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Chou SR, Bailey AC, Baysac K, Oler AJ, Milner JD, Ombrello MJ. Splice site and de novo mutations can cause mixed dominant negative/gain of function PLCG2-associated immune dysregulation with cold urticaria (CU-PLAID). medRxiv 2024:2024.03.16.24304180. [PMID: 38562814 PMCID: PMC10984065 DOI: 10.1101/2024.03.16.24304180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Background Phospholipase Cγ2 (PLCγ2) is an important signaling molecule that receives and transmits signals from various cell surface receptors in most hematopoietic lineages. Variants of PLCG2 cause PLCγ2-associated immune dysregulation (PLAID), a family of conditions that are classified by mutational effect. PLAID with cold urticaria (CU-PLAID) is caused by in-frame deletions of PLCG2 that are dominant negative at physiologic temperatures but become spontaneously active at sub-physiologic temperatures. Objective To identify genetic lesions that cause PLAID by combining RNA sequencing of full-length PLCG2 with whole genome sequencing. Methods We studied nine probands with antibody deficiency and a positive evaporative cooling test, together with two known CU-PLAID patients and three healthy subjects. Illumina sequencing was performed on full-length PLCG2 cDNA synthesized from peripheral blood mononuclear cell RNA and whole genome sequencing was used to identify genetic lesions. Novel alternate transcripts were overexpressed in the Plcg2-deficient DT40 cell overexpression system. ERK phosphorylation was quantified by flow cytometry with and without BCR crosslinking. Results Two probands expressed novel alternative transcripts of PLCG2 with in-frame deletions. The first, expressing PLCG2 without exons 18-19, carried a splice site mutation in intron 19. The second, expressing PLCG2 without exons 19-22, carried a 14kb de novo deletion of PLCG2. DT40 cells overexpressing the exon 18-19 or exon 19-22 deletions failed to phosphorylate ERK in response to BCR crosslinking. Conclusion In addition to autosomal dominant genomic deletions, de novo deletions and splice site mutations of PLCG2 can also cause CU-PLAID. All of these can be identified by cDNA-based sequencing.
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Affiliation(s)
- Sophia R. Chou
- Translational Genetics and Genomics Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health (NIH), Bethesda, MD
| | - Alexis C. Bailey
- Translational Genetics and Genomics Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health (NIH), Bethesda, MD
| | - Kathleen Baysac
- Translational Genetics and Genomics Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health (NIH), Bethesda, MD
| | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Joshua D. Milner
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Michael J. Ombrello
- Translational Genetics and Genomics Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health (NIH), Bethesda, MD
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2
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Delmonte OM, Oguz C, Dobbs K, Myint-Hpu K, Palterer B, Abers MS, Draper D, Truong M, Kaplan IM, Gittelman RM, Zhang Y, Rosen LB, Snow AL, Dalgard CL, Burbelo PD, Imberti L, Sottini A, Quiros-Roldan E, Castelli F, Rossi C, Brugnoni D, Biondi A, Bettini LR, D'Angio M, Bonfanti P, Anderson MV, Saracino A, Chironna M, Di Stefano M, Fiore JR, Santantonio T, Castagnoli R, Marseglia GL, Magliocco M, Bosticardo M, Pala F, Shaw E, Matthews H, Weber SE, Xirasagar S, Barnett J, Oler AJ, Dimitrova D, Bergerson JRE, McDermott DH, Rao VK, Murphy PM, Holland SM, Lisco A, Su HC, Lionakis MS, Cohen JI, Freeman AF, Snyder TM, Lack J, Notarangelo LD. Perturbations of the T-cell receptor repertoire in response to SARS-CoV-2 in immunocompetent and immunocompromised individuals. J Allergy Clin Immunol 2023:S0091-6749(23)02544-7. [PMID: 38154666 DOI: 10.1016/j.jaci.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND Functional T-cell responses are essential for virus clearance and long-term protection after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, whereas certain clinical factors, such as older age and immunocompromise, are associated with worse outcome. OBJECTIVE We sought to study the breadth and magnitude of T-cell responses in patients with coronavirus disease 2019 (COVID-19) and in individuals with inborn errors of immunity (IEIs) who had received COVID-19 mRNA vaccine. METHODS Using high-throughput sequencing and bioinformatics tools to characterize the T-cell receptor β repertoire signatures in 540 individuals after SARS-CoV-2 infection, 31 IEI recipients of COVID-19 mRNA vaccine, and healthy controls, we quantified HLA class I- and class II-restricted SARS-CoV-2-specific responses and also identified several HLA allele-clonotype motif associations in patients with COVID-19, including a subcohort of anti-type 1 interferon (IFN-1)-positive patients. RESULTS Our analysis revealed that elderly patients with COVID-19 with critical disease manifested lower SARS-CoV-2 T-cell clonotype diversity as well as T-cell responses with reduced magnitude, whereas the SARS-CoV-2-specific clonotypes targeted a broad range of HLA class I- and class II-restricted epitopes across the viral proteome. The presence of anti-IFN-I antibodies was associated with certain HLA alleles. Finally, COVID-19 mRNA immunization induced an increase in the breadth of SARS-CoV-2-specific clonotypes in patients with IEIs, including those who had failed to seroconvert. CONCLUSIONS Elderly individuals have impaired capacity to develop broad and sustained T-cell responses after SARS-CoV-2 infection. Genetic factors may play a role in the production of anti-IFN-1 antibodies. COVID-19 mRNA vaccines are effective in inducing T-cell responses in patients with IEIs.
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Affiliation(s)
- Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
| | - Cihan Oguz
- Integrated Data Sciences Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Katherine Myint-Hpu
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Boaz Palterer
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michael S Abers
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Deborah Draper
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Meng Truong
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | | | | | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Lindsey B Rosen
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrew L Snow
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md; Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, Md; The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - Peter D Burbelo
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Md
| | - Luisa Imberti
- Section of Microbiology, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Alessandra Sottini
- Section of Microbiology, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Francesco Castelli
- Department of Infectious and Tropical Diseases, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Camillo Rossi
- Direzione Sanitaria, ASST Spedali Civili, Brescia, Italy
| | - Duilio Brugnoni
- Laboratorio Analisi Chimico-Cliniche, ASST Spedali Civili, Brescia, Italy
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Laura Rachele Bettini
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Mariella D'Angio
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Megan V Anderson
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Annalisa Saracino
- Clinic of Infectious Diseases, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, University of Bari, Bari, Italy
| | - Maria Chironna
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Mariantonietta Di Stefano
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Jose Ramon Fiore
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Teresa Santantonio
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Riccardo Castagnoli
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Gian Luigi Marseglia
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Mary Magliocco
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Elana Shaw
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Helen Matthews
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sarah E Weber
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sandhya Xirasagar
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Jason Barnett
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Dimana Dimitrova
- Center for Immuno-Oncology, National Cancer Institute, National Institutes of Health, Bethesda, Md
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - David H McDermott
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - V Koneti Rao
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Philip M Murphy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrea Lisco
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | | | - Justin Lack
- Integrated Data Sciences Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
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3
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Chaimongkol N, Dábilla N, Tohma K, Matsushima Y, Yardley AB, Levenson EA, Johnson JA, Ahorrio C, Oler AJ, Kim DY, Souza M, Sosnovtsev SV, Parra GI, Green KY. Norovirus evolves as one or more distinct clonal populations in immunocompromised hosts. mBio 2023; 14:e0217723. [PMID: 37905910 PMCID: PMC10746188 DOI: 10.1128/mbio.02177-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 08/30/2023] [Indexed: 11/02/2023] Open
Abstract
Noroviruses are a major cause of acute gastroenteritis worldwide and can establish chronic infection in immunocompromised individuals. To investigate the mechanisms of norovirus evolution during chronic infection, we selected seven representative patients from a National Institutes of Health study cohort who sustained norovirus infection for periods ranging from 73 to 1,492 days. Six patients shed viruses belonging to a single genotype (GII.2[PNA], GII.4 New Orleans[P4], GII.4 Den Haag[P4], GII.3[P21], GII.6[P7], or GII.14[P7]) over the period examined, while one patient sequentially shed two genotypes (GII.6[P7] followed by GII.4 Sydney[P31]). Norovirus genomes from consecutive stool samples were sequenced at high resolution (>3,300 reads/nucleotide position) using the Illumina platform and subjected to bioinformatics analysis. Norovirus sequences could be resolved into one or more discrete clonal RNA genomes that persisted within these patients over time. Phylogenetic analyses inferred that clonal populations originated from a single founder virus and not by reinfection with community strains. Estimated evolutionary rates of clonal populations during persistent infection were similar to those of noroviruses from acute infection in the global database, suggesting that inherently higher RNA-dependent polymerase error rates were not associated with the ability to persist. The high-resolution analysis of norovirus diversity and evolution at the population level described here should allow a better understanding of adaptive mutations sustained during chronic infection. IMPORTANCE Noroviruses are an important cause of chronic diarrhea in patients with compromised immune systems. Presently, there are no effective therapies to clear the virus, which can persist for years in the intestinal tract. The goal of our study was to develop a better understanding of the norovirus strains that are associated with these long-term infections. With the remarkable diversity of norovirus strains detected in the immunocompromised patient cohort we studied, it appears that most, if not all, noroviruses circulating in nature may have the capacity to establish a chronic infection when a person is unable to mount an effective immune response. Our work is the most comprehensive genetic data set generated to date in which near full-length genomes from noroviruses associated with chronic infection were analyzed by high-resolution next-generation sequencing. Analysis of this data set led to our discovery that certain patients in our cohort were shedding noroviruses that could be subdivided into distinct haplotypes or populations of viruses that were co-evolving independently. The ability to track haplotypes of noroviruses during chronic infection will allow us to fine-tune our understanding of how the virus adapts and maintains itself in the human host, and how selective pressures such as antiviral drugs can affect these distinct populations.
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Affiliation(s)
- Natthawan Chaimongkol
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nathânia Dábilla
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Virology and Cell Culture, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Kentaro Tohma
- Division of Viral Products, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yuki Matsushima
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Allison Behrle Yardley
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Eric A. Levenson
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jordan A. Johnson
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Courtney Ahorrio
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Daniel Y. Kim
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Menira Souza
- Laboratory of Virology and Cell Culture, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Stanislav V. Sosnovtsev
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Gabriel I. Parra
- Division of Viral Products, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Kim Y. Green
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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4
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Papendorf JJ, Ebstein F, Alehashemi S, Piotto DGP, Kozlova A, Terreri MT, Shcherbina A, Rastegar A, Rodrigues M, Pereira R, Park S, Lin B, Uss K, Möller S, da Silva Pina AF, Sztajnbok F, Torreggiani S, Niemela J, Stoddard J, Rosenzweig SD, Oler AJ, McNinch C, de Guzman MM, Fonseca A, Micheloni N, Fraga MM, Perazzio SF, Goldbach-Mansky R, de Jesus AA, Krüger E. Identification of eight novel proteasome variants in five unrelated cases of proteasome-associated autoinflammatory syndromes (PRAAS). Front Immunol 2023; 14:1190104. [PMID: 37600812 PMCID: PMC10436547 DOI: 10.3389/fimmu.2023.1190104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/12/2023] [Indexed: 08/22/2023] Open
Abstract
Mutations in genes coding for proteasome subunits and/or proteasome assembly helpers typically cause recurring autoinflammation referred to as chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperatures (CANDLE) or proteasome-associated autoinflammatory syndrome (PRAAS). Patients with CANDLE/PRAAS present with mostly chronically elevated type I interferon scores that emerge as a consequence of increased proteotoxic stress by mechanisms that are not fully understood. Here, we report on five unrelated patients with CANDLE/PRAAS carrying novel inherited proteasome missense and/or nonsense variants. Four patients were compound heterozygous for novel pathogenic variants in the known CANDLE/PRAAS associated genes, PSMB8 and PSMB10, whereas one patient showed additive loss-of-function mutations in PSMB8. Variants in two previously not associated proteasome genes, PSMA5 and PSMC5, were found in a patient who also carried the PSMB8 founder mutation, p.T75M. All newly identified mutations substantially impact the steady-state expression of the affected proteasome subunits and/or their incorporation into mature 26S proteasomes. Our observations expand the spectrum of PRAAS-associated genetic variants and improve a molecular diagnosis and genetic counseling of patients with sterile autoinflammation.
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Affiliation(s)
- Jonas Johannes Papendorf
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany
| | - Frédéric Ebstein
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany
| | - Sara Alehashemi
- Translational Autoinflammatory Diseases Section (TADS), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Daniela Gerent Petry Piotto
- Division of Pediatric Rheumatology, Department of Pediatrics, Universidade Federal de São Paulo (Unifesp), São Paulo, Brazil
| | - Anna Kozlova
- Department of Immunology, D.Rogachev National Medical and Research Center for Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| | - Maria Teresa Terreri
- Division of Pediatric Rheumatology, Department of Pediatrics, Universidade Federal de São Paulo (Unifesp), São Paulo, Brazil
| | - Anna Shcherbina
- Department of Immunology, D.Rogachev National Medical and Research Center for Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| | - Andre Rastegar
- Translational Autoinflammatory Diseases Section (TADS), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Marta Rodrigues
- Division of Pediatric Rheumatology, Department of Pediatrics, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Renan Pereira
- Department of Pediatrics, Universidade Federal de Ciencias da Saude de Porto Alegre, Porto Alegre, Brazil
| | - Sophia Park
- Translational Autoinflammatory Diseases Section (TADS), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Bin Lin
- Translational Autoinflammatory Diseases Section (TADS), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kat Uss
- Translational Autoinflammatory Diseases Section (TADS), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sophie Möller
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany
| | - Ana Flávia da Silva Pina
- Division of Pediatric Rheumatology, Department of Pediatrics, Universidade Federal de São Paulo (Unifesp), São Paulo, Brazil
| | - Flavio Sztajnbok
- Division of Pediatric Rheumatology, Department of Pediatrics, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Sofia Torreggiani
- Translational Autoinflammatory Diseases Section (TADS), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Julie Niemela
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Jennifer Stoddard
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Sergio D. Rosenzweig
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Colton McNinch
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Marietta M. de Guzman
- Section of Pediatric Rheumatology, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX, United States
| | - Adriana Fonseca
- Division of Pediatric Rheumatology, Department of Pediatrics, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Nicole Micheloni
- Division of Pediatric Rheumatology, Department of Pediatrics, Universidade Federal de São Paulo (Unifesp), São Paulo, Brazil
| | - Melissa Mariti Fraga
- Division of Pediatric Rheumatology, Department of Pediatrics, Universidade Federal de São Paulo (Unifesp), São Paulo, Brazil
| | - Sandro Félix Perazzio
- Division of Rheumatology – Department of Medicine, Universidade Federal de São Paulo (Unifesp), Sao Paulo, Brazil
| | - Raphaela Goldbach-Mansky
- Translational Autoinflammatory Diseases Section (TADS), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Adriana A. de Jesus
- Translational Autoinflammatory Diseases Section (TADS), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Elke Krüger
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany
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5
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Beers BJ, Similuk MN, Ghosh R, Seifert BA, Jamal L, Kamen M, Setzer MR, Jodarski C, Duncan R, Hunt D, Mixer M, Cao W, Bi W, Veltri D, Karlins E, Zhang L, Li Z, Oler AJ, Jevtich K, Yu Y, Hullfish H, Bielekova B, Frischmeyer-Guerrerio P, Dang Do A, Huryn LA, Olivier KN, Su HC, Lyons JJ, Zerbe CS, Rao VK, Keller MD, Freeman AF, Holland SM, Franco LM, Walkiewicz MA, Yan J. Chromosomal microarray analysis supplements exome sequencing to diagnose children with suspected inborn errors of immunity. Front Immunol 2023; 14:1172004. [PMID: 37215141 PMCID: PMC10196392 DOI: 10.3389/fimmu.2023.1172004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/04/2023] [Indexed: 05/24/2023] Open
Abstract
Purpose Though copy number variants (CNVs) have been suggested to play a significant role in inborn errors of immunity (IEI), the precise nature of this role remains largely unexplored. We sought to determine the diagnostic contribution of CNVs using genome-wide chromosomal microarray analysis (CMA) in children with IEI. Methods We performed exome sequencing (ES) and CMA for 332 unrelated pediatric probands referred for evaluation of IEI. The analysis included primary, secondary, and incidental findings. Results Of the 332 probands, 134 (40.4%) received molecular diagnoses. Of these, 116/134 (86.6%) were diagnosed by ES alone. An additional 15/134 (11.2%) were diagnosed by CMA alone, including two likely de novo changes. Three (2.2%) participants had diagnostic molecular findings from both ES and CMA, including two compound heterozygotes and one participant with two distinct diagnoses. Half of the participants with CMA contribution to diagnosis had CNVs in at least one non-immune gene, highlighting the clinical complexity of these cases. Overall, CMA contributed to 18/134 diagnoses (13.4%), increasing the overall diagnostic yield by 15.5% beyond ES alone. Conclusion Pairing ES and CMA can provide a comprehensive evaluation to clarify the complex factors that contribute to both immune and non-immune phenotypes. Such a combined approach to genetic testing helps untangle complex phenotypes, not only by clarifying the differential diagnosis, but in some cases by identifying multiple diagnoses contributing to the overall clinical presentation.
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Affiliation(s)
- Breanna J. Beers
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Morgan N. Similuk
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Rajarshi Ghosh
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Bryce A. Seifert
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Leila Jamal
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Michael Kamen
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Michael R. Setzer
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Colleen Jodarski
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Rylee Duncan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Devin Hunt
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Madison Mixer
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Wenjia Cao
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Weimin Bi
- Baylor Genetics, Houston, TX, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Daniel Veltri
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Eric Karlins
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lingwen Zhang
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Zhiwen Li
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Andrew J. Oler
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kathleen Jevtich
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yunting Yu
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Haley Hullfish
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Bibiana Bielekova
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Pamela Frischmeyer-Guerrerio
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - An Dang Do
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Laryssa A. Huryn
- National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Kenneth N. Olivier
- Division of Pulmonary Diseases and Critical Care Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Helen C. Su
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jonathan J. Lyons
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Christa S. Zerbe
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - V. Koneti Rao
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Michael D. Keller
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Alexandra F. Freeman
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Steven M. Holland
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Luis M. Franco
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Magdalena A. Walkiewicz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jia Yan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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6
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Hsu AP, Korzeniowska A, Aguilar CC, Gu J, Karlins E, Oler AJ, Chen G, Reynoso GV, Davis J, Chaput A, Peng T, Sun L, Lack JB, Bays DJ, Stewart ER, Waldman SE, Powell DA, Donovan FM, Desai JV, Pouladi N, Long Priel DA, Yamanaka D, Rosenzweig SD, Niemela JE, Stoddard J, Freeman AF, Zerbe CS, Kuhns DB, Lussier YA, Olivier KN, Boucher RC, Hickman HD, Frelinger J, Fierer J, Shubitz LF, Leto TL, Thompson GR, Galgiani JN, Lionakis MS, Holland SM. Immunogenetics associated with severe coccidioidomycosis. JCI Insight 2022; 7:159491. [PMID: 36166305 PMCID: PMC9746810 DOI: 10.1172/jci.insight.159491] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/21/2022] [Indexed: 12/15/2022] Open
Abstract
Disseminated coccidioidomycosis (DCM) is caused by Coccidioides, pathogenic fungi endemic to the southwestern United States and Mexico. Illness occurs in approximately 30% of those infected, less than 1% of whom develop disseminated disease. To address why some individuals allow dissemination, we enrolled patients with DCM and performed whole-exome sequencing. In an exploratory set of 67 patients with DCM, 2 had haploinsufficient STAT3 mutations, and defects in β-glucan sensing and response were seen in 34 of 67 cases. Damaging CLEC7A and PLCG2 variants were associated with impaired production of β-glucan-stimulated TNF-α from PBMCs compared with healthy controls. Using ancestry-matched controls, damaging CLEC7A and PLCG2 variants were overrepresented in DCM, including CLEC7A Y238* and PLCG2 R268W. A validation cohort of 111 patients with DCM confirmed the PLCG2 R268W, CLEC7A I223S, and CLEC7A Y238* variants. Stimulation with a DECTIN-1 agonist induced DUOX1/DUOXA1-derived hydrogen peroxide [H2O2] in transfected cells. Heterozygous DUOX1 or DUOXA1 variants that impaired H2O2 production were overrepresented in discovery and validation cohorts. Patients with DCM have impaired β-glucan sensing or response affecting TNF-α and H2O2 production. Impaired Coccidioides recognition and decreased cellular response are associated with disseminated coccidioidomycosis.
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Affiliation(s)
- Amy P Hsu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Agnieszka Korzeniowska
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Cynthia C Aguilar
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Jingwen Gu
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Eric Karlins
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Gang Chen
- Marsico Lung Institute and Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Glennys V Reynoso
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Joie Davis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Alexandria Chaput
- Valley Fever Center for Excellence, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA
| | - Tao Peng
- Valley Fever Center for Excellence, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA
| | - Ling Sun
- Marsico Lung Institute and Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Respiratory and Critical Care Medicine, Laboratory of Pulmonary Immunology and Inflammation, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Justin B Lack
- NIAID Collaborative Bioinformatics Resource, NIAID, NIH, Bethesda, Maryland, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Derek J Bays
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Sacramento, California, USA
| | - Ethan R Stewart
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Sacramento, California, USA
| | - Sarah E Waldman
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Sacramento, California, USA
| | - Daniel A Powell
- Valley Fever Center for Excellence, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA.,Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Fariba M Donovan
- Valley Fever Center for Excellence, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA.,Department of Medicine, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA
| | - Jigar V Desai
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Nima Pouladi
- Center for Biomedical Informatics and Biostatistics and.,The Center for Applied Genetics and Genomic Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Debra A Long Priel
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Daisuke Yamanaka
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA.,Laboratory for Immunopharmacology of Microbial Products, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | | | - Julie E Niemela
- Immunology Service, Department of Laboratory Medicine, Clinical Center and
| | - Jennifer Stoddard
- Immunology Service, Department of Laboratory Medicine, Clinical Center and
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Christa S Zerbe
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Douglas B Kuhns
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Yves A Lussier
- Center for Biomedical Informatics and Biostatistics and.,The Center for Applied Genetics and Genomic Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Kenneth N Olivier
- Laboratory of Chronic Airway Infection, Pulmonary Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Richard C Boucher
- Marsico Lung Institute and Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Heather D Hickman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Jeffrey Frelinger
- Valley Fever Center for Excellence, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA.,Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Joshua Fierer
- VA HealthCare San Diego, San Diego, California, USA.,Division of Infectious Diseases, Departments of Pathology and Medicine, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Lisa F Shubitz
- Valley Fever Center for Excellence, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA
| | - Thomas L Leto
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - George R Thompson
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Sacramento, California, USA.,Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, USA
| | - John N Galgiani
- Valley Fever Center for Excellence, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA.,Department of Medicine, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
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7
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Drummond RA, Desai JV, Hsu AP, Oikonomou V, Vinh DC, Acklin JA, Abers MS, Walkiewicz MA, Anzick SL, Swamydas M, Vautier S, Natarajan M, Oler AJ, Yamanaka D, Mayer-Barber KD, Iwakura Y, Bianchi D, Driscoll B, Hauck K, Kline A, Viall NS, Zerbe CS, Ferré EM, Schmitt MM, DiMaggio T, Pittaluga S, Butman JA, Zelazny AM, Shea YR, Arias CA, Ashbaugh C, Mahmood M, Temesgen Z, Theofiles AG, Nigo M, Moudgal V, Bloch KC, Kelly SG, Whitworth MS, Rao G, Whitener CJ, Mafi N, Gea-Banacloche J, Kenyon LC, Miller WR, Boggian K, Gilbert A, Sincock M, Freeman AF, Bennett JE, Hasbun R, Mikelis CM, Kwon-Chung KJ, Belkaid Y, Brown GD, Lim JK, Kuhns DB, Holland SM, Lionakis MS. Human Dectin-1 deficiency impairs macrophage-mediated defense against phaeohyphomycosis. J Clin Invest 2022; 132:e159348. [PMID: 36377664 PMCID: PMC9663159 DOI: 10.1172/jci159348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Subcutaneous phaeohyphomycosis typically affects immunocompetent individuals following traumatic inoculation. Severe or disseminated infection can occur in CARD9 deficiency or after transplantation, but the mechanisms protecting against phaeohyphomycosis remain unclear. We evaluated a patient with progressive, refractory Corynespora cassiicola phaeohyphomycosis and found that he carried biallelic deleterious mutations in CLEC7A encoding the CARD9-coupled, β-glucan-binding receptor, Dectin-1. The patient's PBMCs failed to produce TNF-α and IL-1β in response to β-glucan and/or C. cassiicola. To confirm the cellular and molecular requirements for immunity against C. cassiicola, we developed a mouse model of this infection. Mouse macrophages required Dectin-1 and CARD9 for IL-1β and TNF-α production, which enhanced fungal killing in an interdependent manner. Deficiency of either Dectin-1 or CARD9 was associated with more severe fungal disease, recapitulating the human observation. Because these data implicated impaired Dectin-1 responses in susceptibility to phaeohyphomycosis, we evaluated 17 additional unrelated patients with severe forms of the infection. We found that 12 out of 17 carried deleterious CLEC7A mutations associated with an altered Dectin-1 extracellular C-terminal domain and impaired Dectin-1-dependent cytokine production. Thus, we show that Dectin-1 and CARD9 promote protective TNF-α- and IL-1β-mediated macrophage defense against C. cassiicola. More broadly, we demonstrate that human Dectin-1 deficiency may contribute to susceptibility to severe phaeohyphomycosis by certain dematiaceous fungi.
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Affiliation(s)
| | | | - Amy P. Hsu
- Immunopathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | | | - Donald C. Vinh
- Division of Infectious Diseases, McGill University Health Centre (MUHC), and Infectious Disease Susceptibility Program, Research Institute-MUHC, Montreal, Quebec, Canada
| | - Joshua A. Acklin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | - Sarah L. Anzick
- Research Technologies Branches, NIAID, NIH, Hamilton, Montana, USA
| | | | | | | | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Daisuke Yamanaka
- Laboratory for Immunopharmacology of Microbial Products, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | | | - Yoichiro Iwakura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - David Bianchi
- National Institute of Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland, USA
| | - Brian Driscoll
- National Institute of Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland, USA
| | - Ken Hauck
- National Institute of Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland, USA
| | | | | | - Christa S. Zerbe
- Immunopathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | | | | | | | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, Maryland, USA
| | | | - Adrian M. Zelazny
- Department of Laboratory Medicine, NIH Clinical Center, NIH, Bethesda, Maryland, USA
| | - Yvonne R. Shea
- Department of Laboratory Medicine, NIH Clinical Center, NIH, Bethesda, Maryland, USA
| | - Cesar A. Arias
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Research, Houston Methodist Research Institute, Houston, Texas, USA
| | - Cameron Ashbaugh
- Division of Infectious Diseases, UCSF, San Francisco, California, USA
| | - Maryam Mahmood
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Zelalem Temesgen
- Division of Hospital Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Masayuki Nigo
- Division of Infectious Diseases, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Varsha Moudgal
- Department of Internal Medicine, St. Joseph Mercy Hospital, Ann Arbor, Michigan, USA
| | - Karen C. Bloch
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sean G. Kelly
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Ganesh Rao
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA
| | - Cindy J. Whitener
- Division of Infectious Diseases, Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Neema Mafi
- Division of Infectious Diseases, Mayo Clinic Hospital, Phoenix, Arizona, USA
| | | | - Lawrence C. Kenyon
- Department of Pathology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - William R. Miller
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Research, Houston Methodist Research Institute, Houston, Texas, USA
| | - Katia Boggian
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, Switzerland
| | - Andrea Gilbert
- Department of Pathology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | | | - Alexandra F. Freeman
- Immunopathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | | | - Rodrigo Hasbun
- Department of Internal Medicine, University of Texas Health Science Center, Houston, Texas, USA
| | - Constantinos M. Mikelis
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas, USA
- Department of Pharmacy, University of Patras, Patras, Greece
| | | | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, Maryland, USA
| | - Gordon D. Brown
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Jean K. Lim
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Douglas B. Kuhns
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Steven M. Holland
- Immunopathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
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8
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Carmona-Rivera C, Zhang Y, Dobbs K, Markowitz TE, Dalgard CL, Oler AJ, Claybaugh DR, Draper D, Truong M, Delmonte OM, Licciardi F, Ramenghi U, Crescenzio N, Imberti L, Sottini A, Quaresima V, Fiorini C, Discepolo V, Lo Vecchio A, Guarino A, Pierri L, Catzola A, Biondi A, Bonfanti P, Poli Harlowe MC, Espinosa Y, Astudillo C, Rey-Jurado E, Vial C, de la Cruz J, Gonzalez R, Pinera C, Mays JW, Ng A, Platt A, Drolet B, Moon J, Cowen EW, Kenney H, Weber SE, Castagnoli R, Magliocco M, Stack MA, Montealegre G, Barron K, Fink DL, Kuhns DB, Hewitt SM, Arkin LM, Chertow DS, Su HC, Notarangelo LD, Kaplan MJ. Multicenter analysis of neutrophil extracellular trap dysregulation in adult and pediatric COVID-19. JCI Insight 2022; 7:160332. [PMID: 35852866 PMCID: PMC9534551 DOI: 10.1172/jci.insight.160332] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/14/2022] [Indexed: 12/02/2022] Open
Abstract
Dysregulation in neutrophil extracellular trap (NET) formation and degradation may play a role in the pathogenesis and severity of COVID-19; however, its role in the pediatric manifestations of this disease, including multisystem inflammatory syndrome in children (MIS-C) and chilblain-like lesions (CLLs), otherwise known as “COVID toes,” remains unclear. Studying multinational cohorts, we found that, in CLLs, NETs were significantly increased in serum and skin. There was geographic variability in the prevalence of increased NETs in MIS-C, in association with disease severity. MIS-C and CLL serum samples displayed decreased NET degradation ability, in association with C1q and G-actin or anti-NET antibodies, respectively, but not with genetic variants of DNases. In adult COVID-19, persistent elevations in NETs after disease diagnosis were detected but did not occur in asymptomatic infection. COVID-19–affected adults displayed significant prevalence of impaired NET degradation, in association with anti-DNase1L3, G-actin, and specific disease manifestations, but not with genetic variants of DNases. NETs were detected in many organs of adult patients who died from COVID-19 complications. Infection with the Omicron variant was associated with decreased NET levels when compared with other SARS-CoV-2 strains. These data support a role for NETs in the pathogenesis and severity of COVID-19 in pediatric and adult patients.
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Affiliation(s)
- Carmelo Carmona-Rivera
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID); and
| | | | | | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics, School of Medicine, and the American Genome Center, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
| | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Dillon R. Claybaugh
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
| | | | | | | | | | - Ugo Ramenghi
- Department of Public Health and Pediatric Sciences and
| | - Nicoletta Crescenzio
- Pediatric Hematology, “Regina Margherita” Children Hospital, University of Turin, Turin, Italy
| | - Luisa Imberti
- Centro di Ricerca Emato-oncologica AIL, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Alessandra Sottini
- Centro di Ricerca Emato-oncologica AIL, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Virginia Quaresima
- Centro di Ricerca Emato-oncologica AIL, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Chiara Fiorini
- Centro di Ricerca Emato-oncologica AIL, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Valentina Discepolo
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Andrea Lo Vecchio
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Alfredo Guarino
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Luca Pierri
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Andrea Catzola
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Andrea Biondi
- Department of Pediatrics, University of Milano-Bicocca, European Reference Network (ERN) PaedCan, EuroBloodNet, MetabERN, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital–University of Milano-Bicocca, Monza, Italy
| | - Maria C. Poli Harlowe
- Programa de Inmunogenética e Inmunología Traslacional, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Hospital Roberto del Rio, Santiago, Chile
| | | | | | - Emma Rey-Jurado
- Programa de Inmunogenética e Inmunología Traslacional, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Cecilia Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | - Javiera de la Cruz
- Programa de Inmunogenética e Inmunología Traslacional, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Ricardo Gonzalez
- Pediatric Intensive Care Unit, Hospital Exequiel Gonzalez Cortés, Santiago, Chile
| | - Cecilia Pinera
- Infectious Diseases Unit, Hospital Dr. Exequiel González Cortés, Región Metropolitana, Chile
- Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Jacqueline W. Mays
- National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, Maryland, USA
| | - Ashley Ng
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Andrew Platt
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, and Laboratory of Immunoregulation, NIAID, NIH, Bethesda, Maryland, USA
| | | | | | - Beth Drolet
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - John Moon
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | | | | | | | | | - Mary Magliocco
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID; and
| | - Michael A. Stack
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID; and
| | - Gina Montealegre
- Division of Clinical Research, NIAID, NIH, Bethesda, Maryland, USA
| | - Karyl Barron
- Division of Clinical Research, NIAID, NIH, Bethesda, Maryland, USA
| | - Danielle L. Fink
- Applied/Developmental Research Directorate, Frederick and National Laboratory for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Douglas B. Kuhns
- Applied/Developmental Research Directorate, Frederick and National Laboratory for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Stephen M. Hewitt
- Laboratory of Pathology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Lisa M. Arkin
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Daniel S. Chertow
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, and Laboratory of Immunoregulation, NIAID, NIH, Bethesda, Maryland, USA
| | - Helen C. Su
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID); and
| | | | - Mariana J. Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
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9
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Similuk MN, Yan J, Ghosh R, Oler AJ, Franco LM, Setzer M, Kamen M, Jodarski C, DiMaggio T, Davis J, Gore R, Jamal L, Borges A, Gentile N, Niemela J, Lowe C, Jevtich K, Yu Y, Hullfish H, Hsu AP, Hong C, Littel P, Seifert BA, Milner J, Johnston JJ, Cheng X, Li Z, Veltri D, Huang K, Kaladi K, Barnett J, Zhang L, Vlasenko N, Fan Y, Karlins E, Ganakammal SR, Gilmore R, Tran E, Yun A, Mackey J, Yazhuk S, Lack J, Kuram V, Cao W, Huse S, Frank K, Fahle G, Rosenzweig S, Su Y, Hwang S, Bi W, Bennett J, Myles IA, De Ravin SS, Fussm I, Strober W, Bielekova B, Almeida de Jesus A, Goldbach-Mansky R, Williamson P, Kumar K, Dempsy C, Frischmeyer-Guerrerio P, Eisch R, Bolan H, Metcalfe DD, Komarow H, Carter M, Druey KM, Sereti I, Dropulic L, Klion AD, Khoury P, O' Connell EM, Holland-Thomas NC, Brown T, McDermott DH, Murphy PM, Bundy V, Keller MD, Peng C, Kim H, Norman S, Delmonte OM, Kang E, Su HC, Malech H, Freeman A, Zerbe C, Uzel G, Bergerson JRE, Rao VK, Olivier KN, Lyons JJ, Lisco A, Cohen JI, Lionakis MS, Biesecker LG, Xirasagar S, Notarangelo L, Holland SM, Walkiewicz MA. Clinical Exome Sequencing of 1000 Families with Complex Immune Phenotypes: Towards comprehensive genomic evaluations. J Allergy Clin Immunol 2022; 150:947-954. [PMID: 35753512 PMCID: PMC9547837 DOI: 10.1016/j.jaci.2022.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/07/2022] [Accepted: 06/02/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND Prospective genetic evaluation of patients at our referral research hospital presents clinical research challenges. OBJECTIVE This study sought not only a single-gene explanation for participants' immune-related presentations, but viewed each participant holistically, with the potential to have multiple genetic contributions to their immune-phenotype and other heritable comorbidities relevant to their presentation and health. METHODS We developed a program integrating exome sequencing, chromosomal microarray, phenotyping, results return with genetic counseling, and reanalysis in 1505 individuals from 1000 families with suspected or known inborn errors of immunity. RESULTS Probands were 50.8% female, 71.5% >18 years, and had diverse immune presentations. Overall, 327/1000 probands (32.7%) received 361 molecular diagnoses. These included 17 probands with diagnostic copy number variants, 32 probands with secondary findings, and 31 probands with multiple molecular diagnoses. Reanalysis added 22 molecular diagnoses, predominantly due to new disease-gene associations (9/22, 40.9%). One-quarter of the molecular diagnoses (92/361) did not involve immune-associated genes. Molecular diagnosis was correlated with younger age, male sex, and a higher number of organ systems involved. This program also facilitated the discovery of new gene-disease associations such as SASH3-related immunodeficiency. A review of treatment options and ClinGen actionability curations suggest that at least 251/361 (69.5%) of these molecular diagnoses could translate into >1 management option. CONCLUSION This program contributes to our understanding of the diagnostic and clinical utility whole exome analysis on a large scale. CLINICAL Implication: Comprehensive analysis of exome data has diagnostic and clinical utility for patients with suspected inborn errors of immunity.
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Affiliation(s)
| | - Jia Yan
- Centralized Sequencing Program
- DIR
- NIAID
| | | | - Andrew J Oler
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Luis M Franco
- Functional Immunogenomics Unit
- Systemic Autoimmunity Branch
- National Institute of Arthritis and Musculoskeletal and Skin Diseases
| | | | | | | | - Thomas DiMaggio
- Fungal Pathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
| | - Joie Davis
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Leila Jamal
- Johns Hopkins/NIH Genetic Counseling Training Program; Genetics Branch, Center for Cancer Research, National Cancer Institute; NIH Clinical Center Department of Bioethics
| | | | | | | | - Chenery Lowe
- Health, Behavior, and Society
- Johns Hopkins Bloomberg School of Public Health
| | - Kathleen Jevtich
- School of Medicine
- Uniformed Services University of Health Sciences
| | | | | | - Amy P Hsu
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Patricia Littel
- Genetic Immunotherapy Section
- Laboratory of Clinical Immunology and Microbiology
| | | | | | | | - Xi Cheng
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Zhiwen Li
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Daniel Veltri
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Ke Huang
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Krishnaveni Kaladi
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Jason Barnett
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Lingwen Zhang
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Nikita Vlasenko
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Yongjie Fan
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Eric Karlins
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | | | - Robert Gilmore
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Emily Tran
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Alvin Yun
- Operations and Engineering Branch
- Office of Cyber Infrastructure and Computational Biology
- NIAID
| | - Joseph Mackey
- Operations and Engineering Branch
- Office of Cyber Infrastructure and Computational Biology
- NIAID
| | - Svetlana Yazhuk
- Operations and Engineering Branch
- Office of Cyber Infrastructure and Computational Biology
- NIAID
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | - Vasu Kuram
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | - Wen Cao
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | - Susan Huse
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | | | | | | | - Yan Su
- Immunology Service
- Laboratory Medicine
- NIH
| | - SuJin Hwang
- Tumor Vaccines and Biotechnology Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration
| | - Weimin Bi
- Department of Molecular and Human Genetics
- Baylor Genetics
| | - John Bennett
- Clinical Mycology
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Ian A Myles
- Epithelial Therapeutics Unit
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Suk See De Ravin
- Laboratory of Host Defenses
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Ivan Fussm
- Mucosal Immunity Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Warren Strober
- Mucosal Immunity Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Bibiana Bielekova
- Neuroimmunological Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Adriana Almeida de Jesus
- Translational Autoinflammatory Disease Studies Unit
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Raphaela Goldbach-Mansky
- Translational Autoinflammatory Disease Studies Unit
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Peter Williamson
- Translational Mycology Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Caeden Dempsy
- Food Allergy Research Unit
- Laboratory of Allergic Diseases
- NIAID
| | | | - Robin Eisch
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Hyejeong Bolan
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Dean D Metcalfe
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Hirsh Komarow
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Melody Carter
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Kirk M Druey
- Lung and Vascular Inflammation Section
- Laboratory of Allergic Diseases
- NIAID
| | - Irini Sereti
- HIV Pathogenesis Section
- Laboratory of Immunoregulation
- NIAID
| | - Lesia Dropulic
- Medical Virology Section
- Laboratory of Immunoregulation
- NIAID
| | - Amy D Klion
- Human Eosinophil Section
- Laboratory of Parasitic Diseases
- NIAID
| | - Paneez Khoury
- Human Eosinophil Section
- Laboratory of Parasitic Diseases
- NIAID
| | | | | | - Thomas Brown
- Human Eosinophil Section
- Laboratory of Parasitic Diseases
- NIAID
| | | | - Philip M Murphy
- Molecular Signaling Section
- Laboratory of Molecular Immunology
- NIAID
| | - Vanessa Bundy
- Division of Allergy and Immunology
- Children's National Health System
| | - Michael D Keller
- Division of Allergy and Immunology
- Children's National Health System
| | - Christine Peng
- Division of Allergy and Immunology
- Children's National Health System
| | - Helen Kim
- Division of Allergy and Immunology
- Children's National Health System
| | - Stephanie Norman
- Division of Allergy and Immunology
- Children's National Health System
| | - Ottavia M Delmonte
- Immune Deficiency Genetics Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Elizabeth Kang
- Genetic Immunotherapy Section
- Laboratory of Clinical Immunology and Microbiology
| | - Helen C Su
- Human Immunological Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Harry Malech
- Genetic Immunotherapy Section
- Laboratory of Clinical Immunology and Microbiology
| | - Alexandra Freeman
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Christa Zerbe
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Gulbu Uzel
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Jenna R E Bergerson
- Primary Immune Deficiency Clinic
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - V Koneti Rao
- Primary Immune Deficiency Clinic
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Jonathan J Lyons
- Translational Allergic Immunopathology Unit
- Laboratory of Allergic Diseases
- NIAID
| | - Andrea Lisco
- HIV Pathogenesis Section
- Laboratory of Immunoregulation
- NIAID
| | - Jeffrey I Cohen
- Medical Virology Section
- Laboratory of Infectious Diseases
- NIAID
| | - Michail S Lionakis
- Fungal Pathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
| | | | - Sandhya Xirasagar
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Luigi Notarangelo
- Immune Deficiency Genetics Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Steven M Holland
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
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10
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Yan S, Luo L, Lai PT, Veltri D, Oler AJ, Xirasagar S, Ghosh R, Similuk M, Robinson PN, Lu Z. PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology. J Biomed Inform 2022; 129:104059. [PMID: 35351638 PMCID: PMC11040548 DOI: 10.1016/j.jbi.2022.104059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/23/2022] [Accepted: 03/22/2022] [Indexed: 11/29/2022]
Abstract
The study aims at developing a neural network model to improve the performance of Human Phenotype Ontology (HPO) concept recognition tools. We used the terms, definitions, and comments about the phenotypic concepts in the HPO database to train our model. The document to be analyzed is first split into sentences and annotated with a base method to generate candidate concepts. The sentences, along with the candidate concepts, are then fed into the pre-trained model for re-ranking. Our model comprises the pre-trained BlueBERT and a feature selection module, followed by a contrastive loss. We re-ranked the results generated by three robust HPO annotation tools and compared the performance against most of the existing approaches. The experimental results show that our model can improve the performance of the existing methods. Significantly, it boosted 3.0% and 5.6% in F1 score on the two evaluated datasets compared with the base methods. It removed more than 80% of the false positives predicted by the base methods, resulting in up to 18% improvement in precision. Our model utilizes the descriptive data in the ontology and the contextual information in the sentences for re-ranking. The results indicate that the additional information and the re-ranking model can significantly enhance the precision of HPO concept recognition compared with the base method.
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Affiliation(s)
- Shankai Yan
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Ling Luo
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Po-Ting Lai
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Daniel Veltri
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandhya Xirasagar
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rajarshi Ghosh
- Centralized Sequencing Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Morgan Similuk
- Centralized Sequencing Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Zhiyong Lu
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA.
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11
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Carmona-Rivera C, Zhang Y, Dobbs K, Markowitz TE, Dalgard CL, Oler AJ, Claybaugh DR, Draper D, Truong M, Delmonte OM, Licciardi F, Ramenghi U, Crescenzio N, Imberti L, Sottini A, Quaresima V, Fiorini C, Discepolo V, Lo Vecchio A, Guarino A, Pierri L, Catzola A, Biondi A, Bonfanti P, Poli Harlowe MC, Espinosa Y, Astudillo C, Rey-Jurado E, Vial C, de la Cruz J, Gonzalez R, Pinera C, Mays JW, Ng A, Platt A, Drolet B, Moon J, Cowen EW, Kenney H, Weber SE, Castagnoli R, Magliocco M, Stack MA, Montealegre G, Barron K, Hewitt SM, Arkin LM, Chertow DS, Su HC, Notarangelo LD, Kaplan MJ. Multicenter analysis of neutrophil extracellular trap dysregulation in adult and pediatric COVID-19. medRxiv 2022:2022.02.24.22271475. [PMID: 35262093 PMCID: PMC8902885 DOI: 10.1101/2022.02.24.22271475] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Dysregulation in neutrophil extracellular trap (NET) formation and degradation may play a role in the pathogenesis and severity of COVID-19; however, its role in the pediatric manifestations of this disease including MIS-C and chilblain-like lesions (CLL), otherwise known as "COVID toes", remains unclear. Studying multinational cohorts, we found that, in CLL, NETs were significantly increased in serum and skin. There was geographic variability in the prevalence of increased NETs in MIS-C, in association with disease severity. MIS-C and CLL serum samples displayed decreased NET degradation ability, in association with C1q and G-actin or anti-NET antibodies, respectively, but not with genetic variants of DNases. In adult COVID-19, persistent elevations in NETs post-disease diagnosis were detected but did not occur in asymptomatic infection. COVID-19-affected adults displayed significant prevalence of impaired NET degradation, in association with anti-DNase1L3, G-actin, and specific disease manifestations, but not with genetic variants of DNases. NETs were detected in many organs of adult patients who died from COVID-19 complications. Infection with the Omicron variant was associated with decreased levels of NETs when compared to other SARS-CoV-2 strains. These data support a role for NETs in the pathogenesis and severity of COVID-19 in pediatric and adult patients. Summary NET formation and degradation are dysregulated in pediatric and symptomatic adult patients with various complications of COVID-19, in association with disease severity. NET degradation impairments are multifactorial and associated with natural inhibitors of DNase 1, G-actin and anti-DNase1L3 and anti-NET antibodies. Infection with the Omicron variant is associated with decreased levels of NETs when compared to other SARS-CoV-2 strains.
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Affiliation(s)
- Carmelo Carmona-Rivera
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | | | - Tovah E. Markowitz
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, MD
- Axle Informatics, Bethesda, MD, USA
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics, School of Medicine, Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD and The American Genome Center, USUHS, Bethesda, MD, USA
| | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, MD
| | - Dillon R. Claybaugh
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | | | | | - Francesco Licciardi
- Department of Public Health and Pediatric Sciences, “Regina Margherita” Children’s Hospital, University of Turin, Turin, Italy
| | - Ugo Ramenghi
- Department of Public Health and Pediatric Sciences, “Regina Margherita” Children’s Hospital, University of Turin, Turin, Italy
| | - Nicoletta Crescenzio
- Pediatric Hematology, “Regina Margherita” Children Hospital, University of Turin, Turin, Italy
| | - Luisa Imberti
- Centro di Ricerca Emato-oncologica AIL (CREA), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Alessandra Sottini
- Centro di Ricerca Emato-oncologica AIL (CREA), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Virginia Quaresima
- Centro di Ricerca Emato-oncologica AIL (CREA), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Chiara Fiorini
- Centro di Ricerca Emato-oncologica AIL (CREA), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Valentina Discepolo
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Andrea Lo Vecchio
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Alfredo Guarino
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Luca Pierri
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Andrea Catzola
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Andrea Biondi
- Department of Pediatrics, University of Milano-Bicocca, European Reference Network (ERN) PaedCan, EuroBloodNet, MetabERN, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital–University of Milano-Bicocca, Monza, Italy
| | - Maria Cecilia Poli Harlowe
- Programa de Inmunogenética e Inmunología Traslacional, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Hospital Roberto del Rio, Santiago, Chile
| | | | | | - Emma Rey-Jurado
- Programa de Inmunogenética e Inmunología Traslacional, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Cecilia Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | - Javiera de la Cruz
- Programa de Inmunogenética e Inmunología Traslacional, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Ricardo Gonzalez
- Pediatric Intensive Care Unit, Hospital Exequiel Gonzalez Cortés, Santiago, Chile
| | - Cecilia Pinera
- Infectious Diseases Unit, Hospital Dr. Exequiel González Cortés, Región Metropolitana, Chile
- Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Jacqueline W. Mays
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
| | - Ashley Ng
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Andrew Platt
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, and Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD, USA
| | | | | | - Beth Drolet
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - John Moon
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Edward W. Cowen
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD
| | | | | | | | | | | | | | - Karyl Barron
- Division of Clinical Research, NIAID, NIH, Bethesda, MD
| | - Stephen M. Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Lisa M. Arkin
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Daniel S. Chertow
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, and Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD, USA
| | - Helen C. Su
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | | | - Mariana J. Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
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12
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Kubo S, Fritz JM, Raquer-McKay HM, Kataria R, Vujkovic-Cvijin I, Al-Shaibi A, Yao Y, Zheng L, Zou J, Waldman AD, Jing X, Farley TK, Park AY, Oler AJ, Charles AK, Makhlouf M, AbouMoussa EH, Hasnah R, Saraiva LR, Ganesan S, Al-Subaiey AA, Matthews H, Flano E, Lee HH, Freeman AF, Sefer AP, Sayar E, Çakır E, Karakoc-Aydiner E, Baris S, Belkaid Y, Ozen A, Lo B, Lenardo MJ. Congenital iRHOM2 deficiency causes ADAM17 dysfunction and environmentally directed immunodysregulatory disease. Nat Immunol 2022; 23:75-85. [PMID: 34937930 PMCID: PMC11060421 DOI: 10.1038/s41590-021-01093-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/18/2021] [Accepted: 11/09/2021] [Indexed: 11/08/2022]
Abstract
We report a pleiotropic disease due to loss-of-function mutations in RHBDF2, the gene encoding iRHOM2, in two kindreds with recurrent infections in different organs. One patient had recurrent pneumonia but no colon involvement, another had recurrent infectious hemorrhagic colitis but no lung involvement and the other two experienced recurrent respiratory infections. Loss of iRHOM2, a rhomboid superfamily member that regulates the ADAM17 metalloproteinase, caused defective ADAM17-dependent cleavage and release of cytokines, including tumor-necrosis factor and amphiregulin. To understand the diverse clinical phenotypes, we challenged Rhbdf2-/- mice with Pseudomonas aeruginosa by nasal gavage and observed more severe pneumonia, whereas infection with Citrobacter rodentium caused worse inflammatory colitis than in wild-type mice. The fecal microbiota in the colitis patient had characteristic oral species that can predispose to colitis. Thus, a human immunodeficiency arising from iRHOM2 deficiency causes divergent disease phenotypes that can involve the local microbial environment.
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Affiliation(s)
- Satoshi Kubo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jill M Fritz
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Cooley, LLP in Washington, Washington, DC, USA
| | - Hayley M Raquer-McKay
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Rhea Kataria
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ivan Vujkovic-Cvijin
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Yikun Yao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Juan Zou
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alex D Waldman
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Xinyi Jing
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Taylor K Farley
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Ann Y Park
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | - Reem Hasnah
- Research Branch, Sidra Medicine, Doha, Qatar
| | - Luis R Saraiva
- Research Branch, Sidra Medicine, Doha, Qatar
- Monell Chemical Senses Center, Philadelphia, PA, USA
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Helen Matthews
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emilio Flano
- Discovery Oncology and Immunology, Merck & Co., Inc., Boston, MA, USA
| | - Hyun Hee Lee
- Discovery Oncology and Immunology, Merck & Co., Inc., Boston, MA, USA
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Asena Pınar Sefer
- Division of Allergy and Immunology, Marmara University School of Medicine, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic Center for Primary Immunodeficiency Diseases, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Ersin Sayar
- Department of Pediatric Gastroenterology, Altinbas University Medical Park Bahcelievler Hospital, Istanbul, Turkey
| | - Erkan Çakır
- Division of Pediatric Pulmonology, Department of Pediatrics, Bezmialem Vakif University, School of Medicine, Istanbul, Turkey
| | - Elif Karakoc-Aydiner
- Division of Allergy and Immunology, Marmara University School of Medicine, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic Center for Primary Immunodeficiency Diseases, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Safa Baris
- Division of Allergy and Immunology, Marmara University School of Medicine, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic Center for Primary Immunodeficiency Diseases, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- National Institute of Allergy and Infectious Diseases Microbiome Program, National Institutes of Health, Bethesda, MD, USA
| | - Ahmet Ozen
- Division of Allergy and Immunology, Marmara University School of Medicine, Istanbul, Turkey.
- Istanbul Jeffrey Modell Diagnostic Center for Primary Immunodeficiency Diseases, Istanbul, Turkey.
- The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey.
| | - Bernice Lo
- Research Branch, Sidra Medicine, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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13
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Boso G, Lam O, Bamunusinghe D, Oler AJ, Wollenberg K, Liu Q, Shaffer E, Kozak CA. Patterns of Coevolutionary Adaptations across Time and Space in Mouse Gammaretroviruses and Three Restrictive Host Factors. Viruses 2021; 13:v13091864. [PMID: 34578445 PMCID: PMC8472935 DOI: 10.3390/v13091864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/04/2021] [Accepted: 09/15/2021] [Indexed: 10/26/2022] Open
Abstract
The classical laboratory mouse strains are genetic mosaics of three Mus musculus subspecies that occupy distinct regions of Eurasia. These strains and subspecies carry infectious and endogenous mouse leukemia viruses (MLVs) that can be pathogenic and mutagenic. MLVs evolved in concert with restrictive host factors with some under positive selection, including the XPR1 receptor for xenotropic/polytropic MLVs (X/P-MLVs) and the post-entry restriction factor Fv1. Since positive selection marks host-pathogen genetic conflicts, we examined MLVs for counter-adaptations at sites that interact with XPR1, Fv1, and the CAT1 receptor for ecotropic MLVs (E-MLVs). Results describe different co-adaptive evolutionary paths within the ranges occupied by these virus-infected subspecies. The interface of CAT1, and the otherwise variable E-MLV envelopes, is highly conserved; antiviral protection is afforded by the Fv4 restriction factor. XPR1 and X/P-MLVs variants show coordinate geographic distributions, with receptor critical sites in envelope, under positive selection but with little variation in envelope and XPR1 in mice carrying P-ERVs. The major Fv1 target in the viral capsid is under positive selection, and the distribution of Fv1 alleles is subspecies-correlated. These data document adaptive, spatial and temporal, co-evolutionary trajectories at the critical interfaces of MLVs and the host factors that restrict their replication.
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Affiliation(s)
- Guney Boso
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (G.B.); (O.L.); (D.B.); (Q.L.); (E.S.)
| | - Oscar Lam
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (G.B.); (O.L.); (D.B.); (Q.L.); (E.S.)
| | - Devinka Bamunusinghe
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (G.B.); (O.L.); (D.B.); (Q.L.); (E.S.)
| | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (A.J.O.); (K.W.)
| | - Kurt Wollenberg
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (A.J.O.); (K.W.)
| | - Qingping Liu
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (G.B.); (O.L.); (D.B.); (Q.L.); (E.S.)
| | - Esther Shaffer
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (G.B.); (O.L.); (D.B.); (Q.L.); (E.S.)
| | - Christine A. Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (G.B.); (O.L.); (D.B.); (Q.L.); (E.S.)
- Correspondence:
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14
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Namkoong H, Omae Y, Asakura T, Ishii M, Suzuki S, Morimoto K, Kawai Y, Emoto K, Oler AJ, Szymanski EP, Yoshida M, Matsuda S, Yagi K, Hase I, Nishimura T, Sasaki Y, Asami T, Shiomi T, Matsubara H, Shimada H, Hamamoto J, Jhun BW, Kim SY, Huh HJ, Won HH, Ato M, Kosaki K, Betsuyaku T, Fukunaga K, Kurashima A, Tettelin H, Yanai H, Mahasirimongkol S, Olivier KN, Hoshino Y, Koh WJ, Holland SM, Tokunaga K, Hasegawa N. Genome-wide association study in patients with pulmonary Mycobacterium avium complex disease. Eur Respir J 2021; 58:13993003.02269-2019. [PMID: 33542050 DOI: 10.1183/13993003.02269-2019] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 12/30/2020] [Indexed: 12/26/2022]
Abstract
RATIONALE Nontuberculous mycobacteria (NTM) are environmental mycobacteria that can cause a chronic progressive lung disease. Although epidemiological data indicate potential genetic predisposition, its nature remains unclear. OBJECTIVES We aimed to identify host susceptibility loci for Mycobacterium avium complex (MAC), the most common NTM pathogen. METHODS This genome-wide association study (GWAS) was conducted in Japanese patients with pulmonary MAC and healthy controls, followed by genotyping of candidate single-nucleotide polymorphisms (SNPs) in another Japanese cohort. For verification by Korean and European ancestry, we performed SNP genotyping. RESULTS The GWAS discovery set included 475 pulmonary MAC cases and 417 controls. Both GWAS and replication analysis of 591 pulmonary MAC cases and 718 controls revealed the strongest association with chromosome 16p21, particularly with rs109592 (p=1.64×10-13, OR 0.54), which is in an intronic region of the calcineurin-like EF-hand protein 2 (CHP2). Expression quantitative trait loci analysis demonstrated an association with lung CHP2 expression. CHP2 was expressed in the lung tissue in pulmonary MAC disease. This SNP was associated with the nodular bronchiectasis subtype. Additionally, this SNP was significantly associated with the disease in patients of Korean (p=2.18×10-12, OR 0.54) and European (p=5.12×10-03, OR 0.63) ancestry. CONCLUSIONS We identified rs109592 in the CHP2 locus as a susceptibility marker for pulmonary MAC disease.
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Affiliation(s)
- Ho Namkoong
- Division of Pulmonary Medicine, Dept of Medicine, Keio University School of Medicine, Tokyo, Japan.,Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, USA.,JSPS Overseas Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan.,H. Namkoong and Y. Omae are co-first authors.,H. Namkoong, N. Hasegawa and K. Tokunaga contributed equally to this article as lead authors and supervised the work
| | - Yosuke Omae
- Dept of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project (Toyama), National Center for Global Health and Medicine, Tokyo, Japan.,H. Namkoong and Y. Omae are co-first authors
| | - Takanori Asakura
- Division of Pulmonary Medicine, Dept of Medicine, Keio University School of Medicine, Tokyo, Japan.,Dept of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ishii
- Division of Pulmonary Medicine, Dept of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shoji Suzuki
- Division of Pulmonary Medicine, Dept of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kozo Morimoto
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Yosuke Kawai
- Dept of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project (Toyama), National Center for Global Health and Medicine, Tokyo, Japan
| | - Katsura Emoto
- Dept of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Eva P Szymanski
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Mitsunori Yoshida
- Dept of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shuichi Matsuda
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Kazuma Yagi
- Division of Pulmonary Medicine, Dept of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Isano Hase
- Dept of Respiratory Medicine, National Hospital Organization Utsunomiya Hospital, Tochigi, Japan
| | | | - Yuka Sasaki
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Takahiro Asami
- Division of Pulmonary Medicine, Dept of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Tetsuya Shiomi
- Dept of Pulmonary Medicine, Keiyu Hospital, Kanagawa, Japan
| | | | - Hisato Shimada
- Dept of Pulmonary Medicine, Kawasaki Municipal Ida Hospital, Kanagawa, Japan
| | - Junko Hamamoto
- Division of Pulmonary Medicine, Dept of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hee Jae Huh
- Dept of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
| | - Manabu Ato
- Dept of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Tomoko Betsuyaku
- Division of Pulmonary Medicine, Dept of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Dept of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Atsuyuki Kurashima
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Hervé Tettelin
- Dept of Microbiology and Immunology, School of Medicine, University of Maryland, Bethesda, MD, USA.,Institute for Genome Sciences, School of Medicine, University of Maryland, Bethesda, MD, USA
| | - Hideki Yanai
- Dept of Clinical Laboratory, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Surakameth Mahasirimongkol
- Medical Genetics Center, Medical Life Sciences Institute, Dept of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Kenneth N Olivier
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yoshihiko Hoshino
- Dept of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Katsushi Tokunaga
- Dept of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project (Toyama), National Center for Global Health and Medicine, Tokyo, Japan.,H. Namkoong, N. Hasegawa and K. Tokunaga contributed equally to this article as lead authors and supervised the work
| | - Naoki Hasegawa
- Dept of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan.,H. Namkoong, N. Hasegawa and K. Tokunaga contributed equally to this article as lead authors and supervised the work
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15
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de Jesus AA, Hou Y, Brooks S, Malle L, Biancotto A, Huang Y, Calvo KR, Marrero B, Moir S, Oler AJ, Deng Z, Montealegre Sanchez GA, Ahmed A, Allenspach E, Arabshahi B, Behrens E, Benseler S, Bezrodnik L, Bout-Tabaku S, Brescia AC, Brown D, Burnham JM, Caldirola MS, Carrasco R, Chan AY, Cimaz R, Dancey P, Dare J, DeGuzman M, Dimitriades V, Ferguson I, Ferguson P, Finn L, Gattorno M, Grom AA, Hanson EP, Hashkes PJ, Hedrich CM, Herzog R, Horneff G, Jerath R, Kessler E, Kim H, Kingsbury DJ, Laxer RM, Lee PY, Lee-Kirsch MA, Lewandowski L, Li S, Lilleby V, Mammadova V, Moorthy LN, Nasrullayeva G, O'Neil KM, Onel K, Ozen S, Pan N, Pillet P, Piotto DG, Punaro MG, Reiff A, Reinhardt A, Rider LG, Rivas-Chacon R, Ronis T, Rösen-Wolff A, Roth J, Ruth NM, Rygg M, Schmeling H, Schulert G, Scott C, Seminario G, Shulman A, Sivaraman V, Son MB, Stepanovskiy Y, Stringer E, Taber S, Terreri MT, Tifft C, Torgerson T, Tosi L, Van Royen-Kerkhof A, Wampler Muskardin T, Canna SW, Goldbach-Mansky R. Distinct interferon signatures and cytokine patterns define additional systemic autoinflammatory diseases. J Clin Invest 2020; 130:1669-1682. [PMID: 31874111 DOI: 10.1172/jci129301] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 12/18/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUNDUndifferentiated systemic autoinflammatory diseases (USAIDs) present diagnostic and therapeutic challenges. Chronic interferon (IFN) signaling and cytokine dysregulation may identify diseases with available targeted treatments.METHODSSixty-six consecutively referred USAID patients underwent underwent screening for the presence of an interferon signature using a standardized type-I IFN-response-gene score (IRG-S), cytokine profiling, and genetic evaluation by next-generation sequencing.RESULTSThirty-six USAID patients (55%) had elevated IRG-S. Neutrophilic panniculitis (40% vs. 0%), basal ganglia calcifications (46% vs. 0%), interstitial lung disease (47% vs. 5%), and myositis (60% vs. 10%) were more prevalent in patients with elevated IRG-S. Moderate IRG-S elevation and highly elevated serum IL-18 distinguished 8 patients with pulmonary alveolar proteinosis (PAP) and recurrent macrophage activation syndrome (MAS). Among patients with panniculitis and progressive cytopenias, 2 patients were compound heterozygous for potentially novel LRBA mutations, 4 patients harbored potentially novel splice variants in IKBKG (which encodes NF-κB essential modulator [NEMO]), and 6 patients had de novo frameshift mutations in SAMD9L. Of additional 12 patients with elevated IRG-S and CANDLE-, SAVI- or Aicardi-Goutières syndrome-like (AGS-like) phenotypes, 5 patients carried mutations in either SAMHD1, TREX1, PSMB8, or PSMG2. Two patients had anti-MDA5 autoantibody-positive juvenile dermatomyositis, and 7 could not be classified. Patients with LRBA, IKBKG, and SAMD9L mutations showed a pattern of IRG elevation that suggests prominent NF-κB activation different from the canonical interferonopathies CANDLE, SAVI, and AGS.CONCLUSIONSIn patients with elevated IRG-S, we identified characteristic clinical features and 3 additional autoinflammatory diseases: IL-18-mediated PAP and recurrent MAS (IL-18PAP-MAS), NEMO deleted exon 5-autoinflammatory syndrome (NEMO-NDAS), and SAMD9L-associated autoinflammatory disease (SAMD9L-SAAD). The IRG-S expands the diagnostic armamentarium in evaluating USAIDs and points to different pathways regulating IRG expression.TRIAL REGISTRATIONClinicalTrials.gov NCT02974595.FUNDINGThe Intramural Research Program of the NIH, NIAID, NIAMS, and the Clinical Center.
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Affiliation(s)
- Adriana A de Jesus
- Translational Autoinflammatory Diseases Section (TADS), NIAID/NIH, Bethesda, Maryland, USA
| | - Yangfeng Hou
- Department of Rheumatology, Shandong Provincial Qianfoshan Hospital, Shandong University, Shandong, China
| | - Stephen Brooks
- Biomining and Discovery Section, NIAMS/NIH, Bethesda, Maryland, USA
| | - Louise Malle
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Angelique Biancotto
- Immunology & Inflammation Research Therapeutic Area, Sanofi, Boston, Massachusetts, USA
| | - Yan Huang
- Translational Autoinflammatory Diseases Section (TADS), NIAID/NIH, Bethesda, Maryland, USA
| | - Katherine R Calvo
- Department of Laboratory Medicine (DLM), Clinical Center/NIH, Bethesda, Maryland, USA
| | | | | | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch (BCBB), Office of Cyber Infrastructure and Computational Biology (OCICB), NIAID/NIH, Bethesda, Maryland, USA
| | - Zuoming Deng
- Biomining and Discovery Section, NIAMS/NIH, Bethesda, Maryland, USA
| | | | - Amina Ahmed
- The Autoinflammatory Diseases Consortium.,Levine Children's Hospital, Charlotte, North Carolina, USA
| | - Eric Allenspach
- The Autoinflammatory Diseases Consortium.,Divisions of Immunology & Rheumatology, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, Washington, USA
| | - Bita Arabshahi
- The Autoinflammatory Diseases Consortium.,Virginia Commonwealth University & Pediatric Specialists of Virginia, Fairfax, Virginia, USA
| | - Edward Behrens
- The Autoinflammatory Diseases Consortium.,Division of Rheumatology, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Susanne Benseler
- The Autoinflammatory Diseases Consortium.,Department of Pediatrics, Pediatric Rheumatology Section, Alberta Children's Hospital, University of Calgary, Calgary, Alberta, Canada
| | - Liliana Bezrodnik
- The Autoinflammatory Diseases Consortium.,Immunology Unit, Pediatric Hospital R. Gutierrez, Buenos Aires, Argentina
| | - Sharon Bout-Tabaku
- The Autoinflammatory Diseases Consortium.,Department of Pediatric Medicine, Sidra Medicine, Qatar Foundation, Doha, Qatar
| | - AnneMarie C Brescia
- The Autoinflammatory Diseases Consortium.,Nemours/Alfred I. DuPont Hospital for Children, Wilmington, Delaware, USA
| | - Diane Brown
- The Autoinflammatory Diseases Consortium.,Division of Rheumatology, Children's Hospital Los Angeles & USC, Los Angeles, California, USA
| | - Jon M Burnham
- The Autoinflammatory Diseases Consortium.,Division of Rheumatology, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maria Soledad Caldirola
- The Autoinflammatory Diseases Consortium.,Immunology Unit, Pediatric Hospital R. Gutierrez, Buenos Aires, Argentina
| | - Ruy Carrasco
- The Autoinflammatory Diseases Consortium.,Pediatric Rheumatology, Dell Children's Medical Center of Central Texas, Austin, Texas, USA
| | - Alice Y Chan
- The Autoinflammatory Diseases Consortium.,Divisions of Pediatric AIBMT & Rheumatology, UCSF, San Francisco, California, USA
| | - Rolando Cimaz
- The Autoinflammatory Diseases Consortium.,Department of Clinical Sciences and Community Health, University of Milano, Milan, Italy
| | - Paul Dancey
- The Autoinflammatory Diseases Consortium.,Division of Rheumatology, Janeway Children's Hospital & Rehabilitation Centre, Saint John's, Newfoundland and Labrador, Canada
| | - Jason Dare
- The Autoinflammatory Diseases Consortium.,Division of Pediatric Rheumatology, University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Little Rock, Arkansas, USA
| | - Marietta DeGuzman
- The Autoinflammatory Diseases Consortium.,Department of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, Texas, USA
| | - Victoria Dimitriades
- The Autoinflammatory Diseases Consortium.,Division of Pediatric Allergy, Immunology & Rheumatology, UC Davis Health, Sacramento, California, USA
| | - Ian Ferguson
- The Autoinflammatory Diseases Consortium.,Department of Pediatrics/Pediatric Rheumatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Polly Ferguson
- The Autoinflammatory Diseases Consortium.,Pediatrics Department, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Laura Finn
- The Autoinflammatory Diseases Consortium.,Pathology Department, University of Washington and Seattle Children's Hospital, Seattle, Washington, USA
| | - Marco Gattorno
- The Autoinflammatory Diseases Consortium.,Center for Autoinflammatory Diseases and Immunedeficiencies, IRCCS Giannina Gaslini, Genoa, Italy
| | - Alexei A Grom
- The Autoinflammatory Diseases Consortium.,Division of Rheumatology, Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Eric P Hanson
- The Autoinflammatory Diseases Consortium.,Department of Pediatrics Indiana University School of Medicine and Riley Hospital for Children, Indianapolis, Indiana, USA
| | - Philip J Hashkes
- The Autoinflammatory Diseases Consortium.,Pediatric Rheumatology Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Christian M Hedrich
- The Autoinflammatory Diseases Consortium.,Department of Women's & Children's Health, Institute of Translational Medicine, University of Liverpool & Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, United Kingdom
| | - Ronit Herzog
- The Autoinflammatory Diseases Consortium.,Department of Otolaryngology, Division of Allergy and Immunology, New York University, New York, New York, USA
| | - Gerd Horneff
- The Autoinflammatory Diseases Consortium.,Asklepios Klinik Sankt, Augustin GmbH, St. Augustin, Germany and Department of Pediatric and Adolescents Medicine, University of Cologne, Cologne, Germany
| | - Rita Jerath
- The Autoinflammatory Diseases Consortium.,Augusta University Medical Center, Augusta, Georgia, USA
| | - Elizabeth Kessler
- The Autoinflammatory Diseases Consortium.,Division of Rheumatology, Children's Mercy, Kansas City and University of Missouri, Kansas City, Missouri, USA
| | - Hanna Kim
- The Autoinflammatory Diseases Consortium.,Pediatric Translational Research Branch, NIAMS/NIH, Bethesda, Maryland, USA
| | - Daniel J Kingsbury
- The Autoinflammatory Diseases Consortium.,Randall Children's Hospital at Legacy Emanuel, Portland, Oregon, USA
| | - Ronald M Laxer
- The Autoinflammatory Diseases Consortium.,Division of Pediatric Rheumatology, University of Toronto and The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pui Y Lee
- The Autoinflammatory Diseases Consortium.,Division of Allergy, Immunology and Rheumatology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Min Ae Lee-Kirsch
- The Autoinflammatory Diseases Consortium.,Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Laura Lewandowski
- The Autoinflammatory Diseases Consortium.,Systemic Autoimmunity Branch, NIAMS/NIH, Bethesda, Maryland, USA
| | - Suzanne Li
- The Autoinflammatory Diseases Consortium.,Hackensack University Medical Center, Hackensack Meridian School of Medicine at Seton Hall University, Hackensack, New Jersey, USA
| | - Vibke Lilleby
- The Autoinflammatory Diseases Consortium.,Department of Rheumatology, Pediatric Section, Oslo University Hospital, Oslo, Norway
| | - Vafa Mammadova
- The Autoinflammatory Diseases Consortium.,Azerbaijan Medical University, Baku, Azerbaijan
| | - Lakshmi N Moorthy
- The Autoinflammatory Diseases Consortium.,Rutgers - Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Gulnara Nasrullayeva
- The Autoinflammatory Diseases Consortium.,Azerbaijan Medical University, Baku, Azerbaijan
| | - Kathleen M O'Neil
- The Autoinflammatory Diseases Consortium.,Department of Pediatrics Indiana University School of Medicine and Riley Hospital for Children, Indianapolis, Indiana, USA
| | - Karen Onel
- The Autoinflammatory Diseases Consortium.,Division of Pediatric Rheumatology, Weill Cornell Medicine & Hospital for Special Surgery, New York, New York, USA
| | - Seza Ozen
- The Autoinflammatory Diseases Consortium.,Hacettepe University, Department of Pediatrics, Ankara, Turkey
| | - Nancy Pan
- The Autoinflammatory Diseases Consortium.,Division of Pediatric Rheumatology, Weill Cornell Medicine & Hospital for Special Surgery, New York, New York, USA
| | - Pascal Pillet
- The Autoinflammatory Diseases Consortium.,Children Hospital Pellegrin-Enfants, Bordeaux, France
| | - Daniela Gp Piotto
- The Autoinflammatory Diseases Consortium.,Department of Pediatric Rheumatology, Federal University of Sao Paulo, Sao Paulo, Brazil
| | - Marilynn G Punaro
- The Autoinflammatory Diseases Consortium.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Andreas Reiff
- The Autoinflammatory Diseases Consortium.,Division of Rheumatology, Children's Hospital Los Angeles, Keck School of Medicine, USC, Los Angeles, California, USA
| | - Adam Reinhardt
- The Autoinflammatory Diseases Consortium.,University of Nebraska Medical Center/Children's Hospital and Medical Center, Omaha, Nebraska, USA
| | - Lisa G Rider
- The Autoinflammatory Diseases Consortium.,Environmental Autoimmunity Group, NIEHS/NIH, Bethesda, Maryland, USA
| | - Rafael Rivas-Chacon
- The Autoinflammatory Diseases Consortium.,Department of Pediatric Rheumatology, Nicklaus Children's Hospital, Miami, Florida, USA
| | - Tova Ronis
- The Autoinflammatory Diseases Consortium.,Division of Pediatric Rheumatology, Children's National Health System, Washington, DC, USA
| | - Angela Rösen-Wolff
- The Autoinflammatory Diseases Consortium.,Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Johannes Roth
- The Autoinflammatory Diseases Consortium.,Division of Pediatric Dermatology and Rheumatology, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Natasha Mckerran Ruth
- The Autoinflammatory Diseases Consortium.,Medical University of South Carolina, Charleston, South Carolina, USA
| | - Marite Rygg
- The Autoinflammatory Diseases Consortium.,Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, and Department of Pediatrics, St. Olavs Hospital, Trondheim, Norway
| | - Heinrike Schmeling
- The Autoinflammatory Diseases Consortium.,Department of Pediatrics, Pediatric Rheumatology Section, Alberta Children's Hospital, University of Calgary, Calgary, Alberta, Canada
| | - Grant Schulert
- The Autoinflammatory Diseases Consortium.,Division of Rheumatology, Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Christiaan Scott
- The Autoinflammatory Diseases Consortium.,University of Cape Town, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Gisella Seminario
- The Autoinflammatory Diseases Consortium.,Immunology Unit, Pediatric Hospital R. Gutierrez, Buenos Aires, Argentina
| | - Andrew Shulman
- The Autoinflammatory Diseases Consortium.,Pediatric Rheumatology, Children's Hospital of Orange County, UC Irvine, Irvine, California, USA
| | - Vidya Sivaraman
- The Autoinflammatory Diseases Consortium.,Section of Rheumatology, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Mary Beth Son
- The Autoinflammatory Diseases Consortium.,Division of Immunology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Yuriy Stepanovskiy
- The Autoinflammatory Diseases Consortium.,Department of Pediatric Infectious Diseases and Immunology, Shupyk National Medical Academy for Postgraduate Education, Kiev, Ukraine
| | - Elizabeth Stringer
- The Autoinflammatory Diseases Consortium.,IWK Health Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sara Taber
- The Autoinflammatory Diseases Consortium.,Division of Pediatric Rheumatology, Department of Rheumatology, Hospital for Special Surgery, New York, New York, USA
| | - Maria Teresa Terreri
- The Autoinflammatory Diseases Consortium.,Department of Pediatric Rheumatology, Federal University of Sao Paulo, Sao Paulo, Brazil
| | - Cynthia Tifft
- The Autoinflammatory Diseases Consortium.,Undiagnosed Diseases Program, NHGRI/NIH, Bethesda, Maryland, USA
| | - Troy Torgerson
- The Autoinflammatory Diseases Consortium.,Divisions of Immunology & Rheumatology, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, Washington, USA
| | - Laura Tosi
- The Autoinflammatory Diseases Consortium.,Bone Health Program, Children's National Health System, Washington, DC, USA
| | - Annet Van Royen-Kerkhof
- The Autoinflammatory Diseases Consortium.,Department of Pediatric Immunology and Rheumatology, Wilhelmina Children's Hospital Utrecht, Utrecht, Netherlands
| | - Theresa Wampler Muskardin
- The Autoinflammatory Diseases Consortium.,New York University School of Medicine, New York, New York, USA
| | - Scott W Canna
- Children's Hospital Pittsburgh, Pittsburgh, Pennsylvania, USA
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16
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Ghosh S, Köstel Bal S, Edwards ESJ, Pillay B, Jiménez Heredia R, Erol Cipe F, Rao G, Salzer E, Zoghi S, Abolhassani H, Momen T, Gostick E, Price DA, Zhang Y, Oler AJ, Gonzaga-Jauregui C, Erman B, Metin A, Ilhan I, Haskologlu S, Islamoglu C, Baskin K, Ceylaner S, Yilmaz E, Unal E, Karakukcu M, Berghuis D, Cole T, Gupta AK, Hauck F, Kogler H, Hoepelman AIM, Baris S, Karakoc-Aydiner E, Ozen A, Kager L, Holzinger D, Paulussen M, Krüger R, Meisel R, Oommen PT, Morris E, Neven B, Worth A, van Montfrans J, Fraaij PLA, Choo S, Dogu F, Davies EG, Burns S, Dückers G, Becker RP, von Bernuth H, Latour S, Faraci M, Gattorno M, Su HC, Pan-Hammarström Q, Hammarström L, Lenardo MJ, Ma CS, Niehues T, Aghamohammadi A, Rezaei N, Ikinciogullari A, Tangye SG, Lankester AC, Boztug K. Extended clinical and immunological phenotype and transplant outcome in CD27 and CD70 deficiency. Blood 2020; 136:2638-2655. [PMID: 32603431 PMCID: PMC7735164 DOI: 10.1182/blood.2020006738] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/10/2020] [Indexed: 12/31/2022] Open
Abstract
Biallelic mutations in the genes encoding CD27 or its ligand CD70 underlie inborn errors of immunity (IEIs) characterized predominantly by Epstein-Barr virus (EBV)-associated immune dysregulation, such as chronic viremia, severe infectious mononucleosis, hemophagocytic lymphohistiocytosis (HLH), lymphoproliferation, and malignancy. A comprehensive understanding of the natural history, immune characteristics, and transplant outcomes has remained elusive. Here, in a multi-institutional global collaboration, we collected the clinical information of 49 patients from 29 families (CD27, n = 33; CD70, n = 16), including 24 previously unreported individuals and identified a total of 16 distinct mutations in CD27, and 8 in CD70, respectively. The majority of patients (90%) were EBV+ at diagnosis, but only ∼30% presented with infectious mononucleosis. Lymphoproliferation and lymphoma were the main clinical manifestations (70% and 43%, respectively), and 9 of the CD27-deficient patients developed HLH. Twenty-one patients (43%) developed autoinflammatory features including uveitis, arthritis, and periodic fever. Detailed immunological characterization revealed aberrant generation of memory B and T cells, including a paucity of EBV-specific T cells, and impaired effector function of CD8+ T cells, thereby providing mechanistic insight into cellular defects underpinning the clinical features of disrupted CD27/CD70 signaling. Nineteen patients underwent allogeneic hematopoietic stem cell transplantation (HSCT) prior to adulthood predominantly because of lymphoma, with 95% survival without disease recurrence. Our data highlight the marked predisposition to lymphoma of both CD27- and CD70-deficient patients. The excellent outcome after HSCT supports the timely implementation of this treatment modality particularly in patients presenting with malignant transformation to lymphoma.
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Affiliation(s)
- Sujal Ghosh
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, Düsseldorf, Germany
| | - Sevgi Köstel Bal
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Emily S J Edwards
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St. Vincent's Clinical School, UNSW Sydney, Randwick, NSW, Australia
| | - Bethany Pillay
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St. Vincent's Clinical School, UNSW Sydney, Randwick, NSW, Australia
| | - Raúl Jiménez Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Funda Erol Cipe
- Department of Pediatric Allergy and Immunology, Istinye University, Istanbul, Turkey
| | - Geetha Rao
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Elisabeth Salzer
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Samaneh Zoghi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Abolhassani
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Tooba Momen
- Department of Allergy and Clinical Immunology, Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Emma Gostick
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - David A Price
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Vaccine Research Center
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research
- Clinical Genomics Program, and
| | - Andrew J Oler
- Clinical Genomics Program, and
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD
| | | | - Baran Erman
- Institute of Child Health, Hacettepe University, Ankara, Turkey
- Can Sucak Research Laboratory for Translational Immunology, Center for Genomics and Rare Diseases, Hacettepe University, Ankara, Turkey
| | - Ayse Metin
- Division of Pediatric Allergy and Immunology, University of Health Sciences/Ankara City Hospital/Children's Hospital, Ankara, Turkey
| | - Inci Ilhan
- Division of Pediatric Oncology, University of Health Sciences/Ankara City Hospital/Children's Hospital, Ankara, Turkey
| | - Sule Haskologlu
- Department of Pediatric Allergy and Immunology, School of Medicine, Ankara University, Ankara, Turkey
| | - Candan Islamoglu
- Department of Pediatric Allergy and Immunology, School of Medicine, Ankara University, Ankara, Turkey
| | - Kubra Baskin
- Department of Pediatric Allergy and Immunology, School of Medicine, Ankara University, Ankara, Turkey
| | - Serdar Ceylaner
- Intergen Genetic Diagnosis and Research Center, Ankara, Turkey
| | - Ebru Yilmaz
- Department of Pediatrics, Division of Pediatric Hematology & Oncology & Molecular Biology and Genetic Department, Erciyes University, Kayseri, Turkey
- Gevher Nesibe Genom and Stem Cell Institution, GENKOK Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey
| | - Ekrem Unal
- Department of Pediatrics, Division of Pediatric Hematology & Oncology & Molecular Biology and Genetic Department, Erciyes University, Kayseri, Turkey
- Gevher Nesibe Genom and Stem Cell Institution, GENKOK Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey
| | - Musa Karakukcu
- Department of Pediatrics, Division of Pediatric Hematology & Oncology & Molecular Biology and Genetic Department, Erciyes University, Kayseri, Turkey
- Gevher Nesibe Genom and Stem Cell Institution, GENKOK Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey
| | - Dagmar Berghuis
- Willem-Alexander Children's Hospital, Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Theresa Cole
- Department of Allergy and Immunology, The Royal Children's Hospital, Melbourne, VIC, Australia
| | - Aditya K Gupta
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Fabian Hauck
- Dr von Hauner Children's Hospital, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Hubert Kogler
- St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Andy I M Hoepelman
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Safa Baris
- Division of Allergy and Immunology, Marmara University, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
| | - Elif Karakoc-Aydiner
- Division of Allergy and Immunology, Marmara University, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
| | - Ahmet Ozen
- Division of Allergy and Immunology, Marmara University, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
| | - Leo Kager
- St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Dirk Holzinger
- Department of Pediatric Hematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Michael Paulussen
- Vestische Kinder-und Jugendklinik, Witten/Herdecke University, Datteln, Germany
| | - Renate Krüger
- Department of Pediatric Pulmonology, Immunology, and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Roland Meisel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, Düsseldorf, Germany
| | - Prasad T Oommen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, Düsseldorf, Germany
| | - Emma Morris
- Institute of Immunity & Transplantation, University College London, Royal Free Hospital, London, United Kingdom
| | - Benedicte Neven
- Unité d'Immuno-Hematologie et Rhumatologie, Département de Pédiatrie Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
- INSERM U1163, Imagine Institute, Université de Paris, Paris, France
| | - Austen Worth
- UCL Great Ormond Street Institute of Child Health, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Joris van Montfrans
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, UMC Utrecht, Utrecht, The Netherlands
| | - Pieter L A Fraaij
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
- Department of Pediatrics, Subdivision Infectious Diseases and Immunology, Erasmus MC-Sophia, Rotterdam, The Netherlands
| | - Sharon Choo
- Department of Allergy and Immunology, The Royal Children's Hospital, Melbourne, VIC, Australia
| | - Figen Dogu
- Department of Pediatric Allergy and Immunology, School of Medicine, Ankara University, Ankara, Turkey
| | - E Graham Davies
- UCL Great Ormond Street Institute of Child Health, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Siobhan Burns
- Institute of Immunity & Transplantation, University College London, Royal Free Hospital, London, United Kingdom
- Department of Immunology, Royal Free London National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Gregor Dückers
- Department of Pediatrics, Helios Children's Hospital, Krefeld, Germany
| | - Ruy Perez Becker
- Department of Pediatrics, Helios Children's Hospital, Krefeld, Germany
| | - Horst von Bernuth
- Department of Pediatric Pulmonology, Immunology, and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Immunology, Labor Berlin GmbH, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Berlin, Germany
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV infection, INSERM U1163, Imagine Institute, Université de Paris, Paris, France
| | - Maura Faraci
- Hematopoietic Stem Cell Transplantation Unit and Istituto di Ricovero e Cura Pediatrico a Carattere Scientifico (IRCSS) Istituto Giannina Gaslini Research Institute Genova, Italy
| | - Marco Gattorno
- Center for Autoinflammatory Diseases and Immunodeficiency, Istituto di Ricovero e Cura Pediatrico a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Genova, Italy
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research
- Clinical Genomics Program, and
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition (NEO), Karolinska Institutet, Karolinska, Sweden
| | - Lennart Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Karolinska Institutet, Stockholm, Sweden
- Beijing Genomics Institute (BGI) Shenzhen, Shenzhen, China
| | - Michael J Lenardo
- Clinical Genomics Program, and
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, MD
| | - Cindy S Ma
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St. Vincent's Clinical School, UNSW Sydney, Randwick, NSW, Australia
| | - Tim Niehues
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Primary Immunodeficiency Diseases Network (PIDNet), Universal Scientific Education and Research Network (USERN), Tehran, Iran; and
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Primary Immunodeficiency Diseases Network (PIDNet), Universal Scientific Education and Research Network (USERN), Tehran, Iran; and
| | - Aydan Ikinciogullari
- Department of Pediatric Allergy and Immunology, School of Medicine, Ankara University, Ankara, Turkey
| | - Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St. Vincent's Clinical School, UNSW Sydney, Randwick, NSW, Australia
| | - Arjan C Lankester
- Willem-Alexander Children's Hospital, Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
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17
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Bastard P, Rosen LB, Zhang Q, Michailidis E, Hoffmann HH, Zhang Y, Dorgham K, Philippot Q, Rosain J, Béziat V, Manry J, Shaw E, Haljasmägi L, Peterson P, Lorenzo L, Bizien L, Trouillet-Assant S, Dobbs K, de Jesus AA, Belot A, Kallaste A, Catherinot E, Tandjaoui-Lambiotte Y, Le Pen J, Kerner G, Bigio B, Seeleuthner Y, Yang R, Bolze A, Spaan AN, Delmonte OM, Abers MS, Aiuti A, Casari G, Lampasona V, Piemonti L, Ciceri F, Bilguvar K, Lifton RP, Vasse M, Smadja DM, Migaud M, Hadjadj J, Terrier B, Duffy D, Quintana-Murci L, van de Beek D, Roussel L, Vinh DC, Tangye SG, Haerynck F, Dalmau D, Martinez-Picado J, Brodin P, Nussenzweig MC, Boisson-Dupuis S, Rodríguez-Gallego C, Vogt G, Mogensen TH, Oler AJ, Gu J, Burbelo PD, Cohen JI, Biondi A, Bettini LR, D'Angio M, Bonfanti P, Rossignol P, Mayaux J, Rieux-Laucat F, Husebye ES, Fusco F, Ursini MV, Imberti L, Sottini A, Paghera S, Quiros-Roldan E, Rossi C, Castagnoli R, Montagna D, Licari A, Marseglia GL, Duval X, Ghosn J, Tsang JS, Goldbach-Mansky R, Kisand K, Lionakis MS, Puel A, Zhang SY, Holland SM, Gorochov G, Jouanguy E, Rice CM, Cobat A, Notarangelo LD, Abel L, Su HC, Casanova JL. Autoantibodies against type I IFNs in patients with life-threatening COVID-19. Science 2020; 370:eabd4585. [PMID: 32972996 PMCID: PMC7857397 DOI: 10.1126/science.abd4585] [Citation(s) in RCA: 1683] [Impact Index Per Article: 420.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022]
Abstract
Interindividual clinical variability in the course of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is vast. We report that at least 101 of 987 patients with life-threatening coronavirus disease 2019 (COVID-19) pneumonia had neutralizing immunoglobulin G (IgG) autoantibodies (auto-Abs) against interferon-ω (IFN-ω) (13 patients), against the 13 types of IFN-α (36), or against both (52) at the onset of critical disease; a few also had auto-Abs against the other three type I IFNs. The auto-Abs neutralize the ability of the corresponding type I IFNs to block SARS-CoV-2 infection in vitro. These auto-Abs were not found in 663 individuals with asymptomatic or mild SARS-CoV-2 infection and were present in only 4 of 1227 healthy individuals. Patients with auto-Abs were aged 25 to 87 years and 95 of the 101 were men. A B cell autoimmune phenocopy of inborn errors of type I IFN immunity accounts for life-threatening COVID-19 pneumonia in at least 2.6% of women and 12.5% of men.
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Affiliation(s)
- 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
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Lindsey B Rosen
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Karim Dorgham
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses, (CIMI-Paris), 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
| | - 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
| | - Vivien Béziat
- 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
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jérémy Manry
- 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
| | - Elana Shaw
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Liis Haljasmägi
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Pärt Peterson
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Lazaro Lorenzo
- 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
| | - Lucy Bizien
- 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
| | - Sophie Trouillet-Assant
- Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite, France
- International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Adriana Almeida de Jesus
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Alexandre Belot
- International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France
- National Referee Centre for Rheumatic and AutoImmune and Systemic Diseases in Children (RAISE), Lyon, France
- Lyon Immunopathology Federation (LIFE), Hospices Civils de Lyon, Lyon, France
| | - Anne Kallaste
- Internal Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | | | - Yacine Tandjaoui-Lambiotte
- Avicenne Hospital, Assistance Publique Hôpitaux de Paris (AP-HP), Bobigny, INSERM U1272 Hypoxia and Lung, Bobigny, France
| | - Jeremie Le Pen
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Gaspard Kerner
- 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
| | - Rui Yang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | | | - 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
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Michael S Abers
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Alessandro Aiuti
- IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
| | - Giorgio Casari
- IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
| | - Vito Lampasona
- IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
| | - Lorenzo Piemonti
- IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
| | - Fabio Ciceri
- IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
| | - Kaya Bilguvar
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Genome Analysis, Yale University School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Marc Vasse
- Service de Biologie Clinique and UMR-S 1176, Hôpital Foch, Suresnes, France
| | - David M Smadja
- INSERM UMR-S 1140, Biosurgical Research Laboratory (Carpentier Foundation), Paris University and European Georges Pompidou Hospital, Paris, France
| | - Mélanie Migaud
- 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
| | - Jérome Hadjadj
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, University of Paris, Imagine Institute, Paris, France
| | - Benjamin Terrier
- Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hôpitaux de Paris-Centre (APHP-CUP), University of Paris, Paris, France
| | - Darragh Duffy
- Translational Immunology Laboratory, Institut Pasteur, Paris, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, CNRS UMR 2000, 75015, Paris, France
- Human Genomics and Evolution, Collège de France, Paris, France
| | - Diederik van de Beek
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Lucie Roussel
- Department of Medicine, Division of Infectious Diseases, McGill University Health Centre, Montréal, Québec, Canada
- Infectious Disease Susceptibility Program, Research Institute, McGill University Health Centre, Montréal, Québec, Canada
| | - Donald C Vinh
- Department of Medicine, Division of Infectious Diseases, McGill University Health Centre, Montréal, Québec, Canada
- Infectious Disease Susceptibility Program, Research Institute, McGill University Health Centre, Montréal, Québec, Canada
| | - Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW, Sydney, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Darlinghurst 2010, NSW, Australia
| | - Filomeen Haerynck
- Department of Paediatric Immunology and Pulmonology, Centre for Primary Immunodeficiency Ghent (CPIG), PID Research Laboratory, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
| | - David Dalmau
- Infectious Diseases and HIV Service, Hospital Universitari Mutua Terrassa, Universitat de Barcelona, Fundació Docència i Recerca Mutua Terrassa, Terrassa, Barcelona, Catalonia, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute and Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
- Infectious Diseases and Immunity, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Petter Brodin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Karolinska, Sweden
- Department of Pediatric Rheumatology, Karolinska University Hospital, Karolinska, Sweden
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Stéphanie Boisson-Dupuis
- 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
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Carlos Rodríguez-Gallego
- Department of Immunology, Hospital Universitario de Gran Canaria Dr. Negrín, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Guillaume Vogt
- Neglected Human Genetics Laboratory, INSERM, University of Paris, Paris, France
| | - Trine H Mogensen
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jingwen Gu
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, MD, USA
| | - Peter D Burbelo
- Division of Intramural Research, National Institute of Dental Craniofacial Research (NIDCR), NIH, Bethesda, MD, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale, San Gerardo, Monza, Italy
| | - Laura Rachele Bettini
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale, San Gerardo, Monza, Italy
| | - Mariella D'Angio
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale, San Gerardo, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital - University of Milano-Bicocca, Monza, Italy
| | - Patrick Rossignol
- University of Lorraine, Plurithematic Clinical Investigation Centre INSERM CIC-P 1433, INSERM U1116, CHRU Nancy Hopitaux de Brabois, F-CRIN INI-CRCT (Cardiovascular and Renal Clinical Trialists), Nancy, France
| | - Julien Mayaux
- Intensive Care Unit, Pitié-Salpétrière Hospital, Paris University, AP-HP, Paris, France
| | - Frédéric Rieux-Laucat
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, University of Paris, Imagine Institute, Paris, France
| | - Eystein S Husebye
- Department of Clinical Science and K.G. Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden
| | - Francesca Fusco
- Human Molecular Genetics Laboratory, Institute of Genetics and Biophysics, "A. Buzzati-Traverso" Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Matilde Valeria Ursini
- Human Molecular Genetics Laboratory, Institute of Genetics and Biophysics, "A. Buzzati-Traverso" Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Luisa Imberti
- Centro di Ricerca Emato-oncologica AIL (CREA) Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Alessandra Sottini
- Centro di Ricerca Emato-oncologica AIL (CREA) Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Simone Paghera
- Centro di Ricerca Emato-oncologica AIL (CREA) Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali di Brescia, Brescia, Italy
| | - Camillo Rossi
- Direzione Sanitaria, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Riccardo Castagnoli
- Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Daniela Montagna
- Laboratory of Immunology and Transplantation, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Amelia Licari
- Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Gian Luigi Marseglia
- Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Xavier Duval
- INSERM CIC 1425, Paris, France
- AP-HP, University Hospital of Bichat, Paris, France
- University Paris Diderot, Paris 7, UFR de Médecine-Bichat, Paris, France
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMRS1137, University of Paris, Paris, France
- AP-HP, Bichat Claude Bernard Hospital, Infectious and Tropical Diseases Department, Paris, France
| | - Jade Ghosn
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMRS1137, University of Paris, Paris, France
- AP-HP, Bichat Claude Bernard Hospital, Infectious and Tropical Diseases Department, Paris, France
| | - John S Tsang
- Center for Human Immunology, NIH, Bethesda, MD, USA
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Raphaela Goldbach-Mansky
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kai Kisand
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Anne Puel
- 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
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Shen-Ying Zhang
- 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
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Guy Gorochov
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses, (CIMI-Paris), Paris, France
- Département d'Immunologie, AP-HP, Hôpital Pitié-Salpétrière, Paris, France
| | - Emmanuelle Jouanguy
- 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
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Aurélie Cobat
- 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
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Laurent Abel
- 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
- 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, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jean-Laurent Casanova
- 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
- 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
- Pediatric Hematology and Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
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18
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Zhang Q, Bastard P, Liu Z, Le Pen J, Moncada-Velez M, Chen J, Ogishi M, Sabli IKD, Hodeib S, Korol C, Rosain J, Bilguvar K, Ye J, Bolze A, Bigio B, Yang R, Arias AA, Zhou Q, Zhang Y, Onodi F, Korniotis S, Karpf L, Philippot Q, Chbihi M, Bonnet-Madin L, Dorgham K, Smith N, Schneider WM, Razooky BS, Hoffmann HH, Michailidis E, Moens L, Han JE, Lorenzo L, Bizien L, Meade P, Neehus AL, Ugurbil AC, Corneau A, Kerner G, Zhang P, Rapaport F, Seeleuthner Y, Manry J, Masson C, Schmitt Y, Schlüter A, Le Voyer T, Khan T, Li J, Fellay J, Roussel L, Shahrooei M, Alosaimi MF, Mansouri D, Al-Saud H, Al-Mulla F, Almourfi F, Al-Muhsen SZ, Alsohime F, Al Turki S, Hasanato R, van de Beek D, Biondi A, Bettini LR, D'Angio' M, Bonfanti P, Imberti L, Sottini A, Paghera S, Quiros-Roldan E, Rossi C, Oler AJ, Tompkins MF, Alba C, Vandernoot I, Goffard JC, Smits G, Migeotte I, Haerynck F, Soler-Palacin P, Martin-Nalda A, Colobran R, Morange PE, Keles S, Çölkesen F, Ozcelik T, Yasar KK, Senoglu S, Karabela ŞN, Rodríguez-Gallego C, Novelli G, Hraiech S, Tandjaoui-Lambiotte Y, Duval X, Laouénan C, Snow AL, Dalgard CL, Milner JD, Vinh DC, Mogensen TH, Marr N, Spaan AN, Boisson B, Boisson-Dupuis S, Bustamante J, Puel A, Ciancanelli MJ, Meyts I, Maniatis T, Soumelis V, Amara A, Nussenzweig M, García-Sastre A, Krammer F, Pujol A, Duffy D, Lifton RP, Zhang SY, Gorochov G, Béziat V, Jouanguy E, Sancho-Shimizu V, Rice CM, Abel L, Notarangelo LD, Cobat A, Su HC, Casanova JL. Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science 2020; 370:eabd4570. [PMID: 32972995 PMCID: PMC7857407 DOI: 10.1126/science.abd4570] [Citation(s) in RCA: 1458] [Impact Index Per Article: 364.5] [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: 06/22/2020] [Accepted: 09/16/2020] [Indexed: 12/15/2022]
Abstract
Clinical outcome upon infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ranges from silent infection to lethal coronavirus disease 2019 (COVID-19). We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern Toll-like receptor 3 (TLR3)- and interferon regulatory factor 7 (IRF7)-dependent type I interferon (IFN) immunity to influenza virus in 659 patients with life-threatening COVID-19 pneumonia relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally defined LOF variants underlying autosomal-recessive or autosomal-dominant deficiencies in 23 patients (3.5%) 17 to 77 years of age. We show that human fibroblasts with mutations affecting this circuit are vulnerable to SARS-CoV-2. Inborn errors of TLR3- and IRF7-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in patients with no prior severe infection.
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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, 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
| | - Zhiyong Liu
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jérémie Le Pen
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Marcela Moncada-Velez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jie Chen
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Ira K D Sabli
- Department of Paediatric Infectious Diseases & Virology, Imperial College London, London, UK
| | - Stephanie Hodeib
- Department of Paediatric Infectious Diseases & Virology, Imperial College London, London, UK
| | - Cecilia Korol
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 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
| | - Kaya Bilguvar
- Yale Center for Genome Analysis and Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Junqiang Ye
- Zukerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | | | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Rui Yang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Andrés Augusto Arias
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Primary Immunodeficiencies Group, University of Antioquia UdeA, Medellin, Colombia
- School of Microbiology, University of Antioquia UdeA, Medellin, Colombia
| | - Qinhua Zhou
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Bethesda, MD, USA
| | - Fanny Onodi
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Hôpital Saint-Louis, Paris, France
| | - Sarantis Korniotis
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Hôpital Saint-Louis, Paris, France
| | - Léa Karpf
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Hôpital Saint-Louis, 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
| | - Marwa Chbihi
- 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
| | - Lucie Bonnet-Madin
- Laboratory of Genomes & Cell Biology of Disease, INSERM U944, CNRS UMR 7212, Université de Paris, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Paris, France
| | - Karim Dorgham
- Sorbonne Université, Inserm, Centre d'Immunologie et des Maladies Infectieuses-Paris (CIMI PARIS), Assistance Publique-Hôpitaux de Paris (AP-HP) Hôpital Pitié-Salpêtrière, Paris, France
| | - Nikaïa Smith
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - William M Schneider
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Brandon S Razooky
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Leen Moens
- Laboratory for Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, Department of Pediatrics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Ji Eun Han
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Lazaro Lorenzo
- 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
| | - Lucy Bizien
- 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
| | - Philip Meade
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 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
| | - Aileen Camille Ugurbil
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Aurélien Corneau
- Sorbonne Université, UMS037, PASS, Plateforme de Cytométrie de la Pitié-Salpêtrière CyPS, Paris, France
| | - Gaspard Kerner
- 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
| | - Franck Rapaport
- 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
| | - Jeremy Manry
- 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
| | - Cecile Masson
- Bioinformatics Platform, Structure Fédérative de Recherche Necker, INSERM UMR1163, Université de Paris, Imagine Institute, Paris, France
| | - Yohann Schmitt
- Bioinformatics Platform, Structure Fédérative de Recherche Necker, INSERM UMR1163, Université de Paris, Imagine Institute, Paris, France
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, IDIBELL-Hospital Duran i Reynals, CIBERER U759, and Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - 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
| | - Taushif Khan
- Department of Immunology, Research Branch, Sidra Medicine, Doha, Qatar
| | - Juan Li
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jacques Fellay
- School of Life sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Swiss Institue of Bioinformatics, Lausanne, Switzerland
| | - Lucie Roussel
- Infectious Disease Susceptibility Program, Research Institute, McGill University Health Centre, Montréal, Québec, Canada
| | - 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
| | - Mohammed F Alosaimi
- Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - 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
| | - Haya Al-Saud
- National Center of Genomics Technology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fahd Al-Mulla
- Dasman Diabetes Institute, Department of Genetics and Bioinformatics, Kuwait
| | - Feras Almourfi
- National Center of Genomics Technology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Saleh Zaid Al-Muhsen
- Immunology Research Laboratory, Department of Pediatrics, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Fahad Alsohime
- Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Saeed Al Turki
- Translational Pathology, Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Misery of National Guard Health Affairs, Riyadh, Saudi Arabia
- Cancer & Blood Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Rana Hasanato
- Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Diederik van de Beek
- Amsterdam UMC, Department of Neurology, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Andrea Biondi
- Pediatric Departement and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale, San Gerardo, Monza, Italy
| | - Laura Rachele Bettini
- Pediatric Departement and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale, San Gerardo, Monza, Italy
| | - Mariella D'Angio'
- Pediatric Departement and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale, San Gerardo, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
| | - Luisa Imberti
- CREA Laboratory, Diagnostic Laboratory, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Alessandra Sottini
- CREA Laboratory, Diagnostic Laboratory, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Simone Paghera
- CREA Laboratory, Diagnostic Laboratory, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali di Brescia, Brescia, Italy
| | - Camillo Rossi
- Chief Medical Officer, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, MD, USA
| | - Miranda F Tompkins
- PRIMER, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Camille Alba
- PRIMER, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Isabelle Vandernoot
- Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Christophe Goffard
- Department of Internal Medicine, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Guillaume Smits
- Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Isabelle Migeotte
- Fonds de la Recherche Scientifique (FNRS) and Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Filomeen Haerynck
- Department of Paediatric Immunology and Pulmonology, Centre for Primary Immunodeficiency Ghent (CPIG), PID Research Lab, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
| | - Pere Soler-Palacin
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Andrea Martin-Nalda
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Roger Colobran
- Immunology Division, Genetics Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Vall d'Hebron Barcelona Hospital Campus, UAB, Barcelona, Catalonia, Spain
| | | | - Sevgi Keles
- Necmettin Erbakan University, Meram Medical Faculty, Division of Pediatric Allergy and Immunology, Konya, Turkey
| | - Fatma Çölkesen
- Department of Infectious Diseases and Clinical Microbiology, Konya Training and Research Hospital, Konya, Turkey
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Bilkent-Ankara, Turkey
| | - Kadriye Kart Yasar
- Departments of Infectious Diseases and Clinical Microbiology, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Sevtap Senoglu
- Departments of Infectious Diseases and Clinical Microbiology, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Şemsi Nur Karabela
- Departments of Infectious Diseases and Clinical Microbiology, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Carlos Rodríguez-Gallego
- Department of Immunology, Hospital Universitario de G.C. Dr. Negrín, Canarian Health System, Las Palmas de Gran Canaria, Spain
- University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata," Rome, Italy
| | | | - Yacine Tandjaoui-Lambiotte
- Avicenne Hospital Intensive Care Unit, APHP, Bobigny, INSERM U1272 Hypoxia & Lung, Paris, France
- PH Réanimation CHU Avicenne, Bobigny, INSERM U1272 Hypoxie & Poumon, Paris, France
| | - Xavier Duval
- Université de Paris, IAME UMR-S 1137, INSERM, Paris, France
- Inserm CIC 1425, Paris, France
| | - Cédric Laouénan
- Université de Paris, IAME UMR-S 1137, INSERM, Paris, France
- Inserm CIC 1425, Paris, France
- AP-HP, Département Epidémiologie Biostatistiques et Recherche Clinique, Hôpital Bichat, Paris, France
| | - Andrew L Snow
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Clifton L Dalgard
- PRIMER, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Joshua D Milner
- Division of Pediatric Allergy, Immunology and Rheumatology, Columbia University, New York, USA
| | - Donald C Vinh
- Infectious Disease Susceptibility Program, Research Institute, McGill University Health Centre, Montréal, Québec, Canada
| | - Trine H Mogensen
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Nico Marr
- Department of Immunology, Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, 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, Utrecht UMC, Utrecht, Netherlands
| | - 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
| | - 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
| | - 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
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, France
| | - 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
| | - Michael J Ciancanelli
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Turnstone Biologics, New York, NY, USA
| | - Isabelle Meyts
- Laboratory for Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, Department of Pediatrics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
- Department of Pediatrics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Tom Maniatis
- Zukerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Vassili Soumelis
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Hôpital Saint-Louis, Paris, France
- AP-HP, Hôpital Saint-Louis, Laboratoire d'Immunologie, Paris, France
| | - Ali Amara
- Laboratory of Genomes & Cell Biology of Disease, INSERM U944, CNRS UMR 7212, Université de Paris, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Paris, France
| | - Michel Nussenzweig
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, IDIBELL-Hospital Duran i Reynals, CIBERER U759, and Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Darragh Duffy
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - 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
| | - 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
| | - Guy Gorochov
- Sorbonne Université, Inserm, Centre d'Immunologie et des Maladies Infectieuses-Paris (CIMI PARIS), Assistance Publique-Hôpitaux de Paris (AP-HP) Hôpital Pitié-Salpêtrière, 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
| | - 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
| | - Vanessa Sancho-Shimizu
- Department of Paediatric Infectious Diseases & Virology, Imperial College London, London, UK
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, 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
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Bethesda, MD, USA
| | - 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
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Bethesda, MD, 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
- Pediatric Hematology and Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
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19
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Cook SA, Comrie WA, Poli MC, Similuk M, Oler AJ, Faruqi AJ, Kuhns DB, Yang S, Vargas-Hernández A, Carisey AF, Fournier B, Anderson DE, Price S, Smelkinson M, Abou Chahla W, Forbes LR, Mace EM, Cao TN, Coban-Akdemir ZH, Jhangiani SN, Muzny DM, Gibbs RA, Lupski JR, Orange JS, Cuvelier GDE, Al Hassani M, Al Kaabi N, Al Yafei Z, Jyonouchi S, Raje N, Caldwell JW, Huang Y, Burkhardt JK, Latour S, Chen B, ElGhazali G, Rao VK, Chinn IK, Lenardo MJ. HEM1 deficiency disrupts mTORC2 and F-actin control in inherited immunodysregulatory disease. Science 2020; 369:202-207. [PMID: 32647003 DOI: 10.1126/science.aay5663] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 01/21/2020] [Accepted: 05/29/2020] [Indexed: 12/22/2022]
Abstract
Immunodeficiency often coincides with hyperactive immune disorders such as autoimmunity, lymphoproliferation, or atopy, but this coincidence is rarely understood on a molecular level. We describe five patients from four families with immunodeficiency coupled with atopy, lymphoproliferation, and cytokine overproduction harboring mutations in NCKAP1L, which encodes the hematopoietic-specific HEM1 protein. These mutations cause the loss of the HEM1 protein and the WAVE regulatory complex (WRC) or disrupt binding to the WRC regulator, Arf1, thereby impairing actin polymerization, synapse formation, and immune cell migration. Diminished cortical actin networks caused by WRC loss led to uncontrolled cytokine release and immune hyperresponsiveness. HEM1 loss also blocked mechanistic target of rapamycin complex 2 (mTORC2)-dependent AKT phosphorylation, T cell proliferation, and selected effector functions, leading to immunodeficiency. Thus, the evolutionarily conserved HEM1 protein simultaneously regulates filamentous actin (F-actin) and mTORC2 signaling to achieve equipoise in immune responses.
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Affiliation(s)
- Sarah A Cook
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, and Clinical Genomics Program, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - William A Comrie
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, and Clinical Genomics Program, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.,Neomics Pharmaceuticals, LLC, Gaithersburg, MD, USA
| | - M Cecilia Poli
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Section of Pediatric Immunology, Allergy, and Retrovirology, Texas Children's Hospital, Houston, TX, USA.,Program of Immunogenetics and Translational Immunology, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Morgan Similuk
- Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, MD, USA
| | - Aiman J Faruqi
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, and Clinical Genomics Program, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Douglas B Kuhns
- Neutrophil Monitoring Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sheng Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Alexander Vargas-Hernández
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Section of Pediatric Immunology, Allergy, and Retrovirology, Texas Children's Hospital, Houston, TX, USA
| | - Alexandre F Carisey
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Section of Pediatric Immunology, Allergy, and Retrovirology, Texas Children's Hospital, Houston, TX, USA
| | - Benjamin Fournier
- Laboratory of Lymphocyte Activation and Susceptibility to EBV, INSERM UMR 1163, Paris, France.,University Paris Descartes Sorbonne Paris Cité, Institut des Maladies Génétiques-IMAGINE, Paris, France
| | - D Eric Anderson
- Advanced Mass Spectrometry Facility, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Susan Price
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Margery Smelkinson
- Biological Imaging Section, Research Technologies Branch, NIAID, NIH, Bethesda, MD, USA
| | - Wadih Abou Chahla
- Department of Pediatric Hematology, Jeanne de Flandre Hospital, Centre Hospitalier Universitaire (CHU), Lille, France
| | - Lisa R Forbes
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Section of Pediatric Immunology, Allergy, and Retrovirology, Texas Children's Hospital, Houston, TX, USA
| | - Emily M Mace
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Tram N Cao
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Section of Pediatric Immunology, Allergy, and Retrovirology, Texas Children's Hospital, Houston, TX, USA
| | - Zeynep H Coban-Akdemir
- Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jordan S Orange
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Geoffrey D E Cuvelier
- Section of Pediatric Hematology/Oncology/BMT, CancerCare Manitoba, University of Manitoba, Winnipeg, MB, Canada
| | - Moza Al Hassani
- Sheikh Khalifa Medical City, Abu Dhabi Healthcare Company (SEHA), Abu Dhabi, United Arab Emirates
| | - Nawal Al Kaabi
- Sheikh Khalifa Medical City, Abu Dhabi Healthcare Company (SEHA), Abu Dhabi, United Arab Emirates
| | - Zain Al Yafei
- Sheikh Khalifa Medical City, Abu Dhabi Healthcare Company (SEHA), Abu Dhabi, United Arab Emirates
| | - Soma Jyonouchi
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nikita Raje
- Division of Allergy, Immunology, Pulmonary, and Sleep Medicine, Children's Mercy Hospital, Kansas City, MO, USA.,Department of Internal Medicine and Pediatrics, University of Missouri Kansas City, Kansas City, MO, USA
| | - Jason W Caldwell
- Section of Pulmonary, Critical Care, Allergy and Immunological Diseases, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Yanping Huang
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Janis K Burkhardt
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV, INSERM UMR 1163, Paris, France.,University Paris Descartes Sorbonne Paris Cité, Institut des Maladies Génétiques-IMAGINE, Paris, France
| | - Baoyu Chen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Gehad ElGhazali
- Sheikh Khalifa Medical City, Abu Dhabi Healthcare Company (SEHA), Abu Dhabi, United Arab Emirates
| | - V Koneti Rao
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Ivan K Chinn
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Section of Pediatric Immunology, Allergy, and Retrovirology, Texas Children's Hospital, Houston, TX, USA
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, and Clinical Genomics Program, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.
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20
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Argersinger DP, Natkha VP, Shepard MJ, Thomas AA, Oler AJ, Williamson PR, Chittiboina P, Heiss JD. Intradural cauda equina Candida abscess presenting with hydrocephalus: case report. J Neurosurg Spine 2019; 31:1-4. [PMID: 31470401 PMCID: PMC7339489 DOI: 10.3171/2019.6.spine19271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/25/2019] [Indexed: 11/06/2022]
Abstract
Central nervous system (CNS) candida infections are often associated with a poor prognosis. Typically, CNS candidiasis presents as meningitis or microabscesses. Here, the authors report a patient with a challenging presentation of a CNS Candida infection as a discrete, large cauda equina abscess. The patient initially presented with ventriculomegaly due to fourth ventricular outflow obstruction and a cauda equina mass. The patient was treated with a ventriculoperitoneal shunt and underwent a lumbar laminectomy for exploration of the lumbar lesion. An intradural abscess was encountered during surgery. Fungal wet mount revealed fungal elements and polymerase chain reaction confirmed the presence of Candida albicans. The patient did not have any known predisposition to fungal infections; therefore, the authors performed whole-exome sequencing using peripheral blood mononuclear cell DNA. They found heterozygous missense variants in the following genes: colony-stimulating factor 2 (CSF2) and Ras protein-specific guanine nucleotide-releasing factor 1 (RASGRF1)-genes that have been specifically associated with protection from CNS candidiasis via caspase recruitment domain-containing protein 9 (CARD9) signaling, and phospholipase C gamma 2 (PLCG2)-a lectin receptor involved in candidiasis. The authors' experience suggests that C. albicans can present as a cauda equina abscess. Hydrocephalus, a result of diffuse arachnoiditis, is a potential complication from intradural fungal abscesses.
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Affiliation(s)
- Davis P. Argersinger
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Vitaliy P. Natkha
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Matthew J. Shepard
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
- Department of Neurological Surgery, University of Virginia Health System, Charlottesville, Virginia
| | - Alissa A. Thomas
- University of Vermont Medical Center, Department of Neurological Sciences, Burlington, Vermont
| | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Peter R. Williamson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Prashant Chittiboina
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
- Neurosurgery Unit for Pituitary and Inheritable Disorders, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - John D. Heiss
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
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21
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Matsuda-Lennikov M, Biancalana M, Zou J, Ravell JC, Zheng L, Kanellopoulou C, Jiang P, Notarangelo G, Jing H, Masutani E, Oler AJ, Olano LR, Schulz BL, Lenardo MJ. Magnesium transporter 1 (MAGT1) deficiency causes selective defects in N-linked glycosylation and expression of immune-response genes. J Biol Chem 2019; 294:13638-13656. [PMID: 31337704 DOI: 10.1074/jbc.ra119.008903] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/08/2019] [Indexed: 12/22/2022] Open
Abstract
Magnesium transporter 1 (MAGT1) critically mediates magnesium homeostasis in eukaryotes and is highly-conserved across different evolutionary branches. In humans, loss-of-function mutations in the MAGT1 gene cause X-linked magnesium deficiency with Epstein-Barr virus (EBV) infection and neoplasia (XMEN), a disease that has a broad range of clinical and immunological consequences. We have previously shown that EBV susceptibility in XMEN is associated with defective expression of the antiviral natural-killer group 2 member D (NKG2D) protein and abnormal Mg2+ transport. New evidence suggests that MAGT1 is the human homolog of the yeast OST3/OST6 proteins that form an integral part of the N-linked glycosylation complex, although the exact contributions of these perturbations in the glycosylation pathway to disease pathogenesis are still unknown. Using MS-based glycoproteomics, along with CRISPR/Cas9-KO cell lines, natural killer cell-killing assays, and RNA-Seq experiments, we now demonstrate that humans lacking functional MAGT1 have a selective deficiency in both immune and nonimmune glycoproteins, and we identified several critical glycosylation defects in important immune-response proteins and in the expression of genes involved in immunity, particularly CD28. We show that MAGT1 function is partly interchangeable with that of the paralog protein tumor-suppressor candidate 3 (TUSC3) but that each protein has a different tissue distribution in humans. We observed that MAGT1-dependent glycosylation is sensitive to Mg2+ levels and that reduced Mg2+ impairs immune-cell function via the loss of specific glycoproteins. Our findings reveal that defects in protein glycosylation and gene expression underlie immune defects in an inherited disease due to MAGT1 deficiency.
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Affiliation(s)
- Mami Matsuda-Lennikov
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Matthew Biancalana
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Juan Zou
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Juan C Ravell
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Chrysi Kanellopoulou
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Ping Jiang
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Giulia Notarangelo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Huie Jing
- Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Evan Masutani
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Lisa Renee Olano
- Laboratory of Neurotoxicology, National Institute of Mental Health, Bethesda, Maryland 20892
| | - Benjamin L Schulz
- University of Queensland, School of Chemistry and Molecular Biology, Brisbane, St. Lucia, Queensland 4072, Australia
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892 .,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
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22
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Dorjbal B, Stinson JR, Ma CA, Weinreich MA, Miraghazadeh B, Hartberger JM, Frey-Jakobs S, Weidinger S, Moebus L, Franke A, Schäffer AA, Bulashevska A, Fuchs S, Ehl S, Limaye S, Arkwright PD, Briggs TA, Langley C, Bethune C, Whyte AF, Alachkar H, Nejentsev S, DiMaggio T, Nelson CG, Stone KD, Nason M, Brittain EH, Oler AJ, Veltri DP, Leahy TR, Conlon N, Poli MC, Borzutzky A, Cohen JI, Davis J, Lambert MP, Romberg N, Sullivan KE, Paris K, Freeman AF, Lucas L, Chandrakasan S, Savic S, Hambleton S, Patel SY, Jordan MB, Theos A, Lebensburger J, Atkinson TP, Torgerson TR, Chinn IK, Milner JD, Grimbacher B, Cook MC, Snow AL. Hypomorphic caspase activation and recruitment domain 11 (CARD11) mutations associated with diverse immunologic phenotypes with or without atopic disease. J Allergy Clin Immunol 2019; 143:1482-1495. [PMID: 30170123 PMCID: PMC6395549 DOI: 10.1016/j.jaci.2018.08.013] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/02/2018] [Accepted: 08/13/2018] [Indexed: 01/26/2023]
Abstract
BACKGROUND Caspase activation and recruitment domain 11 (CARD11) encodes a scaffold protein in lymphocytes that links antigen receptor engagement with downstream signaling to nuclear factor κB, c-Jun N-terminal kinase, and mechanistic target of rapamycin complex 1. Germline CARD11 mutations cause several distinct primary immune disorders in human subjects, including severe combined immune deficiency (biallelic null mutations), B-cell expansion with nuclear factor κB and T-cell anergy (heterozygous, gain-of-function mutations), and severe atopic disease (loss-of-function, heterozygous, dominant interfering mutations), which has focused attention on CARD11 mutations discovered by using whole-exome sequencing. OBJECTIVES We sought to determine the molecular actions of an extended allelic series of CARD11 and to characterize the expanding range of clinical phenotypes associated with heterozygous CARD11 loss-of-function alleles. METHODS Cell transfections and primary T-cell assays were used to evaluate signaling and function of CARD11 variants. RESULTS Here we report on an expanded cohort of patients harboring novel heterozygous CARD11 mutations that extend beyond atopy to include other immunologic phenotypes not previously associated with CARD11 mutations. In addition to (and sometimes excluding) severe atopy, heterozygous missense and indel mutations in CARD11 presented with immunologic phenotypes similar to those observed in signal transducer and activator of transcription 3 loss of function, dedicator of cytokinesis 8 deficiency, common variable immunodeficiency, neutropenia, and immune dysregulation, polyendocrinopathy, enteropathy, X-linked-like syndrome. Pathogenic variants exhibited dominant negative activity and were largely confined to the CARD or coiled-coil domains of the CARD11 protein. CONCLUSION These results illuminate a broader phenotypic spectrum associated with CARD11 mutations in human subjects and underscore the need for functional studies to demonstrate that rare gene variants encountered in expected and unexpected phenotypes must nonetheless be validated for pathogenic activity.
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Affiliation(s)
- Batsukh Dorjbal
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - Jeffrey R Stinson
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - Chi A Ma
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michael A Weinreich
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Bahar Miraghazadeh
- Department of Immunology, Canberra Hospital, Canberra, Australia; Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Julia M Hartberger
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stefanie Frey-Jakobs
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stephan Weidinger
- Department of Dermatology, Venereology and Allergology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Lena Moebus
- Department of Dermatology, Venereology and Allergology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, Md
| | - Alla Bulashevska
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian Fuchs
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stephan Ehl
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Peter D Arkwright
- Paediatric Allergy and Immunology & the Manchester Center for Genomic Medicine, University of Manchester, Manchester, United Kingdom
| | - Tracy A Briggs
- Paediatric Allergy and Immunology & the Manchester Center for Genomic Medicine, University of Manchester, Manchester, United Kingdom
| | - Claire Langley
- Paediatric Allergy and Immunology & the Manchester Center for Genomic Medicine, University of Manchester, Manchester, United Kingdom
| | - Claire Bethune
- Department of Clinical Immunology, Plymouth Hospitals NHS Trust, Plymouth, United Kingdom
| | - Andrew F Whyte
- Department of Clinical Immunology, Plymouth Hospitals NHS Trust, Plymouth, United Kingdom
| | - Hana Alachkar
- Immunology, Salford Royal Foundation Trust, Manchester, United Kingdom
| | - Sergey Nejentsev
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Thomas DiMaggio
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Celeste G Nelson
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Kelly D Stone
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Martha Nason
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Erica H Brittain
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrew J Oler
- Bioinformatics and Computational Sciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Daniel P Veltri
- Bioinformatics and Computational Sciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - T Ronan Leahy
- Department of Paediatric Immunology and ID, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Niall Conlon
- Department of Immunology, St James's Hospital, Dublin, Ireland
| | - Maria C Poli
- Department of Pediatrics, Baylor College of Medicine, and the Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, Tex
| | - Arturo Borzutzky
- Department of Pediatrics, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Joie Davis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michele P Lambert
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, and the Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pa
| | - Neil Romberg
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, and the Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pa
| | - Kathleen E Sullivan
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, and the Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pa
| | - Kenneth Paris
- Louisiana State University Health Sciences Center and Children's Hospital, New Orleans, La
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Laura Lucas
- Division of Bone Marrow Transplant, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, Ga
| | - Shanmuganathan Chandrakasan
- Division of Bone Marrow Transplant, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, Ga
| | - Sinisa Savic
- Leeds Institute for Rheumatic and Musculoskeletal Medicine, St James University Hospital, Leeds, United Kingdom
| | - Sophie Hambleton
- Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Smita Y Patel
- Oxford University Hospitals NHS Trust and NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Michael B Jordan
- Division of Bone Marrow Transplantation and Immune Deficiency, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Amy Theos
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Ala
| | - Jeffrey Lebensburger
- Department of Pediatric Hematology Oncology, University of Alabama at Birmingham, Birmingham, Ala
| | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Ala
| | - Troy R Torgerson
- University of Washington School of Medicine and Seattle Children's Hospital, Seattle, Wash
| | - Ivan K Chinn
- Department of Pediatrics, Baylor College of Medicine, and the Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, Tex
| | - Joshua D Milner
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Bodo Grimbacher
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthew C Cook
- Department of Immunology, Canberra Hospital, Canberra, Australia; Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Andrew L Snow
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Md.
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23
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Tawara K, Scott H, Emathinger J, Ide A, Fox R, Greiner D, LaJoie D, Hedeen D, Nandakumar M, Oler AJ, Holzer R, Jorcyk C. Co-Expression of VEGF and IL-6 Family Cytokines is Associated with Decreased Survival in HER2 Negative Breast Cancer Patients: Subtype-Specific IL-6 Family Cytokine-Mediated VEGF Secretion. Transl Oncol 2018; 12:245-255. [PMID: 30439625 PMCID: PMC6234768 DOI: 10.1016/j.tranon.2018.10.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/03/2018] [Accepted: 10/03/2018] [Indexed: 02/06/2023] Open
Abstract
Breast cancer cell-response to inflammatory cytokines such as interleukin-6 (IL-6) and oncostatin M (OSM) may affect the course of clinical disease in a cancer subtype-dependent manner. Furthermore, vascular endothelial growth factor A (VEGF) secretion induced by IL-6 and OSM may also be subtype-dependent. Utilizing datasets from Oncomine, we show that poor survival of invasive ductal carcinoma (IDC) breast cancer patients is correlated with both high VEGF expression and high cytokine or cytokine receptor expression in tumors. Importantly, epidermal growth factor receptor-negative (HER2-), but not HER2-positive (HER2+), patient survival is significantly lower with high tumor co-expression of VEGF and OSM, OSMRβ, IL-6, or IL-6Rα compared to low co-expression. Furthermore, assessment of HER2- breast cancer cells in vitro identified unique signaling differences regulating cytokine-induced VEGF secretion. The levels of VEGF secretion were analyzed by ELISA with siRNAs for hypoxia inducible factor 1 α (HIF1α) and signal transducer and activator of transcription 3 (STAT3). Specifically, we found that estrogen receptor-negative (ER-) MDA-MB-231 cells respond only to OSM through STAT3 signaling, while ER+ T47D cells respond to both OSM and IL-6, though to IL-6 to a lesser extent. Additionally, in the ER+ T47D cells, OSM signals through both STAT3 and HIF1α. These results highlight that the survival of breast cancer patients with high co-expression of VEGF and IL-6 family cytokines is dependent on breast cancer subtype. Thus, the heterogeneity of human breast cancer in relation to IL-6 family cytokines and VEGF may have important implications in clinical treatment options, disease progression, and ultimately patient prognosis.
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Affiliation(s)
- Ken Tawara
- Boise State University, Biomolecular Sciences Program, 1910 University Drive, MS1515, Boise, ID, 83725, USA
| | - Hannah Scott
- Boise State University, Department of Biological Sciences, 1910 University Drive, MS1515, Boise, ID, USA
| | - Jacqueline Emathinger
- Boise State University, Department of Biological Sciences, 1910 University Drive, MS1515, Boise, ID, USA
| | - Alex Ide
- Boise State University, Department of Biological Sciences, 1910 University Drive, MS1515, Boise, ID, USA
| | - Ryan Fox
- Boise State University, Department of Biological Sciences, 1910 University Drive, MS1515, Boise, ID, USA
| | - Daniel Greiner
- Boise State University, Department of Biological Sciences, 1910 University Drive, MS1515, Boise, ID, USA
| | - Dollie LaJoie
- Boise State University, Department of Biological Sciences, 1910 University Drive, MS1515, Boise, ID, USA; University of Utah, Department of Oncological Sciences, Salt Lake City, UT, USA
| | - Danielle Hedeen
- Boise State University, Department of Biological Sciences, 1910 University Drive, MS1515, Boise, ID, USA; University of Utah, Department of Oncological Sciences, Salt Lake City, UT, USA
| | - Madhuri Nandakumar
- Boise State University, Department of Biological Sciences, 1910 University Drive, MS1515, Boise, ID, USA
| | - Andrew J Oler
- Boise State University, Department of Biological Sciences, 1910 University Drive, MS1515, Boise, ID, USA; Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID/NIH, Bethesda, MD, USA
| | - Ryan Holzer
- Boise State University, Department of Biological Sciences, 1910 University Drive, MS1515, Boise, ID, USA; Rosetta Institute of Biomedical Research, San Jose, CA, USA
| | - Cheryl Jorcyk
- Boise State University, Biomolecular Sciences Program, 1910 University Drive, MS1515, Boise, ID, 83725, USA; Boise State University, Department of Biological Sciences, 1910 University Drive, MS1515, Boise, ID, USA.
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24
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Kosik I, Ince WL, Gentles LE, Oler AJ, Kosikova M, Angel M, Magadán JG, Xie H, Brooke CB, Yewdell JW. Correction: Influenza A virus hemagglutinin glycosylation compensates for antibody escape fitness costs. PLoS Pathog 2018; 14:e1007141. [PMID: 29924863 PMCID: PMC6010253 DOI: 10.1371/journal.ppat.1007141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.ppat.1006796.].
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25
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Weber N, Liou D, Dommer J, MacMenamin P, Quiñones M, Misner I, Oler AJ, Wan J, Kim L, Coakley McCarthy M, Ezeji S, Noble K, Hurt DE. Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis. Bioinformatics 2018; 34:1411-1413. [PMID: 29028892 PMCID: PMC5905584 DOI: 10.1093/bioinformatics/btx617] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 02/05/2023] Open
Abstract
Motivation Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools. Results The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights. Nephele integrates common microbiome analysis tools as well as valuable reference datasets like the healthy human subjects cohort of the Human Microbiome Project (HMP). Nephele is built on the Amazon Web Services cloud, which provides centralized and automated storage and compute capacity, thereby reducing the burden on researchers and their institutions. Availability and implementation https://nephele.niaid.nih.gov and https://github.com/niaid/Nephele. Contact darrell.hurt@nih.gov.
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Affiliation(s)
- Nick Weber
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Liou
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Dommer
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Philip MacMenamin
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mariam Quiñones
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ian Misner
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joe Wan
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lewis Kim
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Meghan Coakley McCarthy
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Ezeji
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Karlynn Noble
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Darrell E Hurt
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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26
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Mao L, Kitani A, Similuk M, Oler AJ, Albenberg L, Kelsen J, Aktay A, Quezado M, Yao M, Montgomery-Recht K, Fuss IJ, Strober W. Loss-of-function CARD8 mutation causes NLRP3 inflammasome activation and Crohn's disease. J Clin Invest 2018; 128:1793-1806. [PMID: 29408806 DOI: 10.1172/jci98642] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/30/2018] [Indexed: 12/14/2022] Open
Abstract
In these studies, we evaluated the contribution of the NLRP3 inflammasome to Crohn's disease (CD) in a kindred containing individuals having a missense mutation in CARD8, a protein known to inhibit this inflammasome. Whole exome sequencing and PCR studies identified the affected individuals as having a V44I mutation in a single allele of the T60 isoform of CARD8. The serum levels of IL-1β in the affected individuals were increased compared with those in healthy controls, and their peripheral monocytes produced increased amounts of IL-1β when stimulated by NLRP3 activators. Immunoblot studies probing the basis of these findings showed that mutated T60 CARD8 failed to downregulate the NLRP3 inflammasome because it did not bind to NLRP3 and inhibit its oligomerization. In addition, these studies showed that mutated T60 CARD8 exerted a dominant-negative effect by its capacity to bind to and form oligomers with unmutated T60 or T48 CARD8 that impeded their binding to NLRP3. Finally, inflammasome activation studies revealed that intact but not mutated CARD8 prevented NLRP3 deubiquitination and serine dephosphorylation. CD due to a CARD8 mutation was not effectively treated by anti-TNF-α, but did respond to IL-1β inhibitors. Thus, patients with anti-TNF-α-resistant CD may respond to this treatment option.
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Affiliation(s)
- Liming Mao
- Mucosal Immunity Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Atsushi Kitani
- Mucosal Immunity Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Morgan Similuk
- Clinical Genomics Program, NIAID, NIH, Bethesda, Maryland, USA
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Lindsey Albenberg
- Division of Pediatric Gastroenterology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Judith Kelsen
- Division of Pediatric Gastroenterology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Atiye Aktay
- Division of Pediatric Gastroenterology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Martha Quezado
- Laboratory of Pathology, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Michael Yao
- Mucosal Immunity Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA.,Division of Gastroenterology, Washington DC VA Medical Center, Washington DC, USA
| | - Kim Montgomery-Recht
- Clinical Research Directorate/Clinical Monitoring Research Program, Leidos Biomedical Research Inc., NCI Campus at Frederick, Frederick, Maryland, USA
| | - Ivan J Fuss
- Mucosal Immunity Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Warren Strober
- Mucosal Immunity Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
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Fang D, Cui K, Hu G, Gurram RK, Zhong C, Oler AJ, Yagi R, Zhao M, Sharma S, Liu P, Sun B, Zhao K, Zhu J. Bcl11b, a novel GATA3-interacting protein, suppresses Th1 while limiting Th2 cell differentiation. J Exp Med 2018. [PMID: 29514917 PMCID: PMC5940260 DOI: 10.1084/jem.20171127] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
GATA-binding protein 3 (GATA3) acts as the master transcription factor for type 2 T helper (Th2) cell differentiation and function. However, it is still elusive how GATA3 function is precisely regulated in Th2 cells. Here, we show that the transcription factor B cell lymphoma 11b (Bcl11b), a previously unknown component of GATA3 transcriptional complex, is involved in GATA3-mediated gene regulation. Bcl11b binds to GATA3 through protein-protein interaction, and they colocalize at many important cis-regulatory elements in Th2 cells. The expression of type 2 cytokines, including IL-4, IL-5, and IL-13, is up-regulated in Bcl11b-deficient Th2 cells both in vitro and in vivo; such up-regulation is completely GATA3 dependent. Genome-wide analyses of Bcl11b- and GATA3-regulated genes (from RNA sequencing), cobinding patterns (from chromatin immunoprecipitation sequencing), and Bcl11b-modulated epigenetic modification and gene accessibility suggest that GATA3/Bcl11b complex is involved in limiting Th2 gene expression, as well as in inhibiting non-Th2 gene expression. Thus, Bcl11b controls both GATA3-mediated gene activation and repression in Th2 cells.
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Affiliation(s)
- Difeng Fang
- Molecular and Cellular Immunoregulation Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Kairong Cui
- Laboratory of Epigenome Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Gangqing Hu
- Laboratory of Epigenome Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Rama Krishna Gurram
- Molecular and Cellular Immunoregulation Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Chao Zhong
- Molecular and Cellular Immunoregulation Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Ryoji Yagi
- Molecular and Cellular Immunoregulation Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Ming Zhao
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Suveena Sharma
- Molecular and Cellular Immunoregulation Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Pentao Liu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Bing Sun
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Keji Zhao
- Laboratory of Epigenome Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Jinfang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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28
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Kosik I, Ince WL, Gentles LE, Oler AJ, Kosikova M, Angel M, Magadán JG, Xie H, Brooke CB, Yewdell JW. Influenza A virus hemagglutinin glycosylation compensates for antibody escape fitness costs. PLoS Pathog 2018; 14:e1006796. [PMID: 29346435 PMCID: PMC5773227 DOI: 10.1371/journal.ppat.1006796] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 12/07/2017] [Indexed: 12/31/2022] Open
Abstract
Rapid antigenic evolution enables the persistence of seasonal influenza A and B viruses in human populations despite widespread herd immunity. Understanding viral mechanisms that enable antigenic evolution is critical for designing durable vaccines and therapeutics. Here, we utilize the primerID method of error-correcting viral population sequencing to reveal an unexpected role for hemagglutinin (HA) glycosylation in compensating for fitness defects resulting from escape from anti-HA neutralizing antibodies. Antibody-free propagation following antigenic escape rapidly selected viruses with mutations that modulated receptor binding avidity through the addition of N-linked glycans to the HA globular domain. These findings expand our understanding of the viral mechanisms that maintain fitness during antigenic evolution to include glycan addition, and highlight the immense power of high-definition virus population sequencing to reveal novel viral adaptive mechanisms.
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Affiliation(s)
- Ivan Kosik
- Cellular Biology Section, Laboratory of Viral Diseases, NIAID, Bethesda, Maryland, United States of America
| | - William L. Ince
- Cellular Biology Section, Laboratory of Viral Diseases, NIAID, Bethesda, Maryland, United States of America
- Center for Drug Evaluation and Research, FDA, Silver Spring, Maryland, United States of America
| | - Lauren E. Gentles
- Cellular Biology Section, Laboratory of Viral Diseases, NIAID, Bethesda, Maryland, United States of America
| | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, Bethesda, Maryland, United States of America
| | - Martina Kosikova
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, FDA, Silver Spring, Maryland, United States of America
| | - Matthew Angel
- Cellular Biology Section, Laboratory of Viral Diseases, NIAID, Bethesda, Maryland, United States of America
| | - Javier G. Magadán
- Cellular Biology Section, Laboratory of Viral Diseases, NIAID, Bethesda, Maryland, United States of America
| | - Hang Xie
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, FDA, Silver Spring, Maryland, United States of America
| | - Christopher B. Brooke
- Department of Microbiology, School of Molecular and Cellular Biology, University of Illinois, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Jonathan W. Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, NIAID, Bethesda, Maryland, United States of America
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29
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Bamunusinghe D, Liu Q, Plishka R, Dolan MA, Skorski M, Oler AJ, Yedavalli VRK, Buckler-White A, Hartley JW, Kozak CA. Recombinant Origins of Pathogenic and Nonpathogenic Mouse Gammaretroviruses with Polytropic Host Range. J Virol 2017; 91:e00855-17. [PMID: 28794032 PMCID: PMC5640873 DOI: 10.1128/jvi.00855-17] [Citation(s) in RCA: 12] [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: 05/30/2017] [Accepted: 07/26/2017] [Indexed: 01/06/2023] Open
Abstract
Ecotropic, xenotropic, and polytropic mouse leukemia viruses (E-, X-, and P-MLVs) exist in mice as infectious viruses and endogenous retroviruses (ERVs) inserted into mouse chromosomes. All three MLV subgroups are linked to leukemogenesis, which involves generation of recombinants with polytropic host range. Although P-MLVs are deemed to be the proximal agents of disease induction, few biologically characterized infectious P-MLVs have been sequenced for comparative analysis. We analyzed the complete genomes of 16 naturally occurring infectious P-MLVs, 12 of which were typed for pathogenic potential. We sought to identify ERV progenitors, recombinational hot spots, and segments that are always replaced, never replaced, or linked to pathogenesis or host range. Each P-MLV has an E-MLV backbone with P- or X-ERV replacements that together cover 100% of the recombinant genomes, with different substitution patterns for X- and P-ERVs. Two segments are always replaced, both coding for envelope (Env) protein segments: the N terminus of the surface subunit and the cytoplasmic tail R peptide. Viral gag gene replacements are influenced by host restriction genes Fv1 and Apobec3 Pathogenic potential maps to the env transmembrane subunit segment encoding the N-heptad repeat (HR1). Molecular dynamics simulations identified three novel interdomain salt bridges in the lymphomagenic virus HR1 that could affect structural stability, entry or sensitivity to host immune responses. The long terminal repeats of lymphomagenic P-MLVs are differentially altered by recombinations, duplications, or mutations. This analysis of the naturally occurring, sometimes pathogenic P-MLV recombinants defines the limits and extent of intersubgroup recombination and identifies specific sequence changes linked to pathogenesis and host interactions.IMPORTANCE During virus-induced leukemogenesis, ecotropic mouse leukemia viruses (MLVs) recombine with nonecotropic endogenous retroviruses (ERVs) to produce polytropic MLVs (P-MLVs). Analysis of 16 P-MLV genomes identified two segments consistently replaced: one at the envelope N terminus that alters receptor choice and one in the R peptide at the envelope C terminus, which is removed during virus assembly. Genome-wide analysis shows that nonecotropic replacements in the progenitor ecotropic MLV genome are more extensive than previously appreciated, covering 100% of the genome; contributions from xenotropic and polytropic ERVs differentially alter the regions responsible for receptor determination or subject to APOBEC3 and Fv1 restriction. All pathogenic viruses had modifications in the regulatory elements in their long terminal repeats and differed in a helical segment of envelope involved in entry and targeted by the host immune system. Virus-induced leukemogenesis thus involves generation of complex recombinants, and specific replacements are linked to pathogenesis and host restrictions.
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Affiliation(s)
- Devinka Bamunusinghe
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Qingping Liu
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Ronald Plishka
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Michael A Dolan
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Matthew Skorski
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Venkat R K Yedavalli
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Alicia Buckler-White
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Janet W Hartley
- Laboratory of Immunopathology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Christine A Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
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30
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Lamborn IT, Jing H, Zhang Y, Drutman SB, Abbott JK, Munir S, Bade S, Murdock HM, Santos CP, Brock LG, Masutani E, Fordjour EY, McElwee JJ, Hughes JD, Nichols DP, Belkadi A, Oler AJ, Happel CS, Matthews HF, Abel L, Collins PL, Subbarao K, Gelfand EW, Ciancanelli MJ, Casanova JL, Su HC. Recurrent rhinovirus infections in a child with inherited MDA5 deficiency. J Exp Med 2017; 214:1949-1972. [PMID: 28606988 PMCID: PMC5502429 DOI: 10.1084/jem.20161759] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 04/13/2017] [Accepted: 05/26/2017] [Indexed: 12/15/2022] Open
Abstract
Human MDA5 deficiency features recurrent severe human rhinovirus (HRV) infections. MDA5 serves a protective and nonredundant role in protecting against HRV in the respiratory tract, through its effects on virus sensing and triggering of antiviral IFN signaling. MDA5 is a cytosolic sensor of double-stranded RNA (ds)RNA including viral byproducts and intermediates. We studied a child with life-threatening, recurrent respiratory tract infections, caused by viruses including human rhinovirus (HRV), influenza virus, and respiratory syncytial virus (RSV). We identified in her a homozygous missense mutation in IFIH1 that encodes MDA5. Mutant MDA5 was expressed but did not recognize the synthetic MDA5 agonist/(ds)RNA mimic polyinosinic-polycytidylic acid. When overexpressed, mutant MDA5 failed to drive luciferase activity from the IFNB1 promoter or promoters containing ISRE or NF-κB sequence motifs. In respiratory epithelial cells or fibroblasts, wild-type but not knockdown of MDA5 restricted HRV infection while increasing IFN-stimulated gene expression and IFN-β/λ. However, wild-type MDA5 did not restrict influenza virus or RSV replication. Moreover, nasal epithelial cells from the patient, or fibroblasts gene-edited to express mutant MDA5, showed increased replication of HRV but not influenza or RSV. Thus, human MDA5 deficiency is a novel inborn error of innate and/or intrinsic immunity that causes impaired (ds)RNA sensing, reduced IFN induction, and susceptibility to the common cold virus.
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Affiliation(s)
- Ian T Lamborn
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Department of Pathology and Laboratory Medicine, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Huie Jing
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Yu Zhang
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Scott B Drutman
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Jordan K Abbott
- Immunodeficiency Diagnosis and Treatment Program, Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO
| | - Shirin Munir
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | | | - Heardley M Murdock
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Celia P Santos
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Linda G Brock
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Evan Masutani
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Emmanuel Y Fordjour
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | | | | | - Dave P Nichols
- Division of Pediatric Pulmonary Medicine, Department of Pediatrics, National Jewish Health, Denver, CO
| | - Aziz Belkadi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Necker Hospital for Sick Children, Paris, France
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Corinne S Happel
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Helen F Matthews
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - 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, Institut National de la Santé et de la Recherche Médicale UMR1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Necker Hospital for Sick Children, Paris, France
| | - Peter L Collins
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Kanta Subbarao
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Erwin W Gelfand
- Immunodeficiency Diagnosis and Treatment Program, Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO
| | - Michael J Ciancanelli
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - 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, Institut National de la Santé et de la Recherche Médicale UMR1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Pediatric Immuno-Hematology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France.,Howard Hughes Medical Institute, New York, NY
| | - Helen C Su
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD .,Department of Pathology and Laboratory Medicine, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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31
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Lyons JJ, Yu X, Hughes JD, Le QT, Jamil A, Bai Y, Ho N, Zhao M, Liu Y, O'Connell MP, Trivedi NN, Nelson C, DiMaggio T, Jones N, Matthews H, Lewis KL, Oler AJ, Carlson RJ, Arkwright PD, Hong C, Agama S, Wilson TM, Tucker S, Zhang Y, McElwee JJ, Pao M, Glover SC, Rothenberg ME, Hohman RJ, Stone KD, Caughey GH, Heller T, Metcalfe DD, Biesecker LG, Schwartz LB, Milner JD. Elevated basal serum tryptase identifies a multisystem disorder associated with increased TPSAB1 copy number. Nat Genet 2016; 48:1564-1569. [PMID: 27749843 DOI: 10.1038/ng.3696] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/16/2016] [Indexed: 12/14/2022]
Abstract
Elevated basal serum tryptase levels are present in 4-6% of the general population, but the cause and relevance of such increases are unknown. Previously, we described subjects with dominantly inherited elevated basal serum tryptase levels associated with multisystem complaints including cutaneous flushing and pruritus, dysautonomia, functional gastrointestinal symptoms, chronic pain, and connective tissue abnormalities, including joint hypermobility. Here we report the identification of germline duplications and triplications in the TPSAB1 gene encoding α-tryptase that segregate with inherited increases in basal serum tryptase levels in 35 families presenting with associated multisystem complaints. Individuals harboring alleles encoding three copies of α-tryptase had higher basal serum levels of tryptase and were more symptomatic than those with alleles encoding two copies, suggesting a gene-dose effect. Further, we found in two additional cohorts (172 individuals) that elevated basal serum tryptase levels were exclusively associated with duplication of α-tryptase-encoding sequence in TPSAB1, and affected individuals reported symptom complexes seen in our initial familial cohort. Thus, our findings link duplications in TPSAB1 with irritable bowel syndrome, cutaneous complaints, connective tissue abnormalities, and dysautonomia.
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Affiliation(s)
- Jonathan J Lyons
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Xiaomin Yu
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Jason D Hughes
- Merck Research Laboratories, Merck &Co. Inc., Boston, Massachusetts, USA
| | - Quang T Le
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Ali Jamil
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Yun Bai
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Nancy Ho
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Ming Zhao
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Rockville, Maryland, USA
| | - Yihui Liu
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Michael P O'Connell
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Neil N Trivedi
- Cardiovascular Research Institute and Department of Medicine, University of California at San Francisco, San Francisco, California, USA.,Veterans Affairs Medical Center, San Francisco, California, USA
| | - Celeste Nelson
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas DiMaggio
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Nina Jones
- Clinical Research Directorate/CMRP, SAIC-Frederick, Inc., Frederick National Laboratory for Clinical Research, Frederick, Maryland, USA
| | - Helen Matthews
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Katie L Lewis
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Ryan J Carlson
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D Arkwright
- Institute of Infection, Immunity and Respiratory Medicine, University of Manchester, Royal Manchester Children's Hospital, Manchester, UK
| | - Celine Hong
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Sherene Agama
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Todd M Wilson
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Sofie Tucker
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Yu Zhang
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Joshua J McElwee
- Merck Research Laboratories, Merck &Co. Inc., Boston, Massachusetts, USA
| | - Maryland Pao
- National Institute of Mental Health, US National Institutes of Health, Bethesda, Maryland, USA
| | - Sarah C Glover
- Division of Gastroenterology, Hepatology, and Nutrition, University of Florida, Gainesville, Florida, USA
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Robert J Hohman
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Rockville, Maryland, USA
| | - Kelly D Stone
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - George H Caughey
- Cardiovascular Research Institute and Department of Medicine, University of California at San Francisco, San Francisco, California, USA.,Veterans Affairs Medical Center, San Francisco, California, USA
| | - Theo Heller
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Dean D Metcalfe
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Lawrence B Schwartz
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Joshua D Milner
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA
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32
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Barb JJ, Oler AJ, Kim HS, Chalmers N, Wallen GR, Cashion A, Munson PJ, Ames NJ. Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples. PLoS One 2016; 11:e0148047. [PMID: 26829716 PMCID: PMC4734828 DOI: 10.1371/journal.pone.0148047] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/11/2016] [Indexed: 12/14/2022] Open
Abstract
Objectives There is much speculation on which hypervariable region provides the highest bacterial specificity in 16S rRNA sequencing. The optimum solution to prevent bias and to obtain a comprehensive view of complex bacterial communities would be to sequence the entire 16S rRNA gene; however, this is not possible with second generation standard library design and short-read next-generation sequencing technology. Methods This paper examines a new process using seven hypervariable or V regions of the 16S rRNA (six amplicons: V2, V3, V4, V6-7, V8, and V9) processed simultaneously on the Ion Torrent Personal Genome Machine (Life Technologies, Grand Island, NY). Four mock samples were amplified using the 16S Ion Metagenomics Kit™ (Life Technologies) and their sequencing data is subjected to a novel analytical pipeline. Results Results are presented at family and genus level. The Kullback-Leibler divergence (DKL), a measure of the departure of the computed from the nominal bacterial distribution in the mock samples, was used to infer which region performed best at the family and genus levels. Three different hypervariable regions, V2, V4, and V6-7, produced the lowest divergence compared to the known mock sample. The V9 region gave the highest (worst) average DKL while the V4 gave the lowest (best) average DKL. In addition to having a high DKL, the V9 region in both the forward and reverse directions performed the worst finding only 17% and 53% of the known family level and 12% and 47% of the genus level bacteria, while results from the forward and reverse V4 region identified all 17 family level bacteria. Conclusions The results of our analysis have shown that our sequencing methods using 6 hypervariable regions of the 16S rRNA and subsequent analysis is valid. This method also allowed for the assessment of how well each of the variable regions might perform simultaneously. Our findings will provide the basis for future work intended to assess microbial abundance at different time points throughout a clinical protocol.
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Affiliation(s)
- Jennifer J. Barb
- Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hyung-Suk Kim
- National Institute of Nursing Research, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Natalia Chalmers
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Gwenyth R. Wallen
- Clinical Center Nursing Department, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ann Cashion
- National Institute of Nursing Research, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Peter J. Munson
- Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nancy J. Ames
- Clinical Center Nursing Department, National Institutes of Health, Bethesda, Maryland, United States of America
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33
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Szymanski EP, Leung JM, Fowler CJ, Haney C, Hsu AP, Chen F, Duggal P, Oler AJ, McCormack R, Podack E, Drummond RA, Lionakis MS, Browne SK, Prevots DR, Knowles M, Cutting G, Liu X, Devine SE, Fraser CM, Tettelin H, Olivier KN, Holland SM. Pulmonary Nontuberculous Mycobacterial Infection. A Multisystem, Multigenic Disease. Am J Respir Crit Care Med 2015; 192:618-28. [PMID: 26038974 DOI: 10.1164/rccm.201502-0387oc] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE The clinical features of patients infected with pulmonary nontuberculous mycobacteria (PNTM) are well described, but the genetic components of infection susceptibility are not. OBJECTIVES To examine genetic variants in patients with PNTM, their unaffected family members, and a control group. METHODS Whole-exome sequencing was done on 69 white patients with PNTM and 18 of their white unaffected family members. We performed a candidate gene analysis using immune, cystic fibrosis transmembrance conductance regulator (CFTR), cilia, and connective tissue gene sets. The numbers of patients, family members, and control subjects with variants in each category were compared, as was the average number of variants per person. MEASUREMENTS AND MAIN RESULTS A significantly higher number of patients with PNTM than the other subjects had low-frequency, protein-affecting variants in immune, CFTR, cilia, and connective tissue categories (35, 26, 90, and 90%, respectively). Patients with PNTM also had significantly more cilia and connective tissue variants per person than did control subjects (2.47 and 2.55 compared with 1.38 and 1.40, respectively; P = 1.4 × 10(-6) and P = 2.7 × 10(-8), respectively). Patients with PNTM had an average of 5.26 variants across all categories (1.98 in control subjects; P = 2.8 × 10(-17)), and they were more likely than control subjects to have variants in multiple categories. We observed similar results for family members without PNTM infection, with the exception of the immune category. CONCLUSIONS Patients with PNTM have more low-frequency, protein-affecting variants in immune, CFTR, cilia, and connective tissue genes than their unaffected family members and control subjects. We propose that PNTM infection is a multigenic disease in which combinations of variants across gene categories, plus environmental exposures, increase susceptibility to the infection.
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Affiliation(s)
| | | | | | | | - Amy P Hsu
- 1 Laboratory of Clinical Infectious Diseases
| | - Fei Chen
- 2 Department of Epidemiology, Bloomberg School of Public Health, and
| | - Priya Duggal
- 2 Department of Epidemiology, Bloomberg School of Public Health, and
| | - Andrew J Oler
- 3 Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, and
| | - Ryan McCormack
- 4 Department of Microbiology and Immunology, School of Medicine, University of Miami, Miami, Florida
| | - Eckhard Podack
- 4 Department of Microbiology and Immunology, School of Medicine, University of Miami, Miami, Florida
| | | | | | | | | | - Michael Knowles
- 5 Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; and
| | - Gary Cutting
- 6 McKusick-Nathans Institute of Genetic Medicine, School of Medicine, The Johns Hopkins University, Baltimore, Maryland
| | | | - Scott E Devine
- 7 Institute for Genome Sciences.,8 Department of Medicine, and
| | - Claire M Fraser
- 7 Institute for Genome Sciences.,8 Department of Medicine, and
| | - Hervé Tettelin
- 7 Institute for Genome Sciences.,9 Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland
| | - Kenneth N Olivier
- 10 Cardiovascular and Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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Varshney D, Vavrova-Anderson J, Oler AJ, Cairns BR, White RJ. Selective repression of SINE transcription by RNA polymerase III. Mob Genet Elements 2015; 5:86-91. [PMID: 26942044 DOI: 10.1080/2159256x.2015.1096997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 10/23/2022] Open
Abstract
A million copies of the Alu short interspersed nuclear element (SINE) are scattered throughout the human genome, providing ∼11% of our total DNA. SINEs spread by retrotransposition, using a transcript generated by RNA polymerase (pol) III from an internal promoter. Levels of these pol III-dependent Alu transcripts are far lower than might be expected from the abundance of the template. This was believed to reflect transcriptional suppression through DNA methylation, denying pol III access to most SINEs through chromatin-mediated effects. Contrary to expectations, our recent study found no evidence that methylation of SINE DNA reduces its occupancy or expression by pol III. However, histone H3 associated with SINEs is prominently methylated on lysine 9, a mark that correlates with transcriptional silencing. The SUV39 methyltransferases that deposit this mark can be found at many SINEs. Furthermore, a selective inhibitor of SUV39 stimulates pol III recruitment to these loci, as well as SINE expression. These data suggest that methylation of histone H3 rather than DNA may mediate repression of SINE transcription by pol III, at least under the conditions we studied.
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Affiliation(s)
- Dhaval Varshney
- Centre for Gene Regulation and Expression; University of Dundee ; Dundee, UK
| | - Jana Vavrova-Anderson
- College of Medical; Veterinary and Life Sciences; University of Glasgow ; Glasgow, UK
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch; Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases; National Institutes of Health ; Bethesda, MD USA
| | - Bradley R Cairns
- Department of Oncological Sciences; Huntsman Cancer Institute; University of Utah School of Medicine; Salt Lake City, UT USA; Howard Hughes Medical Institute; University of Utah School of Medicine; Salt Lake City, UT USA
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Golosova O, Henderson R, Vaskin Y, Gabrielian A, Grekhov G, Nagarajan V, Oler AJ, Quiñones M, Hurt D, Fursov M, Huyen Y. Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses. PeerJ 2014; 2:e644. [PMID: 25392756 PMCID: PMC4226638 DOI: 10.7717/peerj.644] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [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: 08/21/2014] [Accepted: 10/09/2014] [Indexed: 02/03/2023] Open
Abstract
The advent of Next Generation Sequencing (NGS) technologies has opened new possibilities for researchers. However, the more biology becomes a data-intensive field, the more biologists have to learn how to process and analyze NGS data with complex computational tools. Even with the availability of common pipeline specifications, it is often a time-consuming and cumbersome task for a bench scientist to install and configure the pipeline tools. We believe that a unified, desktop and biologist-friendly front end to NGS data analysis tools will substantially improve productivity in this field. Here we present NGS pipelines "Variant Calling with SAMtools", "Tuxedo Pipeline for RNA-seq Data Analysis" and "Cistrome Pipeline for ChIP-seq Data Analysis" integrated into the Unipro UGENE desktop toolkit. We describe the available UGENE infrastructure that helps researchers run these pipelines on different datasets, store and investigate the results and re-run the pipelines with the same parameters. These pipeline tools are included in the UGENE NGS package. Individual blocks of these pipelines are also available for expert users to create their own advanced workflows.
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Affiliation(s)
- Olga Golosova
- Unipro Center for Information Technologies , Novosibirsk , Russia
| | - Ross Henderson
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH , Bethesda, MD , USA
| | - Yuriy Vaskin
- Unipro Center for Information Technologies , Novosibirsk , Russia
| | - Andrei Gabrielian
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH , Bethesda, MD , USA
| | - German Grekhov
- Unipro Center for Information Technologies , Novosibirsk , Russia
| | - Vijayaraj Nagarajan
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH , Bethesda, MD , USA
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH , Bethesda, MD , USA
| | - Mariam Quiñones
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH , Bethesda, MD , USA
| | - Darrell Hurt
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH , Bethesda, MD , USA
| | - Mikhail Fursov
- Unipro Center for Information Technologies , Novosibirsk , Russia
| | - Yentram Huyen
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH , Bethesda, MD , USA
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Barry KH, Moore LE, Sampson J, Yan L, Meyer A, Oler AJ, Chung CC, Wang Z, Yeager M, Amundadottir L, Berndt SI. DNA methylation levels at chromosome 8q24 in peripheral blood are associated with 8q24 cancer susceptibility loci. Cancer Prev Res (Phila) 2014; 7:1282-92. [PMID: 25315430 DOI: 10.1158/1940-6207.capr-14-0132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chromosome 8q24 has emerged as an important region for genetic susceptibility to various cancers, but little is known about the contribution of DNA methylation at 8q24. To evaluate variability in DNA methylation levels at 8q24 and the relationship with cancer susceptibility single nucleotide polymorphisms (SNPs) in this region, we quantified DNA methylation levels in peripheral blood at 145 CpG sites nearby 8q24 cancer susceptibility SNPs or MYC using pyrosequencing among 80 Caucasian men in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. For the 60 CpG sites meeting quality control, which also demonstrated temporal stability over a 5-year period, we calculated pairwise Spearman correlations for DNA methylation levels at each CpG site with 42 8q24 cancer susceptibility SNPs. To account for multiple testing, we adjusted P values into q values reflecting the false discovery rate (FDR). In contrast to the MYC CpG sites, most sites nearby the SNPs demonstrated good reproducibility, high methylation levels, and moderate-high between-individual variation. We observed 10 statistically significant (FDR < 0.05) CpG site-SNP correlations. These included correlations between an intergenic CpG site at Chr8:128393157 and the prostate cancer SNP rs16902094 (ρ = -0.54; P = 9.7 × 10(-7); q = 0.002), a PRNCR1 CpG site at Chr8:128167809 and the prostate cancer SNP rs1456315 (ρ = 0.52; P = 1.4 × 10(-6); q = 0.002), and two POU5F1B CpG sites and several prostate/colorectal cancer SNPs (for Chr8:128498051 and rs6983267, ρ = 0.46; P = 2.0 × 10(-5); q = 0.01). This is the first report of correlations between blood DNA methylation levels and cancer susceptibility SNPs at 8q24, suggesting that DNA methylation at this important susceptibility locus may contribute to cancer risk.
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Affiliation(s)
- Kathryn Hughes Barry
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland.
| | - Lee E Moore
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Joshua Sampson
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Liying Yan
- EpigenDx, Inc., Hopkinton, Massachusetts
| | - Ann Meyer
- EpigenDx, Inc., Hopkinton, Massachusetts
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Charles C Chung
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Zhaoming Wang
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Laufey Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Sonja I Berndt
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
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Oler AJ, Traina-Dorge S, Derbes RS, Canella D, Cairns BR, Roy-Engel AM. Alu expression in human cell lines and their retrotranspositional potential. Mob DNA 2012; 3:11. [PMID: 22716230 PMCID: PMC3412727 DOI: 10.1186/1759-8753-3-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 06/20/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The vast majority of the 1.1 million Alu elements are retrotranspositionally inactive, where only a few loci referred to as 'source elements' can generate new Alu insertions. The first step in identifying the active Alu sources is to determine the loci transcribed by RNA polymerase III (pol III). Previous genome-wide analyses from normal and transformed cell lines identified multiple Alu loci occupied by pol III factors, making them candidate source elements. FINDINGS Analysis of the data from these genome-wide studies determined that the majority of pol III-bound Alus belonged to the older subfamilies Alu S and Alu J, which varied between cell lines from 62.5% to 98.7% of the identified loci. The pol III-bound Alus were further scored for estimated retrotransposition potential (ERP) based on the absence or presence of selected sequence features associated with Alu retrotransposition capability. Our analyses indicate that most of the pol III-bound Alu loci candidates identified lack the sequence characteristics important for retrotransposition. CONCLUSIONS These data suggest that Alu expression likely varies by cell type, growth conditions and transformation state. This variation could extend to where the same cell lines in different laboratories present different Alu expression patterns. The vast majority of Alu loci potentially transcribed by RNA pol III lack important sequence features for retrotransposition and the majority of potentially active Alu loci in the genome (scored high ERP) belong to young Alu subfamilies. Our observations suggest that in an in vivo scenario, the contribution of Alu activity on somatic genetic damage may significantly vary between individuals and tissues.
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Affiliation(s)
- Andrew J Oler
- Department of Oncological Sciences, Huntsman Cancer Institute, and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT USA.,Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen Traina-Dorge
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Rebecca S Derbes
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Donatella Canella
- Center for Integrative Genomics (CIG), Faculty of Biology and Medicine, University of Lausanne, Lausanne 1015, Switzerland
| | - Brad R Cairns
- Department of Oncological Sciences, Huntsman Cancer Institute, and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Astrid M Roy-Engel
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University, 1430 Tulane Ave, New Orleans, LA 70112, USA
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Oler AJ, Cairns BR. PP4 dephosphorylates Maf1 to couple multiple stress conditions to RNA polymerase III repression. EMBO J 2012; 31:1440-52. [PMID: 22333918 PMCID: PMC3321174 DOI: 10.1038/emboj.2011.501] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 12/16/2011] [Indexed: 12/22/2022] Open
Abstract
Maf1 is the 'master' repressor of RNA polymerase III (Pol III) transcription in yeast, and is conserved in eukaryotes. Maf1 is a phospho-integrator, with unfavourable growth conditions leading to rapid Maf1 dephosphorylation, nuclear accumulation, binding to RNA Pol III at Pol III genes and transcriptional repression. Here, we establish the protein phosphatase 4 (PP4) complex as the main Maf1 phosphatase, and define the involved catalytic (Pph3), scaffold (Psy2) and regulatory subunits (Rrd1, Tip41), as well as uninvolved subunits (Psy4, Rrd2). Multiple approaches support a central role for PP4 in Maf1 dephosphorylation, Maf1 nuclear localization and the rapid repression of Pol III in the nucleus. PP4 action is likely direct, as a portion of PP4 co-precipitates with Maf1, and purified PP4 dephosphorylates Maf1 in vitro. Furthermore, Pph3 mediates (either largely or fully) rapid Maf1 dephosphorylation in response to diverse stresses, suggesting PP4 plays a key role in the integration of cell nutrition and stress conditions by Maf1 to enable Pol III regulation.
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Affiliation(s)
- Andrew J Oler
- HHMI, Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
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