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García-García A, Pérez de Diego R, Flores C, Rinchai D, Solé-Violán J, Deyà-Martínez À, García-Solis B, Lorenzo-Salazar JM, Hernández-Brito E, Lanz AL, Moens L, Bucciol G, Almuqamam M, Domachowske JB, Colino E, Santos-Perez JL, Marco FM, Pignata C, Bousfiha A, Turvey SE, Bauer S, Haerynck F, Ocejo-Vinyals JG, Lendinez F, Prader S, Naumann-Bartsch N, Pachlopnik Schmid J, Biggs CM, Hildebrand K, Dreesman A, Cárdenes MÁ, Ailal F, Benhsaien I, Giardino G, Molina-Fuentes A, Fortuny C, Madhavarapu S, Conway DH, Prando C, Schidlowski L, Martínez de Saavedra Álvarez MT, Alfaro R, Rodríguez de Castro F, Meyts I, Hauck F, Puel A, Bastard P, Boisson B, Jouanguy E, Abel L, Cobat A, Zhang Q, Casanova JL, Alsina L, Rodríguez-Gallego C. Humans with inherited MyD88 and IRAK-4 deficiencies are predisposed to hypoxemic COVID-19 pneumonia. J Exp Med 2023; 220:e20220170. [PMID: 36880831 PMCID: PMC9998661 DOI: 10.1084/jem.20220170] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 11/11/2022] [Accepted: 01/30/2023] [Indexed: 03/08/2023] Open
Abstract
X-linked recessive deficiency of TLR7, a MyD88- and IRAK-4-dependent endosomal ssRNA sensor, impairs SARS-CoV-2 recognition and type I IFN production in plasmacytoid dendritic cells (pDCs), thereby underlying hypoxemic COVID-19 pneumonia with high penetrance. We report 22 unvaccinated patients with autosomal recessive MyD88 or IRAK-4 deficiency infected with SARS-CoV-2 (mean age: 10.9 yr; 2 mo to 24 yr), originating from 17 kindreds from eight countries on three continents. 16 patients were hospitalized: six with moderate, four with severe, and six with critical pneumonia, one of whom died. The risk of hypoxemic pneumonia increased with age. The risk of invasive mechanical ventilation was also much greater than in age-matched controls from the general population (OR: 74.7, 95% CI: 26.8-207.8, P < 0.001). The patients' susceptibility to SARS-CoV-2 can be attributed to impaired TLR7-dependent type I IFN production by pDCs, which do not sense SARS-CoV-2 correctly. Patients with inherited MyD88 or IRAK-4 deficiency were long thought to be selectively vulnerable to pyogenic bacteria, but also have a high risk of hypoxemic COVID-19 pneumonia.
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Affiliation(s)
- Ana García-García
- Pediatric Allergy and Clinical Immunology Dept., Clinical Immunology and Primary Immunodeficiencies Unit, Hospital Sant Joan de Déu, Barcelona, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children, Institut de Recerca Sant Joan de Déu, Barcelona, Barcelona, Spain
- Clinical Immunology Unit, Hospital Sant Joan de Déu-Hospital Clínic Barcelona, Barcelona, Spain
| | - Rebeca Pérez de Diego
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, La Paz Hospital, Madrid, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Dept. of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Jordi Solé-Violán
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Dept. of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Dept. of Intensive Care Medicine, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Àngela Deyà-Martínez
- Pediatric Allergy and Clinical Immunology Dept., Clinical Immunology and Primary Immunodeficiencies Unit, Hospital Sant Joan de Déu, Barcelona, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children, Institut de Recerca Sant Joan de Déu, Barcelona, Barcelona, Spain
- Clinical Immunology Unit, Hospital Sant Joan de Déu-Hospital Clínic Barcelona, Barcelona, Spain
| | - Blanca García-Solis
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, La Paz Hospital, Madrid, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Elisa Hernández-Brito
- Dept. of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Anna-Lisa Lanz
- Dept. of Pediatrics, Division of Pediatric Immunology and Rheumatology, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Leen Moens
- Laboratory for Inborn Errors of Immunity, Dept. of Microbiology, Immunology and Transplantation KU Leuven, Leuven, Belgium
| | - Giorgia Bucciol
- Laboratory for Inborn Errors of Immunity, Dept. of Microbiology, Immunology and Transplantation KU Leuven, Leuven, Belgium
- Dept. of Pediatrics, Childhood Immunology, UZ Leuven, Leuven, Belgium
| | - Mohamed Almuqamam
- Dept. of Pediatrics, Drexel University College of Medicine, St Christopher’s Hospital for Children, Philadelphia, PA, USA
| | | | - Elena Colino
- Unidad de Enfermedades Infecciosas, Complejo Hospitalario Universitario Insular-Materno Infantil, Las Palmas de Gran Canaria, Spain
| | - Juan Luis Santos-Perez
- Unidad de Gestión Clínica de Pediatría y Cirugía Pediátrica, Hospital Virgen de las Nieves-IBS, Granada, Spain
| | - Francisco M. Marco
- Dept. of Immunology, Alicante University General Hospital Doctor Balmis, Alicante, Spain
- Alicante Institute for Health and Biomedical Research, Alicante, Spain
| | - Claudio Pignata
- Dept. of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | - Aziz Bousfiha
- Dept. of Pediatric Infectious Diseases and Clinical Immunology, Ibn Rushd University Hospital, Casablanca, Morocco
- Clinical Immunology, Autoimmunity and Inflammation Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Stuart E. Turvey
- Dept. of Paediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Stefanie Bauer
- Clinic for Children and Adolescents. Dept. of Hematology and Oncology. University Clinic Erlangen, Erlangen, Germany
| | - Filomeen Haerynck
- Dept. of Pediatric Immunology and Pulmonology, Centre for Primary Immune Deficiency Ghent, Ghent University Hospital, Ghent, Belgium
- Dept. of Internal Medicine and Pediatrics, PID Research Laboratory, Ghent University, Ghent, Belgium
| | | | - Francisco Lendinez
- Dept. of Pediatric Oncohematology, Hospital Materno Infantil Torrecárdenas, Almería, Spain
| | - Seraina Prader
- Division of Immunology and Children’s Research Center, University Children’s Hospital Zurich, Zurich, Switzerland; University of Zurich, Zurich, Switzerland
| | - Nora Naumann-Bartsch
- Clinic for Children and Adolescents. Dept. of Hematology and Oncology. University Clinic Erlangen, Erlangen, Germany
| | - Jana Pachlopnik Schmid
- Division of Immunology and Children’s Research Center, University Children’s Hospital Zurich, Zurich, Switzerland; University of Zurich, Zurich, Switzerland
| | - Catherine M. Biggs
- Dept. of Paediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Kyla Hildebrand
- Dept. of Paediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | | | - Miguel Ángel Cárdenes
- Dept. of Internal Medicine, Unit of Infectious Diseases, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Fatima Ailal
- Dept. of Pediatric Infectious Diseases and Clinical Immunology, Ibn Rushd University Hospital, Casablanca, Morocco
- Clinical Immunology, Autoimmunity and Inflammation Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Ibtihal Benhsaien
- Dept. of Pediatric Infectious Diseases and Clinical Immunology, Ibn Rushd University Hospital, Casablanca, Morocco
- Clinical Immunology, Autoimmunity and Inflammation Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Giuliana Giardino
- Dept. of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy
| | | | - Claudia Fortuny
- Study Group for Immune Dysfunction Diseases in Children, Institut de Recerca Sant Joan de Déu, Barcelona, Barcelona, Spain
- Pediatric Infectious Diseases Unit, Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER of Epidemiology and Public Health, Madrid, Spain; Translational Research Network in Pediatric Infectious Diseases, Madrid, Spain
- Dept. of Surgery and Surgical Specializations, Facultat de Medicina i Ciències de la Salut, University of Barcelona, Barcelona, Spain
| | - Swetha Madhavarapu
- Dept. of Pediatrics, Drexel University College of Medicine, St Christopher’s Hospital for Children, Philadelphia, PA, USA
| | - Daniel H. Conway
- Dept. of Pediatrics, Drexel University College of Medicine, St Christopher’s Hospital for Children, Philadelphia, PA, USA
| | - Carolina Prando
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Hospital Pequeno Príncipe, Curitiba, Brazil
| | - Laire Schidlowski
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Hospital Pequeno Príncipe, Curitiba, Brazil
| | | | - Rafael Alfaro
- Dept. of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Felipe Rodríguez de Castro
- Dept. of Medical and Surgical Sciences, School of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
- Dept. of Respiratory Diseases, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Isabelle Meyts
- Laboratory for Inborn Errors of Immunity, Dept. of Microbiology, Immunology and Transplantation KU Leuven, Leuven, Belgium
- Dept. of Pediatrics, Childhood Immunology, UZ Leuven, Leuven, Belgium
| | - Fabian Hauck
- Dept. of Pediatrics, Division of Pediatric Immunology and Rheumatology, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Paul Bastard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- Pediatric Hematology and Immunology Unit, Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Laia Alsina
- Pediatric Allergy and Clinical Immunology Dept., Clinical Immunology and Primary Immunodeficiencies Unit, Hospital Sant Joan de Déu, Barcelona, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children, Institut de Recerca Sant Joan de Déu, Barcelona, Barcelona, Spain
- Clinical Immunology Unit, Hospital Sant Joan de Déu-Hospital Clínic Barcelona, Barcelona, Spain
- Dept. of Surgery and Surgical Specializations, Facultat de Medicina i Ciències de la Salut, University of Barcelona, Barcelona, Spain
| | - Carlos Rodríguez-Gallego
- Dept. of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Dept. of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Dept. of Medical and Surgical Sciences, School of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
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6
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Sugiyama MG, Cui H, Redka DS, Karimzadeh M, Rujas E, Maan H, Hayat S, Cheung K, Misra R, McPhee JB, Viirre RD, Haller A, Botelho RJ, Karshafian R, Sabatinos SA, Fairn GD, Madani Tonekaboni SA, Windemuth A, Julien JP, Shahani V, MacKinnon SS, Wang B, Antonescu CN. Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease. Sci Rep 2021; 11:23315. [PMID: 34857794 PMCID: PMC8640055 DOI: 10.1038/s41598-021-02432-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022] Open
Abstract
The COVID-19 pandemic has highlighted the urgent need for the identification of new antiviral drug therapies for a variety of diseases. COVID-19 is caused by infection with the human coronavirus SARS-CoV-2, while other related human coronaviruses cause diseases ranging from severe respiratory infections to the common cold. We developed a computational approach to identify new antiviral drug targets and repurpose clinically-relevant drug compounds for the treatment of a range of human coronavirus diseases. Our approach is based on graph convolutional networks (GCN) and involves multiscale host-virus interactome analysis coupled to off-target drug predictions. Cell-based experimental assessment reveals several clinically-relevant drug repurposing candidates predicted by the in silico analyses to have antiviral activity against human coronavirus infection. In particular, we identify the MET inhibitor capmatinib as having potent and broad antiviral activity against several coronaviruses in a MET-independent manner, as well as novel roles for host cell proteins such as IRAK1/4 in supporting human coronavirus infection, which can inform further drug discovery studies.
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Affiliation(s)
- Michael G Sugiyama
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Haotian Cui
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | | | | | - Edurne Rujas
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Hassaan Maan
- Vector Institute, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Peter Munk Cardiac Centre, University Health Centre, Toronto, ON, Canada
| | - Sikander Hayat
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, USA
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Kyle Cheung
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada
| | - Rahul Misra
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Joseph B McPhee
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada
| | - Russell D Viirre
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada
| | - Andrew Haller
- Phoenox Pharma, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Roberto J Botelho
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada
| | - Raffi Karshafian
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
- Institute for Biomedical Engineering, Science and Technology (iBEST), a partnership between Ryerson University and St. Michael's Hospital, Toronto, ON, Canada
- Department of Physics, Ryerson University, Toronto, ON, Canada
| | - Sarah A Sabatinos
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada
| | - Gregory D Fairn
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
- Department of Surgery, University of Toronto, Toronto, ON, Canada
| | | | | | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Immunology, Toronto, ON, Canada
| | | | | | - Bo Wang
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
- Vector Institute, Toronto, ON, Canada.
- Peter Munk Cardiac Centre, University Health Centre, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
| | - Costin N Antonescu
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada.
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada.
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada.
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