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Boeren M, de Vrij N, Ha MK, Valkiers S, Souquette A, Gielis S, Kuznetsova M, Schippers J, Bartholomeus E, Van den Bergh J, Michels N, Aerts O, Leysen J, Bervoets A, Lambert J, Leuridan E, Wens J, Peeters K, Emonds MP, Elias G, Vandamme N, Jansens H, Adriaensen W, Suls A, Vanhee S, Hens N, Smits E, Van Damme P, Thomas PG, Beutels P, Ponsaerts P, Van Tendeloo V, Delputte P, Laukens K, Meysman P, Ogunjimi B. Lack of functional TCR-epitope interaction is associated with herpes zoster through reduced downstream T cell activation. Cell Rep 2024; 43:114062. [PMID: 38588339 DOI: 10.1016/j.celrep.2024.114062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 02/23/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
The role of T cell receptor (TCR) diversity in infectious disease susceptibility is not well understood. We use a systems immunology approach on three cohorts of herpes zoster (HZ) patients and controls to investigate whether TCR diversity against varicella-zoster virus (VZV) influences the risk of HZ. We show that CD4+ T cell TCR diversity against VZV glycoprotein E (gE) and immediate early 63 protein (IE63) after 1-week culture is more restricted in HZ patients. Single-cell RNA and TCR sequencing of VZV-specific T cells shows that T cell activation pathways are significantly decreased after stimulation with VZV peptides in convalescent HZ patients. TCR clustering indicates that TCRs from HZ patients co-cluster more often together than TCRs from controls. Collectively, our results suggest that not only lower VZV-specific TCR diversity but also reduced functional TCR affinity for VZV-specific proteins in HZ patients leads to lower T cell activation and consequently affects the susceptibility for viral reactivation.
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Affiliation(s)
- Marlies Boeren
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Nicky de Vrij
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium; Clinical Immunology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - My K Ha
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Sebastiaan Valkiers
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Aisha Souquette
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sofie Gielis
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Maria Kuznetsova
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Jolien Schippers
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Esther Bartholomeus
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Johan Van den Bergh
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Nele Michels
- Department of Family Medicine and Population Health (FAMPOP), Center for General Practice/Family Medicine, University of Antwerp, Antwerp, Belgium
| | - Olivier Aerts
- Department of Dermatology, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - Julie Leysen
- Department of Dermatology, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - An Bervoets
- Department of Dermatology, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - Julien Lambert
- Department of Dermatology, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - Elke Leuridan
- Centre for the Evaluation of Vaccination (CEV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Johan Wens
- Department of Family Medicine and Population Health (FAMPOP), Center for General Practice/Family Medicine, University of Antwerp, Antwerp, Belgium
| | - Karin Peeters
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Marie-Paule Emonds
- Histocompatibility and Immunogenetic Laboratory, Rode Kruis-Vlaanderen, Mechelen, Belgium
| | - George Elias
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Niels Vandamme
- Data Mining and Modeling for Biomedicine Group, VIB-UGent Center for Inflammation Research, 9052 Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Hilde Jansens
- Department of Clinical Microbiology, Antwerp University Hospital, Antwerp, Belgium
| | - Wim Adriaensen
- Clinical Immunology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Arvid Suls
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Stijn Vanhee
- Laboratory of Immunoregulation and Mucosal Immunology, VIB Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Department of Head and Skin, Ghent University, Ghent, Belgium
| | - Niel Hens
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium; I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Evelien Smits
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium
| | - Pierre Van Damme
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Centre for the Evaluation of Vaccination (CEV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Philippe Beutels
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Peter Ponsaerts
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Viggo Van Tendeloo
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium
| | - Peter Delputte
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium; Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium; Department of Paediatrics, Antwerp University Hospital, Antwerp, Belgium.
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2
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Vandoren R, Boeren M, Schippers J, Bartholomeus E, Mullan K, Michels N, Aerts O, Leysen J, Bervoets A, Lambert J, Leuridan E, Wens J, Peeters K, Emonds MP, Jansens H, Casanova JL, Bastard P, Suls A, Van Tendeloo V, Ponsaerts P, Delputte P, Ogunjimi B, Laukens K, Meysman P. Unravelling the immune signature of herpes zoster: Insights into pathophysiology and the HLA risk profile. J Infect Dis 2024:jiad609. [PMID: 38195164 DOI: 10.1093/infdis/jiad609] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/15/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024] Open
Abstract
The varicella-zoster virus (VZV) infects over 95% of the population. VZV reactivation causes herpes zoster (HZ), known as shingles, primarily affecting the elderly and immunocompromised individuals. However, HZ can also occur in otherwise healthy individuals. We analyzed the immune signature and risk profile in HZ patients using a genome-wide association study across different UK Biobank HZ cohorts. Additionally, we conducted one of the largest HZ HLA association studies to date, coupled with transcriptomic analysis of pathways underlying HZ susceptibility. Our findings highlight the significance of the MHC locus for HZ development, identifying five protective and four risk HLA alleles. This demonstrates that HZ susceptibility is largely governed by variations in the MHC. Furthermore, functional analyses revealed the upregulation of type I interferon and adaptive immune responses. These findings provide fresh molecular insights into the pathophysiology and the activation of innate and adaptive immune responses triggered by symptomatic VZV reactivation.
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Affiliation(s)
- Romi Vandoren
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Marlies Boeren
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH) & Infla-Med Center of Excellence, University of Antwerp, Antwerp, Belgium
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Jolien Schippers
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Esther Bartholomeus
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Kerry Mullan
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Nele Michels
- Department of Family Medicine and Population Health (FAMPOP), Center for general practice/family Medicine, University of Antwerp, Antwerp, Belgium
| | - Olivier Aerts
- Department of Dermatology, Antwerp University Hospital & University of Antwerp, Antwerp, Belgium
| | - Julie Leysen
- Department of Dermatology, Antwerp University Hospital & University of Antwerp, Antwerp, Belgium
| | - An Bervoets
- Department of Dermatology, Antwerp University Hospital & University of Antwerp, Antwerp, Belgium
| | - Julien Lambert
- Department of Dermatology, Antwerp University Hospital & University of Antwerp, Antwerp, Belgium
| | - Elke Leuridan
- Centre for the Evaluation of Vaccination (CEV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Johan Wens
- Department of Family Medicine and Population Health (FAMPOP), Center for general practice/family Medicine, University of Antwerp, Antwerp, Belgium
| | - Karin Peeters
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Marie-Paule Emonds
- Histocompatibility and Immunogenetic Laboratory, Rode Kruis-Vlaanderen, Mechelen, Belgium
| | - Hilde Jansens
- Department of Clinical Microbiology, Antwerp University Hospital, Antwerp, 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, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistante Publique-Hôpitaux de Paris, Paris, France
| | - Arvid Suls
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium
- Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Viggo Van Tendeloo
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Peter Ponsaerts
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Peter Delputte
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH) & Infla-Med Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Department of Paediatrics, Antwerp University Hospital, Antwerp, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
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3
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Ha MK, Bartholomeus E, Van Os L, Dandelooy J, Leysen J, Aerts O, Siozopoulou V, De Smet E, Gielen J, Guerti K, De Maeseneer M, Herregods N, Lechkar B, Wittoek R, Geens E, Claes L, Zaqout M, Dewals W, Lemay A, Tuerlinckx D, Weynants D, Vanlede K, van Berlaer G, Raes M, Verhelst H, Boiy T, Van Damme P, Jansen AC, Meuwissen M, Sabato V, Van Camp G, Suls A, Werff ten Bosch JVD, Dehoorne J, Joos R, Laukens K, Meysman P, Ogunjimi B. Blood transcriptomics to facilitate diagnosis and stratification in pediatric rheumatic diseases - a proof of concept study. Pediatr Rheumatol Online J 2022; 20:91. [PMID: 36253751 PMCID: PMC9575227 DOI: 10.1186/s12969-022-00747-x] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/24/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Transcriptome profiling of blood cells is an efficient tool to study the gene expression signatures of rheumatic diseases. This study aims to improve the early diagnosis of pediatric rheumatic diseases by investigating patients' blood gene expression and applying machine learning on the transcriptome data to develop predictive models. METHODS RNA sequencing was performed on whole blood collected from children with rheumatic diseases. Random Forest classification models were developed based on the transcriptome data of 48 rheumatic patients, 46 children with viral infection, and 35 controls to classify different disease groups. The performance of these classifiers was evaluated by leave-one-out cross-validation. Analyses of differentially expressed genes (DEG), gene ontology (GO), and interferon-stimulated gene (ISG) score were also conducted. RESULTS Our first classifier could differentiate pediatric rheumatic patients from controls and infection cases with high area-under-the-curve (AUC) values (AUC = 0.8 ± 0.1 and 0.7 ± 0.1, respectively). Three other classifiers could distinguish chronic recurrent multifocal osteomyelitis (CRMO), juvenile idiopathic arthritis (JIA), and interferonopathies (IFN) from control and infection cases with AUC ≥ 0.8. DEG and GO analyses reveal that the pathophysiology of CRMO, IFN, and JIA involves innate immune responses including myeloid leukocyte and granulocyte activation, neutrophil activation and degranulation. IFN is specifically mediated by antibacterial and antifungal defense responses, CRMO by cellular response to cytokine, and JIA by cellular response to chemical stimulus. IFN patients particularly had the highest mean ISG score among all disease groups. CONCLUSION Our data show that blood transcriptomics combined with machine learning is a promising diagnostic tool for pediatric rheumatic diseases and may assist physicians in making data-driven and patient-specific decisions in clinical practice.
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Affiliation(s)
- My Kieu Ha
- Center for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium. .,Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium. .,Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium.
| | - Esther Bartholomeus
- grid.5284.b0000 0001 0790 3681Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium ,grid.5284.b0000 0001 0790 3681Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium ,grid.411414.50000 0004 0626 3418Center of Medical Genetics, University of Antwerp, Antwerp University Hospital, Edegem, Belgium
| | - Luc Van Os
- grid.411414.50000 0004 0626 3418Ophthalmology Department, Antwerp University Hospital, Edegem, Belgium
| | - Julie Dandelooy
- grid.411414.50000 0004 0626 3418Dermatology Department, Antwerp University Hospital, Edegem, Belgium
| | - Julie Leysen
- grid.411414.50000 0004 0626 3418Dermatology Department, Antwerp University Hospital, Edegem, Belgium ,grid.5284.b0000 0001 0790 3681Department of Translational Research in Immunology and Inflammation, University of Antwerp, Wilrijk, Belgium
| | - Olivier Aerts
- grid.411414.50000 0004 0626 3418Dermatology Department, Antwerp University Hospital, Edegem, Belgium ,grid.5284.b0000 0001 0790 3681Department of Translational Research in Immunology and Inflammation, University of Antwerp, Wilrijk, Belgium
| | - Vasiliki Siozopoulou
- grid.411414.50000 0004 0626 3418Pathology Department, Antwerp University Hospital, Edegem, Belgium
| | - Eline De Smet
- grid.411414.50000 0004 0626 3418Radiology Department, Antwerp University Hospital, Edegem, Belgium
| | - Jan Gielen
- grid.411414.50000 0004 0626 3418Radiology Department, Antwerp University Hospital, Edegem, Belgium ,grid.5284.b0000 0001 0790 3681Department of Molecular – Morphology – Microscopy, University of Antwerp, Wilrijk, Belgium
| | - Khadija Guerti
- grid.411414.50000 0004 0626 3418Clinical Biology Department, Antwerp University Hospital, Edegem, Belgium
| | | | - Nele Herregods
- grid.410566.00000 0004 0626 3303Radiology Department, Ghent University Hospital, Ghent, Belgium
| | - Bouchra Lechkar
- grid.411414.50000 0004 0626 3418Department of Immunology, Allergology, and Rheumatology, Antwerp University Hospital, Edegem, Belgium
| | - Ruth Wittoek
- grid.410566.00000 0004 0626 3303Rheumatology Department, Ghent University Hospital, Ghent, Belgium ,grid.411414.50000 0004 0626 3418Rheumatology Department, Antwerp Hospital Network, Antwerp, Belgium
| | - Elke Geens
- grid.411414.50000 0004 0626 3418Rheumatology Department, Antwerp Hospital Network, Antwerp, Belgium
| | - Laura Claes
- grid.411414.50000 0004 0626 3418Pediatric Neurology Unit, Antwerp University Hospital, Edegem, Belgium
| | - Mahmoud Zaqout
- grid.411414.50000 0004 0626 3418Pediatric Cardiology Department, Antwerp University Hospital, Edegem, Belgium ,grid.411414.50000 0004 0626 3418Pediatric Cardiology Department, Antwerp Hospital Network, Antwerp, Belgium
| | - Wendy Dewals
- grid.411414.50000 0004 0626 3418Pediatric Cardiology Department, Antwerp University Hospital, Edegem, Belgium
| | - Annelies Lemay
- Department of Pediatrics, Turnhout General Hospital, Turnhout, Belgium
| | - David Tuerlinckx
- grid.7942.80000 0001 2294 713XDepartment of Pediatrics, Catholic University of Louvain, Louvain-la-Neuve, Belgium ,grid.6520.10000 0001 2242 8479Department of Pediatrics, Namur University Hospital Center, Site Dinant, Dinant, Belgium
| | - David Weynants
- grid.6520.10000 0001 2242 8479Department of Pediatrics, Namur University Hospital Center, Site Sainte-Elisabeth, Namur, Belgium
| | - Koen Vanlede
- Department of Pediatrics, Nikolaas General Hospital, Sint-Niklaas, Belgium
| | - Gerlant van Berlaer
- Department of Emergency Medicine/Pediatric Care, Brussels University Hospital, Jette, Belgium
| | - Marc Raes
- grid.414977.80000 0004 0578 1096Department of Pediatrics, Jessa Hospital, Hasselt, Belgium
| | - Helene Verhelst
- grid.410566.00000 0004 0626 3303Department of Pediatric Neurology, Ghent University Hospital, Ghent, Belgium
| | - Tine Boiy
- grid.411414.50000 0004 0626 3418Department of Pediatric Rheumatology, Antwerp University Hospital, Edegem, Belgium
| | - Pierre Van Damme
- grid.5284.b0000 0001 0790 3681Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium ,grid.5284.b0000 0001 0790 3681Center for the Evaluation of Vaccine, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Anna C. Jansen
- grid.411414.50000 0004 0626 3418Pediatric Neurology Unit, Antwerp University Hospital, Edegem, Belgium
| | - Marije Meuwissen
- grid.5284.b0000 0001 0790 3681Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Vito Sabato
- grid.411414.50000 0004 0626 3418Department of Immunology, Allergology, and Rheumatology, Antwerp University Hospital, Edegem, Belgium ,Antwerp Center for Pediatric Rheumatology and Autoinflammatory Diseases, Antwerp, Belgium
| | - Guy Van Camp
- grid.411414.50000 0004 0626 3418Center of Medical Genetics, University of Antwerp, Antwerp University Hospital, Edegem, Belgium
| | - Arvid Suls
- grid.5284.b0000 0001 0790 3681Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| | | | - Joke Dehoorne
- grid.410566.00000 0004 0626 3303Department of Pediatric Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - Rik Joos
- grid.411414.50000 0004 0626 3418Rheumatology Department, Antwerp Hospital Network, Antwerp, Belgium ,grid.411414.50000 0004 0626 3418Department of Pediatric Rheumatology, Antwerp University Hospital, Edegem, Belgium ,Antwerp Center for Pediatric Rheumatology and Autoinflammatory Diseases, Antwerp, Belgium ,grid.410566.00000 0004 0626 3303Department of Pediatric Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - Kris Laukens
- grid.5284.b0000 0001 0790 3681Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium ,grid.5284.b0000 0001 0790 3681ADREM Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium ,grid.5284.b0000 0001 0790 3681Biomedical Informatics Research Network Antwerp, University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- grid.5284.b0000 0001 0790 3681Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium ,grid.5284.b0000 0001 0790 3681ADREM Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium ,grid.5284.b0000 0001 0790 3681Biomedical Informatics Research Network Antwerp, University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- Center for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium. .,Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium. .,Rheumatology Department, Antwerp Hospital Network, Antwerp, Belgium. .,Department of Pediatric Rheumatology, Antwerp University Hospital, Edegem, Belgium. .,Antwerp Center for Pediatric Rheumatology and Autoinflammatory Diseases, Antwerp, Belgium. .,Department of Pediatric Rheumatology, Brussels University Hospital, Jette, Belgium.
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4
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Elias G, Meysman P, Bartholomeus E, De Neuter N, Keersmaekers N, Suls A, Jansens H, Souquette A, De Reu H, Emonds MP, Smits E, Lion E, Thomas PG, Mortier G, Van Damme P, Beutels P, Laukens K, Van Tendeloo V, Ogunjimi B. Preexisting memory CD4 T cells in naïve individuals confer robust immunity upon hepatitis B vaccination. eLife 2022; 11:68388. [PMID: 35074048 PMCID: PMC8824481 DOI: 10.7554/elife.68388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 01/07/2022] [Indexed: 11/22/2022] Open
Abstract
Antigen recognition through the T cell receptor (TCR) αβ heterodimer is one of the primary determinants of the adaptive immune response. Vaccines activate naïve T cells with high specificity to expand and differentiate into memory T cells. However, antigen-specific memory CD4 T cells exist in unexposed antigen-naïve hosts. In this study, we use high-throughput sequencing of memory CD4 TCRβ repertoire and machine learning to show that individuals with preexisting vaccine-reactive memory CD4 T cell clonotypes elicited earlier and higher antibody titers and mounted a more robust CD4 T cell response to hepatitis B vaccine. In addition, integration of TCRβ sequence patterns into a hepatitis B epitope-specific annotation model can predict which individuals will have an early and more vigorous vaccine-elicited immunity. Thus, the presence of preexisting memory T cell clonotypes has a significant impact on immunity and can be used to predict immune responses to vaccination. Immune cells called CD4 T cells help the body build immunity to infections caused by bacteria and viruses, or after vaccination. Receptor proteins on the outside of the cells recognize pathogens, foreign molecules called antigens, or vaccine antigens. Vaccine antigens are usually inactivated bacteria or viruses, or fragments of these pathogens. After recognizing an antigen, CD4 T cells develop into memory CD4 T cells ready to defend against future infections with the pathogen. People who have never been exposed to a pathogen, or have never been vaccinated against it, may nevertheless have preexisting memory cells ready to defend against it. This happens because CD4 T cells can recognize multiple targets, which enables the immune system to be ready to defend against both new and familiar pathogens. Elias, Meysman, Bartholomeus et al. wanted to find out whether having preexisting memory CD4 T cells confers an advantage for vaccine-induced immunity. Thirty-four people who were never exposed to hepatitis B or vaccinated against it participated in the study. These individuals provided blood samples before vaccination, with 2 doses of the hepatitis B vaccine, and at 3 time points afterward. Using next generation immune sequencing and machine learning techniques, Elias et al. analyzed the individuals’ memory CD4 T cells before and after vaccination. The experiments showed that preexisting memory CD4 T cells may determine vaccination outcomes, and people with more preexisting memory cells develop quicker and stronger immunity after vaccination against hepatitis B. This information may help scientists to better understand how people develop immunity to pathogens. It may guide them develop better vaccines or predict who will develop immunity after vaccination.
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Affiliation(s)
- George Elias
- Laboratory of Experimental Hematology (LEH), University of Antwerp
| | - Pieter Meysman
- Biomedical Informatics Research Network Antwerp, Department of Mathematics and Informatics, University of Antwerp
| | | | - Nicolas De Neuter
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Nina Keersmaekers
- Centre for Health Economics Research & Modeling Infectious Diseases, University of Antwerp
| | - Arvid Suls
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Hilde Jansens
- Department of Clinical Microbiology, Antwerp University Hospital
| | - Aisha Souquette
- Department of Immunology, St. Jude Children's Research Hospital
| | - Hans De Reu
- Laboratory of Experimental Hematology, University of Antwerp
| | | | - Evelien Smits
- Laboratory of Experimental Hematology, University of Antwerp
| | - Eva Lion
- Laboratory of Experimental Hematology, University of Antwerp
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital
| | - Geert Mortier
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Pierre Van Damme
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Philippe Beutels
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Kris Laukens
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Viggo Van Tendeloo
- Janssen Research and Development, Immunosciences WWDA, Johnson and Johnson
| | - Benson Ogunjimi
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
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5
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Bartholomeus E, De Neuter N, Suls A, Elias G, van der Heijden S, Keersmaekers N, Jansens H, Van Tendeloo V, Beutels P, Laukens K, Ogunjimi B, Mortier G, Meysman P, Van Damme P. Transcriptomic profiling of different responder types in adults after a Priorix® vaccination. Vaccine 2020; 38:3218-3226. [PMID: 32165045 DOI: 10.1016/j.vaccine.2020.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/24/2020] [Accepted: 03/01/2020] [Indexed: 12/12/2022]
Abstract
Thanks to the recommendation of a combined Measles/Mumps/Rubella (MMR) vaccine, like Priorix®, these childhood diseases are less common now. This is beneficial to limit the spread of these diseases and work towards their elimination. However, the measles, mumps and rubella antibody titers show a large variability in short- and long-term immunity. The recent outbreaks worldwide of measles and mumps and previous studies, which mostly focused on only one of the three virus responses, illustrate that there is a clear need for better understanding the immune responses after vaccination. Our healthy cohort was already primed with the MMR antigens in their childhood. In this study, the adult volunteers received one Priorix® vaccine dose at day 0. First, we defined 4 different groups of responders, based on their antibody titers' evolution over 4 time points (Day 0, 21, 150 and 365). This showed a high variability within and between individuals. Second, we determined transcriptome profiles using 3'mRNA sequencing at day 0, 3 and 7. Using two analytical approaches, "one response group per time point" and "a time comparison per response group", we correlated the short-term gene expression profiles to the different response groups. In general, the list of differentially expressed genes is limited, however, most of them are clearly immune-related and upregulated at day 3 and 7, compared to the baseline day 0. Depending on the specific response group there are overlapping signatures for two of the three viruses. Antibody titers and transcriptomics data showed that an additional Priorix vaccination does not facilitate an equal immune response against the 3 viruses or among different vaccine recipients.
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Affiliation(s)
- Esther Bartholomeus
- Department of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium; AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.
| | - Nicolas De Neuter
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Arvid Suls
- Department of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium; AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - George Elias
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Sanne van der Heijden
- Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Nina Keersmaekers
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Hilde Jansens
- Department of Laboratory Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Viggo Van Tendeloo
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Philippe Beutels
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Department of Paediatrics, Antwerp University Hospital, Edegem, Belgium.
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium; AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Pierre Van Damme
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
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6
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Bartholomeus E, De Neuter N, Lemay A, Pattyn L, Tuerlinckx D, Weynants D, Van Lede K, van Berlaer G, Bulckaert D, Boiy T, Vander Auwera A, Raes M, Van der Linden D, Verhelst H, Van Steijn S, Jonckheer T, Dehoorne J, Joos R, Jansens H, Suls A, Van Damme P, Laukens K, Mortier G, Meysman P, Ogunjimi B. Diagnosing enterovirus meningitis via blood transcriptomics: an alternative for lumbar puncture? J Transl Med 2019; 17:282. [PMID: 31443725 PMCID: PMC6708255 DOI: 10.1186/s12967-019-2037-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/18/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Meningitis can be caused by several viruses and bacteria. Identifying the causative pathogen as quickly as possible is crucial to initiate the most optimal therapy, as acute bacterial meningitis is associated with a significant morbidity and mortality. Bacterial meningitis requires antibiotics, as opposed to enteroviral meningitis, which only requires supportive therapy. Clinical presentation is usually not sufficient to differentiate between viral and bacterial meningitis, thereby necessitating cerebrospinal fluid (CSF) analysis by PCR and/or time-consuming bacterial cultures. However, collecting CSF in children is not always feasible and a rather invasive procedure. METHODS In 12 Belgian hospitals, we obtained acute blood samples from children with signs of meningitis (49 viral and 7 bacterial cases) (aged between 3 months and 16 years). After pathogen confirmation on CSF, the patient was asked to give a convalescent sample after recovery. 3' mRNA sequencing was performed to determine differentially expressed genes (DEGs) to create a host transcriptomic profile. RESULTS Enteroviral meningitis cases displayed the largest upregulated fold change enrichment in type I interferon production, response and signaling pathways. Patients with bacterial meningitis showed a significant upregulation of genes related to macrophage and neutrophil activation. We found several significantly DEGs between enteroviral and bacterial meningitis. Random forest classification showed that we were able to differentiate enteroviral from bacterial meningitis with an AUC of 0.982 on held-out samples. CONCLUSIONS Enteroviral meningitis has an innate immunity signature with type 1 interferons as key players. Our classifier, based on blood host transcriptomic profiles of different meningitis cases, is a possible strong alternative for diagnosing enteroviral meningitis.
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Affiliation(s)
- Esther Bartholomeus
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium.,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Nicolas De Neuter
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Annelies Lemay
- Department of Paediatrics, AZ Turnhout, Turnhout, Belgium
| | - Luc Pattyn
- Department of Paediatrics, AZ Turnhout, Turnhout, Belgium
| | - David Tuerlinckx
- Université Catholique de Louvain/CHU UCL Namur, Site Dinant, Service de Pédiatrie, Dinant, Belgium
| | - David Weynants
- Department of Paediatrics, CHU ULC Namur Ste Elisabeth, Namur, Belgium
| | - Koen Van Lede
- Department of Paediatrics, AZ Nikolaas, Sint-Niklaas, Belgium
| | - Gerlant van Berlaer
- Department of Emergency Medicine/Pediatric Care, University Hospital Brussels, Jette, Belgium
| | - Dominique Bulckaert
- Department of Emergency Medicine/Pediatric Care, University Hospital Brussels, Jette, Belgium
| | - Tine Boiy
- Department of Paediatrics, Antwerp University Hospital, Edegem, Belgium
| | | | - Marc Raes
- Department of Paediatrics, Jessa Hospital, Hasselt, Belgium
| | - Dimitri Van der Linden
- Paediatric Infectious Diseases, Department of Paediatrics, CHU ULC Cliniques Universitaires Saint-Luc, UCLouvain, Brussels, Belgium
| | - Helene Verhelst
- Department of Paediatric Rheumatology, University Hospital, Ghent, Belgium
| | | | - Tijl Jonckheer
- Department of Paediatrics, GZA Sint-Vincentius, Antwerp, Belgium
| | - Joke Dehoorne
- Department of Paediatric Rheumatology, University Hospital, Ghent, Belgium
| | - Rik Joos
- Department of Paediatric Rheumatology, University Hospital, Ghent, Belgium.,Antwerp Center for Paediatric Rheumatology and AutoInflammatory Diseases, Antwerp, Belgium
| | - Hilde Jansens
- Department of Laboratory Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Arvid Suls
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium.,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Geert Mortier
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - Pieter Meysman
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium. .,Department of Paediatrics, Antwerp University Hospital, Edegem, Belgium. .,Antwerp Center for Paediatric Rheumatology and AutoInflammatory Diseases, Antwerp, Belgium. .,Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium. .,Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, 00323/8213251, Antwerp, Belgium. .,Department of Pediatrics, University Hospital Brussels, Jette, Belgium.
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7
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Ibrahim J, Op de Beeck K, Fransen E, Croes L, Beyens M, Suls A, Vanden Berghe W, Peeters M, Van Camp G. Methylation analysis of Gasdermin E shows great promise as a biomarker for colorectal cancer. Cancer Med 2019; 8:2133-2145. [PMID: 30993897 PMCID: PMC6536921 DOI: 10.1002/cam4.2103] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [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: 05/16/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/17/2022] Open
Abstract
In addition to its implication in hereditary hearing loss, the Gasdermin E (GSDME) gene is also a tumor suppressor involved in cancer progression through programmed cell death. GSDME epigenetic silencing through methylation has been shown in some cancer types, but studies are yet to fully explore its diagnostic/prognostic potential in colorectal cancer on a large-scale. We used public data from The Cancer Genome Atlas (TCGA) to investigate differences in GSDME methylation and expression between colorectal cancer and normal colorectal tissue, and between left- and right-sided colorectal cancers in 432 samples. We also explored GSDME's diagnostic capacity as a biomarker for colorectal cancer. We observed differential methylation in all 22 GSDME CpGs between tumor and normal tissues, and in 18 CpGs between the left- and right-sided groups. In the cancer tissue, putative promoter probes were hypermethylated and gene body probes were hypomethylated, while this pattern was inversed in normal tissues. Both putative promoter and gene body CpGs correlated well together but formed distinct methylation patterns with the putative promoter exhibiting the most pronounced methylation differences between tumor and normal tissues. Clinicopathological parameters, excluding age, did not show any effect on CpG methylation. Although the methylation of 5 distinct probes was a good predictor of gene expression, we could not identify an association between GSDME methylation and expression in general. Survival analysis showed no association between GSDME methylation and expression on 5-year patient survival. Through logistic regression, we identified a combination of 2 CpGs, that can discriminate between cancer and normal tissue with high accuracy (AUC = 0.95) irrespective of age and tumor stage. We also validated our model in 3 external methylation datasets, from the Gene Expression Omnibus database, and similar results were reached. Our results suggest that GSDME is a promising biomarker for the detection of colorectal cancer.
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Affiliation(s)
- Joe Ibrahim
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Ken Op de Beeck
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Erik Fransen
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- StatUa Centre for StatisticsUniversity of AntwerpAntwerpBelgium
| | - Lieselot Croes
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Matthias Beyens
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Arvid Suls
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling, Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
| | - Marc Peeters
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Department of Medical OncologyAntwerp University HospitalEdegemBelgium
| | - Guy Van Camp
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
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8
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Bartholomeus E, De Neuter N, Meysman P, Suls A, Keersmaekers N, Elias G, Jansens H, Hens N, Smits E, Van Tendeloo V, Beutels P, Van Damme P, Ogunjimi B, Laukens K, Mortier G. Transcriptome profiling in blood before and after hepatitis B vaccination shows significant differences in gene expression between responders and non-responders. Vaccine 2018; 36:6282-6289. [PMID: 30205979 DOI: 10.1016/j.vaccine.2018.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/31/2018] [Accepted: 09/01/2018] [Indexed: 12/27/2022]
Abstract
INTRODUCTION As the hepatitis B virus is widely spread and responsible for considerable morbidity and mortality, WHO recommends vaccination from infancy to reduce acute infection and chronic carriers. However, current subunit vaccines are not 100% efficacious and leave 5-10% of recipients unprotected. METHODS To evaluate immune responses after Engerix-B vaccination, we determined, using mRNA-sequencing, whole blood early gene expression signatures before, at day 3 and day 7 after the first dose and correlated this with the resulting antibody titer after two vaccine doses. RESULTS Our results indicate that immune related genes are differentially expressed in responders mostly at day 3 and in non-responders mostly at day 7. The most remarkable difference between responders and non-responders were the differentially expressed genes before vaccination. The granulin precursor gene (GRN) was significantly downregulated in responders while upregulated in non-responders at day 0. Furthermore, absolute granulocytes numbers were significantly higher in non-responders at day 0. CONCLUSION The non-responders already showed an activated state of the immune system before vaccination. Furthermore, after vaccination, they exhibited a delayed and partial immune response in comparison to the responders. Our data may indicate that the baseline and untriggered immune system can influence the response upon hepatitis B vaccination.
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Affiliation(s)
- Esther Bartholomeus
- Department of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium; AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Nicolas De Neuter
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Arvid Suls
- Department of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium; AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Nina Keersmaekers
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - George Elias
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Hilde Jansens
- Department of Laboratory Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Niel Hens
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium; Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Evelien Smits
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, Edegem, Belgium; Center for Oncological Research Antwerp, University of Antwerp, Antwerp, Belgium
| | - Viggo Van Tendeloo
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Philippe Beutels
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Pierre Van Damme
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Department of Paediatrics, Antwerp University Hospital, Edegem, Belgium
| | - Kris Laukens
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium; AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.
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9
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De Neuter N, Bartholomeus E, Elias G, Keersmaekers N, Suls A, Jansens H, Smits E, Hens N, Beutels P, Van Damme P, Mortier G, Van Tendeloo V, Laukens K, Meysman P, Ogunjimi B. Memory CD4 + T cell receptor repertoire data mining as a tool for identifying cytomegalovirus serostatus. Genes Immun 2018; 20:255-260. [PMID: 29904098 DOI: 10.1038/s41435-018-0035-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/18/2018] [Accepted: 04/25/2018] [Indexed: 12/17/2022]
Abstract
Pathogens of past and current infections have been identified directly by means of PCR or indirectly by measuring a specific immune response (e.g., antibody titration). Using a novel approach, Emerson and colleagues showed that the cytomegalovirus serostatus can also be accurately determined by using a T cell receptor repertoire data mining approach. In this study, we have sequenced the CD4+ memory T cell receptor repertoire of a Belgian cohort with known cytomegalovirus serostatus. A random forest classifier was trained on the CMV specific T cell receptor repertoire signature and used to classify individuals in the Belgian cohort. This study shows that the novel approach can be reliably replicated with an equivalent performance as that reported by Emerson and colleagues. Additionally, it provides evidence that the T cell receptor repertoire signature is to a large extent present in the CD4+ memory repertoire.
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Affiliation(s)
- Nicolas De Neuter
- Department of Mathematics and Computer Science, Adrem Data Lab, University of Antwerp, Antwerp, Belgium. .,Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium. .,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.
| | - Esther Bartholomeus
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - George Elias
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Nina Keersmaekers
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Arvid Suls
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - Hilde Jansens
- Department of Laboratory Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Evelien Smits
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, Edegem, Belgium.,Center for Oncological Research Antwerp, University of Antwerp, Antwerp, Belgium
| | - Niel Hens
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Interuniversity Institute for Biostatistics and statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium.,Centre for the Evaluation of Vaccination (CEV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Philippe Beutels
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Pierre Van Damme
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for the Evaluation of Vaccination (CEV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Geert Mortier
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - Viggo Van Tendeloo
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Department of Mathematics and Computer Science, Adrem Data Lab, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium.,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- Department of Mathematics and Computer Science, Adrem Data Lab, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium.,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Department of Paediatrics, Antwerp University Hospital, Edegem, Belgium
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10
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Croes L, Beyens M, Fransen E, Ibrahim J, Berghe WV, Suls A, Peeters M, Pauwels P, Camp GV, Op de Beeck K. PO-367 DFNA5 methylation: a potential biomarker for breast cancer, on the basis of a large scale analysis in TCGA. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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11
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Croes L, Beyens M, Fransen E, Ibrahim J, Vanden Berghe W, Suls A, Peeters M, Pauwels P, Van Camp G, Op de Beeck K. Large-scale analysis of DFNA5 methylation reveals its potential as biomarker for breast cancer. Clin Epigenetics 2018; 10:51. [PMID: 29682089 PMCID: PMC5896072 DOI: 10.1186/s13148-018-0479-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/26/2018] [Indexed: 12/17/2022] Open
Abstract
Background Breast cancer is the most frequent cancer among women worldwide. Biomarkers for early detection and prognosis of these patients are needed. We hypothesized that deafness, autosomal dominant 5 (DFNA5) may be a valuable biomarker, based upon strong indications for its role as tumor suppressor gene and its function in regulated cell death. In this study, we aimed to analyze DFNA5 methylation and expression in the largest breast cancer cohort to date using publicly available data from TCGA, in order to further unravel the role of DFNA5 as detection and/or prognostic marker in breast cancer. We analyzed Infinium HumanMethylation450k data, covering 22 different CpGs in the DFNA5 gene (668 breast adenocarcinomas and 85 normal breast samples) and DFNA5 expression (Agilent 244K Custom Gene Expression: 476 breast adenocarcinomas and 56 normal breast samples; RNA-sequencing: 666 breast adenocarcinomas and 71 normal breast samples). Results DFNA5 methylation and expression were significantly different between breast cancer and normal breast samples. Overall, breast cancer samples showed higher DFNA5 methylation in the putative gene promoter compared to normal breast samples, whereas in the gene body and upstream of the putative gene promoter, the opposite is true. Furthermore, DFNA5 methylation, in 10 out of 22 CpGs, and expression were significantly higher in lobular compared to ductal breast cancers. An important result of this study was the identification of a combination of one CpG in the gene promoter (CpG07504598) and one CpG in the gene body (CpG12922093) of DFNA5, which was able to discriminate between breast cancer and normal breast samples (AUC = 0.93). This model was externally validated in three independent datasets. Moreover, we showed that estrogen receptor state is associated with DFNA5 methylation and expression. Finally, we were able to find a significant effect of DFNA5 gene body methylation on a 5-year overall survival time. Conclusions We conclude that DFNA5 methylation shows strong potential as detection and prognostic biomarker for breast cancer.
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Affiliation(s)
- Lieselot Croes
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Matthias Beyens
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Erik Fransen
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,3StatUa Center for Statistics, University of Antwerp, Prinsstraat 13, BE-2000 Antwerp, Belgium
| | - Joe Ibrahim
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Wim Vanden Berghe
- 4Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), University of Antwerp, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Arvid Suls
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium
| | - Marc Peeters
- Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Patrick Pauwels
- Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
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12
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Dejanovic B, Djémié T, Grünewald N, Suls A, Kress V, Hetsch F, Craiu D, Zemel M, Gormley P, Lal D, Myers CT, Mefford HC, Palotie A, Helbig I, Meier JC, De Jonghe P, Weckhuysen S, Schwarz G. Simultaneous impairment of neuronal and metabolic function of mutated gephyrin in a patient with epileptic encephalopathy. EMBO Mol Med 2017; 9:1764. [PMID: 29196314 PMCID: PMC5709744 DOI: 10.15252/emmm.201708525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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13
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Meysman P, De Neuter N, Bartholomeus E, Elias G, Van den Bergh J, Emonds MP, Haasnoot GW, Heynderickx S, Wens J, Michels NR, Lambert J, Lion E, Claas FHJ, Goossens H, Smits E, Van Damme P, Van Tendeloo V, Beutels P, Suls A, Mortier G, Laukens K, Ogunjimi B. Increased herpes zoster risk associated with poor HLA-A immediate early 62 protein (IE62) affinity. Immunogenetics 2017; 70:363-372. [PMID: 29196796 DOI: 10.1007/s00251-017-1047-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 10/03/2017] [Accepted: 11/20/2017] [Indexed: 01/08/2023]
Abstract
Around 30% of individuals will develop herpes zoster (HZ), caused by the varicella zoster virus (VZV), during their life. While several risk factors for HZ, such as immunosuppressive therapy, are well known, the genetic and molecular components that determine the risk of otherwise healthy individuals to develop HZ are still poorly understood. We created a computational model for the Human Leukocyte Antigen (HLA-A, -B, and -C) presentation capacity of peptides derived from the VZV Immediate Early 62 (IE62) protein. This model could then be applied to a HZ cohort with known HLA molecules. We found that HLA-A molecules with poor VZV IE62 presentation capabilities were more common in a cohort of 50 individuals with a history of HZ compared to a nationwide control group, which equated to a HZ risk increase of 60%. This tendency was most pronounced for cases of HZ at a young age, where other risk factors are less prevalent. These findings provide new molecular insights into the development of HZ and reveal a genetic predisposition in those individuals most at risk to develop HZ.
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Affiliation(s)
- Pieter Meysman
- ADREM Data Lab, Department of Mathematics and Computer Science, University of Antwerp, 2020, Antwerp, Belgium. .,Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, 2020, Antwerp, Belgium. .,Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020, Antwerp, Belgium.
| | - Nicolas De Neuter
- ADREM Data Lab, Department of Mathematics and Computer Science, University of Antwerp, 2020, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, 2020, Antwerp, Belgium.,Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020, Antwerp, Belgium
| | - Esther Bartholomeus
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020, Antwerp, Belgium.,Center for Medical Genetics, Antwerp University Hospital, 2650, Edegem, Belgium.,Center for Medical Genetics, University of Antwerp, 2650, Edegem, Belgium
| | - George Elias
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020, Antwerp, Belgium.,Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2650, Antwerp, Belgium.,Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, 2650, Edegem, Belgium
| | - Johan Van den Bergh
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2650, Antwerp, Belgium
| | - Marie-Paule Emonds
- Laboratory for Histocompatibility and Immunogenetics (HILA), Red Cross Flanders, 2800, Mechelen, Belgium
| | - Geert W Haasnoot
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, 2300, Leiden, The Netherlands
| | - Steven Heynderickx
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2650, Antwerp, Belgium.,Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, 2650, Edegem, Belgium
| | - Johan Wens
- Department of Primary and Interdisciplinary Care, University of Antwerp, 2610, Wilrijk, Belgium
| | - Nele R Michels
- Department of Primary and Interdisciplinary Care, University of Antwerp, 2610, Wilrijk, Belgium
| | - Julien Lambert
- Department of Dermatology, Antwerp University Hospital/University of Antwerp, 2650, Edegem, Belgium
| | - Eva Lion
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2650, Antwerp, Belgium.,Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, 2650, Edegem, Belgium
| | - Frans H J Claas
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, 2300, Leiden, The Netherlands
| | - Herman Goossens
- Department of Laboratory Medicine, Antwerp University Hospital, 2650, Edegem, Belgium.,Lab of Medical Microbiology (LMM), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610, Antwerp, Belgium
| | - Evelien Smits
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020, Antwerp, Belgium.,Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2650, Antwerp, Belgium.,Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, 2650, Edegem, Belgium.,Center for Oncological Research Antwerp, University of Antwerp, 2610, Antwerp, Belgium
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610, Antwerp, Belgium
| | - Viggo Van Tendeloo
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020, Antwerp, Belgium.,Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2650, Antwerp, Belgium
| | - Philippe Beutels
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020, Antwerp, Belgium.,Centre for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610, Antwerp, Belgium.,School of Public Health and Community Medicine, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Arvid Suls
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020, Antwerp, Belgium.,Center for Medical Genetics, Antwerp University Hospital, 2650, Edegem, Belgium.,Center for Medical Genetics, University of Antwerp, 2650, Edegem, Belgium
| | - Geert Mortier
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020, Antwerp, Belgium.,Center for Medical Genetics, Antwerp University Hospital, 2650, Edegem, Belgium.,Center for Medical Genetics, University of Antwerp, 2650, Edegem, Belgium
| | - Kris Laukens
- ADREM Data Lab, Department of Mathematics and Computer Science, University of Antwerp, 2020, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, 2020, Antwerp, Belgium.,Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020, Antwerp, Belgium
| | - Benson Ogunjimi
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020, Antwerp, Belgium.,Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2650, Antwerp, Belgium.,Centre for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610, Antwerp, Belgium.,Department of Paediatric Nephrology and Rheumatology, Ghent University Hospital, 9000, Ghent, Belgium.,Department of Paediatrics, Antwerp University Hospital, 2650, Edegem, Belgium
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14
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Hylebos M, Van Camp G, Vandeweyer G, Fransen E, Beyens M, Cornelissen R, Suls A, Pauwels P, van Meerbeeck JP, Op de Beeck K. Large-scale copy number analysis reveals variations in genes not previously associated with malignant pleural mesothelioma. Oncotarget 2017; 8:113673-113686. [PMID: 29371938 PMCID: PMC5768355 DOI: 10.18632/oncotarget.22817] [Citation(s) in RCA: 14] [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: 08/01/2017] [Accepted: 11/15/2017] [Indexed: 12/29/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive tumor that is often causally associated with asbestos exposure. Comparative genomic hybridization techniques and arrays demonstrated a complex set of copy number variations (CNVs) in the MPM-genome. These techniques however have a limited resolution, throughput and flexibility compared to next-generation sequencing platforms. In this study, the presence of CNVs in the MPM-genome was investigated using an MPM-cohort (N = 85) for which genomic microarray data are available through ‘The Cancer Genome Atlas’ (TCGA). To validate these results, the genomes of MPMs and matched normal samples (N = 21) were analyzed using low-pass whole genome sequencing on an ‘Illumina HiSeq’ platform. CNVs were detected using in-house developed analysis pipelines and frequencies of copy number loss and gain were calculated. In both datasets, losses on chromosomes 1, 3, 4, 6, 9, 13 and 22 and gains on chromosomes 1, 5, 7 and 17 were found in at least 25% and 15% of MPMs, respectively. Besides the well-known MPM-associated genes, CDKN2A, NF2 and BAP1, other interesting cancer-associated genes were listed as frequently involved in a copy number loss (e.g. EP300, SETD2 and PBRM1). Moreover, four cancer-associated genes showed a high frequency of copy number gain in both datasets (i.e. TERT, FCGR2B, CD79B and PRKAR1A). A statistically significant association between overall survival and the presence of copy number loss in the CDKN2A-containing region was observed in the TCGA-set. In conclusion, recurrent CNVs were detected in both datasets, occurring in regions harboring known MPM-associated genes and genes not previously linked to MPM.
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Affiliation(s)
- Marieke Hylebos
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Antwerp, Belgium.,Center for Oncological Research, University of Antwerp, 2610 Antwerp, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Antwerp, Belgium.,Center for Oncological Research, University of Antwerp, 2610 Antwerp, Belgium
| | - Geert Vandeweyer
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Antwerp, Belgium
| | - Erik Fransen
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Antwerp, Belgium.,StatUa Center for Statistics, University of Antwerp, 2610 Antwerp, Belgium
| | - Matthias Beyens
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Antwerp, Belgium.,Center for Oncological Research, University of Antwerp, 2610 Antwerp, Belgium
| | - Robin Cornelissen
- Department of Pulmonary Medicine, Erasmus Medical Center Cancer Institute, 3015 Rotterdam, The Netherlands
| | - Arvid Suls
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Antwerp, Belgium
| | - Patrick Pauwels
- Center for Oncological Research, University of Antwerp, 2610 Antwerp, Belgium.,Laboratory of Pathology, Antwerp University Hospital, 2650 Antwerp, Belgium
| | - Jan P van Meerbeeck
- Center for Oncological Research, University of Antwerp, 2610 Antwerp, Belgium.,Thoracic Oncology, Antwerp University Hospital, 2650 Antwerp, Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Antwerp, Belgium.,Center for Oncological Research, University of Antwerp, 2610 Antwerp, Belgium
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15
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Marini C, Hardies K, Pisano T, May P, Weckhuysen S, Cellini E, Suls A, Mei D, Balling R, Jonghe PD, Helbig I, Garozzo D, Guerrini R. Recessive mutations in SLC35A3 cause early onset epileptic encephalopathy with skeletal defects. Am J Med Genet A 2017; 173:1119-1123. [PMID: 28328131 DOI: 10.1002/ajmg.a.38112] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 08/16/2016] [Revised: 10/28/2016] [Accepted: 12/09/2016] [Indexed: 11/08/2022]
Abstract
We describe the clinical and whole genome sequencing (WGS) study of a non-consanguineous Italian family in which two siblings, a boy and a girl, manifesting a severe epileptic encephalopathy (EE) with skeletal abnormalities, carried novel SLC35A3 compound heterozygous mutations. Both siblings exhibited infantile spasms, associated with focal, and tonic vibratory seizures from early infancy. EEG recordings showed a suppression-burst (SB) pattern and multifocal paroxysmal activity in both. In addition both had quadriplegia, acquired microcephaly, and severe intellectual disability. General examination showed distal arthrogryposis predominant in the hands in both siblings and severe left dorso-lumbar convex scoliosis in one. WGS of the siblings-parents quartet identified novel compound heterozygous mutations in SLC35A3 in both children. SLC35A3 encodes the major Golgi uridine diphosphate N-acetylglucosamine transporter. With this study, we add SLC35A3 to the gene list of epilepsies. Neurological symptoms and skeletal abnormalities might result from impaired glycosylation of proteins involved in normal development and function of the central nervous system and skeletal apparatus.
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Affiliation(s)
- Carla Marini
- Neurology Unit and Neurogenetics Laboratories, Meyer Children Hospital, Florence, Italy
| | - Katia Hardies
- Neurogenetics Group, VIB-Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Tiziana Pisano
- Neurology Unit and Neurogenetics Laboratories, Meyer Children Hospital, Florence, Italy
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, Luxembourg.,Institute for Systems Biology (ISB), Seattle, Washington
| | - Sarah Weckhuysen
- Neurogenetics Group, VIB-Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Elena Cellini
- Neurology Unit and Neurogenetics Laboratories, Meyer Children Hospital, Florence, Italy
| | - Arvid Suls
- Neurogenetics Group, VIB-Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Davide Mei
- Neurology Unit and Neurogenetics Laboratories, Meyer Children Hospital, Florence, Italy
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, Luxembourg
| | - Peter D Jonghe
- Neurogenetics Group, VIB-Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Division of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Ingo Helbig
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian-Albrechts University, Kiel, Germany.,Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Domenico Garozzo
- CNR, Institute of Chemistry and Technology of Polymers, Section of Catania, Catania, Italy
| | | | - Renzo Guerrini
- Neurology Unit and Neurogenetics Laboratories, Meyer Children Hospital, Florence, Italy.,University of Florence, Florence, Italy
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16
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Ogunjimi B, Zhang SY, Sørensen KB, Skipper KA, Carter-Timofte M, Kerner G, Luecke S, Prabakaran T, Cai Y, Meester J, Bartholomeus E, Bolar NA, Vandeweyer G, Claes C, Sillis Y, Lorenzo L, Fiorenza RA, Boucherit S, Dielman C, Heynderickx S, Elias G, Kurotova A, Auwera AV, Verstraete L, Lagae L, Verhelst H, Jansen A, Ramet J, Suls A, Smits E, Ceulemans B, Van Laer L, Plat Wilson G, Kreth J, Picard C, Von Bernuth H, Fluss J, Chabrier S, Abel L, Mortier G, Fribourg S, Mikkelsen JG, Casanova JL, Paludan SR, Mogensen TH. Inborn errors in RNA polymerase III underlie severe varicella zoster virus infections. J Clin Invest 2017; 127:3543-3556. [PMID: 28783042 DOI: 10.1172/jci92280] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 06/26/2017] [Indexed: 01/13/2023] Open
Abstract
Varicella zoster virus (VZV) typically causes chickenpox upon primary infection. In rare cases, VZV can give rise to life-threatening disease in otherwise healthy people, but the immunological basis for this remains unexplained. We report 4 cases of acute severe VZV infection affecting the central nervous system or the lungs in unrelated, otherwise healthy children who are heterozygous for rare missense mutations in POLR3A (one patient), POLR3C (one patient), or both (two patients). POLR3A and POLR3C encode subunits of RNA polymerase III. Leukocytes from all 4 patients tested exhibited poor IFN induction in response to synthetic or VZV-derived DNA. Moreover, leukocytes from 3 of the patients displayed defective IFN production upon VZV infection and reduced control of VZV replication. These phenotypes were rescued by transduction with relevant WT alleles. This work demonstrates that monogenic or digenic POLR3A and POLR3C deficiencies confer increased susceptibility to severe VZV disease in otherwise healthy children, providing evidence for an essential role of a DNA sensor in human immunity.
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Affiliation(s)
- Benson Ogunjimi
- Centre for Health Economics Research & Modeling Infectious Diseases, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.,Department of Pediatrics, Antwerp University Hospital, Antwerp, Belgium.,Department of Pediatric Nephrology and Rheumatology, Ghent University Hospital, Ghent, Belgium.,Laboratory of Experimental Hematology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.,Antwerp Unit for Data Analysis and Computation in Immunology & Sequencing, Antwerp, Belgium
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Katrine B Sørensen
- Department of Infectious Diseases, Aarhus University Hospital Skejby, Aarhus, Denmark.,Department of Biomedicine and.,Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Kristian A Skipper
- Department of Biomedicine and.,Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Madalina Carter-Timofte
- Department of Infectious Diseases, Aarhus University Hospital Skejby, Aarhus, Denmark.,Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Gaspard Kerner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Stefanie Luecke
- Department of Biomedicine and.,Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Thaneas Prabakaran
- Department of Biomedicine and.,Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Yujia Cai
- Department of Biomedicine and.,Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Josephina Meester
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Antwerp, Belgium
| | - Esther Bartholomeus
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Antwerp, Belgium
| | - Nikhita Ajit Bolar
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Antwerp, Belgium
| | - Geert Vandeweyer
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Antwerp, Belgium
| | - Charlotte Claes
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Antwerp, Belgium
| | - Yasmine Sillis
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Antwerp, Belgium
| | - Lazaro Lorenzo
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Raffaele A Fiorenza
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Soraya Boucherit
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Charlotte Dielman
- Department of Child Neurology, Queen Paola Child Hospital, Antwerp, Belgium
| | - Steven Heynderickx
- Laboratory of Experimental Hematology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - George Elias
- Laboratory of Experimental Hematology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Andrea Kurotova
- Department of Pediatrics, Sint-Vincentius Hospital, Antwerp, Belgium
| | - Ann Vander Auwera
- Department of Pediatrics, Sint-Augustinus Hospital, Antwerp, Belgium
| | | | - Lieven Lagae
- Department of Development and Regeneration - Section Paediatric Neurology, University Hospitals KULeuven, Leuven, Belgium
| | - Helene Verhelst
- Department of Paediatric Neurology, Ghent University Hospital, Ghent, Belgium
| | - Anna Jansen
- Pediatric Neurology Unit, Department of Pediatrics, UZ Brussel, Brussels, Belgium.,Department of Public Health, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jose Ramet
- Department of Pediatrics, Antwerp University Hospital, Antwerp, Belgium
| | - Arvid Suls
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Antwerp, Belgium
| | - Evelien Smits
- Laboratory of Experimental Hematology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Berten Ceulemans
- Department of Neurology, Pediatric Neurology, Antwerp University Hospital & University of Antwerp, Antwerp, Belgium
| | - Lut Van Laer
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Antwerp, Belgium
| | | | - Jonas Kreth
- Neuropediatric Department, Hospital for Children and Adolescents, gGmbH Klinikum Leverkusen, Leverkusen, Germany
| | - Capucine Picard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Horst Von Bernuth
- Department of Pediatric Pulmonology and Immunology, Charité Berlin - Campus Rudolf Virchow, Berlin, Germany
| | - Joël Fluss
- FMH Pediatric Neurology, Children's Hospital, Geneva, Switzerland
| | - Stephane Chabrier
- CHU Saint-Étienne, French Centre for Paediatric Stroke, Saint-Étienne, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Geert Mortier
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Antwerp, Belgium
| | | | - Jacob Giehm Mikkelsen
- Department of Biomedicine and.,Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,Howard Hughes Medical Institute, New York, New York, USA.,Pediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, Paris, France
| | - Søren R Paludan
- Department of Biomedicine and.,Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Trine H Mogensen
- Department of Infectious Diseases, Aarhus University Hospital Skejby, Aarhus, Denmark.,Department of Biomedicine and.,Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
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17
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Santiago-Sim T, Burrage LC, Ebstein F, Tokita MJ, Miller M, Bi W, Braxton AA, Rosenfeld JA, Shahrour M, Lehmann A, Cogné B, Küry S, Besnard T, Isidor B, Bézieau S, Hazart I, Nagakura H, Immken LL, Littlejohn RO, Roeder E, Kara B, Hardies K, Weckhuysen S, May P, Lemke JR, Elpeleg O, Abu-Libdeh B, James KN, Silhavy JL, Issa MY, Zaki MS, Gleeson JG, Seavitt JR, Dickinson ME, Ljungberg MC, Wells S, Johnson SJ, Teboul L, Eng CM, Yang Y, Kloetzel PM, Heaney JD, Walkiewicz MA, Afawi Z, Balling R, Barisic N, Baulac S, Craiu D, De Jonghe P, Guerrero-Lopez R, Guerrini R, Helbig I, Hjalgrim H, Jähn J, Klein KM, Leguern E, Lerche H, Marini C, Muhle H, Rosenow F, Serratosa J, Sterbová K, Suls A, Moller RS, Striano P, Weber Y, Zara F. Biallelic Variants in OTUD6B Cause an Intellectual Disability Syndrome Associated with Seizures and Dysmorphic Features. Am J Hum Genet 2017; 100:676-688. [PMID: 28343629 DOI: 10.1016/j.ajhg.2017.03.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/21/2017] [Indexed: 10/19/2022] Open
Abstract
Ubiquitination is a posttranslational modification that regulates many cellular processes including protein degradation, intracellular trafficking, cell signaling, and protein-protein interactions. Deubiquitinating enzymes (DUBs), which reverse the process of ubiquitination, are important regulators of the ubiquitin system. OTUD6B encodes a member of the ovarian tumor domain (OTU)-containing subfamily of deubiquitinating enzymes. Herein, we report biallelic pathogenic variants in OTUD6B in 12 individuals from 6 independent families with an intellectual disability syndrome associated with seizures and dysmorphic features. In subjects with predicted loss-of-function alleles, additional features include global developmental delay, microcephaly, absent speech, hypotonia, growth retardation with prenatal onset, feeding difficulties, structural brain abnormalities, congenital malformations including congenital heart disease, and musculoskeletal features. Homozygous Otud6b knockout mice were subviable, smaller in size, and had congenital heart defects, consistent with the severity of loss-of-function variants in humans. Analysis of peripheral blood mononuclear cells from an affected subject showed reduced incorporation of 19S subunits into 26S proteasomes, decreased chymotrypsin-like activity, and accumulation of ubiquitin-protein conjugates. Our findings suggest a role for OTUD6B in proteasome function, establish that defective OTUD6B function underlies a multisystemic human disorder, and provide additional evidence for the emerging relationship between the ubiquitin system and human disease.
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18
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Johannesen K, Marini C, Pfeffer S, Møller RS, Dorn T, Niturad CE, Gardella E, Weber Y, Søndergård M, Hjalgrim H, Nikanorova M, Becker F, Larsen LH, Dahl HA, Maier O, Mei D, Biskup S, Klein KM, Reif PS, Rosenow F, Elias AF, Hudson C, Helbig KL, Schubert-Bast S, Scordo MR, Craiu D, Djémié T, Hoffman-Zacharska D, Caglayan H, Helbig I, Serratosa J, Striano P, De Jonghe P, Weckhuysen S, Suls A, Muru K, Talvik I, Talvik T, Muhle H, Borggraefe I, Rost I, Guerrini R, Lerche H, Lemke JR, Rubboli G, Maljevic S. Phenotypic spectrum of
GABRA1. Neurology 2016; 87:1140-51. [DOI: 10.1212/wnl.0000000000003087] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 06/03/2016] [Indexed: 11/15/2022] Open
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19
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de Kovel CGF, Brilstra EH, van Kempen MJA, Van't Slot R, Nijman IJ, Afawi Z, De Jonghe P, Djémié T, Guerrini R, Hardies K, Helbig I, Hendrickx R, Kanaan M, Kramer U, Lehesjoki AEE, Lemke JR, Marini C, Mei D, Møller RS, Pendziwiat M, Stamberger H, Suls A, Weckhuysen S, Koeleman BPC. Targeted sequencing of 351 candidate genes for epileptic encephalopathy in a large cohort of patients. Mol Genet Genomic Med 2016; 4:568-80. [PMID: 27652284 PMCID: PMC5023942 DOI: 10.1002/mgg3.235] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [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: 04/14/2016] [Revised: 06/17/2016] [Accepted: 06/27/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Many genes are candidates for involvement in epileptic encephalopathy (EE) because one or a few possibly pathogenic variants have been found in patients, but insufficient genetic or functional evidence exists for a definite annotation. METHODS To increase the number of validated EE genes, we sequenced 26 known and 351 candidate genes for EE in 360 patients. Variants in 25 genes known to be involved in EE or related phenotypes were followed up in 41 patients. We prioritized the candidate genes, and followed up 31 variants in this prioritized subset of candidate genes. RESULTS Twenty-nine genotypes in known genes for EE (19) or related diseases (10), dominant as well as recessive or X-linked, were classified as likely pathogenic variants. Among those, likely pathogenic de novo variants were found in EE genes that act dominantly, including the recently identified genes EEF1A2, KCNB1 and the X-linked gene IQSEC2. A de novo frameshift variant in candidate gene HNRNPU was the only de novo variant found among the followed-up candidate genes, and the patient's phenotype was similar to a few recent publications. CONCLUSION Mutations in genes described in OMIM as, for example, intellectual disability gene can lead to phenotypes that get classified as EE in the clinic. We confirmed existing literature reports that de novo loss-of-function HNRNPUmutations lead to severe developmental delay and febrile seizures in the first year of life.
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Affiliation(s)
| | - Eva H Brilstra
- Department of Genetics UMC Utrecht Utrecht The Netherlands
| | | | | | - Isaac J Nijman
- Department of Genetics UMC Utrecht Utrecht The Netherlands
| | - Zaid Afawi
- Tel Aviv Sourasky Medical Center6 Weizmann St.Tel AvivIsrael; Genetics of Epilepsy Research in Israel Tel-Aviv University Medical SchoolTel-AvivIsrael
| | - Peter De Jonghe
- Neurogenetics GroupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium; Division of NeurologyAntwerp University HospitalAntwerpBelgium
| | - Tania Djémié
- Neurogenetics GroupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium
| | - Renzo Guerrini
- Neuroscience Department Children's Hospital Anna Meyer University of Florence Florence Italy
| | - Katia Hardies
- Neurogenetics GroupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium
| | - Ingo Helbig
- Division of NeurologyThe Children's Hospital of PhiladelphiaPhiladephiaPennsylvania; Department of NeuropediatricsUniversity Medical Center Schleswig-HolsteinChristian Albrechts UniversityKielGermany
| | - Rik Hendrickx
- Neurogenetics Group Department of Molecular Genetics VIB Antwerp Belgium
| | - Moine Kanaan
- Pediatric Epilepsy Unit Tel Aviv Sourasky Medical Center Tel Aviv University Tel Aviv Israel
| | - Uri Kramer
- Department of Life Sciences Bethlehem University Bethlehem Palestine
| | - Anna-Elina E Lehesjoki
- Folkhälsan Institute of Genetics Neuroscience Center and Research Programs Unit Molecular Neurology University of Helsinki Helsinki Finland
| | - Johannes R Lemke
- Institute of Human Genetics University of Leipzig Hospitals and Clinics Leipzig Germany
| | - Carla Marini
- Neuroscience Department Children's Hospital Anna Meyer University of Florence Florence Italy
| | - Davide Mei
- Neuroscience Department Children's Hospital Anna Meyer University of Florence Florence Italy
| | - Rikke S Møller
- Danish Epilepsy Centre - FiladelfiaDianalundDenmark; Institute for Regional Health ServicesUniversity of Southern DenmarkDK-5230OdenseDenmark
| | - Manuela Pendziwiat
- Department of Neuropediatrics University Medical Center Schleswig-Holstein Christian Albrechts University Kiel Germany
| | - Hannah Stamberger
- Neurogenetics GroupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium
| | - Arvid Suls
- Neurogenetics GroupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium
| | - Sarah Weckhuysen
- Neurogenetics GroupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium
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20
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Hardies K, Cai Y, Jardel C, Jansen AC, Cao M, May P, Djémié T, Hachon Le Camus C, Keymolen K, Deconinck T, Bhambhani V, Long C, Sajan SA, Helbig KL, Suls A, Balling R, Helbig I, De Jonghe P, Depienne C, De Camilli P, Weckhuysen S. Loss of SYNJ1 dual phosphatase activity leads to early onset refractory seizures and progressive neurological decline. Brain 2016; 139:2420-30. [PMID: 27435091 DOI: 10.1093/brain/aww180] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/07/2016] [Indexed: 12/30/2022] Open
Abstract
SYNJ1 encodes a polyphosphoinositide phosphatase, synaptojanin 1, which contains two consecutive phosphatase domains and plays a prominent role in synaptic vesicle dynamics. Autosomal recessive inherited variants in SYNJ1 have previously been associated with two different neurological diseases: a recurrent homozygous missense variant (p.Arg258Gln) that abolishes Sac1 phosphatase activity was identified in three independent families with early onset parkinsonism, whereas a homozygous nonsense variant (p.Arg136*) causing a severe decrease of mRNA transcript was found in a single patient with intractable epilepsy and tau pathology. We performed whole exome or genome sequencing in three independent sib pairs with early onset refractory seizures and progressive neurological decline, and identified novel segregating recessive SYNJ1 defects. A homozygous missense variant resulting in an amino acid substitution (p.Tyr888Cys) was found to impair, but not abolish, the dual phosphatase activity of SYNJ1, whereas three premature stop variants (homozygote p.Trp843* and compound heterozygote p.Gln647Argfs*6/p.Ser1122Thrfs*3) almost completely abolished mRNA transcript production. A genetic follow-up screening in a large cohort of 543 patients with a wide phenotypical range of epilepsies and intellectual disability revealed no additional pathogenic variants, showing that SYNJ1 deficiency is rare and probably linked to a specific phenotype. While variants leading to early onset parkinsonism selectively abolish Sac1 function, our results provide evidence that a critical reduction of the dual phosphatase activity of SYNJ1 underlies a severe disorder with neonatal refractory epilepsy and a neurodegenerative disease course. These findings further expand the clinical spectrum of synaptic dysregulation in patients with severe epilepsy, and emphasize the importance of this biological pathway in seizure pathophysiology.
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21
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Dejanovic B, Djémié T, Grünewald N, Suls A, Kress V, Hetsch F, Craiu D, Zemel M, Gormley P, Lal D, Myers CT, Mefford HC, Palotie A, Helbig I, Meier JC, De Jonghe P, Weckhuysen S, Schwarz G. Simultaneous impairment of neuronal and metabolic function of mutated gephyrin in a patient with epileptic encephalopathy. EMBO Mol Med 2016; 7:1580-94. [PMID: 26613940 PMCID: PMC4693503 DOI: 10.15252/emmm.201505323] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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] [Indexed: 11/24/2022] Open
Abstract
Synaptic inhibition is essential for shaping the dynamics of neuronal networks, and aberrant inhibition plays an important role in neurological disorders. Gephyrin is a central player at inhibitory postsynapses, directly binds and organizes GABAA and glycine receptors (GABAARs and GlyRs), and is thereby indispensable for normal inhibitory neurotransmission. Additionally, gephyrin catalyzes the synthesis of the molybdenum cofactor (MoCo) in peripheral tissue. We identified a de novo missense mutation (G375D) in the gephyrin gene (GPHN) in a patient with epileptic encephalopathy resembling Dravet syndrome. Although stably expressed and correctly folded, gephyrin‐G375D was non‐synaptically localized in neurons and acted dominant‐negatively on the clustering of wild‐type gephyrin leading to a marked decrease in GABAAR surface expression and GABAergic signaling. We identified a decreased binding affinity between gephyrin‐G375D and the receptors, suggesting that Gly375 is essential for gephyrin–receptor complex formation. Surprisingly, gephyrin‐G375D was also unable to synthesize MoCo and activate MoCo‐dependent enzymes. Thus, we describe a missense mutation that affects both functions of gephyrin and suggest that the identified defect at GABAergic synapses is the mechanism underlying the patient's severe phenotype.
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Affiliation(s)
- Borislav Dejanovic
- Department of Chemistry, Institute of Biochemistry University of Cologne, Cologne, Germany
| | - Tania Djémié
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium Laboratory of Neurogenetics, Institute Born-Bunge University of Antwerp, Antwerp, Belgium
| | - Nora Grünewald
- Department of Chemistry, Institute of Biochemistry University of Cologne, Cologne, Germany
| | - Arvid Suls
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium Laboratory of Neurogenetics, Institute Born-Bunge University of Antwerp, Antwerp, Belgium GENOMED, Center for Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Vanessa Kress
- Department of Chemistry, Institute of Biochemistry University of Cologne, Cologne, Germany
| | - Florian Hetsch
- Division Cell Physiology, Zoological Institute Technische Universität Braunschweig, Braunschweig, Germany
| | - Dana Craiu
- Pediatric Neurology Clinic, Al Obregia Hospital, Bucharest, Romania Department of Neurology, Pediatric Neurology, Psychiatry, Child and Adolescent Psychiatry, and Neurosurgery, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Matthew Zemel
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Padhraig Gormley
- Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton, UK Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) University of Cologne, Cologne, Germany Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dennis Lal
- Cologne Center for Genomics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) University of Cologne, Cologne, Germany Department of Neuropediatrics, University Medical Faculty Giessen and Marburg, Giessen, Germany
| | | | - Candace T Myers
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Aarno Palotie
- Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton, UK Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Ingo Helbig
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein Christian Albrechts University, Kiel, Germany Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jochen C Meier
- Division Cell Physiology, Zoological Institute Technische Universität Braunschweig, Braunschweig, Germany
| | - Peter De Jonghe
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium Laboratory of Neurogenetics, Institute Born-Bunge University of Antwerp, Antwerp, Belgium Division of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Sarah Weckhuysen
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium Laboratory of Neurogenetics, Institute Born-Bunge University of Antwerp, Antwerp, Belgium Inserm U 1127 CNRS UMR 7225 Sorbonne Universités UPMC Univ Paris 06 UMR S 1127 Institut du Cerveau et de la Moelle épinière, ICM, Paris, France Centre de reference épilepsies rares, Epilepsy unit, AP-HP Groupe hospitalier Pitié-Salpêtrière, F-75013, Paris, France
| | - Guenter Schwarz
- Department of Chemistry, Institute of Biochemistry University of Cologne, Cologne, Germany Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) University of Cologne, Cologne, Germany
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22
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Djémié T, Weckhuysen S, von Spiczak S, Carvill GL, Jaehn J, Anttonen AK, Brilstra E, Caglayan HS, de Kovel CG, Depienne C, Gaily E, Gennaro E, Giraldez BG, Gormley P, Guerrero-López R, Guerrini R, Hämäläinen E, Hartmann C, Hernandez-Hernandez L, Hjalgrim H, Koeleman BPC, Leguern E, Lehesjoki AE, Lemke JR, Leu C, Marini C, McMahon JM, Mei D, Møller RS, Muhle H, Myers CT, Nava C, Serratosa JM, Sisodiya SM, Stephani U, Striano P, van Kempen MJA, Verbeek NE, Usluer S, Zara F, Palotie A, Mefford HC, Scheffer IE, De Jonghe P, Helbig I, Suls A. Pitfalls in genetic testing: the story of missed SCN1A mutations. Mol Genet Genomic Med 2016; 4:457-64. [PMID: 27465585 PMCID: PMC4947864 DOI: 10.1002/mgg3.217] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 01/03/2023] Open
Abstract
Background Sanger sequencing, still the standard technique for genetic testing in most diagnostic laboratories and until recently widely used in research, is gradually being complemented by next‐generation sequencing (NGS). No single mutation detection technique is however perfect in identifying all mutations. Therefore, we wondered to what extent inconsistencies between Sanger sequencing and NGS affect the molecular diagnosis of patients. Since mutations in SCN1A, the major gene implicated in epilepsy, are found in the majority of Dravet syndrome (DS) patients, we focused on missed SCN1A mutations. Methods We sent out a survey to 16 genetic centers performing SCN1A testing. Results We collected data on 28 mutations initially missed using Sanger sequencing. All patients were falsely reported as SCN1A mutation‐negative, both due to technical limitations and human errors. Conclusion We illustrate the pitfalls of Sanger sequencing and most importantly provide evidence that SCN1A mutations are an even more frequent cause of DS than already anticipated.
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Affiliation(s)
- Tania Djémié
- Neurogenetics groupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium
| | - Sarah Weckhuysen
- Neurogenetics groupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium; Sorbonne universitésUPMC université Paris 0691-105boulevard de l'HôpitalParis75013France; ICM, CNRS UMR 7225, Inserm U 112747/83, boulevard de l'HôpitalParis75013France; Centre de reference épilepsies raresEpilepsy unit, AP-HP Groupe hospitalier Pitié-SalpêtrièreParis75013France
| | - Sarah von Spiczak
- Department of Neuropediatrics University Medical Center Schleswig-Holstein Kiel Germany
| | - Gemma L Carvill
- Division of Genetic Medicine Department of Pediatrics University of Washington Seattle Washington 98195 USA
| | - Johanna Jaehn
- Department of Neuropediatrics University Medical Center Schleswig-Holstein Kiel Germany
| | - Anna-Kaisa Anttonen
- Folkhälsan Institute of GeneticsHelsinkiFinland; Medical and Clinical GeneticsUniversity of HelsinkiHelsinkiFinland; Helsinki University HospitalHelsinkiFinland
| | - Eva Brilstra
- Department of Medical Genetics University Medical Center Utrecht Utrecht The Netherlands
| | - Hande S Caglayan
- Department of Molecular Biology and Genetics Bogaziçi University Istanbul Turkey
| | - Carolien G de Kovel
- Department of Medical Genetics University Medical Center Utrecht Utrecht The Netherlands
| | - Christel Depienne
- Sorbonne universitésUPMC université Paris 0691-105boulevard de l'HôpitalParis75013France; ICM, CNRS UMR 7225, Inserm U 112747/83, boulevard de l'HôpitalParis75013France; Département de génétiqueAP-HP, hôpital Pitié-Salpêtrière47/83boulevard de l'HôpitalParis75013France
| | - Eija Gaily
- Department of Pediatric Neurology Helsinki University Hospital Helsinki Finland
| | - Elena Gennaro
- Laboratory of Genetics E.O. Ospedali Galliera Genova Italy
| | - Beatriz G Giraldez
- Neurology Laboratory and Epilepsy UnitDepartment of NeurologyInstituto de Investigatión Sanitaria-Fundación Jiménez Díaz, Universidad Autónoma de MadridMadridSpain; IIS-Fundación Jiménez Díaz and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)MadridSpain
| | - Padhraig Gormley
- Psychiatric and Neurodevelopmental Genetics UnitMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusetts02114USA; Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMassachusetts02142USA; Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusetts02142USA; Wellcome Trust Sanger InstituteHinxtonUnited Kingdom
| | - Rosa Guerrero-López
- IIS-Fundación Jiménez Díaz and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Madrid Spain
| | - Renzo Guerrini
- Pediatric Neurology and Neurogenetics Unit and Laboratories A. Meyer Children's Hospital-University of Florence Florence Italy
| | - Eija Hämäläinen
- Wellcome Trust Sanger InstituteHinxtonUnited Kingdom; Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Corinna Hartmann
- Department of Neuropediatrics University Medical Center Schleswig-Holstein Kiel Germany
| | - Laura Hernandez-Hernandez
- Department of Clinical and Experimental EpilepsyNIHR University College London Hospitals Biomedical Research CentreUCL Institute of NeurologyLondonUnited Kingdom; The Epilepsy SocietyChalfont-St-PeterBucksUnited Kingdom
| | - Helle Hjalgrim
- Department of NeurologyDanish Epilepsy CentreDianalundDenmark; Institute for Regional Health researchUniversity of Southern DenmarkOdenseDenmark
| | - Bobby P C Koeleman
- Department of Medical Genetics University Medical Center Utrecht Utrecht The Netherlands
| | - Eric Leguern
- Sorbonne universitésUPMC université Paris 0691-105boulevard de l'HôpitalParis75013France; ICM, CNRS UMR 7225, Inserm U 112747/83, boulevard de l'HôpitalParis75013France; Département de génétiqueAP-HP, hôpital Pitié-Salpêtrière47/83boulevard de l'HôpitalParis75013France
| | - Anna-Elina Lehesjoki
- Folkhälsan Institute of GeneticsHelsinkiFinland; Research Programs UnitMolecular NeurologyUniversity of HelsinkiHelsinkiFinland
| | - Johannes R Lemke
- Institute of Human Genetics University of Leipzig Leipzig Germany
| | - Costin Leu
- Department of Clinical and Experimental Epilepsy NIHR University College London Hospitals Biomedical Research Centre UCL Institute of Neurology London United Kingdom
| | - Carla Marini
- Pediatric Neurology and Neurogenetics Unit and Laboratories A. Meyer Children's Hospital-University of Florence Florence Italy
| | - Jacinta M McMahon
- Epilepsy Research Centre Department of Medicine University of Melbourne Austin Health Melbourne Australia
| | - Davide Mei
- Pediatric Neurology and Neurogenetics Unit and Laboratories A. Meyer Children's Hospital-University of Florence Florence Italy
| | - Rikke S Møller
- Department of NeurologyDanish Epilepsy CentreDianalundDenmark; Institute for Regional Health researchUniversity of Southern DenmarkOdenseDenmark
| | - Hiltrud Muhle
- Department of Neuropediatrics University Medical Center Schleswig-Holstein Kiel Germany
| | - Candace T Myers
- Division of Genetic Medicine Department of Pediatrics University of Washington Seattle Washington 98195 USA
| | - Caroline Nava
- Sorbonne universitésUPMC université Paris 0691-105boulevard de l'HôpitalParis75013France; ICM, CNRS UMR 7225, Inserm U 112747/83, boulevard de l'HôpitalParis75013France; Département de génétiqueAP-HP, hôpital Pitié-Salpêtrière47/83boulevard de l'HôpitalParis75013France
| | - Jose M Serratosa
- Neurology Laboratory and Epilepsy UnitDepartment of NeurologyInstituto de Investigatión Sanitaria-Fundación Jiménez Díaz, Universidad Autónoma de MadridMadridSpain; IIS-Fundación Jiménez Díaz and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)MadridSpain
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental EpilepsyNIHR University College London Hospitals Biomedical Research CentreUCL Institute of NeurologyLondonUnited Kingdom; The Epilepsy SocietyChalfont-St-PeterBucksUnited Kingdom
| | - Ulrich Stephani
- Department of Neuropediatrics University Medical Center Schleswig-Holstein Kiel Germany
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit Department of Neurosciences Rehabilitation Ophthalmology Genetics and Maternal and Child Health University of Genoa 'G. Gaslini' Institute Genova Italy
| | - Marjan J A van Kempen
- Department of Medical Genetics University Medical Center Utrecht Utrecht The Netherlands
| | - Nienke E Verbeek
- Department of Medical Genetics University Medical Center Utrecht Utrecht The Netherlands
| | - Sunay Usluer
- Department of Molecular Biology and Genetics Bogaziçi University Istanbul Turkey
| | - Federico Zara
- Laboratory of Neurogenetics Department of Neurosciences Giannina Gaslini Institute Genova Italy
| | - Aarno Palotie
- Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMassachusetts02142USA; Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Heather C Mefford
- Division of Genetic Medicine Department of Pediatrics University of Washington Seattle Washington 98195 USA
| | - Ingrid E Scheffer
- Epilepsy Research CentreDepartment of MedicineUniversity of MelbourneAustin HealthMelbourneAustralia; Department of PaediatricsUniversity of Melbourne and Royal Children's HospitalParkvilleVictoria3052Australia; Florey Institute of Neuroscience and Mental HealthMelbourneVictoria3084Australia
| | - Peter De Jonghe
- Neurogenetics groupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium; Division of NeurologyAntwerp University HospitalAntwerpBelgium
| | - Ingo Helbig
- Department of NeuropediatricsUniversity Medical Center Schleswig-HolsteinKielGermany; Division of NeurologyChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Arvid Suls
- Neurogenetics groupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium; GENOMEDCenter for Medical GeneticsUniversity of AntwerpAntwerpBelgium
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23
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Hardies K, Weckhuysen S, De Jonghe P, Suls A. Lessons learned from gene identification studies in Mendelian epilepsy disorders. Eur J Hum Genet 2015; 24:961-7. [PMID: 26603999 DOI: 10.1038/ejhg.2015.251] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 10/05/2015] [Accepted: 10/29/2015] [Indexed: 01/23/2023] Open
Abstract
Next-generation sequencing (NGS) technologies are now routinely used for gene identification in Mendelian disorders. Setting up cost-efficient NGS projects and managing the large amount of variants remains, however, a challenging job. Here we provide insights in the decision-making processes before and after the use of NGS in gene identification studies. Genetic factors are thought to have a role in ~70% of all epilepsies, and a variety of inheritance patterns have been described for seizure-associated gene defects. We therefore chose epilepsy as disease model and selected 35 NGS studies that focused on patients with a Mendelian epilepsy disorder. The strategies used for gene identification and their respective outcomes were reviewed. High-throughput NGS strategies have led to the identification of several new epilepsy-causing genes, enlarging our knowledge on both known and novel pathomechanisms. NGS findings have furthermore extended the awareness of phenotypical and genetic heterogeneity. By discussing recent studies we illustrate: (I) the power of NGS for gene identification in Mendelian disorders, (II) the accelerating pace in which this field evolves, and (III) the considerations that have to be made when performing NGS studies. Nonetheless, the enormous rise in gene discovery over the last decade, many patients and families included in gene identification studies still remain without a molecular diagnosis; hence, further genetic research is warranted. On the basis of successful NGS studies in epilepsy, we discuss general approaches to guide human geneticists and clinicians in setting up cost-efficient gene identification NGS studies.
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Affiliation(s)
- Katia Hardies
- VIB-Department of Molecular Genetics, Neurogenetics Group, University of Antwerp, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Sarah Weckhuysen
- VIB-Department of Molecular Genetics, Neurogenetics Group, University of Antwerp, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Peter De Jonghe
- VIB-Department of Molecular Genetics, Neurogenetics Group, University of Antwerp, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Division of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Arvid Suls
- VIB-Department of Molecular Genetics, Neurogenetics Group, University of Antwerp, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
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24
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Hardies K, de Kovel CGF, Weckhuysen S, Asselbergh B, Geuens T, Deconinck T, Azmi A, May P, Brilstra E, Becker F, Barisic N, Craiu D, Braun KP, Lal D, Thiele H, Schubert J, Weber Y, van ‘t Slot R, Nürnberg P, Balling R, Timmerman V, Lerche H, Maudsley S, Helbig I, Suls A, Koeleman BP. Recessive mutations inSLC13A5result in a loss of citrate transport and cause neonatal epilepsy, developmental delay and teeth hypoplasia. Brain 2015; 138:3238-50. [DOI: 10.1093/brain/awv263] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/07/2015] [Indexed: 12/21/2022] Open
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25
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Hedrich U, Syrbe S, Riesch E, Djémié T, Müller S, Møller R, Maher B, Hernandez-Hernandez L, Synofzik M, Caglayan H, Arslan M, Serratosa J, Gonzalez M, Züchner S, Palotie A, Suls A, De Jonghe P, Helbig I, Biskup S, Wolff M, Maljevic S, Schuele-Freyer R, Sisodiya S, Weckhuysen S, Lerche H, Lemke J. V28. KCNA2 mutations cause epileptic encephalopathy by gain- or loss-of channel function. Clin Neurophysiol 2015. [DOI: 10.1016/j.clinph.2015.04.106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Lal D, Ruppert AK, Trucks H, Schulz H, de Kovel CG, Kasteleijn-Nolst Trenité D, Sonsma ACM, Koeleman BP, Lindhout D, Weber YG, Lerche H, Kapser C, Schankin CJ, Kunz WS, Surges R, Elger CE, Gaus V, Schmitz B, Helbig I, Muhle H, Stephani U, Klein KM, Rosenow F, Neubauer BA, Reinthaler EM, Zimprich F, Feucht M, Møller RS, Hjalgrim H, De Jonghe P, Suls A, Lieb W, Franke A, Strauch K, Gieger C, Schurmann C, Schminke U, Nürnberg P, Sander T. Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies. PLoS Genet 2015; 11:e1005226. [PMID: 25950944 PMCID: PMC4423931 DOI: 10.1371/journal.pgen.1005226] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [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: 12/30/2014] [Accepted: 04/16/2015] [Indexed: 01/06/2023] Open
Abstract
Genetic generalised epilepsy (GGE) is the most common form of genetic epilepsy, accounting for 20% of all epilepsies. Genomic copy number variations (CNVs) constitute important genetic risk factors of common GGE syndromes. In our present genome-wide burden analysis, large (≥ 400 kb) and rare (< 1%) autosomal microdeletions with high calling confidence (≥ 200 markers) were assessed by the Affymetrix SNP 6.0 array in European case-control cohorts of 1,366 GGE patients and 5,234 ancestry-matched controls. We aimed to: 1) assess the microdeletion burden in common GGE syndromes, 2) estimate the relative contribution of recurrent microdeletions at genomic rearrangement hotspots and non-recurrent microdeletions, and 3) identify potential candidate genes for GGE. We found a significant excess of microdeletions in 7.3% of GGE patients compared to 4.0% in controls (P = 1.8 x 10-7; OR = 1.9). Recurrent microdeletions at seven known genomic hotspots accounted for 36.9% of all microdeletions identified in the GGE cohort and showed a 7.5-fold increased burden (P = 2.6 x 10-17) relative to controls. Microdeletions affecting either a gene previously implicated in neurodevelopmental disorders (P = 8.0 x 10-18, OR = 4.6) or an evolutionarily conserved brain-expressed gene related to autism spectrum disorder (P = 1.3 x 10-12, OR = 4.1) were significantly enriched in the GGE patients. Microdeletions found only in GGE patients harboured a high proportion of genes previously associated with epilepsy and neuropsychiatric disorders (NRXN1, RBFOX1, PCDH7, KCNA2, EPM2A, RORB, PLCB1). Our results demonstrate that the significantly increased burden of large and rare microdeletions in GGE patients is largely confined to recurrent hotspot microdeletions and microdeletions affecting neurodevelopmental genes, suggesting a strong impact of fundamental neurodevelopmental processes in the pathogenesis of common GGE syndromes.
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Affiliation(s)
- Dennis Lal
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
- EPICURE Consortium
| | - Ann-Kathrin Ruppert
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Holger Trucks
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Herbert Schulz
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Carolien G. de Kovel
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Anja C. M. Sonsma
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P. Koeleman
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dick Lindhout
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
- SEIN Epilepsy Institute in the Netherlands, Hoofddorp, The Netherlands
| | - Yvonne G. Weber
- EPICURE Consortium
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Holger Lerche
- EPICURE Consortium
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Claudia Kapser
- EPICURE Consortium
- Department of Neurology, University of Munich Hospital—Großhadern, Munich, Germany
| | - Christoph J. Schankin
- EPICURE Consortium
- Department of Neurology, University of Munich Hospital—Großhadern, Munich, Germany
| | - Wolfram S. Kunz
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Rainer Surges
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Christian E. Elger
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Verena Gaus
- EPICURE Consortium
- Department of Neurology, Charité University Medicine, Campus Virchow Clinic, Berlin, Germany
| | - Bettina Schmitz
- EPICURE Consortium
- Department of Neurology, Charité University Medicine, Campus Virchow Clinic, Berlin, Germany
- Department of Neurology, Vivantes Humboldt-Klinikum, Berlin, Germany
| | - Ingo Helbig
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Hiltrud Muhle
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Ulrich Stephani
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Karl M. Klein
- EPICURE Consortium
- Epilepsy-Center Hessen, Department of Neurology, Philipps-University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhein-Main, Department of Neurology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
| | - Felix Rosenow
- EPICURE Consortium
- Epilepsy-Center Hessen, Department of Neurology, Philipps-University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhein-Main, Department of Neurology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
| | - Bernd A. Neubauer
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
| | - Eva M. Reinthaler
- EPICURE Consortium
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Fritz Zimprich
- EPICURE Consortium
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Martha Feucht
- EPICURE Consortium
- Department of Pediatrics and Neonatology, Medical University of Vienna, Vienna, Austria
| | - Rikke S. Møller
- EPICURE Consortium
- Department of Neurology, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Helle Hjalgrim
- EPICURE Consortium
- Department of Neurology, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Peter De Jonghe
- EPICURE Consortium
- Neurogenetics Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Arvid Suls
- EPICURE Consortium
- Neurogenetics Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Christian Albrechts University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, and Chair of Genetic Epidemiology, Ludwig-Maximilians-University, Munich, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia Schurmann
- Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University, Greifswald, Germany
| | - Ulf Schminke
- Department of Neurology, University Medicine Greifswald, Ernst Moritz Arndt University, Greifswald, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- EPICURE Consortium
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | | | - Thomas Sander
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
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Pisano T, Numis AL, Heavin SB, Weckhuysen S, Angriman M, Suls A, Podesta B, Thibert RL, Shapiro KA, Guerrini R, Scheffer IE, Marini C, Cilio MR. Early and effective treatment ofKCNQ2encephalopathy. Epilepsia 2015; 56:685-91. [DOI: 10.1111/epi.12984] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Tiziana Pisano
- Neurology Unit and Laboratories; A. Meyer Children's Hospital; Florence Italy
| | - Adam L. Numis
- Department of Neurology; University of California, San Francisco; San Francisco California U.S.A
| | - Sinéad B. Heavin
- Departments of Medicine and Paediatrics; Florey Institute; Austin Health and Royal Children's Hospital; University of Melbourne; Melbourne Victoria Australia
| | - Sarah Weckhuysen
- Neurogenetics Group; Department of Molecular Genetics; VIB; Antwerp Belgium
- Laboratory of Neurogenetics; Institute Born-Bunge; University of Antwerp; Antwerp Belgium
| | | | - Arvid Suls
- Neurogenetics Group; Department of Molecular Genetics; VIB; Antwerp Belgium
- Laboratory of Neurogenetics; Institute Born-Bunge; University of Antwerp; Antwerp Belgium
| | - Barbara Podesta
- Child Neurology and Psychiatry Unit; S. Croce and S. Carlo Hospital; Cuneo Italy
| | - Ronald L. Thibert
- Pediatric Epilepsy Program; Massachusetts General Hospital; Harvard Medical School; Boston Massachusetts U.S.A
| | - Kevin A. Shapiro
- Department of Neurology; University of California, San Francisco; San Francisco California U.S.A
| | - Renzo Guerrini
- Neurology Unit and Laboratories; A. Meyer Children's Hospital; Florence Italy
- University of Florence; Florence Italy
| | - Ingrid E. Scheffer
- Departments of Medicine and Paediatrics; Florey Institute; Austin Health and Royal Children's Hospital; University of Melbourne; Melbourne Victoria Australia
| | - Carla Marini
- Neurology Unit and Laboratories; A. Meyer Children's Hospital; Florence Italy
| | - Maria Roberta Cilio
- Department of Neurology; University of California, San Francisco; San Francisco California U.S.A
- Department of Pediatrics; University of California San Francisco; San Francisco California U.S.A
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Syrbe S, Hedrich UB, Riesch E, Djémié T, Müller S, Møller RS, Maher B, Hernandez-Hernandez L, Synofzik M, Caglayan HS, Arslan M, Serratosa JM, Nothnagel M, May P, Krause R, Löffler H, Detert K, Dorn T, Vogt H, Krämer G, Schöls L, Mullis PE, Linnankivi T, Lehesjoki AE, Sterbova K, Craiu DC, Hoffman-Zacharska D, Korff CM, Weber YG, Steinlin M, Gallati S, Bertsche A, Bernhard MK, Merkenschlager A, Kiess W, Gonzalez M, Züchner S, Palotie A, Suls A, De Jonghe P, Helbig I, Biskup S, Wolff M, Maljevic S, Schüle R, Sisodiya SM, Weckhuysen S, Lerche H, Lemke JR. De novo loss- or gain-of-function mutations in KCNA2 cause epileptic encephalopathy. Nat Genet 2015; 47:393-399. [PMID: 25751627 PMCID: PMC4380508 DOI: 10.1038/ng.3239] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [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: 07/09/2014] [Accepted: 02/06/2015] [Indexed: 02/07/2023]
Abstract
Epileptic encephalopathies are a phenotypically and genetically heterogeneous group of severe epilepsies accompanied by intellectual disability and other neurodevelopmental features. Using next-generation sequencing, we identified four different de novo mutations in KCNA2, encoding the potassium channel KV1.2, in six isolated patients with epileptic encephalopathy (one mutation recurred three times independently). Four individuals presented with febrile and multiple afebrile, often focal seizure types, multifocal epileptiform discharges strongly activated by sleep, mild to moderate intellectual disability, delayed speech development and sometimes ataxia. Functional studies of the two mutations associated with this phenotype showed almost complete loss of function with a dominant-negative effect. Two further individuals presented with a different and more severe epileptic encephalopathy phenotype. They carried mutations inducing a drastic gain-of-function effect leading to permanently open channels. These results establish KCNA2 as a new gene involved in human neurodevelopmental disorders through two different mechanisms, predicting either hyperexcitability or electrical silencing of KV1.2-expressing neurons.
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Affiliation(s)
- Steffen Syrbe
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany.
| | - Ulrike B.S. Hedrich
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
| | - Erik Riesch
- Center for Genomics and Transcriptomics (CeGaT) GmbH, Tübingen, Germany.
- Division of Human Genetics, University Children’s Hospital Inselspital, Bern, Switzerland.
- Swiss Epilepsy Center, Zürich, Switzerland.
| | - Tania Djémié
- Neurogenetics group, Department of Molecular Genetics, VIB, Antwerp, Belgium.
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
| | - Stephan Müller
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
| | - Rikke S. Møller
- Danish Epilepsy Center, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark.
| | - Bridget Maher
- Department of Clinical and Experimental Epilepsy, University College London Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Epilepsy Society, Chalfont-St-Peter, Bucks, SL9 0RJ, UK.
| | - Laura Hernandez-Hernandez
- Department of Clinical and Experimental Epilepsy, University College London Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Epilepsy Society, Chalfont-St-Peter, Bucks, SL9 0RJ, UK.
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
- German Research Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Hande S. Caglayan
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey.
| | - Mutluay Arslan
- Gulhane Military Medical School, Division of Child Neurology, Ankara, Turkey.
| | - José M. Serratosa
- Neurology Lab and Epilepsy Unit, Department of Neurology, IIS — Fundación Jiménez Díaz, UAM, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Colgone, Cologne, Germany
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Heidrun Löffler
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
| | - Katja Detert
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
| | | | | | | | - Ludger Schöls
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
- German Research Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Primus E. Mullis
- Division of Pediatric Endocrinology, University Children’s Hospital Inselspital, Bern, Switzerland.
| | - Tarja Linnankivi
- Pediatric Neurology, Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
| | - Anna-Elina Lehesjoki
- Folkhälsan Institute of Genetics, Helsinki, Helsinki, Finland.
- Neuroscience Center, University of Helsinki, Helsinki, Finland
- Research Program’s Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Katalin Sterbova
- Child Neurology Department, 2nd Faculty of Medicine, Charles University, Motol Hospital, Prague, Czech Republic.
| | - Dana C. Craiu
- Pediatric Neurology Clinic II, Department of Neurology, Pediatric Neurology, Psychiatry, and Neurosurgery, “Carol Davila” University of Medicine, Sector 4, Bucharest, Romania.
- Pediatric Neurology Clinic, “Professor Doctor Alexandru Obregia” Clinical Hospital, Sector 4, Bucharest, Romania.
| | | | - Christian M. Korff
- Child and Adolescent Department, Pediatric Neurology, University Hospitals, Geneva, Switzerland.
| | - Yvonne G. Weber
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
| | - Maja Steinlin
- Division of Neuropediatrics, University Children’s Hospital Inselspital, Bern, Switzerland.
| | - Sabina Gallati
- Division of Human Genetics, University Children’s Hospital Inselspital, Bern, Switzerland.
| | - Astrid Bertsche
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany.
| | - Matthias K. Bernhard
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany.
| | - Andreas Merkenschlager
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany.
| | - Wieland Kiess
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany.
| | | | - Michael Gonzalez
- Dr. JT MacDonald Department for Human Genetics, Hussman Institute for Human Genomics, University of Miami, Miami, USA
| | - Stephan Züchner
- Dr. JT MacDonald Department for Human Genetics, Hussman Institute for Human Genomics, University of Miami, Miami, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
- Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Arvid Suls
- Neurogenetics group, Department of Molecular Genetics, VIB, Antwerp, Belgium.
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
| | - Peter De Jonghe
- Neurogenetics group, Department of Molecular Genetics, VIB, Antwerp, Belgium.
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
- Department of Neurology, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium
| | - Ingo Helbig
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Germany.
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, USA
| | - Saskia Biskup
- Center for Genomics and Transcriptomics (CeGaT) GmbH, Tübingen, Germany.
| | - Markus Wolff
- Department of Neuropediatrics, University of Tübingen, Tübingen, Germany.
| | - Snezana Maljevic
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
| | - Rebecca Schüle
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
- German Research Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Division of Neuropediatrics, University Children’s Hospital Inselspital, Bern, Switzerland.
| | - Sanjay M. Sisodiya
- Department of Clinical and Experimental Epilepsy, University College London Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Epilepsy Society, Chalfont-St-Peter, Bucks, SL9 0RJ, UK.
| | - Sarah Weckhuysen
- Neurogenetics group, Department of Molecular Genetics, VIB, Antwerp, Belgium.
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
| | - Johannes R. Lemke
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany.
- Division of Human Genetics, University Children’s Hospital Inselspital, Bern, Switzerland.
- Department of Diagnostics, Institute of Human Genetics, University of Leipzig, Leipzig, Germany.
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Hartmann C, von Spiczak S, Suls A, Weckhuysen S, Buyse G, Vilain C, Van Bogaert P, De Jonghe P, Cook J, Muhle H, Stephani U, Helbig I, Mefford HC. Investigating the genetic basis of fever-associated syndromic epilepsies using copy number variation analysis. Epilepsia 2015; 56:e26-32. [PMID: 25690317 DOI: 10.1111/epi.12920] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2014] [Indexed: 12/23/2022]
Abstract
Fever-associated syndromic epilepsies ranging from febrile seizures plus (FS+) to Dravet syndrome have a significant genetic component. However, apart from SCN1A mutations in >80% of patients with Dravet syndrome, the genetic underpinnings of these epilepsies remain largely unknown. Therefore, we performed a genome-wide screening for copy number variations (CNVs) in 36 patients with SCN1A-negative fever-associated syndromic epilepsies. Phenotypes included Dravet syndrome (n = 23; 64%), genetic epilepsy with febrile seizures plus (GEFS+) and febrile seizures plus (FS+) (n = 11; 31%) and unclassified fever-associated epilepsies (n = 2; 6%). Array comparative genomic hybridization (CGH) was performed using Agilent 4 × 180K arrays. We identified 13 rare CNVs in 8 (22%) of 36 individuals. These included known pathogenic CNVs in 4 (11%) of 36 patients: a 1q21.1 duplication in a proband with Dravet syndrome, a 14q23.3 deletion in a proband with FS+, and two deletions at 16p11.2 and 1q44 in two individuals with fever-associated epilepsy with concomitant autism and/or intellectual disability. In addition, a 3q13.11 duplication in a patient with FS+ and two de novo duplications at 7p14.2 and 18q12.2 in a patient with atypical Dravet syndrome were classified as likely pathogenic. Six CNVs were of unknown significance. The identified genomic aberrations overlap with known neurodevelopmental disorders, suggesting that fever-associated epilepsy syndromes may be a recurrent clinical presentation of known microdeletion syndromes.
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Affiliation(s)
- Corinna Hartmann
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian-Albrechts-University, Kiel, Germany
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Hardies K, May P, Djémié T, Tarta-Arsene O, Deconinck T, Craiu D, Helbig I, Suls A, Balling R, Weckhuysen S, De Jonghe P, Hirst J. Recessive loss-of-function mutations in AP4S1 cause mild fever-sensitive seizures, developmental delay and spastic paraplegia through loss of AP-4 complex assembly. Hum Mol Genet 2014; 24:2218-27. [PMID: 25552650 DOI: 10.1093/hmg/ddu740] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report two siblings with infantile onset seizures, severe developmental delay and spastic paraplegia, in whom whole-genome sequencing revealed compound heterozygous mutations in the AP4S1 gene, encoding the σ subunit of the adaptor protein complex 4 (AP-4). The effect of the predicted loss-of-function variants (p.Gln46Profs*9 and p.Arg97*) was further investigated in a patient's fibroblast cell line. We show that the premature stop mutations in AP4S1 result in a reduction of all AP-4 subunits and loss of AP-4 complex assembly. Recruitment of the AP-4 accessory protein tepsin, to the membrane was also abolished. In retrospect, the clinical phenotype in the family is consistent with previous reports of the AP-4 deficiency syndrome. Our study reports the second family with mutations in AP4S1 and describes the first two patients with loss of AP4S1 and seizures. We further discuss seizure phenotypes in reported patients, highlighting that seizures are part of the clinical manifestation of the AP-4 deficiency syndrome. We also hypothesize that endosomal trafficking is a common theme between heritable spastic paraplegia and some inherited epilepsies.
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Affiliation(s)
- Katia Hardies
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium, Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg, Institute for Systems Biology, Seattle, USA
| | - Tania Djémié
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium, Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Oana Tarta-Arsene
- Pediatric Neurology Clinic, Al Obregia Hospital, Bucharest, Romania, Department of Neurology, Pediatric Neurology, Psychiatry, Child and Adolescent Psychiatry, and Neurosurgery, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Tine Deconinck
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium, Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Dana Craiu
- Pediatric Neurology Clinic, Al Obregia Hospital, Bucharest, Romania, Department of Neurology, Pediatric Neurology, Psychiatry, Child and Adolescent Psychiatry, and Neurosurgery, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | | | - Ingo Helbig
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian Albrechts University, Kiel, Germany, Division of Neurology, The Children's Hospital of Philadelphia, Philadephia, USA
| | - Arvid Suls
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium, Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Rudy Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sarah Weckhuysen
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium, Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Peter De Jonghe
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium, Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium, Division of Neurology, Antwerp University Hospital, Antwerp, Belgium and
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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31
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Schubert J, Siekierska A, Langlois M, May P, Huneau C, Becker F, Muhle H, Suls A, Lemke JR, de Kovel CGF, Thiele H, Konrad K, Kawalia A, Toliat MR, Sander T, Rüschendorf F, Caliebe A, Nagel I, Kohl B, Kecskés A, Jacmin M, Hardies K, Weckhuysen S, Riesch E, Dorn T, Brilstra EH, Baulac S, Møller RS, Hjalgrim H, Koeleman BPC, Jurkat-Rott K, Lehmann-Horn F, Roach JC, Glusman G, Hood L, Galas DJ, Martin B, de Witte PAM, Biskup S, De Jonghe P, Helbig I, Balling R, Nürnberg P, Crawford AD, Esguerra CV, Weber YG, Lerche H. Mutations in STX1B, encoding a presynaptic protein, cause fever-associated epilepsy syndromes. Nat Genet 2014; 46:1327-32. [DOI: 10.1038/ng.3130] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 10/06/2014] [Indexed: 01/12/2023]
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32
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Picard F, Makrythanasis P, Navarro V, Ishida S, de Bellescize J, Ville D, Weckhuysen S, Fosselle E, Suls A, De Jonghe P, Vasselon Raina M, Lesca G, Depienne C, An-Gourfinkel I, Vlaicu M, Baulac M, Mundwiller E, Couarch P, Combi R, Ferini-Strambi L, Gambardella A, Antonarakis SE, Leguern E, Steinlein O, Baulac S. DEPDC5 mutations in families presenting as autosomal dominant nocturnal frontal lobe epilepsy. Neurology 2014; 82:2101-6. [DOI: 10.1212/wnl.0000000000000488] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Carvill GL, Weckhuysen S, McMahon JM, Hartmann C, Møller RS, Hjalgrim H, Cook J, Geraghty E, O'Roak BJ, Petrou S, Clarke A, Gill D, Sadleir LG, Muhle H, von Spiczak S, Nikanorova M, Hodgson BL, Gazina EV, Suls A, Shendure J, Dibbens LM, De Jonghe P, Helbig I, Berkovic SF, Scheffer IE, Mefford HC. GABRA1 and STXBP1: novel genetic causes of Dravet syndrome. Neurology 2014; 82:1245-53. [PMID: 24623842 PMCID: PMC4001207 DOI: 10.1212/wnl.0000000000000291] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/02/2014] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVE To determine the genes underlying Dravet syndrome in patients who do not have an SCN1A mutation on routine testing. METHODS We performed whole-exome sequencing in 13 SCN1A-negative patients with Dravet syndrome and targeted resequencing in 67 additional patients to identify new genes for this disorder. RESULTS We detected disease-causing mutations in 2 novel genes for Dravet syndrome, with mutations in GABRA1 in 4 cases and STXBP1 in 3. Furthermore, we identified 3 patients with previously undetected SCN1A mutations, suggesting that SCN1A mutations occur in even more than the currently accepted ∼ 75% of cases. CONCLUSIONS We show that GABRA1 and STXBP1 make a significant contribution to Dravet syndrome after SCN1A abnormalities have been excluded. Our results have important implications for diagnostic testing, clinical management, and genetic counseling of patients with this devastating disorder and their families.
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Affiliation(s)
- Gemma L Carvill
- From the Division of Genetic Medicine, Department of Pediatrics (G.L.C., C.H., J.C., E.G., H.C.M.), and the Department of Genome Sciences (J.S.), University of Washington, Seattle; Neurogenetics Group (S.W.), Department of Molecular Genetics, VIB, Antwerp; Laboratory of Neurogenetics (S.W., A.S., P.D.J.), Institute Born-Bunge, University of Antwerp, Belgium; Epilepsy Centre Kempenhaeghe (S.W.), Oosterhout, the Netherlands; Epilepsy Research Centre (J.M.M., S.F.B., I.E.S.), Department of Medicine, University of Melbourne, Austin Health, Australia; Department of Neuropediatrics (C.H., H.M., S.v.S., I.H.), University Medical Center, Schleswig-Holstein, Christian-Albrechts University, Kiel, Germany; Danish Epilepsy Centre (R.S.M., H.H., M.N.), Dianalund; Institute for Regional Health Services (H.H., M.N.), University of Southern Denmark, Odense, Denmark; Department of Molecular and Medical Genetics (B.J.O.), Oregon Health and Science University, Portland; Florey Institute (S.P., A.C., E.V.G., I.E.S.), Victoria; TY Nelson Department of Neurology (D.G.), The Children's Hospital at Westmead, Sydney, NSW, Australia; Department of Paediatrics (L.G.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Epilepsy Research Program (B.L.H., L.M.D.), School of Pharmacy and Medical Sciences, University of South Australia, Adelaide; Division of Neurology (P.D.J.), Antwerp University Hospital, Belgium; and the Department of Paediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Australia
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Djémié T, Weckhuysen S, Holmgren P, Hardies K, Van Dyck T, Hendrickx R, Schoonjans AS, Van Paesschen W, Jansen AC, De Meirleir L, Selim LAM, Girgis MY, Buyse G, Lagae L, Smets K, Smouts I, Claeys KG, Van den Bergh V, Grisar T, Blatt I, Shorer Z, Roelens F, Afawi Z, Helbig I, Ceulemans B, De Jonghe P, Suls A. PRRT2 mutations: exploring the phenotypical boundaries. J Neurol Neurosurg Psychiatry 2014; 85:462-5. [PMID: 24101679 DOI: 10.1136/jnnp-2013-305122] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Mutations in the proline-rich transmembrane protein 2 (PRRT2) gene have been identified in patients with benign (familial) infantile convulsions (B(F)IC), infantile convulsions with choreoathetosis (ICCA) and paroxysmal dyskinesias (PDs). However it remains unknown whether PRRT2 mutations are causal in other epilepsy syndromes. After we discovered a PRRT2 mutation in a large family with ICCA containing one individual with febrile seizures (FS) and one individual with West syndrome, we analysed PRRT2 in a heterogeneous cohort of patients with different types of infantile epilepsy. METHODS We screened a cohort of 460 patients with B(F)IC or ICCA, fever related seizures or infantile epileptic encephalopathies. All patients were tested for point mutations using direct sequencing. RESULTS We identified heterozygous mutations in 16 individuals: 10 familial and 6 sporadic cases. All patients were diagnosed with B(F)IC, ICCA or PD. We were not able to detect mutations in any of the other epilepsy syndromes. Several mutation carriers had learning disabilities and/or impaired fine motor skills later in life. CONCLUSIONS PRRT2 mutations do not seem to be involved in the aetiology of FS or infantile epileptic encephalopathies. Therefore B(F)IC, ICCA and PD remain the core phenotypes associated with PRRT2 mutations. The presence of learning disabilities or neuropsychiatric problems in several mutation carriers calls for additional clinical studies addressing this developmental aspect in more detail.
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Affiliation(s)
- Tania Djémié
- Neurogenetics Group, Department of Molecular Genetics, VIB, , Antwerp, Belgium
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35
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Orhan G, Bock M, Schepers D, Ilina EI, Reichel SN, Löffler H, Jezutkovic N, Weckhuysen S, Mandelstam S, Suls A, Danker T, Guenther E, Scheffer IE, De Jonghe P, Lerche H, Maljevic S. Dominant-negative effects of KCNQ2 mutations are associated with epileptic encephalopathy. Ann Neurol 2014; 75:382-94. [PMID: 24318194 DOI: 10.1002/ana.24080] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 10/21/2013] [Accepted: 11/22/2013] [Indexed: 01/04/2023]
Abstract
OBJECTIVE Mutations in KCNQ2 and KCNQ3, encoding the voltage-gated potassium channels KV 7.2 and KV 7.3, are known to cause benign familial neonatal seizures mainly by haploinsufficiency. Here, we set out to determine the disease mechanism of 7 de novo missense KCNQ2 mutations that were recently described in patients with a severe epileptic encephalopathy including pharmacoresistant seizures and pronounced intellectual disability. METHODS Mutations were inserted into the KCNQ2 cDNA. Potassium currents were recorded using 2-microelectrode voltage clamping, and surface expression was analyzed by a biotinylation assay in cRNA-injected Xenopus laevis oocytes. RESULTS We observed a clear loss of function for all mutations. Strikingly, 5 of 7 mutations exhibited a drastic dominant-negative effect on wild-type KV 7.2 or KV 7.3 subunits, either by globally reducing current amplitudes (3 pore mutations) or by a depolarizing shift of the activation curve (2 voltage sensor mutations) decreasing potassium currents at the subthreshold level at which these channels are known to critically influence neuronal firing. One mutation significantly reduced surface expression. Application of retigabine, a recently marketed KV 7 channel opener, partially reversed these effects for the majority of analyzed mutations. INTERPRETATION The development of severe epilepsy and cognitive decline in children carrying 5 of the 7 studied KCNQ2 mutations can be related to a dominant-negative reduction of the resulting potassium current at subthreshold membrane potentials. Other factors such as genetic modifiers have to be postulated for the remaining 2 mutations. Retigabine or similar drugs may be used as a personalized therapy for this severe disease.
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Affiliation(s)
- Gökce Orhan
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
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36
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Lemke JR, Hendrickx R, Geider K, Laube B, Schwake M, Harvey RJ, James VM, Pepler A, Steiner I, Hörtnagel K, Neidhardt J, Ruf S, Wolff M, Bartholdi D, Caraballo R, Platzer K, Suls A, De Jonghe P, Biskup S, Weckhuysen S. GRIN2B mutations in West syndrome and intellectual disability with focal epilepsy. Ann Neurol 2014; 75:147-54. [PMID: 24272827 PMCID: PMC4223934 DOI: 10.1002/ana.24073] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 11/10/2013] [Accepted: 11/18/2013] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To identify novel epilepsy genes using a panel approach and describe the functional consequences of mutations. METHODS Using a panel approach, we screened 357 patients comprising a vast spectrum of epileptic disorders for defects in genes known to contribute to epilepsy and/or intellectual disability (ID). After detection of mutations in a novel epilepsy gene, we investigated functional effects in Xenopus laevis oocytes and screened a follow-up cohort. RESULTS We revealed de novo mutations in GRIN2B encoding the NR2B subunit of the N-methyl-D-aspartate (NMDA) receptor in 2 individuals with West syndrome and severe developmental delay as well as 1 individual with ID and focal epilepsy. The patient with ID and focal epilepsy had a missense mutation in the extracellular glutamate-binding domain (p.Arg540His), whereas both West syndrome patients carried missense mutations within the NR2B ion channel-forming re-entrant loop (p.Asn615Ile, p.Val618Gly). Subsequent screening of 47 patients with unexplained infantile spasms did not reveal additional de novo mutations, but detected a carrier of a novel inherited GRIN2B splice site variant in close proximity (c.2011-5_2011-4delTC). Mutations p.Asn615Ile and p.Val618Gly cause a significantly reduced Mg(2+) block and higher Ca(2+) permeability, leading to a dramatically increased Ca(2+) influx, whereas p.Arg540His caused less severe disturbance of channel function, corresponding to the milder patient phenotype. INTERPRETATION We identified GRIN2B gain-of-function mutations as a cause of West syndrome with severe developmental delay as well as of ID with childhood onset focal epilepsy. Severely disturbed channel function corresponded to severe clinical phenotypes, underlining the important role of facilitated NMDA receptor signaling in epileptogenesis.
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MESH Headings
- Animals
- Child
- Child, Preschool
- Crystallography, X-Ray
- Epilepsies, Partial/complications
- Epilepsies, Partial/diagnosis
- Epilepsies, Partial/genetics
- Female
- Humans
- Infant, Newborn
- Intellectual Disability/complications
- Intellectual Disability/diagnosis
- Intellectual Disability/genetics
- Mutation/genetics
- Rats
- Receptors, N-Methyl-D-Aspartate/chemistry
- Receptors, N-Methyl-D-Aspartate/genetics
- Spasms, Infantile/complications
- Spasms, Infantile/diagnosis
- Spasms, Infantile/genetics
- Xenopus laevis
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Affiliation(s)
- Johannes R Lemke
- Division of Human Genetics, University Children’s
Hospital InselspitalBern, Switzerland
- Partners of EuroEPINOMICS, RES
consortium
| | - Rik Hendrickx
- Neurogenetics Group, Department of Molecular Genetics,
Vlaams Institute of BiotechnologyAntwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge,
University of AntwerpAntwerp, Belgium
| | - Kirsten Geider
- Department of Neurophysiology and Neurosensory Systems,
Technical University DarmstadtDarmstadt, Germany
| | - Bodo Laube
- Department of Neurophysiology and Neurosensory Systems,
Technical University DarmstadtDarmstadt, Germany
| | - Michael Schwake
- Biochemistry III, Faculty of Chemistry, University of
BielefeldBielefeld, Germany
| | - Robert J Harvey
- Department of Pharmacology, University College London
School of PharmacyLondon, United Kingdom
| | - Victoria M James
- Department of Pharmacology, University College London
School of PharmacyLondon, United Kingdom
| | - Alex Pepler
- Department of Pharmacology, University College London
School of PharmacyLondon, United Kingdom
- CeGaT GmbHTübingen, Germany
| | | | | | - John Neidhardt
- Institute of Medical Molecular Genetics, University of
ZurichSwitzerland
| | - Susanne Ruf
- Department of Neuropediatrics, University of
TübingenTübingen, Germany
| | - Markus Wolff
- Department of Neuropediatrics, University of
TübingenTübingen, Germany
| | - Deborah Bartholdi
- Institute of Clinical GeneticsKlinikum Stuttgart, Stuttgart, Germany
| | - Roberto Caraballo
- Department of Neurology, Juan P. Garrahan Pediatric
HospitalBuenos Aires, Argentina
| | - Konrad Platzer
- Department of Human Genetics, University of
LübeckLübeck, Germany
| | - Arvid Suls
- Partners of EuroEPINOMICS, RES
consortium
- Neurogenetics Group, Department of Molecular Genetics,
Vlaams Institute of BiotechnologyAntwerp, Belgium
| | - Peter De Jonghe
- Partners of EuroEPINOMICS, RES
consortium
- Neurogenetics Group, Department of Molecular Genetics,
Vlaams Institute of BiotechnologyAntwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge,
University of AntwerpAntwerp, Belgium
- Department of Neurology, Antwerp University
HospitalAntwerp, Belgium
| | - Saskia Biskup
- CeGaT GmbHTübingen, Germany
- Institute of Clinical GeneticsKlinikum Stuttgart, Stuttgart, Germany
- Hertie Institute of Clinical Brain Research and German
Center for Neurodegenerative Diseases, University of TübingenTübingen, Germany
| | - Sarah Weckhuysen
- Partners of EuroEPINOMICS, RES
consortium
- Neurogenetics Group, Department of Molecular Genetics,
Vlaams Institute of BiotechnologyAntwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge,
University of AntwerpAntwerp, Belgium
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Suls A, Jaehn JA, Kecskés A, Weber Y, Weckhuysen S, Craiu DC, Siekierska A, Djémié T, Afrikanova T, Gormley P, von Spiczak S, Kluger G, Iliescu CM, Talvik T, Talvik I, Meral C, Caglayan HS, Giraldez BG, Serratosa J, Lemke JR, Hoffman-Zacharska D, Szczepanik E, Barisic N, Komarek V, Hjalgrim H, Møller RS, Linnankivi T, Dimova P, Striano P, Zara F, Marini C, Guerrini R, Depienne C, Baulac S, Kuhlenbäumer G, Crawford AD, Lehesjoki AE, de Witte PAM, Palotie A, Lerche H, Esguerra CV, De Jonghe P, Helbig I. De novo loss-of-function mutations in CHD2 cause a fever-sensitive myoclonic epileptic encephalopathy sharing features with Dravet syndrome. Am J Hum Genet 2013; 93:967-75. [PMID: 24207121 DOI: 10.1016/j.ajhg.2013.09.017] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 05/28/2013] [Accepted: 09/30/2013] [Indexed: 11/18/2022] Open
Abstract
Dravet syndrome is a severe epilepsy syndrome characterized by infantile onset of therapy-resistant, fever-sensitive seizures followed by cognitive decline. Mutations in SCN1A explain about 75% of cases with Dravet syndrome; 90% of these mutations arise de novo. We studied a cohort of nine Dravet-syndrome-affected individuals without an SCN1A mutation (these included some atypical cases with onset at up to 2 years of age) by using whole-exome sequencing in proband-parent trios. In two individuals, we identified a de novo loss-of-function mutation in CHD2 (encoding chromodomain helicase DNA binding protein 2). A third CHD2 mutation was identified in an epileptic proband of a second (stage 2) cohort. All three individuals with a CHD2 mutation had intellectual disability and fever-sensitive generalized seizures, as well as prominent myoclonic seizures starting in the second year of life or later. To explore the functional relevance of CHD2 haploinsufficiency in an in vivo model system, we knocked down chd2 in zebrafish by using targeted morpholino antisense oligomers. chd2-knockdown larvae exhibited altered locomotor activity, and the epileptic nature of this seizure-like behavior was confirmed by field-potential recordings that revealed epileptiform discharges similar to seizures in affected persons. Both altered locomotor activity and epileptiform discharges were absent in appropriate control larvae. Our study provides evidence that de novo loss-of-function mutations in CHD2 are a cause of epileptic encephalopathy with generalized seizures.
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Affiliation(s)
- Arvid Suls
- Neurogenetics group, Department of Molecular Genetics, VIB, 2610 Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, 2610 Antwerp, Belgium
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38
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Weckhuysen S, Ivanovic V, Hendrickx R, Van Coster R, Hjalgrim H, Møller RS, Grønborg S, Schoonjans AS, Ceulemans B, Heavin SB, Eltze C, Horvath R, Casara G, Pisano T, Giordano L, Rostasy K, Haberlandt E, Albrecht B, Bevot A, Benkel I, Syrbe S, Sheidley B, Guerrini R, Poduri A, Lemke JR, Mandelstam S, Scheffer I, Angriman M, Striano P, Marini C, Suls A, De Jonghe P. Extending the KCNQ2 encephalopathy spectrum: clinical and neuroimaging findings in 17 patients. Neurology 2013; 81:1697-703. [PMID: 24107868 DOI: 10.1212/01.wnl.0000435296.72400.a1] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES To determine the frequency of KCNQ2 mutations in patients with neonatal epileptic encephalopathy (NEE), and to expand the phenotypic spectrum of KCNQ2 epileptic encephalopathy. METHODS Eighty-four patients with unexplained NEE were screened for KCNQ2 mutations using classic Sanger sequencing. Clinical data of 6 additional patients with KCNQ2 mutations detected by gene panel were collected. Detailed phenotyping was performed with particular attention to seizure frequency, cognitive outcome, and video-EEG. RESULTS In the cohort, we identified 9 different heterozygous de novo KCNQ2 missense mutations in 11 of 84 patients (13%). Two of 6 missense mutations detected by gene panel were recurrent and present in patients of the cohort. Seizures at onset typically consisted of tonic posturing often associated with focal clonic jerking, and were accompanied by apnea with desaturation. One patient diagnosed by gene panel had seizure onset at the age of 5 months. Based on seizure frequency at onset and cognitive outcome, we delineated 3 clinical subgroups, expanding the spectrum of KCNQ2 encephalopathy to patients with moderate intellectual disability and/or infrequent seizures at onset. Recurrent mutations lead to relatively homogenous phenotypes. One patient responded favorably to retigabine; 5 patients had a good response to carbamazepine. In 6 patients, seizures with bradycardia were recorded. One patient died of probable sudden unexpected death in epilepsy. CONCLUSION KCNQ2 mutations cause approximately 13% of unexplained NEE. Patients present with a wide spectrum of severity and, although rare, infantile epilepsy onset is possible.
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Affiliation(s)
- Sarah Weckhuysen
- From the Neurogenetics Group (S.W., R.H., A.S., P.D.J.), Department of Molecular Genetics, VIB, Antwerp; Laboratory of Neurogenetics (S.W., R.H., A.S., P.D.J.), Institute Born-Bunge, University of Antwerp, Belgium; Epilepsy Centre Kempenhaeghe (S.W.), Oosterhout, the Netherlands; Department of Paediatrics (V.I.), University Hospital Centre Zagreb, Croatia; Division of Pediatric Neurology and Metabolism (R.V.C.), Department of Pediatrics, University Hospital Ghent, Belgium; Danish Epilepsy Centre (H.H., R.S.M.), Dianalund; Institute for Regional Health Research (H.H.), University of Southern Denmark, Odense; Department of Child Neurology (S.G.), Juliane Marie Center, Rigshospital, Copenhagen, Denmark; Pediatric Neurology (A.-S.S., B.C.), Department of Neurology (A.-S.S., B.C., P.D.J.), Antwerp University Hospital, Antwerp University, Antwerp, Belgium; Epilepsy Research Centre (S.B.H., S.M., I.S.), Department of Medicine, University of Melbourne, Austin Health, Australia; Great Ormond Street Hospital (C.E.), London; Institute of Genetic Medicine (R.H.), Newcastle University, UK; Child Neurology and Neurorehabilitation Unit (G.C., M.A.), Department of Pediatrics, Central Hospital of Bolzano; Neurology Unit and laboratories (T.P., R.G., C.M.), A. Meyer Children's Hospital, Florence; Child Neuropsychiatry Unit (L.G.), Spedali Civili, Brescia, Italy; Pädiatrie I (K.R., E.H.), Division of Pediatric Neurology, University Hospital Innsbruck, Austria; University Hospital Essen (B.A.), University Duisburg-Essen; Department of Paediatric Neurology and Developmental Medicine (A.B.), University Children's Hospital Tübingen, Eberhard Karls University of Tübingen; Center for Child Neurology (I.B.), Sana Krankenhaus Gerresheim, Düsseldorf; Department of Neuropediatrics (S.S.), Hospital for Children and Adolescents, University of Leipzig, Germany; Department of Neurology (B.S., A.P.), Boston Children's Hospital, Harvard School of Medicine; Department of Biology (B.S.), Brandeis U
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Hardies K, Weckhuysen S, Peeters E, Holmgren P, Van Esch H, De Jonghe P, Van Paesschen W, Suls A. Duplications of 17q12 can cause familial fever-related epilepsy syndromes. Neurology 2013; 81:1434-40. [PMID: 24049133 DOI: 10.1212/wnl.0b013e3182a84163] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES After we identified a 17q12 duplication cosegregating in a 4-generation family with genetic or generalized epilepsy with febrile seizures plus (GEFS+), we aimed to determine the frequency of 17q12 genomic rearrangements in GEFS+ and a wide spectrum of other epilepsy phenotypes. We furthermore describe seizure prevalence in previously reported patients with a 17q12 duplication or deletion. METHODS We analyzed 433 patients with a broad range of epilepsy phenotypes. The 180k Cytosure ISCA v2 array was used for copy number variation screening in the index patient. Segregation analysis and follow-up studies were performed with the multiplex amplicon quantification technique. RESULTS We identified 2 families in which a 17q12 duplication segregated with febrile-sensitive epilepsy. In the follow-up study, the mutation rate in familial febrile seizures (FS) and GEFS+ phenotypes was 1/222. No 17q12 deletions were detected. Two of the 6 mutation carriers in the initial GEFS+ family had mild intellectual disability, whereas all family members of the second family were of normal intelligence. In the literature, 4 of 43 individuals with a 17q12 duplication and 4 of 55 with the reciprocal deletion were described to have had seizures. CONCLUSIONS Our study shows that 17q12 duplications are a rare cause of familial FS and GEFS+. Although some family members might have intellectual disability, seizures can be the sole clinical symptom. This is the first report on an inherited copy number variation in these self-limiting fever-sensitive epilepsy syndromes, potentially revealing a novel pathomechanism involved in familial FS and GEFS+.
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Affiliation(s)
- Katia Hardies
- From the Neurogenetics Group (K.H., S.W., P.H., P.D.J., A.S.), Department of Molecular Genetics, VIB, Antwerp; Laboratory of Neurogenetics (K.H., S.W., P.H., P.D.J., A.S.), Institute Born-Bunge, University of Antwerp; Department of Neurology (E.P., W.V.P.), University Hospital Gasthuisberg, Leuven; Center for Human Genetics (H.V.E.), University Hospitals Leuven, KU Leuven; and Division of Neurology (P.D.J.), Antwerp University Hospital, Antwerp, Belgium
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40
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Hitomi Y, Heinzen EL, Donatello S, Dahl HH, Damiano JA, McMahon JM, Berkovic SF, Scheffer IE, Legros B, Rai M, Weckhuysen S, Suls A, De Jonghe P, Pandolfo M, Goldstein DB, Van Bogaert P, Depondt C. Mutations in TNK2 in severe autosomal recessive infantile onset epilepsy. Ann Neurol 2013; 74:496-501. [PMID: 23686771 DOI: 10.1002/ana.23934] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 04/30/2013] [Accepted: 05/01/2013] [Indexed: 01/27/2023]
Abstract
We identified a small family with autosomal recessive, infantile onset epilepsy and intellectual disability. Exome sequencing identified a homozygous missense variant in the gene TNK2, encoding a brain-expressed tyrosine kinase. Sequencing of the coding region of TNK2 in 110 patients with a similar phenotype failed to detect further homozygote or compound heterozygote mutations. Pathogenicity of the variant is supported by the results of our functional studies, which demonstrated that the variant abolishes NEDD4 binding to TNK2, preventing its degradation after epidermal growth factor stimulation. Definitive proof of pathogenicity will require confirmation in unrelated patients.
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Affiliation(s)
- Yuki Hitomi
- Duke Center for Human Genome Variation, Duke University School of Medicine, Durham, NC
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Kim YO, Korff CM, Villaluz MMG, Suls A, Weckhuysen S, De Jonghe P, Scheffer IE. Head stereotypies in STXBP1 encephalopathy. Dev Med Child Neurol 2013; 55:769-72. [PMID: 23763664 DOI: 10.1111/dmcn.12197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/03/2013] [Indexed: 12/21/2022]
Abstract
STXBP1 encephalopathy is associated with a range of movement disorders. We observed head stereotypies in three patients. These comprised a slow (<1Hz), high-amplitude, horizontal, 'figure-of-eight' pattern, beginning at age 4-6 years and resulting in neck muscle hypertrophy, in two males; a faster (2-3Hz), side-to-side, 'no' movement, starting at the age of 9 years 6 months was observed in one female. Upper limb and truncal stereotypies and vocalization occurred intermittently with the head movements. The stereotypies increased with excitement but settled with concentration and sleep. Head and upper limb stereotypies are valuable clinical clues to the diagnosis of STXBP1 encephalopathy in patients with profound impairments.
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Affiliation(s)
- Young Ok Kim
- Department of Medicine, Epilepsy Research Centre, The University of Melbourne, Austin Health, Melbourne, Vic., Australia
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42
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Weckhuysen S, Holmgren P, Hendrickx R, Jansen AC, Hasaerts D, Dielman C, de Bellescize J, Boutry-Kryza N, Lesca G, Von Spiczak S, Helbig I, Gill D, Yendle S, Møller RS, Klitten L, Korff C, Godfraind C, Van Rijckevorsel K, De Jonghe P, Hjalgrim H, Scheffer IE, Suls A. Reduction of seizure frequency after epilepsy surgery in a patient with STXBP1 encephalopathy and clinical description of six novel mutation carriers. Epilepsia 2013; 54:e74-80. [PMID: 23409955 DOI: 10.1111/epi.12124] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2013] [Indexed: 01/10/2023]
Abstract
Mutations in STXBP1 have been identified in a subset of patients with early onset epileptic encephalopathy (EE), but the full phenotypic spectrum remains to be delineated. Therefore, we screened a cohort of 160 patients with an unexplained EE, including patients with early myoclonic encephalopathy (EME), Ohtahara syndrome, West syndrome, nonsyndromic EE with onset in the first year, and Lennox-Gastaut syndrome (LGS). We found six de novo mutations in six patients presenting as Ohtahara syndrome (2/6, 33%), West syndrome (1/65, 2%), and nonsyndromic early onset EE (3/64, 5%). No mutations were found in LGS or EME. Only two of four mutation carriers with neonatal seizures had Ohtahara syndrome. Epileptic spasms were present in five of six patients. One patient with normal magnetic resonance imaging (MRI) but focal seizures underwent epilepsy surgery and seizure frequency dropped drastically. Neuropathology showed a focal cortical dysplasia type 1a. There is a need for additional neuropathologic studies to explore whether STXBP1 mutations can lead to structural brain abnormalities.
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Affiliation(s)
- Sarah Weckhuysen
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
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43
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van Harssel JJT, Weckhuysen S, van Kempen MJA, Hardies K, Verbeek NE, de Kovel CGF, Gunning WB, van Daalen E, de Jonge MV, Jansen AC, Vermeulen RJ, Arts WFM, Verhelst H, Fogarasi A, de Rijk-van Andel JF, Kelemen A, Lindhout D, De Jonghe P, Koeleman BPC, Suls A, Brilstra EH. Clinical and genetic aspects of PCDH19-related epilepsy syndromes and the possible role of PCDH19 mutations in males with autism spectrum disorders. Neurogenetics 2013; 14:23-34. [PMID: 23334464 DOI: 10.1007/s10048-013-0353-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 01/02/2013] [Indexed: 11/26/2022]
Abstract
Epilepsy and mental retardation limited to females (EFMR), caused by PCDH19 mutations, has a variable clinical expression that needs further exploration. Onset of epilepsy may be provoked by fever and can resemble Dravet syndrome. Furthermore, transmitting males have no seizures, but are reported to have rigid personalities suggesting possible autism spectrum disorders (ASD). Therefore, this study aimed to determine the phenotypic spectrum associated with PCDH19 mutations in Dravet-like and EFMR female patients and in males with ASD. We screened 120 females suffering from Dravet-like epilepsy, 136 females with EFMR features and 20 males with ASD. Phenotypes and genotypes of the PCDH19 mutation carriers were compared with those of 125 females with EFMR reported in the literature. We report 15 additional patients with a PCDH19 mutation. Review of clinical data of all reported patients showed that the clinical picture of EFMR is heterogeneous, but epilepsy onset in infancy, fever sensitivity and occurrence of seizures in clusters are key features. Seizures remit in the majority of patients during teenage years. Intellectual disability and behavioural disturbances are common. Fifty percent of all mutations are missense mutations, located in the extracellular domains only. Truncating mutations have been identified in all protein domains. One ASD proband carried one missense mutation predicted to have a deleterious effect, suggesting that ASD in males can be associated with PCDH19 mutations.
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Affiliation(s)
- J J T van Harssel
- Department of Medical Genetics, University Medical Center Utrecht, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
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Muhle H, Helbig I, Frøslev TG, Suls A, von Spiczak S, Klitten LL, Dahl HA, Brusgaard K, Neubauer B, De Jonghe P, Tommerup N, Stephani U, Hjalgrim H, Møller RS. The role of SLC2A1 in early onset and childhood absence epilepsies. Epilepsy Res 2013; 105:229-33. [PMID: 23306390 DOI: 10.1016/j.eplepsyres.2012.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 11/24/2012] [Indexed: 11/15/2022]
Abstract
Early Onset Absence Epilepsy constitutes an Idiopathic Generalized Epilepsy with absences starting before the age of four years. Mutations in SLC2A1, encoding the glucose transporter, account for approximately 10% of EOAE cases. The role of SLC2A1 mutations in absence epilepsies with a later onset has not been assessed. We found two mutation carriers in 26 EOAE patients, while no mutations were found in 124 probands affected by CAE or JAE.
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Affiliation(s)
- Hiltrud Muhle
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian-Albrechts University, Kiel, Germany.
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Kim YO, Dibbens L, Marini C, Suls A, Chemaly N, Mei D, McMahon JM, Iona X, Berkovic SF, De Jonghe P, Guerrini R, Nabbout R, Scheffer IE. Do mutations in SCN1B cause Dravet syndrome? Epilepsy Res 2012. [PMID: 23182416 DOI: 10.1016/j.eplepsyres.2012.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 11/17/2022]
Abstract
A homozygous SCN1B mutation was previously identified in a patient with early onset epileptic encephalopathy (EOEE) described as Dravet syndrome (DS) despite a more severe phenotype than DS. We investigated whether SCN1B mutations are a common cause of DS. Patients with DS who did not have a SCN1A sequencing mutation or copy number variation were studied. Genomic DNA was Sanger sequenced for mutations in the 6 exons of SCN1B. In 54 patients with DS recruited from four centres, no SCN1B mutations were identified. SCN1B mutation is not a common cause of DS.
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Affiliation(s)
- Young Ok Kim
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Melbourne, Australia
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Guergueltcheva V, Peeters K, Baets J, Ceuterick-de Groote C, Martin J, Suls A, Vriendt E, Mihaylova V, Chamova T, Almeida-Souza L, Ydens E, Tzekov C, Hadjidekov G, Gospodinova M, Storm K, Reyniers E, Bichev S, van der Ven P, Furst D, Mitev V, Lochmuller H, Timmerman V, Tournev I, De Jonghe P, Jordanova A. G.O.7 Distal myopathy with upper limb predominance caused by filamin C haploinsufficiency. Neuromuscul Disord 2012. [DOI: 10.1016/j.nmd.2012.06.238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Manganelli F, Pisciotta C, Nolano M, Capponi S, Geroldi A, Topa A, Bellone E, Suls A, Mandich P, Santoro L. A novel autosomal dominant GDAP1 mutation in an Italian CMT2 family. J Peripher Nerv Syst 2012; 17:351-5. [DOI: 10.1111/j.1529-8027.2012.00414.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Steffens M, Leu C, Ruppert AK, Zara F, Striano P, Robbiano A, Capovilla G, Tinuper P, Gambardella A, Bianchi A, La Neve A, Crichiutti G, de Kovel CGF, Kasteleijn-Nolst Trenité D, de Haan GJ, Lindhout D, Gaus V, Schmitz B, Janz D, Weber YG, Becker F, Lerche H, Steinhoff BJ, Kleefuß-Lie AA, Kunz WS, Surges R, Elger CE, Muhle H, von Spiczak S, Ostertag P, Helbig I, Stephani U, Møller RS, Hjalgrim H, Dibbens LM, Bellows S, Oliver K, Mullen S, Scheffer IE, Berkovic SF, Everett KV, Gardiner MR, Marini C, Guerrini R, Lehesjoki AE, Siren A, Guipponi M, Malafosse A, Thomas P, Nabbout R, Baulac S, Leguern E, Guerrero R, Serratosa JM, Reif PS, Rosenow F, Mörzinger M, Feucht M, Zimprich F, Kapser C, Schankin CJ, Suls A, Smets K, De Jonghe P, Jordanova A, Caglayan H, Yapici Z, Yalcin DA, Baykan B, Bebek N, Ozbek U, Gieger C, Wichmann HE, Balschun T, Ellinghaus D, Franke A, Meesters C, Becker T, Wienker TF, Hempelmann A, Schulz H, Rüschendorf F, Leber M, Pauck SM, Trucks H, Toliat MR, Nürnberg P, Avanzini G, Koeleman BPC, Sander T. Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32. Hum Mol Genet 2012; 21:5359-72. [PMID: 22949513 DOI: 10.1093/hmg/dds373] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genetic generalized epilepsies (GGEs) have a lifetime prevalence of 0.3% and account for 20-30% of all epilepsies. Despite their high heritability of 80%, the genetic factors predisposing to GGEs remain elusive. To identify susceptibility variants shared across common GGE syndromes, we carried out a two-stage genome-wide association study (GWAS) including 3020 patients with GGEs and 3954 controls of European ancestry. To dissect out syndrome-related variants, we also explored two distinct GGE subgroups comprising 1434 patients with genetic absence epilepsies (GAEs) and 1134 patients with juvenile myoclonic epilepsy (JME). Joint Stage-1 and 2 analyses revealed genome-wide significant associations for GGEs at 2p16.1 (rs13026414, P(meta) = 2.5 × 10(-9), OR[T] = 0.81) and 17q21.32 (rs72823592, P(meta) = 9.3 × 10(-9), OR[A] = 0.77). The search for syndrome-related susceptibility alleles identified significant associations for GAEs at 2q22.3 (rs10496964, P(meta) = 9.1 × 10(-9), OR[T] = 0.68) and at 1q43 for JME (rs12059546, P(meta) = 4.1 × 10(-8), OR[G] = 1.42). Suggestive evidence for an association with GGEs was found in the region 2q24.3 (rs11890028, P(meta) = 4.0 × 10(-6)) nearby the SCN1A gene, which is currently the gene with the largest number of known epilepsy-related mutations. The associated regions harbor high-ranking candidate genes: CHRM3 at 1q43, VRK2 at 2p16.1, ZEB2 at 2q22.3, SCN1A at 2q24.3 and PNPO at 17q21.32. Further replication efforts are necessary to elucidate whether these positional candidate genes contribute to the heritability of the common GGE syndromes.
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Affiliation(s)
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- Institute for Medical Biometry, Informatic and Epidemiology, University of Bonn, Bonn, Germany
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Blumkin L, Suls A, Deconinck T, De Jonghe P, Linder I, Kivity S, Dabby R, Leshinsky-Silver E, Lev D, Lerman-Sagie T. Neonatal seizures associated with a severe neonatal myoclonus like dyskinesia due to a familial KCNQ2 gene mutation. Eur J Paediatr Neurol 2012; 16:356-60. [PMID: 22169383 DOI: 10.1016/j.ejpn.2011.11.004] [Citation(s) in RCA: 11] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 11/09/2011] [Accepted: 11/20/2011] [Indexed: 10/14/2022]
Abstract
UNLABELLED Mutations in the potassium channel gene KCNQ2, usually cause benign familial neonatal epilepsy. This is an autosomal dominant disorder characterized by clusters of seizures occurring in the first days of life. Most patients have normal psychomotor development and spontaneous remission of seizures by 12 months of age. Since Rett and Teubel reported the first family in 1964 and the identification of KCNQ2 gene mutations in this family by Zimprich et al. in 2006, phenotypic variability has been recognized including: later onset of seizures, myokymia in isolation or accompanied by seizures, neurological deficit and mental retardation. We report a mother and son with an atypical presentation of familial neonatal epilepsy. The mother has persistent epilepsy and subnormal intelligence. The son developed a severe dyskinesia clinically compatible with multifocal myoclonus in the neonatal period that only responded to carbamazepine. He also has ataxia and delayed psychomotor development. EMG revealed a spontaneous occurrence of repetitive normal motor potentials in different muscle groups. Genetic analysis identified a heterozygous missense mutation in KCNQ2 in the child and his mother. CONCLUSION KCNQ2 mutations can present with a neonatal onset multifocal myoclonus-like dyskinesia.
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Affiliation(s)
- Lubov Blumkin
- Pediatric Neurology Unit, Wolfson Medical Center, Holon, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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Weckhuysen S, Mandelstam S, Suls A, Audenaert D, Deconinck T, Claes LRF, Deprez L, Smets K, Hristova D, Yordanova I, Jordanova A, Ceulemans B, Jansen A, Hasaerts D, Roelens F, Lagae L, Yendle S, Stanley T, Heron SE, Mulley JC, Berkovic SF, Scheffer IE, de Jonghe P. KCNQ2 encephalopathy: emerging phenotype of a neonatal epileptic encephalopathy. Ann Neurol 2012; 71:15-25. [PMID: 22275249 DOI: 10.1002/ana.22644] [Citation(s) in RCA: 350] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVE KCNQ2 and KCNQ3 mutations are known to be responsible for benign familial neonatal seizures (BFNS). A few reports on patients with a KCNQ2 mutation with a more severe outcome exist, but a definite relationship has not been established. In this study we investigated whether KCNQ2/3 mutations are a frequent cause of epileptic encephalopathies with an early onset and whether a recognizable phenotype exists. METHODS We analyzed 80 patients with unexplained neonatal or early-infantile seizures and associated psychomotor retardation for KCNQ2 and KCNQ3 mutations. Clinical and imaging data were reviewed in detail. RESULTS We found 7 different heterozygous KCNQ2 mutations in 8 patients (8/80; 10%); 6 mutations arose de novo. One parent with a milder phenotype was mosaic for the mutation. No KCNQ3 mutations were found. The 8 patients had onset of intractable seizures in the first week of life with a prominent tonic component. Seizures generally resolved by age 3 years but the children had profound, or less frequently severe, intellectual disability with motor impairment. Electroencephalography (EEG) at onset showed a burst-suppression pattern or multifocal epileptiform activity. Early magnetic resonance imaging (MRI) of the brain showed characteristic hyperintensities in the basal ganglia and thalamus that later resolved. INTERPRETATION KCNQ2 mutations are found in a substantial proportion of patients with a neonatal epileptic encephalopathy with a potentially recognizable electroclinical and radiological phenotype. This suggests that KCNQ2 screening should be included in the diagnostic workup of refractory neonatal seizures of unknown origin.
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Affiliation(s)
- Sarah Weckhuysen
- Neurogenetics Group, VIB-Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
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