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Matuozzo D, Talouarn E, Marchal A, Zhang P, Manry J, Seeleuthner Y, Zhang Y, Bolze A, Chaldebas M, Milisavljevic B, Gervais A, Bastard P, Asano T, Bizien L, Barzaghi F, Abolhassani H, Tayoun AA, Aiuti A, Darazam IA, Allende LM, Alonso-Arias R, Arias AA, Aytekin G, Bergman P, Bondesan S, Bryceson YT, Bustos IG, Cabrera-Marante O, Carcel S, Carrera P, Casari G, Chaïbi K, Colobran R, Condino-Neto A, Covill LE, Delmonte OM, Zein LE, Flores C, Gregersen PK, Gut M, Haerynck F, Halwani R, Hancerli S, Hammarström L, Hatipoğlu N, Karbuz A, Keles S, Kyheng C, Leon-Lopez R, Franco JL, Mansouri D, Martinez-Picado J, Akcan OM, Migeotte I, Morange PE, Morelle G, Martin-Nalda A, Novelli G, Novelli A, Ozcelik T, Palabiyik F, Pan-Hammarström Q, de Diego RP, Planas-Serra L, Pleguezuelo DE, Prando C, Pujol A, Reyes LF, Rivière JG, Rodriguez-Gallego C, Rojas J, Rovere-Querini P, Schlüter A, Shahrooei M, Sobh A, Soler-Palacin P, Tandjaoui-Lambiotte Y, Tipu I, Tresoldi C, Troya J, van de Beek D, Zatz M, Zawadzki P, Al-Muhsen SZ, Alosaimi MF, Alsohime FM, Baris-Feldman H, Butte MJ, Constantinescu SN, Cooper MA, Dalgard CL, Fellay J, Heath JR, Lau YL, Lifton RP, Maniatis T, Mogensen TH, von Bernuth H, Lermine A, Vidaud M, Boland A, Deleuze JF, Nussbaum R, Kahn-Kirby A, Mentre F, Tubiana S, Gorochov G, Tubach F, Hausfater P, Meyts I, Zhang SY, Puel A, Notarangelo LD, Boisson-Dupuis S, Su HC, Boisson B, Jouanguy E, Casanova JL, Zhang Q, Abel L, Cobat A. Correction: Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19. Genome Med 2024; 16:6. [PMID: 38184654 PMCID: PMC10771638 DOI: 10.1186/s13073-023-01278-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2024] Open
Affiliation(s)
- Daniela Matuozzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Estelle Talouarn
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jeremy Manry
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | | | - Matthieu Chaldebas
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Baptiste Milisavljevic
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Takaki Asano
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Federica Barzaghi
- Department of Paediatric Immunohematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran, Iran
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Ilad Alavi Darazam
- Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Infectious Diseases and Tropical Medicine, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Luis M Allende
- Immunology Department, University Hospital 12 de Octubre, Research Institute imas12 and Complutense University, Madrid, Spain
| | - Rebeca Alonso-Arias
- Immunology Department, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Andrés Augusto Arias
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Department of Microbiology and Parasitology, Primary Immunodeficiencies Group, School of Medicine, University of Antioquia UdeA, 050010, Medellin, Colombia
- School of Microbiology, University of Antioquia UdeA, 050010, Medellin, Colombia
| | - Gokhan Aytekin
- Deparment of Internal Medicine, Division of Allergy and Immunology, Konya City Hospital, Konya, Turkey
| | - Peter Bergman
- Department of Infectious Diseases, The Immunodeficiency Unit, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Clinical Immunology, Stockholm, Sweden
| | - Simone Bondesan
- Clinical Genomics, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Yenan T Bryceson
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | | | - Oscar Cabrera-Marante
- Institute of Biomedical Research of IdiPAZ, University Hospital "La Paz", Madrid, Spain
| | - Sheila Carcel
- Unidad de Gestión Clínica de Cuidados Intensivos, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), Córdoba, Spain
| | - Paola Carrera
- Clinical Genomics, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Giorgio Casari
- Division of Genetics and Cell Biology, Genome-Phenome Relationship, San Raffaele Hospital, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Khalil Chaïbi
- Anesthesiology and Critical Care Medicine Department, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris, Bobigny, France
- Common and Rare Kidney Diseases, Sorbonne University, INSERM UMR-S 1155, Paris, France
| | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Genetics Department, Immunology Division, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Antonio Condino-Neto
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Laura E Covill
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Loubna El Zein
- Biology Department, Lebanese University, Beirut, Lebanon
| | - Carlos Flores
- Genomics Division, Institute of Technology and Renewable Energies (ITER), Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Carlos III Health Institute, Madrid, Spain
- Research Unit, University Hospital of Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Peter K Gregersen
- Feinstein Institute for Medical Research, Northwell Health USA, Manhasset, NY, USA
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Filomeen Haerynck
- Department of Internal Diseases and Pediatrics, Primary Immune Deficiency Research Laboratory, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent, Belgium
| | - Rabih Halwani
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Selda Hancerli
- Department of Pediatrics (Infectious Diseases), Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Nevin Hatipoğlu
- Pediatric Infectious Diseases Unit, Bakirkoy Dr Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Adem Karbuz
- Department of Pediatric Infectious Disease, Dr. Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Sevgi Keles
- Meram Medical Faculty, Division of Pediatric Allergy and Immunology, Necmettin Erbakan University, Konya, Turkey
| | - Christèle Kyheng
- Department of General Paediatrics, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Rafael Leon-Lopez
- Unidad de Gestión Clínica de Cuidados Intensivos, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), Córdoba, Spain
| | - Jose Luis Franco
- Primary Immunodeficiencies Group, School of Microbiology, University of Antioquia UdeA, Medellin, Colombia
| | - Davood Mansouri
- The Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Clinical Immunology and Infectious Diseases, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute and Institute for Health Science Research Germans Trias I Pujol (IGTP), Badalona, Spain
- Institute for Health Science Research Germans Trias I Pujol (IGTP), Badalona, Spain
- Department of Infectious Diseases and Immunity, University of Vic-Central University of Catalonia, Vic, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ozge Metin Akcan
- Meram Medical Faculty, Division of Pediatric Allergy and Immunology, Necmettin Erbakan University, Konya, Turkey
| | - Isabelle Migeotte
- Centre de Génétique Humaine de L'Université Libre de Bruxelles, Hôpital Erasme, Brussels, Belgium
| | - Pierre-Emmanuel Morange
- Laboratory of Haematology, La Timone Hospital, Marseille, France
- C2VN, INSERM, INRAE, Aix-Marseille University, Marseille, France
| | - Guillaume Morelle
- Department of General Paediatrics, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Andrea Martin-Nalda
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Figen Palabiyik
- Pediatric Infectious Diseases Unit, Bakirkoy Dr Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | | | - Rebeca Pérez de Diego
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, University Hospital "La Paz", Madrid, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Daniel E Pleguezuelo
- Immunology Department, University Hospital 12 de Octubre, Research Institute imas12 and Complutense University, Madrid, Spain
| | - Carolina Prando
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
| | - Aurora Pujol
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | | | - Jacques G Rivière
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Carlos Rodriguez-Gallego
- Department of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Department of Clinical Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Julian Rojas
- Primary Immunodeficiencies Group, School of Microbiology, University of Antioquia UdeA, Medellin, Colombia
| | - Patrizia Rovere-Querini
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Mohammad Shahrooei
- Specialized Immunology Laboratory of Dr Shahrooei, Sina Medical Complex, Ahvaz, Iran
- Department of Microbiology and Immunology, Clinical and Diagnostic Immunology, KU Leuven, Leuven, Belgium
| | - Ali Sobh
- Department of Pediatrics, Mansoura University Children's Hospital, Mansoura University Faculty of Medicine, Mansoura, Egypt
| | - Pere Soler-Palacin
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Yacine Tandjaoui-Lambiotte
- Hypoxia and Lung, INSERM U1272, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris, Bobigny, France
| | - Imran Tipu
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Cristina Tresoldi
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Jesus Troya
- Department of Internal Medicine, Infanta Leonor University Hospital, Madrid, Spain
| | - Diederik van de Beek
- Department of Neurology, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Mayana Zatz
- Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Pawel Zawadzki
- MNM Bioscience Inc, Cambridge, MA, USA
- Faculty of Physics, Adam Mickiewicz University, Poznan, Poland
| | - Saleh Zaid Al-Muhsen
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Faraj Alosaimi
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Fahad M Alsohime
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Hagit Baris-Feldman
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Manish J Butte
- Departments of Pediatrics and Microbiology, Immunology, and Molecular Genetics, Division of Immunology, Allergy, and Rheumatology, University of California Los Angeles, Los Angeles, CA, USA
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research, Brussels, Belgium
- SIGN Unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Brussels, Belgium
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, Oxford University, Oxford, UK
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Yu-Lung Lau
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Richard P Lifton
- Laboratory of Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
| | - Tom Maniatis
- Zukerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Horst von Bernuth
- Department of Paediatric Respiratory Medicine, Immunology, and Critical Care Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Alban Lermine
- Laboratoire de Biologie Médicale Multisites Seqoia, MG2025, MG2025, Paris, France
| | - Michel Vidaud
- Laboratoire de Biologie Médicale Multisites Seqoia, MG2025, MG2025, Paris, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | | | | | - France Mentre
- Unité de Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sarah Tubiana
- Centre d'Investigation Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Guy Gorochov
- Département d'immunologie, INSERM Centre d'Immunologie Et Des Maladies Infectieuses CIMI-Paris, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Florence Tubach
- Département de Santé Publique, Unité de Recherche Clinique PSL-CFX, CIC-1901, Institut Pierre Louis d'Epidémiologie Et de Santé Publique, INSERM, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France
- GRC-14 BIOFAST Sorbonn Université, UMR INSERM 1166, IHU ICAN, Sorbonne Université, Paris, France
| | - Isabelle Meyts
- Department of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Luigi D Notarangelo
- Laboratory of Host Defenses, NIAID, National Institutes of Health, Bethesda, MA, USA
| | - Stephanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Bertrand Boisson
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.
- University Paris Cité, Imagine Institute, Paris, France.
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.
- University Paris Cité, Imagine Institute, Paris, France.
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
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Bucciol G, Moens L, Ogishi M, Rinchai D, Matuozzo D, Momenilandi M, Kerrouche N, Cale CM, Treffeisen ER, Al Salamah M, Al-Saud BK, Lachaux A, Duclaux-Loras R, Meignien M, Bousfiha A, Benhsaien I, Shcherbina A, Roppelt A, Gothe F, Houhou-Fidouh N, Hackett SJ, Bartnikas LM, Maciag MC, Alosaimi MF, Chou J, Mohammed RW, Freij BJ, Jouanguy E, Zhang SY, Boisson-Dupuis S, Béziat V, Zhang Q, Duncan CJ, Hambleton S, Casanova JL, Meyts I. Human inherited complete STAT2 deficiency underlies inflammatory viral diseases. J Clin Invest 2023; 133:e168321. [PMID: 36976641 PMCID: PMC10266780 DOI: 10.1172/jci168321] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 12/22/2022] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
STAT2 is a transcription factor activated by type I and III IFNs. We report 23 patients with loss-of-function variants causing autosomal recessive (AR) complete STAT2 deficiency. Both cells transfected with mutant STAT2 alleles and the patients' cells displayed impaired expression of IFN-stimulated genes and impaired control of in vitro viral infections. Clinical manifestations from early childhood onward included severe adverse reaction to live attenuated viral vaccines (LAV) and severe viral infections, particularly critical influenza pneumonia, critical COVID-19 pneumonia, and herpes simplex virus type 1 (HSV-1) encephalitis. The patients displayed various types of hyperinflammation, often triggered by viral infection or after LAV administration, which probably attested to unresolved viral infection in the absence of STAT2-dependent types I and III IFN immunity. Transcriptomic analysis revealed that circulating monocytes, neutrophils, and CD8+ memory T cells contributed to this inflammation. Several patients died from viral infection or heart failure during a febrile illness with no identified etiology. Notably, the highest mortality occurred during early childhood. These findings show that AR complete STAT2 deficiency underlay severe viral diseases and substantially impacts survival.
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Affiliation(s)
- Giorgia Bucciol
- Laboratory of Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Leuven University Hospitals, Leuven, Belgium
| | - Leen Moens
- Laboratory of Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Daniela Matuozzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris Cité, Imagine Institute, Paris, France
| | - Mana Momenilandi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris Cité, Imagine Institute, Paris, France
| | - Nacim Kerrouche
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Catherine M. Cale
- Department of Immunology, Great Ormond Street Hospital, London, United Kingdom
| | - Elsa R. Treffeisen
- Division of Immunology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Mohammad Al Salamah
- King Abdullah Specialist Children’s Hospital and International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Ministry of the National Guard–Health Affairs, Riyadh, Saudi Arabia
| | - Bandar K. Al-Saud
- Pediatric Department, Section of Immunology and Allergy, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Alain Lachaux
- Gastroenterology, Hepatology and Nutrition Unit, University and Pediatric Hospital of Lyon, and Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Autophagy, Infection and Immunity, Lyon, France
| | - Remi Duclaux-Loras
- Gastroenterology, Hepatology and Nutrition Unit, University and Pediatric Hospital of Lyon, and Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Autophagy, Infection and Immunity, Lyon, France
| | - Marie Meignien
- Internal Medicine and Vascular Pathology Service, University Hospital of Lyon, Lyon, France
| | - Aziz Bousfiha
- Clinical Immunology, Inflammation and Allergy Laboratory (LICIA), Faculty of Medicine and Pharmacy, King Hassan II University, Casablanca, Morocco
- Clinical Immunology Unit, Pediatric Infectious Disease Department Children’s Hospital, Ibn Rochd University Hospital, Casablanca, Morocco
| | - Ibtihal Benhsaien
- Clinical Immunology, Inflammation and Allergy Laboratory (LICIA), Faculty of Medicine and Pharmacy, King Hassan II University, Casablanca, Morocco
- Clinical Immunology Unit, Pediatric Infectious Disease Department Children’s Hospital, Ibn Rochd University Hospital, Casablanca, Morocco
| | - Anna Shcherbina
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna Roppelt
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | | | - Florian Gothe
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Nadhira Houhou-Fidouh
- Department of Virology, INSERM, Infection, Antimicrobiens, Modélisation, Evolution, UMR 1137, Bichat–Claude Bernard Hospital, University of Paris, Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Scott J. Hackett
- Department of Paediatrics, Birmingham Chest Clinic and Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Lisa M. Bartnikas
- Division of Immunology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Michelle C. Maciag
- Division of Immunology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Mohammed F. Alosaimi
- Immunology Research Laboratory, Department of Pediatrics, King Saud University, Riyadh, Saudi Arabia
| | - Janet Chou
- Division of Immunology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Reem W. Mohammed
- Pediatric Department, Section of Immunology and Allergy, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Bishara J. Freij
- Pediatric Infectious Diseases Section, Beaumont Children’s Hospital, Royal Oak, Michigan, USA
- Oakland University William Beaumont School of Medicine, Rochester, Michigan, USA
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris Cité, Imagine Institute, Paris, France
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris Cité, Imagine Institute, Paris, France
| | - Stephanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris Cité, Imagine Institute, Paris, France
| | - Vivien Béziat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris Cité, Imagine Institute, Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris Cité, Imagine Institute, Paris, France
| | - Christopher J.A. Duncan
- The COVID Human Genetic Effort is detailed in Supplemental Acknowledgments
- Department of Infectious Disease and Tropical Medicine, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom, and
| | - Sophie Hambleton
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, United Kingdom
- Great North Children’s Hospital, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris Cité, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Assistance Publique–Hôpitaux de Paris, Paris, France
- Howard Hughes Medical Institute, New York, New York, USA
| | - Isabelle Meyts
- Laboratory of Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Leuven University Hospitals, Leuven, Belgium
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3
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Liu Z, Garcia Reino EJ, Harschnitz O, Guo H, Chan YH, Khobrekar NV, Hasek ML, Dobbs K, Rinchai D, Materna M, Matuozzo D, Lee D, Bastard P, Chen J, Lee YS, Kim SK, Zhao S, Amin P, Lorenzo L, Seeleuthner Y, Chevalier R, Mazzola L, Gay C, Stephan JL, Milisavljevic B, Boucherit S, Rozenberg F, Perez de Diego R, Dix RD, Marr N, Béziat V, Cobat A, Aubart M, Abel L, Chabrier S, Smith GA, Notarangelo LD, Mocarski ES, Studer L, Casanova JL, Zhang SY. Encephalitis and poor neuronal death-mediated control of herpes simplex virus in human inherited RIPK3 deficiency. Sci Immunol 2023; 8:eade2860. [PMID: 37083451 PMCID: PMC10337828 DOI: 10.1126/sciimmunol.ade2860] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 03/30/2023] [Indexed: 04/22/2023]
Abstract
Inborn errors of TLR3-dependent type I IFN immunity in cortical neurons underlie forebrain herpes simplex virus-1 (HSV-1) encephalitis (HSE) due to uncontrolled viral growth and subsequent cell death. We report an otherwise healthy patient with HSE who was compound heterozygous for nonsense (R422*) and frameshift (P493fs9*) RIPK3 variants. Receptor-interacting protein kinase 3 (RIPK3) is a ubiquitous cytoplasmic kinase regulating cell death outcomes, including apoptosis and necroptosis. In vitro, the R422* and P493fs9* RIPK3 proteins impaired cellular apoptosis and necroptosis upon TLR3, TLR4, or TNFR1 stimulation and ZBP1/DAI-mediated necroptotic cell death after HSV-1 infection. The patient's fibroblasts displayed no detectable RIPK3 expression. After TNFR1 or TLR3 stimulation, the patient's cells did not undergo apoptosis or necroptosis. After HSV-1 infection, the cells supported excessive viral growth despite normal induction of antiviral IFN-β and IFN-stimulated genes (ISGs). This phenotype was, nevertheless, rescued by application of exogenous type I IFN. The patient's human pluripotent stem cell (hPSC)-derived cortical neurons displayed impaired cell death and enhanced viral growth after HSV-1 infection, as did isogenic RIPK3-knockout hPSC-derived cortical neurons. Inherited RIPK3 deficiency therefore confers a predisposition to HSE by impairing the cell death-dependent control of HSV-1 in cortical neurons but not their production of or response to type I IFNs.
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Affiliation(s)
- Zhiyong Liu
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Eduardo J Garcia Reino
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Oliver Harschnitz
- The Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY, USA
- Human Technopole, Viale Rita Levi-Montalcini, Milan, Italy
| | - Hongyan Guo
- Department of Microbiology and Immunology, Emory Vaccine Center, Emory University, GA, USA
- School of Medicine, Atlanta, GA, USA
- Louisiana State University Health Sciences Center at Shreveport (LSUHSC-S), Shreveport, LA, USA
| | - Yi-Hao Chan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Noopur V Khobrekar
- The Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | - Mary L Hasek
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Marie Materna
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Daniela Matuozzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Danyel Lee
- 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
- Paris City University, 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
- Paris City University, Imagine Institute, Paris, France
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Jie Chen
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Yoon Seung Lee
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | | | - Shuxiang Zhao
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Param Amin
- The Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Remi Chevalier
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Laure Mazzola
- Department of Pediatrics, Hôpital Nord, Saint-Etienne, Paris, France
| | - Claire Gay
- Department of Pediatrics, Hôpital Nord, Saint-Etienne, Paris, France
| | | | - Baptiste Milisavljevic
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Soraya Boucherit
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Flore Rozenberg
- Laboratory of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Cochin Hospital, Paris, France
| | - Rebeca Perez de Diego
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, La Paz Hospital, Madrid, Spain
- Innate Immunity Group, IdiPAZ Institute for Health Research, La Paz Hospital, Madrid, Spain
- Interdepartmental Group of Immunodeficiencies, Madrid, Spain
| | - Richard D Dix
- Viral Immunology Center, Department of Biology, Georgia State University, Atlanta, GA, USA
- Department of Ophthalmology, Emory University School of Medicine, Atlanta, GA, USA
| | - Nico Marr
- Research Branch, Sidra Medicine, Doha, Qatar
- Institute of Translational Immunology, Brandenburg Medical School, Brandenburg an der Havel, Germany
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Vivien Béziat
- 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
- Paris City University, Imagine Institute, Paris, France
| | - Aurelie Cobat
- 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
- Paris City University, Imagine Institute, Paris, France
| | - Mélodie Aubart
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Pediatric Neurology Department, Necker Hospital for Sick Children, APHP, Paris City University, 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
- Paris City University, Imagine Institute, Paris, France
| | - Stephane Chabrier
- Department of Pediatrics, Hôpital Nord, Saint-Etienne, Paris, France
| | - Gregory A Smith
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Edward S Mocarski
- Department of Microbiology and Immunology, Emory Vaccine Center, Emory University, GA, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | - 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
- Paris City University, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Shen-Ying 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
- Paris City University, Imagine Institute, Paris, France
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4
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Matuozzo D, Talouarn E, Marchal A, Zhang P, Manry J, Seeleuthner Y, Zhang Y, Bolze A, Chaldebas M, Milisavljevic B, Gervais A, Bastard P, Asano T, Bizien L, Barzaghi F, Abolhassani H, Abou Tayoun A, Aiuti A, Alavi Darazam I, Allende LM, Alonso-Arias R, Arias AA, Aytekin G, Bergman P, Bondesan S, Bryceson YT, Bustos IG, Cabrera-Marante O, Carcel S, Carrera P, Casari G, Chaïbi K, Colobran R, Condino-Neto A, Covill LE, Delmonte OM, El Zein L, Flores C, Gregersen PK, Gut M, Haerynck F, Halwani R, Hancerli S, Hammarström L, Hatipoğlu N, Karbuz A, Keles S, Kyheng C, Leon-Lopez R, Franco JL, Mansouri D, Martinez-Picado J, Metin Akcan O, Migeotte I, Morange PE, Morelle G, Martin-Nalda A, Novelli G, Novelli A, Ozcelik T, Palabiyik F, Pan-Hammarström Q, de Diego RP, Planas-Serra L, Pleguezuelo DE, Prando C, Pujol A, Reyes LF, Rivière JG, Rodriguez-Gallego C, Rojas J, Rovere-Querini P, Schlüter A, Shahrooei M, Sobh A, Soler-Palacin P, Tandjaoui-Lambiotte Y, Tipu I, Tresoldi C, Troya J, van de Beek D, Zatz M, Zawadzki P, Al-Muhsen SZ, Alosaimi MF, Alsohime FM, Baris-Feldman H, Butte MJ, Constantinescu SN, Cooper MA, Dalgard CL, Fellay J, Heath JR, Lau YL, Lifton RP, Maniatis T, Mogensen TH, von Bernuth H, Lermine A, Vidaud M, Boland A, Deleuze JF, Nussbaum R, Kahn-Kirby A, Mentre F, Tubiana S, Gorochov G, Tubach F, Hausfater P, Meyts I, Zhang SY, Puel A, Notarangelo LD, Boisson-Dupuis S, Su HC, Boisson B, Jouanguy E, Casanova JL, Zhang Q, Abel L, Cobat A. Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19. Genome Med 2023; 15:22. [PMID: 37020259 PMCID: PMC10074346 DOI: 10.1186/s13073-023-01173-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [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: 09/15/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases. METHODS We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded. RESULTS No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P = 1.1 × 10-4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3-8.2], P = 2.1 × 10-4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1-2635.4], P = 3.4 × 10-3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3-8.4], P = 7.7 × 10-8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10-5). CONCLUSIONS Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.
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Affiliation(s)
- Daniela Matuozzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Estelle Talouarn
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jeremy Manry
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | | | - Matthieu Chaldebas
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Baptiste Milisavljevic
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Takaki Asano
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Federica Barzaghi
- Department of Paediatric Immunohematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran, Iran
| | - Ahmad Abou Tayoun
- Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Ilad Alavi Darazam
- Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Infectious Diseases and Tropical Medicine, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Luis M Allende
- Immunology Department, University Hospital 12 de Octubre, Research Institute imas12 and Complutense University, Madrid, Spain
| | - Rebeca Alonso-Arias
- Immunology Department, Hospital Universitario Central de Asturias; Health Research Institute of Principality of Asturias, Oviedo, Spain
| | - Andrés Augusto Arias
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Department of Microbiology and Parasitology, Primary Immunodeficiencies Group, School of Medicine, University of Antioquia UdeA, 050010, Medellin, Colombia
- School of Microbiology, University of Antioquia UdeA, 050010, Medellin, Colombia
| | - Gokhan Aytekin
- Deparment of Internal Medicine, Division of Allergy and Immunology, Konya City Hospital, Konya, Turkey
| | - Peter Bergman
- Department of Infectious Diseases, The Immunodeficiency Unit, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Clinical Immunology, Stockholm, Sweden
| | - Simone Bondesan
- Clinical Genomics, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Yenan T Bryceson
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | | | - Oscar Cabrera-Marante
- Institute of Biomedical Research of IdiPAZ, University Hospital "La Paz", Madrid, Spain
| | - Sheila Carcel
- Unidad de Gestión Clínica de Cuidados Intensivos, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), Córdoba, Spain
| | - Paola Carrera
- Clinical Genomics, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Giorgio Casari
- Division of Genetics and Cell Biology, Genome-Phenome Relationship, San Raffaele Hospital, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Khalil Chaïbi
- Intensive Care Unit Department, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris, Bobigny, France
- Common and Rare Kidney Diseases, Sorbonne University, INSERM UMR-S 1155, Paris, France
| | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Genetics Department, Immunology Division, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Antonio Condino-Neto
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Laura E Covill
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Loubna El Zein
- Biology Department, Lebanese University, Beirut, Lebanon
| | - Carlos Flores
- Genomics Division, Institute of Technology and Renewable Energies (ITER), Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Carlos III Health Institute, Madrid, Spain
- Research Unit, University Hospital of Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Peter K Gregersen
- Feinstein Institute for Medical Research, Northwell Health USA, Manhasset, NY, USA
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Filomeen Haerynck
- Department of Internal Diseases and Pediatrics, Primary Immune Deficiency Research Laboratory, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent, Belgium
| | - Rabih Halwani
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Selda Hancerli
- Department of Pediatrics (Infectious Diseases), Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Nevin Hatipoğlu
- Pediatric Infectious Diseases Unit, Bakirkoy Dr Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Adem Karbuz
- Department of Pediatric Infectious Disease, Dr. Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Sevgi Keles
- Meram Medical Faculty, Pediatric Infectious Diseases Department, Necmettin Erbakan University, Konya, Turkey
| | - Christèle Kyheng
- Department of General Paediatrics, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Rafael Leon-Lopez
- Unidad de Gestión Clínica de Cuidados Intensivos, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), Córdoba, Spain
| | - Jose Luis Franco
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia UDEA, Medellin, 050010, Colombia
| | - Davood Mansouri
- The Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Clinical Immunology and Infectious Diseases, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute and Institute for Health Science Research Germans Trias I Pujol (IGTP), Badalona, Spain
- Institute for Health Science Research Germans Trias I Pujol (IGTP), Badalona, Spain
- Department of Infectious Diseases and Immunity, University of Vic-Central University of Catalonia, Vic, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ozge Metin Akcan
- Meram Medical Faculty, Pediatric Infectious Diseases Department, Necmettin Erbakan University, Konya, Turkey
| | - Isabelle Migeotte
- Centre de Génétique Humaine de L'Université Libre de Bruxelles, Hôpital Erasme, Brussels, Belgium
| | - Pierre-Emmanuel Morange
- Laboratory of Haematology, La Timone Hospital, Marseille, France
- C2VN, INSERM, INRAE, Aix-Marseille University, Marseille, France
| | - Guillaume Morelle
- Department of General Paediatrics, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Andrea Martin-Nalda
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection and Immunity in Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Figen Palabiyik
- Pediatric Infectious Diseases Unit, Bakirkoy Dr Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | | | - Rebeca Pérez de Diego
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, University Hospital "La Paz", Madrid, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Daniel E Pleguezuelo
- Immunology Department, University Hospital 12 de Octubre, Research Institute imas12 and Complutense University, Madrid, Spain
| | - Carolina Prando
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
| | - Aurora Pujol
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | | | - Jacques G Rivière
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection and Immunity in Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Carlos Rodriguez-Gallego
- Department of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Department of Clinical Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Julian Rojas
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia UDEA, Medellin, 050010, Colombia
| | - Patrizia Rovere-Querini
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Mohammad Shahrooei
- Specialized Immunology Laboratory of Dr Shahrooei, Sina Medical Complex, Ahvaz, Iran
- Department of Microbiology and Immunology, Clinical and Diagnostic Immunology, KU Leuven, Leuven, Belgium
| | - Ali Sobh
- Department of Pediatrics, Mansoura University Children's Hospital, Mansoura University Faculty of Medicine, Mansoura, Egypt
| | - Pere Soler-Palacin
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection and Immunity in Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Yacine Tandjaoui-Lambiotte
- Hypoxia and Lung, INSERM U1272, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris, Bobigny, France
| | - Imran Tipu
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Cristina Tresoldi
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Jesus Troya
- Department of Internal Medicine, Infanta Leonor University Hospital, Madrid, Spain
| | - Diederik van de Beek
- Department of Neurology, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Mayana Zatz
- Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Pawel Zawadzki
- Gordion Bioscience Inc, Cambridge, MA, USA
- Faculty of Physics, Adam Mickiewicz University, Poznan, Poland
| | - Saleh Zaid Al-Muhsen
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Faraj Alosaimi
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Fahad M Alsohime
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Hagit Baris-Feldman
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Manish J Butte
- Departments of Pediatrics and Microbiology, Immunology, and Molecular Genetics, Division of Immunology, Allergy, and Rheumatology, University of California Los Angeles, Los Angeles, CA, USA
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research, Brussels, Belgium
- SIGN Unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Brussels, Belgium
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, Oxford University, Oxford, UK
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Yu-Lung Lau
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Richard P Lifton
- Laboratory of Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
| | - Tom Maniatis
- Zukerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Horst von Bernuth
- Department of Paediatric Respiratory Medicine, Immunology, and Critical Care Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Alban Lermine
- Laboratoire de Biologie Médicale Multisites Seqoia, MG2025, MG2025, Paris, France
| | - Michel Vidaud
- Laboratoire de Biologie Médicale Multisites Seqoia, MG2025, MG2025, Paris, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | | | | | - France Mentre
- Unité de Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sarah Tubiana
- Centre d'Investigation Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Guy Gorochov
- Sorbonne Université, INSERM Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Département d'immunologie Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Florence Tubach
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié Salpêtrière, Département de Santé Publique, Unité de Recherche Clinique PSL-CFX , CIC-1901, Paris, France
| | - Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France
- GRC-14 BIOFAST Sorbonn Université, UMR INSERM 1135, CIMI, Sorbonne Université, Paris, France
| | - Isabelle Meyts
- Department of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Luigi D Notarangelo
- Laboratory of Host Defenses, NIAID, National Institutes of Health, Bethesda, MA, USA
| | - Stephanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Bertrand Boisson
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.
- University Paris Cité, Imagine Institute, Paris, France.
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.
- University Paris Cité, Imagine Institute, Paris, France.
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
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5
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Matuozzo D, Talouarn E, Marchal A, Manry J, Seeleuthner Y, Zhang Y, Bolze A, Chaldebas M, Milisavljevic B, Zhang P, Gervais A, Bastard P, Asano T, Bizien L, Barzaghi F, Abolhassani H, Tayoun AA, Aiuti A, Darazam IA, Allende LM, Alonso-Arias R, Arias AA, Aytekin G, Bergman P, Bondesan S, Bryceson YT, Bustos IG, Cabrera-Marante O, Carcel S, Carrera P, Casari G, Chaïbi K, Colobran R, Condino-Neto A, Covill LE, El Zein L, Flores C, Gregersen PK, Gut M, Haerynck F, Halwani R, Hancerli S, Hammarström L, Hatipoğlu N, Karbuz A, Keles S, Kyheng C, Leon-Lopez R, Franco JL, Mansouri D, Martinez-Picado J, Akcan OM, Migeotte I, Morange PE, Morelle G, Martin-Nalda A, Novelli G, Novelli A, Ozcelik T, Palabiyik F, Pan-Hammarström Q, Pérez de Diego R, Planas-Serra L, Pleguezuelo DE, Prando C, Pujol A, Reyes LF, Rivière JG, Rodriguez-Gallego C, Rojas J, Rovere-Querini P, Schlüter A, Shahrooei M, Sobh A, Soler-Palacin P, Tandjaoui-Lambiotte Y, Tipu I, Tresoldi C, Troya J, van de Beek D, Zatz M, Zawadzki P, Al-Muhsen SZ, Baris-Feldman H, Butte MJ, Constantinescu SN, Cooper MA, Dalgard CL, Fellay J, Heath JR, Lau YL, Lifton RP, Maniatis T, Mogensen TH, von Bernuth H, Lermine A, Vidaud M, Boland A, Deleuze JF, Nussbaum R, Kahn-Kirby A, Mentre F, Tubiana S, Gorochov G, Tubach F, Hausfater P, Meyts I, Zhang SY, Puel A, Notarangelo LD, Boisson-Dupuis S, Su HC, Boisson B, Jouanguy E, Casanova JL, Zhang Q, Abel L, Cobat A. Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19. medRxiv 2022:2022.10.22.22281221. [PMID: 36324795 PMCID: PMC9628204 DOI: 10.1101/2022.10.22.22281221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Background We previously reported inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity in 1-5% of unvaccinated patients with life-threatening COVID-19, and auto-antibodies against type I IFN in another 15-20% of cases. Methods We report here a genome-wide rare variant burden association analysis in 3,269 unvaccinated patients with life-threatening COVID-19 (1,301 previously reported and 1,968 new patients), and 1,373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. A quarter of the patients tested had antibodies against type I IFN (234 of 928) and were excluded from the analysis. Results No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7 , with an OR of 27.68 (95%CI:1.5-528.7, P= 1.1×10 -4 ), in analyses restricted to biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR=3.70 [95%CI:1.3-8.2], P= 2.1×10 -4 ). Adding the recently reported TYK2 COVID-19 locus strengthened this enrichment, particularly under a recessive model (OR=19.65 [95%CI:2.1-2635.4]; P= 3.4×10 -3 ). When these 14 loci and TLR7 were considered, all individuals hemizygous ( n =20) or homozygous ( n =5) for pLOF or bLOF variants were patients (OR=39.19 [95%CI:5.2-5037.0], P =4.7×10 -7 ), who also showed an enrichment in heterozygous variants (OR=2.36 [95%CI:1.0-5.9], P =0.02). Finally, the patients with pLOF or bLOF variants at these 15 loci were significantly younger (mean age [SD]=43.3 [20.3] years) than the other patients (56.0 [17.3] years; P= 1.68×10 -5 ). Conclusions Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.
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6
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Zhang Q, Matuozzo D, Le Pen J, Lee D, Moens L, Asano T, Bohlen J, Liu Z, Moncada-Velez M, Kendir-Demirkol Y, Jing H, Bizien L, Marchal A, Abolhassani H, Delafontaine S, Bucciol G, Bayhan GI, Keles S, Kiykim A, Hancerli S, Haerynck F, Florkin B, Hatipoglu N, Ozcelik T, Morelle G, Zatz M, Ng LF, Lye DC, Young BE, Leo YS, Dalgard CL, Lifton RP, Renia L, Meyts I, Jouanguy E, Hammarström L, Pan-Hammarström Q, Boisson B, Bastard P, Su HC, Boisson-Dupuis S, Abel L, Rice CM, Zhang SY, Cobat A, Casanova JL. Recessive inborn errors of type I IFN immunity in children with COVID-19 pneumonia. J Exp Med 2022; 219:213287. [PMID: 35708626 PMCID: PMC9206114 DOI: 10.1084/jem.20220131] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [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: 01/23/2022] [Revised: 05/01/2022] [Accepted: 05/24/2022] [Indexed: 12/16/2022] Open
Abstract
Recessive or dominant inborn errors of type I interferon (IFN) immunity can underlie critical COVID-19 pneumonia in unvaccinated adults. The risk of COVID-19 pneumonia in unvaccinated children, which is much lower than in unvaccinated adults, remains unexplained. In an international cohort of 112 children (<16 yr old) hospitalized for COVID-19 pneumonia, we report 12 children (10.7%) aged 1.5-13 yr with critical (7 children), severe (3), and moderate (2) pneumonia and 4 of the 15 known clinically recessive and biochemically complete inborn errors of type I IFN immunity: X-linked recessive TLR7 deficiency (7 children) and autosomal recessive IFNAR1 (1), STAT2 (1), or TYK2 (3) deficiencies. Fibroblasts deficient for IFNAR1, STAT2, or TYK2 are highly vulnerable to SARS-CoV-2. These 15 deficiencies were not found in 1,224 children and adults with benign SARS-CoV-2 infection without pneumonia (P = 1.2 × 10-11) and with overlapping age, sex, consanguinity, and ethnicity characteristics. Recessive complete deficiencies of type I IFN immunity may underlie ∼10% of hospitalizations for COVID-19 pneumonia in children.
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Affiliation(s)
- Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Daniela Matuozzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Jérémie Le Pen
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY
| | - Danyel Lee
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Leen Moens
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY
| | - Takaki Asano
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Jonathan Bohlen
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Zhiyong Liu
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Marcela Moncada-Velez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Yasemin Kendir-Demirkol
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Huie Jing
- Laboratory of Clinical Immunology and Microbiology, Intramural Research Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Selket Delafontaine
- Laboratory for Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Giorgia Bucciol
- Laboratory for Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | | | | | - Sevgi Keles
- Necmettin Erbakan University, Meram Medical Faculty, Division of Pediatric Allergy and Immunology, Konya, Turkey
| | - Ayca Kiykim
- Istanbul University-Cerrahpasa, Pediatric Allergy and Immunology, Istanbul, Turkey
| | - Selda Hancerli
- Department of Pediatrics (Infectious Diseases), Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Filomeen Haerynck
- Department of Pediatric Immunology and Pulmonology, Department of Internal Medicine and Pediatrics, Centre for Primary Immunodeficiency Ghent, PID Research Laboratory, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
| | - Benoit Florkin
- Department of Pediatrics, Hôpital de la Citadelle, Liége, Belgium
| | - Nevin Hatipoglu
- Pediatric Infectious Diseases Unit, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Bilkent-Ankara, Turkey
| | - Guillaume Morelle
- Department of General Pediatrics, Bicêtre Hospital, Assistance Publique – Hôpitaux de Paris, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Mayana Zatz
- Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Lisa F.P. Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Richard P. Lifton
- Laboratory of Genetics and Genomics, The Rockefeller University, New York, NY
- Department of Genetics, Yale University School of Medicine, New Haven, CT
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Isabelle Meyts
- Laboratory for Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | | | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Paul Bastard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Helen C. Su
- Laboratory of Clinical Immunology and Microbiology, Intramural Research Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Charles M. Rice
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Aurélie Cobat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, 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
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7
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O'Neill MB, Quach H, Pothlichet J, Aquino Y, Bisiaux A, Zidane N, Deschamps M, Libri V, Hasan M, Zhang SY, Zhang Q, Matuozzo D, Cobat A, Abel L, Casanova JL, Naffakh N, Rotival M, Quintana-Murci L. Single-Cell and Bulk RNA-Sequencing Reveal Differences in Monocyte Susceptibility to Influenza A Virus Infection Between Africans and Europeans. Front Immunol 2021; 12:768189. [PMID: 34912340 PMCID: PMC8667309 DOI: 10.3389/fimmu.2021.768189] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/27/2021] [Indexed: 01/02/2023] Open
Abstract
There is considerable inter-individual and inter-population variability in response to viruses. The potential of monocytes to elicit type-I interferon responses has attracted attention to their role in viral infections. Here, we use single-cell RNA-sequencing to characterize the role of cellular heterogeneity in human variation of monocyte responses to influenza A virus (IAV) exposure. We show widespread inter-individual variability in the percentage of IAV-infected monocytes. Notably, individuals with high cellular susceptibility to IAV are characterized by a lower activation at basal state of an IRF/STAT-induced transcriptional network, which includes antiviral genes such as IFITM3, MX1 and OAS3. Upon IAV challenge, we find that cells escaping viral infection display increased mRNA expression of type-I interferon stimulated genes and decreased expression of ribosomal genes, relative to both infected cells and those never exposed to IAV. We also uncover a stronger resistance of CD16+ monocytes to IAV infection, together with CD16+ -specific mRNA expression of IL6 and TNF in response to IAV. Finally, using flow cytometry and bulk RNA-sequencing across 200 individuals of African and European ancestry, we observe a higher number of CD16 + monocytes and lower susceptibility to IAV infection among monocytes from individuals of African-descent. Based on these data, we hypothesize that higher basal monocyte activation, driven by environmental factors and/or weak-effect genetic variants, underlies the lower cellular susceptibility to IAV infection of individuals of African ancestry relative to those of European ancestry. Further studies are now required to investigate how such cellular differences in IAV susceptibility translate into population differences in clinical outcomes and susceptibility to severe influenza.
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Affiliation(s)
- Mary B O'Neill
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Hélène Quach
- Muséum National d'Histoire Naturelle, UMR7206, Centre National de la Recherche Scientifique (CNRS), Université de Paris, Paris, France
| | | | - Yann Aquino
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, Centre National de la Recherche Scientifique (CNRS), Paris, France.,Sorbonne Université, Collège doctoral, Paris, France
| | - Aurélie Bisiaux
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Nora Zidane
- Biodiversity and Epidemiology of Bacterial Pathogens Unit, Institut Pasteur, Paris, France
| | - Matthieu Deschamps
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Valentina Libri
- Cytometry and Biomarkers UTechS, Institut Pasteur, Paris, France
| | - Milena Hasan
- Cytometry and Biomarkers UTechS, Institut Pasteur, Paris, France
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, United States.,Laboratory of Human Genetics of Infectious Diseases, Necker Hospital for Sick Children, INSERM UMR 1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris University, Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, United States.,Laboratory of Human Genetics of Infectious Diseases, Necker Hospital for Sick Children, INSERM UMR 1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris University, Paris, France
| | - Daniela Matuozzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Hospital for Sick Children, INSERM UMR 1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris University, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Hospital for Sick Children, INSERM UMR 1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris University, Paris, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, United States.,Laboratory of Human Genetics of Infectious Diseases, Necker Hospital for Sick Children, INSERM UMR 1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris University, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, United States.,Laboratory of Human Genetics of Infectious Diseases, Necker Hospital for Sick Children, INSERM UMR 1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris University, Paris, France.,Howard Hughes Medical Institute, New York, NY, United States
| | - Nadia Naffakh
- RNA Biology of Influenza Virus Unit, Institut Pasteur, Paris, France
| | - Maxime Rotival
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, Centre National de la Recherche Scientifique (CNRS), Paris, France.,Chair of Human Genomics and Evolution, Collège de France, Paris, France
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8
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Asano T, Boisson B, Onodi F, Matuozzo D, Moncada-Velez M, Maglorius Renkilaraj MRL, Zhang P, Meertens L, Bolze A, Materna M, Korniotis S, Gervais A, Talouarn E, Bigio B, Seeleuthner Y, Bilguvar K, Zhang Y, Neehus AL, Ogishi M, Pelham SJ, Le Voyer T, Rosain J, Philippot Q, Soler-Palacín P, Colobran R, Martin-Nalda A, Rivière JG, Tandjaoui-Lambiotte Y, Chaïbi K, Shahrooei M, Darazam IA, Olyaei NA, Mansouri D, Hatipoğlu N, Palabiyik F, Ozcelik T, Novelli G, Novelli A, Casari G, Aiuti A, Carrera P, Bondesan S, Barzaghi F, Rovere-Querini P, Tresoldi C, Franco JL, Rojas J, Reyes LF, Bustos IG, Arias AA, Morelle G, Christèle K, Troya J, Planas-Serra L, Schlüter A, Gut M, Pujol A, Allende LM, Rodriguez-Gallego C, Flores C, Cabrera-Marante O, Pleguezuelo DE, de Diego RP, Keles S, Aytekin G, Akcan OM, Bryceson YT, Bergman P, Brodin P, Smole D, Smith CIE, Norlin AC, Campbell TM, Covill LE, Hammarström L, Pan-Hammarström Q, Abolhassani H, Mane S, Marr N, Ata M, Al Ali F, Khan T, Spaan AN, Dalgard CL, Bonfanti P, Biondi A, Tubiana S, Burdet C, Nussbaum R, Kahn-Kirby A, Snow AL, Bustamante J, Puel A, Boisson-Dupuis S, Zhang SY, Béziat V, Lifton RP, Bastard P, Notarangelo LD, Abel L, Su HC, Jouanguy E, Amara A, Soumelis V, Cobat A, Zhang Q, Casanova JL. X-linked recessive TLR7 deficiency in ~1% of men under 60 years old with life-threatening COVID-19. Sci Immunol 2021; 6:eabl4348. [PMID: 34413140 PMCID: PMC8532080 DOI: 10.1126/sciimmunol.abl4348] [Citation(s) in RCA: 233] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/12/2021] [Indexed: 01/16/2023]
Abstract
Autosomal inborn errors of type I IFN immunity and autoantibodies against these cytokines underlie at least 10% of critical COVID-19 pneumonia cases. We report very rare, biochemically deleterious X-linked TLR7 variants in 16 unrelated male individuals aged 7 to 71 years (mean: 36.7 years) from a cohort of 1,202 male patients aged 0.5 to 99 years (mean: 52.9 years) with unexplained critical COVID-19 pneumonia. None of the 331 asymptomatically or mildly infected male individuals aged 1.3 to 102 years (mean: 38.7 years) tested carry such TLR7 variants (p = 3.5 × 10-5). The phenotypes of five hemizygous relatives of index cases infected with SARS-CoV-2 include asymptomatic or mild infection (n=2, 5 and 38 years), or moderate (n=1, 5 years), severe (n=1, 27 years), or critical (n=1, 29 years) pneumonia. Two boys (aged 7 and 12 years) from a cohort of 262 male patients with severe COVID-19 pneumonia (mean: 51.0 years) are hemizygous for a deleterious TLR7 variant. The cumulative allele frequency for deleterious TLR7 variants in the male general population is < 6.5x10-4 We also show that blood B cell lines and myeloid cell subsets from the patients do not respond to TLR7 stimulation, a phenotype rescued by wild-type TLR7 The patients' blood plasmacytoid dendritic cells (pDCs) produce low levels of type I IFNs in response to SARS-CoV-2. Overall, X-linked recessive TLR7 deficiency is a highly penetrant genetic etiology of critical COVID-19 pneumonia, in about 1.8% of male patients below the age of 60 years. Human TLR7 and pDCs are essential for protective type I IFN immunity against SARS-CoV-2 in the respiratory tract.
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Affiliation(s)
- Takaki Asano
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The 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 of Paris, Imagine Institute, Paris, France
| | - Fanny Onodi
- Laboratory of Genomes & Cell Biology of Disease, INSERM U944, CNRS UMR7212, University of Paris, Research Institute of Saint-Louis, Saint-Louis Hospital, Paris, France
| | - Daniela Matuozzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Marcela Moncada-Velez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Majistor Raj Luxman Maglorius Renkilaraj
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Laurent Meertens
- Laboratory of Genomes & Cell Biology of Disease, INSERM U944, CNRS UMR7212, University of Paris, Research Institute of Saint-Louis, Saint-Louis Hospital, Paris, France
| | | | - Marie Materna
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | | | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Estelle Talouarn
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Kaya Bilguvar
- Yale Center for Genome Analysis and Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Anna-Lena Neehus
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Simon J Pelham
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Tom Le Voyer
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Pere Soler-Palacín
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
| | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Diagnostic Immunology Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Immunology Division, Genetics Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Andrea Martin-Nalda
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
| | - Jacques G Rivière
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
| | - Yacine Tandjaoui-Lambiotte
- AP-HP, Avicenne Hospital, Intensive Care Unit, Bobigny, France
- INSERM U1272 Hypoxia & Lung, Bobigny, France
| | - Khalil Chaïbi
- Anesthesiology and Critical Care Medicine Department, APHP, Avicenne Hospital, Bobigny, France
- Common and Rare Kidney Diseases, Sorbonne University, INSERM UMR-S 1155, Paris, France
| | - Mohammad Shahrooei
- Specialized Immunology Laboratory of Dr. Shahrooei, Sina Medical Complex, Ahvaz, Iran
- Department of Microbiology and Immunology, Clinical and Diagnostic Immunology, KU Leuven, Leuven, Belgium
| | - Ilad Alavi Darazam
- Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Infectious Diseases and Tropical Medicine, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nasrin Alipour Olyaei
- Specialized Immunology Laboratory of Dr. Shahrooei, Sina Medical Complex, Ahvaz, Iran
- Department of Microbiology and Immunology, Clinical and Diagnostic Immunology, KU Leuven, Leuven, Belgium
| | - Davood Mansouri
- Department of Clinical Immunology and Infectious Diseases, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- The Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Shahid Beheshti, University of Medical Sciences, Tehran, Iran
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti, Iran
| | - Nevin Hatipoğlu
- Pediatric Infectious Diseases Unit, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Figen Palabiyik
- Pediatric Infectious Diseases Unit, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, University of Bilkent, Bilkent-Ankara, Turkey
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata," Rome, and Neuromed Institute, IRCCS, Pozzilli (IS), Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Giorgio Casari
- Vita-Salute San Raffaele University, Milan, Italy
- Clinical Genomics, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Aiuti
- Vita-Salute San Raffaele University, Milan, Italy
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) and Pediatric Immunohematology Unit and BMT Program, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paola Carrera
- Clinical Genomics, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Simone Bondesan
- Clinical Genomics, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Barzaghi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) and Pediatric Immunohematology Unit and BMT Program, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Patrizia Rovere-Querini
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Cristina Tresoldi
- Molecular Hematology Unit, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Jose Luis Franco
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia, Medellín, Colombia
| | - Julian Rojas
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia, Medellín, Colombia
| | | | | | - Andres Augusto Arias
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia, Medellín, Colombia
- School of Microbiology, University of Antioquia UdeA, Medellín, Colombia
| | - Guillaume Morelle
- Department of General Pediatrics, Hôpital Bicêtre, AP-HP, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Kyheng Christèle
- Department of General Pediatrics, Hôpital Bicêtre, AP-HP, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Jesús Troya
- Department of Internal Medicine, Infanta Leonor University Hospital, Madrid, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Spain
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, 08028, Barcelona, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Luis M Allende
- Immunology Department, University Hospital 12 de Octubre, Research Institute Hospital 12 de Octubre (I+12), Madrid, Spain
- Complutense University, Madrid, Spain
| | - Carlos Rodriguez-Gallego
- Department of Immunology, University Hospital of Gran Canaria Dr. Negrín, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Department of Clinical Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Carlos Flores
- Genomics Division, Institute of Technology and Renewable Energies (ITER), Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Health Institute of Carlos III, Madrid, Spain
- Research Unit, University Hospital of N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Institute of Biomedical technologies (ITB), University of La Laguna, San Cristóbal de La Laguna, Spain
| | - Oscar Cabrera-Marante
- Immunology Department, University Hospital 12 de Octubre, Research Institute Hospital 12 de Octubre (I+12), Madrid, Spain
| | - Daniel E Pleguezuelo
- Immunology Department, University Hospital 12 de Octubre, Research Institute Hospital 12 de Octubre (I+12), Madrid, Spain
| | - Rebeca Pérez de Diego
- Institute of Biomedical Research of IdiPAZ, University Hospital "La Paz", Madrid, Spain
| | - Sevgi Keles
- Necmettin Erbakan University, Meram Medical Faculty, Division of Pediatric Allergy and Immunology, Konya, Turkey
| | - Gokhan Aytekin
- Konya City Hospital, Division of Allergy and Immunology, Konya, Turkey
| | - Ozge Metin Akcan
- Necmettin Erbakan University, Meram Medical Faculty, Division of Pediatric Allergy and Immunology, Konya, Turkey
| | - Yenan T Bryceson
- Centre for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Peter Bergman
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, Stockholm, Sweden
- The Immunodeficiency Unit, Infectious Disease Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Petter Brodin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institute, Solna, Sweden
| | - Daniel Smole
- Central Hospital-Anesthesia and Intensive Care Unit, Karlstad, Sweden
| | - C I Edvard Smith
- Department of Laboratory Medicine, Division of Biomolecular and Cellular Medicine, Karolinska Institute, Stockholm, Sweden
- The Immunodeficiency Unit, Infectious Disease Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Anna-Carin Norlin
- The Immunodeficiency Unit, Infectious Disease Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Tessa M Campbell
- Centre for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Laura E Covill
- Centre for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | | | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nico Marr
- Department of Immunology, Research Branch, Sidra Medicine, Doha, Qatar
| | - Manar Ata
- Department of Immunology, Research Branch, Sidra Medicine, Doha, Qatar
| | - Fatima Al Ali
- Department of Immunology, Research Branch, Sidra Medicine, Doha, Qatar
| | - Taushif Khan
- Department of Immunology, Research Branch, Sidra Medicine, Doha, Qatar
| | - András N Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM- Ospedale San Gerardo, Monza, Italy
| | - Sarah Tubiana
- Centre d'Investigation Clinique, INSERM CIC 1425, Paris, France
- Hôpital Bichat Claude Bernard, APHP, Paris, France
| | - Charles Burdet
- Centre d'Investigation Clinique, INSERM CIC 1425, Paris, France
- Université de Paris, IAME, INSERM UMR 1137, Paris, France
| | | | | | - Andrew L Snow
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The 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 of Paris, Imagine Institute, Paris, France
- Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, Paris, France, EU
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The 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 of Paris, Imagine Institute, Paris, France
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The 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 of Paris, Imagine Institute, Paris, France
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The 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 of Paris, Imagine Institute, Paris, France
| | - Vivien Béziat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The 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 of Paris, Imagine Institute, Paris, France
| | - Richard P Lifton
- Yale Center for Genome Analysis and Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Laboratory of Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The 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 of Paris, Imagine Institute, Paris, France
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The 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 of Paris, Imagine Institute, Paris, France
| | - Ali Amara
- Laboratory of Genomes & Cell Biology of Disease, INSERM U944, CNRS UMR7212, University of Paris, Research Institute of Saint-Louis, Saint-Louis Hospital, Paris, France
| | - Vassili Soumelis
- University of Paris, INSERM U976, F-75006 Paris, France
- APHP, Hôpital Saint-Louis, Department of Immunology-Histocompatibility, 75010 Paris, France
| | - Aurélie Cobat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The 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 of Paris, Imagine Institute, Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The 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 of Paris, Imagine Institute, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
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9
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Zhang P, Cobat A, Lee YS, Wu Y, Bayrak CS, Boccon-Gibod C, Matuozzo D, Lorenzo L, Jain A, Boucherit S, Vallée L, Stüve B, Chabrier S, Casanova JL, Abel L, Zhang SY, Itan Y. A computational approach for detecting physiological homogeneity in the midst of genetic heterogeneity. Am J Hum Genet 2021; 108:1012-1025. [PMID: 34015270 DOI: 10.1016/j.ajhg.2021.04.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023] Open
Abstract
The human genetic dissection of clinical phenotypes is complicated by genetic heterogeneity. Gene burden approaches that detect genetic signals in case-control studies are underpowered in genetically heterogeneous cohorts. We therefore developed a genome-wide computational method, network-based heterogeneity clustering (NHC), to detect physiological homogeneity in the midst of genetic heterogeneity. Simulation studies showed our method to be capable of systematically converging genes in biological proximity on the background biological interaction network, and capturing gene clusters harboring presumably deleterious variants, in an efficient and unbiased manner. We applied NHC to whole-exome sequencing data from a cohort of 122 individuals with herpes simplex encephalitis (HSE), including 13 individuals with previously published monogenic inborn errors of TLR3-dependent IFN-α/β immunity. The top gene cluster identified by our approach successfully detected and prioritized all causal variants of five TLR3 pathway genes in the 13 previously reported individuals. This approach also suggested candidate variants of three reported genes and four candidate genes from the same pathway in another ten previously unstudied individuals. TLR3 responsiveness was impaired in dermal fibroblasts from four of the five individuals tested, suggesting that the variants detected were causal for HSE. NHC is, therefore, an effective and unbiased approach for unraveling genetic heterogeneity by detecting physiological homogeneity.
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Affiliation(s)
- Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA.
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris 75015, France; University of Paris, Imagine Institute, Paris 75015, France
| | - Yoon-Seung Lee
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Yiming Wu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cigdem Sevim Bayrak
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Clémentine Boccon-Gibod
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Daniela Matuozzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris 75015, France; University of Paris, Imagine Institute, Paris 75015, France
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris 75015, France; University of Paris, Imagine Institute, Paris 75015, France
| | - Aayushee Jain
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Soraya Boucherit
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris 75015, France; University of Paris, Imagine Institute, Paris 75015, France
| | - Louis Vallée
- Neuropediatric Department, Roger Salengro Hospital, Lille 59037, France
| | - Burkhard Stüve
- Clinics of the City of Cologne gGmbH, Cologne 53323, Germany
| | - Stéphane Chabrier
- CHU Saint-Étienne, French Centre for Pediatric Stroke, Saint-Étienne, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris 75015, France; University of Paris, Imagine Institute, Paris 75015, France; Howard Hughes Medical Institute, New York, NY 10065, USA.
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris 75015, France; University of Paris, Imagine Institute, Paris 75015, France
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris 75015, France; University of Paris, Imagine Institute, Paris 75015, France
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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