1
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Fernández JJ, Marin A, Rosales R, Penrice-Randal R, Mlcochova P, Alvarez Y, Villalon-Letelier F, Yildiz S, Pérez E, Rathnasinghe R, Cupic A, Kehrer T, Uccellini MB, Alonso S, Martínez F, McGovern BL, Clark JJ, Sharma P, Bayón Y, Alonso A, Albrecht RA, White KM, Schotsaert M, Miorin L, Stewart JP, Hiscox JA, Gupta RK, Irigoyen N, García-Sastre A, Crespo MS, Fernández N. The IRE1α-XBP1 arm of the unfolded protein response is a host factor activated in SARS-CoV-2 infection. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167193. [PMID: 38648902 DOI: 10.1016/j.bbadis.2024.167193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 03/30/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
SARS-CoV-2 infection can cause severe pneumonia, wherein exacerbated inflammation plays a major role. This is reminiscent of the process commonly termed cytokine storm, a condition dependent on a disproportionated production of cytokines. This state involves the activation of the innate immune response by viral patterns and coincides with the biosynthesis of the biomass required for viral replication, which may overwhelm the capacity of the endoplasmic reticulum and drive the unfolded protein response (UPR). The UPR is a signal transduction pathway composed of three branches that is initiated by a set of sensors: inositol-requiring protein 1 (IRE1), protein kinase RNA-like ER kinase (PERK), and activating transcription factor 6 (ATF6). These sensors control adaptive processes, including the transcriptional regulation of proinflammatory cytokines. Based on this background, the role of the UPR in SARS-CoV-2 replication and the ensuing inflammatory response was investigated using in vivo and in vitro models of infection. Mice and Syrian hamsters infected with SARS-CoV-2 showed a sole activation of the Ire1α-Xbp1 arm of the UPR associated with a robust production of proinflammatory cytokines. Human lung epithelial cells showed the dependence of viral replication on the expression of UPR-target proteins branching on the IRE1α-XBP1 arm and to a lower extent on the PERK route. Likewise, activation of the IRE1α-XBP1 branch by Spike (S) proteins from different variants of concern was a uniform finding. These results show that the IRE1α-XBP1 system enhances viral replication and cytokine expression and may represent a potential therapeutic target in SARS-CoV-2 severe pneumonia.
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Affiliation(s)
- Jose Javier Fernández
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arturo Marin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rebekah Penrice-Randal
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Yolanda Alvarez
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain; Departamento de Bioquímica, Biología Molecular y Fisiología, Universidad de Valladolid, 47003 Valladolid, Spain
| | | | - Soner Yildiz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Enrique Pérez
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain
| | - Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anastasija Cupic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa B Uccellini
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara Alonso
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain
| | - Fernando Martínez
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain
| | - Briana Lynn McGovern
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jordan J Clark
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Parul Sharma
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Yolanda Bayón
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain; Departamento de Bioquímica, Biología Molecular y Fisiología, Universidad de Valladolid, 47003 Valladolid, Spain
| | - Andrés Alonso
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James P Stewart
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Department of Infectious Disease, University of Georgia, GA, USA
| | - Julian A Hiscox
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Infectious Diseases Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore; Department of Preventive Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Mariano Sánchez Crespo
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain.
| | - Nieves Fernández
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain; Departamento de Bioquímica, Biología Molecular y Fisiología, Universidad de Valladolid, 47003 Valladolid, Spain
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2
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Gillum DR, Schwartz A, Albrecht RA, Moritz RL. Seven Opportunities for Effective Biosafety and Biosecurity Governance. Health Secur 2024. [PMID: 38608244 DOI: 10.1089/hs.2023.0189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024] Open
Affiliation(s)
- David R Gillum
- David R. Gillum, MS, is Associate Vice President, Compliance and Research Administration, University of Nevada, Reno, Reno, NV. David R. Gillum is also cofounders of Tutela Strategies, LLC, Reno, NV
| | - Antony Schwartz
- Antony Schwartz, PhD, is Director - Biological Safety, Biosafety Officer, and Responsible Official and Institutional Contact for Dual-Use Research, Occupational and Environmental Safety Office, Duke University, Durham, NC. Antony Schwartz is also cofounders of Tutela Strategies, LLC, Reno, NV
| | - Randy A Albrecht
- Randy A. Albrecht, PhD, is Senior Director, Biosafety, and Director, Emerging Pathogens Facility, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Rebecca L Moritz
- Rebecca L. Moritz, MS, is Director and Responsible Official and Institutional Contact for Dual-Use Research, Office of Research Collaboration and Compliance, Colorado State University, Fort Collins, CO. Rebecca L. Moritz is also cofounders of Tutela Strategies, LLC, Reno, NV
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3
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Meade PS, Bandawane P, Bushfield K, Hoxie I, Azcona KR, Burgos D, Choudhury S, Diaby A, Diallo M, Gaynor K, Huang A, Kante K, Khan SN, Kim W, Ajayi PK, Roubidoux E, Nelson S, McMahon R, Albrecht RA, Krammer F, Marizzi C. Detection of clade 2.3.4.4b highly pathogenic H5N1 influenza virus in New York City. bioRxiv 2024:2024.04.04.588061. [PMID: 38617218 PMCID: PMC11014507 DOI: 10.1101/2024.04.04.588061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Highly pathogenic avian influenza viruses of the H5N1 clade 2.3.4.4b arrived in North America in the winter of 2021/2022. These viruses have spread across the Americas causing morbidity and mortality in both wild and domestic birds as well as some mammalian species, including cattle. Many surveillance programs in wildlife as well as commercial poultry operations have detected these viruses. Here we conducted surveillance of avian species in the urban environment in New York City. We detected highly pathogenic H5N1 viruses in six samples from four different bird species and performed full genome sequencing. Sequence analysis showed the presence of multiple different genotypes. Our work highlights that the interface between animals and humans that may give rise to zoonotic infections or even pandemics is not limited to rural environments and commercial poultry operations but extends into the heart of our urban centers.
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Affiliation(s)
- Philip S. Meade
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pooja Bandawane
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kaitlyn Bushfield
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Irene Hoxie
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Karla R. Azcona
- New York City Virus Hunters Program, BioBus, New York, NY, USA
| | - Daneidy Burgos
- New York City Virus Hunters Program, BioBus, New York, NY, USA
| | - Sadia Choudhury
- New York City Virus Hunters Program, BioBus, New York, NY, USA
| | - Adama Diaby
- New York City Virus Hunters Program, BioBus, New York, NY, USA
| | - Mariama Diallo
- New York City Virus Hunters Program, BioBus, New York, NY, USA
| | - Kailani Gaynor
- New York City Virus Hunters Program, BioBus, New York, NY, USA
| | - Aaron Huang
- New York City Virus Hunters Program, BioBus, New York, NY, USA
| | - Kadiatou Kante
- New York City Virus Hunters Program, BioBus, New York, NY, USA
| | | | - William Kim
- New York City Virus Hunters Program, BioBus, New York, NY, USA
| | | | - Ericka Roubidoux
- Department of Host Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Sasha Nelson
- Animal Care Centers of New York, New York, NY, USA
| | | | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria
| | - Christine Marizzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- New York City Virus Hunters Program, BioBus, New York, NY, USA
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4
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Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, Braberg H, Zhou Y, Metreveli G, Harjai B, Tummino TA, Melnyk JE, Soucheray M, Batra J, Pache L, Martin-Sancho L, Carlson-Stevermer J, Jureka AS, Basler CF, Shokat KM, Shoichet BK, Shriver LP, Johnson JR, Shaw ML, Chanda SK, Roden DM, Carter TC, Kottyan LC, Chisholm RL, Pacheco JA, Smith ME, Schrodi SJ, Albrecht RA, Vignuzzi M, Zuliani-Alvarez L, Swaney DL, Eckhardt M, Wolinsky SM, White KM, Hultquist JF, Kaake RM, García-Sastre A, Krogan NJ. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nat Commun 2023; 14:6030. [PMID: 37758692 PMCID: PMC10533562 DOI: 10.1038/s41467-023-41442-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza A Virus (IAV) is a recurring respiratory virus with limited availability of antiviral therapies. Understanding host proteins essential for IAV infection can identify targets for alternative host-directed therapies (HDTs). Using affinity purification-mass spectrometry and global phosphoproteomic and protein abundance analyses using three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions and identify 13 IAV-modulated kinases. Whole exome sequencing of patients who experienced severe influenza reveals several genes, including scaffold protein AHNAK, with predicted loss-of-function variants that are also identified in our proteomic analyses. Of our identified host factors, 54 significantly alter IAV infection upon siRNA knockdown, and two factors, AHNAK and coatomer subunit COPB1, are also essential for productive infection by SARS-CoV-2. Finally, 16 compounds targeting our identified host factors suppress IAV replication, with two targeting CDK2 and FLT3 showing pan-antiviral activity across influenza and coronavirus families. This study provides a comprehensive network model of IAV infection in human cells, identifying functional host targets for pan-viral HDT.
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Affiliation(s)
- Kelsey M Haas
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Michael J McGregor
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Mehdi Bouhaddou
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Thong T Nguyen
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Billy W Newton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
| | - Matthew Urbanowski
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Heejin Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Michael A P Williams
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Veronica V Rezelj
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Alexandra Hardy
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Andrea Fossati
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Erica J Stevenson
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Ellie Sukerman
- Division of Infectious Diseases, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Tiffany Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sudhir Penugonda
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal and IRYCIS, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Yuan Zhou
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Giorgi Metreveli
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bhavya Harjai
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Tia A Tummino
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
- Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - James E Melnyk
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Margaret Soucheray
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Jyoti Batra
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Lars Pache
- Infectious and Inflammatory Disease Center, Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Laura Martin-Sancho
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Infectious Disease, Imperial College London, London, SW7 2BX, UK
| | - Jared Carlson-Stevermer
- Synthego Corporation, Redwood City, CA, 94063, USA
- Serotiny Inc., South San Francisco, CA, 94080, USA
| | - Alexander S Jureka
- Molecular Virology and Vaccine Team, Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization & Respiratory Diseases, Centers for Disease Control & Prevention, Atlanta, GA, 30333, USA
- General Dynamics Information Technology, Federal Civilian Division, Atlanta, GA, 30329, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Brian K Shoichet
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Leah P Shriver
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63105, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63105, USA
| | - Jeffrey R Johnson
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Megan L Shaw
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medical Biosciences, University of the Western Cape, Bellville, 7535, Western Cape, South Africa
| | - Sumit K Chanda
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Tonia C Carter
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, 54449, USA
| | - Leah C Kottyan
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Maureen E Smith
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Steven J Schrodi
- Laboratory of Genetics, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI, 53706, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marco Vignuzzi
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Lorena Zuliani-Alvarez
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Danielle L Swaney
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Manon Eckhardt
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Kris M White
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Judd F Hultquist
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA.
| | - Robyn M Kaake
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
| | - Adolfo García-Sastre
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
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5
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Runstadler JA, Lowen AC, Kayali G, Tompkins SM, Albrecht RA, Fouchier RAM, Stallknecht DE, Lakdawala SS, Goodrum FD, Casadevall A, Enquist LW, Alwine JC, Imperiale MJ, Schultz-Cherry S, Webby RJ. Field Research Is Essential to Counter Virological Threats. J Virol 2023; 97:e0054423. [PMID: 37166327 DOI: 10.1128/jvi.00544-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The interface between humans and wildlife is changing and, with it, the potential for pathogen introduction into humans has increased. Avian influenza is a prominent example, with an ongoing outbreak showing the unprecedented expansion of both geographic and host ranges. Research in the field is essential to understand this and other zoonotic threats. Only by monitoring dynamic viral populations and defining their biology in situ can we gather the information needed to ensure effective pandemic preparation.
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Affiliation(s)
- Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Boston, Massachusetts, USA
- Center for Research on Influenza Pathogenesis and Transmission (CRIPT) CEIRR, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, USA
| | - Ghazi Kayali
- Human-Link DMCC, Dubai, UAE
- University of Texas School of Public Health, Houston, Texas, USA
- St Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, Tennessee, USA
| | - S Mark Tompkins
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, USA
- Center for Influenza Disease and Emergence Research (CIDER) CEIRR, Athens, Georgia, USA
| | - Randy A Albrecht
- Center for Research on Influenza Pathogenesis and Transmission (CRIPT) CEIRR, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ron A M Fouchier
- Center for Research on Influenza Pathogenesis and Transmission (CRIPT) CEIRR, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - David E Stallknecht
- St Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, Tennessee, USA
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Seema S Lakdawala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Penn Center of Excellence for Influenza Research and Response (Penn-CEIRR), Philadelphia, Pennsylvania, USA
| | - Felicia D Goodrum
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, USA
| | - Lynn W Enquist
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - James C Alwine
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael J Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Stacey Schultz-Cherry
- St Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, Tennessee, USA
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Richard J Webby
- St Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, Tennessee, USA
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
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6
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Chung YT, Kuan CY, Liao GR, Albrecht RA, Tseng YY, Hsu YC, Ou SC, Hsu WL. A variant NS1 protein from H5N2 avian influenza virus suppresses PKR activation and promotes replication and virulence in mammals. Emerg Microbes Infect 2022; 11:2291-2303. [PMID: 35979918 PMCID: PMC9559317 DOI: 10.1080/22221751.2022.2114853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) frequently receive global attention as threats to public health. The NS1 protein is a key virulence factor known to impair host antiviral responses. The study herein revealed HPAIV H5N2 NS gene encoded additional protein; a truncated NS1 variant, designated NS3, produced by alternative splicing of the NS transcript. To examine the function of NS3 during infection, we generated recombinant viruses expressing either full-length NS1 (RG-AIV-T375G) or NS3 (RG-AIV-NS3). Interestingly, RG-AIV-NS3 virus produced higher titres than RG-AIV-T375G in multiple mammalian cell lines. However, RG-AIV-T375G exhibited a replication advantage over RG-AIV-NS3 in chicken DF-1 cells, indicating that host cell identity dictates the effect of NS3 on viral replication. In mice and mammalian cells, RG-AIV-NS3 infection elicited higher level of cytokines, including IFN-β, MX and TNF-α, potentially due to its higher replication activity. Based on mini-genome assay, NS3 had pronounced effects on viral replication machinery. Surprisingly, NS3 retained an interaction with PKR and suppressed PKR activation despite its lack of amino-acid residues 126-167. The poor replication ability of RG-AIV-T375G was partially restored in cells deficient in PKR suggesting that full-length NS1 may be insufficient to suppress PKR function. Notably, virulence of the full-length NS1-expressing RG-AIV-T375G virus was highly attenuated in mice when compared to RG-AIV-NS3. In summary, our study reveals the existence and function of a previously unidentified H5N2 viral protein, NS3. We found that NS3 is functionally distinct from NS1 protein, as it enhances viral replication and pathogenicity in mammalian systems, potentially via suppression of PKR activity.
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Affiliation(s)
- Yun-Ting Chung
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Ying Kuan
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Guan-Ru Liao
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Randy A Albrecht
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yeu-Yang Tseng
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Yu-Chen Hsu
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Shan-Chia Ou
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Wei-Li Hsu
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
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7
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Nogales A, Steel J, Liu WC, Lowen AC, Rodriguez L, Chiem K, Cox A, García-Sastre A, Albrecht RA, Dewhurst S, Martínez-Sobrido L. Mutation L319Q in the PB1 Polymerase Subunit Improves Attenuation of a Candidate Live-Attenuated Influenza A Virus Vaccine. Microbiol Spectr 2022; 10:e0007822. [PMID: 35583364 PMCID: PMC9241597 DOI: 10.1128/spectrum.00078-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/25/2022] [Indexed: 01/11/2023] Open
Abstract
Influenza A viruses (IAV) remain emerging threats to human public health. Live-attenuated influenza vaccines (LAIV) are one of the most effective prophylactic options to prevent disease caused by influenza infections. However, licensed LAIV remain restricted for use in 2- to 49-year-old healthy and nonpregnant people. Therefore, development of LAIV with increased safety, immunogenicity, and protective efficacy is highly desired. The U.S.-licensed LAIV is based on the master donor virus (MDV) A/Ann Arbor/6/60 H2N2 backbone, which was generated by adaptation of the virus to growth at low temperatures. Introducing the genetic signature of the U.S. MDV into the backbone of other IAV strains resulted in varying levels of attenuation. While the U.S. MDV mutations conferred an attenuated phenotype to other IAV strains, the same amino acid changes did not significantly attenuate the pandemic A/California/04/09 H1N1 (pH1N1) strain. To attenuate pH1N1, we replaced the conserved leucine at position 319 with glutamine (L319Q) in PB1 and analyzed the in vitro and in vivo properties of pH1N1 viruses containing either PB1 L319Q alone or in combination with the U.S. MDV mutations using two animal models of influenza infection and transmission, ferrets and guinea pigs. Our results demonstrated that L319Q substitution in the pH1N1 PB1 alone or in combination with the mutations of the U.S. MDV resulted in reduced pathogenicity (ferrets) and transmission (guinea pigs), and an enhanced temperature sensitive phenotype. These results demonstrate the feasibility of generating an attenuated MDV based on the backbone of a contemporary pH1N1 IAV strain. IMPORTANCE Vaccination represents the most effective strategy to reduce the impact of seasonal IAV infections. Although LAIV are superior in inducing protection and sterilizing immunity, they are not recommended for many individuals who are at high risk for severe disease. Thus, development of safer and more effective LAIV are needed. A concern with the current MDV used to generate the U.S.-licensed LAIV is that it is based on a virus isolated in 1960. Moreover, mutations that confer the temperature-sensitive, cold-adapted, and attenuated phenotype of the U.S. MDV resulted in low level of attenuation in the contemporary pandemic A/California/04/09 H1N1 (pH1N1). Here, we show that introduction of PB1 L319Q substitution, alone or in combination with the U.S. MDV mutations, resulted in pH1N1 attenuation. These findings support the development of a novel LAIV MDV based on a contemporary pH1N1 strain as a medical countermeasure against currently circulating H1N1 IAV.
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Affiliation(s)
- Aitor Nogales
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
- Animal Health Research Centre (CISA), Centro Nacional Instituto de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Madrid, Spain
| | - John Steel
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Laura Rodriguez
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
- Agencia Española de Medicamentos y Productos Sanitarios, Madrid, Spain
| | - Kevin Chiem
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
- Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Andrew Cox
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stephen Dewhurst
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
- Texas Biomedical Research Institute, San Antonio, Texas, USA
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8
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van der Heide V, Jangra S, Cohen P, Rathnasinghe R, Aslam S, Aydillo T, Geanon D, Handler D, Kelley G, Lee B, Rahman A, Dawson T, Qi J, D'Souza D, Kim-Schulze S, Panzer JK, Caicedo A, Kusmartseva I, Posgai AL, Atkinson MA, Albrecht RA, García-Sastre A, Rosenberg BR, Schotsaert M, Homann D. Limited extent and consequences of pancreatic SARS-CoV-2 infection. Cell Rep 2022; 38:110508. [PMID: 35247306 PMCID: PMC8858708 DOI: 10.1016/j.celrep.2022.110508] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/17/2021] [Accepted: 02/16/2022] [Indexed: 02/05/2023] Open
Abstract
Concerns that infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), may cause new-onset diabetes persist in an evolving research landscape, and precise risk assessment is hampered by, at times, conflicting evidence. Here, leveraging comprehensive single-cell analyses of in vitro SARS-CoV-2-infected human pancreatic islets, we demonstrate that productive infection is strictly dependent on the SARS-CoV-2 entry receptor ACE2 and targets practically all pancreatic cell types. Importantly, the infection remains highly circumscribed and largely non-cytopathic and, despite a high viral burden in infected subsets, promotes only modest cellular perturbations and inflammatory responses. Similar experimental outcomes are also observed after islet infection with endemic coronaviruses. Thus, the limits of pancreatic SARS-CoV-2 infection, even under in vitro conditions of enhanced virus exposure, challenge the proposition that in vivo targeting of β cells by SARS-CoV-2 precipitates new-onset diabetes. Whether restricted pancreatic damage and immunological alterations accrued by COVID-19 increase cumulative diabetes risk, however, remains to be evaluated.
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Affiliation(s)
- Verena van der Heide
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Phillip Cohen
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sadaf Aslam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Geanon
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Diana Handler
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Geoffrey Kelley
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Lee
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adeeb Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Travis Dawson
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jingjing Qi
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Darwin D'Souza
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Julia K Panzer
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Alejandro Caicedo
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Irina Kusmartseva
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, College of Medicine, Gainesville, FL, USA
| | - Amanda L Posgai
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, College of Medicine, Gainesville, FL, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, College of Medicine, Gainesville, FL, USA; Department of Pediatrics, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Dirk Homann
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Diabetes Obesity & Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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9
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Escalera A, Gonzalez-Reiche AS, Aslam S, Mena I, Laporte M, Pearl RL, Fossati A, Rathnasinghe R, Alshammary H, van de Guchte A, Farrugia K, Qin Y, Bouhaddou M, Kehrer T, Zuliani-Alvarez L, Meekins DA, Balaraman V, McDowell C, Richt JA, Bajic G, Sordillo EM, Dejosez M, Zwaka TP, Krogan NJ, Simon V, Albrecht RA, van Bakel H, García-Sastre A, Aydillo T. Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission. Cell Host Microbe 2022; 30:373-387.e7. [PMID: 35150638 PMCID: PMC8776496 DOI: 10.1016/j.chom.2022.01.006] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/06/2021] [Accepted: 01/14/2022] [Indexed: 11/29/2022]
Abstract
SARS-CoV-2 lineages have diverged into highly prevalent variants termed "variants of concern" (VOCs). Here, we characterized emerging SARS-CoV-2 spike polymorphisms in vitro and in vivo to understand their impact on transmissibility and virus pathogenicity and fitness. We demonstrate that the substitution S:655Y, represented in the gamma and omicron VOCs, enhances viral replication and spike protein cleavage. The S:655Y substitution was transmitted more efficiently than its ancestor S:655H in the hamster infection model and was able to outcompete S:655H in the hamster model and in a human primary airway system. Finally, we analyzed a set of emerging SARS-CoV-2 variants to investigate how different sets of mutations may impact spike processing. All VOCs tested exhibited increased spike cleavage and fusogenic capacity. Taken together, our study demonstrates that the spike mutations present in VOCs that become epidemiologically prevalent in humans are linked to an increase in spike processing and virus transmission.
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Affiliation(s)
- Alba Escalera
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sadaf Aslam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Manon Laporte
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rebecca L Pearl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrea Fossati
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2140, USA
| | - Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Keith Farrugia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yiren Qin
- Huffington Center for Cell-based Research in Parkinson's Disease, Black Family Stem Cell Institute, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2140, USA
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lorena Zuliani-Alvarez
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2140, USA
| | - David A Meekins
- Department of Diagnostic Medicine/Pathobiology and Center of Excellence for Emerging and Zoonotic Animal Diseases, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Velmurugan Balaraman
- Department of Diagnostic Medicine/Pathobiology and Center of Excellence for Emerging and Zoonotic Animal Diseases, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Chester McDowell
- Department of Diagnostic Medicine/Pathobiology and Center of Excellence for Emerging and Zoonotic Animal Diseases, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Jürgen A Richt
- Department of Diagnostic Medicine/Pathobiology and Center of Excellence for Emerging and Zoonotic Animal Diseases, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marion Dejosez
- Huffington Center for Cell-based Research in Parkinson's Disease, Black Family Stem Cell Institute, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Thomas P Zwaka
- Huffington Center for Cell-based Research in Parkinson's Disease, Black Family Stem Cell Institute, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Nevan J Krogan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2140, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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10
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Peña N, Zhang W, Watkins C, Halucha M, Alshammary H, Hernandez MM, Liu WC, Albrecht RA, Garcia-Sastre A, Simon V, Katanski C, Pan T. Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations. Front Cell Dev Biol 2022; 10:768356. [PMID: 35186917 PMCID: PMC8851031 DOI: 10.3389/fcell.2022.768356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/18/2022] [Indexed: 11/24/2022] Open
Abstract
Viruses package host RNAs in their virions which are associated with a range of functions in the viral life cycle. Previous transcriptomic profiling of host RNA packaging mostly focused on retroviruses. Which host RNAs are packaged in other viruses at the transcriptome level has not been thoroughly examined. Here we perform proof-of-concept studies using both small RNA and large RNA sequencing of six different SARS-CoV-2 viral isolates grown on VeroE6 cells to profile host RNAs present in cell free viral preparations and to explore SARS-CoV-2 genomic RNA modifications. We find selective enrichment of specific host transfer RNAs (tRNAs), tRNA fragments and signal recognition particle (SRP) RNA in SARS-CoV-2 viral preparations. Different viral preparations contain the same set of host RNAs, suggesting a common mechanism of packaging. We estimate that a single SARS-CoV-2 particle likely contains up to one SRP RNA and four tRNA molecules. We identify tRNA modification differences between the tRNAs present in viral preparations and those in the uninfected VeroE6 host cells. Furthermore, we find uncharacterized candidate modifications in the SARS-CoV-2 genomic RNA. Our results reveal an under-studied aspect of viral-host interactions that may be explored for viral therapeutics.
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Affiliation(s)
- Noah Peña
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, United States
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Christopher Watkins
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Mateusz Halucha
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Matthew M. Hernandez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Adolfo Garcia-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Christopher Katanski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
- Committee on Microbiology, University of Chicago, Chicago, IL, United States
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11
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Siddiq MM, Chan AT, Miorin L, Yadaw AS, Beaumont KG, Kehrer T, Cupic A, White KM, Tolentino RE, Hu B, Stern AD, Tavassoly I, Hansen J, Sebra R, Martinez P, Prabha S, Dubois N, Schaniel C, Iyengar-Kapuganti R, Kukar N, Giustino G, Sud K, Nirenberg S, Kovatch P, Albrecht RA, Goldfarb J, Croft L, McLaughlin MA, Argulian E, Lerakis S, Narula J, García-Sastre A, Iyengar R. Functional Effects of Cardiomyocyte Injury in COVID-19. J Virol 2022; 96:e0106321. [PMID: 34669512 PMCID: PMC8791272 DOI: 10.1128/jvi.01063-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/18/2021] [Indexed: 01/19/2023] Open
Abstract
COVID-19 affects multiple organs. Clinical data from the Mount Sinai Health System show that substantial numbers of COVID-19 patients without prior heart disease develop cardiac dysfunction. How COVID-19 patients develop cardiac disease is not known. We integrated cell biological and physiological analyses of human cardiomyocytes differentiated from human induced pluripotent stem cells (hiPSCs) infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the presence of interleukins (ILs) with clinical findings related to laboratory values in COVID-19 patients to identify plausible mechanisms of cardiac disease in COVID-19 patients. We infected hiPSC-derived cardiomyocytes from healthy human subjects with SARS-CoV-2 in the absence and presence of IL-6 and IL-1β. Infection resulted in increased numbers of multinucleated cells. Interleukin treatment and infection resulted in disorganization of myofibrils, extracellular release of troponin I, and reduced and erratic beating. Infection resulted in decreased expression of mRNA encoding key proteins of the cardiomyocyte contractile apparatus. Although interleukins did not increase the extent of infection, they increased the contractile dysfunction associated with viral infection of cardiomyocytes, resulting in cessation of beating. Clinical data from hospitalized patients from the Mount Sinai Health System show that a significant portion of COVID-19 patients without history of heart disease have elevated troponin and interleukin levels. A substantial subset of these patients showed reduced left ventricular function by echocardiography. Our laboratory observations, combined with the clinical data, indicate that direct effects on cardiomyocytes by interleukins and SARS-CoV-2 infection might underlie heart disease in COVID-19 patients. IMPORTANCE SARS-CoV-2 infects multiple organs, including the heart. Analyses of hospitalized patients show that a substantial number without prior indication of heart disease or comorbidities show significant injury to heart tissue, assessed by increased levels of troponin in blood. We studied the cell biological and physiological effects of virus infection of healthy human iPSC-derived cardiomyocytes in culture. Virus infection with interleukins disorganizes myofibrils, increases cell size and the numbers of multinucleated cells, and suppresses the expression of proteins of the contractile apparatus. Viral infection of cardiomyocytes in culture triggers release of troponin similar to elevation in levels of COVID-19 patients with heart disease. Viral infection in the presence of interleukins slows down and desynchronizes the beating of cardiomyocytes in culture. The cell-level physiological changes are similar to decreases in left ventricular ejection seen in imaging of patients' hearts. These observations suggest that direct injury to heart tissue by virus can be one underlying cause of heart disease in COVID-19.
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Affiliation(s)
- Mustafa M. Siddiq
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Angel T. Chan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine and Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Arjun S. Yadaw
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kristin G. Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anastasija Cupic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kris M. White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Rosa E. Tolentino
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bin Hu
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alan D. Stern
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Iman Tavassoly
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jens Hansen
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, a Mount Sinai Venture, Stamford, Connecticut, USA
| | - Pedro Martinez
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Som Prabha
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nicole Dubois
- Department of Cell Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christoph Schaniel
- Black Family Stem Cell Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Hematology & Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Rupa Iyengar-Kapuganti
- Division of Cardiology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nina Kukar
- Division of Cardiology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gennaro Giustino
- Black Family Stem Cell Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Hematology & Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Karan Sud
- Division of Cardiology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sharon Nirenberg
- Department of Scientific Computing and Data Science, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Patricia Kovatch
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Scientific Computing and Data Science, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joseph Goldfarb
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lori Croft
- Division of Cardiology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Maryann A. McLaughlin
- Division of Cardiology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Edgar Argulian
- Division of Cardiology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stamatios Lerakis
- Division of Cardiology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jagat Narula
- Division of Cardiology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ravi Iyengar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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12
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Muñoz-Fontela C, Widerspick L, Albrecht RA, Beer M, Carroll MW, de Wit E, Diamond MS, Dowling WE, Funnell SGP, García-Sastre A, Gerhards NM, de Jong R, Munster VJ, Neyts J, Perlman S, Reed DS, Richt JA, Riveros-Balta X, Roy CJ, Salguero FJ, Schotsaert M, Schwartz LM, Seder RA, Segalés J, Vasan SS, Henao-Restrepo AM, Barouch DH. Advances and gaps in SARS-CoV-2 infection models. PLoS Pathog 2022; 18:e1010161. [PMID: 35025969 PMCID: PMC8757994 DOI: 10.1371/journal.ppat.1010161] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The global response to Coronavirus Disease 2019 (COVID-19) is now facing new challenges such as vaccine inequity and the emergence of SARS-CoV-2 variants of concern (VOCs). Preclinical models of disease, in particular animal models, are essential to investigate VOC pathogenesis, vaccine correlates of protection and postexposure therapies. Here, we provide an update from the World Health Organization (WHO) COVID-19 modeling expert group (WHO-COM) assembled by WHO, regarding advances in preclinical models. In particular, we discuss how animal model research is playing a key role to evaluate VOC virulence, transmission and immune escape, and how animal models are being refined to recapitulate COVID-19 demographic variables such as comorbidities and age.
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Affiliation(s)
- César Muñoz-Fontela
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Lina Widerspick
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Randy A. Albrecht
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Martin Beer
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Miles W. Carroll
- National Infection Service, Public Health England, Salisbury, United Kingdom
- Pandemic Sciences Centre, Nuffield Department of Medicine, Oxford University, United Kingdom
| | - Emmie de Wit
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Michael S. Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - William E. Dowling
- Coalition for Epidemic Preparedness Innovations (CEPI), Washington, Washington, DC, United States of America
| | - Simon G. P. Funnell
- National Infection Service, Public Health England, Salisbury, United Kingdom
| | - Adolfo García-Sastre
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | | | - Rineke de Jong
- Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Vincent J. Munster
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Johan Neyts
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, United States of America
| | - Douglas S. Reed
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Juergen A. Richt
- Kansas State University, College of Veterinary Medicine, Manhattan, Kansas, United States of America
| | | | - Chad J. Roy
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | | | - Michael Schotsaert
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | | | - Robert A. Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Joaquim Segalés
- Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus UAB, and Departament de Sanitat i Anatomia animals, Facultat de Veterinària, UAB, Barcelona, Spain
| | - Seshadri S. Vasan
- Australian Centre for Disease Preparedness, CSIRO, Geelong, Australia
| | | | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
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13
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Horiuchi S, Wu H, Liu WC, Schmitt N, Provot J, Liu Y, Bentebibel SE, Albrecht RA, Schotsaert M, Forst CV, Zhang B, Ueno H. Tox2 is required for the maintenance of GC T FH cells and the generation of memory T FH cells. Sci Adv 2021; 7:eabj1249. [PMID: 34623911 PMCID: PMC8500513 DOI: 10.1126/sciadv.abj1249] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Memory T follicular helper (TFH) cells play an essential role to induce secondary antibody response by providing help to memory and naïve B cells. Here, we show that the transcription factor Tox2 is vital for the maintenance of TFH cells in germinal centers (GCs) and the generation of memory TFH cells. High Tox2 expression was almost exclusive to GC TFH cells among human tonsillar and blood CD4+ T cell subsets. Tox2 overexpression maintained the expression of TFH-associated genes in T cell receptor–stimulated human GC TFH cells and inhibited their spontaneous conversion into TH1-like cells. Tox2-deficient mice displayed impaired secondary TFH cell expansion upon reimmunization with an antigen and upon secondary infection with a heterologous influenza virus. Collectively, our study shows that Tox2 is highly integrated into establishment of durable GC TFH cell responses and development of memory TFH cells in mice and humans.
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Affiliation(s)
- Shu Horiuchi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX 75204, USA
| | - Hanchih Wu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Biomedical Translation Research Center, Academia Sinica, Taipei 11571, Taiwan
| | - Nathalie Schmitt
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX 75204, USA
- ImmunoConcEpT, CNRS UMR 5164, Bordeaux University, Bordeaux 33076, France
| | - Jonathan Provot
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX 75204, USA
| | - Yang Liu
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX 75204, USA
| | | | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christian V. Forst
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bin Zhang
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hideki Ueno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX 75204, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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14
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Martin-Sancho L, Tripathi S, Rodriguez-Frandsen A, Pache L, Sanchez-Aparicio M, McGregor MJ, Haas KM, Swaney DL, Nguyen TT, Mamede JI, Churas C, Pratt D, Rosenthal SB, Riva L, Nguyen C, Beltran-Raygoza N, Soonthornvacharin S, Wang G, Jimenez-Morales D, De Jesus PD, Moulton HM, Stein DA, Chang MW, Benner C, Ideker T, Albrecht RA, Hultquist JF, Krogan NJ, García-Sastre A, Chanda SK. Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy. Nat Microbiol 2021; 6:1319-1333. [PMID: 34556855 PMCID: PMC9683089 DOI: 10.1038/s41564-021-00964-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/18/2021] [Indexed: 02/07/2023]
Abstract
The fate of influenza A virus (IAV) infection in the host cell depends on the balance between cellular defence mechanisms and viral evasion strategies. To illuminate the landscape of IAV cellular restriction, we generated and integrated global genetic loss-of-function screens with transcriptomics and proteomics data. Our multi-omics analysis revealed a subset of both IFN-dependent and independent cellular defence mechanisms that inhibit IAV replication. Amongst these, the autophagy regulator TBC1 domain family member 5 (TBC1D5), which binds Rab7 to enable fusion of autophagosomes and lysosomes, was found to control IAV replication in vitro and in vivo and to promote lysosomal targeting of IAV M2 protein. Notably, IAV M2 was observed to abrogate TBC1D5-Rab7 binding through a physical interaction with TBC1D5 via its cytoplasmic tail. Our results provide evidence for the molecular mechanism utilised by IAV M2 protein to escape lysosomal degradation and traffic to the cell membrane, where it supports IAV budding and growth.
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Affiliation(s)
- Laura Martin-Sancho
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Shashank Tripathi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Infectious Disease Research, Microbiology & Cell Biology Department, Indian Institute of Science, Bangalore, India
| | - Ariel Rodriguez-Frandsen
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Lars Pache
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Maite Sanchez-Aparicio
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael J McGregor
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Kelsey M Haas
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Thong T Nguyen
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - João I Mamede
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Christopher Churas
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Dexter Pratt
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sara B Rosenthal
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Laura Riva
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Courtney Nguyen
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Nish Beltran-Raygoza
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Stephen Soonthornvacharin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Guojun Wang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Jimenez-Morales
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
| | - Paul D De Jesus
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Hong M Moulton
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - David A Stein
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Max W Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chris Benner
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judd F Hultquist
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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15
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Tseng YY, Kuan CY, Mibayashi M, Chen CJ, Palese P, Albrecht RA, Hsu WL. Interaction between NS1 and Cellular MAVS Contributes to NS1 Mitochondria Targeting. Viruses 2021; 13:1909. [PMID: 34696339 PMCID: PMC8537625 DOI: 10.3390/v13101909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022] Open
Abstract
Influenza A virus nonstructural protein 1 (NS1) plays an important role in evading host innate immunity. NS1 inhibits interferon (IFN) responses via multiple mechanisms, including sequestering dsRNA and suppressing retinoic acid-inducible gene I (RIG-I) signaling by interacting with RIG-I and tripartite motif-containing protein 25 (TRIM25). In the current study, we demonstrated the mitochondrial localization of NS1 at the early stage of influenza virus infection. Since NS1 does not contain mitochondria-targeting signals, we suspected that there is an association between the NS1 and mitochondrial proteins. This hypothesis was tested by demonstrating the interaction of NS1 with mitochondrial antiviral-signaling protein (MAVS) in a RIG-I-independent manner. Importantly, the association with MAVS facilitated the mitochondrial localization of NS1 and thereby significantly impeded MAVS-mediated Type I IFN production.
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Affiliation(s)
- Yeu-Yang Tseng
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung 402, Taiwan; (Y.-Y.T.); (C.-Y.K.)
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Chih-Ying Kuan
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung 402, Taiwan; (Y.-Y.T.); (C.-Y.K.)
| | - Masaki Mibayashi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (C.-J.C.); (P.P.); (R.A.A.)
| | - Chi-Jene Chen
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (C.-J.C.); (P.P.); (R.A.A.)
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (C.-J.C.); (P.P.); (R.A.A.)
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (C.-J.C.); (P.P.); (R.A.A.)
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wei-Li Hsu
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung 402, Taiwan; (Y.-Y.T.); (C.-Y.K.)
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16
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Sindelar M, Stancliffe E, Schwaiger-Haber M, Anbukumar DS, Adkins-Travis K, Goss CW, O’Halloran JA, Mudd PA, Liu WC, Albrecht RA, García-Sastre A, Shriver LP, Patti GJ. Longitudinal metabolomics of human plasma reveals prognostic markers of COVID-19 disease severity. Cell Rep Med 2021; 2:100369. [PMID: 34308390 PMCID: PMC8292035 DOI: 10.1016/j.xcrm.2021.100369] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/01/2021] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
There is an urgent need to identify which COVID-19 patients will develop life-threatening illness so that medical resources can be optimally allocated and rapid treatment can be administered early in the disease course, when clinical management is most effective. To aid in the prognostic classification of disease severity, we perform untargeted metabolomics on plasma from 339 patients, with samples collected at six longitudinal time points. Using the temporal metabolic profiles and machine learning, we build a predictive model of disease severity. We discover that a panel of metabolites measured at the time of study entry successfully determines disease severity. Through analysis of longitudinal samples, we confirm that most of these markers are directly related to disease progression and that their levels return to baseline upon disease recovery. Finally, we validate that these metabolites are also altered in a hamster model of COVID-19.
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Affiliation(s)
- Miriam Sindelar
- Department of Chemistry, Washington University, St. Louis, MO, USA
- Department of Medicine, Washington University, St. Louis, MO, USA
| | - Ethan Stancliffe
- Department of Chemistry, Washington University, St. Louis, MO, USA
- Department of Medicine, Washington University, St. Louis, MO, USA
| | - Michaela Schwaiger-Haber
- Department of Chemistry, Washington University, St. Louis, MO, USA
- Department of Medicine, Washington University, St. Louis, MO, USA
| | - Dhanalakshmi S. Anbukumar
- Department of Chemistry, Washington University, St. Louis, MO, USA
- Department of Medicine, Washington University, St. Louis, MO, USA
| | | | - Charles W. Goss
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Philip A. Mudd
- Department of Emergency Medicine, Washington University, St. Louis, MO, USA
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Leah P. Shriver
- Department of Chemistry, Washington University, St. Louis, MO, USA
- Department of Medicine, Washington University, St. Louis, MO, USA
| | - Gary J. Patti
- Department of Chemistry, Washington University, St. Louis, MO, USA
- Department of Medicine, Washington University, St. Louis, MO, USA
- Siteman Cancer Center, Washington University, St. Louis, MO, USA
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17
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El Jamal SM, Pujadas E, Ramos I, Bryce C, Grimes ZM, Amanat F, Tsankova NM, Mussa Z, Olson S, Salem F, Miorin L, Aydillo T, Schotsaert M, Albrecht RA, Liu WC, Marjanovic N, Francoeur N, Sebra R, Sealfon SC, García-Sastre A, Fowkes M, Cordon-Cardo C, Westra WH. Tissue-based SARS-CoV-2 detection in fatal COVID-19 infections: Sustained direct viral-induced damage is not necessary to drive disease progression. Hum Pathol 2021; 114:110-119. [PMID: 33961839 PMCID: PMC8095022 DOI: 10.1016/j.humpath.2021.04.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an ongoing pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although viral infection is known to trigger inflammatory processes contributing to tissue injury and organ failure, it is unclear whether direct viral damage is needed to sustain cellular injury. An understanding of pathogenic mechanisms has been handicapped by the absence of optimized methods to visualize the presence and distribution of SARS-CoV-2 in damaged tissues. We first developed a positive control cell line (Vero E6) to validate SARS-CoV-2 detection assays. We then evaluated multiple organs (lungs, kidneys, heart, liver, brain, intestines, lymph nodes, and spleen) from fourteen COVID-19 autopsy cases using immunohistochemistry (IHC) for the spike and the nucleoprotein proteins, and RNA in situ hybridization (RNA ISH) for the spike protein mRNA. Tissue detection assays were compared with quantitative polymerase chain reaction (qPCR)-based detection. SARS-CoV-2 was histologically detected in the Vero E6 positive cell line control, 1 of 14 (7%) lungs, and none (0%) of the other 59 organs. There was perfect concordance between the IHC and RNA ISH results. qPCR confirmed high viral load in the SARS-CoV-2 ISH-positive lung tissue, and absent or low viral load in all ISH-negative tissues. In patients who die of COVID-19-related organ failure, SARS-CoV-2 is largely not detectable using tissue-based assays. Even in lungs showing widespread injury, SARS-CoV-2 viral RNA or proteins were detected in only a small minority of cases. This observation supports the concept that viral infection is primarily a trigger for multiple-organ pathogenic proinflammatory responses. Direct viral tissue damage is a transient phenomenon that is generally not sustained throughout disease progression.
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Affiliation(s)
- Siraj M El Jamal
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA.
| | - Elisabet Pujadas
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Irene Ramos
- Department of Neurology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029 USA
| | - Clare Bryce
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Zachary M Grimes
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Fatima Amanat
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Nadejda M Tsankova
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Zarmeen Mussa
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Sara Olson
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Fadi Salem
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Lisa Miorin
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Global Health and Emerging Pathogens Institute, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Teresa Aydillo
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Global Health and Emerging Pathogens Institute, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Michael Schotsaert
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Global Health and Emerging Pathogens Institute, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Randy A Albrecht
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Global Health and Emerging Pathogens Institute, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Wen-Chun Liu
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Global Health and Emerging Pathogens Institute, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Biomedical Translation Research Center, Academia Sinica, Taipei, 11571, Taiwan
| | - Nada Marjanovic
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Nancy Francoeur
- Department of Genetics and Genomic Sciences, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Sema4, Stamford, CT, 10029, USA
| | - Stuart C Sealfon
- Department of Neurology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029 USA
| | - Adolfo García-Sastre
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Global Health and Emerging Pathogens Institute, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Department of Medicine, Division of Infectious Diseases, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Mary Fowkes
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Carlos Cordon-Cardo
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - William H Westra
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA.
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18
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Si L, Bai H, Rodas M, Cao W, Oh CY, Jiang A, Moller R, Hoagland D, Oishi K, Horiuchi S, Uhl S, Blanco-Melo D, Albrecht RA, Liu WC, Jordan T, Nilsson-Payant BE, Golynker I, Frere J, Logue J, Haupt R, McGrath M, Weston S, Zhang T, Plebani R, Soong M, Nurani A, Kim SM, Zhu DY, Benam KH, Goyal G, Gilpin SE, Prantil-Baun R, Gygi SP, Powers RK, Carlson KE, Frieman M, tenOever BR, Ingber DE. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics. Nat Biomed Eng 2021; 5:815-829. [PMID: 33941899 PMCID: PMC8387338 DOI: 10.1038/s41551-021-00718-9] [Citation(s) in RCA: 174] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/19/2021] [Indexed: 02/05/2023]
Abstract
The rapid repurposing of antivirals is particularly pressing during pandemics. However, rapid assays for assessing candidate drugs typically involve in vitro screens and cell lines that do not recapitulate human physiology at the tissue and organ levels. Here we show that a microfluidic bronchial-airway-on-a-chip lined by highly differentiated human bronchial-airway epithelium and pulmonary endothelium can model viral infection, strain-dependent virulence, cytokine production and the recruitment of circulating immune cells. In airway chips infected with influenza A, the co-administration of nafamostat with oseltamivir doubled the treatment-time window for oseltamivir. In chips infected with pseudotyped severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), clinically relevant doses of the antimalarial drug amodiaquine inhibited infection but clinical doses of hydroxychloroquine and other antiviral drugs that inhibit the entry of pseudotyped SARS-CoV-2 in cell lines under static conditions did not. We also show that amodiaquine showed substantial prophylactic and therapeutic activities in hamsters challenged with native SARS-CoV-2. The human airway-on-a-chip may accelerate the identification of therapeutics and prophylactics with repurposing potential.
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Affiliation(s)
- Longlong Si
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Haiqing Bai
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Melissa Rodas
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Wuji Cao
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Crystal Yuri Oh
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Amanda Jiang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Rasmus Moller
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daisy Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kohei Oishi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shu Horiuchi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Skyler Uhl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Blanco-Melo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tristan Jordan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ilona Golynker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Justin Frere
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James Logue
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robert Haupt
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Marisa McGrath
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Stuart Weston
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Roberto Plebani
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Center on Advanced Studies and Technology (CAST), Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Mercy Soong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Atiq Nurani
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Seong Min Kim
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Danni Y Zhu
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Kambez H Benam
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Girija Goyal
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Sarah E Gilpin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Rachelle Prantil-Baun
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Rani K Powers
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Kenneth E Carlson
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, USA.
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19
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Ho JSY, Mok BWY, Campisi L, Jordan T, Yildiz S, Parameswaran S, Wayman JA, Gaudreault NN, Meekins DA, Indran SV, Morozov I, Trujillo JD, Fstkchyan YS, Rathnasinghe R, Zhu Z, Zheng S, Zhao N, White K, Ray-Jones H, Malysheva V, Thiecke MJ, Lau SY, Liu H, Zhang AJ, Lee ACY, Liu WC, Jangra S, Escalera A, Aydillo T, Melo BS, Guccione E, Sebra R, Shum E, Bakker J, Kaufman DA, Moreira AL, Carossino M, Balasuriya UBR, Byun M, Albrecht RA, Schotsaert M, Garcia-Sastre A, Chanda SK, Miraldi ER, Jeyasekharan AD, TenOever BR, Spivakov M, Weirauch MT, Heinz S, Chen H, Benner C, Richt JA, Marazzi I. TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation. Cell 2021; 184:2618-2632.e17. [PMID: 33836156 PMCID: PMC8008343 DOI: 10.1016/j.cell.2021.03.051] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/05/2021] [Accepted: 03/24/2021] [Indexed: 12/29/2022]
Abstract
The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently affecting millions of lives worldwide. Large retrospective studies indicate that an elevated level of inflammatory cytokines and pro-inflammatory factors are associated with both increased disease severity and mortality. Here, using multidimensional epigenetic, transcriptional, in vitro, and in vivo analyses, we report that topoisomerase 1 (TOP1) inhibition suppresses lethal inflammation induced by SARS-CoV-2. Therapeutic treatment with two doses of topotecan (TPT), an FDA-approved TOP1 inhibitor, suppresses infection-induced inflammation in hamsters. TPT treatment as late as 4 days post-infection reduces morbidity and rescues mortality in a transgenic mouse model. These results support the potential of TOP1 inhibition as an effective host-directed therapy against severe SARS-CoV-2 infection. TPT and its derivatives are inexpensive clinical-grade inhibitors available in most countries. Clinical trials are needed to evaluate the efficacy of repurposing TOP1 inhibitors for severe coronavirus disease 2019 (COVID-19) in humans.
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Affiliation(s)
- Jessica Sook Yuin Ho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bobo Wing-Yee Mok
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine (HKUMed), The University of Hong Kong, Hong Kong
| | - Laura Campisi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tristan Jordan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Soner Yildiz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Joseph A Wayman
- Divisions of Immunobiology and Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45229, USA
| | - Natasha N Gaudreault
- Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - David A Meekins
- Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Sabarish V Indran
- Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Igor Morozov
- Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Jessie D Trujillo
- Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Yesai S Fstkchyan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zeyu Zhu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Simin Zheng
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nan Zhao
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kris White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Helen Ray-Jones
- MRC London Institute of Medical Sciences, London W12 0NN, UK
| | | | | | - Siu-Ying Lau
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine (HKUMed), The University of Hong Kong, Hong Kong
| | - Honglian Liu
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine (HKUMed), The University of Hong Kong, Hong Kong
| | - Anna Junxia Zhang
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine (HKUMed), The University of Hong Kong, Hong Kong
| | - Andrew Chak-Yiu Lee
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine (HKUMed), The University of Hong Kong, Hong Kong
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alba Escalera
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Betsaida Salom Melo
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ernesto Guccione
- Tisch Cancer Institute, Department of Oncological Sciences and Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Sema4, a Mount Sinai venture, Stamford, CT, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elaine Shum
- Division of Medical Oncology and Hematology, NYU Langone Perlmutter Cancer Center, New York, NY 10016, USA
| | - Jan Bakker
- Pontificia Universidad Católica de Chile, Santiago, Chile; Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Editor in Chief, Journal of Critical Care, NYU School of Medicine, Columbia University College of Physicians & Surgeons, New York, NY, USA
| | - David A Kaufman
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, NYU School of Medicine, New York, NY, USA
| | - Andre L Moreira
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Udeni B R Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Minji Byun
- Department of Medicine, Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo Garcia-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Department of Oncological Sciences and Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, NY 10029, USA
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Emily R Miraldi
- Divisions of Immunobiology and Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45229, USA
| | - Anand D Jeyasekharan
- Department of Haematology-Oncology, National University Hospital and Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore, Singapore
| | - Benjamin R TenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45229, USA; Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sven Heinz
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92092, USA
| | - Honglin Chen
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine (HKUMed), The University of Hong Kong, Hong Kong
| | - Christopher Benner
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92092, USA
| | - Juergen A Richt
- Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), Kansas State University, Manhattan, KS, USA; Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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20
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Sindelar M, Stancliffe E, Schwaiger-Haber M, Anbukumar DS, Albrecht RA, Liu WC, Travis KA, García-Sastre A, Shriver LP, Patti GJ. Longitudinal Metabolomics of Human Plasma Reveals Robust Prognostic Markers of COVID-19 Disease Severity. medRxiv 2021:2021.02.05.21251173. [PMID: 33564793 PMCID: PMC7872388 DOI: 10.1101/2021.02.05.21251173] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There is an urgent need to identify which COVID-19 patients will develop life-threatening illness so that scarce medical resources can be optimally allocated and rapid treatment can be administered early in the disease course, when clinical management is most effective. To aid in the prognostic classification of disease severity, we performed untargeted metabolomics profiling of 341 patients with plasma samples collected at six longitudinal time points. Using the temporal metabolic profiles and machine learning, we then built a predictive model of disease severity. We determined that the levels of 25 metabolites measured at the time of hospital admission successfully predict future disease severity. Through analysis of longitudinal samples, we confirmed that these prognostic markers are directly related to disease progression and that their levels are restored to baseline upon disease recovery. Finally, we validated that these metabolites are also altered in a hamster model of COVID-19. Our results indicate that metabolic changes associated with COVID-19 severity can be effectively used to stratify patients and inform resource allocation during the pandemic.
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Affiliation(s)
- Miriam Sindelar
- Department of Chemistry, Washington University, St. Louis, MO
- Department of Medicine, Washington University, St. Louis, MO
- These authors contributed equally
| | - Ethan Stancliffe
- Department of Chemistry, Washington University, St. Louis, MO
- Department of Medicine, Washington University, St. Louis, MO
- These authors contributed equally
| | - Michaela Schwaiger-Haber
- Department of Chemistry, Washington University, St. Louis, MO
- Department of Medicine, Washington University, St. Louis, MO
- These authors contributed equally
| | - Dhanalakshmi S. Anbukumar
- Department of Chemistry, Washington University, St. Louis, MO
- Department of Medicine, Washington University, St. Louis, MO
- These authors contributed equally
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY
- Current affiliation: Biomedical Translation Research Center, Academia Sinica, Taipei, 11571, Taiwan
| | | | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Leah P. Shriver
- Department of Chemistry, Washington University, St. Louis, MO
- Department of Medicine, Washington University, St. Louis, MO
| | - Gary J. Patti
- Department of Chemistry, Washington University, St. Louis, MO
- Department of Medicine, Washington University, St. Louis, MO
- Siteman Cancer Center, Washington University, St. Louis, MO
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21
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Liu WC, Nachbagauer R, Stadlbauer D, Strohmeier S, Solórzano A, Berlanda-Scorza F, Innis BL, García-Sastre A, Palese P, Krammer F, Albrecht RA. Chimeric Hemagglutinin-Based Live-Attenuated Vaccines Confer Durable Protective Immunity against Influenza A Viruses in a Preclinical Ferret Model. Vaccines (Basel) 2021; 9:vaccines9010040. [PMID: 33440898 PMCID: PMC7826668 DOI: 10.3390/vaccines9010040] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/01/2021] [Accepted: 01/07/2021] [Indexed: 02/06/2023] Open
Abstract
Epidemic or pandemic influenza can annually cause significant morbidity and mortality in humans. We developed novel chimeric hemagglutinin (cHA)-based universal influenza virus vaccines, which contain a conserved HA stalk domain from a 2009 pandemic H1N1 (pH1N1) strain combined with globular head domains from avian influenza A viruses. Our previous reports demonstrated that prime-boost sequential immunizations induced robust antibody responses directed toward the conserved HA stalk domain in ferrets. Herein, we further followed vaccinated animals for one year to compare the efficacy and durability of these vaccines in the preclinical ferret model of influenza. Although all cHA-based immunization regimens induced durable HA stalk-specific and heterosubtypic antibody responses in ferrets, sequential immunization with live-attenuated influenza virus vaccines (LAIV-LAIV) conferred the best protection against upper respiratory tract infection by a pH1N1 influenza A virus. The findings from this study suggest that our sequential immunization strategy for a cHA-based universal influenza virus vaccine provides durable protective humoral and cellular immunity against influenza virus infection.
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Affiliation(s)
- Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.-C.L.); (R.N.); (D.S.); (S.S.); (A.S.); (A.G.-S.); (P.P.); (F.K.)
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Biomedical Translation Research Center, Academia Sinica, Taipei 11571, Taiwan;
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.-C.L.); (R.N.); (D.S.); (S.S.); (A.S.); (A.G.-S.); (P.P.); (F.K.)
- Moderna Therapeutics, Inc., Cambridge, MA 02141, USA
| | - Daniel Stadlbauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.-C.L.); (R.N.); (D.S.); (S.S.); (A.S.); (A.G.-S.); (P.P.); (F.K.)
| | - Shirin Strohmeier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.-C.L.); (R.N.); (D.S.); (S.S.); (A.S.); (A.G.-S.); (P.P.); (F.K.)
| | - Alicia Solórzano
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.-C.L.); (R.N.); (D.S.); (S.S.); (A.S.); (A.G.-S.); (P.P.); (F.K.)
| | | | - Bruce L. Innis
- Biomedical Translation Research Center, Academia Sinica, Taipei 11571, Taiwan;
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.-C.L.); (R.N.); (D.S.); (S.S.); (A.S.); (A.G.-S.); (P.P.); (F.K.)
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.-C.L.); (R.N.); (D.S.); (S.S.); (A.S.); (A.G.-S.); (P.P.); (F.K.)
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.-C.L.); (R.N.); (D.S.); (S.S.); (A.S.); (A.G.-S.); (P.P.); (F.K.)
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.-C.L.); (R.N.); (D.S.); (S.S.); (A.S.); (A.G.-S.); (P.P.); (F.K.)
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence:
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22
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Sun W, McCroskery S, Liu WC, Leist SR, Liu Y, Albrecht RA, Slamanig S, Oliva J, Amanat F, Schäfer A, Dinnon KH, Innis BL, García-Sastre A, Krammer F, Baric RS, Palese P. A Newcastle Disease Virus (NDV) Expressing a Membrane-Anchored Spike as a Cost-Effective Inactivated SARS-CoV-2 Vaccine. Vaccines (Basel) 2020; 8:vaccines8040771. [PMID: 33348607 PMCID: PMC7766959 DOI: 10.3390/vaccines8040771] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 12/18/2022] Open
Abstract
A successful severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine must not only be safe and protective, but must also meet the demand on a global scale at a low cost. Using the current influenza virus vaccine production capacity to manufacture an egg-based inactivated Newcastle disease virus (NDV)/SARS-CoV-2 vaccine would meet that challenge. Here, we report pre-clinical evaluations of an inactivated NDV chimera stably expressing the membrane-anchored form of the spike (NDV-S) as a potent coronavirus disease 2019 (COVID-19) vaccine in mice and hamsters. The inactivated NDV-S vaccine was immunogenic, inducing strong binding and/or neutralizing antibodies in both animal models. More importantly, the inactivated NDV-S vaccine protected animals from SARS-CoV-2 infections. In the presence of an adjuvant, antigen-sparing could be achieved, which would further reduce the cost while maintaining the protective efficacy of the vaccine.
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Affiliation(s)
- Weina Sun
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.S.); (S.M.); (W.-C.L.); (Y.L.); (R.A.A.); (S.S.); (J.O.); (F.A.); (A.G.-S.); (F.K.)
| | - Stephen McCroskery
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.S.); (S.M.); (W.-C.L.); (Y.L.); (R.A.A.); (S.S.); (J.O.); (F.A.); (A.G.-S.); (F.K.)
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.S.); (S.M.); (W.-C.L.); (Y.L.); (R.A.A.); (S.S.); (J.O.); (F.A.); (A.G.-S.); (F.K.)
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Biomedical Translation Research Center, Academia Sinica, Taipei 11571, Taiwan
| | - Sarah R. Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.); (A.S.); (R.S.B.)
| | - Yonghong Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.S.); (S.M.); (W.-C.L.); (Y.L.); (R.A.A.); (S.S.); (J.O.); (F.A.); (A.G.-S.); (F.K.)
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.S.); (S.M.); (W.-C.L.); (Y.L.); (R.A.A.); (S.S.); (J.O.); (F.A.); (A.G.-S.); (F.K.)
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stefan Slamanig
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.S.); (S.M.); (W.-C.L.); (Y.L.); (R.A.A.); (S.S.); (J.O.); (F.A.); (A.G.-S.); (F.K.)
| | - Justine Oliva
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.S.); (S.M.); (W.-C.L.); (Y.L.); (R.A.A.); (S.S.); (J.O.); (F.A.); (A.G.-S.); (F.K.)
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.S.); (S.M.); (W.-C.L.); (Y.L.); (R.A.A.); (S.S.); (J.O.); (F.A.); (A.G.-S.); (F.K.)
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.); (A.S.); (R.S.B.)
| | - Kenneth H. Dinnon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | | | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.S.); (S.M.); (W.-C.L.); (Y.L.); (R.A.A.); (S.S.); (J.O.); (F.A.); (A.G.-S.); (F.K.)
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.S.); (S.M.); (W.-C.L.); (Y.L.); (R.A.A.); (S.S.); (J.O.); (F.A.); (A.G.-S.); (F.K.)
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.R.L.); (A.S.); (R.S.B.)
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (W.S.); (S.M.); (W.-C.L.); (Y.L.); (R.A.A.); (S.S.); (J.O.); (F.A.); (A.G.-S.); (F.K.)
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence:
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23
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Subrahmanyam PB, Holmes TH, Lin D, Su LF, Obermoser G, Banchereau J, Pascual V, García-Sastre A, Albrecht RA, Palucka K, Davis MM, Maecker HT. Mass Cytometry Defines Virus-Specific CD4 + T Cells in Influenza Vaccination. Immunohorizons 2020; 4:774-788. [PMID: 33310880 PMCID: PMC7891553 DOI: 10.4049/immunohorizons.1900097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 11/12/2020] [Indexed: 11/19/2022] Open
Abstract
The antiviral response to influenza virus is complex and multifaceted, involving many immune cell subsets. There is an urgent need to understand the role of CD4+ T cells, which orchestrate an effective antiviral response, to improve vaccine design strategies. In this study, we analyzed PBMCs from human participants immunized with influenza vaccine, using high-dimensional single-cell proteomic immune profiling by mass cytometry. Data were analyzed using a novel clustering algorithm, denoised ragged pruning, to define possible influenza virus–specific clusters of CD4+ T cells. Denoised ragged pruning identified six clusters of cells. Among these, one cluster (Cluster 3) was found to increase in abundance following stimulation with influenza virus peptide ex vivo. A separate cluster (Cluster 4) was found to expand in abundance between days 0 and 7 postvaccination, indicating that it is vaccine responsive. We examined the expression profiles of all six clusters to characterize their lineage, functionality, and possible role in the response to influenza vaccine. Clusters 3 and 4 consisted of effector memory cells, with high CD154 expression. Cluster 3 expressed cytokines like IL-2, IFN-γ, and TNF-α, whereas Cluster 4 expressed IL-17. Interestingly, some participants had low abundance of Clusters 3 and 4, whereas others had higher abundance of one of these clusters compared with the other. Taken together, we present an approach for identifying novel influenza virus–reactive CD4+ T cell subsets, a method that could help advance understanding of the immune response to influenza, predict responsiveness to vaccines, and aid in better vaccine design.
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Affiliation(s)
- Priyanka B Subrahmanyam
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305
| | - Tyson H Holmes
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305
| | - Dongxia Lin
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305
| | - Laura F Su
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305
| | - Gerlinde Obermoser
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX 75246
| | | | - Virginia Pascual
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX 75246
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029.,Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029; and.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Karolina Palucka
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX 75246
| | - Mark M Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305
| | - Holden T Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305;
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24
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Yuin Ho JS, Wing-Yee Mok B, Campisi L, Jordan T, Yildiz S, Parameswaran S, Wayman JA, Gaudreault NN, Meekins DA, Indran SV, Morozov I, Trujillo JD, Fstkchyan YS, Rathnasinghe R, Zhu Z, Zheng S, Zhao N, White K, Ray-Jones H, Malysheva V, Thiecke MJ, Lau SY, Liu H, Junxia Zhang A, Chak-Yiu Lee A, Liu WC, Aydillo T, Salom Melo B, Guccione E, Sebra R, Shum E, Bakker J, Kaufman DA, Moreira AL, Carossino M, Balasuriya UBR, Byun M, Miraldi ER, Albrecht RA, Schotsaert M, Garcia-Sastre A, Chanda SK, Jeyasekharan AD, TenOever BR, Spivakov M, Weirauch MT, Heinz S, Chen H, Benner C, Richt JA, Marazzi I. Topoisomerase 1 inhibition therapy protects against SARS-CoV-2-induced inflammation and death in animal models. bioRxiv 2020. [PMID: 33299999 DOI: 10.1101/2020.12.01.404483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is currently affecting millions of lives worldwide. Large retrospective studies indicate that an elevated level of inflammatory cytokines and pro-inflammatory factors are associated with both increased disease severity and mortality. Here, using multidimensional epigenetic, transcriptional, in vitro and in vivo analyses, we report that Topoisomerase 1 (Top1) inhibition suppresses lethal inflammation induced by SARS-CoV-2. Therapeutic treatment with two doses of Topotecan (TPT), a FDA-approved Top1 inhibitor, suppresses infection-induced inflammation in hamsters. TPT treatment as late as four days post-infection reduces morbidity and rescues mortality in a transgenic mouse model. These results support the potential of Top1 inhibition as an effective host-directed therapy against severe SARS-CoV-2 infection. TPT and its derivatives are inexpensive clinical-grade inhibitors available in most countries. Clinical trials are needed to evaluate the efficacy of repurposing Top1 inhibitors for COVID-19 in humans.
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25
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Javaid W, Ehni J, Gonzalez-Reiche AS, Carreño JM, Hirsch E, Tan J, Khan Z, Kriti D, Ly T, Kranitzky B, Barnett B, Cera F, Prespa L, Moss M, Albrecht RA, Mustafa A, Herbison I, Hernandez MM, Pak TR, Alshammary H, Sebra R, Smith M, Krammer F, Gitman MR, Sordillo EM, Simon V, van Bakel H. Real-Time Investigation of a Large Nosocomial Influenza A Outbreak Informed by Genomic Epidemiology. Clin Infect Dis 2020; 73:e4375-e4383. [PMID: 33252647 DOI: 10.1093/cid/ciaa1781] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Nosocomial respiratory virus outbreaks represent serious public health challenges. Rapid and precise identification of cases and tracing of transmission chains is critical to end outbreaks and to inform prevention measures. METHODS We combined conventional surveillance with influenza A virus (IAV) genome sequencing to identify and contain a large IAV outbreak in a metropolitan healthcare system. A total of 381 individuals, including 91 inpatients and 290 health care workers (HCWs), were included in the investigation. RESULTS During a 12-day period in early 2019, infection preventionists identified 89 HCWs and 18 inpatients as cases of influenza-like illness (ILI), using an amended definition without the requirement for fever. Sequencing of IAV genomes from available nasopharyngeal (NP) specimens identified 66 individuals infected with a nearly identical strain of influenza A H1N1pdm09 (43 HCWs, 17 inpatients, and 6 with unspecified affiliation). All HCWs infected with the outbreak strain had received the seasonal influenza virus vaccination. Characterization of five representative outbreak viral isolates did not show antigenic drift. In conjunction with IAV genome sequencing, mining of electronic records pinpointed the origin of the outbreak as a single patient and a few interactions in the emergency department that occurred one day prior to the index ILI cluster. CONCLUSIONS We used precision surveillance to delineate a large nosocomial IAV outbreak, mapping the source of the outbreak to a single patient rather than HCWs as initially assumed based on conventional epidemiology. These findings have important ramifications for more effective prevention strategies to curb nosocomial respiratory virus outbreaks.
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Affiliation(s)
- Waleed Javaid
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Infection Prevention, Mount Sinai Beth Israel, New York, NY
| | - Jordan Ehni
- Department of Infection Prevention, Mount Sinai Beth Israel, New York, NY
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Elena Hirsch
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jessica Tan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Zenab Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Divya Kriti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Thanh Ly
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Bethany Kranitzky
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Barbara Barnett
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Emergency Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Freddy Cera
- Clinical Laboratory, Mount Sinai Beth Israel, New York, NY
| | - Lenny Prespa
- Clinical Laboratory, Mount Sinai Beth Israel, New York, NY
| | - Marie Moss
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY.,The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ala Mustafa
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ilka Herbison
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Matthew M Hernandez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Theodore R Pak
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa R Gitman
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Emilia Mia Sordillo
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Biochemistry and Molecular Genomics, University of Louisville, Louisville, KY
| | - Viviana Simon
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY.,The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Biochemistry and Molecular Genomics, University of Louisville, Louisville, KY
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Biochemistry and Molecular Genomics, University of Louisville, Louisville, KY
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26
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Muñoz-Fontela C, Dowling WE, Funnell SGP, Gsell PS, Riveros-Balta AX, Albrecht RA, Andersen H, Baric RS, Carroll MW, Cavaleri M, Qin C, Crozier I, Dallmeier K, de Waal L, de Wit E, Delang L, Dohm E, Duprex WP, Falzarano D, Finch CL, Frieman MB, Graham BS, Gralinski LE, Guilfoyle K, Haagmans BL, Hamilton GA, Hartman AL, Herfst S, Kaptein SJF, Klimstra WB, Knezevic I, Krause PR, Kuhn JH, Le Grand R, Lewis MG, Liu WC, Maisonnasse P, McElroy AK, Munster V, Oreshkova N, Rasmussen AL, Rocha-Pereira J, Rockx B, Rodríguez E, Rogers TF, Salguero FJ, Schotsaert M, Stittelaar KJ, Thibaut HJ, Tseng CT, Vergara-Alert J, Beer M, Brasel T, Chan JFW, García-Sastre A, Neyts J, Perlman S, Reed DS, Richt JA, Roy CJ, Segalés J, Vasan SS, Henao-Restrepo AM, Barouch DH. Animal models for COVID-19. Nature 2020; 586:509-515. [PMID: 32967005 PMCID: PMC8136862 DOI: 10.1038/s41586-020-2787-6] [Citation(s) in RCA: 572] [Impact Index Per Article: 143.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the aetiological agent of coronavirus disease 2019 (COVID-19), an emerging respiratory infection caused by the introduction of a novel coronavirus into humans late in 2019 (first detected in Hubei province, China). As of 18 September 2020, SARS-CoV-2 has spread to 215 countries, has infected more than 30 million people and has caused more than 950,000 deaths. As humans do not have pre-existing immunity to SARS-CoV-2, there is an urgent need to develop therapeutic agents and vaccines to mitigate the current pandemic and to prevent the re-emergence of COVID-19. In February 2020, the World Health Organization (WHO) assembled an international panel to develop animal models for COVID-19 to accelerate the testing of vaccines and therapeutic agents. Here we summarize the findings to date and provides relevant information for preclinical testing of vaccine candidates and therapeutic agents for COVID-19.
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Affiliation(s)
- César Muñoz-Fontela
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - William E Dowling
- Centre for Epidemic Preparedness Innovations (CEPI), Washington, DC, USA
| | | | | | | | - Randy A Albrecht
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Miles W Carroll
- National Infection Service, Public Health England, Salisbury, UK
| | | | - Chuan Qin
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking, China
| | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | | | - Emmie de Wit
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Leen Delang
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Erik Dohm
- Animal Resources Program, University of Alabama at Birmingham, Birmingham, AL, USA
| | - W Paul Duprex
- Department of Microbiology and Molecular Genetics, Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Darryl Falzarano
- VIDO-Intervac, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Courtney L Finch
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Matthew B Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Bart L Haagmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Amy L Hartman
- Department of Microbiology and Molecular Genetics, Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Suzanne J F Kaptein
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - William B Klimstra
- Department of Immunology, Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Philip R Krause
- Center for Biologics Evaluation and Research, FDA, Silver Spring, MD, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Roger Le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Inserm, CEA, Université Paris-Saclay, Paris, France
| | | | - Wen-Chun Liu
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pauline Maisonnasse
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Inserm, CEA, Université Paris-Saclay, Paris, France
| | - Anita K McElroy
- Division of Pediatric Infectious Diseases, Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Vincent Munster
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Nadia Oreshkova
- Wageningen Bioveterinary Research (WBVR), Wageningen University and Research, Lelystad, The Netherlands
| | - Angela L Rasmussen
- Center for Infection and Immunity, Columbia Mailman |School of Public Health, New York, NY, USA
| | - Joana Rocha-Pereira
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Barry Rockx
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Estefanía Rodríguez
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Thomas F Rogers
- Division of Infectious Diseases, University of California San Diego, San Diego, CA, USA
| | | | - Michael Schotsaert
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Chien-Te Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Júlia Vergara-Alert
- Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Trevor Brasel
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jasper F W Chan
- Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Adolfo García-Sastre
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Douglas S Reed
- Department of Immunology, Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Juergen A Richt
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Chad J Roy
- Tulane National Primate Research Center, Covington, LA, USA
| | - Joaquim Segalés
- Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, Bellaterra, Spain
| | - Seshadri S Vasan
- Australian Centre for Disease Preparedness, CSIRO, Geelong, Victoria, Australia
- Department of Health Sciences, University of York, York, UK
| | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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27
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Amanat F, White KM, Miorin L, Strohmeier S, McMahon M, Meade P, Liu W, Albrecht RA, Simon V, Martinez‐Sobrido L, Moran T, García‐Sastre A, Krammer F. An In Vitro Microneutralization Assay for SARS-CoV-2 Serology and Drug Screening. Curr Protoc Microbiol 2020; 58:e108. [PMID: 32585083 PMCID: PMC7361222 DOI: 10.1002/cpmc.108] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the city of Wuhan, Hubei Province, China, in late 2019. Since then, the virus has spread globally and caused a pandemic. Assays that can measure the antiviral activity of antibodies or antiviral compounds are needed for SARS-CoV-2 vaccine and drug development. Here, we describe in detail a microneutralization assay, which can be used to assess in a quantitative manner if antibodies or drugs can block entry and/or replication of SARS-CoV-2 in vitro. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Microneutralization assay to test inhibition of virus by antibodies (purified antibodies or serum/plasma) Basic Protocol 2: Screening of anti-SARS-CoV-2 compounds in vitro Support Protocol: SARS-CoV-2 propagation.
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Affiliation(s)
- Fatima Amanat
- Graduate School of Biomedical SciencesIcahn School of Medicine at Mount SinaiNew YorkNew York
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Kris M. White
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew York
- Global Health Emerging Pathogens InstituteIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Lisa Miorin
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew York
- Global Health Emerging Pathogens InstituteIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Shirin Strohmeier
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Meagan McMahon
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Philip Meade
- Graduate School of Biomedical SciencesIcahn School of Medicine at Mount SinaiNew YorkNew York
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Wen‐Chun Liu
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew York
- Global Health Emerging Pathogens InstituteIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Randy A. Albrecht
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew York
- Global Health Emerging Pathogens InstituteIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Viviana Simon
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew York
- Global Health Emerging Pathogens InstituteIcahn School of Medicine at Mount SinaiNew YorkNew York
- Division of Infectious Diseases, Department of MedicineIcahn School of Medicine at Mount SinaiNew YorkNew York
| | | | - Thomas Moran
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Adolfo García‐Sastre
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew York
- Global Health Emerging Pathogens InstituteIcahn School of Medicine at Mount SinaiNew YorkNew York
- Division of Infectious Diseases, Department of MedicineIcahn School of Medicine at Mount SinaiNew YorkNew York
- Tisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Florian Krammer
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew York
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28
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Sun W, McCroskery S, Liu WC, Leist SR, Liu Y, Albrecht RA, Slamanig S, Oliva J, Amanat F, Schaefer A, Dinnon KH, Innis BL, Garcia-Sastre A, Krammer F, Baric RS, Palese P. A Newcastle disease virus (NDV) expressing membrane-anchored spike as a cost-effective inactivated SARS-CoV-2 vaccine. bioRxiv 2020. [PMID: 32766572 DOI: 10.1101/2020.07.30.229120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A successful SARS-CoV-2 vaccine must be not only safe and protective but must also meet the demand on a global scale at low cost. Using the current influenza virus vaccine production capacity to manufacture an egg-based inactivated Newcastle disease virus (NDV)/SARS-CoV-2 vaccine would meet that challenge. Here, we report pre-clinical evaluations of an inactivated NDV chimera stably expressing the membrane-anchored form of the spike (NDV-S) as a potent COVID-19 vaccine in mice and hamsters. The inactivated NDV-S vaccine was immunogenic, inducing strong binding and/or neutralizing antibodies in both animal models. More importantly, the inactivated NDV-S vaccine protected animals from SARS-CoV-2 infections or significantly attenuated SARS-CoV-2 induced disease. In the presence of an adjuvant, antigen-sparing could be achieved, which would further reduce the cost while maintaining the protective efficacy of the vaccine.
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29
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Blanco-Melo D, Nilsson-Payant BE, Liu WC, Uhl S, Hoagland D, Møller R, Jordan TX, Oishi K, Panis M, Sachs D, Wang TT, Schwartz RE, Lim JK, Albrecht RA, tenOever BR. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19. Cell 2020; 181:1036-1045.e9. [PMID: 32416070 PMCID: PMC7227586 DOI: 10.1016/j.cell.2020.04.026] [Citation(s) in RCA: 2888] [Impact Index Per Article: 722.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 11/25/2022]
Abstract
Viral pandemics, such as the one caused by SARS-CoV-2, pose an imminent threat to humanity. Because of its recent emergence, there is a paucity of information regarding viral behavior and host response following SARS-CoV-2 infection. Here we offer an in-depth analysis of the transcriptional response to SARS-CoV-2 compared with other respiratory viruses. Cell and animal models of SARS-CoV-2 infection, in addition to transcriptional and serum profiling of COVID-19 patients, consistently revealed a unique and inappropriate inflammatory response. This response is defined by low levels of type I and III interferons juxtaposed to elevated chemokines and high expression of IL-6. We propose that reduced innate antiviral defenses coupled with exuberant inflammatory cytokine production are the defining and driving features of COVID-19.
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Affiliation(s)
- Daniel Blanco-Melo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin E Nilsson-Payant
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Skyler Uhl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daisy Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rasmus Møller
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tristan X Jordan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kohei Oishi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maryline Panis
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Sachs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Taia T Wang
- Divison of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Jean K Lim
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Bernstein DI, Guptill J, Naficy A, Nachbagauer R, Berlanda-Scorza F, Feser J, Wilson PC, Solórzano A, Van der Wielen M, Walter EB, Albrecht RA, Buschle KN, Chen YQ, Claeys C, Dickey M, Dugan HL, Ermler ME, Freeman D, Gao M, Gast C, Guthmiller JJ, Hai R, Henry C, Lan LYL, McNeal M, Palm AKE, Shaw DG, Stamper CT, Sun W, Sutton V, Tepora ME, Wahid R, Wenzel H, Wohlbold TJ, Innis BL, García-Sastre A, Palese P, Krammer F. Immunogenicity of chimeric haemagglutinin-based, universal influenza virus vaccine candidates: interim results of a randomised, placebo-controlled, phase 1 clinical trial. Lancet Infect Dis 2020; 20:80-91. [PMID: 31630990 PMCID: PMC6928577 DOI: 10.1016/s1473-3099(19)30393-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/10/2019] [Accepted: 06/20/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Influenza viruses cause substantial annual morbidity and mortality globally. Current vaccines protect against influenza only when well matched to the circulating strains. However, antigenic drift can cause considerable mismatches between vaccine and circulating strains, substantially reducing vaccine effectiveness. Moreover, current seasonal vaccines are ineffective against pandemic influenza, and production of a vaccine matched to a newly emerging virus strain takes months. Therefore, there is an unmet medical need for a broadly protective influenza virus vaccine. We aimed to test the ability of chimeric H1 haemagglutinin-based universal influenza virus vaccine candidates to induce broadly cross-reactive antibodies targeting the stalk domain of group 1 haemagglutinin-expressing influenza viruses. METHODS We did a randomised, observer-blinded, phase 1 study in healthy adults in two centres in the USA. Participants were randomly assigned to one of three prime-boost, chimeric haemagglutinin-based vaccine regimens or one of two placebo groups. The vaccine regimens included a chimeric H8/1, intranasal, live-attenuated vaccine on day 1 followed by a non-adjuvanted, chimeric H5/1, intramuscular, inactivated vaccine on day 85; the same regimen but with the inactivated vaccine being adjuvanted with AS03; and an AS03-adjuvanted, chimeric H8/1, intramuscular, inactivated vaccine followed by an AS03-adjuvanted, chimeric H5/1, intramuscular, inactivated vaccine. In this planned interim analysis, the primary endpoints of reactogenicity and safety were assessed by blinded study group. We also assessed anti-H1 haemagglutinin stalk, anti-H2, anti-H9, and anti-H18 IgG antibody titres and plasmablast and memory B-cell responses in peripheral blood. This trial is registered with ClinicalTrials.gov, number NCT03300050. FINDINGS Between Oct 10, 2017, and Nov 27, 2017, 65 participants were enrolled and randomly assigned. The adjuvanted inactivated vaccine, but not the live-attenuated vaccine, induced a substantial serum IgG antibody response after the prime immunisation, with a seven times increase in anti-H1 stalk antibody titres on day 29. After boost immunisation, all vaccine regimens induced detectable anti-H1 stalk antibody (2·2-5·6 times induction over baseline), cross-reactive serum IgG antibody, and peripheral blood plasmablast responses. An unsolicited adverse event was reported for 29 (48%) of 61 participants. Solicited local adverse events were reported in 12 (48%) of 25 participants following prime vaccination with intramuscular study product or placebo, in 12 (33%) of 36 after prime immunisation with intranasal study product or placebo, and in 18 (32%) of 56 following booster doses of study product or placebo. Solicited systemic adverse events were reported in 14 (56%) of 25 after prime immunisation with intramuscular study product or placebo, in 22 (61%) of 36 after immunisation with intranasal study product or placebo, and in 21 (38%) of 56 after booster doses of study product or placebo. Disaggregated safety data were not available at the time of this interim analysis. INTERPRETATION The tested chimeric haemagglutinin-based, universal influenza virus vaccine regimens elicited cross-reactive serum IgG antibodies that targeted the conserved haemagglutinin stalk domain. This is the first proof-of-principle study to show that high anti-stalk titres can be induced by a rationally designed vaccine in humans and opens up avenues for further development of universal influenza virus vaccines. On the basis of the blinded study group, the vaccine regimens were tolerable and no safety concerns were observed. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
- David I Bernstein
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jeffrey Guptill
- Duke Early Phase Clinical Research Unit, Duke Clinical Research Institute, Durham, NC, USA
| | - Abdollah Naficy
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Jodi Feser
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Patrick C Wilson
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL, USA; The Committee on Immunology, University of Chicago, Chicago, IL, USA
| | - Alicia Solórzano
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Emmanuel B Walter
- Duke Early Phase Clinical Research Unit, Duke Clinical Research Institute, Durham, NC, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen N Buschle
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yao-Qing Chen
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Michelle Dickey
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Haley L Dugan
- The Committee on Immunology, University of Chicago, Chicago, IL, USA
| | - Megan E Ermler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; GlaxoSmithKline, Collegeville, PA, USA
| | - Debra Freeman
- Duke Early Phase Clinical Research Unit, Duke Clinical Research Institute, Durham, NC, USA
| | - Min Gao
- Duke Early Phase Clinical Research Unit, Duke Clinical Research Institute, Durham, NC, USA
| | - Christopher Gast
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Jenna J Guthmiller
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Rong Hai
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Carole Henry
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Linda Yu-Ling Lan
- The Committee on Immunology, University of Chicago, Chicago, IL, USA
| | - Monica McNeal
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anna-Karin E Palm
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Dustin G Shaw
- The Committee on Immunology, University of Chicago, Chicago, IL, USA
| | | | - Weina Sun
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Victoria Sutton
- Duke Early Phase Clinical Research Unit, Duke Clinical Research Institute, Durham, NC, USA
| | - Micah E Tepora
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Rahnuma Wahid
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Heather Wenzel
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Teddy John Wohlbold
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce L Innis
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Ramos I, Smith G, Ruf-Zamojski F, Martínez-Romero C, Fribourg M, Carbajal EA, Hartmann BM, Nair VD, Marjanovic N, Monteagudo PL, DeJesus VA, Mutetwa T, Zamojski M, Tan GS, Jayaprakash C, Zaslavsky E, Albrecht RA, Sealfon SC, García-Sastre A, Fernandez-Sesma A. Innate Immune Response to Influenza Virus at Single-Cell Resolution in Human Epithelial Cells Revealed Paracrine Induction of Interferon Lambda 1. J Virol 2019; 93:e00559-19. [PMID: 31375585 PMCID: PMC6798124 DOI: 10.1128/jvi.00559-19] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/07/2019] [Indexed: 12/14/2022] Open
Abstract
Early interactions of influenza A virus (IAV) with respiratory epithelium might determine the outcome of infection. The study of global cellular innate immune responses often masks multiple aspects of the mechanisms by which populations of cells work as organized and heterogeneous systems to defeat virus infection, and how the virus counteracts these systems. In this study, we experimentally dissected the dynamics of IAV and human epithelial respiratory cell interaction during early infection at the single-cell level. We found that the number of viruses infecting a cell (multiplicity of infection [MOI]) influences the magnitude of virus antagonism of the host innate antiviral response. Infections performed at high MOIs resulted in increased viral gene expression per cell and stronger antagonist effect than infections at low MOIs. In addition, single-cell patterns of expression of interferons (IFN) and IFN-stimulated genes (ISGs) provided important insights into the contributions of the infected and bystander cells to the innate immune responses during infection. Specifically, the expression of multiple ISGs was lower in infected than in bystander cells. In contrast with other IFNs, IFN lambda 1 (IFNL1) showed a widespread pattern of expression, suggesting a different cell-to-cell propagation mechanism more reliant on paracrine signaling. Finally, we measured the dynamics of the antiviral response in primary human epithelial cells, which highlighted the importance of early innate immune responses at inhibiting virus spread.IMPORTANCE Influenza A virus (IAV) is a respiratory pathogen of high importance to public health. Annual epidemics of seasonal IAV infections in humans are a significant public health and economic burden. IAV also causes sporadic pandemics, which can have devastating effects. The main target cells for IAV replication are epithelial cells in the respiratory epithelium. The cellular innate immune responses induced in these cells upon infection are critical for defense against the virus, and therefore, it is important to understand the complex interactions between the virus and the host cells. In this study, we investigated the innate immune response to IAV in the respiratory epithelium at the single-cell level, providing a better understanding on how a population of epithelial cells functions as a complex system to orchestrate the response to virus infection and how the virus counteracts this system.
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Affiliation(s)
- Irene Ramos
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gregory Smith
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Frederique Ruf-Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carles Martínez-Romero
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Miguel Fribourg
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Edwin A Carbajal
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Boris M Hartmann
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Venugopalan D Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nada Marjanovic
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paula L Monteagudo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Veronica A DeJesus
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Tinaye Mutetwa
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michel Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gene S Tan
- Infectious Diseases, J. Craig Venter Institute, La Jolla, California, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | | | - Elena Zaslavsky
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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32
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McMahon M, Asthagiri Arunkumar G, Liu WC, Stadlbauer D, Albrecht RA, Pavot V, Aramouni M, Lambe T, Gilbert SC, Krammer F. Vaccination With Viral Vectors Expressing Chimeric Hemagglutinin, NP and M1 Antigens Protects Ferrets Against Influenza Virus Challenge. Front Immunol 2019; 10:2005. [PMID: 31497029 PMCID: PMC6712942 DOI: 10.3389/fimmu.2019.02005] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/07/2019] [Indexed: 12/25/2022] Open
Abstract
Seasonal influenza viruses cause significant morbidity and mortality in the global population every year. Although seasonal vaccination limits disease, mismatches between the circulating strain and the vaccine strain can severely impair vaccine effectiveness. Because of this, there is an urgent need for a universal vaccine that induces broad protection against drifted seasonal and emerging pandemic influenza viruses. Targeting the conserved stalk region of the influenza virus hemagglutinin (HA), the major glycoprotein on the surface of the virus, results in the production of broadly protective antibody responses. Furthermore, replication deficient viral vectors based on Chimpanzee Adenovirus Oxford 1 (ChAdOx1) and modified vaccinia Ankara (MVA) virus expressing the influenza virus internal antigens, the nucleoprotein (NP) and matrix 1 (M1) protein, can induce strong heterosubtypic influenza virus-specific T cell responses in vaccinated individuals. Here, we combine these two platforms to evaluate the efficacy of a viral vectored vaccination regimen in protecting ferrets from H3N2 influenza virus infection. We observed that viral vectored vaccines expressing both stalk-targeting, chimeric HA constructs, and the NP+M1 fusion protein, in a prime-boost regimen resulted in the production of antibodies toward group 2 HAs, the HA stalk, NP and M1, as well as in induction of influenza virus-specific-IFNγ responses. The immune response induced by this vaccination regime ultimately reduced viral titers in the respiratory tract of influenza virus infected ferrets. Overall, these results improve our understanding of vaccination platforms capable of harnessing both cellular and humoral immunity with the goal of developing a universal influenza virus vaccine.
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Affiliation(s)
- Meagan McMahon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Guha Asthagiri Arunkumar
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Daniel Stadlbauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vincent Pavot
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Mario Aramouni
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Teresa Lambe
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Sarah C. Gilbert
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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33
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Sanyal M, Holmes TH, Maecker HT, Albrecht RA, Dekker CL, He XS, Greenberg HB. Diminished B-Cell Response After Repeat Influenza Vaccination. J Infect Dis 2019; 219:1586-1595. [PMID: 30496437 PMCID: PMC6473172 DOI: 10.1093/infdis/jiy685] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/26/2018] [Indexed: 12/11/2022] Open
Abstract
Annual vaccination with influenza vaccines is recommended for protection against influenza in the United States. Past clinical studies and meta-analysis, however, have reported conflicting results on the benefits of annual vaccination. B-cell responses elicited following repeat influenza vaccinations over multiple seasons have not been examined in detail. We analyzed the B-cell and antibody (Ab) responses in volunteers vaccinated yearly, from 2010 or 2011 through 2014, with seasonal trivalent inactivated influenza vaccines. Statistical analyses were designed to help correct for possible bias due to reduced sample size in the later years of the study. We show that, after the second annual vaccination, the frequency of vaccine-specific plasmablasts and the binding reactivity of plasmablast-derived polyclonal Abs are reduced and do not increase in subsequent years. Similar trends are observed with the serum hemagglutination inhibition Ab response after each annual vaccination, as well as the binding reactivity of plasmablast-derived polyclonal Abs to the hemagglutinin of influenza A virus vaccine components, even with changes in the seasonal vaccine components during the study. Our findings indicate a diminished B-cell response to annual vaccination with seasonal trivalent influenza vaccine. These results emphasize the need for developing improved strategies to enhance the immunogenicity and efficacy of annual influenza vaccination.
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Affiliation(s)
- Mrinmoy Sanyal
- Department of Medicine, Stanford University School of Medicine, Stanford
- Department of Biochemistry, Stanford University School of Medicine, Stanford
- VA Palo Alto Health Care System, Palo Alto, California
| | - Tyson H Holmes
- Department of Medicine, Stanford University School of Medicine, Stanford
| | - Holden T Maecker
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Cornelia L Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford
| | - Xiao-Song He
- Department of Medicine, Stanford University School of Medicine, Stanford
- VA Palo Alto Health Care System, Palo Alto, California
| | - Harry B Greenberg
- Department of Medicine, Stanford University School of Medicine, Stanford
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford
- VA Palo Alto Health Care System, Palo Alto, California
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34
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Liu WC, Nachbagauer R, Stadlbauer D, Solórzano A, Berlanda-Scorza F, García-Sastre A, Palese P, Krammer F, Albrecht RA. Sequential Immunization With Live-Attenuated Chimeric Hemagglutinin-Based Vaccines Confers Heterosubtypic Immunity Against Influenza A Viruses in a Preclinical Ferret Model. Front Immunol 2019; 10:756. [PMID: 31105689 PMCID: PMC6499175 DOI: 10.3389/fimmu.2019.00756] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022] Open
Abstract
Due to continuous antigenic drift and occasional antigenic shift, influenza viruses escape from human adaptive immunity resulting in significant morbidity and mortality in humans. Therefore, to avoid the need for annual reformulation and readministration of seasonal influenza virus vaccines, we are developing a novel chimeric hemagglutinin (cHA)-based universal influenza virus vaccine, which is comprised of sequential immunization with antigens containing a conserved stalk domain derived from a circulating pandemic H1N1 strain in combination with “exotic” head domains. Here, we show that this prime-boost sequential immunization strategy redirects antibody responses toward the conserved stalk region. We compared the vaccine efficacy elicited by distinct vaccination approaches in the preclinical ferret model of influenza. All ferrets immunized with cHA-based vaccines developed stalk-specific and broadly cross-reactive antibody responses. Two consecutive vaccinations with live-attenuated influenza viruses (LAIV-LAIV) conferred superior protection against pH1N1 and H6N1 challenge infection. Sequential immunization with LAIV followed by inactivated influenza vaccine (LAIV-IIV regimen) also induced robust antibody responses. Importantly, the LAIV-LAIV immunization regimen also induced HA stalk-specific CD4+IFN-γ+ and CD8+IFN-γ+ effector T cell responses in peripheral blood that were recalled by pH1N1 viral challenge. The findings from this preclinical study suggest that an LAIV-LAIV vaccination regimen would be more efficient in providing broadly protective immunity against influenza virus infection as compared to other approaches tested here.
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Affiliation(s)
- Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Daniel Stadlbauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Alicia Solórzano
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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35
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Liu STH, Behzadi MA, Sun W, Freyn AW, Liu WC, Broecker F, Albrecht RA, Bouvier NM, Simon V, Nachbagauer R, Krammer F, Palese P. Antigenic sites in influenza H1 hemagglutinin display species-specific immunodominance. J Clin Invest 2018; 128:4992-4996. [PMID: 30188868 DOI: 10.1172/jci122895] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/21/2018] [Indexed: 12/12/2022] Open
Abstract
Hemagglutination inhibition (HI) titers are a major correlate of protection for influenza-related illness. The influenza virus hemagglutinin possesses antigenic sites that are the targets of HI active antibodies. Here, a panel of mutant viruses each lacking a classically defined antigenic site was created to compare the species-specific immunodominance of the antigenic sites in a clinically relevant hemagglutinin. HI active antibodies of antisera from influenza virus-infected mice targeted sites Sb and Ca2. HI active antibodies of guinea pigs were not directed against any specific antigenic site, although trends were observed toward Sb, Ca2, and Sa. HI titers of antisera from infected ferrets were significantly affected by site Sa. HI active antibodies of adult humans followed yet another immunodominance pattern, in which sites Sb and Sa were immunodominant. When comparing the HI profiles among different species by antigenic cartography, animals and humans grouped separately. This study provides characterizations of the antibody-mediated immune responses against the head domain of a recent H1 hemagglutinin in animals and humans.
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Affiliation(s)
- Sean T H Liu
- Department of Microbiology.,Division of Infectious Diseases, and
| | | | | | | | | | | | - Randy A Albrecht
- Department of Microbiology.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nicole M Bouvier
- Department of Microbiology.,Division of Infectious Diseases, and
| | - Viviana Simon
- Department of Microbiology.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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36
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Heinz S, Texari L, Hayes MGB, Urbanowski M, Chang MW, Givarkes N, Rialdi A, White KM, Albrecht RA, Pache L, Marazzi I, García-Sastre A, Shaw ML, Benner C. Transcription Elongation Can Affect Genome 3D Structure. Cell 2018; 174:1522-1536.e22. [PMID: 30146161 PMCID: PMC6130916 DOI: 10.1016/j.cell.2018.07.047] [Citation(s) in RCA: 249] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 04/23/2018] [Accepted: 07/26/2018] [Indexed: 11/25/2022]
Abstract
How transcription affects genome 3D organization is not well understood. We found that during influenza A (IAV) infection, rampant transcription rapidly reorganizes host cell chromatin interactions. These changes occur at the ends of highly transcribed genes, where global inhibition of transcription termination by IAV NS1 protein causes readthrough transcription for hundreds of kilobases. In these readthrough regions, elongating RNA polymerase II disrupts chromatin interactions by inducing cohesin displacement from CTCF sites, leading to locus decompaction. Readthrough transcription into heterochromatin regions switches them from the inert (B) to the permissive (A) chromatin compartment and enables transcription factor binding. Data from non-viral transcription stimuli show that transcription similarly affects cohesin-mediated chromatin contacts within gene bodies. Conversely, inhibition of transcription elongation allows cohesin to accumulate at previously transcribed intragenic CTCF sites and to mediate chromatin looping and compaction. Our data indicate that transcription elongation by RNA polymerase II remodels genome 3D architecture.
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Affiliation(s)
- Sven Heinz
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0640, USA.
| | - Lorane Texari
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0640, USA
| | - Michael G B Hayes
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0640, USA
| | - Matthew Urbanowski
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Max W Chang
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0640, USA
| | - Ninvita Givarkes
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0640, USA
| | - Alexander Rialdi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Lars Pache
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Megan L Shaw
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Christopher Benner
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0640, USA.
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37
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Nachbagauer R, Krammer F, Albrecht RA. A Live-Attenuated Prime, Inactivated Boost Vaccination Strategy with Chimeric Hemagglutinin-Based Universal Influenza Virus Vaccines Provides Protection in Ferrets: A Confirmatory Study. Vaccines (Basel) 2018; 6:vaccines6030047. [PMID: 30044403 PMCID: PMC6161119 DOI: 10.3390/vaccines6030047] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/14/2018] [Accepted: 07/17/2018] [Indexed: 12/11/2022] Open
Abstract
Influenza viruses cause severe diseases and mortality in humans on an annual basis. The current influenza virus vaccines can confer protection when they are well-matched with the circulating strains. However, due to constant changes of the virus surface glycoproteins, the vaccine efficacy can drop substantially in some seasons. In addition, the current seasonal influenza virus vaccines do not protect from avian influenza viruses of human pandemic potential. Novel influenza virus vaccines that aim to elicit antibodies against conserved epitopes like the hemagglutinin stalk could not only reduce the burden of drifted seasonal viruses but potentially also protect humans from infection with zoonotic and emerging pandemic influenza viruses. In this paper, we generated influenza virus vaccine constructs that express chimeric hemagglutinins consisting of exotic, avian head domains and a consistent stalk domain of a seasonal virus. Using such viruses in a sequential immunization regimen can redirect the immune response towards conserved epitopes. In this study, male ferrets received a live-attenuated vaccine virus based on the A/Ann Arbor/6/60 strain expressing a chimeric H8/1 (cH8/1) hemagglutinin, which was followed by a heterologous booster vaccination with a cH5/1N1 formalin inactivated non-adjuvanted whole virus. This group was compared to a second group that received a cH8/1N1 inactivated vaccine followed by a cH5/1N1 inactivated vaccine. Both groups showed a reduction in viral titers in the upper respiratory tract after the A(H1N1)pdm09 virus challenge. Animals that received the live-attenuated vaccine had low or undetectable titers in the lower respiratory tract. The results support the further development of chimeric hemagglutinin-based vaccination strategies. The outcome of this study confirms and corroborates findings from female ferrets primed with a A/Leningrad/134/17/57-based live attenuated cH8/1N1 vaccine followed by vaccination with an AS03-adjuvanted cH5/1N1 split virus vaccine 10.
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Affiliation(s)
- Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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38
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Bangaru S, Zhang H, Gilchuk IM, Voss TG, Irving RP, Gilchuk P, Matta P, Zhu X, Lang S, Nieusma T, Richt JA, Albrecht RA, Vanderven HA, Bombardi R, Kent SJ, Ward AB, Wilson IA, Crowe JE. A multifunctional human monoclonal neutralizing antibody that targets a unique conserved epitope on influenza HA. Nat Commun 2018; 9:2669. [PMID: 29991715 PMCID: PMC6039445 DOI: 10.1038/s41467-018-04704-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 05/16/2018] [Indexed: 11/09/2022] Open
Abstract
The high rate of antigenic drift in seasonal influenza viruses necessitates frequent changes in vaccine composition. Recent seasonal H3 vaccines do not protect against swine-origin H3N2 variant (H3N2v) strains that recently have caused severe human infections. Here, we report a human VH1-69 gene-encoded monoclonal antibody (mAb) designated H3v-47 that exhibits potent cross-reactive neutralization activity against human and swine H3N2 viruses that circulated since 1989. The crystal structure and electron microscopy reconstruction of H3v-47 Fab with the H3N2v hemagglutinin (HA) identify a unique epitope spanning the vestigial esterase and receptor-binding subdomains that is distinct from that of any known neutralizing antibody for influenza A H3 viruses. MAb H3v-47 functions largely by blocking viral egress from infected cells. Interestingly, H3v-47 also engages Fcγ receptor and mediates antibody dependent cellular cytotoxicity (ADCC). This newly identified conserved epitope can be used in design of novel immunogens for development of broadly protective H3 vaccines. Broadly neutralizing antibodies are potential therapeutics and can aid rational vaccine development. Here, the authors show that the human monoclonal antibody H3v-47 recognizes a highly conserved epitope in HA of H3N2 viruses, inhibits virus replication by blocking egress and other mechanisms, and protects mice from disease.
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Affiliation(s)
- Sandhya Bangaru
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Heng Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Iuliia M Gilchuk
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Thomas G Voss
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Ryan P Irving
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Pavlo Gilchuk
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Pranathi Matta
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Shanshan Lang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Travis Nieusma
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Juergen A Richt
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Randy A Albrecht
- Department of Microbiology, Global Health and Emerging Pathogens Institute, at Icahn School of Medicine at Mount Sina, New York, NY, 10029, USA
| | - Hillary A Vanderven
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Robin Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA. .,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - James E Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA. .,The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA. .,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
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39
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Hartmann BM, Albrecht RA, Zaslavsky E, Nudelman G, Pincas H, Marjanovic N, Schotsaert M, Martínez-Romero C, Fenutria R, Ingram JP, Ramos I, Fernandez-Sesma A, Balachandran S, García-Sastre A, Sealfon SC. Pandemic H1N1 influenza A viruses suppress immunogenic RIPK3-driven dendritic cell death. Nat Commun 2017; 8:1931. [PMID: 29203926 PMCID: PMC5715119 DOI: 10.1038/s41467-017-02035-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 11/02/2017] [Indexed: 12/15/2022] Open
Abstract
The risk of emerging pandemic influenza A viruses (IAVs) that approach the devastating 1918 strain motivates finding strain-specific host–pathogen mechanisms. During infection, dendritic cells (DC) mature into antigen-presenting cells that activate T cells, linking innate to adaptive immunity. DC infection with seasonal IAVs, but not with the 1918 and 2009 pandemic strains, induces global RNA degradation. Here, we show that DC infection with seasonal IAV causes immunogenic RIPK3-mediated cell death. Pandemic IAV suppresses this immunogenic DC cell death. Only DC infected with seasonal IAV, but not with pandemic IAV, enhance maturation of uninfected DC and T cell proliferation. In vivo, circulating T cell levels are reduced after pandemic, but not seasonal, IAV infection. Using recombinant viruses, we identify the HA genomic segment as the mediator of cell death inhibition. These results show how pandemic influenza viruses subvert the immune response. The differences in virus-host interactions resulting in distinct pathogenicity of seasonal and pandemic influenza A viruses (IAV) are not well understood. Here, the authors show that the hemagglutinin segment from pandemic, but not seasonal, IAV suppresses RIPK3-mediated dendritic cell death, thereby reducing T cell activation.
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Affiliation(s)
- Boris M Hartmann
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Randy A Albrecht
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hanna Pincas
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nada Marjanovic
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Schotsaert
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carles Martínez-Romero
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rafael Fenutria
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Irene Ramos
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ana Fernandez-Sesma
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Adolfo García-Sastre
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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40
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Silvin A, Yu CI, Lahaye X, Imperatore F, Brault JB, Cardinaud S, Becker C, Kwan WH, Conrad C, Maurin M, Goudot C, Marques-Ladeira S, Wang Y, Pascual V, Anguiano E, Albrecht RA, Iannacone M, García-Sastre A, Goud B, Dalod M, Moris A, Merad M, Palucka AK, Manel N. Constitutive resistance to viral infection in human CD141 + dendritic cells. Sci Immunol 2017; 2:2/13/eaai8071. [PMID: 28783704 DOI: 10.1126/sciimmunol.aai8071] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 03/09/2017] [Accepted: 05/17/2017] [Indexed: 12/24/2022]
Abstract
Dendritic cells (DCs) are critical for the launching of protective T cell immunity in response to viral infection. Viruses can directly infect DCs, thereby compromising their viability and suppressing their ability to activate immune responses. How DC function is maintained in light of this paradox is not understood. By analyzing the susceptibility of primary human DC subsets to viral infections, we report that CD141+ DCs have an innate resistance to infection by a broad range of enveloped viruses, including HIV and influenza virus. In contrast, CD1c+ DCs are susceptible to infection, which enables viral antigen production but impairs their immune functions and survival. The ability of CD141+ DCs to resist infection is conferred by RAB15, a vesicle-trafficking protein constitutively expressed in this DC subset. We show that CD141+ DCs rely on viral antigens produced in bystander cells to launch cross-presentation-driven T cell responses. By dissociating viral infection from antigen presentation, this mechanism protects the functional capacity of DCs to launch adaptive immunity against viral infection.
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Affiliation(s)
- Aymeric Silvin
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Chun I Yu
- Baylor Institute for Immunology Research, Dallas, TX 75204, USA.,The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.,The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Xavier Lahaye
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Francesco Imperatore
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille University, UM2, INSERM U1104, CNRS UMR7280, France
| | - Jean-Baptiste Brault
- Institut Curie, PSL Research University, CNRS, UMR144, Molecular Mechanisms of Intracellular Transport, 75005 Paris, France
| | - Sylvain Cardinaud
- Centre d'Immunologie et des Maladies Infectieuses-Paris, Pierre and Marie Curie University UMRS C7, INSERM U1135, CNRS ERL 8255, Paris, France.,INSERM U955, IMRB Equipe-16, Vaccine Research Institute (VRI), F-94010, Creteil, France
| | - Christian Becker
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine; and Immunology Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Wing-Hong Kwan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cécile Conrad
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Mathieu Maurin
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Christel Goudot
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Santy Marques-Ladeira
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Yuanyuan Wang
- Baylor Institute for Immunology Research, Dallas, TX 75204, USA
| | | | | | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matteo Iannacone
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bruno Goud
- Institut Curie, PSL Research University, CNRS, UMR144, Molecular Mechanisms of Intracellular Transport, 75005 Paris, France
| | - Marc Dalod
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille University, UM2, INSERM U1104, CNRS UMR7280, France
| | - Arnaud Moris
- Centre d'Immunologie et des Maladies Infectieuses-Paris, Pierre and Marie Curie University UMRS C7, INSERM U1135, CNRS ERL 8255, Paris, France
| | - Miriam Merad
- Precision Immunology Institute, Human Immune Monitoring Center, Tisch Cancer institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - A Karolina Palucka
- Baylor Institute for Immunology Research, Dallas, TX 75204, USA. .,The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.,The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Nicolas Manel
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France.
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41
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Rialdi A, Hultquist J, Jimenez-Morales D, Peralta Z, Campisi L, Fenouil R, Moshkina N, Wang ZZ, Laffleur B, Kaake RM, McGregor MJ, Haas K, Pefanis E, Albrecht RA, Pache L, Chanda S, Jen J, Ochando J, Byun M, Basu U, García-Sastre A, Krogan N, van Bakel H, Marazzi I. The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity. Cell 2017; 169:679-692.e14. [PMID: 28475896 DOI: 10.1016/j.cell.2017.04.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 03/08/2017] [Accepted: 04/14/2017] [Indexed: 01/08/2023]
Abstract
The nuclear RNA exosome is an essential multi-subunit complex that controls RNA homeostasis. Congenital mutations in RNA exosome genes are associated with neurodegenerative diseases. Little is known about the role of the RNA exosome in the cellular response to pathogens. Here, using NGS and human and mouse genetics, we show that influenza A virus (IAV) ribogenesis and growth are suppressed by impaired RNA exosome activity. Mechanistically, the nuclear RNA exosome coordinates the initial steps of viral transcription with RNAPII at host promoters. The viral polymerase complex co-opts the nuclear RNA exosome complex and cellular RNAs en route to 3' end degradation. Exosome deficiency uncouples chromatin targeting of the viral polymerase complex and the formation of cellular:viral RNA hybrids, which are essential RNA intermediates that license transcription of antisense genomic viral RNAs. Our results suggest that evolutionary arms races have shaped the cellular RNA quality control machinery.
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Affiliation(s)
- Alexander Rialdi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Judd Hultquist
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2140, USA
| | - David Jimenez-Morales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2140, USA
| | - Zuleyma Peralta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Laura Campisi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Romain Fenouil
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Natasha Moshkina
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Zhen Zhen Wang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Brice Laffleur
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Robyn M Kaake
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2140, USA
| | - Michael J McGregor
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2140, USA
| | - Kelsey Haas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2140, USA
| | - Evangelos Pefanis
- Regeneron Pharmaceuticals and Regeneron Genetics Center, Tarrytown, NY 10591, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Lars Pache
- Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Sumit Chanda
- Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Joanna Jen
- Department of Neurology, University of California, Los Angeles, CA 90095, USA
| | - Jordi Ochando
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Minji Byun
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Uttiya Basu
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2140, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA.
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Tundup S, Kandasamy M, Perez JT, Mena N, Steel J, Nagy T, Albrecht RA, Manicassamy B. Endothelial cell tropism is a determinant of H5N1 pathogenesis in mammalian species. PLoS Pathog 2017; 13:e1006270. [PMID: 28282445 PMCID: PMC5362246 DOI: 10.1371/journal.ppat.1006270] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 03/22/2017] [Accepted: 03/02/2017] [Indexed: 12/19/2022] Open
Abstract
The cellular and molecular mechanisms underpinning the unusually high virulence of highly pathogenic avian influenza H5N1 viruses in mammalian species remains unknown. Here, we investigated if the cell tropism of H5N1 virus is a determinant of enhanced virulence in mammalian species. We engineered H5N1 viruses with restricted cell tropism through the exploitation of cell type-specific microRNA expression by incorporating microRNA target sites into the viral genome. Restriction of H5N1 replication in endothelial cells via miR-126 ameliorated disease symptoms, prevented systemic viral spread and limited mortality, despite showing similar levels of peak viral replication in the lungs as compared to control virus-infected mice. Similarly, restriction of H5N1 replication in endothelial cells resulted in ameliorated disease symptoms and decreased viral spread in ferrets. Our studies demonstrate that H5N1 infection of endothelial cells results in excessive production of cytokines and reduces endothelial barrier integrity in the lungs, which culminates in vascular leakage and viral pneumonia. Importantly, our studies suggest a need for a combinational therapy that targets viral components, suppresses host immune responses, and improves endothelial barrier integrity for the treatment of highly pathogenic H5N1 virus infections. In healthy individuals, the symptoms of seasonal influenza virus infection are mild and the infection is cleared within 4–7 days. However, infection with highly pathogenic avian influenza virus (H5N1) can be severe and often results in fatal pneumonia even in healthy adults. While it is known that both viral and host factors play a role in enhanced disease progression, the molecular mechanisms for the high virulence of H5N1 virus are not completely understood. In this study, we engineered avian influenza H5N1 viruses incapable of replicating in endothelial cells and evaluated disease symptoms in mice and ferrets. Our studies show that H5N1 infection of endothelial cells causes severe disease and death of infected animals in part due to the damage of endothelial cells lining the blood vessels, which results in leakage of fluid into the lungs (pneumonia).
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Affiliation(s)
- Smanla Tundup
- Department of Microbiology, University of Chicago, Chicago, IL, United States of America
- Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, IL, United States of America
| | - Matheswaran Kandasamy
- Department of Microbiology, University of Chicago, Chicago, IL, United States of America
- Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, IL, United States of America
| | - Jasmine T. Perez
- Department of Microbiology, University of Chicago, Chicago, IL, United States of America
| | - Nacho Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - John Steel
- Department of Microbiology, Emory University, Atlanta, GA, United States of America
| | - Tamas Nagy
- Comparative Pathology Laboratory, University of Georgia, Athens, GA, United States of America
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Balaji Manicassamy
- Department of Microbiology, University of Chicago, Chicago, IL, United States of America
- Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, IL, United States of America
- * E-mail:
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Tripathi S, Balasubramaniam VRMT, Brown JA, Mena I, Grant A, Bardina SV, Maringer K, Schwarz MC, Maestre AM, Sourisseau M, Albrecht RA, Krammer F, Evans MJ, Fernandez-Sesma A, Lim JK, García-Sastre A. A novel Zika virus mouse model reveals strain specific differences in virus pathogenesis and host inflammatory immune responses. PLoS Pathog 2017; 13:e1006258. [PMID: 28278235 PMCID: PMC5373643 DOI: 10.1371/journal.ppat.1006258] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/30/2017] [Accepted: 02/24/2017] [Indexed: 11/21/2022] Open
Abstract
Zika virus (ZIKV) is a mosquito borne flavivirus, which was a neglected tropical pathogen until it emerged and spread across the Pacific Area and the Americas, causing large human outbreaks associated with fetal abnormalities and neurological disease in adults. The factors that contributed to the emergence, spread and change in pathogenesis of ZIKV are not understood. We previously reported that ZIKV evades cellular antiviral responses by targeting STAT2 for degradation in human cells. In this study, we demonstrate that Stat2-/- mice are highly susceptible to ZIKV infection, recapitulate virus spread to the central nervous system (CNS), gonads and other visceral organs, and display neurological symptoms. Further, we exploit this model to compare ZIKV pathogenesis caused by a panel of ZIKV strains of a range of spatiotemporal history of isolation and representing African and Asian lineages. We observed that African ZIKV strains induce short episodes of severe neurological symptoms followed by lethality. In comparison, Asian strains manifest prolonged signs of neuronal malfunctions, occasionally causing death of the Stat2-/- mice. African ZIKV strains induced higher levels of inflammatory cytokines and markers associated with cellular infiltration in the infected brain in mice, which may explain exacerbated pathogenesis in comparison to those of the Asian lineage. Interestingly, viral RNA levels in different organs did not correlate with the pathogenicity of the different strains. Taken together, we have established a new murine model that supports ZIKV infection and demonstrate its utility in highlighting intrinsic differences in the inflammatory response induced by different ZIKV strains leading to severity of disease. This study paves the way for the future interrogation of strain-specific changes in the ZIKV genome and their contribution to viral pathogenesis. Zika virus is the most recent viral pathogen to cause a global public health emergency. It is distinct from other flaviviruses in its ability to cause transplacental infection, fetal abnormalities and vector independent transmission through body fluids in humans. Over the last year, there has been rapid progress in the development of animal models, which can be used to study ZIKV pathogenesis. In this study, we demonstrate for the first time that Stat2-/- mice are highly susceptible to ZIKV infection and recapitulate aspects of ZIKV pathogenesis and disease. We use this model to delineate whether strain specific differences in ZIKV pathogenesis exist, using diverse strains representing both African and Asian lineages. We show that African strains in general are more virulent than Asian strains and their pathogenicity associates closely with the degree of inflammatory immune response in the CNS of infected mice, and does not necessarily correlate with viral RNA levels. Thus, we establish Stat2-/- mice as new model to study ZIKV pathogenesis and use it to characterize inherent differences in the virulence among ZIKV strains. More importantly, we also highlight a potential role of the host inflammatory immune response in mediating differential pathogenesis among ZIKV strains.
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Affiliation(s)
- Shashank Tripathi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Vinod R. M. T. Balasubramaniam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Julia A. Brown
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Graduate School of Biological Sciences at the Icahn School of Medicine at Mount Sinai, Microbiology Training Area, New York, New York, United States of America
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Alesha Grant
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Graduate School of Biological Sciences at the Icahn School of Medicine at Mount Sinai, Microbiology Training Area, New York, New York, United States of America
| | - Susana V. Bardina
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Graduate School of Biological Sciences at the Icahn School of Medicine at Mount Sinai, Microbiology Training Area, New York, New York, United States of America
| | - Kevin Maringer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Megan C. Schwarz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ana M. Maestre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Marion Sourisseau
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Matthew J. Evans
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jean K. Lim
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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Branagan AR, Duffy E, Albrecht RA, Cooper DL, Seropian S, Parker TL, Gan G, Li F, Zelterman D, Boddupalli CS, Zhang L, Verma R, Ferencz TM, Dhodapkar MV. Clinical and Serologic Responses After a Two-dose Series of High-dose Influenza Vaccine in Plasma Cell Disorders: A Prospective, Single-arm Trial. Clin Lymphoma Myeloma Leuk 2017; 17:296-304.e2. [PMID: 28343904 DOI: 10.1016/j.clml.2017.02.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/12/2017] [Accepted: 02/28/2017] [Indexed: 02/05/2023]
Abstract
BACKGROUND Patients with multiple myeloma (MM) and other plasma cell disorders are highly susceptible to influenza infections, which are major causes of morbidity in this population, despite the routine administration of a seasonal influenza vaccination. Existing data are limited by small and retrospective studies, which suggest poor seroprotection rates of < 20% after standard influenza vaccination in patients with MM. PATIENTS AND METHODS Patients with plasma cell dyscrasia (n = 51) were treated with a 2-dose series of high-dose inactivated trivalent influenza vaccine during the 2014 to 2015 influenza season. Laboratory-confirmed influenza infections were identified through seasonal surveillance, sera were collected for influenza hemagglutination antibody inhibition (HAI) titer assays, and logistic regression models were used to identify the clinical correlates to the HAI serologic responses. RESULTS Influenza vaccine was well tolerated, without any vaccine-related grade ≥ 2 adverse events. Only 3 patients (6%) experienced laboratory-confirmed influenza. The rates of HAI seroprotection against all 3 vaccine strains (A/California/7/2009 [H1N1] pdm09-like virus; A/Texas/50/2012 [H3N2]-like virus; and a B/Massachusetts/2/2012-like virus) increased from 4% at baseline to 49% and 65% after 1 and 2 doses, respectively. The risk factors associated with a lower likelihood of HAI serologic response included plasma cell disorder requiring therapy, less than a partial response found on disease response assessment, and active conventional chemotherapy. Alternatively, active therapy with an immunomodulatory drug alone or with a proteasome inhibitor was associated with a greater likelihood of an HAI serologic response. CONCLUSION These data have demonstrated that, in contrast to the historically poor results with standard influenza vaccination, this novel high-dose booster vaccination strategy leads to high rates of seroprotection. Randomized controlled studies are needed to compare this novel strategy to the standard vaccination strategy.
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Affiliation(s)
- Andrew R Branagan
- Yale Cancer Center, New Haven, CT; Yale School of Medicine, New Haven, CT.
| | | | | | - Dennis L Cooper
- Yale Cancer Center, New Haven, CT; Yale School of Medicine, New Haven, CT
| | - Stuart Seropian
- Yale Cancer Center, New Haven, CT; Yale School of Medicine, New Haven, CT
| | - Terri L Parker
- Yale Cancer Center, New Haven, CT; Yale School of Medicine, New Haven, CT
| | | | | | | | | | - Lin Zhang
- Yale Cancer Center, New Haven, CT; Yale School of Medicine, New Haven, CT
| | - Rakesh Verma
- Yale Cancer Center, New Haven, CT; Yale School of Medicine, New Haven, CT
| | | | - Madhav V Dhodapkar
- Yale Cancer Center, New Haven, CT; Yale School of Medicine, New Haven, CT
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45
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Nachbagauer R, Choi A, Hirsh A, Margine I, Iida S, Barrera A, Ferres M, Albrecht RA, García-Sastre A, Bouvier NM, Ito K, Medina RA, Palese P, Krammer F. Defining the antibody cross-reactome directed against the influenza virus surface glycoproteins. Nat Immunol 2017; 18:464-473. [PMID: 28192418 PMCID: PMC5360498 DOI: 10.1038/ni.3684] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/06/2017] [Indexed: 12/14/2022]
Abstract
Influenza virus infections induce antibodies against the viral surface glycoproteins hemagglutinin and neuraminidase, and these responses can be broadly protective. To test the breadth and magnitude of antibody responses, mice, guinea pigs and ferrets were sequentially infected with divergent H1N1 or H3N2 viruses. Antibody responses were measured by ELISA against an extensive panel of recombinant glycoproteins representing the viral diversity in nature. Guinea pigs developed high titers of broadly cross-reactive antibodies; mice and ferrets exhibited narrower humoral responses. Then, we compared antibody responses after H1N1 or H3N2 infections in humans and found markedly broad responses and cogent evidence for original antigenic sin. This work will inform universal influenza vaccine design and can guide pandemic preparedness efforts against emerging influenza viruses.
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Affiliation(s)
- Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Angela Choi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ariana Hirsh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Irina Margine
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sayaka Iida
- Division of Bioinformatics, Hokkaido University Research Center for Zoonosis Control, Kitaku, Japan
| | - Aldo Barrera
- Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcela Ferres
- Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nicole M Bouvier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kimihito Ito
- Division of Bioinformatics, Hokkaido University Research Center for Zoonosis Control, Kitaku, Japan
| | - Rafael A Medina
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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46
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Hartmann BM, Albrecht RA, Marjanovic N, Sealfon SC. Suppression of dendritic cell necroptosis by pandemic influenza virus. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.78.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The public health risk of a new pandemic influenza virus (IAV) approaching the scope and mortality of the devastating 1918 strain makes it important to identify virus-host mechanisms unique to pandemic strains. Human dendritic cell infection by two different H1N1 seasonal IAV strains (1991 and 1999) induces widespread RNA degradation and programmed cell death beginning at 4 h after infection. Characteristic of necroptosis, the cell death showed nuclear condensation and fragmentation that was caspase independent and RIP3 kinase dependent. Notably, infection with the pandemic 1918 and 2009 H1N1 IAV strains did not induce dendritic cell RNA degradation and necroptosis. Furthermore, necroptosis induced in dendritic cells by poly I:C exposure was suppressed by concomitant infection with the pandemic 2009 IAV. These results indicate that infection with the pandemic viruses not only fails to induce the dendritic cell necroptosis seen with the seasonal IAV strains, but that it actively suppresses necroptosis. Virus chimera studies implicate the HA virus segment as mediating the necroptosis inhibition by the pandemic IAV strains. Necroptosis leads to the release of intracellular components which serve as danger associated molecular patterns (DAMP), making this a highly immunogenic cell death mechanism. Consistent with this view, we find that the suppression of virus-induced necroptosis by the pandemic IAV reduces T cell activation. These studies show that pandemic viruses are unique in suppressing a key immunological danger signal. The suppression of the generation of DAMPs from infected immune cells may contribute to the pathogenicity of pandemic H1N1 IAV viruses.
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Fribourg Casajuana ML, Hartmann BM, Tabbaa OP, Ramos I, Zaslavsky E, Nudelman G, Albrecht RA, Merad M, Hayot F, Jayaprakash C, Kleinstein SH, Garcia-Sastre A, Sealfon SC. Single cell variability in pro-inflammatory and antiviral gene responses in dendritic cells. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.202.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Type I interferons (IFNs) can have both protective and deleterious effects in chronic infection and autoimmune disease. Cellular responses to type I IFNs are mediated by IFN-stimulated genes (ISGs), are cell type-dependent, and likely cell specific. Varying responses of individual cells to immune signals, such as type I IFNs, may be critical in orchestrating context and microenvironment appropriate immune responses. Simulations of an agent-based mathematical model of viral infection suggested that within each cell, the levels of pro-inflammatory ISGs induced by STAT dimers and the antiviral ISGs induced by the ISGF-3 heterotrimer can show low correlation. We used RNAseq to study global single-cell correlation of ISG groups in human peripheral blood CD1c+ dendritic cells infected with an influenza A H1N1 virus. Consonant with the simulations, distinct groups of ISGs were identified that showed high levels of single cell expression correlation within, but low to negative correlations across ISG subgroups. Using multiple probe FISH we find low single cell correlation of the pro-inflammatory ISG IL6 and the antiviral ISG RIG-I induction in cells stimulated with type I IFN. The single cell correlations in the induction of the two genes were 0.56, 0.55 and 0.19 in human peripheral blood plasmacytoid dendritic cells, monocytes, and monocyte-derived dendritic cells respectively. The generation of uncorrelated pro-inflammatory and antiviral ISG single cell responses within a dendritic cell population can increase the breadth of the immune response to noxious stimuli.
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Loi M, Müller A, Steinbach K, Niven J, Barreira da Silva R, Paul P, Ligeon LA, Caruso A, Albrecht RA, Becker AC, Annaheim N, Nowag H, Dengjel J, García-Sastre A, Merkler D, Münz C, Gannagé M. Macroautophagy Proteins Control MHC Class I Levels on Dendritic Cells and Shape Anti-viral CD8(+) T Cell Responses. Cell Rep 2016; 15:1076-1087. [PMID: 27117419 DOI: 10.1016/j.celrep.2016.04.002] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/10/2016] [Accepted: 03/27/2016] [Indexed: 01/08/2023] Open
Abstract
The macroautophagy machinery has been implicated in MHC class II restricted antigen presentation. Here, we report that this machinery assists in the internalization of MHC class I molecules. In the absence of the autophagy factors Atg5 and Atg7, MHC class I surface levels are elevated due to decreased endocytosis and degradation. Internalization of MHC class I molecules occurs less efficiently if AAK1 cannot be recruited via Atg8/LC3B. In the absence of Atg-dependent MHC class I internalization, dendritic cells stimulate CD8(+) T cell responses more efficiently in vitro and in vivo. During viral infections, lack of Atg5 results in enhanced influenza- and LCMV-specific CD8(+) T cell responses in vivo. Elevated influenza-specific CD8(+) T cell responses are associated with better immune control of this infection. Thus, the macroautophagy machinery orchestrates T cell immunity by supporting MHC class II but compromises MHC class I restricted antigen presentation.
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Affiliation(s)
- Monica Loi
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, 8057 Zürich, Switzerland
| | - Anne Müller
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, 8057 Zürich, Switzerland
| | - Karin Steinbach
- Department of Pathology and Immunology, School of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Jennifer Niven
- Department of Pathology and Immunology, School of Medicine, University of Geneva, 1211 Geneva, Switzerland; Division of Rheumatology, Department of Internal Medicine, University Hospital, Geneva 1205, Switzerland
| | - Rosa Barreira da Silva
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, 8057 Zürich, Switzerland
| | - Petra Paul
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, 8057 Zürich, Switzerland
| | - Laure-Anne Ligeon
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, 8057 Zürich, Switzerland
| | - Assunta Caruso
- Department of Pathology and Immunology, School of Medicine, University of Geneva, 1211 Geneva, Switzerland; Division of Rheumatology, Department of Internal Medicine, University Hospital, Geneva 1205, Switzerland
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrea C Becker
- Department of Dermatology, Medical Center; ZBSA Center for Biological Systems Analysis; BIOSS Centre for Biological Signalling Studies; and FRIAS Freiburg Institute for Advanced Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Nicolas Annaheim
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, 8057 Zürich, Switzerland
| | - Heike Nowag
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, 8057 Zürich, Switzerland
| | - Jörn Dengjel
- Department of Dermatology, Medical Center; ZBSA Center for Biological Systems Analysis; BIOSS Centre for Biological Signalling Studies; and FRIAS Freiburg Institute for Advanced Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Doron Merkler
- Department of Pathology and Immunology, School of Medicine, University of Geneva, 1211 Geneva, Switzerland; Department of Neuropathology, University Medical Center, 37099 Göttingen, Germany
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, 8057 Zürich, Switzerland.
| | - Monique Gannagé
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, 8057 Zürich, Switzerland; Department of Pathology and Immunology, School of Medicine, University of Geneva, 1211 Geneva, Switzerland; Division of Rheumatology, Department of Internal Medicine, University Hospital, Geneva 1205, Switzerland.
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49
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Hussein ITM, Ma EJ, Hill NJ, Meixell BW, Lindberg M, Albrecht RA, Bahl J, Runstadler JA. A point mutation in the polymerase protein PB2 allows a reassortant H9N2 influenza isolate of wild-bird origin to replicate in human cells. Infect Genet Evol 2016; 41:279-288. [PMID: 27101787 DOI: 10.1016/j.meegid.2016.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/08/2016] [Accepted: 04/10/2016] [Indexed: 12/09/2022]
Abstract
H9N2 influenza A viruses are on the list of potentially pandemic subtypes. Therefore, it is important to understand how genomic reassortment and genetic polymorphisms affect phenotypes of H9N2 viruses circulating in the wild bird reservoir. A comparative genetic analysis of North American H9N2 isolates of wild bird origin identified a naturally occurring reassortant virus containing gene segments derived from both North American and Eurasian lineage ancestors. The PB2 segment of this virus encodes 10 amino acid changes that distinguish it from other H9 strains circulating in North America. G590S, one of the 10 amino acid substitutions observed, was present in ~12% of H9 viruses worldwide. This mutation combined with R591 has been reported as a marker of pathogenicity for human pandemic 2009 H1N1 viruses. Screening by polymerase reporter assay of all the natural polymorphisms at these two positions identified G590/K591 and S590/K591 as the most active, with the highest polymerase activity recorded for the SK polymorphism. Rescued viruses containing these two polymorphic combinations replicated more efficiently in MDCK cells and they were the only ones tested that were capable of establishing productive infection in NHBE cells. A global analysis of all PB2 sequences identified the K591 signature in six viral HA/NA subtypes isolated from several hosts in seven geographic locations. Interestingly, introducing the K591 mutation into the PB2 of a human-adapted H3N2 virus did not affect its polymerase activity. Our findings demonstrate that a single point mutation in the PB2 of a low pathogenic H9N2 isolate could have a significant effect on viral phenotype and increase its propensity to infect mammals. However, this effect is not universal, warranting caution in interpreting point mutations without considering protein sequence context.
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Affiliation(s)
- Islam T M Hussein
- Department of Biological Engineering and Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric J Ma
- Department of Biological Engineering and Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nichola J Hill
- Department of Biological Engineering and Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brandt W Meixell
- U.S. Geological Survey, Alaska Science Center, Anchorage, AK 99508, USA
| | - Mark Lindberg
- Institute of Arctic Biology, University of Alaska Fairbanks, AK 99775, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Justin Bahl
- Center for Infectious Diseases, The University of Texas School of Public Health, Houston, TX, USA
| | - Jonathan A Runstadler
- Department of Biological Engineering and Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA.
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50
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Thornburg NJ, Zhang H, Bangaru S, Sapparapu G, Kose N, Lampley RM, Bombardi RG, Yu Y, Graham S, Branchizio A, Yoder SM, Rock MT, Creech CB, Edwards KM, Lee D, Li S, Wilson IA, García-Sastre A, Albrecht RA, Crowe JE. H7N9 influenza virus neutralizing antibodies that possess few somatic mutations. J Clin Invest 2016; 126:1482-94. [PMID: 26950424 PMCID: PMC4811156 DOI: 10.1172/jci85317] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/21/2016] [Indexed: 01/08/2023] Open
Abstract
Avian H7N9 influenza viruses are group 2 influenza A viruses that have been identified as the etiologic agent for a current major outbreak that began in China in 2013 and may pose a pandemic threat. Here, we examined the human H7-reactive antibody response in 75 recipients of a monovalent inactivated A/Shanghai/02/2013 H7N9 vaccine. After 2 doses of vaccine, the majority of donors had memory B cells that secreted IgGs specific for H7 HA, with dominant responses against single HA subtypes, although frequencies of H7-reactive B cells ranged widely between donors. We isolated 12 naturally occurring mAbs with low half-maximal effective concentrations for binding, 5 of which possessed neutralizing and HA-inhibiting activities. The 5 neutralizing mAbs exhibited narrow breadth of reactivity with influenza H7 strains. Epitope-mapping studies using neutralization escape mutant analysis, deuterium exchange mass spectrometry, and x-ray crystallography revealed that these neutralizing mAbs bind near the receptor-binding pocket on HA. All 5 neutralizing mAbs possessed low numbers of somatic mutations, suggesting the clones arose from naive B cells. The most potent mAb, H7.167, was tested as a prophylactic treatment in a mouse intranasal virus challenge study, and systemic administration of the mAb markedly reduced viral lung titers.
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MESH Headings
- Adult
- Animals
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Binding Sites, Antibody/genetics
- Binding Sites, Antibody/immunology
- Epitope Mapping
- Epitopes/genetics
- Epitopes/immunology
- Female
- Humans
- Influenza A Virus, H7N9 Subtype/genetics
- Influenza A Virus, H7N9 Subtype/immunology
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/genetics
- Influenza Vaccines/immunology
- Male
- Mice
- Middle Aged
- Mutation
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Affiliation(s)
- Natalie J. Thornburg
- The Vanderbilt Vaccine Center and
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, USA
| | - Heng Zhang
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | | | - Gopal Sapparapu
- The Vanderbilt Vaccine Center and
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, USA
| | | | | | | | | | | | | | - Sandra M. Yoder
- The Vanderbilt Vaccine Center and
- Vanderbilt Vaccine Research Program, Vanderbilt University, Nashville, Tennessee, USA
| | - Michael T. Rock
- The Vanderbilt Vaccine Center and
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Vaccine Research Program, Vanderbilt University, Nashville, Tennessee, USA
| | - C. Buddy Creech
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Vaccine Research Program, Vanderbilt University, Nashville, Tennessee, USA
| | - Kathryn M. Edwards
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Vaccine Research Program, Vanderbilt University, Nashville, Tennessee, USA
| | - David Lee
- Department of Medicine and Biomedical Sciences Graduate Program, School of Medicine, UCSD, San Diego, California, USA
| | - Sheng Li
- Department of Medicine and Biomedical Sciences Graduate Program, School of Medicine, UCSD, San Diego, California, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Adolfo García-Sastre
- Department of Microbiology
- Global Health and Emerging Pathogens Institute, and
- Department of Medicine, Division of Infectious Diseases at Icahn School of Medicine at Mount Sinai (ISMMS), New York, New York, USA
| | - Randy A. Albrecht
- Department of Microbiology
- Global Health and Emerging Pathogens Institute, and
| | - James E. Crowe
- The Vanderbilt Vaccine Center and
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, USA
- Departments of Pathology, Microbiology, and Immunology, and
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