellier Cedex 5, France
| | - Gilles Gadea
- Centre National de la Recherche Scientifique, UMR 5237, Centre de Recherche en Biochimie Macromoléculaire, Université Montpellier, 1919 route de Mende, 34293 Montpellier Cedex 5, France
| | - E Louise Lagerqvist
- Centre National de la Recherche Scientifique, UMR5203, Institut de Génomique Fonctionnelle, Institut National de la Santé et de la Recherche Médicale, U661, Université Montpellier, route de Cardonille, 34094 Montpellier, France
| | - Muriel Busson
- Plateforme Imagerie du Petit Animal de Montpellier (IPAM), Institut de Recherche en Cancérologie de Montpellier Inserm U896, Université Montpellier, ICM Val d'Aurelle Campus Val d'Aurelle, 208 Rue des Apothicaires, 34298 Montpellier Cedex 5, France
| | - Nathalie Cahuzac
- Eurobiodev, 2040 avenue du Père Soulas, 34090 Montpellier, France
| | - Carsten Brock
- Eurofins Cerep, Le bois L'Evèque, 86600 Celle L'Evescault, France
| | - Frederic Hollande
- Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Veronique Gire
- Centre National de la Recherche Scientifique, UMR 5237, Centre de Recherche en Biochimie Macromoléculaire, Université Montpellier, 1919 route de Mende, 34293 Montpellier Cedex 5, France
| | - Julie Pannequin
- Centre National de la Recherche Scientifique, UMR5203, Institut de Génomique Fonctionnelle, Institut National de la Santé et de la Recherche Médicale, U661, Université Montpellier, route de Cardonille, 34094 Montpellier, France
| | - Pierre Roux
- Centre National de la Recherche Scientifique, UMR 5237, Centre de Recherche en Biochimie Macromoléculaire, Université Montpellier, 1919 route de Mende, 34293 Montpellier Cedex 5, France.
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Abstract
During their nuclear replication stage, influenza viruses hijack the host splicing machinery to process some of their RNA segments, the M and NS segments. In this review, we provide an overview of the current knowledge gathered on this interplay between influenza viruses and the cellular spliceosome, with a particular focus on influenza A viruses (IAV). These viruses have developed accurate regulation mechanisms to reassign the host spliceosome to alter host cellular expression and enable an optimal expression of specific spliced viral products throughout infection. Moreover, IAV segments undergoing splicing display high levels of similarity with human consensus splice sites and their viral transcripts show noteworthy secondary structures. Sequence alignments and consensus analyses, along with recently published studies, suggest both conservation and evolution of viral splice site sequences and structure for improved adaptation to the host. Altogether, these results emphasize the ability of IAV to be well adapted to the host's splicing machinery, and further investigations may contribute to a better understanding of splicing regulation with regard to viral replication, host range, and pathogenesis.
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32
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Dimitrakopoulou K, Dimitrakopoulos GN, Wilk E, Tsimpouris C, Sgarbas KN, Schughart K, Bezerianos A. Influenza A immunomics and public health omics: the dynamic pathway interplay in host response to H1N1 infection. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:167-83. [PMID: 24512282 DOI: 10.1089/omi.2013.0062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Towards unraveling the influenza A (H1N1) immunome, this work aims at constructing the murine host response pathway interactome. To accomplish that, an ensemble of dynamic and time-varying Gene Regulatory Network Inference methodologies was recruited to set a confident interactome based on mouse time series transcriptome data (day 1-day 60). The proposed H1N1 interactome demonstrated significant transformations among activated and suppressed pathways in time. Enhanced interplay was observed at day 1, while the maximal network complexity was reached at day 8 (correlated with viral clearance and iBALT tissue formation) and one interaction was present at day 40. Next, we searched for common interactivity features between the murine-adapted PR8 strain and other influenza A subtypes/strains. For this, two other interactomes, describing the murine host response against H5N1 and H1N1pdm, were constructed, which in turn validated many of the observed interactions (in the period day 1-day 7). The H1N1 interactome revealed the role of cell cycle both in innate and adaptive immunity (day 1-day 14). Also, pathogen sensory pathways (e.g., RIG-I) displayed long-lasting association with cytokine/chemokine signaling (until day 8). Interestingly, the above observations were also supported by the H5N1 and H1N1pdm models. It also elucidated the enhanced coupling of the activated innate pathways with the suppressed PPAR signaling to keep low inflammation until viral clearance (until day 14). Further, it showed that interactions reflecting phagocytosis processes continued long after the viral clearance and the establishment of adaptive immunity (day 8-day 40). Additionally, interactions involving B cell receptor pathway were evident since day 1. These results collectively inform the emerging field of public health omics and future clinical studies aimed at deciphering dynamic host responses to infectious agents.
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Abstract
To replicate their genomes in cells and generate new progeny, viruses typically require factors provided by the cells that they have infected. Subversion of the cellular machinery that controls replication of the infected host cell is a common activity of many viruses. Viruses employ different strategies to deregulate cell cycle checkpoint controls and modulate cell proliferation pathways. A number of DNA and RNA viruses encode proteins that target critical cell cycle regulators to achieve cellular conditions that are beneficial for viral replication. Many DNA viruses induce quiescent cells to enter the cell cycle; this is thought to increase pools of deoxynucleotides and thus, facilitate viral replication. In contrast, some viruses can arrest cells in a particular phase of the cell cycle that is favorable for replication of the specific virus. Cell cycle arrest may inhibit early cell death of infected cells, allow the cells to evade immune defenses, or help promote virus assembly. Although beneficial for the viral life cycle, virus-mediated alterations in normal cell cycle control mechanisms could have detrimental effects on cellular physiology and may ultimately contribute to pathologies associated with the viral infection, including cell transformation and cancer progression and maintenance. In this chapter, we summarize various strategies employed by DNA and RNA viruses to modulate the replication cycle of the virus-infected cell. When known, we describe how these virus-associated effects influence replication of the virus and contribute to diseases associated with infection by that specific virus.
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Affiliation(s)
- Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania USA
| | - Mariana C. Gadaleta
- Dept of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, USA
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34
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Abstract
Immunity to respiratory virus infection is governed by complex biological networks that influence disease progression and pathogenesis. Systems biology provides an opportunity to explore and understand these multifaceted interactions based on integration and modeling of multiple biological parameters. In this review, we describe new and refined systems-based approaches used to model, identify, and validate novel targets within complex networks following influenza and coronavirus infection. In addition, we propose avenues for extension and expansion that can revolutionize our understanding of infectious disease processes. Together, we hope to provide a window into the unique and expansive opportunity presented by systems biology to understand complex disease processes within the context of infectious diseases.
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Affiliation(s)
- Vineet D. Menachery
- Department of EpidemiologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Ralph S. Baric
- Department of EpidemiologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
- Department of Microbiology and ImmunologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
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35
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Terrier O, Diederichs A, Dubois J, Cartet G, Lina B, Bourdon JC, Rosa-Calatrava M. Influenza NS1 interacts with p53 and alters its binding to p53-responsive genes, in a promoter-dependent manner. FEBS Lett 2013; 587:2965-71. [PMID: 23954291 DOI: 10.1016/j.febslet.2013.08.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/12/2013] [Accepted: 08/05/2013] [Indexed: 11/25/2022]
Abstract
The interplay between influenza A viruses (IAV) and p53 has only been reported in a limited number of studies, mainly focusing on the antiviral role of p53. We investigated the impact of IAV infection on p53 stability and transcriptional activity. Our results indicate that IAV-induced stabilization of p53 only partially correlates with modulation of p53 transcriptional activity measured during infection. Moreover, we show that the viral non-structural protein 1 (NS1) is able to inhibit p53 transcriptional activity, in a promoter-dependent manner. Based on these data, we propose that NS1 may contribute to p53-mediated cell fate decision during IAV infection.
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Affiliation(s)
- Olivier Terrier
- Laboratoire de Virologie et Pathologie Humaine VirPath, Equipe VirCell, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France.
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36
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Terrier O, Textoris J, Carron C, Marcel V, Bourdon JC, Rosa-Calatrava M. Host microRNA molecular signatures associated with human H1N1 and H3N2 influenza A viruses reveal an unanticipated antiviral activity for miR-146a. J Gen Virol 2013; 94:985-995. [PMID: 23343627 DOI: 10.1099/vir.0.049528-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
While post-transcriptional regulation of gene expression by microRNAs (miRNAs) has been shown to be involved in influenza virus replication cycle, only a few studies have further investigated this aspect in a human cellular model infected with human influenza viruses. In this study, we performed miRNA global profiling in human lung epithelial cells (A549) infected by two different subtypes of human influenza A viruses (H1N1 and H3N2). We identified a common miRNA signature in response to infection by the two different strains, highlighting a pool of five miRNAs commonly deregulated, which are known to be involved in the innate immune response or apoptosis. Among the five miRNA hits, the only upregulated miRNA in response to influenza infection corresponded to miR-146a. Based on a previously published gene expression dataset, we extracted inversely correlated miR-146a target genes and determined their first-level interactants. This functional analysis revealed eight distinct biological processes strongly associated with these interactants: Toll-like receptor pathway, innate immune response, cytokine production and apoptosis. To better understand the biological significance of miR-146a upregulation, using a reporter assay and a specific anti-miR-146a inhibitor, we confirmed that infection increased the endogenous miR-146a promoter activity and that inhibition of miR-146a significantly increased viral propagation. Altogether, our results suggest a functional role of miR-146a in the outcome of influenza infection, at the crossroads of several biological processes.
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Affiliation(s)
- Olivier Terrier
- Laboratoire de Virologie et Pathologie Humaine VirPath, Equipe VirCell, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Julien Textoris
- Laboratoire d'Immunologie, UMR CNRS 7278, INSERM U1095, Faculté de Médecine Timone, Marseille, France
| | - Coralie Carron
- Laboratoire de Virologie et Pathologie Humaine VirPath, Equipe VirCell, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Virginie Marcel
- Division of Medical Sciences, Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital, Dundee, Scotland, UK
| | - Jean-Christophe Bourdon
- Division of Medical Sciences, Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital, Dundee, Scotland, UK
| | - Manuel Rosa-Calatrava
- Laboratoire de Virologie et Pathologie Humaine VirPath, Equipe VirCell, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
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37
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Influenza A virus NS1 induces G0/G1 cell cycle arrest by inhibiting the expression and activity of RhoA protein. J Virol 2013; 87:3039-52. [PMID: 23283961 DOI: 10.1128/jvi.03176-12] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Influenza A virus is an important pathogenic virus known to induce host cell cycle arrest in G(0)/G(1) phase and create beneficial conditions for viral replication. However, how the virus achieves arrest remains unclear. We investigated the mechanisms underlying this process and found that the nonstructural protein 1 (NS1) is required. Based on this finding, we generated a viable influenza A virus (H1N1) lacking the entire NS1 gene to study the function of this protein in cell cycle regulation. In addition to some cell cycle regulators that were changed, the concentration and activity of RhoA protein, which is thought to be pivotal for G(1)/S phase transition, were also decreased with overexpressing NS1. And in the meantime, the phosphorylation level of cell cycle regulator pRb, downstream of RhoA kinase, was decreased in an NS1-dependent manner. These findings indicate that the NS1 protein induces G(0)/G(1) cell cycle arrest mainly through interfering with the RhoA/pRb signaling cascade, thus providing favorable conditions for viral protein accumulation and replication. We further investigated the NS1 protein of avian influenza virus (H5N1) and found that it can also decrease the expression and activity of RhoA, suggesting that the H5N1 virus may affect the cell cycle through the same mechanism. The NS1/RhoA/pRb cascade, which can induce the G(0)/G(1) cell cycle arrest identified here, provides a unified explanation for the seemingly different NS1 functions involved in viral replication events. Our findings shed light on the mechanism of influenza virus replication and open new avenues for understanding the interaction between pathogens and hosts.
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38
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Sato Y, Tsurumi T. Genome guardian p53 and viral infections. Rev Med Virol 2012; 23:213-20. [PMID: 23255396 DOI: 10.1002/rmv.1738] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/18/2012] [Accepted: 11/20/2012] [Indexed: 01/07/2023]
Abstract
Because virus infections elicit various cellular responses that inhibit viral replication and growth, viruses must intervene to attenuate antiviral measures in order to thrive. The genome guardian p53 plays a central part not only in DNA damage responses, inducing cell cycle arrest or apoptosis, but also in the innate host immune control of viral infections by orchestrating diverse signaling pathways originating from many different cellular receptors and sensors. Many viruses have acquired sophisticated mechanisms to regulate p53 functions by deploying subversive proteins and modulating its post-transcriptional status. In this review, we overview the mechanisms by which DNA and RNA viruses manage p53 signaling in favor of their continued survival.
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Affiliation(s)
- Yoshitaka Sato
- Division of Virology, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan
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Influenza A viruses control expression of proviral human p53 isoforms p53β and Delta133p53α. J Virol 2012; 86:8452-60. [PMID: 22647703 DOI: 10.1128/jvi.07143-11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Previous studies have described the role of p53 isoforms, including p53β and Δ133p53α, in the modulation of the activity of full-length p53, which regulates cell fate. In the context of influenza virus infection, an interplay between influenza viruses and p53 has been described, with p53 being involved in the antiviral response. However, the role of physiological p53 isoforms has never been explored in this context. Here, we demonstrate that p53 isoforms play a role in influenza A virus infection by using silencing and transient expression strategies in human lung epithelial cells. In addition, with the help of a panel of different influenza viruses from different subtypes, we also show that infection differentially regulates the expressions of p53β and Δ133p53α. Altogether, our results highlight the role of p53 isoforms in the viral cycle of influenza A viruses, with p53β and Δ133p53α acting as regulators of viral production in a p53-dependent manner.
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