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      Gain-of-function human UNC93B1 variants cause systemic lupus erythematosus and chilblain lupus

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      1 , 2 , 3 , 4 , 5 , 6 , 1 , 5 , 1 , 1 , 7 , 8 , 2 , 9 , 10 , 2 , 9 , 10 , 2 , 10 , 2 , 9 , 10 , 2 , 10 , 4 , 11 , 12 , 12 , 12 , 13 , 14 , 15 , 16 , 17 , 7 , 18 , 4 , 2 , 9 , 10 , 19 , 20 , 1 , 4 , 16 , , 5 , 1 , 7 , 18 , 2 , 10 , 1
      The Journal of Experimental Medicine
      Rockefeller University Press

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          Abstract

          David et al. describe UNC93B1 missense substitutions causing systemic lupus erythematosus or chilblain lupus, inherited as either autosomal dominant or autosomal recessive traits. In vitro and ex vivo assays show that these variants confer differential hypermorphic TLR7 and TLR8 signaling.

          Abstract

          UNC93B1 is a transmembrane domain protein mediating the signaling of endosomal Toll-like receptors (TLRs). We report five families harboring rare missense substitutions (I317M, G325C, L330R, R466S, and R525P) in UNC93B1 causing systemic lupus erythematosus (SLE) or chilblain lupus (CBL) as either autosomal dominant or autosomal recessive traits. As for a D34A mutation causing murine lupus, we recorded a gain of TLR7 and, to a lesser extent, TLR8 activity with the I317M (in vitro) and G325C (in vitro and ex vivo) variants in the context of SLE. Contrastingly, in three families segregating CBL, the L330R, R466S, and R525P variants were isomorphic with respect to TLR7 activity in vitro and, for R525P, ex vivo. Rather, these variants demonstrated a gain of TLR8 activity. We observed enhanced interaction of the G325C, L330R, and R466S variants with TLR8, but not the R525P substitution, indicating different disease mechanisms. Overall, these observations suggest that UNC93B1 mutations cause monogenic SLE or CBL due to differentially enhanced TLR7 and TLR8 signaling.

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          The Protein Data Bank.

          The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
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            ColabFold: making protein folding accessible to all

            ColabFold offers accelerated prediction of protein structures and complexes by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold’s 40−60-fold faster search and optimized model utilization enables prediction of close to 1,000 structures per day on a server with one graphics processing unit. Coupled with Google Colaboratory, ColabFold becomes a free and accessible platform for protein folding. ColabFold is open-source software available at https://github.com/sokrypton/ColabFold and its novel environmental databases are available at https://colabfold.mmseqs.com . ColabFold is a free and accessible platform for protein folding that provides accelerated prediction of protein structures and complexes using AlphaFold2 or RoseTTAFold.
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              Inborn errors of type I IFN immunity in patients with life-threatening COVID-19

              The genetics underlying severe COVID-19 The immune system is complex and involves many genes, including those that encode cytokines known as interferons (IFNs). Individuals that lack specific IFNs can be more susceptible to infectious diseases. Furthermore, the autoantibody system dampens IFN response to prevent damage from pathogen-induced inflammation. Two studies now examine the likelihood that genetics affects the risk of severe coronavirus disease 2019 (COVID-19) through components of this system (see the Perspective by Beck and Aksentijevich). Q. Zhang et al. used a candidate gene approach and identified patients with severe COVID-19 who have mutations in genes involved in the regulation of type I and III IFN immunity. They found enrichment of these genes in patients and conclude that genetics may determine the clinical course of the infection. Bastard et al. identified individuals with high titers of neutralizing autoantibodies against type I IFN-α2 and IFN-ω in about 10% of patients with severe COVID-19 pneumonia. These autoantibodies were not found either in infected people who were asymptomatic or had milder phenotype or in healthy individuals. Together, these studies identify a means by which individuals at highest risk of life-threatening COVID-19 can be identified. Science, this issue p. eabd4570, p. eabd4585; see also p. 404
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                Author and article information

                Contributors
                Role: ConceptualizationRole: InvestigationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: Methodology
                Role: Formal analysisRole: SoftwareRole: Visualization
                Role: ConceptualizationRole: Investigation
                Role: InvestigationRole: Writing - review & editing
                Role: Formal analysisRole: Investigation
                Role: InvestigationRole: Methodology
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Validation
                Role: InvestigationRole: Resources
                Role: Formal analysis
                Role: Formal analysis
                Role: Formal analysisRole: Writing - review & editing
                Role: Formal analysisRole: Software
                Role: Data curationRole: Formal analysis
                Role: Investigation
                Role: Investigation
                Role: Data curationRole: InvestigationRole: ResourcesRole: Writing - review & editing
                Role: Data curationRole: InvestigationRole: Writing - review & editing
                Role: Resources
                Role: Resources
                Role: Resources
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: Writing - review & editing
                Role: InvestigationRole: Writing - review & editing
                Role: Data curationRole: InvestigationRole: ValidationRole: Writing - review & editing
                Role: Writing - review & editing
                Role: Formal analysisRole: Writing - review & editing
                Role: Funding acquisitionRole: SupervisionRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - review & editing
                Role: ConceptualizationRole: ResourcesRole: SupervisionRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Formal analysisRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - review & editing
                Journal
                J Exp Med
                J Exp Med
                jem
                The Journal of Experimental Medicine
                Rockefeller University Press
                0022-1007
                1540-9538
                05 August 2024
                13 June 2024
                13 June 2024
                : 221
                : 8
                : e20232066
                Affiliations
                [1 ]Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163 ( https://ror.org/02vjkv261) , Paris, France
                [2 ]Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children ( https://ror.org/02vjkv261) , Paris, France
                [3 ]Department of Microbiology and Parasitology, Group of Primary Immunodeficiencies, School of Medicine, University of Antioquia; , Medellín, Colombia
                [4 ]MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh ( https://ror.org/011jsc803) , Edinburgh, UK
                [5 ]Faculté de Médecine Necker, Institut Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, Université Paris Cité ( https://ror.org/02vjkv261) , Paris, France
                [6 ]Faculty of Biology, Medicine and Health, Division of Evolution and Genomic Sciences, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester; , Manchester, UK
                [7 ]Department of Paediatric Hematology-Immunology and Rheumatology, Necker-Enfants Malades Hospital, ( https://ror.org/05tr67282) Assistance publique–hôpitaux de Paris (AP-HP), Paris, France
                [8 ]Bioinformatics Core Facility, Université Paris Cité-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633; , Paris, France
                [9 ]St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University ( https://ror.org/0420db125) , New York, NY, USA
                [10 ]Imagine Institute, Université Paris Cité ( https://ror.org/05f82e368) , Paris, France
                [11 ]Université Toulouse Paul Sabatier; , Toulouse, France
                [12 ]Paediatric Rheumatology, Royal Aberdeen Children’s Hospital ( https://ror.org/0264d9934) , Aberdeen, UK
                [13 ]Department of Paediatric Rheumatology, Royal Hospital for Children; , Glasgow, UK
                [14 ]Department of Pediatrics, Pediatric Rheumatology, Christian Medical College ( https://ror.org/00c7kvd80) , Vellore, India
                [15 ]Medical and Surgical Unit of Congenital and Paediatric Cardiology, Reference Centre for Complex Congenital Heart Defects—M3C, University Hospital Necker-Enfants Malades ( https://ror.org/05tr67282) , Paris, France
                [16 ]Université Paris Cité ( https://ror.org/05f82e368) , Paris, France
                [17 ]Department of Dermatology, Hospital Necker-Enfants Malades, AP-HP. Université Paris Cité ( https://ror.org/05f82e368) , Paris, France
                [18 ]Centre for Inflammatory Rheumatism, AutoImmune Diseases and Systemic Interferonopathies in Children (RAISE); , Paris, France
                [19 ]Howard Hughes Medical Institute; , New York, NY, USA
                [20 ]Department of Pediatrics, Necker Hospital for Sick Children; , Paris, France
                Author notes
                Correspondence to Yanick J Crow: yanickcrow@ 123456mac.com
                [*]

                C.A. Arango-Franco, M. Badonyi, and J. Fouchet contributed equally to this paper.

                [**]

                B. Manoury, M.-L. Frémond, J. Bohlen, and A. Lepelley contributed equally to this paper.

                Disclosures: C. Paul reported personal fees from Abbvie, Boehringer, BMS, Eli Lilly, and Janssen; grants from Novartis; and personal fees from Pfizer, Sanofi, Pierre Fabre, and UCB outside the submitted work. D. Bonnet reported personal fees from Novartis and MSD outside the submitted work. No other disclosures were reported.

                Author information
                https://orcid.org/0000-0001-6455-3251
                https://orcid.org/0000-0002-7404-0860
                https://orcid.org/0000-0002-8305-5618
                https://orcid.org/0009-0009-4572-5084
                https://orcid.org/0000-0002-4223-0571
                https://orcid.org/0009-0003-3261-7670
                https://orcid.org/0000-0002-5056-9444
                https://orcid.org/0000-0002-4678-3026
                https://orcid.org/0009-0007-0462-8224
                https://orcid.org/0000-0001-7870-7821
                https://orcid.org/0000-0001-7209-6257
                https://orcid.org/0000-0001-7016-6493
                https://orcid.org/0000-0002-5016-0446
                https://orcid.org/0000-0002-4020-824X
                https://orcid.org/0000-0002-8775-3368
                https://orcid.org/0009-0001-9620-1549
                https://orcid.org/0000-0003-0165-5263
                https://orcid.org/0009-0006-1627-4366
                https://orcid.org/0009-0006-3812-1889
                https://orcid.org/0009-0005-6660-8144
                https://orcid.org/0009-0003-2835-3772
                https://orcid.org/0000-0003-2137-7475
                https://orcid.org/0000-0002-8722-5805
                https://orcid.org/0000-0001-8772-0905
                https://orcid.org/0000-0001-8476-8196
                https://orcid.org/0000-0003-4132-0628
                https://orcid.org/0000-0002-7782-4169
                https://orcid.org/0000-0001-7211-7564
                https://orcid.org/0000-0002-4827-4110
                https://orcid.org/0000-0002-2798-9141
                https://orcid.org/0000-0003-0458-9484
                https://orcid.org/0000-0001-8656-7291
                Article
                jem.20232066
                10.1084/jem.20232066
                11176256
                38869500
                9a833344-760d-428c-b59a-2cf2b097f7ce
                © 2024 David et al.

                This article is available under a Creative Commons License (Attribution 4.0 International, as described at https://creativecommons.org/licenses/by/4.0/).

                History
                : 10 November 2023
                : 29 March 2024
                : 15 May 2024
                Funding
                Funded by: Fondation pour la Recherche Médicale, DOI http://dx.doi.org/10.13039/501100002915;
                Award ID: FDM202106013329
                Funded by: European Research Council, DOI http://dx.doi.org/10.13039/501100000781;
                Award ID: 786142 E-T1IFNs
                Award ID: 101001169
                Funded by: Medical Research Council, DOI http://dx.doi.org/10.13039/501100000265;
                Award ID: MC_UU_00035/11
                Funded by: Agence Nationale de la Recherche, DOI http://dx.doi.org/10.13039/501100001665;
                Award ID: ANR-10-IAHU-01
                Award ID: ANR-23-CE15-0015-02
                Award ID: ANR-10-LABX-62-IBEID
                Award ID: ANR-23-CE15-0015-02
                Funded by: Howard Hughes Medical Institute, DOI http://dx.doi.org/10.13039/100000011;
                Funded by: Rockefeller University, DOI http://dx.doi.org/10.13039/100012007;
                Funded by: St. Giles Foundation, DOI http://dx.doi.org/10.13039/100002350;
                Funded by: French Foundation for Medical Research, DOI http://dx.doi.org/10.13039/501100002915;
                Award ID: EQU201903007798
                Funded by: European Union’s Horizon 2020 research and innovation program, DOI http://dx.doi.org/10.13039/501100007601;
                Award ID: 824110
                Funded by: Square Foundation;
                Funded by: Grandir—Fonds de solidarité pour l’enfance;
                Funded by: General Atlantic Foundation;
                Funded by: Institut National de la Santé et de la Recherche Médicale, DOI http://dx.doi.org/10.13039/501100001677;
                Funded by: Paris Cité University, DOI http://dx.doi.org/10.13039/501100009516;
                Funded by: European Molecular Biology Organization, DOI http://dx.doi.org/10.13039/100004410;
                Categories
                Brief Definitive Report
                Human Disease Genetics
                Innate Immunity and Inflammation
                Autoimmunity

                Medicine
                Medicine

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