51
|
Sefik E, Israelow B, Zhao J, Qu R, Song E, Mirza H, Kaffe E, Halene S, Meffre E, Kluger Y, Nussenzweig M, Wilen CB, Iwasaki A, Flavell RA. A humanized mouse model of chronic COVID-19 to evaluate disease mechanisms and treatment options. Res Sq 2021:rs.3.rs-279341. [PMID: 33758831 PMCID: PMC7987100 DOI: 10.21203/rs.3.rs-279341/v1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Coronavirus-associated acute respiratory disease, called coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). More than 90 million people have been infected with SARS-CoV-2 and more than 2 million people have died of complications due to COVID-19 worldwide. COVID-19, in its severe form, presents with an uncontrolled, hyperactive immune response and severe immunological injury or organ damage that accounts for morbidity and mortality. Even in the absence of complications, COVID-19 can last for several months with lingering effects of an overactive immune system. Dysregulated myeloid and lymphocyte compartments have been implicated in lung immunopathology. Currently, there are limited clinically-tested treatments of COVID-19 with disparities in the apparent efficacy in patients. Accurate model systems are essential to rapidly evaluate promising discoveries but most currently available in mice, ferrets and hamsters do not recapitulate sustained immunopathology described in COVID19 patients. Here, we present a comprehensively humanized mouse COVID-19 model that faithfully recapitulates the innate and adaptive human immune responses during infection with SARS-CoV-2 by adapting recombinant adeno-associated virus (AAV)-driven gene therapy to deliver human ACE2 to the lungs 1 of MISTRG6 mice. Our unique model allows for the first time the study of chronic disease due to infection with SARS-CoV-2 in the context of patient-derived antibodies to characterize in real time the potential culprits of the observed human driving immunopathology; most importantly this model provides a live view into the aberrant macrophage response that is thought to be the effector of disease morbidity and ARDS in patients. Application of therapeutics such as patient-derived antibodies and steroids to our model allowed separation of the two aspects of the immune response, infectious viral clearance and immunopathology. Inflammatory cells seeded early in infection drove immune-patholgy later, but this very same early anti-viral response was also crucial to contain infection.
Collapse
Affiliation(s)
- Esen Sefik
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Ben Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Jun Zhao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Rihao Qu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Haris Mirza
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Eleanna Kaffe
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Stephanie Halene
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
| | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Yuval Kluger
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Michel Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT,USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
52
|
Chen JS, Alfajaro MM, Chow RD, Wei J, Filler RB, Eisenbarth SC, Wilen CB. Non-steroidal anti-inflammatory drugs dampen the cytokine and antibody response to SARS-CoV-2 infection. J Virol 2021; 95:JVI.00014-21. [PMID: 33441348 PMCID: PMC8092681 DOI: 10.1128/jvi.00014-21] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022] Open
Abstract
Identifying drugs that regulate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and its symptoms has been a pressing area of investigation during the coronavirus disease 2019 (COVID-19) pandemic. Nonsteroidal anti-inflammatory drugs (NSAIDs), which are frequently used for the relief of pain and inflammation, could modulate both SARS-CoV-2 infection and the host response to the virus. NSAIDs inhibit the enzymes cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2), which mediate the production of prostaglandins (PGs). As PGs play diverse biological roles in homeostasis and inflammatory responses, inhibiting PG production with NSAIDs could affect COVID-19 pathogenesis in multiple ways, including: (1) altering susceptibility to infection by modifying expression of angiotensin-converting enzyme 2 (ACE2), the cell entry receptor for SARS-CoV-2; (2) regulating replication of SARS-CoV-2 in host cells; and (3) modulating the immune response to SARS-CoV-2. Here, we investigate these potential roles. We demonstrate that SARS-CoV-2 infection upregulates COX-2 in diverse human cell culture and mouse systems. However, suppression of COX-2 by two commonly used NSAIDs, ibuprofen and meloxicam, had no effect on ACE2 expression, viral entry, or viral replication. In contrast, in a mouse model of SARS-CoV-2 infection, NSAID treatment reduced production of pro-inflammatory cytokines and impaired the humoral immune response to SARS-CoV-2 as demonstrated by reduced neutralizing antibody titers. Our findings indicate that NSAID treatment may influence COVID-19 outcomes by dampening the inflammatory response and production of protective antibodies rather than modifying susceptibility to infection or viral replication.ImportancePublic health officials have raised concerns about the use of nonsteroidal anti-inflammatory drugs (NSAIDs) for treating symptoms of coronavirus disease 2019 (COVID-19). NSAIDs inhibit the enzymes cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2), which are critical for the generation of prostaglandins - lipid molecules with diverse roles in homeostasis and inflammation. Inhibition of prostaglandin production by NSAIDs could therefore have multiple effects on COVID-19 pathogenesis. Here, we demonstrate that NSAID treatment reduced both the antibody and pro-inflammatory cytokine response to SARS-CoV-2 infection. The ability of NSAIDs to modulate the immune response to SARS-CoV-2 infection has important implications for COVID-19 pathogenesis in patients. Whether this occurs in humans and whether it is beneficial or detrimental to the host remains an important area of future investigation. This also raises the possibility that NSAIDs may alter the immune response to SARS-CoV-2 vaccination.
Collapse
Affiliation(s)
- Jennifer S Chen
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Ryan D Chow
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jin Wei
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie C Eisenbarth
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
53
|
Walker FC, Hassan E, Peterson ST, Rodgers R, Schriefer LA, Thompson CE, Li Y, Kalugotla G, Blum-Johnston C, Lawrence D, McCune BT, Graziano VR, Lushniak L, Lee S, Roth AN, Karst SM, Nice TJ, Miner JJ, Wilen CB, Baldridge MT. Norovirus evolution in immunodeficient mice reveals potentiated pathogenicity via a single nucleotide change in the viral capsid. PLoS Pathog 2021; 17:e1009402. [PMID: 33705489 PMCID: PMC7987144 DOI: 10.1371/journal.ppat.1009402] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 03/23/2021] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
Interferons (IFNs) are key controllers of viral replication, with intact IFN responses suppressing virus growth and spread. Using the murine norovirus (MNoV) system, we show that IFNs exert selective pressure to limit the pathogenic evolutionary potential of this enteric virus. In animals lacking type I IFN signaling, the nonlethal MNoV strain CR6 rapidly acquired enhanced virulence via conversion of a single nucleotide. This nucleotide change resulted in amino acid substitution F514I in the viral capsid, which led to >10,000-fold higher replication in systemic organs including the brain. Pathogenicity was mediated by enhanced recruitment and infection of intestinal myeloid cells and increased extraintestinal dissemination of virus. Interestingly, the trade-off for this mutation was reduced fitness in an IFN-competent host, in which CR6 bearing F514I exhibited decreased intestinal replication and shedding. In an immunodeficient context, a spontaneous amino acid change can thus convert a relatively avirulent viral strain into a lethal pathogen.
Collapse
Affiliation(s)
- Forrest C. Walker
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ebrahim Hassan
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Stefan T. Peterson
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rachel Rodgers
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lawrence A. Schriefer
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Cassandra E. Thompson
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yuhao Li
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gowri Kalugotla
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Carla Blum-Johnston
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Dylan Lawrence
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Broc T. McCune
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Vincent R. Graziano
- Departments of Laboratory Medicine & Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Larissa Lushniak
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sanghyun Lee
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Alexa N. Roth
- Department of Molecular Genetics & Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Stephanie M. Karst
- Department of Molecular Genetics & Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Timothy J. Nice
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Jonathan J. Miner
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Craig B. Wilen
- Departments of Laboratory Medicine & Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Megan T. Baldridge
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| |
Collapse
|
54
|
Ravindra NG, Alfajaro MM, Gasque V, Huston NC, Wan H, Szigeti-Buck K, Yasumoto Y, Greaney AM, Habet V, Chow RD, Chen JS, Wei J, Filler RB, Wang B, Wang G, Niklason LE, Montgomery RR, Eisenbarth SC, Chen S, Williams A, Iwasaki A, Horvath TL, Foxman EF, Pierce RW, Pyle AM, van Dijk D, Wilen CB. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. PLoS Biol 2021; 19:e3001143. [PMID: 33730024 PMCID: PMC8007021 DOI: 10.1371/journal.pbio.3001143] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 03/29/2021] [Accepted: 02/08/2021] [Indexed: 01/21/2023] Open
Abstract
There are currently limited Food and Drug Administration (FDA)-approved drugs and vaccines for the treatment or prevention of Coronavirus Disease 2019 (COVID-19). Enhanced understanding of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and pathogenesis is critical for the development of therapeutics. To provide insight into viral replication, cell tropism, and host-viral interactions of SARS-CoV-2, we performed single-cell (sc) RNA sequencing (RNA-seq) of experimentally infected human bronchial epithelial cells (HBECs) in air-liquid interface (ALI) cultures over a time course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target at the onset of infection, which we confirmed by electron and immunofluorescence microscopy. Over the course of infection, the cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell-intrinsic expression of type I and type III interferons (IFNs) and interleukin (IL)-6 but not IL-1. This results in expression of interferon-stimulated genes (ISGs) in both infected and bystander cells. This provides a detailed characterization of genes, cell types, and cell state changes associated with SARS-CoV-2 infection in the human airway.
Collapse
Affiliation(s)
- Neal G. Ravindra
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School Medicine, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Victor Gasque
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School Medicine, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
- Universite Claude Bernard Lyon 1, Faculte de Medecine Lyon Est, Lyon, France
- Department de Bioinformatique, Univ Evry, Universite Paris-Saclay, Paris, France
| | - Nicholas C. Huston
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Klara Szigeti-Buck
- Department of Comparative Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, United of States of America
| | - Yuki Yasumoto
- Department of Comparative Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, United of States of America
| | - Allison M. Greaney
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
| | - Victoria Habet
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Ryan D. Chow
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Jennifer S. Chen
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Jin Wei
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Renata B. Filler
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Bao Wang
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Guilin Wang
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Laura E. Niklason
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
- Department of Anesthesiology, Yale University, New Haven, Connecticut, United States of America
| | - Ruth R. Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Stephanie C. Eisenbarth
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Sidi Chen
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Adam Williams
- The Jackson Laboratory, Farmington, Connecticut, United States of America
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Tamas L. Horvath
- Department of Comparative Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, United of States of America
| | - Ellen F. Foxman
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Richard W. Pierce
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Anna Marie Pyle
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - David van Dijk
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School Medicine, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| |
Collapse
|
55
|
Huston NC, Wan H, Strine MS, de Cesaris Araujo Tavares R, Wilen CB, Pyle AM. Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. Mol Cell 2021; 81:584-598.e5. [PMID: 33444546 PMCID: PMC7775661 DOI: 10.1016/j.molcel.2020.12.041] [Citation(s) in RCA: 157] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/06/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2) is the positive-sense RNA virus that causes coronavirus disease 2019 (COVID-19). The genome of SARS-CoV-2 is unique among viral RNAs in its vast potential to form RNA structures, yet as much as 97% of its 30 kilobases have not been structurally explored. Here, we apply a novel long amplicon strategy to determine the secondary structure of the SARS-CoV-2 RNA genome at single-nucleotide resolution in infected cells. Our in-depth structural analysis reveals networks of well-folded RNA structures throughout Orf1ab and reveals aspects of SARS-CoV-2 genome architecture that distinguish it from other RNA viruses. Evolutionary analysis shows that several features of the SARS-CoV-2 genomic structure are conserved across β-coronaviruses, and we pinpoint regions of well-folded RNA structure that merit downstream functional analysis. The native, secondary structure of SARS-CoV-2 presented here is a roadmap that will facilitate focused studies on the viral life cycle, facilitate primer design, and guide the identification of RNA drug targets against COVID-19.
Collapse
Affiliation(s)
- Nicholas C Huston
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Madison S Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06519, USA
| | | | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06519, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Department of Chemistry, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| |
Collapse
|
56
|
Brestoff JR, Wilen CB, Moley JR, Li Y, Zou W, Malvin NP, Rowen MN, Saunders BT, Ma H, Mack MR, Hykes BL, Balce DR, Orvedahl A, Williams JW, Rohatgi N, Wang X, McAllaster MR, Handley SA, Kim BS, Doench JG, Zinselmeyer BH, Diamond MS, Virgin HW, Gelman AE, Teitelbaum SL. Intercellular Mitochondria Transfer to Macrophages Regulates White Adipose Tissue Homeostasis and Is Impaired in Obesity. Cell Metab 2021; 33:270-282.e8. [PMID: 33278339 PMCID: PMC7858234 DOI: 10.1016/j.cmet.2020.11.008] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/03/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023]
Abstract
Recent studies suggest that mitochondria can be transferred between cells to support the survival of metabolically compromised cells. However, whether intercellular mitochondria transfer occurs in white adipose tissue (WAT) or regulates metabolic homeostasis in vivo remains unknown. We found that macrophages acquire mitochondria from neighboring adipocytes in vivo and that this process defines a transcriptionally distinct macrophage subpopulation. A genome-wide CRISPR-Cas9 knockout screen revealed that mitochondria uptake depends on heparan sulfates (HS). High-fat diet (HFD)-induced obese mice exhibit lower HS levels on WAT macrophages and decreased intercellular mitochondria transfer from adipocytes to macrophages. Deletion of the HS biosynthetic gene Ext1 in myeloid cells decreases mitochondria uptake by WAT macrophages, increases WAT mass, lowers energy expenditure, and exacerbates HFD-induced obesity in vivo. Collectively, this study suggests that adipocytes and macrophages employ intercellular mitochondria transfer as a mechanism of immunometabolic crosstalk that regulates metabolic homeostasis and is impaired in obesity.
Collapse
Affiliation(s)
- Jonathan R Brestoff
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Craig B Wilen
- Department of Laboratory Medicine and Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - John R Moley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yongjia Li
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Wei Zou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole P Malvin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marina N Rowen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian T Saunders
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hongming Ma
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Madison R Mack
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barry L Hykes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dale R Balce
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Vir Biotechnology, San Francisco, CA 94158, USA
| | - Anthony Orvedahl
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jesse W Williams
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nidhi Rohatgi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiaoyan Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael R McAllaster
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian S Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bernd H Zinselmeyer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Vir Biotechnology, San Francisco, CA 94158, USA; Department of Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andrew E Gelman
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven L Teitelbaum
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
57
|
Song E, Zhang C, Israelow B, Lu-Culligan A, Prado AV, Skriabine S, Lu P, Weizman OE, Liu F, Dai Y, Szigeti-Buck K, Yasumoto Y, Wang G, Castaldi C, Heltke J, Ng E, Wheeler J, Alfajaro MM, Levavasseur E, Fontes B, Ravindra NG, Van Dijk D, Mane S, Gunel M, Ring A, Kazmi SAJ, Zhang K, Wilen CB, Horvath TL, Plu I, Haik S, Thomas JL, Louvi A, Farhadian SF, Huttner A, Seilhean D, Renier N, Bilguvar K, Iwasaki A. Neuroinvasion of SARS-CoV-2 in human and mouse brain. J Exp Med 2021; 218:211674. [PMID: 33433624 PMCID: PMC7808299 DOI: 10.1084/jem.20202135] [Citation(s) in RCA: 572] [Impact Index Per Article: 190.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/23/2020] [Accepted: 12/10/2020] [Indexed: 12/28/2022] Open
Abstract
Although COVID-19 is considered to be primarily a respiratory disease, SARS-CoV-2 affects multiple organ systems including the central nervous system (CNS). Yet, there is no consensus on the consequences of CNS infections. Here, we used three independent approaches to probe the capacity of SARS-CoV-2 to infect the brain. First, using human brain organoids, we observed clear evidence of infection with accompanying metabolic changes in infected and neighboring neurons. However, no evidence for type I interferon responses was detected. We demonstrate that neuronal infection can be prevented by blocking ACE2 with antibodies or by administering cerebrospinal fluid from a COVID-19 patient. Second, using mice overexpressing human ACE2, we demonstrate SARS-CoV-2 neuroinvasion in vivo. Finally, in autopsies from patients who died of COVID-19, we detect SARS-CoV-2 in cortical neurons and note pathological features associated with infection with minimal immune cell infiltrates. These results provide evidence for the neuroinvasive capacity of SARS-CoV-2 and an unexpected consequence of direct infection of neurons by SARS-CoV-2.
Collapse
Affiliation(s)
- Eric Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Ce Zhang
- Department of Genetics, Yale School of Medicine, New Haven, CT.,Department of Neuroscience, Yale School of Medicine, New Haven, CT
| | - Benjamin Israelow
- Department of Immunobiology, Yale School of Medicine, New Haven, CT.,Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT
| | | | - Alba Vieites Prado
- Sorbonne Université, INSERM U1127, French National Centre for Scientific Research, Joint Research Unit 7225, Paris Brain Institute, Institut du Cerveau et de la Moelle Épinière, Paris, France
| | - Sophie Skriabine
- Sorbonne Université, INSERM U1127, French National Centre for Scientific Research, Joint Research Unit 7225, Paris Brain Institute, Institut du Cerveau et de la Moelle Épinière, Paris, France
| | - Peiwen Lu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Orr-El Weizman
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT.,Department of Biomedical Engineering, Yale University, New Haven, CT
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Klara Szigeti-Buck
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT
| | - Yuki Yasumoto
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT
| | - Guilin Wang
- Yale Center for Genome Analysis, West Haven, CT
| | | | | | - Evelyn Ng
- Yale Center for Genome Analysis, West Haven, CT
| | | | - Mia Madel Alfajaro
- Department of Immunobiology, Yale School of Medicine, New Haven, CT.,Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Etienne Levavasseur
- Sorbonne Université, INSERM U1127, French National Centre for Scientific Research, Joint Research Unit 7225, Paris Brain Institute, Institut du Cerveau et de la Moelle Épinière, Paris, France
| | - Benjamin Fontes
- Yale Environmental Health and Safety, Yale University, New Haven, CT
| | - Neal G Ravindra
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT.,Department of Computer Science, Yale University, New Haven, CT
| | - David Van Dijk
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT.,Department of Computer Science, Yale University, New Haven, CT
| | - Shrikant Mane
- Department of Genetics, Yale School of Medicine, New Haven, CT.,Yale Center for Genome Analysis, West Haven, CT
| | - Murat Gunel
- Department of Genetics, Yale School of Medicine, New Haven, CT.,Department of Neuroscience, Yale School of Medicine, New Haven, CT.,Department of Neurosurgery, Yale School of Medicine, New Haven, CT
| | - Aaron Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | | | - Kai Zhang
- Department of Laboratory Medicine, Geisinger Medical Center, Danville, PA
| | - Craig B Wilen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT.,Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Tamas L Horvath
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT
| | - Isabelle Plu
- Sorbonne Université, INSERM U1127, French National Centre for Scientific Research, Joint Research Unit 7225, Paris Brain Institute, Institut du Cerveau et de la Moelle Épinière, Paris, France.,Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Neuropathologie, Paris, France
| | - Stephane Haik
- Sorbonne Université, INSERM U1127, French National Centre for Scientific Research, Joint Research Unit 7225, Paris Brain Institute, Institut du Cerveau et de la Moelle Épinière, Paris, France.,Yale Environmental Health and Safety, Yale University, New Haven, CT.,Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Neuropathologie, Paris, France.,Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Cellule nationale de référence des maladies de Creutzfeldt-Jakob, Paris, France
| | - Jean-Leon Thomas
- Sorbonne Université, INSERM U1127, French National Centre for Scientific Research, Joint Research Unit 7225, Paris Brain Institute, Institut du Cerveau et de la Moelle Épinière, Paris, France.,Department of Neurology, Yale School of Medicine, New Haven, CT
| | - Angeliki Louvi
- Department of Neuroscience, Yale School of Medicine, New Haven, CT.,Department of Neurosurgery, Yale School of Medicine, New Haven, CT
| | - Shelli F Farhadian
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT.,Department of Neurology, Yale School of Medicine, New Haven, CT
| | - Anita Huttner
- Department of Pathology, Yale School of Medicine, New Haven, CT
| | - Danielle Seilhean
- Sorbonne Université, INSERM U1127, French National Centre for Scientific Research, Joint Research Unit 7225, Paris Brain Institute, Institut du Cerveau et de la Moelle Épinière, Paris, France.,Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Neuropathologie, Paris, France
| | - Nicolas Renier
- Sorbonne Université, INSERM U1127, French National Centre for Scientific Research, Joint Research Unit 7225, Paris Brain Institute, Institut du Cerveau et de la Moelle Épinière, Paris, France
| | - Kaya Bilguvar
- Department of Genetics, Yale School of Medicine, New Haven, CT.,Yale Center for Genome Analysis, West Haven, CT
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT.,Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Chevy Chase, MD
| |
Collapse
|
58
|
Tada T, Fan C, Chen JS, Kaur R, Stapleford KA, Gristick H, Dcosta BM, Wilen CB, Nimigean CM, Landau NR. An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. Cell Rep 2020; 33:108528. [PMID: 33326798 PMCID: PMC7705358 DOI: 10.1016/j.celrep.2020.108528] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/26/2020] [Accepted: 11/24/2020] [Indexed: 12/20/2022] Open
Abstract
Soluble forms of angiotensin-converting enzyme 2 (ACE2) have recently been shown to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We report on an improved soluble ACE2, termed a "microbody," in which the ACE2 ectodomain is fused to Fc domain 3 of the immunoglobulin (Ig) heavy chain. The protein is smaller than previously described ACE2-Ig Fc fusion proteins and contains an H345A mutation in the ACE2 catalytic active site that inactivates the enzyme without reducing its affinity for the SARS-CoV-2 spike. The disulfide-bonded ACE2 microbody protein inhibits entry of SARS-CoV-2 spike protein pseudotyped virus and replication of live SARS-CoV-2 in vitro and in a mouse model. Its potency is 10-fold higher than soluble ACE2, and it can act after virus bound to the cell. The microbody inhibits the entry of β coronaviruses and virus with the variant D614G spike. The ACE2 microbody may be a valuable therapeutic for coronavirus disease 2019 (COVID-19) that is active against viral variants and future coronaviruses.
Collapse
Affiliation(s)
- Takuya Tada
- Department of Microbiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Chen Fan
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Jennifer S Chen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Ramanjit Kaur
- Department of Microbiology, NYU Langone Medical Center, New York, NY 10016, USA
| | | | - Harry Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Belinda M Dcosta
- Department of Microbiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU Langone Medical Center, New York, NY 10016, USA.
| |
Collapse
|
59
|
Abstract
Testing for SARS-CoV-2 has attracted a tremendous amount of attention as a tool to manage the ongoing COVID-19 pandemic. Although diagnostic laboratory testing is used ubiquitously by physicians and encountered regularly by individuals receiving medical care, several aspects of test interpretation are incompletely understood by medical communities and the general population, creating a significant challenge in minimizing the damage caused by disease spread through informed decision making and proper testing utilization. Here, general principles of test interpretation are reviewed and applied to specific examples, such as whether asymptomatic individuals should be tested, what it means to test positive (or negative), and how to interpret tests for "immunity passports." Unexpectedly, the answers seem to run contrary to many of the popular narratives about testing as a tool for managing COVID-19. Although testing is an important and essential part of managing diseases such as COVID-19, improper utilization can have unintended negative consequences.
Collapse
Affiliation(s)
- Edward C Stites
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037 USA
| | - Craig B Wilen
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, CT 06520 USA
| |
Collapse
|
60
|
Israelow B, Song E, Mao T, Lu P, Meir A, Liu F, Alfajaro MM, Wei J, Dong H, Homer RJ, Ring A, Wilen CB, Iwasaki A. Mouse model of SARS-CoV-2 reveals inflammatory role of type I interferon signaling. J Exp Med 2020; 217:e20201241. [PMID: 32750141 PMCID: PMC7401025 DOI: 10.1084/jem.20201241] [Citation(s) in RCA: 307] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/15/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-Cov-2) has caused over 13,000,000 cases of coronavirus disease (COVID-19) with a significant fatality rate. Laboratory mice have been the stalwart of therapeutic and vaccine development; however, they do not support infection by SARS-CoV-2 due to the virus's inability to use the mouse orthologue of its human entry receptor angiotensin-converting enzyme 2 (hACE2). While hACE2 transgenic mice support infection and pathogenesis, these mice are currently limited in availability and are restricted to a single genetic background. Here we report the development of a mouse model of SARS-CoV-2 based on adeno-associated virus (AAV)-mediated expression of hACE2. These mice support viral replication and exhibit pathological findings found in COVID-19 patients. Moreover, we show that type I interferons do not control SARS-CoV-2 replication in vivo but are significant drivers of pathological responses. Thus, the AAV-hACE2 mouse model enables rapid deployment for in-depth analysis following robust SARS-CoV-2 infection with authentic patient-derived virus in mice of diverse genetic backgrounds.
Collapse
Affiliation(s)
- Benjamin Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Peiwen Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Amit Meir
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT
| | - Feimei Liu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Mia Madel Alfajaro
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT
| | - Jin Wei
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT
| | - Huiping Dong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Robert J. Homer
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | - Aaron Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Craig B. Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Chevy Chase, MD
| |
Collapse
|
61
|
Wei J, Alfajaro MM, DeWeirdt PC, Hanna RE, Lu-Culligan WJ, Cai WL, Strine MS, Zhang SM, Graziano VR, Schmitz CO, Chen JS, Mankowski MC, Filler RB, Ravindra NG, Gasque V, de Miguel FJ, Patil A, Chen H, Oguntuyo KY, Abriola L, Surovtseva YV, Orchard RC, Lee B, Lindenbach BD, Politi K, van Dijk D, Kadoch C, Simon MD, Yan Q, Doench JG, Wilen CB. Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection. Cell 2020; 184:76-91.e13. [PMID: 33147444 PMCID: PMC7574718 DOI: 10.1016/j.cell.2020.10.028] [Citation(s) in RCA: 328] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/11/2020] [Accepted: 10/15/2020] [Indexed: 12/17/2022]
Abstract
Identification of host genes essential for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may reveal novel therapeutic targets and inform our understanding of coronavirus disease 2019 (COVID-19) pathogenesis. Here we performed genome-wide CRISPR screens in Vero-E6 cells with SARS-CoV-2, Middle East respiratory syndrome CoV (MERS-CoV), bat CoV HKU5 expressing the SARS-CoV-1 spike, and vesicular stomatitis virus (VSV) expressing the SARS-CoV-2 spike. We identified known SARS-CoV-2 host factors, including the receptor ACE2 and protease Cathepsin L. We additionally discovered pro-viral genes and pathways, including HMGB1 and the SWI/SNF chromatin remodeling complex, that are SARS lineage and pan-coronavirus specific, respectively. We show that HMGB1 regulates ACE2 expression and is critical for entry of SARS-CoV-2, SARS-CoV-1, and NL63. We also show that small-molecule antagonists of identified gene products inhibited SARS-CoV-2 infection in monkey and human cells, demonstrating the conserved role of these genetic hits across species. This identifies potential therapeutic targets for SARS-CoV-2 and reveals SARS lineage-specific and pan-CoV host factors that regulate susceptibility to highly pathogenic CoVs.
Collapse
Affiliation(s)
- Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Peter C DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ruth E Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William J Lu-Culligan
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA; Department of Cell Biology, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Wesley L Cai
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Madison S Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shang-Min Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Vincent R Graziano
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Cameron O Schmitz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jennifer S Chen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Madeleine C Mankowski
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Neal G Ravindra
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Victor Gasque
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Fernando J de Miguel
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Ajinkya Patil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Huacui Chen
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kasopefoluwa Y Oguntuyo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Robert C Orchard
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06520, USA
| | - Katerina Politi
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA; Department of Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - David van Dijk
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
| |
Collapse
|
62
|
Flynn RA, Belk JA, Qi Y, Yasumoto Y, Schmitz CO, Mumbach MR, Limaye A, Wei J, Alfajaro MM, Parker KR, Chang HY, Horvath TL, Carette JE, Bertozzi C, Wilen CB, Satpathy AT. Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection. bioRxiv 2020:2020.10.06.327445. [PMID: 33052334 PMCID: PMC7553159 DOI: 10.1101/2020.10.06.327445] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a pandemic with growing global mortality. There is an urgent need to understand the molecular pathways required for host infection and anti-viral immunity. Using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), we identified 309 host proteins that bind the SARS-CoV-2 RNA during active infection. Integration of this data with viral ChIRP-MS data from three other positive-sense RNA viruses defined pan-viral and SARS-CoV-2-specific host interactions. Functional interrogation of these factors with a genome-wide CRISPR screen revealed that the vast majority of viral RNA-binding proteins protect the host from virus-induced cell death, and we identified known and novel anti-viral proteins that regulate SARS-CoV-2 pathogenicity. Finally, our RNA-centric approach demonstrated a physical connection between SARS-CoV-2 RNA and host mitochondria, which we validated with functional and electron microscopy data, providing new insights into a more general virus-specific protein logic for mitochondrial interactions. Altogether, these data provide a comprehensive catalogue of SARS-CoV-2 RNA-host protein interactions, which may inform future studies to understand the mechanisms of viral pathogenesis, as well as nominate host pathways that could be targeted for therapeutic benefit. HIGHLIGHTS · ChIRP-MS of SARS-CoV-2 RNA identifies a comprehensive viral RNA-host protein interaction network during infection across two species· Comparison to RNA-protein interaction networks with Zika virus, dengue virus, and rhinovirus identify SARS-CoV-2-specific and pan-viral RNA protein complexes and highlights distinct intracellular trafficking pathways· Intersection of ChIRP-MS and genome-wide CRISPR screens identify novel SARS-CoV-2-binding proteins with pro- and anti-viral function· Viral RNA-RNA and RNA-protein interactions reveal specific SARS-CoV-2-mediated mitochondrial dysfunction during infection.
Collapse
Affiliation(s)
- Ryan A. Flynn
- Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA
- These authors contributed equally
| | - Julia A. Belk
- Department of Computer Science, Stanford University, Stanford, CA
- Department of Pathology, Stanford University, Stanford, CA
- These authors contributed equally
| | - Yanyan Qi
- Department of Pathology, Stanford University, Stanford, CA
| | - Yuki Yasumoto
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT
| | - Cameron O. Schmitz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Maxwell R. Mumbach
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA
| | - Aditi Limaye
- Department of Pathology, Stanford University, Stanford, CA
| | - Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Kevin R. Parker
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
| | - Tamas L. Horvath
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT
| | - Jan E. Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA
| | - Carolyn Bertozzi
- Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | | |
Collapse
|
63
|
Chen JS, Alfajaro MM, Wei J, Chow RD, Filler RB, Eisenbarth SC, Wilen CB. Cyclooxgenase-2 is induced by SARS-CoV-2 infection but does not affect viral entry or replication. bioRxiv 2020:2020.09.24.312769. [PMID: 32995789 PMCID: PMC7523115 DOI: 10.1101/2020.09.24.312769] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Identifying drugs that regulate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and its symptoms has been a pressing area of investigation during the coronavirus disease 2019 (COVID-19) pandemic. Nonsteroidal anti-inflammatory drugs (NSAIDs), which are frequently used for the relief of pain and inflammation, could modulate both SARS-CoV-2 infection and the host response to the virus. NSAIDs inhibit the enzymes cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2), which mediate the production of prostaglandins (PGs). PGE2, one of the most abundant PGs, has diverse biological roles in homeostasis and inflammatory responses. Previous studies have shown that NSAID treatment or inhibition of PGE2 receptor signaling leads to upregulation of angiotensin-converting enzyme 2 (ACE2), the cell entry receptor for SARS-CoV-2, thus raising concerns that NSAIDs could increase susceptibility to infection. COX/PGE2 signaling has also been shown to regulate the replication of many viruses, but it is not yet known whether it plays a role in SARS-CoV-2 replication. The purpose of this study was to dissect the effect of NSAIDs on COVID-19 in terms of SARS-CoV-2 entry and replication. We found that SARS-CoV-2 infection induced COX-2 upregulation in diverse human cell culture and mouse systems. However, suppression of COX-2/PGE2 signaling by two commonly used NSAIDs, ibuprofen and meloxicam, had no effect on ACE2 expression, viral entry, or viral replication. Our findings suggest that COX-2 signaling driven by SARS-CoV-2 may instead play a role in regulating the lung inflammation and injury observed in COVID-19 patients.
Collapse
Affiliation(s)
- Jennifer S. Chen
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jin Wei
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Ryan D. Chow
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Renata B. Filler
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie C. Eisenbarth
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
64
|
Song E, Zhang C, Israelow B, Lu-Culligan A, Prado AV, Skriabine S, Lu P, Weizman OE, Liu F, Dai Y, Szigeti-Buck K, Yasumoto Y, Wang G, Castaldi C, Heltke J, Ng E, Wheeler J, Alfajaro MM, Levavasseur E, Fontes B, Ravindra NG, Van Dijk D, Mane S, Gunel M, Ring A, Kazmi SAJ, Zhang K, Wilen CB, Horvath TL, Plu I, Haik S, Thomas JL, Louvi A, Farhadian SF, Huttner A, Seilhean D, Renier N, Bilguvar K, Iwasaki A. Neuroinvasion of SARS-CoV-2 in human and mouse brain. bioRxiv 2020:2020.06.25.169946. [PMID: 32935108 PMCID: PMC7491522 DOI: 10.1101/2020.06.25.169946] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although COVID-19 is considered to be primarily a respiratory disease, SARS-CoV-2 affects multiple organ systems including the central nervous system (CNS). Yet, there is no consensus whether the virus can infect the brain, or what the consequences of CNS infection are. Here, we used three independent approaches to probe the capacity of SARS-CoV-2 to infect the brain. First, using human brain organoids, we observed clear evidence of infection with accompanying metabolic changes in the infected and neighboring neurons. However, no evidence for the type I interferon responses was detected. We demonstrate that neuronal infection can be prevented either by blocking ACE2 with antibodies or by administering cerebrospinal fluid from a COVID-19 patient. Second, using mice overexpressing human ACE2, we demonstrate in vivo that SARS-CoV-2 neuroinvasion, but not respiratory infection, is associated with mortality. Finally, in brain autopsy from patients who died of COVID-19, we detect SARS-CoV-2 in the cortical neurons, and note pathologic features associated with infection with minimal immune cell infiltrates. These results provide evidence for the neuroinvasive capacity of SARS-CoV2, and an unexpected consequence of direct infection of neurons by SARS-CoV-2.
Collapse
Affiliation(s)
- Eric Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ce Zhang
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Benjamin Israelow
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06510, USA
| | - Alice Lu-Culligan
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Alba Vieites Prado
- Sorbonne Université, INSERM U1127, CNRS UMR 7225, Paris Brain Institute - ICM, Paris, France
| | - Sophie Skriabine
- Sorbonne Université, INSERM U1127, CNRS UMR 7225, Paris Brain Institute - ICM, Paris, France
| | - Peiwen Lu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Orr-El Weizman
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Klara Szigeti-Buck
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA
| | - Yuki Yasumoto
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Guilin Wang
- Yale Center for Genome Analysis, West Haven, CT 06510, USA
| | | | - Jaime Heltke
- Yale Center for Genome Analysis, West Haven, CT 06510, USA
| | - Evelyn Ng
- Yale Center for Genome Analysis, West Haven, CT 06510, USA
| | - John Wheeler
- Yale Center for Genome Analysis, West Haven, CT 06510, USA
| | - Mia Madel Alfajaro
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Etienne Levavasseur
- Sorbonne Université, INSERM U1127, CNRS UMR 7225, Paris Brain Institute - ICM, Paris, France
| | - Benjamin Fontes
- Yale Environmental Health and Safety, Yale University, New Haven, CT 06510, USA
| | - Neal G. Ravindra
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Computer Science, Yale University, New Haven, CT 06510, USA
| | - David Van Dijk
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Computer Science, Yale University, New Haven, CT 06510, USA
| | - Shrikant Mane
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Center for Genome Analysis, West Haven, CT 06510, USA
| | - Murat Gunel
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA
| | - Aaron Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Syed A. Jaffar Kazmi
- Department of Laboratory Medicine, Geisinger Medical Center, Danville, Pennsylvania
| | - Kai Zhang
- Department of Laboratory Medicine, Geisinger Medical Center, Danville, Pennsylvania
| | - Craig B Wilen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Tamas L. Horvath
- Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Isabelle Plu
- Sorbonne Université, INSERM U1127, CNRS UMR 7225, Paris Brain Institute - ICM, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Neuropathologie, Paris, France
| | - Stephane Haik
- Sorbonne Université, INSERM U1127, CNRS UMR 7225, Paris Brain Institute - ICM, Paris, France
- Yale Environmental Health and Safety, Yale University, New Haven, CT 06510, USA
- Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Neuropathologie, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Cellule nationale de référence des maladies de Creutzfeldt-Jakob, Paris, France
| | - Jean-Leon Thomas
- Sorbonne Université, INSERM U1127, CNRS UMR 7225, Paris Brain Institute - ICM, Paris, France
- Department of Neurology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Angeliki Louvi
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shelli F. Farhadian
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Anita Huttner
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Danielle Seilhean
- Sorbonne Université, INSERM U1127, CNRS UMR 7225, Paris Brain Institute - ICM, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Neuropathologie, Paris, France
| | - Nicolas Renier
- Sorbonne Université, INSERM U1127, CNRS UMR 7225, Paris Brain Institute - ICM, Paris, France
| | - Kaya Bilguvar
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Center for Genome Analysis, West Haven, CT 06510, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT 06510, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lead Contact
| |
Collapse
|
65
|
Ott IM, Strine MS, Watkins AE, Boot M, Kalinich CC, Harden CA, Vogels CB, Casanovas-Massana A, Moore AJ, Muenker MC, Nakahata M, Tokuyama M, Nelson A, Fournier J, Bermejo S, Campbell M, Datta R, Dela Cruz CS, Farhadian SF, Ko AI, Iwasaki A, Grubaugh ND, Wilen CB, Wyllie AL. Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices. medRxiv 2020:2020.08.03.20165233. [PMID: 32793924 PMCID: PMC7418742 DOI: 10.1101/2020.08.03.20165233] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Most currently approved strategies for the collection of saliva for COVID-19 diagnostics require specialized tubes containing buffers promoted for the stabilization of SARS-CoV-2 RNA and virus inactivation. Yet many of these are expensive, in limited supply, and not necessarily validated specifically for viral RNA. While saliva is a promising sample type as it can be reliably self-collected for the sensitive detection of SARS-CoV-2, the expense and availability of these collection tubes are prohibitive to mass testing efforts. Therefore, we investigated the stability of SARS-CoV-2 RNA and infectious virus detection from saliva without supplementation. We tested RNA stability over extended periods of time (2-25 days) and at temperatures representing at-home storage and elevated temperatures which might be experienced when cold chain transport may be unavailable. We found SARS-CoV-2 RNA in saliva from infected individuals is stable at 4°C, room temperature (~19°C), and 30°C for prolonged periods and found limited evidence for viral replication in saliva. This work demonstrates that expensive saliva collection options involving RNA stabilization and virus inactivation buffers are not always needed, permitting the use of cheaper collection options. Affordable testing methods are urgently needed to meet current testing demands and for continued surveillance in reopening strategies.
Collapse
Affiliation(s)
- Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Madison S. Strine
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Anne E. Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Maikel Boot
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Christina A. Harden
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Adam J. Moore
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - M. Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Maura Nakahata
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Maria Tokuyama
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Allison Nelson
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA
| | - John Fournier
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Santos Bermejo
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Melissa Campbell
- Department of Pediatrics, Division of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Rupak Datta
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA
| | | | - Charles S. Dela Cruz
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Shelli F. Farhadian
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Albert I. Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
- Howard Hughes Medical Institute, New Haven, CT 06510, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Anne L. Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| |
Collapse
|
66
|
Ravindra NG, Alfajaro MM, Gasque V, Habet V, Wei J, Filler RB, Huston NC, Wan H, Szigeti-Buck K, Wang B, Wang G, Montgomery RR, Eisenbarth SC, Williams A, Pyle AM, Iwasaki A, Horvath TL, Foxman EF, Pierce RW, van Dijk D, Wilen CB. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium. bioRxiv 2020:2020.05.06.081695. [PMID: 32511382 PMCID: PMC7263511 DOI: 10.1101/2020.05.06.081695] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
SARS-CoV-2, the causative agent of COVID-19, has tragically burdened individuals and institutions around the world. There are currently no approved drugs or vaccines for the treatment or prevention of COVID-19. Enhanced understanding of SARS-CoV-2 infection and pathogenesis is critical for the development of therapeutics. To reveal insight into viral replication, cell tropism, and host-viral interactions of SARS-CoV-2 we performed single-cell RNA sequencing of experimentally infected human bronchial epithelial cells (HBECs) in air-liquid interface cultures over a time-course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target of infection, which we confirmed by electron microscopy. Over the course of infection, cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell-intrinsic expression of type I and type III IFNs and IL6 but not IL1. This results in expression of interferon-stimulated genes in both infected and bystander cells. We observe similar gene expression changes from a COVID-19 patient ex vivo. In addition, we developed a new computational method termed CONditional DENSity Embedding (CONDENSE) to characterize and compare temporal gene dynamics in response to infection, which revealed genes relating to endothelin, angio-genesis, interferon, and inflammation-causing signaling pathways. In this study, we conducted an in-depth analysis of SARS-CoV-2 infection in HBECs and a COVID-19 patient and revealed genes, cell types, and cell state changes associated with infection.
Collapse
Affiliation(s)
- Neal G. Ravindra
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Victor Gasque
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
- Université Claude Bernard Lyon 1, Faculté de Médecine Lyon Est, Lyon, France
- Département de Bioinformatique, Univ Evry, Université Paris-Saclay, Paris, France
| | - Victoria Habet
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Renata B. Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Nicholas C. Huston
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT, USA
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA
| | - Klara Szigeti-Buck
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Bao Wang
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Guilin Wang
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
| | - Ruth R. Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Stephanie C. Eisenbarth
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | | | - Anna Marie Pyle
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tamas L. Horvath
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ellen F. Foxman
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Richard W. Pierce
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - David van Dijk
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
67
|
Wei J, Alfajaro MM, Hanna RE, DeWeirdt PC, Strine MS, Lu-Culligan WJ, Zhang SM, Graziano VR, Schmitz CO, Chen JS, Mankowski MC, Filler RB, Gasque V, de Miguel F, Chen H, Oguntuyo K, Abriola L, Surovtseva YV, Orchard RC, Lee B, Lindenbach B, Politi K, van Dijk D, Simon MD, Yan Q, Doench JG, Wilen CB. Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection. bioRxiv 2020:2020.06.16.155101. [PMID: 32869025 PMCID: PMC7457610 DOI: 10.1101/2020.06.16.155101] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Identification of host genes essential for SARS-CoV-2 infection may reveal novel therapeutic targets and inform our understanding of COVID-19 pathogenesis. Here we performed a genome-wide CRISPR screen with SARS-CoV-2 and identified known SARS-CoV-2 host factors including the receptor ACE2 and protease Cathepsin L. We additionally discovered novel pro-viral genes and pathways including the SWI/SNF chromatin remodeling complex and key components of the TGF-β signaling pathway. Small molecule inhibitors of these pathways prevented SARS-CoV-2-induced cell death. We also revealed that the alarmin HMGB1 is critical for SARS-CoV-2 replication. In contrast, loss of the histone H3.3 chaperone complex sensitized cells to virus-induced death. Together this study reveals potential therapeutic targets for SARS-CoV-2 and highlights host genes that may regulate COVID-19 pathogenesis.
Collapse
Affiliation(s)
- Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ruth E. Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter C. DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Madison S. Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - William J. Lu-Culligan
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University, New Haven, CT, USA
| | - Shang-Min Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Vincent R. Graziano
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Cameron O. Schmitz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jennifer S. Chen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Madeleine C. Mankowski
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Renata B. Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Victor Gasque
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Fernando de Miguel
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Huacui Chen
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | | | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | | | - Robert C. Orchard
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Benhur Lee
- Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brett Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Katerina Politi
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - David van Dijk
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
| | - Matthew D. Simon
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
68
|
Israelow B, Song E, Mao T, Lu P, Meir A, Liu F, Alfajaro MM, Wei J, Dong H, Homer RJ, Ring A, Wilen CB, Iwasaki A. Mouse model of SARS-CoV-2 reveals inflammatory role of type I interferon signaling. SSRN 2020:3628297. [PMID: 32714125 PMCID: PMC7366812 DOI: 10.2139/ssrn.3628297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 06/16/2020] [Indexed: 12/15/2022]
Abstract
Severe Acute Respiratory Syndrome- Coronavirus 2 (SARS-Cov-2) has caused over 5,000,000 cases of Coronavirus disease (COVID-19) with significant fatality rate.1-3 Due to the urgency of this global pandemic, numerous therapeutic and vaccine trials have begun without customary safety and efficacy studies.4 Laboratory mice have been the stalwart of these types of studies; however, they do not support infection by SARS-CoV-2 due to the inability of its spike (S) protein to engage the mouse ortholog of its human entry receptor angiotensin-converting enzyme 2 (hACE2). While hACE2 transgenic mice support infection and pathogenesis,5 these mice are currently limited in availability and are restricted to a single genetic background. Here we report the development of a mouse model of SARS-CoV-2 based on adeno associated virus (AAV)-mediated expression of hACE2. These mice support viral replication and antibody production and exhibit pathologic findings found in COVID-19 patients as well as non-human primate models. Moreover, we show that type I interferons are unable to control SARS-CoV2 replication and drive pathologic responses. Thus, the hACE2-AAV mouse model enables rapid deployment for in-depth analysis following robust SARS-CoV-2 infection with authentic patient-derived virus in mice of diverse genetic backgrounds. This represents a much-needed platform for rapidly testing prophylactic and therapeutic strategies to combat COVID-19.
Collapse
Affiliation(s)
- Benjamin Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Peiwen Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Amit Meir
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Feimei Liu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jin Wei
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Huiping Dong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Robert J Homer
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Aaron Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| |
Collapse
|
69
|
Israelow B, Song E, Mao T, Lu P, Meir A, Liu F, Alfajaro MM, Wei J, Dong H, Homer RJ, Ring A, Wilen CB, Iwasaki A. Mouse model of SARS-CoV-2 reveals inflammatory role of type I interferon signaling. bioRxiv 2020. [PMID: 32577647 PMCID: PMC7302201 DOI: 10.1101/2020.05.27.118893] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Severe Acute Respiratory Syndrome- Coronavirus 2 (SARS-Cov-2) has caused over 5,000,000 cases of Coronavirus disease (COVID-19) with significant fatality rate.1–3 Due to the urgency of this global pandemic, numerous therapeutic and vaccine trials have begun without customary safety and efficacy studies.4 Laboratory mice have been the stalwart of these types of studies; however, they do not support infection by SARS-CoV-2 due to the inability of its spike (S) protein to engage the mouse ortholog of its human entry receptor angiotensin-converting enzyme 2 (hACE2). While hACE2 transgenic mice support infection and pathogenesis,5 these mice are currently limited in availability and are restricted to a single genetic background. Here we report the development of a mouse model of SARS-CoV-2 based on adeno associated virus (AAV)-mediated expression of hACE2. These mice support viral replication and antibody production and exhibit pathologic findings found in COVID-19 patients as well as non-human primate models. Moreover, we show that type I interferons are unable to control SARS-CoV2 replication and drive pathologic responses. Thus, the hACE2-AAV mouse model enables rapid deployment for in-depth analysis following robust SARS-CoV-2 infection with authentic patient-derived virus in mice of diverse genetic backgrounds. This represents a much-needed platform for rapidly testing prophylactic and therapeutic strategies to combat COVID-19.
Collapse
Affiliation(s)
- Benjamin Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Peiwen Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Amit Meir
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Feimei Liu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jin Wei
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Huiping Dong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Robert J Homer
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Aaron Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| |
Collapse
|
70
|
Graziano VR, Walker FC, Kennedy EA, Wei J, Ettayebi K, Strine MS, Filler RB, Hassan E, Hsieh LL, Kim AS, Kolawole AO, Wobus CE, Lindesmith LC, Baric RS, Estes MK, Orchard RC, Baldridge MT, Wilen CB. CD300lf is the primary physiologic receptor of murine norovirus but not human norovirus. PLoS Pathog 2020; 16:e1008242. [PMID: 32251490 PMCID: PMC7162533 DOI: 10.1371/journal.ppat.1008242] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/16/2020] [Accepted: 03/03/2020] [Indexed: 12/18/2022] Open
Abstract
Murine norovirus (MNoV) is an important model of human norovirus (HNoV) and mucosal virus infection more broadly. Viral receptor utilization is a major determinant of cell tropism, host range, and pathogenesis. The bona fide receptor for HNoV is unknown. Recently, we identified CD300lf as a proteinaceous receptor for MNoV. Interestingly, its paralogue CD300ld was also sufficient for MNoV infection in vitro. Here we explored whether CD300lf is the sole physiologic receptor in vivo and whether HNoV can use a CD300 ortholog as an entry receptor. We report that both CD300ld and CD300lf are sufficient for infection by diverse MNoV strains in vitro. We further demonstrate that CD300lf is essential for both oral and parenteral MNoV infection and to elicit anti-MNoV humoral responses in vivo. In mice deficient in STAT1 signaling, CD300lf is required for MNoV-induced lethality. Finally, we demonstrate that human CD300lf (huCD300lf) is not essential for HNoV infection, nor does huCD300lf inhibit binding of HNoV virus-like particles to glycans. Thus, we report huCD300lf is not a receptor for HNoV.
Collapse
Affiliation(s)
- Vincent R. Graziano
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Forrest C. Walker
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Elizabeth A. Kennedy
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Jin Wei
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Khalil Ettayebi
- Departments of Medicine and Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Madison S. Strine
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Renata B. Filler
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Ebrahim Hassan
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Leon L. Hsieh
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Arthur S. Kim
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Abimbola O. Kolawole
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Lisa C. Lindesmith
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Mary K. Estes
- Departments of Medicine and Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Robert C. Orchard
- Department of Immunology, University of Texas Southwestern Medical School, Dallas, Texas, United States of America
| | - Megan T. Baldridge
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Craig B. Wilen
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| |
Collapse
|
71
|
Wang YT, Zaitsev K, Lu Q, Li S, Schaiff WT, Kim KW, Droit L, Wilen CB, Desai C, Balce DR, Orchard RC, Orvedahl A, Park S, Kreamalmeyer D, Handley SA, Pfeifer JD, Baldridge MT, Artyomov MN, Stallings CL, Virgin HW. Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes. Nat Microbiol 2020; 5:272-281. [PMID: 31959973 PMCID: PMC7147835 DOI: 10.1038/s41564-019-0633-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 11/05/2019] [Indexed: 02/07/2023]
Abstract
Innate and adaptive immune responses that prime myeloid cells, such as macrophages, protect against pathogens1,2. However, if left uncontrolled, these responses may lead to detrimental inflammation3. Macrophages, particularly those resident in tissues, must therefore remain quiescent between infections despite chronic stimulation by commensal microorganisms. The genes required for quiescence of tissue-resident macrophages are not well understood. Autophagy, an evolutionarily conserved cellular process by which cytoplasmic contents are targeted for lysosomal digestion, has homeostatic functions including maintenance of protein and organelle integrity and regulation of metabolism4. Recent research has shown that degradative autophagy, as well as various combinations of autophagy genes, regulate immunity and inflammation5-12. Here, we delineate a function of the autophagy proteins Beclin 1 and FIP200-but not of other essential autophagy components ATG5, ATG16L1 or ATG7-in mediating quiescence of tissue-resident macrophages by limiting the effects of systemic interferon-γ. The perturbation of quiescence in mice that lack Beclin 1 or FIP200 in myeloid cells results in spontaneous immune activation and resistance to Listeria monocytogenes infection. While antibiotic-treated wild-type mice display diminished macrophage responses to inflammatory stimuli, this is not observed in mice that lack Beclin 1 in myeloid cells, establishing the dominance of this gene over effects of the bacterial microbiota. Thus, select autophagy genes, but not all genes essential for degradative autophagy, have a key function in maintaining immune quiescence of tissue-resident macrophages, resulting in genetically programmed susceptibility to bacterial infection.
Collapse
Affiliation(s)
- Ya-Ting Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
| | - Konstantin Zaitsev
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Computer Technologies Department, ITMO University, St Petersburg, Russia
| | - Qun Lu
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Shan Li
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO, USA
| | - W Timothy Schaiff
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Vir Biotechnology, San Francisco, CA, USA
| | - Ki-Wook Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL, USA
| | - Lindsay Droit
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Craig B Wilen
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Chandni Desai
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Dale R Balce
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Vir Biotechnology, San Francisco, CA, USA
| | - Robert C Orchard
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anthony Orvedahl
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Sunmin Park
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Darren Kreamalmeyer
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - John D Pfeifer
- Lauren V. Ackerman Laboratory of Surgical Pathology, Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University Medical Center, St Louis, MO, USA
| | - Megan T Baldridge
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
- Vir Biotechnology, San Francisco, CA, USA.
| |
Collapse
|
72
|
Grau KR, Zhu S, Peterson ST, Helm EW, Philip D, Phillips M, Hernandez A, Turula H, Frasse P, Graziano VR, Wilen CB, Wobus CE, Baldridge MT, Karst SM. The intestinal regionalization of acute norovirus infection is regulated by the microbiota via bile acid-mediated priming of type III interferon. Nat Microbiol 2020; 5:84-92. [PMID: 31768030 PMCID: PMC6925324 DOI: 10.1038/s41564-019-0602-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/03/2019] [Indexed: 01/07/2023]
Abstract
Evidence has accumulated to demonstrate that the intestinal microbiota enhances mammalian enteric virus infections1. For example, we and others previously reported that commensal bacteria stimulate acute and persistent murine norovirus infections2-4. However, in apparent contradiction of these results, the virulence of murine norovirus infection was unaffected by antibiotic treatment. This prompted us to perform a detailed investigation of murine norovirus infection in microbially deplete mice, revealing a more complex picture in which commensal bacteria inhibit viral infection of the proximal small intestine while simultaneously stimulating the infection of distal regions of the gut. Thus, commensal bacteria can regulate viral regionalization along the intestinal tract. We further show that the mechanism underlying bacteria-dependent inhibition of norovirus infection in the proximal gut involves bile acid priming of type III interferon. Finally, the regional effects of the microbiota on norovirus infection may result from distinct regional expression profiles of key bile acid receptors that regulate the type III interferon response. Overall, these findings reveal that the biotransformation of host metabolites by the intestinal microbiota directly and regionally impacts infection by a pathogenic enteric virus.
Collapse
Affiliation(s)
- Katrina R Grau
- Department of Molecular Genetics & Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Shu Zhu
- Department of Molecular Genetics & Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Stefan T Peterson
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Emily W Helm
- Department of Molecular Genetics & Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Drake Philip
- Department of Molecular Genetics & Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Matthew Phillips
- Department of Molecular Genetics & Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Abel Hernandez
- Department of Molecular Genetics & Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Holly Turula
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Philip Frasse
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Vincent R Graziano
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Craig B Wilen
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Megan T Baldridge
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA.
| | - Stephanie M Karst
- Department of Molecular Genetics & Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
73
|
Hosmillo M, Lu J, McAllaster MR, Eaglesham JB, Wang X, Emmott E, Domingues P, Chaudhry Y, Fitzmaurice TJ, Tung MKH, Panas MD, McInerney G, Locker N, Wilen CB, Goodfellow IG. Noroviruses subvert the core stress granule component G3BP1 to promote viral VPg-dependent translation. eLife 2019; 8:e46681. [PMID: 31403400 PMCID: PMC6739877 DOI: 10.7554/elife.46681] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
Knowledge of the host factors required for norovirus replication has been hindered by the challenges associated with culturing human noroviruses. We have combined proteomic analysis of the viral translation and replication complexes with a CRISPR screen, to identify host factors required for norovirus infection. The core stress granule component G3BP1 was identified as a host factor essential for efficient human and murine norovirus infection, demonstrating a conserved function across the Norovirus genus. Furthermore, we show that G3BP1 functions in the novel paradigm of viral VPg-dependent translation initiation, contributing to the assembly of translation complexes on the VPg-linked viral positive sense RNA genome by facilitating ribosome recruitment. Our data uncovers a novel function for G3BP1 in the life cycle of positive sense RNA viruses and identifies the first host factor with pan-norovirus pro-viral activity.
Collapse
Affiliation(s)
- Myra Hosmillo
- Division of Virology, Department of PathologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Jia Lu
- Division of Virology, Department of PathologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Michael R McAllaster
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
| | - James B Eaglesham
- Division of Virology, Department of PathologyUniversity of CambridgeCambridgeUnited Kingdom
- Department of MicrobiologyHarvard Medical SchoolBostonUnited States
| | - Xinjie Wang
- Division of Virology, Department of PathologyUniversity of CambridgeCambridgeUnited Kingdom
- Institute for Brain Research and RehabilitationSouth China Normal UniversityGuangzhouChina
| | - Edward Emmott
- Division of Virology, Department of PathologyUniversity of CambridgeCambridgeUnited Kingdom
- Department of BioengineeringNortheastern UniversityBostonUnited States
- Barnett Institute for Chemical and Biological AnalysesNortheastern UniversityBostonUnited States
| | - Patricia Domingues
- Division of Virology, Department of PathologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Yasmin Chaudhry
- Division of Virology, Department of PathologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Tim J Fitzmaurice
- Division of Virology, Department of PathologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Matthew KH Tung
- Division of Virology, Department of PathologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Marc Dominik Panas
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstituteStockholmSweden
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstituteStockholmSweden
| | - Nicolas Locker
- School of Biosciences and MedicineUniversity of SurreyGuildfordUnited Kingdom
| | - Craig B Wilen
- Department of Laboratory MedicineYale School of MedicineNew HavenUnited States
| | - Ian G Goodfellow
- Division of Virology, Department of PathologyUniversity of CambridgeCambridgeUnited Kingdom
| |
Collapse
|
74
|
Lee S, Liu H, Wilen CB, Sychev ZE, Desai C, Hykes BL, Orchard RC, McCune BT, Kim KW, Nice TJ, Handley SA, Baldridge MT, Amarasinghe GK, Virgin HW. A Secreted Viral Nonstructural Protein Determines Intestinal Norovirus Pathogenesis. Cell Host Microbe 2019; 25:845-857.e5. [PMID: 31130511 PMCID: PMC6622463 DOI: 10.1016/j.chom.2019.04.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/08/2019] [Accepted: 04/15/2019] [Indexed: 12/18/2022]
Abstract
Murine norovirus (MNoV) infects a low percentage of enteric tuft cells and can persist in these cells for months following acute infection. Both tuft-cell tropism and resistance to interferon-λ (IFN-λ)-mediated clearance during persistent infection requires the viral nonstructural protein 1/2 (NS1/2). We show that processing of NS1/2 yields NS1, an unconventionally secreted viral protein that is central for IFN-λ resistance. MNoV infection globally suppresses intestinal IFN-λ responses, which is attributable to secreted NS1. MNoV NS1 secretion is triggered by caspase-3 cleavage of NS1/2, and a secreted form of human NoV NS1 is also observed. NS1 secretion is essential for intestinal infection and resistance to IFN-λ in vivo. NS1 vaccination alone protects against MNoV challenge, despite the lack of induction of neutralizing anti-capsid antibodies previously shown to confer protection. Thus, despite infecting a low number of tuft cells, NS1 secretion allows MNoV to globally suppress IFN responses and promote persistence.
Collapse
Affiliation(s)
- Sanghyun Lee
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Hejun Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Craig B Wilen
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Zoi E Sychev
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chandni Desai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barry L Hykes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert C Orchard
- Department of Immunology, the University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Broc T McCune
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ki-Wook Kim
- Department of Pharmacology and Center for Stem Cell and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Timothy J Nice
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Megan T Baldridge
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
75
|
Abstract
Human norovirus is a major human pathogen causing the majority of cases of viral gastroenteritis globally. Viral entry is the first step of the viral life cycle and is a significant determinant of cell tropism, host range, immune interactions, and pathogenesis. Bile salts and histo-blood group antigens are key mediators of norovirus entry; however, the molecular mechanisms by which these molecules promote infection and the identity of a potential human norovirus receptor remain unknown. Recently, there have been several important advances in norovirus entry biology including the identification of CD300lf as the receptor for murine norovirus and of the role of the minor capsid protein VP2 in viral genome release. Here, we will review the current understanding about norovirus attachment and entry and highlight important future directions.
Collapse
Affiliation(s)
- Vincent R Graziano
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Jin Wei
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Craig B Wilen
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
| |
Collapse
|
76
|
Liu TC, Kern JT, VanDussen KL, Xiong S, Kaiko GE, Wilen CB, Rajala MW, Caruso R, Holtzman MJ, Gao F, McGovern DP, Nunez G, Head RD, Stappenbeck TS. Interaction between smoking and ATG16L1T300A triggers Paneth cell defects in Crohn's disease. J Clin Invest 2018; 128:5110-5122. [PMID: 30137026 DOI: 10.1172/jci120453] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 08/21/2018] [Indexed: 12/14/2022] Open
Abstract
It is suggested that subtyping of complex inflammatory diseases can be based on genetic susceptibility and relevant environmental exposure (G+E). We propose that using matched cellular phenotypes in human subjects and corresponding preclinical models with the same G+E combinations is useful to this end. As an example, defective Paneth cells can subtype Crohn's disease (CD) subjects; Paneth cell defects have been linked to multiple CD susceptibility genes and are associated with poor outcome. We hypothesized that CD susceptibility genes interact with cigarette smoking, a major CD environmental risk factor, to trigger Paneth cell defects. We found that both CD subjects and mice with ATG16L1T300A (T300A; a prevalent CD susceptibility allele) developed Paneth cell defects triggered by tobacco smoke. Transcriptional analysis of full-thickness ileum and Paneth cell-enriched crypt base cells showed the T300A-smoking combination altered distinct pathways, including proapoptosis, metabolic dysregulation, and selective downregulation of the PPARγ pathway. Pharmacologic intervention by either apoptosis inhibitor or PPARγ agonist rosiglitazone prevented smoking-induced crypt apoptosis and Paneth cell defects in T300A mice and mice with conditional Paneth cell-specific knockout of Atg16l1. This study demonstrates how explicit G+E can drive disease-relevant phenotype and provides rational strategies for identifying actionable targets.
Collapse
Affiliation(s)
- Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Justin T Kern
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Shanshan Xiong
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Gerard E Kaiko
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Craig B Wilen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Michael W Rajala
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Roberta Caruso
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | | | - Feng Gao
- Department of Surgery, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Dermot Pb McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gabriel Nunez
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Richard D Head
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| |
Collapse
|
77
|
Nelson CA, Wilen CB, Dai YN, Orchard RC, Kim AS, Stegeman RA, Hsieh LL, Smith TJ, Virgin HW, Fremont DH. Structural basis for murine norovirus engagement of bile acids and the CD300lf receptor. Proc Natl Acad Sci U S A 2018; 115:E9201-E9210. [PMID: 30194229 PMCID: PMC6166816 DOI: 10.1073/pnas.1805797115] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Murine norovirus (MNoV) is closely related to human norovirus (HNoV), an infectious agent responsible for acute gastroenteritis worldwide. Here we report the X-ray crystal structure of the dimeric MNoV VP1 protruding (P) domain in complex with its cellular receptor CD300lf. CD300lf binds the P domain with a 2:2 stoichiometry, engaging a cleft between the AB and DE loops of the P2 subdomain at a site that overlaps the epitopes of neutralizing antibodies. We also identify that bile acids are cofactors enhancing MNoV cell-binding and infectivity. Structures of CD300lf-P domain in complex with glycochenodeoxycholic acid (GCDCA) and lithocholic acid (LCA) reveal two bile acid binding sites at the P domain dimer interface distant from receptor binding sites. The structural determinants for receptor and bile acid binding are supported by numerous biophysical assays utilizing interface residue mutations. We find that the monomeric affinity of CD300lf for the P domain is low and is divalent cation dependent. We have also determined the crystal structure of CD300lf in complex with phosphocholine, revealing that MNoV engages its receptor in a manner mimicking host ligands including similar metal coordination. Docking of the cocomplex structures onto a cryo-EM-derived model of MNoV suggests that each virion can make multiple CD300lf engagements, and thus, infection may be driven by the avidity of cell surface clustered CD300lf. These studies identify multiple potential modulators of norovirus infection that may act to regulate the interaction between the viral capsid P domain and its cognate cellular receptor.
Collapse
Affiliation(s)
- Christopher A Nelson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Craig B Wilen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Ya-Nan Dai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Robert C Orchard
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Arthur S Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Roderick A Stegeman
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Leon L Hsieh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Thomas J Smith
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| |
Collapse
|
78
|
Orchard RC, Wilen CB, Virgin HW. Sphingolipid biosynthesis induces a conformational change in the murine norovirus receptor and facilitates viral infection. Nat Microbiol 2018; 3:1109-1114. [PMID: 30127493 PMCID: PMC6158067 DOI: 10.1038/s41564-018-0221-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/19/2018] [Indexed: 12/24/2022]
Abstract
Cellular susceptibility to viral infections is in part determined by the presence of a host cellular receptor. Here we use murine norovirus as a model to uncover an unappreciated connection between an intracellular lipid biosynthetic enzyme and a receptor conformation permissive for viral infection. The serine palmitoyltransferase (SPT) complex is required for de novo sphingolipid biosynthesis and we find that its absence impairs the ability of murine norovirus to bind and enter cells. While, the SPT complex is dispensable for the surface expression of the norovirus receptor, CD300lf, SPT activity is required for CD300lf to adopt a conformation permissive for viral binding. Addition of extracellular ceramide to SPT deficient cells chemically complements both the conformational changes of CD300lf and the cellular susceptibility to murine norovirus infection. Taken together, these data indicate that intracellular sphingolipid biosynthesis regulates the conformation of the murine norovirus receptor, and therefore the tropism of murine norovirus. This indicates that intracellular biosynthetic pathways can regulate viral tropism even when the receptor for a virus is expressed on the target cell surface.
Collapse
Affiliation(s)
- Robert C Orchard
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Craig B Wilen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
79
|
Wilen CB, Lee S, Hsieh LL, Orchard RC, Desai C, Hykes BL, McAllaster MR, Balce DR, Feehley T, Brestoff JR, Hickey CA, Yokoyama CC, Wang YT, MacDuff DA, Kreamalmayer D, Howitt MR, Neil JA, Cadwell K, Allen PM, Handley SA, van Lookeren Campagne M, Baldridge MT, Virgin HW. Tropism for tuft cells determines immune promotion of norovirus pathogenesis. Science 2018; 360:204-208. [PMID: 29650672 PMCID: PMC6039974 DOI: 10.1126/science.aar3799] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/05/2018] [Indexed: 12/12/2022]
Abstract
Complex interactions between host immunity and the microbiome regulate norovirus infection. However, the mechanism of host immune promotion of enteric virus infection remains obscure. The cellular tropism of noroviruses is also unknown. Recently, we identified CD300lf as a murine norovirus (MNoV) receptor. In this study, we have shown that tuft cells, a rare type of intestinal epithelial cell, express CD300lf and are the target cell for MNoV in the mouse intestine. We found that type 2 cytokines, which induce tuft cell proliferation, promote MNoV infection in vivo. These cytokines can replace the effect of commensal microbiota in promoting virus infection. Our work thus provides insight into how the immune system and microbes can coordinately promote enteric viral infection.
Collapse
Affiliation(s)
- Craig B Wilen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sanghyun Lee
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Leon L Hsieh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert C Orchard
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chandni Desai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barry L Hykes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael R McAllaster
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dale R Balce
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Taylor Feehley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jonathan R Brestoff
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christina A Hickey
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christine C Yokoyama
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ya-Ting Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Donna A MacDuff
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - Darren Kreamalmayer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael R Howitt
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jessica A Neil
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Paul M Allen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Megan T Baldridge
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
80
|
Lee S, Wilen CB, Orvedahl A, McCune BT, Kim KW, Orchard RC, Peterson ST, Nice TJ, Baldridge MT, Virgin HW. Norovirus Cell Tropism Is Determined by Combinatorial Action of a Viral Non-structural Protein and Host Cytokine. Cell Host Microbe 2017; 22:449-459.e4. [PMID: 28966054 PMCID: PMC5679710 DOI: 10.1016/j.chom.2017.08.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/19/2017] [Accepted: 08/29/2017] [Indexed: 01/24/2023]
Abstract
Cellular tropism during persistent viral infection is commonly conferred by the interaction of a viral surface protein with a host receptor complex. Norovirus, the leading global cause of gastroenteritis, can be persistently shed during infection, but its in vivo cellular tropism and tropism determinants remain unidentified. Using murine norovirus (MNoV), we determine that a small number of intestinal epithelial cells (IECs) serve as the reservoir for fecal shedding and persistence. The viral non-structural protein NS1, rather than a viral surface protein, determines IEC tropism. Expression of NS1 from a persistent MNoV strain is sufficient for an acute MNoV strain to target IECs and persist. In addition, interferon-lambda (IFN-λ) is a key host determinant blocking MNoV infection in IECs. The inability of acute MNoV to shed and persist is rescued in Ifnlr1-/- mice, suggesting that NS1 evades IFN-λ-mediated antiviral immunity. Thus, NS1 and IFN-λ interactions govern IEC tropism and persistence of MNoV.
Collapse
Affiliation(s)
- Sanghyun Lee
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Craig B Wilen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Anthony Orvedahl
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Broc T McCune
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ki-Wook Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert C Orchard
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Stefan T Peterson
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Timothy J Nice
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
| | - Megan T Baldridge
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA.
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
81
|
Wilen CB, Booth GS, Grossman BJ, Lane WJ, Szklarski PC, Jackups R. Using direct antiglobulin test results to reduce unnecessary cold agglutinin testing. Transfusion 2017; 57:1480-1484. [DOI: 10.1111/trf.14059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 01/06/2017] [Accepted: 01/14/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Craig B. Wilen
- Department of Pathology and Immunology; Washington University School of Medicine; St Louis Missouri
| | - Garrett S. Booth
- Department of Pathology; Vanderbilt University Medical Center; Nashville Tennessee
| | - Brenda J. Grossman
- Department of Pathology and Immunology; Washington University School of Medicine; St Louis Missouri
| | - William J. Lane
- Department of Pathology; Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
| | - Penny C. Szklarski
- Department of Pathology; Vanderbilt University Medical Center; Nashville Tennessee
| | - Ronald Jackups
- Department of Pathology and Immunology; Washington University School of Medicine; St Louis Missouri
| |
Collapse
|
82
|
Orchard RC, Wilen CB, Doench JG, Baldridge MT, McCune BT, Lee YCJ, Lee S, Pruett-Miller SM, Nelson CA, Fremont DH, Virgin HW. Discovery of a proteinaceous cellular receptor for a norovirus. Science 2016; 353:933-6. [PMID: 27540007 DOI: 10.1126/science.aaf1220] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 07/29/2016] [Indexed: 12/26/2022]
Abstract
Noroviruses (NoVs) are a leading cause of gastroenteritis globally, yet the host factors required for NoV infection are poorly understood. We identified host molecules that are essential for murine NoV (MNoV)-induced cell death, including CD300lf as a proteinaceous receptor. We found that CD300lf is essential for MNoV binding and replication in cell lines and primary cells. Additionally, Cd300lf(-/-) mice are resistant to MNoV infection. Expression of CD300lf in human cells breaks the species barrier that would otherwise restrict MNoV replication. The crystal structure of the CD300lf ectodomain reveals a potential ligand-binding cleft composed of residues that are critical for MNoV infection. Therefore, the presence of a proteinaceous receptor is the primary determinant of MNoV species tropism, whereas other components of cellular machinery required for NoV replication are conserved between humans and mice.
Collapse
Affiliation(s)
- Robert C Orchard
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Craig B Wilen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Megan T Baldridge
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Broc T McCune
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ying-Chiang J Lee
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sanghyun Lee
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shondra M Pruett-Miller
- Genome Engineering and iPSC Center, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christopher A Nelson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
83
|
Monaco CL, Gootenberg DB, Zhao G, Handley SA, Ghebremichael MS, Lim ES, Lankowski A, Baldridge MT, Wilen CB, Flagg M, Norman JM, Keller BC, Luévano JM, Wang D, Boum Y, Martin JN, Hunt PW, Bangsberg DR, Siedner MJ, Kwon DS, Virgin HW. Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome. Cell Host Microbe 2016; 19:311-22. [PMID: 26962942 PMCID: PMC4821831 DOI: 10.1016/j.chom.2016.02.011] [Citation(s) in RCA: 264] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/31/2015] [Accepted: 02/19/2016] [Indexed: 02/07/2023]
Abstract
Human immunodeficiency virus (HIV) infection is associated with increased intestinal translocation of microbial products and enteropathy as well as alterations in gut bacterial communities. However, whether the enteric virome contributes to this infection and resulting immunodeficiency remains unknown. We characterized the enteric virome and bacterial microbiome in a cohort of Ugandan patients, including HIV-uninfected or HIV-infected subjects and those either treated with anti-retroviral therapy (ART) or untreated. Low peripheral CD4 T cell counts were associated with an expansion of enteric adenovirus sequences and this increase was independent of ART treatment. Additionally, the enteric bacterial microbiome of patients with lower CD4 T counts exhibited reduced phylogenetic diversity and richness with specific bacteria showing differential abundance, including increases in Enterobacteriaceae, which have been associated with inflammation. Thus, immunodeficiency in progressive HIV infection is associated with alterations in the enteric virome and bacterial microbiome, which may contribute to AIDS-associated enteropathy and disease progression.
Collapse
Affiliation(s)
- Cynthia L Monaco
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Guoyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - Efrem S Lim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Alex Lankowski
- Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Megan T Baldridge
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Craig B Wilen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Meaghan Flagg
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | - Brian C Keller
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - David Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Yap Boum
- Médecins Sans Frontières Epicentre, 1956 Mbarara, Uganda
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Peter W Hunt
- Department of Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - David R Bangsberg
- Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Harvard School of Public Health, Boston, MA 02114, USA
| | - Mark J Siedner
- Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Douglas S Kwon
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| |
Collapse
|
84
|
Lu Q, Yokoyama CC, Williams JW, Baldridge MT, Jin X, DesRochers B, Bricker T, Wilen CB, Bagaitkar J, Loginicheva E, Sergushichev A, Kreamalmeyer D, Keller BC, Zhao Y, Kambal A, Green DR, Martinez J, Dinauer MC, Holtzman MJ, Crouch EC, Beatty W, Boon ACM, Zhang H, Randolph GJ, Artyomov MN, Virgin HW. Homeostatic Control of Innate Lung Inflammation by Vici Syndrome Gene Epg5 and Additional Autophagy Genes Promotes Influenza Pathogenesis. Cell Host Microbe 2016; 19:102-13. [PMID: 26764600 PMCID: PMC4714358 DOI: 10.1016/j.chom.2015.12.011] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/11/2015] [Accepted: 12/18/2015] [Indexed: 12/21/2022]
Abstract
Mutations in the autophagy gene EPG5 are linked to the multisystem human disease Vici syndrome, which is characterized in part by pulmonary abnormalities, including recurrent infections. We found that Epg5-deficient mice exhibited elevated baseline innate immune cellular and cytokine-based lung inflammation and were resistant to lethal influenza virus infection. Lung transcriptomics, bone marrow transplantation experiments, and analysis of cellular cytokine expression indicated that Epg5 plays a role in lung physiology through its function in macrophages. Deletion of other autophagy genes including Atg14, Fip200, Atg5, and Atg7 in myeloid cells also led to elevated basal lung inflammation and influenza resistance. This suggests that Epg5 and other Atg genes function in macrophages to limit innate immune inflammation in the lung. Disruption of this normal homeostatic dampening of lung inflammation results in increased resistance to influenza, suggesting that normal homeostatic mechanisms that limit basal tissue inflammation support some infectious diseases.
Collapse
Affiliation(s)
- Qun Lu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christine C Yokoyama
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jesse W Williams
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Megan T Baldridge
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiaohua Jin
- Department of Internal Medicine (Pulmonary and Critical Care Medicine), Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brittany DesRochers
- Department of Internal Medicine (Pulmonary and Critical Care Medicine), Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Traci Bricker
- Department of Internal Medicine (Pulmonary and Critical Care Medicine), Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Craig B Wilen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Juhi Bagaitkar
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pediatrics (Hematology/Oncology), Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ekaterina Loginicheva
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alexey Sergushichev
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Computer Technologies Department, ITMO University, St. Petersburg 197101, Russia
| | - Darren Kreamalmeyer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian C Keller
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Internal Medicine (Pulmonary and Critical Care Medicine), Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yan Zhao
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Amal Kambal
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jennifer Martinez
- Immunity, Inflammation, and Disease Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27703, USA
| | - Mary C Dinauer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pediatrics (Hematology/Oncology), Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Holtzman
- Department of Internal Medicine (Pulmonary and Critical Care Medicine), Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erika C Crouch
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Wandy Beatty
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Adrianus C M Boon
- Department of Internal Medicine (Pulmonary and Critical Care Medicine), Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hong Zhang
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Gwendalyn J Randolph
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
85
|
Wilen CB, Szymanski JJ, Hung S, Rajan A, Lavigne PM, Char DM, Geltman EM, Scott MG. Impact on Patient Management and Outcome of Switching between 2 Contemporary Sensitive Cardiac Troponin Assays. Clin Chem 2015; 61:870-6. [DOI: 10.1373/clinchem.2015.238089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/23/2015] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Myocardial infarction is characterized by an increase of cardiac troponin I (cTnI) above the 99th percentile of a reference population. Our hospital switched from 1 contemporary cTnI assay to another and observed a doubling of cTnI results above the assays' respective 99th percentile cutoffs. We investigated the potential impact on inpatient management and outcomes.
METHODS
We performed a retrospective cohort study of 45 498 individuals with ≥1 cTnI result between January 2013 and June 2014. The Dimension cTnI assay was used in 2013; the Abbott Architect cTnI assay was used in 2014.
RESULTS
Before switching cTnI assays, 19.2% (4742/30 872) of patients had at least 1 of the first 3 cTnIs above the 99th percentile (0.07 μg/L). After switching to the Architect cTnI assay, 31.4% (4034/14 626) of patients had at least 1 cTnI above the 99th percentile (0.03 μg/L). This increase was due to the difference in the assays' 99th percentile cutoffs. Having an increased cTnI reported on the Architect assay that would not have been reported as such on the Dimension assay (0.03–0.06 μg/L) correlated with increased inpatient mortality, length of stay, non–ST elevation myocardial infarction diagnosis, therapeutic heparin use, and percutaneous coronary intervention, relative to individuals with cTnI <0.03 μg/L.
CONCLUSIONS
The changes observed in patient outcomes and management were likely due to the increased sensitivity and lower 99th percentile cutoff of the Architect assay. It is important to recognize the potential impact that differences in sensitivity and assay configuration may have on patient management.
Collapse
Affiliation(s)
| | | | | | | | - Paul M Lavigne
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | | | - Edward M Geltman
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | | |
Collapse
|
86
|
Abstract
Infectious diarrhea is a major cause of morbidity. A rapid and inexpensive assay for the diagnosis of infectious gastroenteritis would expedite appropriate therapy and prevent unnecessary and potentially invasive testing. This article summarizes assays for the diagnosis of infectious gastroenteritis based on the host response to bacterial, viral, or parasitic infection. This includes both systemic biomarkers (such as C-reactive protein, erythrocyte sedimentation rate, and serum cytokines) and fecal biomarkers (such as lactoferrin, fecal leukocyte analysis, and calprotectin). Although some of these assays have value as adjunct diagnostics, they lack sensitivity and specificity as stand-alone tests in this setting.
Collapse
Affiliation(s)
- Mark D Gonzalez
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, Washington University in St. Louis, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Craig B Wilen
- Department of Pathology and Immunology, Washington University School of Medicine, Washington University in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, Washington University in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
| |
Collapse
|
87
|
Petersen J, Drake MJ, Bruce EA, Riblett AM, Didigu CA, Wilen CB, Malani N, Male F, Lee FH, Bushman FD, Cherry S, Doms RW, Bates P, Briley K. The major cellular sterol regulatory pathway is required for Andes virus infection. PLoS Pathog 2014; 10:e1003911. [PMID: 24516383 PMCID: PMC3916400 DOI: 10.1371/journal.ppat.1003911] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 12/18/2013] [Indexed: 12/21/2022] Open
Abstract
The Bunyaviridae comprise a large family of RNA viruses with worldwide distribution and includes the pathogenic New World hantavirus, Andes virus (ANDV). Host factors needed for hantavirus entry remain largely enigmatic and therapeutics are unavailable. To identify cellular requirements for ANDV infection, we performed two parallel genetic screens. Analysis of a large library of insertionally mutagenized human haploid cells and a siRNA genomic screen converged on components (SREBP-2, SCAP, S1P and S2P) of the sterol regulatory pathway as critically important for infection by ANDV. The significance of this pathway was confirmed using functionally deficient cells, TALEN-mediated gene disruption, RNA interference and pharmacologic inhibition. Disruption of sterol regulatory complex function impaired ANDV internalization without affecting virus binding. Pharmacologic manipulation of cholesterol levels demonstrated that ANDV entry is sensitive to changes in cellular cholesterol and raises the possibility that clinically approved regulators of sterol synthesis may prove useful for combating ANDV infection. As obligate, intracellular parasites viruses are dependent upon the host cell for numerous factors and processes. However, for many important viruses few of the required host factors have been identified. Hantaviruses are rodent-borne viruses that are associated with severe human disease. Transmission to humans occurs sporadically with a recent notable example in Yosemite National park. In the present study, we utilized two independent genetic strategies to discover cellular factors needed for replication of the highly pathogenic hantavirus Andes virus. We found that four genes, encoding components of a complex involved in regulation of cholesterol synthesis and uptake, were critical for Andes virus infection. Drugs that inhibit an enzyme in this complex or that reduce cellular cholesterol levels effectively blocked Andes virus infection, suggesting new ways for combating this pathogenic virus.
Collapse
Affiliation(s)
- Josiah Petersen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mary Jane Drake
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Emily A. Bruce
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Amber M. Riblett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Chukwuka A. Didigu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Craig B. Wilen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nirav Malani
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Frances Male
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Fang-Hua Lee
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sara Cherry
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Robert W. Doms
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Paul Bates
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (PB); (KB)
| | - Kenneth Briley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (PB); (KB)
| |
Collapse
|
88
|
Parrish NF, Li H, Hora B, Berg A, Wilen CB, Decker J, Iyer SS, Zajic L, O’Brien M, Salazar-Gonzalez JF, Salazar MG, Parrish EH, Ding H, Kumar A, Ochsenbauer C, Bhardwaj N, Doms RW, Kappes JC, Gao F, Haynes BF, Korber B, Hahn BH, Shaw GM. C106 Distinguishing Features of Transmitted/Founder HIV-1. J Acquir Immune Defic Syndr 2013. [DOI: 10.1097/01.qai.0000429225.92253.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
89
|
Abstract
The first step of the human immunodeficiency virus (HIV) replication cycle-binding and entry into the host cell-plays a major role in determining viral tropism and the ability of HIV to degrade the human immune system. HIV uses a complex series of steps to deliver its genome into the host cell cytoplasm while simultaneously evading the host immune response. To infect cells, the HIV protein envelope (Env) binds to the primary cellular receptor CD4 and then to a cellular coreceptor. This sequential binding triggers fusion of the viral and host cell membranes, initiating infection. Revealing the mechanism of HIV entry has profound implications for viral tropism, transmission, pathogenesis, and therapeutic intervention. Here, we provide an overview into the mechanism of HIV entry, provide historical context to key discoveries, discuss recent advances, and speculate on future directions in the field.
Collapse
Affiliation(s)
- Craig B Wilen
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | |
Collapse
|
90
|
Parrish NF, Wilen CB, Banks LB, Iyer SS, Pfaff JM, Salazar-Gonzalez JF, Salazar MG, Decker JM, Parrish EH, Berg A, Hopper J, Hora B, Kumar A, Mahlokozera T, Yuan S, Coleman C, Vermeulen M, Ding H, Ochsenbauer C, Tilton JC, Permar SR, Kappes JC, Betts MR, Busch MP, Gao F, Montefiori D, Haynes BF, Shaw GM, Hahn BH, Doms RW. Transmitted/founder and chronic subtype C HIV-1 use CD4 and CCR5 receptors with equal efficiency and are not inhibited by blocking the integrin α4β7. PLoS Pathog 2012; 8:e1002686. [PMID: 22693444 PMCID: PMC3364951 DOI: 10.1371/journal.ppat.1002686] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 03/23/2012] [Indexed: 12/25/2022] Open
Abstract
Sexual transmission of human immunodeficiency virus type 1 (HIV-1) most often results from productive infection by a single transmitted/founder (T/F) virus, indicating a stringent mucosal bottleneck. Understanding the viral traits that overcome this bottleneck could have important implications for HIV-1 vaccine design and other prevention strategies. Most T/F viruses use CCR5 to infect target cells and some encode envelope glycoproteins (Envs) that contain fewer potential N-linked glycosylation sites and shorter V1/V2 variable loops than Envs from chronic viruses. Moreover, it has been reported that the gp120 subunits of certain transmitted Envs bind to the gut-homing integrin α4β7, possibly enhancing virus entry and cell-to-cell spread. Here we sought to determine whether subtype C T/F viruses, which are responsible for the majority of new HIV-1 infections worldwide, share biological properties that increase their transmission fitness, including preferential α4β7 engagement. Using single genome amplification, we generated panels of both T/F (n = 20) and chronic (n = 20) Env constructs as well as full-length T/F (n = 6) and chronic (n = 4) infectious molecular clones (IMCs). We found that T/F and chronic control Envs were indistinguishable in the efficiency with which they used CD4 and CCR5. Both groups of Envs also exhibited the same CD4+ T cell subset tropism and showed similar sensitivity to neutralization by CD4 binding site (CD4bs) antibodies. Finally, saturating concentrations of anti-α4β7 antibodies failed to inhibit infection and replication of T/F as well as chronic control viruses, although the growth of the tissue culture-adapted strain SF162 was modestly impaired. These results indicate that the population bottleneck associated with mucosal HIV-1 acquisition is not due to the selection of T/F viruses that use α4β7, CD4 or CCR5 more efficiently. Most new HIV-1 infections worldwide are caused by the sexual transmission of subtype C viruses, which are prevalent in Asia and southern Africa. While chronically infected individuals harbor a genetically diverse set of viruses, most new infections are established by single variants, termed transmitted/founder (T/F) viruses. This raises the question whether certain viral variants have particular properties allowing them to more efficiently overcome the transmission bottleneck. Preferential binding of the viral envelope (Env) to the integrin α4β7 has been hypothesized as one important feature of transmitted viruses. Here, we compared Envs from subtype C viruses that were transmitted to those that were prevalent in chronic infections for efficiency in utilizing α4β7, CD4 and CCR5 for cell entry and replication. We found that transmitted and chronic Envs engaged CD4 and CCR5 with equal efficiency, and that blocking the interaction between Env and α4β7 failed to inhibit replication of T/F as well as control viruses. While the search for determinants of transmission fitness remains an important goal, preferential CD4, CCR5 or α4β7 interactions do not appear to represent distinguishing features of T/F viruses.
Collapse
Affiliation(s)
- Nicholas F. Parrish
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Craig B. Wilen
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lauren B. Banks
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shilpa S. Iyer
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jennifer M. Pfaff
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jesus F. Salazar-Gonzalez
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Maria G. Salazar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Julie M. Decker
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Erica H. Parrish
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Anna Berg
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Jennifer Hopper
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Amit Kumar
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Tatenda Mahlokozera
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Sally Yuan
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Charl Coleman
- Donation Testing Department, South African National Blood Service, Roodepoort, Gauteng, South Africa
| | - Marion Vermeulen
- Donation Testing Department, South African National Blood Service, Roodepoort, Gauteng, South Africa
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Christina Ochsenbauer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - John C. Tilton
- Department of General Medical Sciences, Center for Proteomics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Sallie R. Permar
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - John C. Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michael R. Betts
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael P. Busch
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - George M. Shaw
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Beatrice H. Hahn
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (BHH); (RWD)
| | - Robert W. Doms
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (BHH); (RWD)
| |
Collapse
|
91
|
Abstract
Human immunodeficiency virus (HIV) entry is a complex and intricate process that facilitates delivery of the viral genome to the host cell. The only viral surface protein, Envelope (Env), is composed of a trimer of gp120 and gp41 heterodimers. It is essentially a fusion machine cloaked in a shroud of carbohydrate structures and variable loops of amino acids that enable it to evade the humoral immune response. For entry to occur gp120 sequentially engages the host protein CD4 and then one of two chemokine coreceptors, either CCR5 or CXCR4. CD4 binding facilitates exposure and formation of the coreceptor-binding site, and coreceptor binding then triggers the membrane fusion machinery in the gp41 subunit. Our understanding of HIV entry has led to the development of successful small molecule inhibitors for the clinical treatment of HIV infection as well as insights into viral tropism and pathogenesis.
Collapse
Affiliation(s)
- Craig B Wilen
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | |
Collapse
|
92
|
Jiang C, Parrish NF, Wilen CB, Li H, Chen Y, Pavlicek JW, Berg A, Lu X, Song H, Tilton JC, Pfaff JM, Henning EA, Decker JM, Moody MA, Drinker MS, Schutte R, Freel S, Tomaras GD, Nedellec R, Mosier DE, Haynes BF, Shaw GM, Hahn BH, Doms RW, Gao F. Primary infection by a human immunodeficiency virus with atypical coreceptor tropism. J Virol 2011; 85:10669-81. [PMID: 21835785 PMCID: PMC3187499 DOI: 10.1128/jvi.05249-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 08/02/2011] [Indexed: 01/23/2023] Open
Abstract
The great majority of human immunodeficiency virus type 1 (HIV-1) strains enter CD4+ target cells by interacting with one of two coreceptors, CCR5 or CXCR4. Here we describe a transmitted/founder (T/F) virus (ZP6248) that was profoundly impaired in its ability to utilize CCR5 and CXCR4 coreceptors on multiple CD4+ cell lines as well as primary human CD4+ T cells and macrophages in vitro yet replicated to very high titers (>80 million RNA copies/ml) in an acutely infected individual. Interestingly, the envelope (Env) glycoprotein of this clade B virus had a rare GPEK sequence in the crown of its third variable loop (V3) rather than the consensus GPGR sequence. Extensive sequencing of sequential plasma samples showed that the GPEK sequence was present in virtually all Envs, including those from the earliest time points after infection. The molecularly cloned (single) T/F virus was able to replicate, albeit poorly, in cells obtained from ccr5Δ32 homozygous donors. The ZP6248 T/F virus could also infect cell lines overexpressing the alternative coreceptors GPR15, APJ, and FPRL-1. A single mutation in the V3 crown sequence (GPEK->GPGK) of ZP6248 restored its infectivity in CCR5+ cells but reduced its ability to replicate in GPR15+ cells, indicating that the V3 crown motif played an important role in usage of this alternative coreceptor. These results suggest that the ZP6248 T/F virus established an acute in vivo infection by using coreceptor(s) other than CCR5 or CXCR4 or that the CCR5 coreceptor existed in an unusual conformation in this individual.
Collapse
MESH Headings
- Amino Acid Motifs
- Amino Acid Substitution/genetics
- Apelin Receptors
- CD4-Positive T-Lymphocytes/virology
- Cells, Cultured
- Gene Expression
- HIV-1/physiology
- Humans
- Macrophages/virology
- Receptors, Formyl Peptide/genetics
- Receptors, Formyl Peptide/metabolism
- Receptors, G-Protein-Coupled/genetics
- Receptors, G-Protein-Coupled/metabolism
- Receptors, HIV/metabolism
- Receptors, Lipoxin/genetics
- Receptors, Lipoxin/metabolism
- Receptors, Peptide/genetics
- Receptors, Peptide/metabolism
- Viral Tropism
- env Gene Products, Human Immunodeficiency Virus/genetics
Collapse
Affiliation(s)
| | | | - Craig B. Wilen
- Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | | | - Yue Chen
- Duke Human Vaccine Institute
- Departments of Medicine
| | | | - Anna Berg
- Duke Human Vaccine Institute
- Departments of Medicine
| | - Xiaozhi Lu
- Duke Human Vaccine Institute
- Departments of Medicine
| | | | - John C. Tilton
- Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Jennifer M. Pfaff
- Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | | | | | - M. Anthony Moody
- Duke Human Vaccine Institute
- Pediatrics, Duke University Medical Center, Durham, North Carolina 27710
| | | | | | | | | | - Rebecca Nedellec
- Department of Immunology & Microbial Science, The Scripps Research Institute, La Jolla, California 92037
| | - Donald E. Mosier
- Department of Immunology & Microbial Science, The Scripps Research Institute, La Jolla, California 92037
| | | | - George M. Shaw
- Departments of Medicine
- Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Beatrice H. Hahn
- Departments of Medicine
- Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Robert W. Doms
- Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Feng Gao
- Duke Human Vaccine Institute
- Departments of Medicine
| |
Collapse
|
93
|
Wilen CB, Wang J, Tilton JC, Miller JC, Kim KA, Rebar EJ, Sherrill-Mix SA, Patro SC, Secreto AJ, Jordan APO, Lee G, Kahn J, Aye PP, Bunnell BA, Lackner AA, Hoxie JA, Danet-Desnoyers GA, Bushman FD, Riley JL, Gregory PD, June CH, Holmes MC, Doms RW. Engineering HIV-resistant human CD4+ T cells with CXCR4-specific zinc-finger nucleases. PLoS Pathog 2011; 7:e1002020. [PMID: 21533216 PMCID: PMC3077364 DOI: 10.1371/journal.ppat.1002020] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 02/18/2011] [Indexed: 11/18/2022] Open
Abstract
HIV-1 entry requires the cell surface expression of CD4 and either the CCR5 or CXCR4 coreceptors on host cells. Individuals homozygous for the ccr5Δ32 polymorphism do not express CCR5 and are protected from infection by CCR5-tropic (R5) virus strains. As an approach to inactivating CCR5, we introduced CCR5-specific zinc-finger nucleases into human CD4+ T cells prior to adoptive transfer, but the need to protect cells from virus strains that use CXCR4 (X4) in place of or in addition to CCR5 (R5X4) remains. Here we describe engineering a pair of zinc finger nucleases that, when introduced into human T cells, efficiently disrupt cxcr4 by cleavage and error-prone non-homologous DNA end-joining. The resulting cells proliferated normally and were resistant to infection by X4-tropic HIV-1 strains. CXCR4 could also be inactivated in ccr5Δ32 CD4+ T cells, and we show that such cells were resistant to all strains of HIV-1 tested. Loss of CXCR4 also provided protection from X4 HIV-1 in a humanized mouse model, though this protection was lost over time due to the emergence of R5-tropic viral mutants. These data suggest that CXCR4-specific ZFNs may prove useful in establishing resistance to CXCR4-tropic HIV for autologous transplant in HIV-infected individuals.
Collapse
Affiliation(s)
- Craig B. Wilen
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jianbin Wang
- Sangamo BioSciences, Richmond, California, United States of America
| | - John C. Tilton
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | | | - Kenneth A. Kim
- Sangamo BioSciences, Richmond, California, United States of America
| | - Edward J. Rebar
- Sangamo BioSciences, Richmond, California, United States of America
| | - Scott A. Sherrill-Mix
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Sean C. Patro
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Anthony J. Secreto
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Andrea P. O. Jordan
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Gary Lee
- Sangamo BioSciences, Richmond, California, United States of America
| | - Joshua Kahn
- Sangamo BioSciences, Richmond, California, United States of America
| | - Pyone P. Aye
- Divisions of Regenerative Medicine and Comparative Pathology, Tulane National Primate Research Center, Tulane University School of Medicine, Covington, Louisiana, United States of America
| | - Bruce A. Bunnell
- Divisions of Regenerative Medicine and Comparative Pathology, Tulane National Primate Research Center, Tulane University School of Medicine, Covington, Louisiana, United States of America
| | - Andrew A. Lackner
- Divisions of Regenerative Medicine and Comparative Pathology, Tulane National Primate Research Center, Tulane University School of Medicine, Covington, Louisiana, United States of America
| | - James A. Hoxie
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Gwenn A. Danet-Desnoyers
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - James L. Riley
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | | | - Carl H. June
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | | | - Robert W. Doms
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|