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Dueñas Rey A, Del Pozo Valero M, Bouckaert M, Wood KA, Van den Broeck F, Daich Varela M, Thomas HB, Van Heetvelde M, De Bruyne M, Van de Sompele S, Bauwens M, Lenaerts H, Mahieu Q, Josifova D, Rivolta C, O'Keefe RT, Ellingford J, Webster AR, Arno G, Ayuso C, De Zaeytijd J, Leroy BP, De Baere E, Coppieters F. Combining a prioritization strategy and functional studies nominates 5'UTR variants underlying inherited retinal disease. Genome Med 2024; 16:7. [PMID: 38184646 PMCID: PMC10771650 DOI: 10.1186/s13073-023-01277-1] [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: 06/16/2023] [Accepted: 12/15/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND 5' untranslated regions (5'UTRs) are essential modulators of protein translation. Predicting the impact of 5'UTR variants is challenging and rarely performed in routine diagnostics. Here, we present a combined approach of a comprehensive prioritization strategy and functional assays to evaluate 5'UTR variation in two large cohorts of patients with inherited retinal diseases (IRDs). METHODS We performed an isoform-level re-analysis of retinal RNA-seq data to identify the protein-coding transcripts of 378 IRD genes with highest expression in retina. We evaluated the coverage of their 5'UTRs by different whole exome sequencing (WES) kits. The selected 5'UTRs were analyzed in whole genome sequencing (WGS) and WES data from IRD sub-cohorts from the 100,000 Genomes Project (n = 2397 WGS) and an in-house database (n = 1682 WES), respectively. Identified variants were annotated for 5'UTR-relevant features and classified into seven categories based on their predicted functional consequence. We developed a variant prioritization strategy by integrating population frequency, specific criteria for each category, and family and phenotypic data. A selection of candidate variants underwent functional validation using diverse approaches. RESULTS Isoform-level re-quantification of retinal gene expression revealed 76 IRD genes with a non-canonical retina-enriched isoform, of which 20 display a fully distinct 5'UTR compared to that of their canonical isoform. Depending on the probe design, 3-20% of IRD genes have 5'UTRs fully captured by WES. After analyzing these regions in both cohorts, we prioritized 11 (likely) pathogenic variants in 10 genes (ARL3, MERTK, NDP, NMNAT1, NPHP4, PAX6, PRPF31, PRPF4, RDH12, RD3), of which 7 were novel. Functional analyses further supported the pathogenicity of three variants. Mis-splicing was demonstrated for the PRPF31:c.-9+1G>T variant. The MERTK:c.-125G>A variant, overlapping a transcriptional start site, was shown to significantly reduce both luciferase mRNA levels and activity. The RDH12:c.-123C>T variant was found in cis with the hypomorphic RDH12:c.701G>A (p.Arg234His) variant in 11 patients. This 5'UTR variant, predicted to introduce an upstream open reading frame, was shown to result in reduced RDH12 protein but unaltered mRNA levels. CONCLUSIONS This study demonstrates the importance of 5'UTR variants implicated in IRDs and provides a systematic approach for 5'UTR annotation and validation that is applicable to other inherited diseases.
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Affiliation(s)
- Alfredo Dueñas Rey
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marta Del Pozo Valero
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Manon Bouckaert
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Katherine A Wood
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Filip Van den Broeck
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Malena Daich Varela
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Huw B Thomas
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Mattias Van Heetvelde
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Stijn Van de Sompele
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Hanne Lenaerts
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Quinten Mahieu
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | | | - Carlo Rivolta
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Raymond T O'Keefe
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Jamie Ellingford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
- Genomics England, London, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
- Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium.
- Department of Pharmaceutics, Ghent University, Ghent, Belgium.
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2
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Panneman DM, Hitti-Malin RJ, Holtes LK, de Bruijn SE, Reurink J, Boonen EGM, Khan MI, Ali M, Andréasson S, De Baere E, Banfi S, Bauwens M, Ben-Yosef T, Bocquet B, De Bruyne M, de la Cerda B, Coppieters F, Farinelli P, Guignard T, Inglehearn CF, Karali M, Kjellström U, Koenekoop R, de Koning B, Leroy BP, McKibbin M, Meunier I, Nikopoulos K, Nishiguchi KM, Poulter JA, Rivolta C, Rodríguez de la Rúa E, Saunders P, Simonelli F, Tatour Y, Testa F, Thiadens AAHJ, Toomes C, Tracewska AM, Tran HV, Ushida H, Vaclavik V, Verhoeven VJM, van de Vorst M, Gilissen C, Hoischen A, Cremers FPM, Roosing S. Cost-effective sequence analysis of 113 genes in 1,192 probands with retinitis pigmentosa and Leber congenital amaurosis. Front Cell Dev Biol 2023; 11:1112270. [PMID: 36819107 PMCID: PMC9936074 DOI: 10.3389/fcell.2023.1112270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction: Retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) are two groups of inherited retinal diseases (IRDs) where the rod photoreceptors degenerate followed by the cone photoreceptors of the retina. A genetic diagnosis for IRDs is challenging since >280 genes are associated with these conditions. While whole exome sequencing (WES) is commonly used by diagnostic facilities, the costs and required infrastructure prevent its global applicability. Previous studies have shown the cost-effectiveness of sequence analysis using single molecule Molecular Inversion Probes (smMIPs) in a cohort of patients diagnosed with Stargardt disease and other maculopathies. Methods: Here, we introduce a smMIPs panel that targets the exons and splice sites of all currently known genes associated with RP and LCA, the entire RPE65 gene, known causative deep-intronic variants leading to pseudo-exons, and part of the RP17 region associated with autosomal dominant RP, by using a total of 16,812 smMIPs. The RP-LCA smMIPs panel was used to screen 1,192 probands from an international cohort of predominantly RP and LCA cases. Results and discussion: After genetic analysis, a diagnostic yield of 56% was obtained which is on par with results from WES analysis. The effectiveness and the reduced costs compared to WES renders the RP-LCA smMIPs panel a competitive approach to provide IRD patients with a genetic diagnosis, especially in countries with restricted access to genetic testing.
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Affiliation(s)
- Daan M. Panneman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands,*Correspondence: Daan M. Panneman,
| | - Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lara K. Holtes
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Janine Reurink
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Erica G. M. Boonen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Muhammad Imran Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Sten Andréasson
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy,Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Béatrice Bocquet
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, Montpellier, France,Institute for Neurosciences of Montpellier (INM), L’Institut National de la Santé et de la Recherche Médicale, University of Montpellier, L’Institut National de la Santé et de la Recherche Médicale, Montpellier, France
| | - Marieke De Bruyne
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Berta de la Cerda
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), Seville, Spain
| | - Frauke Coppieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium,Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Pietro Farinelli
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Thomas Guignard
- Chromosomal Genetics Unit, University Hospital of Montpellier, Montpellier, France
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Marianthi Karali
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy,Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Ulrika Kjellström
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Robert Koenekoop
- McGill University Health Center (MUHC) Research Institute, Montreal, QC, Canada,Departments of Paediatric Surgery, Human Genetics, and Adult Ophthalmology, McGill University Health Center, Montreal, QC, Canada
| | - Bart de Koning
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, Netherlands
| | - Bart P. Leroy
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium,Department of Head & Skin, Ghent University, Ghent, Belgium,Division of Ophthalmology & Center for Cellular & Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Martin McKibbin
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom,Department of Ophthalmology, St. James’s University Hospital, Leeds, United Kingdom
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, Montpellier, France,Institute for Neurosciences of Montpellier (INM), L’Institut National de la Santé et de la Recherche Médicale, University of Montpellier, L’Institut National de la Santé et de la Recherche Médicale, Montpellier, France
| | | | - Koji M. Nishiguchi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - James A. Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland,Department of Ophthalmology, University of Basel, Basel, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Enrique Rodríguez de la Rúa
- Department of Ophthalmology, Retics Patologia Ocular, OFTARED, Instituto de Salud Carlos III, University Hospital Virgen Macarena, Madrid, Spain
| | | | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Yasmin Tatour
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Anna M. Tracewska
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hoai Viet Tran
- Oculogenetic Unit, University Eye Hospital Jules Gonin, Geneva, Switzerland
| | - Hiroaki Ushida
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Veronika Vaclavik
- Oculogenetic Unit, University Eye Hospital Jules Gonin, Geneva, Switzerland
| | - Virginie J. M. Verhoeven
- Department of Ophthalmology, Erasmus, Rotterdam, Netherlands,Department of Clinical Genetics, Erasmus, Rotterdam, Netherlands
| | - Maartje van de Vorst
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
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Naesens L, Muppala S, Acharya D, Nemegeer J, Bogaert D, Lee JH, Staes K, Debacker V, De Bleser P, De Bruyne M, De Baere E, van Gent M, Liu G, Lambrecht BN, Staal J, Kerre T, Beyaert R, Maelfait J, Tavernier SJ, Gack MU, Haerynck F. GTF3A mutations predispose to herpes simplex encephalitis by disrupting biogenesis of the host-derived RIG-I ligand RNA5SP141. Sci Immunol 2022; 7:eabq4531. [PMID: 36399538 PMCID: PMC10075094 DOI: 10.1126/sciimmunol.abq4531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Herpes simplex virus 1 (HSV-1) infects several billion people worldwide and can cause life-threatening herpes simplex encephalitis (HSE) in some patients. Monogenic defects in components of the type I interferon system have been identified in patients with HSE, emphasizing the role of inborn errors of immunity underlying HSE pathogenesis. Here, we identify compound heterozygous loss-of-function mutations in the gene GTF3A encoding for transcription factor IIIA (TFIIIA), a component of the RNA polymerase III complex, in a patient with common variable immunodeficiency and HSE. Patient fibroblasts and GTF3A gene-edited cells displayed impaired HSV-1-induced innate immune responses and enhanced HSV-1 replication. Chromatin immunoprecipitation sequencing analysis identified the 5S ribosomal RNA pseudogene 141 (RNA5SP141), an endogenous ligand of the RNA sensor RIG-I, as a transcriptional target of TFIIIA. GTF3A mutant cells exhibited diminished RNA5SP141 expression and abrogated RIG-I activation upon HSV-1 infection. Our work unveils a crucial role for TFIIIA in transcriptional regulation of a cellular RIG-I agonist and shows that GTF3A genetic defects lead to impaired cell-intrinsic anti-HSV-1 responses and can predispose to HSE.
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Affiliation(s)
- Leslie Naesens
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, FL, USA
| | - Santoshi Muppala
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, FL, USA
| | - Dhiraj Acharya
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, FL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Josephine Nemegeer
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Laboratory of Molecular Signaling and Cell death, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Delfien Bogaert
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Jung-Hyun Lee
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, FL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Katrien Staes
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Veronique Debacker
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Pieter De Bleser
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Laboratory of Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Marieke De Bruyne
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Michiel van Gent
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, FL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, FL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Bart N. Lambrecht
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Jens Staal
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Laboratory of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Tessa Kerre
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Department of Hematology, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Rudi Beyaert
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Laboratory of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Jonathan Maelfait
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Laboratory of Molecular Signaling and Cell death, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Simon J. Tavernier
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Laboratory of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Michaela U. Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, FL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
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4
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Naesens L, Nemegeer J, Roelens F, Vallaeys L, Meuwissen M, Janssens K, Verloo P, Ogunjimi B, Hemelsoet D, Hoste L, Roels L, De Bruyne M, De Baere E, Van Dorpe J, Dendooven A, Sieben A, Rice GI, Kerre T, Beyaert R, Uggenti C, Crow YJ, Tavernier SJ, Maelfait J, Haerynck F. Mutations in RNU7-1 Weaken Secondary RNA Structure, Induce MCP-1 and CXCL10 in CSF, and Result in Aicardi-Goutières Syndrome with Severe End-Organ Involvement. J Clin Immunol 2022; 42:962-974. [PMID: 35320431 PMCID: PMC9402729 DOI: 10.1007/s10875-022-01209-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 10/06/2021] [Accepted: 01/07/2022] [Indexed: 01/19/2023]
Abstract
BACKGROUND Aicardi-Goutières syndrome (AGS) is a type I interferonopathy usually characterized by early-onset neurologic regression. Biallelic mutations in LSM11 and RNU7-1, components of the U7 small nuclear ribonucleoprotein (snRNP) complex, have been identified in a limited number of genetically unexplained AGS cases. Impairment of U7 snRNP function results in misprocessing of replication-dependent histone (RDH) pre-mRNA and disturbance of histone occupancy of nuclear DNA, ultimately driving cGAS-dependent type I interferon (IFN-I) release. OBJECTIVE We performed a clinical, genetic, and immunological workup of 3 unrelated patients with uncharacterized AGS. METHODS Whole exome sequencing (WES) and targeted Sanger sequencing of RNU7-1 were performed. Primary fibroblasts were used for mechanistic studies. IFN-I signature and STAT1/2 phosphorylation were assessed in peripheral blood. Cytokines were profiled on serum and cerebrospinal fluid (CSF). Histopathology was examined on brain and kidney tissue. RESULTS Sequencing revealed compound heterozygous RNU7-1 mutations, resulting in impaired RDH pre-mRNA processing. The 3' stem-loop mutations reduced stability of the secondary U7 snRNA structure. A discrete IFN-I signature in peripheral blood was paralleled by MCP-1 (CCL2) and CXCL10 upregulation in CSF. Histopathological analysis of the kidney showed thrombotic microangiopathy. We observed dysregulated STAT phosphorylation upon cytokine stimulation. Clinical overview of all reported patients with RNU7-1-related disease revealed high mortality and high incidence of organ involvement compared to other AGS genotypes. CONCLUSIONS Targeted RNU7-1 sequencing is recommended in genetically unexplained AGS cases. CSF cytokine profiling represents an additional diagnostic tool to identify aberrant IFN-I signaling. Clinical follow-up of RNU7-1-mutated patients should include screening for severe end-organ involvement including liver disease and nephropathy.
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Affiliation(s)
- Leslie Naesens
- Department of Internal Medicine and Pediatrics, Ghent University, 9000, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, 9000, Ghent, Belgium
| | - Josephine Nemegeer
- VIB-UGent Center for Inflammation Research, 9052, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9052, Ghent, Belgium
| | - Filip Roelens
- Department of Pediatrics, Algemeen Ziekenhuis Delta, 8800, Roeselare, Belgium
| | - Lore Vallaeys
- Department of Pediatrics, Algemeen Ziekenhuis Groeninge, 8500, Kortrijk, Belgium
| | - Marije Meuwissen
- Department of Medical Genetics, University of Antwerp, 2000, Antwerp, Belgium
- Department of Medical Genetics, Antwerp University Hospital, 2650, Antwerp, Belgium
| | - Katrien Janssens
- Department of Medical Genetics, University of Antwerp, 2000, Antwerp, Belgium
- Department of Medical Genetics, Antwerp University Hospital, 2650, Antwerp, Belgium
| | - Patrick Verloo
- Department of Pediatrics, Division of Pediatric Neurology, University Hospital Ghent, 9000, Ghent, Belgium
| | - Benson Ogunjimi
- Department of Pediatrics, Antwerp University Hospital, 2650, Edegem, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610, Antwerp, Belgium
| | - Dimitri Hemelsoet
- Department of Neurology, Ghent University Hospital, 9000, Ghent, Belgium
| | - Levi Hoste
- Department of Internal Medicine and Pediatrics, Ghent University, 9000, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, 9000, Ghent, Belgium
| | - Lisa Roels
- Department of Internal Medicine and Pediatrics, Ghent University, 9000, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, 9000, Ghent, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000, Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, 9000, Ghent, Belgium
| | - Amélie Dendooven
- Department of Pathology, Ghent University Hospital, 9000, Ghent, Belgium
- Department of Pathology, Antwerp University Hospital, 9000, Ghent, Belgium
| | - Anne Sieben
- Department of Neurology, Ghent University Hospital, 9000, Ghent, Belgium
- Department of Pathology, Antwerp University Hospital, 9000, Ghent, Belgium
| | - Gillian I Rice
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Tessa Kerre
- Department of Hematology, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, 9000, Ghent, Belgium
| | - Rudi Beyaert
- Department of Biomedical Molecular Biology, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Inflammation Research, Laboratory of Molecular Signal Transduction in Inflammation, VIB, 9052, Ghent, Belgium
| | - Carolina Uggenti
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Yanick J Crow
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- Laboratory of Neurogenetics and Neuroinflammation, University of Paris, Imagine Institute, Paris, France
| | - Simon J Tavernier
- Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, 9000, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9052, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
- VIB-UGent Center for Inflammation Research, Laboratory of Molecular Signal Transduction in Inflammation, VIB, 9052, Ghent, Belgium
| | - Jonathan Maelfait
- VIB-UGent Center for Inflammation Research, 9052, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9052, Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Ghent University, 9000, Ghent, Belgium.
- Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, 9000, Ghent, Belgium.
- Department of Pediatric Pulmonology, Infectious Diseases and Immunology, Ghent University Hospital, Corneel Heymanslaan 10, Ghent, Belgium.
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5
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Faizi N, Casteels I, Termote B, Coucke P, De Baere E, De Bruyne M, Balikova I. High myopia and vitreal veils in a patient with Poretti- Boltshauser syndrome due to a novel homozygous LAMA1 mutation. Ophthalmic Genet 2022; 43:653-657. [PMID: 35535551 DOI: 10.1080/13816810.2022.2068045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Nawid Faizi
- Department of Ophthalmology, University Hospital Leuven, Leuven, Belgium
| | - Ingele Casteels
- Department of Ophthalmology, University Hospital Leuven, Leuven, Belgium
| | - Bruno Termote
- Department of Radiology, Jessa Hospital Hasselt, Hasselt, Belgium
| | - Paul Coucke
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Marieke De Bruyne
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Irina Balikova
- Department of Ophthalmology, University Hospital Leuven, Leuven, Belgium
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6
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Strubbe S, De Bruyne M, Pannicke U, Beyls E, Vandekerckhove B, Leclercq G, De Baere E, Bordon V, Vral A, Schwarz K, Haerynck F, Taghon T. A Novel Non-Coding Variant in DCLRE1C Results in Deregulated Splicing and Induces SCID Through the Generation of a Truncated ARTEMIS Protein That Fails to Support V(D)J Recombination and DNA Damage Repair. Front Immunol 2021; 12:674226. [PMID: 34220820 PMCID: PMC8248492 DOI: 10.3389/fimmu.2021.674226] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Severe Combined Immune Deficiency (SCID) is a primary deficiency of the immune system in which opportunistic and recurring infections are often fatal during neonatal or infant life. SCID is caused by an increasing number of genetic defects that induce an abrogation of T lymphocyte development or function in which B and NK cells might be affected as well. Because of the increased availability and usage of next-generation sequencing (NGS), many novel variants in SCID genes are being identified and cause a heterogeneous disease spectrum. However, the molecular and functional implications of these new variants, of which some are non-coding, are often not characterized in detail. Using targeted NGS, we identified a novel homozygous c.465-1G>C splice acceptor site variant in the DCLRE1C gene in a T-B-NK+ SCID patient and fully characterized the molecular and functional impact. By performing a minigene splicing reporter assay, we revealed deregulated splicing of the DCLRE1C transcript since a cryptic splice acceptor in exon 7 was employed. This induced a frameshift and the generation of a p.Arg155Serfs*15 premature termination codon (PTC) within all DCLRE1C splice variants, resulting in the absence of full-length ARTEMIS protein. Consistently, a V(D)J recombination assay and a G0 micronucleus assay demonstrated the inability of the predicted mutant ARTEMIS protein to perform V(D)J recombination and DNA damage repair, respectively. Together, these experiments molecularly and functionally clarify how a newly identified c.465-1G>C variant in the DCLRE1C gene is responsible for inducing SCID. In a clinical context, this demonstrates how the experimental validation of new gene variants, that are identified by NGS, can facilitate the diagnosis of SCID which can be vital for implementing appropriate therapies.
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Affiliation(s)
- Steven Strubbe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | | | - Ulrich Pannicke
- The Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Elien Beyls
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Bart Vandekerckhove
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Georges Leclercq
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Victoria Bordon
- Department of Internal Medicine and Pediatrics, Division of Pediatric Hemato-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Anne Vral
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Klaus Schwarz
- The Institute for Transfusion Medicine, University of Ulm, Ulm, Germany.,Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, Germa Red Cross Blood Service Baden-Württemberg - Hessen, Ulm, Germany
| | - Filomeen Haerynck
- Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Division of Pediatric Immunology and Pulmonology, Ghent University Hospital, Ghent, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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7
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De Zaeytijd J, Van Cauwenbergh C, De Bruyne M, Van Heetvelde M, De Baere E, Coppieters F, Leroy BP. ISOLATED MACULOPATHY AND MODERATE ROD-CONE DYSTROPHY REPRESENT THE MILDER END OF THE RDH12-RELATED RETINAL DYSTROPHY SPECTRUM. Retina 2021; 41:1346-1355. [PMID: 34001834 DOI: 10.1097/iae.0000000000003028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE To describe an isolated maculopathy and an intermediate rod-cone dystrophy phenotype as the milder end of the RDH12-related retinal dystrophy spectrum. METHODS Seven patients (17-34 years of age) underwent an extensive ophthalmic workup including psychophysical and electrophysiological testing and multimodal imaging. RESULTS Three patients have isolated macular disease. Best-corrected visual acuity (BCVA) ranges from 20/125 to 20/40 with normal visual fields or only limited central, relative scotomata, and normal full-field ERGs. Both optical coherence tomography scans and autofluorescent imaging hint at relatively better-preserved foveal quality initially. An intermediate rod-cone phenotype in four patients is characterized by a central retinal dystrophy extending just beyond the vascular arcades, characteristic peripapillary sparing, and additional scattered atrophic patches. Again, foveal quality is initially better on optical coherence tomography scans. Best-corrected visual acuity ranges from counting fingers to 20/32. Goldmann visual fields vary from central scotomata to severe generalized abnormalities. ERGs range between mild and severe rod-cone dysfunction. Nine distinct RDH12 pathogenic variants, two of which are novel, are identified. CONCLUSION The classic phenotype of RDH12-related early-onset retinal dystrophy is expanded to include an isolated maculopathy and intermediate dystrophy phenotype, characterized by its later onset and milder course with a fair visual potential until much later in life, emphasizing the phenotypic heterogeneity of RDH12-related retinopathy.
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Affiliation(s)
- Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Caroline Van Cauwenbergh
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Mattias Van Heetvelde
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bart P Leroy
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; and
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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8
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De Zaeytijd J, Coppieters F, De Bruyne M, Van Royen J, Roels D, Six R, Van Cauwenbergh C, De Baere E, Leroy BP. Longitudinal phenotypic study of late-onset retinal degeneration due to a founder variant c.562C>A p.(Pro188Thr) in the C1QTNF5 gene. Ophthalmic Genet 2021; 42:521-532. [PMID: 33949280 DOI: 10.1080/13816810.2021.1923041] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Background: Late-onset retinal degeneration (L-ORD) is a rare autosomal dominant retinal dystrophy related to C1QTNF5 gene variants.Materials and methods: Twenty-six patients (21-81 years) with L-ORD due to c.562C>A p.(Pro188Thr) with a mean follow-up time of 8 years (range 1-37 years) underwent an extensive ophthalmic work-up.Results: Best-corrected visual acuity (BCVA) and visual fields were maintained up to 50 to 55 years (n = 8), with a gradual decline, but conservation of functional central vision between 55 to 65 years (n = 15), followed by a steep decrease in overall visual function beyond 65 years (n = 9). Classic anterior segment findings in L-ORD of abnormally long, anteriorly inserted lens zonules were absent in most patients (n = 24/26). In contrast, findings of iris transillumination and sphincter pupillae atrophy with poor dilation were novel. Patients presented with three completely different initial fundus phenotypes: adjoining pavingstone-like atrophic patches (type 1) (n = 6/20); tiny yellow-white subretinal dots (type 2) (n = 8/20); or larger yellow, thick, round sub-RPE drusenoid deposits (type 3) (n = 4/20). Two patients had a mixed phenotype. Although different in presentation phenotype, patients eventually all progressed to a common panretinal atrophy with diffuse intraretinal pigment migration beyond the age of 65. Progression pace, and thus visual prognosis, differed depending on presentation phenotype. Specifically, type 2 appears to have a more benign course.Conclusions: Phenotypic analysis showed three distinct presenting phenotypes with a considerable intrafamilial variability both in age of onset of clinical signs and in disease progression, with a fair visual potential (>20/40) until the seventh decade.Abbreviations: L-ORD: Late-onset retinal degeneration; C1QTNF5: complement 1Q tumor necrosis factor 5; OCT: Ocular coherence tomography; BCVA: Best-corrected visual acuity; RPE: Retinal pigment epithelium; ffERG: Full-field electroretinography; IRD: Inherited retinal dystrophy; CNV: Choroidal neovascularization; LAZ: Long anteriorly inserted zonules; AMPK: AMP-activated protein kinase; IOP: Intraocular pressure; cSLO: confocal scanning laser ophthalmoscopy; BAF: Blue light autofluorescence; NIR-AF: Near-infrared autofluorescence; NIR-R: Near-infrared reflectance; RF: Red-free; SD-OCT: Spectral domain ocular coherence tomography; HRR: Hardy-Rand-Rittler pseudo-isochromatic plates; AS: anterior segment; UBM: ultrasound biomicroscopy; PCR: Polymerase chain reaction; SNP: Single nucleotide polymorphism; VEGF: Vascular endothelial growth factor; IZ: Interdigitation zone; EZ: Ellipsoid zone; ELM: External limiting membrane; LP: Light perception; AMD: Age-related macular degeneration; SFD: Sorsby fundus dystrophy.
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Affiliation(s)
- Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jasper Van Royen
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Dimitri Roels
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Rani Six
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Caroline Van Cauwenbergh
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bart P Leroy
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Head & Skin, Ghent University, Ghent, Belgium.,Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Center for Cellular & Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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9
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Ascari G, Rendtorff ND, De Bruyne M, De Zaeytijd J, Van Lint M, Bauwens M, Van Heetvelde M, Arno G, Jacob J, Creytens D, Van Dorpe J, Van Laethem T, Rosseel T, De Pooter T, De Rijk P, De Coster W, Menten B, Rey AD, Strazisar M, Bertelsen M, Tranebjaerg L, De Baere E. Long-Read Sequencing to Unravel Complex Structural Variants of CEP78 Leading to Cone-Rod Dystrophy and Hearing Loss. Front Cell Dev Biol 2021; 9:664317. [PMID: 33968938 PMCID: PMC8097100 DOI: 10.3389/fcell.2021.664317] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Abstract
Inactivating variants as well as a missense variant in the centrosomal CEP78 gene have been identified in autosomal recessive cone-rod dystrophy with hearing loss (CRDHL), a rare syndromic inherited retinal disease distinct from Usher syndrome. Apart from this, a complex structural variant (SV) implicating CEP78 has been reported in CRDHL. Here we aimed to expand the genetic architecture of typical CRDHL by the identification of complex SVs of the CEP78 region and characterization of their underlying mechanisms. Approaches used for the identification of the SVs are shallow whole-genome sequencing (sWGS) combined with quantitative polymerase chain reaction (PCR) and long-range PCR, or ExomeDepth analysis on whole-exome sequencing (WES) data. Targeted or whole-genome nanopore long-read sequencing (LRS) was used to delineate breakpoint junctions at the nucleotide level. For all SVs cases, the effect of the SVs on CEP78 expression was assessed using quantitative PCR on patient-derived RNA. Apart from two novel canonical CEP78 splice variants and a frameshifting single-nucleotide variant (SNV), two SVs affecting CEP78 were identified in three unrelated individuals with CRDHL: a heterozygous total gene deletion of 235 kb and a partial gene deletion of 15 kb in a heterozygous and homozygous state, respectively. Assessment of the molecular consequences of the SVs on patient's materials displayed a loss-of-function effect. Delineation and characterization of the 15-kb deletion using targeted LRS revealed the previously described complex CEP78 SV, suggestive of a recurrent genomic rearrangement. A founder haplotype was demonstrated for the latter SV in cases of Belgian and British origin, respectively. The novel 235-kb deletion was delineated using whole-genome LRS. Breakpoint analysis showed microhomology and pointed to a replication-based underlying mechanism. Moreover, data mining of bulk and single-cell human and mouse transcriptional datasets, together with CEP78 immunostaining on human retina, linked the CEP78 expression domain with its phenotypic manifestations. Overall, this study supports that the CEP78 locus is prone to distinct SVs and that SV analysis should be considered in a genetic workup of CRDHL. Finally, it demonstrated the power of sWGS and both targeted and whole-genome LRS in identifying and characterizing complex SVs in patients with ocular diseases.
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Affiliation(s)
- Giulia Ascari
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Nanna D Rendtorff
- The Kennedy Center, Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Michel Van Lint
- Department of Ophthalmology, Antwerp University Hospital, Antwerp, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Mattias Van Heetvelde
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Gavin Arno
- Great Ormond Street Hospital, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom.,UCL Institute of Ophthalmology, London, United Kingdom
| | - Julie Jacob
- Department of Ophthalmology, University Hospitals Leuven, Leuven, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Thalia Van Laethem
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tim De Pooter
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Peter De Rijk
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Alfredo Dueñas Rey
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Mojca Strazisar
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Mette Bertelsen
- The Kennedy Center, Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Ophthalmology, Rigshospitalet-Glostrup, University of Copenhagen, Glostrup, Denmark
| | - Lisbeth Tranebjaerg
- The Kennedy Center, Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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10
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Strubbe I, Van Cauwenbergh C, De Zaeytijd J, De Jaegere S, De Bruyne M, Rosseel T, Van de Sompele S, De Baere E, Leroy BP. Phenocopy of a heterozygous carrier of X-linked retinitis pigmentosa due to mosaicism for a RHO variant. Sci Rep 2021; 11:117. [PMID: 33420188 PMCID: PMC7794345 DOI: 10.1038/s41598-020-80400-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 07/03/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022] Open
Abstract
We describe both phenotype and pathogenesis in two male siblings with typical retinitis pigmentosa (RP) and the potentially X-linked RP (XLRP) carrier phenotype in their mother. Two affected sons, two unaffected daughters, and their mother underwent detailed ophthalmological assessments including Goldmann perimetry, color vision testing, multimodal imaging and ISCEV-standard electroretinography. Genetic testing consisted of targeted next-generation sequencing (NGS) of known XLRP genes and whole exome sequencing (WES) of known inherited retinal disease genes (RetNet-WES). Variant validation and segregation analysis were performed by Sanger sequencing. The mutational load of the RHO variant in the mother was assessed in DNA from leucocytes, buccal cells and hair follicles using targeted NGS. Both affected sons showed signs of classical RP, while the mother displayed patches of hyperautofluorescence on blue light autofluorescence imaging and regional, intraretinal, spicular pigmentation, reminiscent of a carrier phenotype of XLRP. XLRP testing was negative. RetNet-WES testing revealed RHO variant c.404G > C p.(Arg135Pro) in a mosaic state (21% of the reads) in the mother and in a heterozygous state in both sons. Targeted NGQSS of the RHO variant in different maternal tissues showed a mutation load between 25.06% and 41.72%. We report for the first time that somatic mosaicism of RHO variant c.404G > C p.(Arg135Pro) mimics the phenotype of a female carrier of XLRP, in combination with heterozygosity for the variant in the two affected sons.
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Affiliation(s)
- Ine Strubbe
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Caroline Van Cauwenbergh
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Sarah De Jaegere
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Stijn Van de Sompele
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Elfride De Baere
- Department of Head & Skin, Ghent University, Ghent, Belgium. .,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium. .,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
| | - Bart P Leroy
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium. .,Department of Head & Skin, Ghent University, Ghent, Belgium. .,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium. .,Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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11
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Van Damme KFA, Tavernier S, Van Roy N, De Leeuw E, Declercq J, Bosteels C, Maes B, De Bruyne M, Bogaert D, Bosteels V, Hoste L, Naesens L, Maes P, Grifoni A, Weiskopf D, Sette A, Depuydt P, Van Braeckel E, Haerynck F, Lambrecht BN. Case Report: Convalescent Plasma, a Targeted Therapy for Patients with CVID and Severe COVID-19. Front Immunol 2020; 11:596761. [PMID: 33329586 PMCID: PMC7714937 DOI: 10.3389/fimmu.2020.596761] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/26/2020] [Indexed: 12/27/2022] Open
Abstract
The disease course of COVID-19 in patients with immunodeficiencies is unclear, as well as the optimal therapeutic strategy. We report a case of a 37-year old male with common variable immunodeficiency disorder and a severe SARS-CoV-2 infection. After administration of convalescent plasma, the patient's condition improved rapidly. Despite clinical recovery, viral RNA remained detectable up to 60 days after onset of symptoms. We propose that convalescent plasma might be considered as a treatment option in patients with CVID and severe COVID-19. In addition, in patients with immunodeficiencies, a different clinical course is possible, with prolonged viral shedding.
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Affiliation(s)
- Karel F A Van Damme
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Simon Tavernier
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Nele Van Roy
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Elisabeth De Leeuw
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Jozefien Declercq
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Cédric Bosteels
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Bastiaan Maes
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Delfien Bogaert
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Victor Bosteels
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Laboratory of ER Stress and Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Levi Hoste
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Leslie Naesens
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Piet Maes
- Department of Microbiology, Immunology, and Transplantation, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), CA, United States
| | - Pieter Depuydt
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Department of Intensive Care, Ghent University Hospital, Ghent, Belgium
| | - Eva Van Braeckel
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Bart N Lambrecht
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium.,Department of Pulmonary Medicine, Erasmus Medical Center, Rotterdam, Netherlands
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12
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Backers L, Parton B, De Bruyne M, Tavernier SJ, Van Den Bogaert K, Lambrecht BN, Haerynck F, Claes KBM. Missing heritability in Bloom syndrome: First report of a deep intronic variant leading to pseudo-exon activation in the BLM gene. Clin Genet 2020; 99:292-297. [PMID: 33073370 DOI: 10.1111/cge.13859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 07/20/2020] [Revised: 09/17/2020] [Accepted: 09/30/2020] [Indexed: 12/16/2022]
Abstract
Pathogenic biallelic variants in the BLM/RECQL3 gene cause a rare autosomal recessive disorder called Bloom syndrome (BS). This syndrome is characterized by severe growth delay, immunodeficiency, dermatological manifestations and a predisposition to a wide variety of cancers, often multiple and very early in life. Literature shows that the main mode of BLM inactivation is protein translation termination. We expanded the molecular spectrum of BS by reporting the first deep intronic variant causing intron exonisation. We describe a patient with a clinical phenotype of BS and a strong increase in sister chromatid exchanges (SCE), who was found to be compound heterozygous for a novel nonsense variant c.3379C>T, p.(Gln1127Ter) in exon 18 and a deep intronic variant c.3020-258A>G in intron 15 of the BLM gene. The deep intronic variant creates a high-quality de novo donor splice site, which leads to retention of two intron segments. Both pseudo-exons introduce a premature stop codon into the reading frame and abolish BLM protein expression, confirmed by Western Blot analysis. These findings illustrate the role of non-coding variation in Mendelian disorders and herewith highlight an unmet need in routine testing of Mendelian disorders, being the added value of RNA-based approaches to provide a complete molecular diagnosis.
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Affiliation(s)
- Lynn Backers
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Bram Parton
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Simon J Tavernier
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Kris Van Den Bogaert
- Center for Human Genetics, University Hospitals Leuven - Catholic University Leuven, Leuven, Belgium
| | - Bart N Lambrecht
- Unit of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Kathleen B M Claes
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
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13
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Béziat V, Tavernier SJ, Chen YH, Ma CS, Materna M, Laurence A, Staal J, Aschenbrenner D, Roels L, Worley L, Claes K, Gartner L, Kohn LA, De Bruyne M, Schmitz-Abe K, Charbonnier LM, Keles S, Nammour J, Vladikine N, Luxman Maglorius Renkilaraj MR, Seeleuthner Y, Migaud M, Rosain J, Jeljeli M, Boisson B, Van Braeckel E, Rosenfeld JA, Dai H, Burrage LC, Murdock DR, Lambrecht BN, Avettand-Fenoel V, Vogel TP, Network UD, Esther CR, Haskologlu S, Dogu F, Ciznar P, Boutboul D, Ouachée-Chardin M, Amourette J, Lebras MN, Gauvain C, Tcherakian C, Ikinciogullari A, Beyaert R, Abel L, Milner JD, Grimbacher B, Couderc LJ, Butte MJ, Freeman AF, Catherinot É, Fieschi C, Chatila TA, Tangye SG, Uhlig HH, Haerynck F, Casanova JL, Puel A. Correction: Dominant-negative mutations in human IL6ST underlie hyper-IgE syndrome. J Exp Med 2020; 217:151847. [PMID: 32516385 PMCID: PMC7336304 DOI: 10.1084/jem.2019180405272020c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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14
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Béziat V, Tavernier SJ, Chen YH, Ma CS, Materna M, Laurence A, Staal J, Aschenbrenner D, Roels L, Worley L, Claes K, Gartner L, Kohn LA, De Bruyne M, Schmitz-Abe K, Charbonnier LM, Keles S, Nammour J, Vladikine N, Maglorius Renkilaraj MRL, Seeleuthner Y, Migaud M, Rosain J, Jeljeli M, Boisson B, Van Braeckel E, Rosenfeld JA, Dai H, Burrage LC, Murdock DR, Lambrecht BN, Avettand-Fenoel V, Vogel TP, Esther CR, Haskologlu S, Dogu F, Ciznar P, Boutboul D, Ouachée-Chardin M, Amourette J, Lebras MN, Gauvain C, Tcherakian C, Ikinciogullari A, Beyaert R, Abel L, Milner JD, Grimbacher B, Couderc LJ, Butte MJ, Freeman AF, Catherinot É, Fieschi C, Chatila TA, Tangye SG, Uhlig HH, Haerynck F, Casanova JL, Puel A. Dominant-negative mutations in human IL6ST underlie hyper-IgE syndrome. J Exp Med 2020; 217:e20191804. [PMID: 32207811 PMCID: PMC7971136 DOI: 10.1084/jem.20191804] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [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: 09/25/2019] [Revised: 01/14/2020] [Accepted: 02/18/2020] [Indexed: 11/29/2022] Open
Abstract
Autosomal dominant hyper-IgE syndrome (AD-HIES) is typically caused by dominant-negative (DN) STAT3 mutations. Patients suffer from cold staphylococcal lesions and mucocutaneous candidiasis, severe allergy, and skeletal abnormalities. We report 12 patients from 8 unrelated kindreds with AD-HIES due to DN IL6ST mutations. We identified seven different truncating mutations, one of which was recurrent. The mutant alleles encode GP130 receptors bearing the transmembrane domain but lacking both the recycling motif and all four STAT3-recruiting tyrosine residues. Upon overexpression, the mutant proteins accumulate at the cell surface and are loss of function and DN for cellular responses to IL-6, IL-11, LIF, and OSM. Moreover, the patients' heterozygous leukocytes and fibroblasts respond poorly to IL-6 and IL-11. Consistently, patients with STAT3 and IL6ST mutations display infectious and allergic manifestations of IL-6R deficiency, and some of the skeletal abnormalities of IL-11R deficiency. DN STAT3 and IL6ST mutations thus appear to underlie clinical phenocopies through impairment of the IL-6 and IL-11 response pathways.
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Affiliation(s)
- Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, 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
| | - Simon J. Tavernier
- Primary Immune Deficiency Research Laboratory, Department of Internal Diseases and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
- VIB-UGent Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, Ghent, Belgium
| | - Yin-Huai Chen
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Cindy S. Ma
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Marie Materna
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Arian Laurence
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Jens Staal
- VIB-UGent Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, Ghent, Belgium
| | - Dominik Aschenbrenner
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Lisa Roels
- Primary Immune Deficiency Research Laboratory, Department of Internal Diseases and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
| | - Lisa Worley
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Kathleen Claes
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Lisa Gartner
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Lisa A. Kohn
- Division of Immunology, Allergy, and Rheumatology, Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA
| | - Marieke De Bruyne
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Klaus Schmitz-Abe
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Louis-Marie Charbonnier
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Division of Immunology, Boston Children’s Hospital, Boston, MA
| | - Sevgi Keles
- Necmettin Erbakan University, Meram Medical Faculty, Division of Pediatric Allergy and Immunology, Konya, Turkey
| | - Justine Nammour
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Natasha Vladikine
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Majistor Raj Luxman Maglorius Renkilaraj
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Mohamed Jeljeli
- Cochin University Hospital, Biological Immunology Unit, Assistance Publique Hôpitaux de Paris (AP-HP), Paris, France
| | - Bertrand Boisson
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, 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
| | - Eva Van Braeckel
- Department of Respiratory Medicine, Ghent University Hospital, Ghent Belgium
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Lindsay C. Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - David R. Murdock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Bart N. Lambrecht
- VIB-UGent Center for Inflammation Research, Unit of Immunoregulation and Mucosal Immunology, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Véronique Avettand-Fenoel
- Laboratory of Clinical Microbiology, Virology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Tiphanie P. Vogel
- Division of Rheumatology, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | | | - Charles R. Esther
- Pediatric Pulmonology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sule Haskologlu
- Division of Pediatric Immunology and Allergy, Ankara University School of Medicine, Sıhhıye, Ankara, Turkey
| | - Figen Dogu
- Division of Pediatric Immunology and Allergy, Ankara University School of Medicine, Sıhhıye, Ankara, Turkey
| | - Peter Ciznar
- Department of Pediatrics, Faculty of Medicine Comenius University and Children's University Hospital, Bratislava, Slovakia
| | - David Boutboul
- Clinical Immunology Department, Saint Louis Hospital, AP-HP de Paris University of Paris, Paris, France
| | - Marie Ouachée-Chardin
- Department of Pediatric Hematology and Immunology, Robert Debré Hospital, AP-HP, Paris, France
| | - Jean Amourette
- Pulmonology Department, Centre Hospitalier d'Arras, Arras, France
| | - Marie-Noëlle Lebras
- Pediatric Pulmonology, Infectious Disease and Internal Medicine Department, AP-HP, Robert Debré Hospital, Paris, France
| | - Clément Gauvain
- Thoracic Oncology Department, Lille University Hospital, Lille, France
| | | | - Aydan Ikinciogullari
- Division of Pediatric Immunology and Allergy, Ankara University School of Medicine, Sıhhıye, Ankara, Turkey
| | - Rudi Beyaert
- VIB-UGent Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, Ghent, Belgium
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, 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
| | - Joshua D. Milner
- National Institute of Allergy and Infectious Diseases, Bethesda, MD
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert Ludwig University of Freiburg, Freiburg, Germany
- German Center for Infection Research, Satellite Center Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signaling Studies, Albert Ludwig University, Freiburg, Germany
- RESIST, Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany
- Institute of Immunity and Transplantation, Royal Free Hospital, University College London, London, UK
| | - Louis-Jean Couderc
- Hôpital Foch, Pulmonology Department, Suresnes, France
- Simone Veil Faculty of Life Sciences, Versailles-Paris Saclay University, UPRES EA-220, Suresnes, France
| | - Manish J. Butte
- Division of Immunology, Allergy, and Rheumatology, Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA
| | | | | | - Claire Fieschi
- Clinical Immunology Department, Saint Louis Hospital, AP-HP de Paris University of Paris, Paris, France
- INSERM UMR1126, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Talal A. Chatila
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Division of Immunology, Boston Children’s Hospital, Boston, MA
| | - Stuart G. Tangye
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Holm H. Uhlig
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Filomeen Haerynck
- Primary Immune Deficiency Research Laboratory, Department of Internal Diseases and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Division of Pediatric Immunology and Pulmonology, Ghent University Hospital, Ghent, Belgium
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, 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
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
- Howard Hughes Medical Institute, New York, NY
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, 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
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15
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Bogaert DJ, Laureys G, Naesens L, Mazure D, De Bruyne M, Hsu AP, Bordon V, Wouters E, Tavernier SJ, Lambrecht BN, De Baere E, Haerynck F, Kerre T. GATA2 deficiency and haematopoietic stem cell transplantation: challenges for the clinical practitioner. Br J Haematol 2019; 188:768-773. [PMID: 31710708 DOI: 10.1111/bjh.16247] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 07/02/2019] [Accepted: 08/15/2019] [Indexed: 12/12/2022]
Abstract
GATA2 deficiency, first described in 2011, is a bone marrow failure disorder resulting in a complex haematological and immunodeficiency syndrome characterised by cytopenias, severe infections, myelodysplasia and leukaemia. The only curative treatment is allogeneic haematopoietic stem cell transplantation (HSCT). Although knowledge on this syndrome has greatly expanded, in clinical practice many challenges remain. In particular, guidelines on optimal donor and stem cell source and conditioning regimens regarding HSCT are lacking. Additionally, genetic analysis of GATA2 is technically cumbersome and could easily result in false-negative results. With this report, we wish to raise awareness of these pitfalls amongst physicians dealing with haematological malignancies and primary immunodeficiencies.
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Affiliation(s)
- Delfien J Bogaert
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium.,Department of Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Genevieve Laureys
- Department of Pediatrics, Division of Pediatric Hemato-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Leslie Naesens
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium.,Department of Hematology, Ghent University Hospital, Ghent, Belgium
| | - Dominiek Mazure
- Department of Hematology, Ghent University Hospital, Ghent, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Amy P Hsu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Victoria Bordon
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium.,Department of Pediatrics, Division of Pediatric Hemato-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Erik Wouters
- Department of Hematology, General Hospital OLV Aalst, Aalst, Belgium
| | - Simon J Tavernier
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium.,Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent, Belgium
| | - Bart N Lambrecht
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium.,Center for Inflammation Research, Laboratory of Immunoregulation, VIB, Ghent, Belgium.,Department of Pulmonology, Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Filomeen Haerynck
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium.,Department of Pediatrics, Division of Pediatric Pulmonology, Infectious Diseases and Immunology, Ghent University Hospital, Ghent, Belgium
| | - Tessa Kerre
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium.,Department of Hematology, Ghent University Hospital, Ghent, Belgium
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16
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De Bruyne M, Hoste L, Bogaert DJ, Van den Bossche L, Tavernier SJ, Parthoens E, Migaud M, Konopnicki D, Yombi JC, Lambrecht BN, van Daele S, Alves de Medeiros AK, Brochez L, Beyaert R, De Baere E, Puel A, Casanova JL, Goffard JC, Savvides SN, Haerynck F, Staal J, Dullaers M. A CARD9 Founder Mutation Disrupts NF-κB Signaling by Inhibiting BCL10 and MALT1 Recruitment and Signalosome Formation. Front Immunol 2018; 9:2366. [PMID: 30429846 PMCID: PMC6220056 DOI: 10.3389/fimmu.2018.02366] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/24/2018] [Indexed: 12/12/2022] Open
Abstract
Background: Inherited CARD9 deficiency constitutes a primary immunodeficiency predisposing uniquely to chronic and invasive fungal infections. Certain mutations are shown to negatively impact CARD9 protein expression and/or NF-κB activation, but the underlying biochemical mechanism remains to be fully understood. Objectives: To investigate a possible founder origin of a known CARD9 R70W mutation in five families of Turkish origin. To explore the biochemical mechanism of immunodeficiency by R70W CARD9. Methods: We performed haplotype analysis using microsatellite markers and SNPs. We designed a model system exploiting a gain-of-function (GOF) CARD9 L213LI mutant that triggers constitutive NF-κB activation, analogous to an oncogenic CARD11 mutant, to study NF-κB signaling and signalosome formation. We performed reporter assays, immunoprecipitation and confocal imaging on HEK cells overexpressing different CARD9 variants. Results: We identified a common haplotype, thus providing evidence for a common Turkish founder. CARD9 R70W failed to activate NF-κB and abrogated NF-κB activation by WT CARD9 and by GOF CARD9. Notably, R70W CARD9 also exerted negative effects on NF-κB activation by CARD10, CARD11, and CARD14. Consistent with the NF-κB results, the R70W mutation prevented GOF CARD9 to pull down the signalosome partner proteins BCL10 and MALT1. This reflected into drastic reduction of BCL10 filamentous assemblies in a cellular context. Indeed, structural analysis revealed that position R70 in CARD9 maps at the putative interface between successive CARD domains in CARD9 filaments. Conclusions: The R70W mutation in CARD9 prevents NF-κB activation by inhibiting productive interactions with downstream BCL10 and MALT1, necessary for assembly of the filamentous CARD9-BCL10-MALT1 signalosome.
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Affiliation(s)
- Marieke De Bruyne
- Primary Immunodeficiency Research Lab, Department of Pulmonary Medicine, Centre for Primary Immunodeficiencies, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Pediatric Immunology and Pulmonology, Centre for Primary Immunodeficiencies, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
| | - Levi Hoste
- Primary Immunodeficiency Research Lab, Department of Pulmonary Medicine, Centre for Primary Immunodeficiencies, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,Department of Pediatric Immunology and Pulmonology, Centre for Primary Immunodeficiencies, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
| | - Delfien J Bogaert
- Primary Immunodeficiency Research Lab, Department of Pulmonary Medicine, Centre for Primary Immunodeficiencies, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Pediatric Immunology and Pulmonology, Centre for Primary Immunodeficiencies, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,Laboratory of Immunoregulation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Lien Van den Bossche
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Simon J Tavernier
- Primary Immunodeficiency Research Lab, Department of Pulmonary Medicine, Centre for Primary Immunodeficiencies, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,Laboratory of Immunoregulation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Eef Parthoens
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.,VIB Bioimaging Core, VIB, Ghent, Belgium
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Medical School, Imagine Institute, Paris Descartes University, Paris, France
| | - Deborah Konopnicki
- Infectious Diseases Department, Saint-Pierre University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean Cyr Yombi
- Department of Internal Medicine and Infectious Diseases, Cliniques Universitaires Saint Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Bart N Lambrecht
- Laboratory of Immunoregulation, VIB-UGent Center for Inflammation Research, Ghent, Belgium.,Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Sabine van Daele
- Department of Pediatric Immunology and Pulmonology, Centre for Primary Immunodeficiencies, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
| | | | - Lieve Brochez
- Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Rudi Beyaert
- Unit of Molecular Signal Transduction in Inflammation, Department of Biomedical Molecular Biology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Medical School, Imagine Institute, Paris Descartes University, Paris, France
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Medical School, Imagine Institute, Paris Descartes University, Paris, France.,St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller University, New York, NY, United States; Pediatric Hematology-Immunology Unit, Necker Hospital, New York, NY, United States
| | | | - Savvas N Savvides
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Filomeen Haerynck
- Primary Immunodeficiency Research Lab, Department of Pulmonary Medicine, Centre for Primary Immunodeficiencies, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,Department of Pediatric Immunology and Pulmonology, Centre for Primary Immunodeficiencies, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
| | - Jens Staal
- Unit of Molecular Signal Transduction in Inflammation, Department of Biomedical Molecular Biology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
| | - Melissa Dullaers
- Primary Immunodeficiency Research Lab, Department of Pulmonary Medicine, Centre for Primary Immunodeficiencies, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,Laboratory of Immunoregulation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
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17
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De Bruyne M, Bogaert DJ, Venken K, Van den Bossche L, Bonroy C, Roels L, Tavernier SJ, van de Vijver E, Driessen A, van Gijn M, Gámez-Diaz L, Elewaut D, Grimbacher B, Haerynck F, Moes N, Dullaers M. A novel LPS-responsive beige-like anchor protein (LRBA) mutation presents with normal cytotoxic T lymphocyte-associated protein 4 (CTLA-4) and overactive T H17 immunity. J Allergy Clin Immunol 2018; 142:1968-1971. [PMID: 30193839 DOI: 10.1016/j.jaci.2018.08.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 08/14/2018] [Accepted: 08/24/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Marieke De Bruyne
- Clinical Immunology Research Lab, Department of Pulmonary Medicine, Ghent University Hospital, Ghent, Belgium; Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium; Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium; Department of Pediatrics, Division of Pediatric Immunology and Pulmonology, Ghent University Hospital, Ghent, Belgium
| | - Delfien J Bogaert
- Clinical Immunology Research Lab, Department of Pulmonary Medicine, Ghent University Hospital, Ghent, Belgium; Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium; Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium; Department of Pediatrics, Division of Pediatric Immunology and Pulmonology, Ghent University Hospital, Ghent, Belgium; Laboratory of Immunoregulation, VIB-UGent Inflammation Research Center, Ghent, Belgium
| | - Koen Venken
- Department of Rheumatology, Ghent University Hospital, Ghent, Belgium; Unit for Molecular Immunology and Inflammation, VIB-UGent Inflammation Research Center, Ghent, Belgium
| | - Lien Van den Bossche
- Clinical Immunology Research Lab, Department of Pulmonary Medicine, Ghent University Hospital, Ghent, Belgium; Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
| | - Carolien Bonroy
- Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium; Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Lisa Roels
- Clinical Immunology Research Lab, Department of Pulmonary Medicine, Ghent University Hospital, Ghent, Belgium; Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
| | - Simon J Tavernier
- Clinical Immunology Research Lab, Department of Pulmonary Medicine, Ghent University Hospital, Ghent, Belgium; Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium; Laboratory of Immunoregulation, VIB-UGent Inflammation Research Center, Ghent, Belgium
| | - Els van de Vijver
- Department of Pediatric Gastroenterology, Antwerp University Hospital, Edegem, Belgium; Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium
| | - Ann Driessen
- Department of Pathology, Antwerp University Hospital, Edegem, Belgium; Molecular imaging, Pathology, Radiotherapy & Oncology (MIPRO), Faculty of Medicine and Healthcare Sciences, University of Antwerp, Antwerp, Belgium
| | - Marielle van Gijn
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Laura Gámez-Diaz
- Center for Chronic Immunodeficiency, University Medical Center of Freiburg, University of Freiburg, Freiburg, Germany
| | - Dirk Elewaut
- Department of Rheumatology, Ghent University Hospital, Ghent, Belgium; Unit for Molecular Immunology and Inflammation, VIB-UGent Inflammation Research Center, Ghent, Belgium
| | - Bodo Grimbacher
- Center for Chronic Immunodeficiency, University Medical Center of Freiburg, University of Freiburg, Freiburg, Germany
| | - Filomeen Haerynck
- Clinical Immunology Research Lab, Department of Pulmonary Medicine, Ghent University Hospital, Ghent, Belgium; Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium; Department of Pediatrics, Division of Pediatric Immunology and Pulmonology, Ghent University Hospital, Ghent, Belgium
| | - Nicolette Moes
- Department of Pediatric Gastroenterology, Antwerp University Hospital, Edegem, Belgium; Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium.
| | - Melissa Dullaers
- Clinical Immunology Research Lab, Department of Pulmonary Medicine, Ghent University Hospital, Ghent, Belgium; Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium; Laboratory of Immunoregulation, VIB-UGent Inflammation Research Center, Ghent, Belgium; Department of Internal Medicine, Ghent University, Ghent, Belgium
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18
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Hoste L, De Baets F, Van Daele S, Schelstraete P, Boon M, De Bruyne M, Dullaers M, Coppieters F, Haerynck F. When One Rare Disease Hides Another: Kartagener Syndrome Masking FMF. Clin Pediatr (Phila) 2018; 57:981-985. [PMID: 28952366 DOI: 10.1177/0009922817733705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Levi Hoste
- 1 Ghent University Hospital, Ghent, Belgium
| | | | | | | | - Mieke Boon
- 2 University Hospital Gasthuisberg, Leuven, Belgium
| | | | - Melissa Dullaers
- 3 Ghent University, Ghent, Belgium.,4 VIB Inflammation Research Center, Ghent, Belgium
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19
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Bogaert DJ, Dullaers M, Kuehn HS, Leroy BP, Niemela JE, De Wilde H, De Schryver S, De Bruyne M, Coppieters F, Lambrecht BN, De Baets F, Rosenzweig SD, De Baere E, Haerynck F. Early-onset primary antibody deficiency resembling common variable immunodeficiency challenges the diagnosis of Wiedeman-Steiner and Roifman syndromes. Sci Rep 2017. [PMID: 28623346 PMCID: PMC5473876 DOI: 10.1038/s41598-017-02434-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 12/11/2022] Open
Abstract
Syndromic primary immunodeficiencies are rare genetic disorders that affect both the immune system and other organ systems. More often, the immune defect is not the major clinical problem and is sometimes only recognized after a diagnosis has been made based on extra-immunological abnormalities. Here, we report two sibling pairs with syndromic primary immunodeficiencies that exceptionally presented with a phenotype resembling early-onset common variable immunodeficiency, while extra-immunological characteristics were not apparent at that time. Additional features not typically associated with common variable immunodeficiency were diagnosed only later, including skeletal and organ anomalies and mild facial dysmorphism. Whole exome sequencing revealed KMT2A-associated Wiedemann-Steiner syndrome in one sibling pair and their mother. In the other sibling pair, targeted testing of the known disease gene for Roifman syndrome (RNU4ATAC) provided a definite diagnosis. With this study, we underline the importance of an early-stage and thorough genetic assessment in paediatric patients with a common variable immunodeficiency phenotype, to establish a conclusive diagnosis and guide patient management. In addition, this study extends the mutational and immunophenotypical spectrum of Wiedemann-Steiner and Roifman syndromes and highlights potential directions for future pathophysiological research.
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Affiliation(s)
- Delfien J Bogaert
- Clinical Immunology Research Lab, Department of Pulmonary Medicine, Centre for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,Department of Paediatric Immunology and Pulmonology, Centre for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium.,Laboratory of Immunoregulation, VIB Inflammation Research Centre, Ghent, Belgium
| | - Melissa Dullaers
- Clinical Immunology Research Lab, Department of Pulmonary Medicine, Centre for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,Laboratory of Immunoregulation, VIB Inflammation Research Centre, Ghent, Belgium.,Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, NIH Clinical Centre, National Institutes of Health, Bethesda, MD, USA
| | - Bart P Leroy
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Julie E Niemela
- Immunology Service, Department of Laboratory Medicine, NIH Clinical Centre, National Institutes of Health, Bethesda, MD, USA
| | - Hans De Wilde
- Department of Paediatric Cardiology, Ghent University Hospital, Ghent, Belgium
| | - Sarah De Schryver
- Department of Paediatric Allergy and Immunology, Montreal Children's Hospital, Montreal, QC, Canada
| | - Marieke De Bruyne
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Bart N Lambrecht
- Laboratory of Immunoregulation, VIB Inflammation Research Centre, Ghent, Belgium.,Department of Internal Medicine, Ghent University, Ghent, Belgium.,Department of Pulmonology, Ghent University Hospital, Ghent, Belgium
| | - Frans De Baets
- Department of Paediatric Immunology and Pulmonology, Centre for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, NIH Clinical Centre, National Institutes of Health, Bethesda, MD, USA
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Filomeen Haerynck
- Clinical Immunology Research Lab, Department of Pulmonary Medicine, Centre for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium. .,Department of Paediatric Immunology and Pulmonology, Centre for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.
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20
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Bogaert DJA, De Bruyne M, Debacker V, Depuydt P, De Preter K, Bonroy C, Philippé J, Bordon V, Lambrecht BN, Kerre T, Cerutti A, Vermaelen KY, Haerynck F, Dullaers M. The immunophenotypic fingerprint of patients with primary antibody deficiencies is partially present in their asymptomatic first-degree relatives. Haematologica 2016; 102:192-202. [PMID: 27634199 DOI: 10.3324/haematol.2016.149112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/08/2016] [Indexed: 11/09/2022] Open
Abstract
The etiology of primary antibody deficiencies is largely unknown. Beside rare monogenic forms, the majority of cases seem to have a more complex genetic basis. Whereas common variable immunodeficiency has been investigated in depth, there are only a few reports on milder primary antibody deficiencies such as idiopathic primary hypogammaglobulinemia and IgG subclass deficiency. We performed flow cytometric immunophenotyping in 33 patients with common variable immunodeficiency, 23 with idiopathic primary hypogammaglobulinemia and 21 with IgG subclass deficiency, as well as in 47 asymptomatic first-degree family members of patients and 101 unrelated healthy controls. All three groups of patients showed decreased memory B- and naïve T-cell subsets and decreased B-cell activating factor receptor expression. In contrast, circulating follicular helper T-cell frequency and expression of inducible T-cell co-stimulator and chemokine receptors were only significantly altered in patients with common variable immunodeficiency. Asymptomatic first-degree family members of patients demonstrated similar, albeit intermediate, alterations in naïve and memory B- and T-cell subsets. About 13% of asymptomatic relatives had an abnormal peripheral B-cell composition. Furthermore, asymptomatic relatives showed decreased levels of CD4+ recent thymic emigrants and increased central memory T cells. Serum IgG and IgM levels were also significantly lower in asymptomatic relatives than in healthy controls. We conclude that, in our cohort, the immunophenotypic landscape of primary antibody deficiencies comprises a spectrum, in which some alterations are shared between all primary antibody deficiencies whereas others are only associated with common variable immunodeficiency. Importantly, asymptomatic first-degree family members of patients were found to have an intermediate phenotype for peripheral B- and T-cell subsets.
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Affiliation(s)
- Delfien J A Bogaert
- Clinical Immunology Research Laboratory, Department of Pulmonary Medicine, Ghent University Hospital, Belgium.,Department of Pediatric Immunology and Pulmonology, Centre for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Belgium.,Center for Medical Genetics, Ghent University and Ghent University Hospital, Belgium.,Laboratory of Immunoregulation, VIB Inflammation Research Center, Ghent, Belgium
| | - Marieke De Bruyne
- Clinical Immunology Research Laboratory, Department of Pulmonary Medicine, Ghent University Hospital, Belgium.,Center for Medical Genetics, Ghent University and Ghent University Hospital, Belgium
| | - Veronique Debacker
- Clinical Immunology Research Laboratory, Department of Pulmonary Medicine, Ghent University Hospital, Belgium.,Tumor Immunology Laboratory, Department of Pulmonary Medicine, Ghent University Hospital, Belgium
| | - Pauline Depuydt
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Belgium.,Cancer Research Institute, Ghent University, Belgium
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Belgium.,Cancer Research Institute, Ghent University, Belgium
| | - Carolien Bonroy
- Department of Laboratory Medicine, Ghent University Hospital, Belgium
| | - Jan Philippé
- Department of Laboratory Medicine, Ghent University Hospital, Belgium.,Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Belgium
| | - Victoria Bordon
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Belgium
| | - Bart N Lambrecht
- Laboratory of Immunoregulation, VIB Inflammation Research Center, Ghent, Belgium.,Department of Internal Medicine, Ghent University, Belgium.,Department of Pulmonology, Ghent University Hospital, Belgium
| | - Tessa Kerre
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Belgium.,Department of Internal Medicine, Ghent University, Belgium.,Department of Hematology, Ghent University Hospital, Belgium
| | - Andrea Cerutti
- Department of Medicine, The Immunology Institute, Mount Sinai School of Medicine, New York, NY, USA and.,B Cell Biology Laboratory, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Karim Y Vermaelen
- Tumor Immunology Laboratory, Department of Pulmonary Medicine, Ghent University Hospital, Belgium.,Department of Internal Medicine, Ghent University, Belgium.,Department of Pulmonology, Ghent University Hospital, Belgium
| | - Filomeen Haerynck
- Clinical Immunology Research Laboratory, Department of Pulmonary Medicine, Ghent University Hospital, Belgium.,Department of Pediatric Immunology and Pulmonology, Centre for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Belgium
| | - Melissa Dullaers
- Clinical Immunology Research Laboratory, Department of Pulmonary Medicine, Ghent University Hospital, Belgium .,Laboratory of Immunoregulation, VIB Inflammation Research Center, Ghent, Belgium.,Department of Internal Medicine, Ghent University, Belgium
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21
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Coppieters F, Todeschini AL, Fujimaki T, Baert A, De Bruyne M, Van Cauwenbergh C, Verdin H, Bauwens M, Ongenaert M, Kondo M, Meire F, Murakami A, Veitia RA, Leroy BP, De Baere E. Hidden Genetic Variation in LCA9-Associated Congenital Blindness Explained by 5'UTR Mutations and Copy-Number Variations of NMNAT1. Hum Mutat 2015; 36:1188-96. [PMID: 26316326 PMCID: PMC5054839 DOI: 10.1002/humu.22899] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 04/15/2015] [Accepted: 08/19/2015] [Indexed: 11/28/2022]
Abstract
Leber congenital amaurosis (LCA) is a severe autosomal‐recessive retinal dystrophy leading to congenital blindness. A recently identified LCA gene is NMNAT1, located in the LCA9 locus. Although most mutations in blindness genes are coding variations, there is accumulating evidence for hidden noncoding defects or structural variations (SVs). The starting point of this study was an LCA9‐associated consanguineous family in which no coding mutations were found in the LCA9 region. Exploring the untranslated regions of NMNAT1 revealed a novel homozygous 5′UTR variant, c.‐70A>T. Moreover, an adjacent 5′UTR variant, c.‐69C>T, was identified in a second consanguineous family displaying a similar phenotype. Both 5′UTR variants resulted in decreased NMNAT1 mRNA abundance in patients’ lymphocytes, and caused decreased luciferase activity in human retinal pigment epithelial RPE‐1 cells. Second, we unraveled pseudohomozygosity of a coding NMNAT1 mutation in two unrelated LCA patients by the identification of two distinct heterozygous partial NMNAT1 deletions. Molecular characterization of the breakpoint junctions revealed a complex Alu‐rich genomic architecture. Our study uncovered hidden genetic variation in NMNAT1‐associated LCA and emphasized a shift from coding to noncoding regulatory mutations and repeat‐mediated SVs in the molecular pathogenesis of heterogeneous recessive disorders such as hereditary blindness.
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Affiliation(s)
| | | | - Takuro Fujimaki
- Department of Ophthalmology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Annelot Baert
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | | | | | - Hannah Verdin
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Maté Ongenaert
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Mineo Kondo
- Department of Ophthalmology, Mie University Graduate School of Medicine, Mie, Japan
| | - Françoise Meire
- Department of Ophthalmology, Queen Fabiola Children's University Hospital, Brussels, Belgium
| | - Akira Murakami
- Department of Ophthalmology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Reiner A Veitia
- Institut Jacques Monod, UMR 7592 CNRS-Université Paris Diderot, Paris, France
| | - Bart P Leroy
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium.,Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
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