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Loeb K, Lemaille C, Frederick C, Wallace HL, Kindrachuk J. Harnessing high-throughput OMICS in emerging zoonotic virus preparedness and response activities. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167337. [PMID: 38986821 DOI: 10.1016/j.bbadis.2024.167337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Emerging and re-emerging viruses pose unpredictable and significant challenges to global health. Emerging zoonotic infectious diseases, which are transmitted between humans and non-human animals, have been estimated to be responsible for nearly two-thirds of emerging infectious disease events and emergence events attributed to these pathogens have been increasing in frequency with the potential for high global health and economic burdens. In this review we will focus on the application of highthroughput OMICS approaches to emerging zoonotic virus investigtations. We highlight the key contributions of transcriptome and proteome investigations to emerging zoonotic virus preparedness and response activities with a focus on SARS-CoV-2, avian influenza virus subtype H5N1, and Orthoebolavirus investigations.
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Affiliation(s)
- Kristi Loeb
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Candice Lemaille
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Christina Frederick
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Hannah L Wallace
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Jason Kindrachuk
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada; Manitoba Centre for Proteomics and Systems Biology, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada; Department of Internal Medicine, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada.
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2
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Sobarzo A, Moné Y, Lang S, Gelkop S, Brangel P, Kuehne AI, McKendry RA, Mell JC, Ahmed A, Davis C, Dye JM, Lutwama JJ, Lobel L, Veas F, Ehrlich GD. Long-term Sudan Virus Ebola Survivors Maintain Multiple Antiviral Defense Mechanisms. J Infect Dis 2024; 230:426-437. [PMID: 38066574 DOI: 10.1093/infdis/jiad555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND The critical issues of sustained memory immunity following ebolavirus disease among long-term survivors are still unclear. METHODS Here, we examine virus-specific immune and inflammatory responses following in vitro challengd in 12 Sudan virus (SUDV) long-term survivors from Uganda's 2000-2001 Gulu outbreak, 15 years after recovery. Total RNA from isolated SUDV-stimulated and unstimulated peripheral blood mononuclear cells was extracted and analyzed. Matched serum samples were also collected to determine SUDV IgG levels and functionality. RESULTS We detected persistent humoral (58%, 7 of 12) and cellular (33%, 4 of 12) immune responses in SUDV long-term survivors and identified critical molecular mechanisms of innate and adaptive immunity. Gene expression in immune pathways, the interferon signaling system, antiviral defense response, and activation and regulation of T- and B-cell responses were observed. SUDV long-term survivors also maintained robust virus-specific IgG antibodies capable of polyfunctional responses, including neutralizing and innate Fc effector functions. CONCLUSIONS Data integration identified significant correlations among humoral and cellular immune responses and pinpointed a specific innate and adaptive gene expression signature associated with long-lasting immunity. This could help identify natural and vaccine correlates of protection against ebolavirus disease.
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MESH Headings
- Hemorrhagic Fever, Ebola/immunology
- Hemorrhagic Fever, Ebola/virology
- Humans
- Ebolavirus/immunology
- Survivors
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Uganda/epidemiology
- Adult
- Female
- Male
- Immunoglobulin G/blood
- Immunoglobulin G/immunology
- Immunity, Innate
- Leukocytes, Mononuclear/immunology
- Immunity, Humoral
- Middle Aged
- Immunity, Cellular
- Adaptive Immunity
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
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Affiliation(s)
- Ariel Sobarzo
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- The Pre-Clinical Research Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yves Moné
- Department of Microbiology and Immunology, Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Genomic Core Facility, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Steven Lang
- Department of Microbiology and Immunology, Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Genomic Core Facility, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Sigal Gelkop
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Polina Brangel
- London Centre for Nanotechnology, Division of Medicine, University College London, London, United Kingdom
| | - Ana I Kuehne
- Viral Immunology Branch, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Rachel A McKendry
- London Centre for Nanotechnology, Division of Medicine, University College London, London, United Kingdom
| | - Joshua Chang Mell
- Department of Microbiology and Immunology, Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Genomic Core Facility, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Azad Ahmed
- Department of Microbiology and Immunology, Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Genomic Core Facility, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Claytus Davis
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - John M Dye
- Viral Immunology Branch, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Julius Julian Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infection, Uganda Virus Research Institute, Entebbe, Uganda
| | - Leslie Lobel
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Francisco Veas
- Molecular Comparative Immuno-Physiopathology Lab, French Institute of Research for Development Health Branch of UMR5151 and UMR Research Unit-Ministry of Defense, Faculty of Pharmacy, University of Montpellier, Montpellier, France
- Copernicus Integrated Solutions for Biosafety Risks, Faculty of Pharmacy, Montpellier University Montpellier, France
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Genomic Core Facility, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
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3
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Fletcher P, Clancy CS, O’Donnell KL, Doratt BM, Malherbe DC, Rhoderick JF, Feldmann F, Hanley PW, Takada A, Messaoudi I, Marzi A. Pathogenic differences of cynomolgus macaques after Taï Forest virus infection depend on the viral stock propagation. PLoS Pathog 2024; 20:e1012290. [PMID: 38861571 PMCID: PMC11195944 DOI: 10.1371/journal.ppat.1012290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/24/2024] [Accepted: 05/24/2024] [Indexed: 06/13/2024] Open
Abstract
Taï Forest virus (TAFV) is a negative-sense RNA virus in the Filoviridae family. TAFV has caused only a single human infection, but several disease outbreaks in chimpanzees have been linked to this virus. Limited research has been done on this human-pathogenic virus. We sought to establish an animal model to assess TAFV disease progression and pathogenicity at our facility. We had access to two different viral stock preparations from different institutions, both originating from the single human case. Type I interferon receptor knockout mice were inoculated with TAFV stock 1 or stock 2 by the intraperitoneal route. Inoculation resulted in 100% survival with no disease regardless of viral stock preparation or infectious dose. Next, cynomolgus macaques were inoculated with TAFV stock 1 or stock 2. Inoculation with TAFV stock 1 resulted in 100% survival and robust TAFV glycoprotein-specific IgG responses including neutralizing antibodies. In contrast, macaques infected with TAFV stock 2 developed disease and were euthanized 8-11 days after infection exhibiting viremia, thrombocytopenia, and increased inflammatory mediators identified by transcriptional analysis. Histopathologic analysis of tissue samples collected at necropsy confirmed classic filovirus disease in numerous organs. Genomic differences in both stock preparations were mapped to several viral genes which may have contributed to disease severity. Taken together, we demonstrate that infection with the two TAFV stocks resulted in no disease in mice and opposing disease phenotypes in cynomolgus macaques, highlighting the impact of viral stock propagation on pathogenicity in animal models.
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Affiliation(s)
- Paige Fletcher
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Chad S. Clancy
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Kyle L. O’Donnell
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Brianna M. Doratt
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, United States of America
| | - Delphine C. Malherbe
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, United States of America
| | - Joseph F. Rhoderick
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Patrick W. Hanley
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, United States of America
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
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4
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Ratnasiri K, Zheng H, Toh J, Yao Z, Duran V, Donato M, Roederer M, Kamath M, Todd JPM, Gagne M, Foulds KE, Francica JR, Corbett KS, Douek DC, Seder RA, Einav S, Blish CA, Khatri P. Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans. Cell Rep 2024; 43:113706. [PMID: 38294906 PMCID: PMC10915397 DOI: 10.1016/j.celrep.2024.113706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/02/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Viral pandemics and epidemics pose a significant global threat. While macaque models of viral disease are routinely used, it remains unclear how conserved antiviral responses are between macaques and humans. Therefore, we conducted a cross-species analysis of transcriptomic data from over 6,088 blood samples from macaques and humans infected with one of 31 viruses. Our findings demonstrate that irrespective of primate or viral species, there are conserved antiviral responses that are consistent across infection phase (acute, chronic, or latent) and viral genome type (DNA or RNA viruses). Leveraging longitudinal data from experimental challenges, we identify virus-specific response kinetics such as host responses to Coronaviridae and Orthomyxoviridae infections peaking 1-3 days earlier than responses to Filoviridae and Arenaviridae viral infections. Our results underscore macaque studies as a powerful tool for understanding viral pathogenesis and immune responses that translate to humans, with implications for viral therapeutic development and pandemic preparedness.
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Affiliation(s)
- Kalani Ratnasiri
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jiaying Toh
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhiyuan Yao
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Veronica Duran
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Michele Donato
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megha Kamath
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John-Paul M Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph R Francica
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shirit Einav
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Catherine A Blish
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.
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5
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Guito JC, Arnold CE, Schuh AJ, Amman BR, Sealy TK, Spengler JR, Harmon JR, Coleman-McCray JD, Sanchez-Lockhart M, Palacios GF, Towner JS, Prescott JB. Peripheral immune responses to filoviruses in a reservoir versus spillover hosts reveal transcriptional correlates of disease. Front Immunol 2024; 14:1306501. [PMID: 38259437 PMCID: PMC10800976 DOI: 10.3389/fimmu.2023.1306501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/27/2023] [Indexed: 01/24/2024] Open
Abstract
Several filoviruses, including Marburg virus (MARV), cause severe disease in humans and nonhuman primates (NHPs). However, the Egyptian rousette bat (ERB, Rousettus aegyptiacus), the only known MARV reservoir, shows no overt illness upon natural or experimental infection, which, like other bat hosts of zoonoses, is due to well-adapted, likely species-specific immune features. Despite advances in understanding reservoir immune responses to filoviruses, ERB peripheral blood responses to MARV and how they compare to those of diseased filovirus-infected spillover hosts remain ill-defined. We thus conducted a longitudinal analysis of ERB blood gene responses during acute MARV infection. These data were then contrasted with a compilation of published primate blood response studies to elucidate gene correlates of filovirus protection versus disease. Our work expands on previous findings in MARV-infected ERBs by supporting both host resistance and disease tolerance mechanisms, offers insight into the peripheral immunocellular repertoire during infection, and provides the most direct known cross-examination between reservoir and spillover hosts of the most prevalently-regulated response genes, pathways and activities associated with differences in filovirus pathogenesis and pathogenicity.
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Affiliation(s)
- Jonathan C. Guito
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Catherine E. Arnold
- Biological Defense Research Directorate, Naval Medical Research Center, Frederick, MD, United States
- RD-CBR, Research and Development Directorate, Chemical and Biological Technologies Directorate, Research Center of Excellence, Defense Threat Reduction Agency, Fort Belvoir, VA, United States
| | - Amy J. Schuh
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Brian R. Amman
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Tara K. Sealy
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jessica R. Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jessica R. Harmon
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Joann D. Coleman-McCray
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, Molecular Biology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - Gustavo F. Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jonathan S. Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Joseph B. Prescott
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
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6
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Normandin E, Triana S, Raju SS, Lan TCT, Lagerborg K, Rudy M, Adams GC, DeRuff KC, Logue J, Liu D, Strebinger D, Rao A, Messer KS, Sacks M, Adams RD, Janosko K, Kotliar D, Shah R, Crozier I, Rinn JL, Melé M, Honko AN, Zhang F, Babadi M, Luban J, Bennett RS, Shalek AK, Barkas N, Lin AE, Hensley LE, Sabeti PC, Siddle KJ. Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses. CELL GENOMICS 2023; 3:100440. [PMID: 38169842 PMCID: PMC10759212 DOI: 10.1016/j.xgen.2023.100440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/27/2023] [Accepted: 10/15/2023] [Indexed: 01/05/2024]
Abstract
Ebola virus (EBOV) causes Ebola virus disease (EVD), marked by severe hemorrhagic fever; however, the mechanisms underlying the disease remain unclear. To assess the molecular basis of EVD across time, we performed RNA sequencing on 17 tissues from a natural history study of 21 rhesus monkeys, developing new methods to characterize host-pathogen dynamics. We identified alterations in host gene expression with previously unknown tissue-specific changes, including downregulation of genes related to tissue connectivity. EBOV was widely disseminated throughout the body; using a new, broadly applicable deconvolution method, we found that viral load correlated with increased monocyte presence. Patterns of viral variation between tissues differentiated primary infections from compartmentalized infections, and several variants impacted viral fitness in a EBOV/Kikwit minigenome system, suggesting that functionally significant variants can emerge during early infection. This comprehensive portrait of host-pathogen dynamics in EVD illuminates new features of pathogenesis and establishes resources to study other emerging pathogens.
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Affiliation(s)
- Erica Normandin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sergio Triana
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA.
| | - Siddharth S Raju
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Tammy C T Lan
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Molecular and Cellular Biology, Harvard University, Boston, MA, USA
| | - Kim Lagerborg
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Melissa Rudy
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Gordon C Adams
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - James Logue
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - David Liu
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Daniel Strebinger
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arya Rao
- Columbia University, New York, NY, USA; Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA 02115, USA
| | | | - Molly Sacks
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ricky D Adams
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Krisztina Janosko
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Dylan Kotliar
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rickey Shah
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Catalonia, Spain
| | - Anna N Honko
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Feng Zhang
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mehrtash Babadi
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jeremy Luban
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA; Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Richard S Bennett
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Alex K Shalek
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Nikolaos Barkas
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Aaron E Lin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Katherine J Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.
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7
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Ambikan AT, Elaldi N, Svensson-Akusjärvi S, Bagci B, Pektas AN, Hewson R, Bagci G, Arasli M, Appelberg S, Mardinoglu A, Sood V, Végvári Á, Benfeitas R, Gupta S, Cetin I, Mirazimi A, Neogi U. Systems-level temporal immune-metabolic profile in Crimean-Congo hemorrhagic fever virus infection. Proc Natl Acad Sci U S A 2023; 120:e2304722120. [PMID: 37669378 PMCID: PMC10500270 DOI: 10.1073/pnas.2304722120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/21/2023] [Indexed: 09/07/2023] Open
Abstract
Crimean-Congo hemorrhagic fever (CCHF) caused by CCHF virus (CCHFV) is one of the epidemic-prone diseases prioritized by the World Health Organisation as public health emergency with an urgent need for accelerated research. The trajectory of host response against CCHFV is multifarious and remains unknown. Here, we reported the temporal spectrum of pathogenesis following the CCHFV infection using genome-wide blood transcriptomics analysis followed by advanced systems biology analysis, temporal immune-pathogenic alterations, and context-specific progressive and postinfection genome-scale metabolic models (GSMM) on samples collected during the acute (T0), early convalescent (T1), and convalescent-phase (T2). The interplay between the retinoic acid-inducible gene-I-like/nucleotide-binding oligomerization domain-like receptor and tumor necrosis factor signaling governed the trajectory of antiviral immune responses. The rearrangement of intracellular metabolic fluxes toward the amino acid metabolism and metabolic shift toward oxidative phosphorylation and fatty acid oxidation during acute CCHFV infection determine the pathogenicity. The upregulation of the tricarboxylic acid cycle during CCHFV infection, compared to the noninfected healthy control and between the severity groups, indicated an increased energy demand and cellular stress. The upregulation of glycolysis and pyruvate metabolism potentiated energy generation through alternative pathways associated with the severity of the infection. The downregulation of metabolic processes at the convalescent phase identified by blood cell transcriptomics and single-cell type proteomics of five immune cells (CD4+ and CD8+ T cells, CD14+ monocytes, B cells, and NK cells) potentially leads to metabolic rewiring through the recovery due to hyperactivity during the acute phase leading to post-viral fatigue syndrome.
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Affiliation(s)
- Anoop T. Ambikan
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm-14152, Sweden
| | - Nazif Elaldi
- Department of Infectious Diseases and Clinical Microbiology, Medical Faculty, Sivas Cumhuriyet University, Sivas58140, Turkey
| | - Sara Svensson-Akusjärvi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm-14152, Sweden
| | - Binnur Bagci
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Sivas Cumhuriyet University, Sivas, Turkey
| | - Ayse Nur Pektas
- Cumhuriyet University Advanced Technology Application and Research Center, Sivas Cumhuriyet University, Sivas58140, Turkey
| | - Roger Hewson
- United Kingdom Health Security Agency, Porton Down, Salisbury, WiltshireSP4 0JG, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Gokhan Bagci
- Department of Biochemistry, Faculty of Medicine, Altinbas University, Istanbul34147, Turkey
| | - Mehmet Arasli
- Department of Immunology, Medical Faculty, Bulent Ecevit University, Zonguldak67600, Turkey
| | - Sofia Appelberg
- Public Health Agency of Sweden, Solna, Stockholm-17165, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, Kungliga Tekniska Högskolan–Royal Institute of Technology, Stockholm-17121, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, LondonWC2R 2LS, United Kingdom
| | - Vikas Sood
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm-14152, Sweden
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard University, Delhi110062, India
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm-17177, Sweden
| | - Rui Benfeitas
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm-14152, Sweden
| | - Soham Gupta
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm-14152, Sweden
| | - Ilhan Cetin
- Department of Public Health, Medical Faculty, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - Ali Mirazimi
- Public Health Agency of Sweden, Solna, Stockholm-17165, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm-14152, Sweden
- National Veterinary Institute, Uppsala-75189, Sweden
| | - Ujjwal Neogi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm-14152, Sweden
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8
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Speranza E. Understanding virus-host interactions in tissues. Nat Microbiol 2023; 8:1397-1407. [PMID: 37488255 DOI: 10.1038/s41564-023-01434-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/20/2023] [Indexed: 07/26/2023]
Abstract
Although virus-host interactions are usually studied in a single cell type using in vitro assays in immortalized cell lines or isolated cell populations, it is important to remember that what is happening inside one infected cell does not translate to understanding how an infected cell behaves in a tissue, organ or whole organism. Infections occur in complex tissue environments, which contain a host of factors that can alter the course of the infection, including immune cells, non-immune cells and extracellular-matrix components. These factors affect how the host responds to the virus and form the basis of the protective response. To understand virus infection, tools are needed that can profile the tissue environment. This Review highlights methods to study virus-host interactions in the infection microenvironment.
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Affiliation(s)
- Emily Speranza
- Cleveland Clinic Lerner Research Institute, Port Saint Lucie, FL, USA.
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9
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Doughan A, Adingo W, Salifu SP. RNA-seq research landscape in Africa: systematic review reveals disparities and opportunities. Eur J Med Res 2023; 28:244. [PMID: 37480073 PMCID: PMC10362609 DOI: 10.1186/s40001-023-01206-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 06/30/2023] [Indexed: 07/23/2023] Open
Abstract
RNA sequencing has emerged as the standard method for transcriptome profiling of several human diseases. We performed a systematic review detailing the state of RNA-seq analyses in Africa from its inception till February 2022. Our goal was to provide an update on the state of RNA-seq analyses in Africa, including research gaps, funding information, participants information, authorship and collaborations. Following the PRISMA guidelines, we performed an exhaustive literature search for RNA-seq studies conducted in Africa, using PubMed, Scopus and Academic Search Complete (EBSCOhost). The output was exported to Endnote X9 for analyses. The initial literature search yielded 10,369 articles spread across PubMed (4916), Scopus (4847) and EBSCOhost (580). By applying our exclusion criteria, 28 full-text articles remained and were thoroughly analyzed. Overall, 17 human diseases were studied, including cancers (10/28), infectious disease (4/28), parasitic disease (4/28), autoimmune disorders (2/28) and neglected tropical diseases (2/28). Majority of the articles were published in PLoS Pathogens, BioMed Central and Nature. The National Institutes of Health (42.4%), the Bill & Melinda Gates Foundation (7.5%) and the Wellcome Trust (7.5%) were the top funders of the research studies. Eleven African countries contributed to the participant group, with 57% located in Eastern Africa, 23.1% from Western and 16.7% from Southern Africa. The extremely low number of RNA-seq research studies in Africa is worrying and calls for an immediate investment in research by the African governments. The funding agencies and institutional review boards should also ensure that African collaborators are treated equitably in the course of the research projects.
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Affiliation(s)
- Albert Doughan
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Wisdom Adingo
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Samson Pandam Salifu
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana.
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana.
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10
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Dong X, Tree J, Banadyga L, He S, Zhu W, Tipton T, Gouriet J, Qiu X, Elmore MJ, Hall Y, Carroll M, Hiscox JA. Linked Mutations in the Ebola Virus Polymerase Are Associated with Organ Specific Phenotypes. Microbiol Spectr 2023; 11:e0415422. [PMID: 36946725 PMCID: PMC10101120 DOI: 10.1128/spectrum.04154-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/20/2023] [Indexed: 03/23/2023] Open
Abstract
Ebola virus (EBOV) causes a severe infection called Ebola virus disease (EVD). The pathogenesis of EBOV infection is complex, and outcome has been associated with a variety of immunological and cellular factors. Disease can result from several mechanisms, including direct organ and endothelial cell damage as a result of viral replication. During the2013 to 2016 Western Africa EBOV outbreak, several mutants emerged, with changes in the genes of nucleoprotein (NP), glycoprotein (GP), and the large (L) protein. Reverse genetic analysis has been used to investigate whether these mutations played any role in pathogenesis with mixed results depending on the experimental system used. Previous studies investigated the impact of three single nonsynonymous mutations (GP-A82V, NP-R111C, and L-D759G) on the fatality rate of mouse and ferret models and suggested that the L-D759G mutation decreased the virulence of EBOV. In this study, the effect of these three mutations was further evaluated by deep sequencing to determine viral population genetics and the host response in longitudinal samples of blood, liver, kidney, spleen, and lung tissues taken from the previous ferret model. The data indicated that the mutations were maintained in the different tissues, but the frequency of minor genomic mutations were different. In addition, compared to wild-type virus, the recombinant mutants had different within host effects, where the D759G (and accompanying Q986H) substitution in the L protein resulted in an upregulation of the immune response in the kidney, liver, spleen, and lungs. Together these studies provide insights into the biology of EBOV mutants both between and within hosts. IMPORTANCE Ebola virus infection can have dramatic effects on the human body which manifest in Ebola virus disease. The outcome of infection is either survival or death and in the former group with the potential of longer-term health consequences and persistent infection. Disease severity is undoubtedly associated with the host response, often with overt inflammatory responses correlated with poorer outcomes. The scale of the2013 to 2016 Western African Ebola virus outbreak revealed new aspects of viral biology. This included the emergence of mutants with potentially altered virulence. Biobanked tissue from ferret models of EBOV infected with different mutants that emerged in the Western Africa outbreak was used to investigate the effect of EBOV genomic variation in different tissues. Overall, the work provided insights into the population genetics of EBOV and showed that different organs in an animal model can respond differently to variants of EBOV.
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Affiliation(s)
- Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Julia Tree
- UK-Health Security Agency, Salisbury, United Kingdom
| | - Logan Banadyga
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Shihua He
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Wenjun Zhu
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Tom Tipton
- UK-Health Security Agency, Salisbury, United Kingdom
| | - Jade Gouriet
- UK-Health Security Agency, Salisbury, United Kingdom
| | - Xiangguo Qiu
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | | | - Yper Hall
- UK-Health Security Agency, Salisbury, United Kingdom
| | - Miles Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
- Pandemic Sciences Institute, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Infectious Diseases Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore
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11
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Spengler JR, Welch SR, Ritter JM, Harmon JR, Coleman-McCray JD, Genzer SC, Seixas JN, Scholte FEM, Davies KA, Bradfute SB, Montgomery JM, Spiropoulou CF. Mouse models of Ebola virus tolerance and lethality: characterization of CD-1 mice infected with wild-type, guinea pig-adapted, or mouse-adapted virus. Antiviral Res 2023; 210:105496. [PMID: 36567020 DOI: 10.1016/j.antiviral.2022.105496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Development of lethal models of Ebola virus disease has been achieved by the serial passage of virus isolates from human cases in mice and guinea pigs. Use of mice infected with non-adapted virus has been limited due to the absence of overt clinical disease. In recent years, newly recognized sequelae identified in human cases has highlighted the importance of continued investigations of non-lethal infection both in humans and animal models. Here, we revisit the use of rodent-adapted and non-adapted Ebola virus (EBOV) in mice to investigate infection tolerance and future utility of these models in pathogenesis and therapeutic intervention studies. We found that like non-adapted wild-type EBOV, guinea pig-adapted EBOV resulted in widespread tissue infection, variably associated with tissue pathology, and alterations in clinical and immunological analytes in the absence of overt disease. Notably, infection with either non-lethal variant did not greatly differ from lethal mouse-adapted EBOV until near the time end-point criteria are reached in these mice. These data support future investigations of pathogenesis, convalescence, and sequelae in mouse models of virus tolerance.
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Affiliation(s)
- Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Stephen R Welch
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jana M Ritter
- Infectious Disease Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jessica R Harmon
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - JoAnn D Coleman-McCray
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sarah C Genzer
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Josilene N Seixas
- Infectious Disease Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Florine E M Scholte
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Katherine A Davies
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Steven B Bradfute
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Joel M Montgomery
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
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12
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Jayaprakash AD, Ronk AJ, Prasad AN, Covington MF, Stein KR, Schwarz TM, Hekmaty S, Fenton KA, Geisbert TW, Basler CF, Bukreyev A, Sachidanandam R. Marburg and Ebola Virus Infections Elicit a Complex, Muted Inflammatory State in Bats. Viruses 2023; 15:350. [PMID: 36851566 PMCID: PMC9958679 DOI: 10.3390/v15020350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/21/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
The Marburg and Ebola filoviruses cause a severe, often fatal, disease in humans and nonhuman primates but have only subclinical effects in bats, including Egyptian rousettes, which are a natural reservoir of Marburg virus. A fundamental question is why these viruses are highly pathogenic in humans but fail to cause disease in bats. To address this question, we infected one cohort of Egyptian rousette bats with Marburg virus and another cohort with Ebola virus and harvested multiple tissues for mRNA expression analysis. While virus transcripts were found primarily in the liver, principal component analysis (PCA) revealed coordinated changes across multiple tissues. Gene signatures in kidney and liver pointed at induction of vasodilation, reduction in coagulation, and changes in the regulation of iron metabolism. Signatures of immune response detected in spleen and liver indicated a robust anti-inflammatory state signified by macrophages in the M2 state and an active T cell response. The evolutionary divergence between bats and humans of many responsive genes might provide a framework for understanding the differing outcomes upon infection by filoviruses. In this study, we outline multiple interconnected pathways that respond to infection by MARV and EBOV, providing insights into the complexity of the mechanisms that enable bats to resist the disease caused by filoviral infections. The results have the potential to aid in the development of new strategies to effectively mitigate and treat the disease caused by these viruses in humans.
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Affiliation(s)
| | - Adam J. Ronk
- Department of Pathology, the University Texas Medical Branch, Galveston, TX 77555, USA
- Galveston National Laboratory, the University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Abhishek N. Prasad
- Department of Pathology, the University Texas Medical Branch, Galveston, TX 77555, USA
- Galveston National Laboratory, the University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Kathryn R. Stein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Toni M. Schwarz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Saboor Hekmaty
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karla A. Fenton
- Galveston National Laboratory, the University of Texas Medical Branch, Galveston, TX 77555, USA
- Department Microbiology & Immunology, the University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Thomas W. Geisbert
- Galveston National Laboratory, the University of Texas Medical Branch, Galveston, TX 77555, USA
- Department Microbiology & Immunology, the University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Christopher F. Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Bukreyev
- Department of Pathology, the University Texas Medical Branch, Galveston, TX 77555, USA
- Galveston National Laboratory, the University of Texas Medical Branch, Galveston, TX 77555, USA
- Department Microbiology & Immunology, the University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ravi Sachidanandam
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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13
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Gedda MR, Danaher P, Shao L, Ongkeko M, Chen L, Dinh A, Thioye Sall M, Reddy OL, Bailey C, Wahba A, Dzekunova I, Somerville R, De Giorgi V, Jin P, West K, Panch SR, Stroncek DF. Longitudinal transcriptional analysis of peripheral blood leukocytes in COVID-19 convalescent donors. J Transl Med 2022; 20:587. [PMID: 36510222 PMCID: PMC9742656 DOI: 10.1186/s12967-022-03751-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND SARS-CoV2 can induce a strong host immune response. Many studies have evaluated antibody response following SARS-CoV2 infections. This study investigated the immune response and T cell receptor diversity in people who had recovered from SARS-CoV2 infection (COVID-19). METHODS Using the nCounter platform, we compared transcriptomic profiles of 162 COVID-19 convalescent donors (CCD) and 40 healthy donors (HD). 69 of the 162 CCDs had two or more time points sampled. RESULTS After eliminating the effects of demographic factors, we found extensive differential gene expression up to 241 days into the convalescent period. The differentially expressed genes were involved in several pathways, including virus-host interaction, interleukin and JAK-STAT signaling, T-cell co-stimulation, and immune exhaustion. A subset of 21 CCD samples was found to be highly "perturbed," characterized by overexpression of PLAU, IL1B, NFKB1, PLEK, LCP2, IRF3, MTOR, IL18BP, RACK1, TGFB1, and others. In addition, one of the clusters, P1 (n = 8) CCD samples, showed enhanced TCR diversity in 7 VJ pairs (TRAV9.1_TCRVA_014.1, TRBV6.8_TCRVB_016.1, TRAV7_TCRVA_008.1, TRGV9_ENST00000444775.1, TRAV18_TCRVA_026.1, TRGV4_ENST00000390345.1, TRAV11_TCRVA_017.1). Multiplexed cytokine analysis revealed anomalies in SCF, SCGF-b, and MCP-1 expression in this subset. CONCLUSIONS Persistent alterations in inflammatory pathways and T-cell activation/exhaustion markers for months after active infection may help shed light on the pathophysiology of a prolonged post-viral syndrome observed following recovery from COVID-19 infection. Future studies may inform the ability to identify druggable targets involving these pathways to mitigate the long-term effects of COVID-19 infection. TRIAL REGISTRATION https://clinicaltrials.gov/ct2/show/NCT04360278 Registered April 24, 2020.
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Affiliation(s)
- Mallikarjuna R. Gedda
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA ,grid.280030.90000 0001 2150 6316Section of Retinal Ganglion Cell Biology, Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Patrick Danaher
- grid.510973.90000 0004 5375 2863NanoString Technologies, Seattle, WA 98109 USA
| | - Lipei Shao
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Martin Ongkeko
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Leonard Chen
- grid.94365.3d0000 0001 2297 5165Blood Services Section, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Anh Dinh
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Mame Thioye Sall
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Opal L. Reddy
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Christina Bailey
- grid.510973.90000 0004 5375 2863NanoString Technologies, Seattle, WA 98109 USA
| | - Amy Wahba
- grid.510973.90000 0004 5375 2863NanoString Technologies, Seattle, WA 98109 USA
| | - Inna Dzekunova
- grid.510973.90000 0004 5375 2863NanoString Technologies, Seattle, WA 98109 USA
| | - Robert Somerville
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Valeria De Giorgi
- grid.94365.3d0000 0001 2297 5165Infectious Disease Section, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Ping Jin
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Kamille West
- grid.94365.3d0000 0001 2297 5165Blood Services Section, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sandhya R. Panch
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA ,grid.34477.330000000122986657Department of Medicine (Hematology Division), University of Washington/Fred Hutchinson Cancer Center, Seattle, WA 98109 USA
| | - David F. Stroncek
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
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14
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Penrice-Randal R, Dong X, Shapanis AG, Gardner A, Harding N, Legebeke J, Lord J, Vallejo AF, Poole S, Brendish NJ, Hartley C, Williams AP, Wheway G, Polak ME, Strazzeri F, Schofield JPR, Skipp PJ, Hiscox JA, Clark TW, Baralle D. Blood gene expression predicts intensive care unit admission in hospitalised patients with COVID-19. Front Immunol 2022; 13:988685. [PMID: 36203591 PMCID: PMC9530807 DOI: 10.3389/fimmu.2022.988685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe COVID-19 pandemic has created pressure on healthcare systems worldwide. Tools that can stratify individuals according to prognosis could allow for more efficient allocation of healthcare resources and thus improved patient outcomes. It is currently unclear if blood gene expression signatures derived from patients at the point of admission to hospital could provide useful prognostic information.MethodsGene expression of whole blood obtained at the point of admission from a cohort of 78 patients hospitalised with COVID-19 during the first wave was measured by high resolution RNA sequencing. Gene signatures predictive of admission to Intensive Care Unit were identified and tested using machine learning and topological data analysis, TopMD.ResultsThe best gene expression signature predictive of ICU admission was defined using topological data analysis with an accuracy: 0.72 and ROC AUC: 0.76. The gene signature was primarily based on differentially activated pathways controlling epidermal growth factor receptor (EGFR) presentation, Peroxisome proliferator-activated receptor alpha (PPAR-α) signalling and Transforming growth factor beta (TGF-β) signalling.ConclusionsGene expression signatures from blood taken at the point of admission to hospital predicted ICU admission of treatment naïve patients with COVID-19.
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Affiliation(s)
- Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- TopMD Precision Medicine Ltd, Southampton, United Kingdom
- *Correspondence: Rebekah Penrice-Randal,
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Andrew George Shapanis
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Aaron Gardner
- TopMD Precision Medicine Ltd, Southampton, United Kingdom
| | | | - Jelmer Legebeke
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
| | - Jenny Lord
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andres F. Vallejo
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Stephen Poole
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Nathan J. Brendish
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Catherine Hartley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Anthony P. Williams
- Cancer Sciences Division, Faculty of Medicine, University Hospital Southampton, Southampton, United Kingdom
| | - Gabrielle Wheway
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Marta E. Polak
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | - Paul J. Skipp
- TopMD Precision Medicine Ltd, Southampton, United Kingdom
- Centre for Proteomic Research, School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- ASTAR Infectious Diseases Laboratories (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR) Singapore, Singapore, Singapore
| | - Tristan W. Clark
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
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15
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Scoon WA, Mancio-Silva L, Suder EL, Villacorta-Martin C, Lindstrom-Vautrin J, Bernbaum JG, Mazur S, Johnson RF, Olejnik J, Flores EY, Mithal A, Wang F, Hume AJ, Kaserman JE, March-Riera S, Wilson AA, Bhatia SN, Mühlberger E, Mostoslavsky G. Ebola virus infection induces a delayed type I IFN response in bystander cells and the shutdown of key liver genes in human iPSC-derived hepatocytes. Stem Cell Reports 2022; 17:2286-2302. [PMID: 36084636 PMCID: PMC9561183 DOI: 10.1016/j.stemcr.2022.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 01/26/2023] Open
Abstract
Liver damage and an exacerbated inflammatory response are hallmarks of Ebola virus (EBOV) infection. Little is known about the intrinsic response to infection in human hepatocytes and their contribution to inflammation. Here, we present an induced pluripotent stem cell (iPSC)-derived hepatocyte-like cell (HLC) platform to define the hepato-intrinsic response to EBOV infection. We used this platform to show robust EBOV infection, with characteristic ultrastructural changes and evidence for viral replication. Transcriptomics analysis revealed a delayed response with minimal early transcriptomic changes, followed by a general downregulation of hepatic function and upregulation of interferon signaling, providing a potential mechanism by which hepatocytes participate in disease severity and liver damage. Using RNA-fluorescence in situ hybridization (FISH), we showed that IFNB1 and CXCL10 were mainly expressed in non-infected bystander cells. We did not observe an inflammatory signature during infection. In conclusion, iPSC-HLCs are an immune competent platform to study responses to EBOV infection.
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Affiliation(s)
- Whitney A. Scoon
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, 620 Albany Street, Boston, MA 02118, USA,Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Liliana Mancio-Silva
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, MA 02139, USA
| | - Ellen L. Suder
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, 620 Albany Street, Boston, MA 02118, USA,Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA
| | - Jonathan Lindstrom-Vautrin
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA
| | - John G. Bernbaum
- Integrated Research Facility, Division of Clinical Research, National Institute for Allergy and Infectious Disease, National Institutes of Health, Frederick, MD 21702, USA
| | - Steve Mazur
- Integrated Research Facility, Division of Clinical Research, National Institute for Allergy and Infectious Disease, National Institutes of Health, Frederick, MD 21702, USA
| | - Reed F. Johnson
- Integrated Research Facility, Division of Clinical Research, National Institute for Allergy and Infectious Disease, National Institutes of Health, Frederick, MD 21702, USA,Emerging Viral Pathogens Section, Laboratory of Immunoregulation, Division of Intramural Research, National Institute for Allergy and Infectious Disease, National Institutes of Health, Frederick, MD 21702, USA
| | - Judith Olejnik
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, 620 Albany Street, Boston, MA 02118, USA,Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Elizabeth Y. Flores
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, 620 Albany Street, Boston, MA 02118, USA,Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Aditya Mithal
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA,Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Feiya Wang
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA
| | - Adam J. Hume
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, 620 Albany Street, Boston, MA 02118, USA,Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Joseph E. Kaserman
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Sandra March-Riera
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, MA 02139, USA
| | - Andrew A. Wilson
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Sangeeta N. Bhatia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, MA 02139, USA,Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA,Broad Institute, Cambridge, MA 02139, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Elke Mühlberger
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, 620 Albany Street, Boston, MA 02118, USA; Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA.
| | - Gustavo Mostoslavsky
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, 670 Albany Street, Suite 209, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, 620 Albany Street, Boston, MA 02118, USA; Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA; Section of Gastroenterology, Department of Medicine, Boston University School of Medicine, 670 Albany Street, Suite 209, Boston, MA 02118, USA.
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16
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Cruz-Pulido D, Ouma WZ, Kenney SP. Differing coronavirus genres alter shared host signaling pathways upon viral infection. Sci Rep 2022; 12:9744. [PMID: 35697915 PMCID: PMC9189807 DOI: 10.1038/s41598-022-13396-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/24/2022] [Indexed: 11/11/2022] Open
Abstract
Coronaviruses are important viral pathogens across a range of animal species including humans. They have a high potential for cross-species transmission as evidenced by the emergence of COVID-19 and may be the origin of future pandemics. There is therefore an urgent need to study coronaviruses in depth and to identify new therapeutic targets. This study shows that distant coronaviruses such as Alpha-, Beta-, and Deltacoronaviruses can share common host immune associated pathways and genes. Differentially expressed genes (DEGs) in the transcription profile of epithelial cell lines infected with swine acute diarrhea syndrome, severe acute respiratory syndrome coronavirus 2, or porcine deltacoronavirus, showed that DEGs within 10 common immune associated pathways were upregulated upon infection. Twenty Three pathways and 21 DEGs across 10 immune response associated pathways were shared by these viruses. These 21 DEGs can serve as focused targets for therapeutics against newly emerging coronaviruses. We were able to show that even though there is a positive correlation between PDCoV and SARS-CoV-2 infections, these viruses could be using different strategies for efficient replication in their cells from their natural hosts. To the best of our knowledge, this is the first report of comparative host transcriptome analysis across distant coronavirus genres.
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Affiliation(s)
- Diana Cruz-Pulido
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Department of Animal Sciences, Center for Food Animal Health, The Ohio State University, Wooster, OH, 44691, USA
| | | | - Scott P Kenney
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Animal Sciences, Center for Food Animal Health, The Ohio State University, Wooster, OH, 44691, USA.
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17
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Mellors J, Tipton T, Fehling SK, Akoi Bore J, Koundouno FR, Hall Y, Hudson J, Alexander F, Longet S, Taylor S, Gorringe A, Magassouba N, Konde MK, Hiscox J, Strecker T, Carroll M. Complement-Mediated Neutralisation Identified in Ebola Virus Disease Survivor Plasma: Implications for Protection and Pathogenesis. Front Immunol 2022; 13:857481. [PMID: 35493467 PMCID: PMC9039621 DOI: 10.3389/fimmu.2022.857481] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
The 2013-2016 Ebola virus (EBOV) epidemic in West Africa was unprecedented in case numbers and fatalities, and sporadic outbreaks continue to arise. Antibodies to the EBOV glycoprotein (GP) are strongly associated with survival and their use in immunotherapy is often initially based on their performance in neutralisation assays. Other immune effector functions also contribute to EBOV protection but are more complex to measure. Their interactions with the complement system in particular are comparatively under-researched and commonly excluded from cellular immunoassays. Using EBOV convalescent plasma samples from the 2013-2016 epidemic, we investigated antibody and complement-mediated neutralisation and how these interactions can influence immunity in response to EBOV-GP and its secreted form (EBOV-sGP). We defined two cohorts: one with low-neutralising titres in relation to EBOV-GP IgG titres (LN cohort) and the other with a direct linear relationship between neutralisation and EBOV-GP IgG titres (N cohort). Using flow cytometry antibody-dependent complement deposition (ADCD) assays, we found that the LN cohort was equally efficient at mediating ADCD in response to the EBOV-GP but was significantly lower in response to the EBOV-sGP, compared to the N cohort. Using wild-type EBOV neutralisation assays with a cohort of the LN plasma, we observed a significant increase in neutralisation associated with the addition of pooled human plasma as a source of complement. Flow cytometry ADCD was also applied using the GP of the highly virulent Sudan virus (SUDV) of the Sudan ebolavirus species. There are no licensed vaccines or therapeutics against SUDV and it overlaps in endemicity with EBOV. We found that the LN plasma was significantly less efficient at cross-reacting and mediating ADCD. Overall, we found a differential response in ADCD between LN and N plasma in response to various Ebolavirus glycoproteins, and that these interactions could significantly improve EBOV neutralisation for selected LN plasma samples. Preservation of the complement system in immunoassays could augment our understanding of neutralisation and thus protection against infection.
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Affiliation(s)
- Jack Mellors
- Department of Research and Evaluation, United Kingdom (UK) Health Security Agency, Salisbury, United Kingdom.,Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,Wellcome Centre for Human Genetics and the Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Tom Tipton
- Wellcome Centre for Human Genetics and the Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Joseph Akoi Bore
- Center for Training and Research on Priority Diseases including Malaria in Guinea, Conakry, Guinea.,Department of Research, Ministry of Health Guinea, Conakry, Guinea
| | - Fara Raymond Koundouno
- Department of Research, Ministry of Health Guinea, Conakry, Guinea.,Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Yper Hall
- Department of Research and Evaluation, United Kingdom (UK) Health Security Agency, Salisbury, United Kingdom
| | - Jacob Hudson
- Department of Research and Evaluation, United Kingdom (UK) Health Security Agency, Salisbury, United Kingdom.,School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom.,Department of Biochemical Sciences, School of Biosciences and Medicine, University of Surrey, Surrey, United Kingdom
| | - Frances Alexander
- Department of Research and Evaluation, United Kingdom (UK) Health Security Agency, Salisbury, United Kingdom
| | - Stephanie Longet
- Wellcome Centre for Human Genetics and the Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephen Taylor
- Department of Research and Evaluation, United Kingdom (UK) Health Security Agency, Salisbury, United Kingdom
| | - Andrew Gorringe
- Department of Research and Evaluation, United Kingdom (UK) Health Security Agency, Salisbury, United Kingdom
| | - N'Faly Magassouba
- Viral Haemorrhagic Fever Reference Department, Projet Laboratoire Fièvres Hémorragiques, Conakry, Guinea
| | - Mandy Kader Konde
- Center for Training and Research on Priority Diseases including Malaria in Guinea, Conakry, Guinea
| | - Julian Hiscox
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Thomas Strecker
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Miles Carroll
- Wellcome Centre for Human Genetics and the Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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18
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Abstract
Ebola virus (EBV) disease (EVD) is a highly virulent systemic disease characterized by an aggressive systemic inflammatory response and impaired vascular and coagulation systems, often leading to uncontrolled hemorrhaging and death. In this study, the proteomes of 38 sequential plasma samples from 12 confirmed EVD patients were analyzed. Of these 12 cases, 9 patients received treatment with interferon beta 1a (IFN-β-1a), 8 survived EVD, and 4 died; 2 of these 4 fatalities had received IFN-β-1a. Our analytical strategy combined three platforms targeting different plasma subproteomes: a liquid chromatography-mass spectrometry (LC-MS)-based analysis of the classical plasma proteome, a protocol that combines the depletion of abundant plasma proteins and LC-MS to detect less abundant plasma proteins, and an antibody-based cytokine/chemokine multiplex assay. These complementary platforms provided comprehensive data on 1,000 host and viral proteins. Examination of the early plasma proteomes revealed protein signatures that differentiated between fatalities and survivors. Moreover, IFN-β-1a treatment was associated with a distinct protein signature. Next, we examined those proteins whose abundances reflected viral load measurements and the disease course: resolution or progression. Our data identified a prognostic 4-protein biomarker panel (histone H1-5, moesin, kininogen 1, and ribosomal protein L35 [RPL35]) that predicted EVD outcomes more accurately than the onset viral load. IMPORTANCE As evidenced by the 2013-2016 outbreak in West Africa, Ebola virus (EBV) disease (EVD) poses a major global health threat. In this study, we characterized the plasma proteomes of 12 individuals infected with EBV, using two different LC-MS-based proteomics platforms and an antibody-based multiplexed cytokine/chemokine assay. Clear differences were observed in the host proteome between individuals who survived and those who died, at both early and late stages of the disease. From our analysis, we derived a 4-protein prognostic biomarker panel that may help direct care. Given the ease of implementation, a panel of these 4 proteins or subsets thereof has the potential to be widely applied in an emergency setting in resource-limited regions.
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19
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Hume AJ, Heiden B, Olejnik J, Suder EL, Ross S, Scoon WA, Bullitt E, Ericsson M, White MR, Turcinovic J, Thao TTN, Hekman RM, Kaserman JE, Huang J, Alysandratos KD, Toth GE, Jakab F, Kotton DN, Wilson AA, Emili A, Thiel V, Connor JH, Kemenesi G, Cifuentes D, Mühlberger E. Recombinant Lloviu virus as a tool to study viral replication and host responses. PLoS Pathog 2022; 18:e1010268. [PMID: 35120176 PMCID: PMC8849519 DOI: 10.1371/journal.ppat.1010268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/16/2022] [Accepted: 01/11/2022] [Indexed: 01/06/2023] Open
Abstract
Next generation sequencing has revealed the presence of numerous RNA viruses in animal reservoir hosts, including many closely related to known human pathogens. Despite their zoonotic potential, most of these viruses remain understudied due to not yet being cultured. While reverse genetic systems can facilitate virus rescue, this is often hindered by missing viral genome ends. A prime example is Lloviu virus (LLOV), an uncultured filovirus that is closely related to the highly pathogenic Ebola virus. Using minigenome systems, we complemented the missing LLOV genomic ends and identified cis-acting elements required for LLOV replication that were lacking in the published sequence. We leveraged these data to generate recombinant full-length LLOV clones and rescue infectious virus. Similar to other filoviruses, recombinant LLOV (rLLOV) forms filamentous virions and induces the formation of characteristic inclusions in the cytoplasm of the infected cells, as shown by electron microscopy. Known target cells of Ebola virus, including macrophages and hepatocytes, are permissive to rLLOV infection, suggesting that humans could be potential hosts. However, inflammatory responses in human macrophages, a hallmark of Ebola virus disease, are not induced by rLLOV. Additional tropism testing identified pneumocytes as capable of robust rLLOV and Ebola virus infection. We also used rLLOV to test antivirals targeting multiple facets of the replication cycle. Rescue of uncultured viruses of pathogenic concern represents a valuable tool in our arsenal for pandemic preparedness. Due to increasing utilization of high-throughput sequencing technologies, RNA sequences of many unknown viruses have been discovered in bats and other animal species. Research on the pathogenic potential of these viruses is hampered by incomplete viral genome sequences and difficulties in isolating infectious virus from the animal hosts. One example of these potentially zoonotic pathogens is Lloviu virus (LLOV), a filovirus which is closely related to Ebola virus. Here we applied molecular virological approaches, including minigenome assays, to complement the incomplete LLOV genome ends with sequences from related viruses and identify cis-acting elements required for LLOV replication and transcription that were missing in the published LLOV sequence. The resulting full-length clones were used to generate infectious recombinant LLOV. We used this virus for electron microscopic analyses, infection studies in human cells, host response analysis, and antiviral drug testing. Our results provide new insights into the pathogenic potential of LLOV and delineate a roadmap for studying uncultured viruses.
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Affiliation(s)
- Adam J. Hume
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- * E-mail: (AJH); (EM)
| | - Baylee Heiden
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Judith Olejnik
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Ellen L. Suder
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Stephen Ross
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Whitney A. Scoon
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Maria Ericsson
- Department of Cell Biology, Harvard Medical School; Boston, Massachusetts, United States of America
| | - Mitchell R. White
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- Program in Bioinformatics, Boston University; Boston, Massachusetts, United States of America
| | - Tran T. N. Thao
- Institute of Virology and Immunology (IVI); Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern; Bern, Switzerland
| | - Ryan M. Hekman
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
- Center for Network Systems Biology, Boston University; Boston, Massachusetts, United States of America
| | - Joseph E. Kaserman
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Gabor E. Toth
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs; Pécs, Hungary
| | - Ferenc Jakab
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs; Pécs, Hungary
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston Medical Center; Boston, Massachusetts, United States of America
| | - Andrew A. Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center; Boston, Massachusetts, United States of America
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
- Center for Network Systems Biology, Boston University; Boston, Massachusetts, United States of America
- Department of Biology, Boston University; Boston, Massachusetts, United States of America
| | - Volker Thiel
- Institute of Virology and Immunology (IVI); Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern; Bern, Switzerland
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
| | - Gabor Kemenesi
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs; Pécs, Hungary
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine; Boston, Massachusetts, United States of America
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine; Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University; Boston, Massachusetts, United States of America
- * E-mail: (AJH); (EM)
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20
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Artificial Intelligence in Blood Transcriptomics. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Dose-Dependent Response to Infection with Ebola Virus in the Ferret Model and Evidence of Viral Evolution in the Eye. J Virol 2021; 95:e0083321. [PMID: 34586862 PMCID: PMC8610581 DOI: 10.1128/jvi.00833-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Filoviruses cause high-consequence infections with limited approved medical countermeasures (MCMs). MCM development is dependent upon well-characterized animal models for the assessment of antiviral agents and vaccines. Following large-scale Ebola virus (EBOV) disease outbreaks in Africa, some survivors are left with long-term sequelae and persistent virus in immune-privileged sites for many years. We report the characterization of the ferret as a model for Ebola virus infection, reproducing disease and lethality observed in humans. The onset of clinical signs is rapid, and EBOV is detected in the blood, oral, and rectal swabs and all tissues studied. We identify viral RNA in the eye (a site of immune privilege) and report on specific genomic changes in EBOV present in this structure. Thus, the ferret model has utility in testing MCMs that prevent or treat long-term EBOV persistence in immune-privileged sites. IMPORTANCE Recent reemergence of Ebola in Guinea that caused over 28,000 cases between 2013 and 2016 has been linked to the original virus from that region. It appears the virus has remained in the region for at least 5 years and is likely to have been maintained in humans. Persistence of Ebola in areas of the body for extended periods of time has been observed, such as in the eye and semen. Despite the importance of reintroduction of Ebola from this route, such events are rare in the population, which makes studying medical interventions to clear persistent virus difficult. We studied various doses of Ebola in ferrets and detected virus in the eyes of most ferrets. We believe this model will enable the study of medical interventions that promote clearance of Ebola virus from sites that promote persistence.
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22
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Silva JMF, Nagata T, Melo FL, Elena SF. Heterogeneity in the Response of Different Subtypes of Drosophila melanogaster Midgut Cells to Viral Infections. Viruses 2021; 13:2284. [PMID: 34835089 PMCID: PMC8623525 DOI: 10.3390/v13112284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/05/2021] [Accepted: 11/13/2021] [Indexed: 11/29/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) offers the possibility to monitor both host and pathogens transcriptomes at the cellular level. Here, public scRNA-seq datasets from Drosophila melanogaster midgut cells were used to compare the differences in replication strategy and cellular responses between two fly picorna-like viruses, Thika virus (TV) and D. melanogaster Nora virus (DMelNV). TV exhibited lower levels of viral RNA accumulation but infected a higher number of cells compared to DMelNV. In both cases, viral RNA accumulation varied according to cell subtype. The cellular heat shock response to TV and DMelNV infection was cell-subtype- and virus-specific. Disruption of bottleneck genes at later stages of infection in the systemic response, as well as of translation-related genes in the cellular response to DMelNV in two cell subtypes, may affect the virus replication.
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Affiliation(s)
- João M. F. Silva
- Departamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, Brazil; (J.M.F.S.); (T.N.); (F.L.M.)
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, 46980 Paterna, València, Spain
| | - Tatsuya Nagata
- Departamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, Brazil; (J.M.F.S.); (T.N.); (F.L.M.)
| | - Fernando L. Melo
- Departamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, Brazil; (J.M.F.S.); (T.N.); (F.L.M.)
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, 46980 Paterna, València, Spain
- The Santa Fe Institute, Santa Fe, NM 87501, USA
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23
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Pathogenic and transcriptomic differences of emerging SARS-CoV-2 variants in the Syrian golden hamster model. EBioMedicine 2021; 73:103675. [PMID: 34758415 PMCID: PMC8572342 DOI: 10.1016/j.ebiom.2021.103675] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/06/2021] [Accepted: 10/19/2021] [Indexed: 12/19/2022] Open
Abstract
Background Following the discovery of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid spread throughout the world, new viral variants of concern (VOC) have emerged. There is a critical need to understand the impact of the emerging variants on host response and disease dynamics to facilitate the development of vaccines and therapeutics. Methods Syrian golden hamsters are the leading small animal model that recapitulates key aspects of severe coronavirus disease 2019 (COVID-19). We performed intranasal inoculation of SARS-CoV-2 into hamsters with the ancestral virus (nCoV-WA1-2020) or VOC first identified in the United Kingdom (B.1.1.7, alpha) and South Africa (B.1.351, beta) and analyzed viral loads and host responses. Findings Similar gross and histopathologic pulmonary lesions were observed after infection with all three variants. Although differences in viral genomic copy numbers were noted in the lungs and oral swabs of challenged animals, infectious titers in the lungs were comparable between the variants. Antibody neutralization capacities varied, dependent on the original challenge virus and cross-variant protective capacity. Transcriptional profiling of lung samples 4 days post-challenge (DPC) indicated significant induction of antiviral pathways in response to all three challenges with a more robust inflammatory signature in response to B.1.1.7 infection. Furthermore, no additional mutations in the spike protein were detected at 4 DPC. Interpretations Although disease severity and viral shedding were not significantly different, the emerging VOC induced distinct humoral responses and transcriptional profiles compared to the ancestral virus. These observations suggest potential differences in acute early responses or alterations in immune modulation by VOC. Funding Intramural Research Program, NIAID, NIH; National Center for Research Resources, NIH; National Center for Advancing Translational Sciences, NIH.
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24
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Paparisto E, Hunt NR, Labach DS, Coleman MD, Di Gravio EJ, Dodge MJ, Friesen NJ, Côté M, Müller A, Hoenen T, Barr SD. Interferon-Induced HERC5 Inhibits Ebola Virus Particle Production and Is Antagonized by Ebola Glycoprotein. Cells 2021; 10:cells10092399. [PMID: 34572049 PMCID: PMC8472148 DOI: 10.3390/cells10092399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/11/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022] Open
Abstract
Survival following Ebola virus (EBOV) infection correlates with the ability to mount an early and robust interferon (IFN) response. The host IFN-induced proteins that contribute to controlling EBOV replication are not fully known. Among the top genes with the strongest early increases in expression after infection in vivo is IFN-induced HERC5. Using a transcription- and replication-competent VLP system, we showed that HERC5 inhibits EBOV virus-like particle (VLP) replication by depleting EBOV mRNAs. The HERC5 RCC1-like domain was necessary and sufficient for this inhibition and did not require zinc finger antiviral protein (ZAP). Moreover, we showed that EBOV (Zaire) glycoprotein (GP) but not Marburg virus GP antagonized HERC5 early during infection. Our data identify a novel ‘protagonist–antagonistic’ relationship between HERC5 and GP in the early stages of EBOV infection that could be exploited for the development of novel antiviral therapeutics.
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Affiliation(s)
- Ermela Paparisto
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Nina R. Hunt
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Daniel S. Labach
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Macon D. Coleman
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Eric J. Di Gravio
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Mackenzie J. Dodge
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Nicole J. Friesen
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Marceline Côté
- Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Roger-Guindon Hall Room 4214, Ottawa, ON K1H 8M5 , Canada;
| | - Andreas Müller
- Friedrich-Loeffler-Institut, Institute of Molecular Virology and Cell Biology, Südufer 10, 17493 Greifswald—Insel Riems, Germany; (A.M.); (T.H.)
| | - Thomas Hoenen
- Friedrich-Loeffler-Institut, Institute of Molecular Virology and Cell Biology, Südufer 10, 17493 Greifswald—Insel Riems, Germany; (A.M.); (T.H.)
| | - Stephen D. Barr
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
- Correspondence:
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25
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Maroney KJ, Pinski AN, Marzi A, Messaoudi I. Transcriptional Analysis of Infection With Early or Late Isolates From the 2013-2016 West Africa Ebola Virus Epidemic Does Not Suggest Attenuated Pathogenicity as a Result of Genetic Variation. Front Microbiol 2021; 12:714817. [PMID: 34484156 PMCID: PMC8415004 DOI: 10.3389/fmicb.2021.714817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
The 2013-2016 West Africa Ebola virus (EBOV) epidemic caused by the EBOV-Makona isolate is the largest and longest recorded to date. It incurred over 28,000 infections and ∼11,000 deaths. Early in this epidemic, several mutations in viral glycoprotein (A82V), nucleoprotein (R111C), and polymerase L (D759G) emerged and stabilized. In vitro studies of these new EBOV-Makona isolates showed enhanced fitness and viral replication capacity. However, in vivo studies in mice and rhesus macaques did not provide any evidence of enhanced viral fitness or shedding. Infection with late isolates carrying or early isolates lacking (early) these mutations resulted in uniformly lethal disease in nonhuman primates (NHPs), albeit with slightly delayed kinetics with late isolates. The recent report of a possible reemergence of EBOV from a persistent infection in a survivor of the epidemic highlights the urgency for understanding the impact of genetic variation on EBOV pathogenesis. However, potential molecular differences in host responses remain unknown. To address this gap in knowledge, we conducted the first comparative analysis of the host responses to lethal infection with EBOV-Mayinga and EBOV-Makona isolates using bivariate, longitudinal, regression, and discrimination transcriptomic analyses. Our analysis shows a conserved core of differentially expressed genes (DEGs) involved in antiviral defense, immune cell activation, and inflammatory processes in response to EBOV-Makona and EBOV-Mayinga infections. Additionally, EBOV-Makona and EBOV-Mayinga infections could be discriminated based on the expression pattern of a small subset of genes. Transcriptional responses to EBOV-Makona isolates that emerged later during the epidemic, specifically those from Mali and Liberia, lacked signatures of profound lymphopenia and excessive inflammation seen following infection with EBOV-Mayinga and early EBOV-Makona isolate C07. Overall, these findings provide novel insight into the mechanisms underlying the lower case fatality rate (CFR) observed with EBOV-Makona compared to EBOV-Mayinga.
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Affiliation(s)
- Kevin J Maroney
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Amanda N Pinski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Rocky Mountain Laboratories, Hamilton, MT, United States
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States.,Center for Virus Research, University of California, Irvine, Irvine, CA, United States.,Institute for Immunology, University of California, Irvine, Irvine, CA, United States
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26
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Beckmann ND, Comella PH, Cheng E, Lepow L, Beckmann AG, Tyler SR, Mouskas K, Simons NW, Hoffman GE, Francoeur NJ, Del Valle DM, Kang G, Do A, Moya E, Wilkins L, Le Berichel J, Chang C, Marvin R, Calorossi S, Lansky A, Walker L, Yi N, Yu A, Chung J, Hartnett M, Eaton M, Hatem S, Jamal H, Akyatan A, Tabachnikova A, Liharska LE, Cotter L, Fennessy B, Vaid A, Barturen G, Shah H, Wang YC, Sridhar SH, Soto J, Bose S, Madrid K, Ellis E, Merzier E, Vlachos K, Fishman N, Tin M, Smith M, Xie H, Patel M, Nie K, Argueta K, Harris J, Karekar N, Batchelor C, Lacunza J, Yishak M, Tuballes K, Scott I, Kumar A, Jaladanki S, Agashe C, Thompson R, Clark E, Losic B, Peters L, Roussos P, Zhu J, Wang W, Kasarskis A, Glicksberg BS, Nadkarni G, Bogunovic D, Elaiho C, Gangadharan S, Ofori-Amanfo G, Alesso-Carra K, Onel K, Wilson KM, Argmann C, Bunyavanich S, Alarcón-Riquelme ME, Marron TU, Rahman A, Kim-Schulze S, Gnjatic S, Gelb BD, Merad M, Sebra R, Schadt EE, Charney AW. Downregulation of exhausted cytotoxic T cells in gene expression networks of multisystem inflammatory syndrome in children. Nat Commun 2021; 12:4854. [PMID: 34381049 PMCID: PMC8357784 DOI: 10.1038/s41467-021-24981-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 07/19/2021] [Indexed: 02/07/2023] Open
Abstract
Multisystem inflammatory syndrome in children (MIS-C) presents with fever, inflammation and pathology of multiple organs in individuals under 21 years of age in the weeks following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Although an autoimmune pathogenesis has been proposed, the genes, pathways and cell types causal to this new disease remain unknown. Here we perform RNA sequencing of blood from patients with MIS-C and controls to find disease-associated genes clustered in a co-expression module annotated to CD56dimCD57+ natural killer (NK) cells and exhausted CD8+ T cells. A similar transcriptome signature is replicated in an independent cohort of Kawasaki disease (KD), the related condition after which MIS-C was initially named. Probing a probabilistic causal network previously constructed from over 1,000 blood transcriptomes both validates the structure of this module and reveals nine key regulators, including TBX21, a central coordinator of exhausted CD8+ T cell differentiation. Together, this unbiased, transcriptome-wide survey implicates downregulation of NK cells and cytotoxic T cell exhaustion in the pathogenesis of MIS-C.
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Affiliation(s)
- Noam D Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA.
| | - Phillip H Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Esther Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lauren Lepow
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aviva G Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott R Tyler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Konstantinos Mouskas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicole W Simons
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nancy J Francoeur
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | | | - Gurpawan Kang
- Department of Medicine, Division of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anh Do
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Emily Moya
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lillian Wilkins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Le Berichel
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christie Chang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Marvin
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sharlene Calorossi
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alona Lansky
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Walker
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nancy Yi
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alex Yu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan Chung
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Melody Eaton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sandra Hatem
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hajra Jamal
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alara Akyatan
- Department of of Rehabilitation and Human Performance, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra Tabachnikova
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lora E Liharska
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liam Cotter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Fennessy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Akhil Vaid
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Guillermo Barturen
- Department of Medical Genomics, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government (GENYO), Granada, Spain
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shwetha Hara Sridhar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Juan Soto
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Swaroop Bose
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Kent Madrid
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Ethan Ellis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Elyze Merzier
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Konstantinos Vlachos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Nataly Fishman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Manying Tin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Melissa Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Hui Xie
- 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
| | - Manishkumar Patel
- 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
| | - Kai Nie
- 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
| | - Kimberly Argueta
- 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
| | - Jocelyn Harris
- 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
| | - Neha Karekar
- 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
| | - Craig Batchelor
- 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
| | - Jose Lacunza
- 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
| | - Mahlet Yishak
- 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
| | - Kevin Tuballes
- 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
| | - Ieisha Scott
- 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
| | - Arvind Kumar
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Suraj Jaladanki
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charuta Agashe
- 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
| | - Ryan Thompson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Evan Clark
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lauren Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panagiotis Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jun Zhu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wenhui Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish Nadkarni
- Mount Sinai COVID Informatics Center, New York, NY, USA
- Department of Medicine, Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, New York, NY, USA
| | - Dusan Bogunovic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cordelia Elaiho
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sandeep Gangadharan
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - George Ofori-Amanfo
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kasey Alesso-Carra
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kenan Onel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Karen M Wilson
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marta E Alarcón-Riquelme
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas U Marron
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adeeb Rahman
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- 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
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- 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
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- 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
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- 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
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
- Black Family Stem Cell Institute, New York, NY, USA
- Sema4, a Mount Sinai Venture, Stamford, CT, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA.
- Sema4, a Mount Sinai Venture, Stamford, CT, USA.
| | - Alexander W Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mount Sinai COVID Informatics Center, New York, NY, USA.
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27
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Bundibugyo ebolavirus Survival Is Associated with Early Activation of Adaptive Immunity and Reduced Myeloid-Derived Suppressor Cell Signaling. mBio 2021; 12:e0151721. [PMID: 34372693 PMCID: PMC8406165 DOI: 10.1128/mbio.01517-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ebolaviruses Bundibugyo virus (BDBV) and Ebola virus (EBOV) cause fatal hemorrhagic disease in humans and nonhuman primates. While the host response to EBOV is well characterized, less is known about BDBV infection. Moreover, immune signatures that mediate natural protection against all ebolaviruses remain poorly defined. To explore these knowledge gaps, we transcriptionally profiled BDBV-infected rhesus macaques, a disease model that results in incomplete lethality. This approach enabled us to identify prognostic indicators. As expected, survival (∼60%) correlated with reduced clinical pathology and circulating infectious virus, although peak viral RNA loads were not significantly different between surviving and nonsurviving macaques. Survivors had higher anti-BDBV antibody titers and transcriptionally derived cytotoxic T cell-, memory B cell-, and plasma cell-type quantities, demonstrating activation of adaptive immunity. Conversely, a poor prognosis was associated with lack of an appropriate adaptive response, sustained innate immune signaling, and higher expression of myeloid-derived suppressor cell (MDSC)-related transcripts (S100A8, S100A9, CEBPB, PTGS2, CXCR1, and LILRA3). MDSCs are potent immunosuppressors of cellular and humoral immunity, and therefore, they represent a potential therapeutic target. Circulating plasminogen activator inhibitor 1 (PAI-1) and tissue plasminogen activator (tPA) levels were also elevated in nonsurvivors and in survivors exhibiting severe illness, emphasizing the importance of maintaining coagulation homeostasis to control disease progression.
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28
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O’donnell KL, Pinski AN, Clancy CS, Gourdine T, Shifflett K, Fletcher P, Messaoudi I, Marzi A. Pathogenic and transcriptomic differences of emerging SARS-CoV-2 variants in the Syrian golden hamster model.. [PMID: 34268506 PMCID: PMC8282094 DOI: 10.1101/2021.07.11.451964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Following the discovery of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid spread throughout the world, new viral variants of concern (VOC) have emerged. There is a critical need to understand the impact of the emerging variants on host response and disease dynamics to facilitate the development of vaccines and therapeutics. Syrian golden hamsters are the leading small animal model that recapitulates key aspects of severe coronavirus disease 2019 (COVID-19). In this study, we show that intranasal inoculation of SARS-CoV-2 into hamsters with the ancestral virus (nCoV-WA1–2020) or VOC first identified in the United Kingdom (B.1.1.7) and South Africa (B.1.351) led to similar gross and histopathologic pulmonary lesions. Although differences in viral genomic copy numbers were noted in the lungs and oral swabs of challenged animals, infectious titers in the lungs were comparable. Antibody neutralization capacities varied, dependent on the original challenge virus and cross-variant protective capacity. Transcriptional profiling indicated significant induction of antiviral pathways in response to all three challenges with a more robust inflammatory signature in response to B.1.1.7. Furthermore, no additional mutations in the spike protein were detected at peak disease. In conclusion, the emerging VOC showed distinct humoral responses and transcriptional profiles in the hamster model compared to the ancestral virus.
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29
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Pinski AN, Maroney KJ, Marzi A, Messaoudi I. Distinct transcriptional responses to fatal Ebola virus infection in cynomolgus and rhesus macaques suggest species-specific immune responses. Emerg Microbes Infect 2021; 10:1320-1330. [PMID: 34112056 PMCID: PMC8253202 DOI: 10.1080/22221751.2021.1942229] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Ebola virus (EBOV) is a negative single-stranded RNA virus within the Filoviridae family and the causative agent of Ebola virus disease (EVD). Nonhuman primates (NHPs), including cynomolgus and rhesus macaques, are considered the gold standard animal model to interrogate mechanisms of EBOV pathogenesis. However, despite significant genetic similarity (>90%), NHP species display different clinical presentation following EBOV infection, notably a ∼1-2 days delay in disease progression. Consequently, evaluation of therapeutics is generally conducted in rhesus macaques, whereas cynomolgus macaques are utilized to determine efficacy of preventative treatments, notably vaccines. This observation is in line with reported differences in disease severity and host responses between these two NHP following infection with simian varicella virus, influenza A and SARS-CoV-2. However, the molecular underpinnings of these differential outcomes following viral infections remain poorly defined. In this study, we compared published transcriptional profiles obtained from cynomolgus and rhesus macaques infected with the EBOV-Makona Guinea C07 using bivariate and regression analyses to elucidate differences in host responses. We report the presence of a shared core of differentially expressed genes (DEGs) reflecting EVD pathology, including aberrant inflammation, lymphopenia, and coagulopathy. However, the magnitudes of change differed between the two macaque species. These findings suggest that the differential clinical presentation of EVD in these two species is mediated by altered transcriptional responses.
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Affiliation(s)
- Amanda N Pinski
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine CA, USA
| | - Kevin J Maroney
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine CA, USA
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine CA, USA.,Center for Virus Research, University of California Irvine, Irvine, CA, USA.,Institute for Immunology, University of California Irvine, Irvine, CA, USA
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30
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Dynamic Host Immune and Transcriptomic Responses to Respiratory Syncytial Virus Infection in a Vaccination-Challenge Mouse Model. Virol Sin 2021; 36:1327-1340. [PMID: 34138405 DOI: 10.1007/s12250-021-00418-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the major cause of lower respiratory tract infections in children. Inactivated RSV vaccine was developed in the late 1960's, but the vaccine-enhanced disease (VED) occurred to vaccinated infants upon subsequent natural RSV infection. The excessive inflammatory immunopathology in the lungs might be involved in the VED, but the underlying mechanisms remain not fully understood. In this study, we utilized UV-inactivated RSV in the prime/boost approach followed by RSV challenge in BALB/c mice to mimic RSV VED. The dynamic virus load, cytokines, histology and transcriptome profiles in lung tissues of mice were investigated from day 1 to day 6 post-infection. Compared to PBS-treated mice, UV-RSV vaccination leads to a Th2 type inflammatory response characterized by enhanced histopathology, reduced Treg cells and increased IL4+CD4 T cells in the lung. Enhanced production of several Th2 type cytokines (IL-4, IL-5, IL-10) and TGF-β, reduction of IL-6 and IL-17 were observed in UV-RSV vaccinated mice. A total of 5582 differentially expressed (DE) genes between PBS-treated or vaccinated mice and naïve mice were identified by RNA-Seq. Eleven conserved high-influential modules (HMs) were recognized, majorly grouped into regulatory networks related to cell cycle and cell metabolism, signal transduction, immune and inflammatory responses. At an early time post-infection, the vaccinated mice showed obvious decreased expression patterns of DE genes in 11 HMs compared to PBS-treated mice. The extracellular matrix (HM5) and immune responses (HM8) revealed tremendous differences in expression and regulation characteristics of transcripts between PBS-treated and vaccinated mice at both early and late time points. The highly connected genes in HM5 and HM8 networks were further validated by RT-qPCR. These findings reveal the relationship between RSV VED and immune responses, which could benefit the development of novel RSV vaccines.
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31
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Feng B, Zhang D, Wang Q, Yu F, Zou Q, Xie G, Wang R, Yang X, Chen W, Lou B, Zheng S, Chen Y. Effects of angiotensin II receptor blocker usage on viral load, antibody dynamics, and transcriptional characteristics among COVID-19 patients with hypertension. J Zhejiang Univ Sci B 2021; 22:330-340. [PMID: 33835767 PMCID: PMC8042529 DOI: 10.1631/jzus.b2000730] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Epidemiological evidence suggests that patients with hypertension infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are at increased risk of acute lung injury. However, it is still not clear whether this increased risk is related to the usage of renin-angiotensin system (RAS) blockers. We collected medical records of coronavirus disease 2019 (COVID-19) patients from the First Affiliated Hospital, Zhejiang University School of Medicine (Hangzhou, China), and evaluated the potential impact of an angiotensin II receptor blocker (ARB) on the clinical outcomes of COVID-19 patients with hypertension. A total of 30 hypertensive COVID-19 patients were enrolled, of which 17 were classified as non-ARB group and the remaining 13 as ARB group based on the antihypertensive therapies they received. Compared with the non-ARB group, patients in the ARB group had a lower proportion of severe cases and intensive care unit (ICU) admission as well as shortened length of hospital stay, and manifested favorable results in most of the laboratory testing. Viral loads in the ARB group were lower than those in the non-ARB group throughout the disease course. No significant difference in the time of seroconversion or antibody levels was observed between the two groups. The median levels of soluble angiotensin-converting enzyme 2 (sACE2) in serum and urine samples were similar in both groups, and there were no significant correlations between serum sACE2 and biomarkers of disease severity. Transcriptional analysis showed 125 differentially expressed genes which mainly were enriched in oxygen transport, bicarbonate transport, and blood coagulation. Our results suggest that ARB usage is not associated with aggravation of COVID-19. These findings support the maintenance of ARB treatment in hypertensive patients diagnosed with COVID-19.
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Affiliation(s)
- Baihuan Feng
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou 310003, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou 310003, China
| | - Dan Zhang
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou 310003, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou 310003, China
| | - Qi Wang
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou 310003, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou 310003, China
| | - Fei Yu
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou 310003, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou 310003, China
| | - Qianda Zou
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou 310003, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou 310003, China
| | - Guoliang Xie
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou 310003, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou 310003, China
| | - Ruonan Wang
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou 310003, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou 310003, China
| | - Xianzhi Yang
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou 310003, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou 310003, China
| | - Weizhen Chen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou 310003, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou 310003, China
| | - Bin Lou
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou 310003, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou 310003, China
| | - Shufa Zheng
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China. .,Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou 310003, China. .,Institute of Laboratory Medicine, Zhejiang University, Hangzhou 310003, China.
| | - Yu Chen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou 310003, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou 310003, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
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32
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Zheng H, Rao AM, Dermadi D, Toh J, Murphy Jones L, Donato M, Liu Y, Su Y, Dai CL, Kornilov SA, Karagiannis M, Marantos T, Hasin-Brumshtein Y, He YD, Giamarellos-Bourboulis EJ, Heath JR, Khatri P. Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses. Immunity 2021; 54:753-768.e5. [PMID: 33765435 PMCID: PMC7988739 DOI: 10.1016/j.immuni.2021.03.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/03/2020] [Accepted: 03/01/2021] [Indexed: 02/08/2023]
Abstract
Viral infections induce a conserved host response distinct from bacterial infections. We hypothesized that the conserved response is associated with disease severity and is distinct between patients with different outcomes. To test this, we integrated 4,780 blood transcriptome profiles from patients aged 0 to 90 years infected with one of 16 viruses, including SARS-CoV-2, Ebola, chikungunya, and influenza, across 34 cohorts from 18 countries, and single-cell RNA sequencing profiles of 702,970 immune cells from 289 samples across three cohorts. Severe viral infection was associated with increased hematopoiesis, myelopoiesis, and myeloid-derived suppressor cells. We identified protective and detrimental gene modules that defined distinct trajectories associated with mild versus severe outcomes. The interferon response was decoupled from the protective host response in patients with severe outcomes. These findings were consistent, irrespective of age and virus, and provide insights to accelerate the development of diagnostics and host-directed therapies to improve global pandemic preparedness.
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Affiliation(s)
- Hong Zheng
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Aditya M Rao
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Immunology program, Stanford University, CA 94305, USA
| | - Denis Dermadi
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Jiaying Toh
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Immunology program, Stanford University, CA 94305, USA
| | - Lara Murphy Jones
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA; Division of Critical Care Medicine, Department of Pediatrics, School of Medicine, Stanford University, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Yiran Liu
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Cancer Biology program, Stanford University, CA 94305, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA, USA
| | - Cheng L Dai
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Minas Karagiannis
- 4(th) Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
| | - Theodoros Marantos
- 4(th) Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
| | | | | | | | - James R Heath
- Institute for Systems Biology, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA.
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33
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Diallo I, Ho J, Laffont B, Laugier J, Benmoussa A, Lambert M, Husseini Z, Soule G, Kozak R, Kobinger GP, Provost P. Altered microRNA Transcriptome in Cultured Human Liver Cells upon Infection with Ebola Virus. Int J Mol Sci 2021; 22:ijms22073792. [PMID: 33917562 PMCID: PMC8038836 DOI: 10.3390/ijms22073792] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/27/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ebola virus (EBOV) is a virulent pathogen, notorious for inducing life-threatening hemorrhagic fever, that has been responsible for several outbreaks in Africa and remains a public health threat. Yet, its pathogenesis is still not completely understood. Although there have been numerous studies on host transcriptional response to EBOV, with an emphasis on the clinical features, the impact of EBOV infection on post-transcriptional regulatory elements, such as microRNAs (miRNAs), remains largely unexplored. MiRNAs are involved in inflammation and immunity and are believed to be important modulators of the host response to viral infection. Here, we have used small RNA sequencing (sRNA-Seq), qPCR and functional analyses to obtain the first comparative miRNA transcriptome (miRNome) of a human liver cell line (Huh7) infected with one of the following three EBOV strains: Mayinga (responsible for the first Zaire outbreak in 1976), Makona (responsible for the West Africa outbreak in 2013–2016) and the epizootic Reston (presumably innocuous to humans). Our results highlight specific miRNA-based immunity pathways and substantial differences between the strains beyond their clinical manifestation and pathogenicity. These analyses shed new light into the molecular signature of liver cells upon EBOV infection and reveal new insights into miRNA-based virus attack and host defense strategy.
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Affiliation(s)
- Idrissa Diallo
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
| | - Jeffrey Ho
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
| | - Benoit Laffont
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
| | - Jonathan Laugier
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
| | - Abderrahim Benmoussa
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
| | - Marine Lambert
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
| | - Zeinab Husseini
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
| | - Geoff Soule
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3B 3M9, Canada; (G.S.); (R.K.)
| | - Robert Kozak
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3B 3M9, Canada; (G.S.); (R.K.)
- Division of Microbiology, Department of Laboratory Medicine & Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Gary P. Kobinger
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3B 3M9, Canada; (G.S.); (R.K.)
- Département de Microbiologie Médicale, Université du Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Patrick Provost
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
- CHUQ Research Center/CHUL Pavilion, 2705 Blvd Laurier, Room T1-65, Quebec, QC G1V 4G2, Canada
- Correspondence: ; Tel.: +1-418-525-4444 (ext. 48842)
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34
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Salguero FJ, White AD, Slack GS, Fotheringham SA, Bewley KR, Gooch KE, Longet S, Humphries HE, Watson RJ, Hunter L, Ryan KA, Hall Y, Sibley L, Sarfas C, Allen L, Aram M, Brunt E, Brown P, Buttigieg KR, Cavell BE, Cobb R, Coombes NS, Darby A, Daykin-Pont O, Elmore MJ, Garcia-Dorival I, Gkolfinos K, Godwin KJ, Gouriet J, Halkerston R, Harris DJ, Hender T, Ho CMK, Kennard CL, Knott D, Leung S, Lucas V, Mabbutt A, Morrison AL, Nelson C, Ngabo D, Paterson J, Penn EJ, Pullan S, Taylor I, Tipton T, Thomas S, Tree JA, Turner C, Vamos E, Wand N, Wiblin NR, Charlton S, Dong X, Hallis B, Pearson G, Rayner EL, Nicholson AG, Funnell SG, Hiscox JA, Dennis MJ, Gleeson FV, Sharpe S, Carroll MW. Comparison of rhesus and cynomolgus macaques as an infection model for COVID-19. Nat Commun 2021; 12:1260. [PMID: 33627662 PMCID: PMC7904795 DOI: 10.1038/s41467-021-21389-9] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
A novel coronavirus, SARS-CoV-2, has been identified as the causative agent of the current COVID-19 pandemic. Animal models, and in particular non-human primates, are essential to understand the pathogenesis of emerging diseases and to assess the safety and efficacy of novel vaccines and therapeutics. Here, we show that SARS-CoV-2 replicates in the upper and lower respiratory tract and causes pulmonary lesions in both rhesus and cynomolgus macaques. Immune responses against SARS-CoV-2 are also similar in both species and equivalent to those reported in milder infections and convalescent human patients. This finding is reiterated by our transcriptional analysis of respiratory samples revealing the global response to infection. We describe a new method for lung histopathology scoring that will provide a metric to enable clearer decision making for this key endpoint. In contrast to prior publications, in which rhesus are accepted to be the preferred study species, we provide convincing evidence that both macaque species authentically represent mild to moderate forms of COVID-19 observed in the majority of the human population and both species should be used to evaluate the safety and efficacy of interventions against SARS-CoV-2. Importantly, accessing cynomolgus macaques will greatly alleviate the pressures on current rhesus stocks.
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Affiliation(s)
- Francisco J Salguero
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Andrew D White
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Gillian S Slack
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Susan A Fotheringham
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Kevin R Bewley
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Karen E Gooch
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Stephanie Longet
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Holly E Humphries
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Robert J Watson
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Laura Hunter
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Kathryn A Ryan
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Yper Hall
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Laura Sibley
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Charlotte Sarfas
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Lauren Allen
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Marilyn Aram
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Emily Brunt
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Phillip Brown
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Karen R Buttigieg
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Breeze E Cavell
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Rebecca Cobb
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Naomi S Coombes
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Alistair Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Owen Daykin-Pont
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Michael J Elmore
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Isabel Garcia-Dorival
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Konstantinos Gkolfinos
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Kerry J Godwin
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Jade Gouriet
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Rachel Halkerston
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Debbie J Harris
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Thomas Hender
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Catherine M K Ho
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Chelsea L Kennard
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Daniel Knott
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Stephanie Leung
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Vanessa Lucas
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Adam Mabbutt
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Alexandra L Morrison
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Charlotte Nelson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Didier Ngabo
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Jemma Paterson
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Elizabeth J Penn
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Steve Pullan
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Irene Taylor
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Tom Tipton
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Stephen Thomas
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Julia A Tree
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Carrie Turner
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Edith Vamos
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Nadina Wand
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Nathan R Wiblin
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Sue Charlton
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Bassam Hallis
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Geoffrey Pearson
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Emma L Rayner
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Andrew G Nicholson
- Royal Brompton and Harefield NHS Foundation Trust, and National Heart and Lung Institute, Imperial College, London, UK
| | - Simon G Funnell
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Infectious Diseases Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore
| | - Mike J Dennis
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | | | - Sally Sharpe
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK
| | - Miles W Carroll
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire, UK.
- Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, OX3 7BN, UK.
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Longet S, Mellors J, Carroll MW, Tipton T. Ebolavirus: Comparison of Survivor Immunology and Animal Models in the Search for a Correlate of Protection. Front Immunol 2021; 11:599568. [PMID: 33679690 PMCID: PMC7935512 DOI: 10.3389/fimmu.2020.599568] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/29/2020] [Indexed: 01/21/2023] Open
Abstract
Ebola viruses are enveloped, single-stranded RNA viruses belonging to the Filoviridae family and can cause Ebola virus disease (EVD), a serious haemorrhagic illness with up to 90% mortality. The disease was first detected in Zaire (currently the Democratic Republic of Congo) in 1976. Since its discovery, Ebola virus has caused sporadic outbreaks in Africa and was responsible for the largest 2013-2016 EVD epidemic in West Africa, which resulted in more than 28,600 cases and over 11,300 deaths. This epidemic strengthened international scientific efforts to contain the virus and develop therapeutics and vaccines. Immunology studies in animal models and survivors, as well as clinical trials have been crucial to understand Ebola virus pathogenesis and host immune responses, which has supported vaccine development. This review discusses the major findings that have emerged from animal models, studies in survivors and vaccine clinical trials and explains how these investigations have helped in the search for a correlate of protection.
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Affiliation(s)
- Stephanie Longet
- Public Health England, National Infection Service, Salisbury, United Kingdom
| | - Jack Mellors
- Public Health England, National Infection Service, Salisbury, United Kingdom
| | - Miles W. Carroll
- Public Health England, National Infection Service, Salisbury, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Tom Tipton
- Public Health England, National Infection Service, Salisbury, United Kingdom
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36
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Grais RF, Kennedy SB, Mahon BE, Dubey SA, Grant-Klein RJ, Liu K, Hartzel J, Coller BA, Welebob C, Hanson ME, Simon JK. Estimation of the correlates of protection of the rVSVΔG-ZEBOV-GP Zaire ebolavirus vaccine: a post-hoc analysis of data from phase 2/3 clinical trials. LANCET MICROBE 2021; 2:e70-e78. [DOI: 10.1016/s2666-5247(20)30198-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/06/2020] [Accepted: 11/10/2020] [Indexed: 12/25/2022]
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Rogers KJ, Shtanko O, Stunz LL, Mallinger LN, Arkee T, Schmidt ME, Bohan D, Brunton B, White JM, Varga SM, Butler NS, Bishop GA, Maury W. Frontline Science: CD40 signaling restricts RNA virus replication in Mϕs, leading to rapid innate immune control of acute virus infection. J Leukoc Biol 2021; 109:309-325. [PMID: 32441445 PMCID: PMC7774454 DOI: 10.1002/jlb.4hi0420-285rr] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 01/03/2023] Open
Abstract
Many acute viral infections target tissue Mϕs, yet the mechanisms of Mϕ-mediated control of viruses are poorly understood. Here, we report that CD40 expressed by peritoneal Mϕs restricts early infection of a broad range of RNA viruses. Loss of CD40 expression enhanced virus replication as early as 12-24 h of infection and, conversely, stimulation of CD40 signaling with an agonistic Ab blocked infection. With peritoneal cell populations infected with the filovirus, wild-type (WT) Ebola virus (EBOV), or a BSL2 model virus, recombinant vesicular stomatitis virus encoding Ebola virus glycoprotein (rVSV/EBOV GP), we examined the mechanism conferring protection. Here, we demonstrate that restricted virus replication in Mϕs required CD154/CD40 interactions that stimulated IL-12 production through TRAF6-dependent signaling. In turn, IL-12 production resulted in IFN-γ production, which induced proinflammatory polarization of Mϕs, protecting the cells from infection. These CD40-dependent events protected mice against virus challenge. CD40-/- mice were exquisitely sensitive to intraperitoneal challenge with a dose of rVSV/EBOV GP that was sublethal to CD40+/+ mice, exhibiting viremia within 12 h of infection and rapidly succumbing to infection. This study identifies a previously unappreciated role for Mϕ-intrinsic CD40 signaling in controlling acute virus infection.
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Affiliation(s)
- Kai J. Rogers
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States
| | - Olena Shtanko
- Host-Pathogen Interactions, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Laura L. Stunz
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States
| | - Laura N. Mallinger
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States
| | - Tina Arkee
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, United States
| | - Megan E. Schmidt
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, United States
| | - Dana Bohan
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, United States
| | - Bethany Brunton
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States
| | - Judith M. White
- Department of Cell Biology, University of Virginia, Charlottesville, VA, United States
| | - Steve M. Varga
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, United States
| | - Noah S. Butler
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, United States
| | - Gail A. Bishop
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, United States
- Department of Internal Medicine, University of Iowa, Iowa City, IA, United States
- Iowa City VA Health Care System, Iowa City, Iowa City, IA, United States
| | - Wendy Maury
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, United States
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38
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Bosworth A, Rickett NY, Dong X, Ng LFP, García-Dorival I, Matthews DA, Fletcher T, Jacobs M, Thomson EC, Carroll MW, Hiscox JA. Analysis of an Ebola virus disease survivor whose host and viral markers were predictive of death indicates the effectiveness of medical countermeasures and supportive care. Genome Med 2021; 13:5. [PMID: 33430949 PMCID: PMC7798020 DOI: 10.1186/s13073-020-00811-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 11/12/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Ebola virus disease (EVD) is an often-fatal infection where the effectiveness of medical countermeasures is uncertain. During the West African outbreak (2013-2016), several patients were treated with different types of anti-viral therapies including monoclonal antibody-based cocktails that had the potential to neutralise Ebola virus (EBOV). However, at the time, the efficacy of these therapies was uncertain. Given the scale of the outbreak, several clinical phenotypes came to the forefront including the ability of the same virus to cause recrudescence in the same patient-perhaps through persisting in immune privileged sites. Several key questions remained including establishing if monoclonal antibody therapy was effective in humans with severe EVD, whether virus escape mutants were selected during treatment, and what is the potential mechanism(s) of persistence. This was made possible through longitudinal samples taken from a UK patient with EVD. METHODS Several different sample types, plasma and cerebrospinal fluid, were collected and sequenced using Illumina-based RNAseq. Sequence reads were mapped both to EBOV and the human genome and differential gene expression analysis used to identify changes in the abundance of gene transcripts as infection progressed. Digital Cell Quantitation analysis was used to predict the immune phenotype in samples derived from blood. RESULTS The findings were compared to equivalent data from West African patients. The study found that both virus and host markers were predictive of a fatal outcome. This suggested that the extensive supportive care, and most likely the application of the medical countermeasure ZMab (a monoclonal antibody cocktail), contributed to survival of the UK patient. The switch from progression to a 'fatal' outcome to a 'survival' outcome could be seen in both the viral and host markers. The UK patient also suffered a recrudescence infection 10 months after the initial infection. Analysis of the sequencing data indicated that the virus entered a period of reduced or minimal replication, rather than other potential mechanisms of persistence-such as defective interfering genomes. CONCLUSIONS The data showed that comprehensive supportive care and the application of medical countermeasures are worth pursuing despite an initial unfavourable prognosis.
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Affiliation(s)
- Andrew Bosworth
- Public Health England, Manor Farm Road, Porton Down, Salisbury, UK
- Clinical Virology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health Research, Liverpool, UK
| | - Natasha Y Rickett
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health Research, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Lisa F P Ng
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health Research, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Infectious Disease Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore
| | - Isabel García-Dorival
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - David A Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Tom Fletcher
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health Research, Liverpool, UK
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Michael Jacobs
- Department of Infection, Royal Free London NHS Foundation Trust, London, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
| | - Miles W Carroll
- Public Health England, Manor Farm Road, Porton Down, Salisbury, UK.
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health Research, Liverpool, UK.
- Nufield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Julian A Hiscox
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health Research, Liverpool, UK.
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
- Infectious Disease Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore.
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Warnat-Herresthal S, Oestreich M, Schultze JL, Becker M. Artificial Intelligence in Blood Transcriptomics. Artif Intell Med 2021. [DOI: 10.1007/978-3-030-58080-3_262-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Kotliar D, Lin AE, Logue J, Hughes TK, Khoury NM, Raju SS, Wadsworth MH, Chen H, Kurtz JR, Dighero-Kemp B, Bjornson ZB, Mukherjee N, Sellers BA, Tran N, Bauer MR, Adams GC, Adams R, Rinn JL, Melé M, Schaffner SF, Nolan GP, Barnes KG, Hensley LE, McIlwain DR, Shalek AK, Sabeti PC, Bennett RS. Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics. Cell 2020; 183:1383-1401.e19. [PMID: 33159858 PMCID: PMC7707107 DOI: 10.1016/j.cell.2020.10.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/10/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022]
Abstract
Ebola virus (EBOV) causes epidemics with high mortality yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. Here, we used single-cell transcriptomics and CyTOF-based single-cell protein quantification to characterize peripheral immune cells during EBOV infection in rhesus monkeys. We obtained 100,000 transcriptomes and 15,000,000 protein profiles, finding that immature, proliferative monocyte-lineage cells with reduced antigen-presentation capacity replace conventional monocyte subsets, while lymphocytes upregulate apoptosis genes and decline in abundance. By quantifying intracellular viral RNA, we identify molecular determinants of tropism among circulating immune cells and examine temporal dynamics in viral and host gene expression. Within infected cells, EBOV downregulates STAT1 mRNA and interferon signaling, and it upregulates putative pro-viral genes (e.g., DYNLL1 and HSPA5), nominating pathways the virus manipulates for its replication. This study sheds light on EBOV tropism, replication dynamics, and elicited immune response and provides a framework for characterizing host-virus interactions under maximum containment.
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Affiliation(s)
- Dylan Kotliar
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Aaron E Lin
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA.
| | - James Logue
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Travis K Hughes
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Nadine M Khoury
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Siddharth S Raju
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marc H Wadsworth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Han Chen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Jonathan R Kurtz
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Bonnie Dighero-Kemp
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Zach B Bjornson
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Brian A Sellers
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, MD 20814, USA
| | - Nancy Tran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Matthew R Bauer
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gordon C Adams
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ricky Adams
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - John L Rinn
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Marta Melé
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia 08034, Spain
| | - Stephen F Schaffner
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kayla G Barnes
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
| | - David R McIlwain
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Pardis C Sabeti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Richard S Bennett
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
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To B or Not to B: Mechanisms of Protection Conferred by rVSV-EBOV-GP and the Roles of Innate and Adaptive Immunity. Microorganisms 2020; 8:microorganisms8101473. [PMID: 32992829 PMCID: PMC7600878 DOI: 10.3390/microorganisms8101473] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 12/28/2022] Open
Abstract
Zaire Ebola virus (EBOV) is a member of the Filoviridae family of negative sense, single-stranded RNA viruses. EBOV infection causes Ebola virus disease (EVD), characterized by coagulopathy, lymphopenia, and multi-organ failure, which can culminate in death. In 2019, the FDA approved the first vaccine against EBOV, a recombinant live-attenuated viral vector wherein the G protein of vesicular stomatitis virus is replaced with the glycoprotein (GP) of EBOV (rVSV-EBOV-GP, Ervebo® by Merck). This vaccine demonstrates high efficacy in nonhuman primates by providing prophylactic, rapid, and post-exposure protection. In humans, rVSV-EBOV-GP demonstrated 100% protection in several phase III clinical trials in over 10,000 individuals during the 2013–2016 West Africa epidemic. As of 2020, over 218,000 doses of rVSV-EBOV-GP have been administered to individuals with high risk of EBOV exposure. Despite licensure and robust preclinical studies, the mechanisms of rVSV-EBOV-GP-mediated protection are not fully understood. Such knowledge is crucial for understanding vaccine-mediated correlates of protection from EVD and to aid the further design and development of therapeutics against filoviruses. Here, we summarize the current literature regarding the host response to vaccination and EBOV exposure, and evidence regarding innate and adaptive immune mechanisms involved in rVSV-EBOV-GP-mediated protection, with a focus on the host transcriptional response. Current data strongly suggest a protective synergy between rapid innate and humoral immunity.
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42
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McClain MT, Constantine FJ, Nicholson BP, Nichols M, Burke TW, Henao R, Jones DC, Hudson LL, Jaggers LB, Veldman T, Mazur A, Park LP, Suchindran S, Tsalik EL, Ginsburg GS, Woods CW. A blood-based host gene expression assay for early detection of respiratory viral infection: an index-cluster prospective cohort study. THE LANCET. INFECTIOUS DISEASES 2020; 21:396-404. [PMID: 32979932 PMCID: PMC7515566 DOI: 10.1016/s1473-3099(20)30486-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 01/31/2023]
Abstract
Background Early and accurate identification of individuals with viral infections is crucial for clinical management and public health interventions. We aimed to assess the ability of transcriptomic biomarkers to identify naturally acquired respiratory viral infection before typical symptoms are present. Methods In this index-cluster study, we prospectively recruited a cohort of undergraduate students (aged 18–25 years) at Duke University (Durham, NC, USA) over a period of 5 academic years. To identify index cases, we monitored students for the entire academic year, for the presence and severity of eight symptoms of respiratory tract infection using a daily web-based survey, with symptoms rated on a scale of 0–4. Index cases were defined as individuals who reported a 6-point increase in cumulative daily symptom score. Suspected index cases were visited by study staff to confirm the presence of reported symptoms of illness and to collect biospecimen samples. We then identified clusters of close contacts of index cases (ie, individuals who lived in close proximity to index cases, close friends, and partners) who were presumed to be at increased risk of developing symptomatic respiratory tract infection while under observation. We monitored each close contact for 5 days for symptoms and viral shedding and measured transcriptomic responses at each timepoint each day using a blood-based 36-gene RT-PCR assay. Findings Between Sept 1, 2009, and April 10, 2015, we enrolled 1465 participants. Of 264 index cases with respiratory tract infection symptoms, 150 (57%) had a viral cause confirmed by RT-PCR. Of their 555 close contacts, 106 (19%) developed symptomatic respiratory tract infection with a proven viral cause during the observation window, of whom 60 (57%) had the same virus as their associated index case. Nine viruses were detected in total. The transcriptomic assay accurately predicted viral infection at the time of maximum symptom severity (mean area under the receiver operating characteristic curve [AUROC] 0·94 [95% CI 0·92–0·96]), as well as at 1 day (0·87 [95% CI 0·84–0·90]), 2 days (0·85 [0·82–0·88]), and 3 days (0·74 [0·71–0·77]) before peak illness, when symptoms were minimal or absent and 22 (62%) of 35 individuals, 25 (69%) of 36 individuals, and 24 (82%) of 29 individuals, respectively, had no detectable viral shedding. Interpretation Transcriptional biomarkers accurately predict and diagnose infection across diverse viral causes and stages of disease and thus might prove useful for guiding the administration of early effective therapy, quarantine decisions, and other clinical and public health interventions in the setting of endemic and pandemic infectious diseases. Funding US Defense Advanced Research Projects Agency.
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Affiliation(s)
- Micah T McClain
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA.
| | - Florica J Constantine
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Marshall Nichols
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Lori L Hudson
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - L Brett Jaggers
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Timothy Veldman
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Anna Mazur
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Lawrence P Park
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
| | - Sunil Suchindran
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
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Dong X, Munoz-Basagoiti J, Rickett NY, Pollakis G, Paxton WA, Günther S, Kerber R, Ng LFP, Elmore MJ, Magassouba N, Carroll MW, Matthews DA, Hiscox JA. Variation around the dominant viral genome sequence contributes to viral load and outcome in patients with Ebola virus disease. Genome Biol 2020; 21:238. [PMID: 32894206 PMCID: PMC7475720 DOI: 10.1186/s13059-020-02148-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Viral load is a major contributor to outcome in patients with Ebola virus disease (EVD), with high values leading to a fatal outcome. Evidence from the 2013-2016 Ebola virus (EBOV) outbreak indicated that different genotypes of the virus can have different phenotypes in patients. Additionally, due to the error-prone nature of viral RNA synthesis in an individual patient, the EBOV genome exists around a dominant viral genome sequence. The minor variants within a patient may contribute to the overall phenotype in terms of viral protein function. To investigate the effects of these minor variants, blood samples from patients with acute EVD were deeply sequenced. RESULTS We examine the minor variant frequency between patients with acute EVD who survived infection with those who died. Non-synonymous differences in viral proteins were identified that have implications for viral protein function. The greatest frequency of substitution was identified at three codon sites in the L gene-which encodes the viral RNA-dependent RNA polymerase (RdRp). Recapitulating this in an assay for virus replication, these substitutions result in aberrant viral RNA synthesis and correlate with patient outcome. CONCLUSIONS Together, these findings support the notion that in patients who survived EVD, in some cases, the genetic variability of the virus resulted in deleterious mutations that affected viral protein function, leading to reduced viral load. Such mutations may also lead to persistent strains of the virus and be associated with recrudescent infections.
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Affiliation(s)
- Xiaofeng Dong
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jordana Munoz-Basagoiti
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Natasha Y. Rickett
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Georgios Pollakis
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - William A. Paxton
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Romy Kerber
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Lisa F. P. Ng
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- Singapore Immunology Network, A*STAR, Singapore, Singapore
| | | | - N’faly Magassouba
- Laboratoire des fièvres hémorragiques en Guinée, Université Gamal Abdel Nasser de Conakry, Conakry, Guinea
| | - Miles W. Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- Public Health England, Salisbury, UK
| | - David A. Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Singapore, Singapore
| | - Julian A. Hiscox
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- Singapore Immunology Network, A*STAR, Singapore, Singapore
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Beckmann ND, Comella PH, Cheng E, Lepow L, Beckmann AG, Mouskas K, Simons NW, Hoffman GE, Francoeur NJ, Del Valle DM, Kang G, Moya E, Wilkins L, Le Berichel J, Chang C, Marvin R, Calorossi S, Lansky A, Walker L, Yi N, Yu A, Hartnett M, Eaton M, Hatem S, Jamal H, Akyatan A, Tabachnikova A, Liharska LE, Cotter L, Fennessey B, Vaid A, Barturen G, Tyler SR, Shah H, Wang YC, Sridhar SH, Soto J, Bose S, Madrid K, Ellis E, Merzier E, Vlachos K, Fishman N, Tin M, Smith M, Xie H, Patel M, Argueta K, Harris J, Karekar N, Batchelor C, Lacunza J, Yishak M, Tuballes K, Scott L, Kumar A, Jaladanki S, Thompson R, Clark E, Losic B, Zhu J, Wang W, Kasarskis A, Glicksberg BS, Nadkarni G, Bogunovic D, Elaiho C, Gangadharan S, Ofori-Amanfo G, Alesso-Carra K, Onel K, Wilson KM, Argmann C, Alarcón-Riquelme ME, Marron TU, Rahman A, Kim-Schulze S, Gnjatic S, Gelb BD, Merad M, Sebra R, Schadt EE, Charney AW. Cytotoxic lymphocytes are dysregulated in multisystem inflammatory syndrome in children. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.08.29.20182899. [PMID: 32909006 PMCID: PMC7480058 DOI: 10.1101/2020.08.29.20182899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Multisystem inflammatory syndrome in children (MIS-C) presents with fever, inflammation and multiple organ involvement in individuals under 21 years following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. To identify genes, pathways and cell types driving MIS-C, we sequenced the blood transcriptomes of MIS-C cases, pediatric cases of coronavirus disease 2019, and healthy controls. We define a MIS-C transcriptional signature partially shared with the transcriptional response to SARS-CoV-2 infection and with the signature of Kawasaki disease, a clinically similar condition. By projecting the MIS-C signature onto a co-expression network, we identified disease gene modules and found genes downregulated in MIS-C clustered in a module enriched for the transcriptional signatures of exhausted CD8 + T-cells and CD56 dim CD57 + NK cells. Bayesian network analyses revealed nine key regulators of this module, including TBX21 , a central coordinator of exhausted CD8 + T-cell differentiation. Together, these findings suggest dysregulated cytotoxic lymphocyte response to SARS-Cov-2 infection in MIS-C.
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Affiliation(s)
- Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Phillip H. Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Esther Cheng
- Department of Genetics and Genomic Sciences, 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
| | - Lauren Lepow
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aviva G. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Konstantinos Mouskas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nicole W. Simons
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gabriel E. Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nancy J. Francoeur
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Diane Marie Del Valle
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gurpawan Kang
- Department of Medicine, division of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emily Moya
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lillian Wilkins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jessica Le Berichel
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christie Chang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Marvin
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sharlene Calorossi
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alona Lansky
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Laura Walker
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nancy Yi
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alex Yu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matthew Hartnett
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melody Eaton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sandra Hatem
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hajra Jamal
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alara Akyatan
- Department of of Rehabilitation and Human Performance, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexandra Tabachnikova
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lora E. Liharska
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Liam Cotter
- Department of Genetics and Genomic Sciences, 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
| | - Brian Fennessey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Akhil Vaid
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Guillermo Barturen
- Department of Medical Genomics, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government (GENYO), 18007 Urb. los Vergeles, Granada, Spain
| | - Scott R. Tyler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ying-chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shwetha Hara Sridhar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Juan Soto
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Swaroop Bose
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Kent Madrid
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Ethan Ellis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Elyze Merzier
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Konstantinos Vlachos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Nataly Fishman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Manying Tin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Melissa Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Hui Xie
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Manishkumar Patel
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimberly Argueta
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jocelyn Harris
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Neha Karekar
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Craig Batchelor
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jose Lacunza
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mahlet Yishak
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kevin Tuballes
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Leisha Scott
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Arvind Kumar
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Suraj Jaladanki
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ryan Thompson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Evan Clark
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jun Zhu
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wenhui Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew Kasarskis
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Benjamin S. Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Girish Nadkarni
- Mount Sinai COVID Informatics Center, New York, NY 10029, USA
- Department of Medicine, Mount Sinai, New York, NY 10029, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, New York, NY 10029, USA
- Charles Bronfman Institute for Personalized Medicine, New York, NY 10029, USA
| | - Dusan Bogunovic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Cordelia Elaiho
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sandeep Gangadharan
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - George Ofori-Amanfo
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kasey Alesso-Carra
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kenan Onel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karen M. Wilson
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marta E. Alarcón-Riquelme
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Thomas U. Marron
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adeeb Rahman
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Seunghee Kim-Schulze
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medicine, division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bruce D. Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mindich Child Health and Development Institute at Mount Sinai, New York, NY 10029, USA
| | - Miriam Merad
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Black Family Stem Cell Institute, New York, NY 10029, USA
- Sema4, a Mount Sinai venture, Stamford CT, 06902, USA
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Sema4, a Mount Sinai venture, Stamford CT, 06902, USA
| | - Alexander W. Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai COVID Informatics Center, New York, NY 10029, USA
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45
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Long-lasting severe immune dysfunction in Ebola virus disease survivors. Nat Commun 2020; 11:3730. [PMID: 32709840 PMCID: PMC7381622 DOI: 10.1038/s41467-020-17489-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 06/29/2020] [Indexed: 12/30/2022] Open
Abstract
Long-term follow up studies from Ebola virus disease (EVD) survivors (EBOV_S) are lacking. Here, we evaluate immune and gene expression profiles in 35 Guinean EBOV_S from the last West African outbreak, a median of 23 months (IQR [18–25]) after discharge from treatment center. Compared with healthy donors, EBOV_S exhibit increases of blood markers of inflammation, intestinal tissue damage, T cell and B cell activation and a depletion of circulating dendritic cells. All survivors have EBOV-specific IgG antibodies and robust and polyfunctional EBOV-specific memory T-cell responses. Deep sequencing of the genes expressed in blood reveals an enrichment in ‘inflammation’ and ‘antiviral’ pathways. Integrated analyses identify specific immune markers associated with the persistence of clinical symptoms. This study identifies a set of biological and genetic markers that could be used to define a signature of “chronic Ebola virus disease (CEVD)”. Patients who have recovered from Ebola virus can have ongoing health problems. Here, the authors show that 35 Guinean survivors of the last West African Ebola epidemic have a chronic disease with high inflammatory cytokine expression and other markers of immune activation as well as evidence of intestinal tissue damage nearly two years after their release from hospital.
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Di Paola N, Sanchez-Lockhart M, Zeng X, Kuhn JH, Palacios G. Viral genomics in Ebola virus research. Nat Rev Microbiol 2020; 18:365-378. [PMID: 32367066 PMCID: PMC7223634 DOI: 10.1038/s41579-020-0354-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 12/20/2022]
Abstract
Filoviruses such as Ebola virus continue to pose a substantial health risk to humans. Advances in the sequencing and functional characterization of both pathogen and host genomes have provided a wealth of knowledge to clinicians, epidemiologists and public health responders during outbreaks of high-consequence viral disease. Here, we describe how genomics has been historically used to investigate Ebola virus disease outbreaks and how new technologies allow for rapid, large-scale data generation at the point of care. We highlight how genomics extends beyond consensus-level sequencing of the virus to include intra-host viral transcriptomics and the characterization of host responses in acute and persistently infected patients. Similar genomics techniques can also be applied to the characterization of non-human primate animal models and to known natural reservoirs of filoviruses, and metagenomic sequencing can be the key to the discovery of novel filoviruses. Finally, we outline the importance of reverse genetics systems that can swiftly characterize filoviruses as soon as their genome sequences are available.
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Affiliation(s)
- Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Mariano Sanchez-Lockhart
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Xiankun Zeng
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, 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
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA.
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Greenberg A, Huber BR, Liu DX, Logue JP, Hischak AMW, Hart RJ, Abbott M, Isic N, Hisada YM, Mackman N, Bennett RS, Hensley LE, Connor JH, Crossland NA. Quantification of Viral and Host Biomarkers in the Liver of Rhesus Macaques: A Longitudinal Study of Zaire Ebolavirus Strain Kikwit (EBOV/Kik). THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:1449-1460. [PMID: 32275904 PMCID: PMC7322367 DOI: 10.1016/j.ajpath.2020.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 12/21/2022]
Abstract
Zaire ebolavirus (EBOV) causes Ebola virus disease (EVD), which carries a fatality rate between 25% and 90% in humans. Liver pathology is a hallmark of terminal EVD; however, little is known about temporal disease progression. We used multiplexed fluorescent immunohistochemistry and in situ hybridization in combination with whole slide imaging and image analysis (IA) to quantitatively characterize temporospatial signatures of viral and host factors as related to EBOV pathogenesis. Eighteen rhesus monkeys euthanized between 3 and 8 days post-infection, and 3 uninfected controls were enrolled in this study. Compared with semiquantitative histomorphologic ordinal scoring, quantitative IA detected subtle and progressive features of early and terminal EVD that was not feasible with routine approaches. Sinusoidal macrophages were the earliest cells to respond to infection, expressing proinflammatory cytokine interleukin 6 (IL6) mRNA, which was subsequently also observed in fibrovascular compartments. The mRNA of interferon-stimulated gene-15 (ISG-15), also known as ISG15 ubiquitin like modifier (ISG15), was observed early, with a progressive and ubiquitous hybridization signature involving mesenchymal and epithelial compartments. ISG-15 mRNA was prominent near infected cells, but not in infected cells, supporting the hypothesis that bystander cells produce a robust interferon gene response. This study contributes to our current understanding of early EVD progression and illustrates the value that digital pathology and quantitative IA serve in infectious disease research.
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Affiliation(s)
- Alexandra Greenberg
- Graduate Medical Sciences, Boston University School of Medicine, Boston, Massachusetts
| | - Bertrand R Huber
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
| | - David X Liu
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - James P Logue
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Amanda M W Hischak
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Randy J Hart
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Maureen Abbott
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Nejra Isic
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Yohei M Hisada
- Division of Hematology and Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Nigel Mackman
- Division of Hematology and Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Richard S Bennett
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Lisa E Hensley
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - John H Connor
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Nicholas A Crossland
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts.
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Previremic Identification of Ebola or Marburg Virus Infection Using Integrated Host-Transcriptome and Viral Genome Detection. mBio 2020; 11:mBio.01157-20. [PMID: 32546624 PMCID: PMC7298714 DOI: 10.1128/mbio.01157-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Current molecular tests that identify infection with high-consequence viruses such as Ebola virus and Marburg virus are based on the detection of virus material in the blood. These viruses do not undergo significant early replication in the blood and, instead, replicate in organs such as the liver and spleen. Thus, virus begins to accumulate in the blood only after significant replication has already occurred in those organs, making viremia an indicator of infection only after initial stages have become established. Here, we show that a multianalyte assay can correctly identify the infectious agent in nonhuman primates (NHPs) prior to viremia through tracking host infection response transcripts. This illustrates that a single-tube, sample-to-answer format assay could be used to advance the time at which the type of infection can be determined and thereby improve outcomes. Outbreaks of filoviruses, such as those caused by the Ebola (EBOV) and Marburg (MARV) virus, are difficult to detect and control. The initial clinical symptoms of these diseases are nonspecific and can mimic other endemic pathogens. This makes confident diagnosis based on clinical symptoms alone impossible. Molecular diagnostics for these diseases that rely on the detection of viral RNA in the blood are only effective after significant disease progression. As an approach to identify these infections earlier in the disease course, we tested the effectiveness of viral RNA detection combined with an assessment of sentinel host mRNAs that are upregulated following filovirus infection. RNAseq analysis of EBOV-infected nonhuman primates identified host RNAs that are upregulated at early stages of infection. NanoString probes that recognized these host-response RNAs were combined with probes that recognized viral RNA and were used to classify viral infection both prior to viremia and postviremia. This approach was highly successful at identifying samples from nonhuman primate subjects and correctly distinguished the causative agent in a previremic stage in 10 EBOV and 5 MARV samples. This work suggests that unified host response/viral fingerprint assays can enable diagnosis of disease earlier than testing for viral nucleic acid alone, which could decrease transmission events and increase therapeutic effectiveness.
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McElroy AK, Akondy RS, Mcllwain DR, Chen H, Bjornson-Hooper Z, Mukherjee N, Mehta AK, Nolan G, Nichol ST, Spiropoulou CF. Immunologic timeline of Ebola virus disease and recovery in humans. JCI Insight 2020; 5:137260. [PMID: 32434986 PMCID: PMC7259516 DOI: 10.1172/jci.insight.137260] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
A complete understanding of human immune responses to Ebola virus infection is limited by the availability of specimens and the requirement for biosafety level 4 (BSL-4) containment. In an effort to bridge this gap, we evaluated cryopreserved PBMCs from 4 patients who survived Ebola virus disease (EVD) using an established mass cytometry antibody panel to characterize various cell populations during both the acute and convalescent phases. Acute loss of nonclassical monocytes and myeloid DCs, especially CD1c+ DCs, was noted. Classical monocyte proliferation and CD38 upregulation on plasmacytoid DCs coincided with declining viral load. Unsupervised analysis of cell abundance demonstrated acute declines in monocytic, NK, and T cell populations, but some populations, many of myeloid origin, increased in abundance during the acute phase, suggesting emergency hematopoiesis. Despite cell losses during the acute phase, upregulation of Ki-67 correlated with recovery of cell populations over time. These data provide insights into the human immune response during EVD.
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Affiliation(s)
- Anita K McElroy
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Division of Pediatric Infectious Diseases and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rama S Akondy
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - David R Mcllwain
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Han Chen
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Zach Bjornson-Hooper
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Nilanjan Mukherjee
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Aneesh K Mehta
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Garry Nolan
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Stuart T Nichol
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Early Transcriptional Changes within Liver, Adrenal Gland, and Lymphoid Tissues Significantly Contribute to Ebola Virus Pathogenesis in Cynomolgus Macaques. J Virol 2020; 94:JVI.00250-20. [PMID: 32213610 DOI: 10.1128/jvi.00250-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/11/2020] [Indexed: 01/05/2023] Open
Abstract
Ebola virus (EBOV) continues to pose a significant threat to human health, as evidenced by the 2013-2016 epidemic in West Africa and the ongoing outbreak in the Democratic Republic of the Congo. EBOV causes hemorrhagic fever, organ damage, and shock culminating in death, with case fatality rates as high as 90%. This high lethality combined with the paucity of licensed medical countermeasures makes EBOV a critical human pathogen. Although EBOV infection results in significant damage to the liver and the adrenal glands, little is known about the molecular signatures of injury in these organs. Moreover, while changes in peripheral blood cells are becoming increasingly understood, the host responses within organs and lymphoid tissues remain poorly characterized. To address this knowledge gap, we tracked longitudinal transcriptional changes in tissues collected from EBOV-Makona-infected cynomolgus macaques. Following infection, both liver and adrenal glands exhibited significant and early downregulation of genes involved in metabolism, coagulation, hormone synthesis, and angiogenesis; upregulated genes were associated with inflammation. Analysis of lymphoid tissues showed early upregulation of genes that play a role in innate immunity and inflammation and downregulation of genes associated with cell cycle and adaptive immunity. Moreover, transient activation of innate immune responses and downregulation of humoral immune responses in lymphoid tissues were confirmed with flow cytometry. Together, these data suggest that the liver, adrenal gland, and lymphatic organs are important sites of EBOV infection and that dysregulating the function of these vital organs contributes to the development of Ebola virus disease.IMPORTANCE Ebola virus (EBOV) remains a high-priority pathogen since it continues to cause outbreaks with high case fatality rates. Although it is well established that EBOV results in severe organ damage, our understanding of tissue injury in the liver, adrenal glands, and lymphoid tissues remains limited. We begin to address this knowledge gap by conducting longitudinal gene expression studies in these tissues, which were collected from EBOV-infected cynomolgus macaques. We report robust and early gene expression changes within these tissues, indicating they are primary sites of EBOV infection. Furthermore, genes involved in metabolism, coagulation, and adaptive immunity were downregulated, while inflammation-related genes were upregulated. These results indicate significant tissue damage consistent with the development of hemorrhagic fever and lymphopenia. Our study provides novel insight into EBOV-host interactions and elucidates how host responses within the liver, adrenal glands, and lymphoid tissues contribute to EBOV pathogenesis.
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