1
|
Rots D, Choufani S, Faundes V, Dingemans AJM, Joss S, Foulds N, Jones EA, Stewart S, Vasudevan P, Dabir T, Park SM, Jewell R, Brown N, Pais L, Jacquemont S, Jizi K, Ravenswaaij-Arts CMAV, Kroes HY, Stumpel CTRM, Ockeloen CW, Diets IJ, Nizon M, Vincent M, Cogné B, Besnard T, Kambouris M, Anderson E, Zackai EH, McDougall C, Donoghue S, O'Donnell-Luria A, Valivullah Z, O'Leary M, Srivastava S, Byers H, Leslie N, Mazzola S, Tiller GE, Vera M, Shen JJ, Boles R, Jain V, Brischoux-Boucher E, Kinning E, Simpson BN, Giltay JC, Harris J, Keren B, Guimier A, Marijon P, Vries BBAD, Motter CS, Mendelsohn BA, Coffino S, Gerkes EH, Afenjar A, Visconti P, Bacchelli E, Maestrini E, Delahaye-Duriez A, Gooch C, Hendriks Y, Adams H, Thauvin-Robinet C, Josephi-Taylor S, Bertoli M, Parker MJ, Rutten JW, Caluseriu O, Vernon HJ, Kaziyev J, Zhu J, Kremen J, Frazier Z, Osika H, Breault D, Nair S, Lewis SME, Ceroni F, Viggiano M, Posar A, Brittain H, Giovanna T, Giulia G, Quteineh L, Ha-Vinh Leuchter R, Zonneveld-Huijssoon E, Mellado C, Marey I, Coudert A, Aracena Alvarez MI, Kennis MGP, Bouman A, Roifman M, Amorós Rodríguez MI, Ortigoza-Escobar JD, Vernimmen V, Sinnema M, Pfundt R, Brunner HG, Vissers LELM, Kleefstra T, Weksberg R, Banka S. Pathogenic variants in KMT2C result in a neurodevelopmental disorder distinct from Kleefstra and Kabuki syndromes. Am J Hum Genet 2024; 111:1626-1642. [PMID: 39013459 PMCID: PMC11339626 DOI: 10.1016/j.ajhg.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/08/2024] [Accepted: 06/19/2024] [Indexed: 07/18/2024] Open
Abstract
Trithorax-related H3K4 methyltransferases, KMT2C and KMT2D, are critical epigenetic modifiers. Haploinsufficiency of KMT2C was only recently recognized as a cause of neurodevelopmental disorder (NDD), so the clinical and molecular spectrums of the KMT2C-related NDD (now designated as Kleefstra syndrome 2) are largely unknown. We ascertained 98 individuals with rare KMT2C variants, including 75 with protein-truncating variants (PTVs). Notably, ∼15% of KMT2C PTVs were inherited. Although the most highly expressed KMT2C transcript consists of only the last four exons, pathogenic PTVs were found in almost all the exons of this large gene. KMT2C variant interpretation can be challenging due to segmental duplications and clonal hematopoesis-induced artifacts. Using samples from 27 affected individuals, divided into discovery and validation cohorts, we generated a moderate strength disorder-specific KMT2C DNA methylation (DNAm) signature and demonstrate its utility in classifying non-truncating variants. Based on 81 individuals with pathogenic/likely pathogenic variants, we demonstrate that the KMT2C-related NDD is characterized by developmental delay, intellectual disability, behavioral and psychiatric problems, hypotonia, seizures, short stature, and other comorbidities. The facial module of PhenoScore, applied to photographs of 34 affected individuals, reveals that the KMT2C-related facial gestalt is significantly different from the general NDD population. Finally, using PhenoScore and DNAm signatures, we demonstrate that the KMT2C-related NDD is clinically and epigenetically distinct from Kleefstra and Kabuki syndromes. Overall, we define the clinical features, molecular spectrum, and DNAm signature of the KMT2C-related NDD and demonstrate they are distinct from Kleefstra and Kabuki syndromes highlighting the need to rename this condition.
Collapse
Affiliation(s)
- Dmitrijs Rots
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands; Genetics Laboratory, Children's Clinical University Hospital, Riga, Latvia
| | - Sanaa Choufani
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Victor Faundes
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de Los Alimentos (INTA), Universidad de Chile, Santiago, Chile; Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Shelagh Joss
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Glasgow, UK
| | - Nicola Foulds
- Wessex Clinical Genetics Services, University Hospital Southampton NHS Foundation Trust, Southampton SO16 5YA, UK
| | - Elizabeth A Jones
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Sarah Stewart
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Pradeep Vasudevan
- Department of Clinical Genetics, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester LE1 7RH, UK
| | - Tabib Dabir
- Northern Ireland Regional Genetics Centre, Belfast City Hospital, Belfast, UK
| | - Soo-Mi Park
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Rosalyn Jewell
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Natasha Brown
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, Royal Children's Hospital, The University of Melbourne, Melbourne, VIC, Australia
| | - Lynn Pais
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Khadijé Jizi
- Service de Génétique Médicale, CHU Ste-Justine, Montréal, QC, Canada
| | | | - Hester Y Kroes
- Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Constance T R M Stumpel
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands; GROW-School for Oncology and Reproduction, Maastricht, the Netherlands
| | - Charlotte W Ockeloen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Illja J Diets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mathilde Nizon
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Marie Vincent
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Benjamin Cogné
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Thomas Besnard
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Marios Kambouris
- Division of Genetics, Department of Pathology and Laboratory Medicine Department, Sidra Medicine, Doha, Qatar
| | - Emily Anderson
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Carey McDougall
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah Donoghue
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Anne O'Donnell-Luria
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zaheer Valivullah
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Melanie O'Leary
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | | | - Heather Byers
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Nancy Leslie
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sarah Mazzola
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, OH, USA
| | - George E Tiller
- Department of Genetics, Kaiser Permanente, Los Angeles, CA, USA
| | - Moin Vera
- Department of Genetics, Kaiser Permanente, Los Angeles, CA, USA
| | - Joseph J Shen
- Division of Genetics, Department of Pediatrics, UCSF Fresno, Fresno, CA, USA; Division of Genomic Medicine, Department of Pediatrics, University of California Davis, Sacramento, CA, USA
| | | | - Vani Jain
- All Wales Medical Genomics Service, Wales Genomic Health Centre, Cardiff Edge Business Park, Longwood Drive, Whitchurch, Cardiff CF14 7YU, UK
| | | | - Esther Kinning
- Clinical Genetics, Birmingham Women's and Children's, Birmingham, UK
| | - Brittany N Simpson
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Jacques C Giltay
- Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jacqueline Harris
- Kennedy Krieger Institute, Baltimore, MD, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Boris Keren
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Anne Guimier
- Service de Médecine Genomique des Maladies Rares, CRMR Anomalies Du Développement, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Pierre Marijon
- Laboratoire de Biologie Médicale Multisites Seqoia FMG2025, 75014 Paris, France
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | | | - Samantha Coffino
- Department of Pediatric Neurology, Kaiser Permanente, Oakland, CA, USA
| | - Erica H Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Afenjar
- APHP Sorbonne Université, Centre de Référence Malformations et Maladies Congénitales Du Cervelet et Déficiences Intellectuelles de Causes Rares, Département de Génétique et Embryologie Médicale, Hôpital Trousseau, Paris, France
| | - Paola Visconti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, UOSI Disturbi Dello Spettro Autistico, Bologna, Italy
| | - Elena Bacchelli
- Pharmacy and Biotechnology Department, University of Bologna, Bologna, Italy
| | - Elena Maestrini
- Pharmacy and Biotechnology Department, University of Bologna, Bologna, Italy
| | | | - Catherine Gooch
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Yvonne Hendriks
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hieab Adams
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Sarah Josephi-Taylor
- Department of Clinical Genetics, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Marta Bertoli
- Northern Genetics Service, Newcastle Upon Tyne NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Michael J Parker
- Department of Clinical Genetics, Sheffield Children's Hospital, Sheffield, UK
| | - Julie W Rutten
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, Edmonton, Canada
| | - Hilary J Vernon
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jonah Kaziyev
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jia Zhu
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jessica Kremen
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zoe Frazier
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hailey Osika
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - David Breault
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sreelata Nair
- Department of Fetal Medicine, Lifeline Super Specialty Hospital, Kerala, India
| | - Suzanne M E Lewis
- Department of Medical Genetics, BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Fabiola Ceroni
- Pharmacy and Biotechnology Department, University of Bologna, Bologna, Italy; Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Marta Viggiano
- Pharmacy and Biotechnology Department, University of Bologna, Bologna, Italy
| | - Annio Posar
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, UOSI Disturbi Dello Spettro Autistico, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Helen Brittain
- Department of Clinical Genetics, Birmingham Women's & Children's NHS Trust, Birmingham, UK
| | - Traficante Giovanna
- Medical Genetics Unit, Meyer Children's Hospital IRCCS Florence, Florence, Italy
| | - Gori Giulia
- Medical Genetics Unit,Meyer Children's Hospital IRCCS, Florence, Italy
| | - Lina Quteineh
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Russia Ha-Vinh Leuchter
- Division of Development and Growth, Department of Pediatrics, University of Geneva, Geneva, Switzerland
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cecilia Mellado
- Sección de Genética y Errores Congénitos Del Metabolismo, División de Pediatría, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | | | - Mariana Inés Aracena Alvarez
- Unit of Genetics and Metabolic Diseases, Division of Pediatrics, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Milou G P Kennis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Arianne Bouman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Maian Roifman
- The Prenatal Diagnosis and Medical Genetics Program, Division of Maternal Fetal Medicine, Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Canada
| | | | - Juan Dario Ortigoza-Escobar
- Movement Disorders Unit, Institut de Recerca Sant Joan de Déu, CIBERER-ISCIII and European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
| | - Vivian Vernimmen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands; GROW-School for Oncology and Reproduction, Maastricht, the Netherlands
| | - Margje Sinnema
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands; Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, the Netherlands.
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Division of Clinical and Metabolic Genetics, Department of Pediatrics, the Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada.
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| |
Collapse
|
2
|
Schmidt A, Danyel M, Grundmann K, Brunet T, Klinkhammer H, Hsieh TC, Engels H, Peters S, Knaus A, Moosa S, Averdunk L, Boschann F, Sczakiel HL, Schwartzmann S, Mensah MA, Pantel JT, Holtgrewe M, Bösch A, Weiß C, Weinhold N, Suter AA, Stoltenburg C, Neugebauer J, Kallinich T, Kaindl AM, Holzhauer S, Bührer C, Bufler P, Kornak U, Ott CE, Schülke M, Nguyen HHP, Hoffjan S, Grasemann C, Rothoeft T, Brinkmann F, Matar N, Sivalingam S, Perne C, Mangold E, Kreiss M, Cremer K, Betz RC, Mücke M, Grigull L, Klockgether T, Spier I, Heimbach A, Bender T, Brand F, Stieber C, Morawiec AM, Karakostas P, Schäfer VS, Bernsen S, Weydt P, Castro-Gomez S, Aziz A, Grobe-Einsler M, Kimmich O, Kobeleva X, Önder D, Lesmann H, Kumar S, Tacik P, Basin MA, Incardona P, Lee-Kirsch MA, Berner R, Schuetz C, Körholz J, Kretschmer T, Di Donato N, Schröck E, Heinen A, Reuner U, Hanßke AM, Kaiser FJ, Manka E, Munteanu M, Kuechler A, Cordula K, Hirtz R, Schlapakow E, Schlein C, Lisfeld J, Kubisch C, Herget T, Hempel M, Weiler-Normann C, Ullrich K, Schramm C, Rudolph C, Rillig F, Groffmann M, Muntau A, Tibelius A, Schwaibold EMC, Schaaf CP, Zawada M, Kaufmann L, Hinderhofer K, Okun PM, Kotzaeridou U, Hoffmann GF, Choukair D, Bettendorf M, Spielmann M, Ripke A, Pauly M, Münchau A, Lohmann K, Hüning I, Hanker B, Bäumer T, Herzog R, Hellenbroich Y, Westphal DS, Strom T, Kovacs R, Riedhammer KM, Mayerhanser K, Graf E, Brugger M, Hoefele J, Oexle K, Mirza-Schreiber N, Berutti R, Schatz U, Krenn M, Makowski C, Weigand H, Schröder S, Rohlfs M, Vill K, Hauck F, Borggraefe I, Müller-Felber W, Kurth I, Elbracht M, Knopp C, Begemann M, Kraft F, Lemke JR, Hentschel J, Platzer K, Strehlow V, Abou Jamra R, Kehrer M, Demidov G, Beck-Wödl S, Graessner H, Sturm M, Zeltner L, Schöls LJ, Magg J, Bevot A, Kehrer C, Kaiser N, Turro E, Horn D, Grüters-Kieslich A, Klein C, Mundlos S, Nöthen M, Riess O, Meitinger T, Krude H, Krawitz PM, Haack T, Ehmke N, Wagner M. Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings. Nat Genet 2024; 56:1644-1653. [PMID: 39039281 PMCID: PMC11319204 DOI: 10.1038/s41588-024-01836-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 06/18/2024] [Indexed: 07/24/2024]
Abstract
Individuals with ultrarare disorders pose a structural challenge for healthcare systems since expert clinical knowledge is required to establish diagnoses. In TRANSLATE NAMSE, a 3-year prospective study, we evaluated a novel diagnostic concept based on multidisciplinary expertise in Germany. Here we present the systematic investigation of the phenotypic and molecular genetic data of 1,577 patients who had undergone exome sequencing and were partially analyzed with next-generation phenotyping approaches. Molecular genetic diagnoses were established in 32% of the patients totaling 370 distinct molecular genetic causes, most with prevalence below 1:50,000. During the diagnostic process, 34 novel and 23 candidate genotype-phenotype associations were identified, mainly in individuals with neurodevelopmental disorders. Sequencing data of the subcohort that consented to computer-assisted analysis of their facial images with GestaltMatcher could be prioritized more efficiently compared with approaches based solely on clinical features and molecular scores. Our study demonstrates the synergy of using next-generation sequencing and phenotyping for diagnosing ultrarare diseases in routine healthcare and discovering novel etiologies by multidisciplinary teams.
Collapse
Affiliation(s)
- Axel Schmidt
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Magdalena Danyel
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Kathrin Grundmann
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
- Institut für Medizinische Biometrie, Informatik und Epidemiologie, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Shahida Moosa
- Institute for Medical Genetics, Stellenbosch University, Cape Town, South Africa
| | - Luisa Averdunk
- Department of Pediatrics, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Felix Boschann
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Henrike Lisa Sczakiel
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sarina Schwartzmann
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Atta Mensah
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jean Tori Pantel
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Manuel Holtgrewe
- Core Uni Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Annemarie Bösch
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia Weiß
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Natalie Weinhold
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Aude-Annick Suter
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Corinna Stoltenburg
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Julia Neugebauer
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Tillmann Kallinich
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Angela M Kaindl
- Department of Pediatric Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Center for Chronically Sick Children, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute of Cell and Neurobiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Susanne Holzhauer
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Bührer
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Philip Bufler
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Uwe Kornak
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Claus-Eric Ott
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Schülke
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Sabine Hoffjan
- Department of Human Genetics, Ruhr University Bochum, Bochum, Germany
| | - Corinna Grasemann
- Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany
| | - Tobias Rothoeft
- Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany
| | - Folke Brinkmann
- Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany
| | - Nora Matar
- Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany
| | - Sugirthan Sivalingam
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Claudia Perne
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Martina Kreiss
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Regina C Betz
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Martin Mücke
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Lorenz Grigull
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Thomas Klockgether
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Isabel Spier
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - André Heimbach
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Tim Bender
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Fabian Brand
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Christiane Stieber
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Alexandra Marzena Morawiec
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Pantelis Karakostas
- Clinic for Internal Medicine III, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Valentin S Schäfer
- Clinic for Internal Medicine III, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Sarah Bernsen
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Patrick Weydt
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Sergio Castro-Gomez
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Ahmad Aziz
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Marcus Grobe-Einsler
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Okka Kimmich
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Xenia Kobeleva
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Demet Önder
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Hellen Lesmann
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Sheetal Kumar
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Pawel Tacik
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Meghna Ahuja Basin
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Pietro Incardona
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Min Ae Lee-Kirsch
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Reinhard Berner
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Catharina Schuetz
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Julia Körholz
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Tanita Kretschmer
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Nataliya Di Donato
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Evelin Schröck
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - André Heinen
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Ulrike Reuner
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Neurology, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Amalia-Mihaela Hanßke
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Frank J Kaiser
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Eva Manka
- Department of Pediatrics II, University Hospital Essen, Essen, Germany
| | - Martin Munteanu
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Kiewert Cordula
- Department of Pediatrics II, University Hospital Essen, Essen, Germany
| | - Raphael Hirtz
- Department of Pediatrics II, University Hospital Essen, Essen, Germany
| | - Elena Schlapakow
- Department of Neurology, University Hospital Halle, Halle, Germany
| | - Christian Schlein
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Jasmin Lisfeld
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Christina Weiler-Normann
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Kurt Ullrich
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Schramm
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Cornelia Rudolph
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Franziska Rillig
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Maximilian Groffmann
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Ania Muntau
- Department of Pediatrics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | - Michal Zawada
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Lilian Kaufmann
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Pamela M Okun
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Urania Kotzaeridou
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Georg F Hoffmann
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniela Choukair
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Markus Bettendorf
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Malte Spielmann
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Annekatrin Ripke
- Center for Rare Diseases, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Martje Pauly
- Department of Neurology, University Hospital Schleswig-Holstein, Lübeck, Germany
- Institute for Neurogenetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Alexander Münchau
- Center for Rare Diseases, University Hospital Schleswig-Holstein, Lübeck, Germany
- Institute of Systems Motor Science, University of Lübeck, Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Irina Hüning
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Britta Hanker
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Tobias Bäumer
- Center for Rare Diseases, University Hospital Schleswig-Holstein, Lübeck, Germany
- Institute of Systems Motor Science, University of Lübeck, Lübeck, Germany
| | - Rebecca Herzog
- Center for Rare Diseases, University Hospital Schleswig-Holstein, Lübeck, Germany
- Department of Neurology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Yorck Hellenbroich
- Department of Human Genetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Dominik S Westphal
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Tim Strom
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Reka Kovacs
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
- Department of Nephrology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Katharina Mayerhanser
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Konrad Oexle
- Institute of Neurogenomics, Helmholtz Zentrum München, München, Germany
| | | | - Riccardo Berutti
- Institute of Neurogenomics, Helmholtz Zentrum München, München, Germany
| | - Ulrich Schatz
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Martin Krenn
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
- Department of Neurology, Medical University of Vienna, Wien, Austria
| | - Christine Makowski
- Department of Paediatrics, Adolescent Medicine and Neonatology, München, Germany
| | - Heike Weigand
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Sebastian Schröder
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Meino Rohlfs
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Katharina Vill
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Fabian Hauck
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Ingo Borggraefe
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | | | - Ingo Kurth
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Cordula Knopp
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Florian Kraft
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Vincent Strehlow
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Martin Kehrer
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - German Demidov
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Stefanie Beck-Wödl
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Holm Graessner
- Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Lena Zeltner
- Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Ludger J Schöls
- Department of Neurology, University of Tübingen, Tübingen, Germany
| | - Janine Magg
- Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Andrea Bevot
- Department of Pediatric Neurology and Developmental Medicine, University of Tübingen, Tübingen, Germany
| | - Christiane Kehrer
- Department of Pediatric Neurology and Developmental Medicine, University of Tübingen, Tübingen, Germany
| | - Nadja Kaiser
- Department of Pediatric Neurology and Developmental Medicine, University of Tübingen, Tübingen, Germany
| | - Ernest Turro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Denise Horn
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Christoph Klein
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Stefan Mundlos
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Nöthen
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Olaf Riess
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Heiko Krude
- Berlin Centre for Rare Diseases, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter M Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany.
| | - Tobias Haack
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Nadja Ehmke
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, München, Germany
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| |
Collapse
|
3
|
Thomsen M, Marth K, Loens S, Everding J, Junker J, Borngräber F, Ott F, Jesús S, Gelderblom M, Odorfer T, Kuhlenbäumer G, Kim HJ, Schaeffer E, Becktepe J, Kasten M, Brüggemann N, Pfister R, Kollewe K, Krauss JK, Lohmann E, Hinrichs F, Berg D, Jeon B, Busch H, Altenmüller E, Mir P, Kamm C, Volkmann J, Zittel S, Ferbert A, Zeuner KE, Rolfs A, Bauer P, Kühn AA, Bäumer T, Klein C, Lohmann K. Large-Scale Screening: Phenotypic and Mutational Spectrum in Isolated and Combined Dystonia Genes. Mov Disord 2024; 39:526-538. [PMID: 38214203 DOI: 10.1002/mds.29693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/16/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Pathogenic variants in several genes have been linked to genetic forms of isolated or combined dystonia. The phenotypic and genetic spectrum and the frequency of pathogenic variants in these genes have not yet been fully elucidated, neither in patients with dystonia nor with other, sometimes co-occurring movement disorders such as Parkinson's disease (PD). OBJECTIVES To screen >2000 patients with dystonia or PD for rare variants in known dystonia-causing genes. METHODS We screened 1207 dystonia patients from Germany (DysTract consortium), Spain, and South Korea, and 1036 PD patients from Germany for pathogenic variants using a next-generation sequencing gene panel. The impact on DNA methylation of KMT2B variants was evaluated by analyzing the gene's characteristic episignature. RESULTS We identified 171 carriers (109 with dystonia [9.0%]; 62 with PD [6.0%]) of 131 rare variants (minor allele frequency <0.005). A total of 52 patients (48 dystonia [4.0%]; four PD [0.4%, all with GCH1 variants]) carried 33 different (likely) pathogenic variants, of which 17 were not previously reported. Pathogenic biallelic variants in PRKRA were not found. Episignature analysis of 48 KMT2B variants revealed that only two of these should be considered (likely) pathogenic. CONCLUSION This study confirms pathogenic variants in GCH1, GNAL, KMT2B, SGCE, THAP1, and TOR1A as relevant causes in dystonia and expands the mutational spectrum. Of note, likely pathogenic variants only in GCH1 were also found among PD patients. For DYT-KMT2B, the recently described episignature served as a reliable readout to determine the functional effect of newly identified variants. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
Collapse
Affiliation(s)
- Mirja Thomsen
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Katrin Marth
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Department of Neurology, University Hospital Rostock, Rostock, Germany
| | - Sebastian Loens
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Institute of Systems Motor Science, CBBM, University of Lübeck, Lübeck, Germany
| | - Judith Everding
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Department of Neurology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johanna Junker
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Department of Neurology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | | | - Fabian Ott
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Silvia Jesús
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Mathias Gelderblom
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Odorfer
- Department of Neurology, University Hospital Würzburg, Würzburg, Germany
| | - Gregor Kuhlenbäumer
- Department of Neurology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Han-Joon Kim
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea
| | - Eva Schaeffer
- Department of Neurology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Jos Becktepe
- Department of Neurology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Meike Kasten
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Department of Psychiatry, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Department of Neurology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | | | - Katja Kollewe
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Joachim K Krauss
- Department of Neurosurgery, Hannover Medical School, Hannover, Germany
| | - Ebba Lohmann
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE)-Tübingen, Tübingen, Germany
| | - Frauke Hinrichs
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Daniela Berg
- Department of Neurology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Beomseok Jeon
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea
| | - Hauke Busch
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Eckart Altenmüller
- Institute of Music Physiology and Musicians' Medicine, Hanover University of Music, Drama and Media, Hanover, Germany
| | - Pablo Mir
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Christoph Kamm
- Department of Neurology, University Hospital Rostock, Rostock, Germany
| | - Jens Volkmann
- Department of Neurology, University Hospital Würzburg, Würzburg, Germany
| | - Simone Zittel
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Kirsten E Zeuner
- Department of Neurology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Arndt Rolfs
- Medical Faculty, University of Rostock, Rostock, Germany
- Agyany Pharmaceuticals, Jerusalem, Israel
| | | | - Andrea A Kühn
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Tobias Bäumer
- Institute of Systems Motor Science, CBBM, University of Lübeck, Lübeck, Germany
- Department of Neurology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
- Center of Rare Diseases, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| |
Collapse
|
4
|
Bouhamdani N, McConkey H, Leblanc A, Sadikovic B, Amor MB. Diagnostic utility of DNA methylation episignature analysis for early diagnosis of KMT2B-related disorders: case report. Front Genet 2024; 15:1346044. [PMID: 38425714 PMCID: PMC10902455 DOI: 10.3389/fgene.2024.1346044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
The lysine methyltransferase 2B (KMT2B) gene product is important for epigenetic modifications associated with active gene transcription in normal development and in maintaining proper neural function. Pathogenic variants in KMT2B have been associated with childhood-onset Dystonia-28 and Intellectual developmental disorder, autosomal dominant 68 (MRD 68) for cases of neurodevelopmental impairment without dystonia (DYT28; OMIM 617284 and MRD68; OMIM 619934, respectively). Since its first description in 2016, approximately one hundred KMT2B genetic variants have been reported with heterogeneous phenotypes, including atypical patterns of dystonia evolution and non-dystonic neurodevelopmental phenotypes. KMT2B-related disorders share many overlapping phenotypic characteristics with other neurodevelopmental disorders and delayed dystonia, that can appear later in childhood, often delaying clinical diagnosis. Furthermore, conventional genetic testing may not always provide actionable information (e.g., gene panel selection based on early clinical presentation or variants of uncertain significance), which prevents patients and families from obtaining early access to treatments and support. Herein, we describe the early diagnosis of KMT2B-related neurodevelopmental disorder by DNA methylation episignature testing in a 4-year-old patient without features of dystonia at diagnosis, which is reported to develop in more than 80% of KMT2B-related disorder cases. The proband, a 4-year-old female of Jewish-Israeli descent, presented with speech delay, microcephaly, poor weight gain, attention-deficit and hyperactivity disorder, dysmorphism, intellectual disabilities and joint hyperlaxity, but presented no signs of dystonia at initial evaluation. Episignature screening in this pre-symptomatic patient enabled accurate genetic diagnosis and timely and actionable intervention earlier in the natural history of Childhood-onset Dystonia-28.
Collapse
Affiliation(s)
- Nadia Bouhamdani
- Vitalité Health Network, Moncton, NB, Canada
- Faculty of medicine and health sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre de Formation Médicale du Nouveau-Brunswick, Université de Moncton, Moncton, NB, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry Western University, London, ON, Canada
| | - Amélie Leblanc
- Vitalité Health Network, Moncton, NB, Canada
- Faculty of medicine and health sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre de Formation Médicale du Nouveau-Brunswick, Université de Moncton, Moncton, NB, Canada
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry Western University, London, ON, Canada
| | - Mouna Ben Amor
- Vitalité Health Network, Moncton, NB, Canada
- Faculty of medicine and health sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre de Formation Médicale du Nouveau-Brunswick, Université de Moncton, Moncton, NB, Canada
| |
Collapse
|
5
|
Husson T, Lecoquierre F, Nicolas G, Richard AC, Afenjar A, Audebert-Bellanger S, Badens C, Bilan F, Bizaoui V, Boland A, Bonnet-Dupeyron MN, Brischoux-Boucher E, Bonnet C, Bournez M, Boute O, Brunelle P, Caumes R, Charles P, Chassaing N, Chatron N, Cogné B, Colin E, Cormier-Daire V, Dard R, Dauriat B, Delanne J, Deleuze JF, Demurger F, Denommé-Pichon AS, Depienne C, Dieux A, Dubourg C, Edery P, El Chehadeh S, Faivre L, Fergelot P, Fradin M, Garde A, Geneviève D, Gilbert-Dussardier B, Goizet C, Goldenberg A, Gouy E, Guerrot AM, Guimier A, Harzalla I, Héron D, Isidor B, Lacombe D, Le Guillou Horn X, Keren B, Kuechler A, Lacaze E, Lavillaureix A, Lehalle D, Lesca G, Lespinasse J, Levy J, Lyonnet S, Morel G, Jean-Marçais N, Marlin S, Marsili L, Mignot C, Nambot S, Nizon M, Olaso R, Pasquier L, Perrin L, Petit F, Pingault V, Piton A, Prieur F, Putoux A, Planes M, Odent S, Quélin C, Quemener-Redon S, Rama M, Rio M, Rossi M, Schaefer E, Rondeau S, Saugier-Veber P, Smol T, Sigaudy S, Touraine R, Mau-Them FT, Trimouille A, Van Gils J, Vanlerberghe C, Vantalon V, Vera G, Vincent M, Ziegler A, Guillin O, Campion D, Charbonnier C. Episignatures in practice: independent evaluation of published episignatures for the molecular diagnostics of ten neurodevelopmental disorders. Eur J Hum Genet 2024; 32:190-199. [PMID: 37872275 PMCID: PMC10853222 DOI: 10.1038/s41431-023-01474-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/29/2023] [Accepted: 09/28/2023] [Indexed: 10/25/2023] Open
Abstract
Variants of uncertain significance (VUS) are a significant issue for the molecular diagnosis of rare diseases. The publication of episignatures as effective biomarkers of certain Mendelian neurodevelopmental disorders has raised hopes to help classify VUS. However, prediction abilities of most published episignatures have not been independently investigated yet, which is a prerequisite for an informed and rigorous use in a diagnostic setting. We generated DNA methylation data from 101 carriers of (likely) pathogenic variants in ten different genes, 57 VUS carriers, and 25 healthy controls. Combining published episignature information and new validation data with a k-nearest-neighbour classifier within a leave-one-out scheme, we provide unbiased specificity and sensitivity estimates for each of the signatures. Our procedure reached 100% specificity, but the sensitivities unexpectedly spanned a very large spectrum. While ATRX, DNMT3A, KMT2D, and NSD1 signatures displayed a 100% sensitivity, CREBBP-RSTS and one of the CHD8 signatures reached <40% sensitivity on our dataset. Remaining Cornelia de Lange syndrome, KMT2A, KDM5C and CHD7 signatures reached 70-100% sensitivity at best with unstable performances, suffering from heterogeneous methylation profiles among cases and rare discordant samples. Our results call for cautiousness and demonstrate that episignatures do not perform equally well. Some signatures are ready for confident use in a diagnostic setting. Yet, it is imperative to characterise the actual validity perimeter and interpretation of each episignature with the help of larger validation sample sizes and in a broader set of episignatures.
Collapse
Affiliation(s)
- Thomas Husson
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Psychiatry, F-76000, Rouen, France
- Department of Research, Centre hospitalier du Rouvray, Sotteville-Lès-Rouen, France
| | - François Lecoquierre
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Anne-Claire Richard
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Alexandra Afenjar
- APHP. Sorbonne Université, Centre de Référence Malformations et maladies congénitales du cervelet et déficiences intellectuelles de causes rares, département de génétique et embryologie médicale, Hôpital Trousseau, F-75012, Paris, France
| | | | - Catherine Badens
- Aix Marseille Univ, INSERM, MMG, Marseille, France; APHM, service de génétique, Marseille, France
| | - Frédéric Bilan
- CHU de Poitiers, Service de Génétique Médicale and Université de Poitiers, INSERM U1084, LNEC, F- 86000, Poitiers, France
| | - Varoona Bizaoui
- Service de génétique et neurodéveloppement, Pôle de Santé Mentale Enfant et Adolescent, Centre Hospitalier de l'Estran, Pontorson, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | | | - Elise Brischoux-Boucher
- Centre de génétique humaine, CHU Besancon, Universite de Bourgogne Franche-Comte, Besancon, France
| | - Céline Bonnet
- Laboratoire de génétique médicale, CHRU Nancy, Nancy, France
- Université de Lorraine, INSERM UMR_S1256, NGERE, F-54000, Nancy, France
| | - Marie Bournez
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
| | - Odile Boute
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
| | - Perrine Brunelle
- Univ. Lille, CHU Lille, ULR 7364 - RADEME - Institut de Génétique Médicale, F-59000, Lille, France
| | - Roseline Caumes
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
| | - Perrine Charles
- Département de génétique clinique, centre de référence des déficiences intellectuelles de causes rares, GHU Pitié Salpêtrière, Paris, France
| | | | - Nicolas Chatron
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261 -INSERM U1315, Université de Lyon - Université Claude Bernard Lyon 1, Lyon, France
| | - Benjamin Cogné
- Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- CHU Nantes, Service de Génétique Médicale, Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
| | - Estelle Colin
- Service de Génétique Médicale, CHU Angers, Angers, France
| | - Valérie Cormier-Daire
- Service de médecine génomique des maladies rares, hôpital Necker Enfants Malades, Paris, France
- Université Paris Cité, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Rodolphe Dard
- Génétique médicale, CHI Poissy-Saint-Germain-en-Laye, 78300, Poissy, France
| | - Benjamin Dauriat
- Service de cytogénétique et génétique médicale, Hôpital Mère Enfant, CHU Limoges, Limoges, France
| | - Julian Delanne
- Centre de Génétique et Centre de référence « Déficiences intellectuelles de causes rares », FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | | | - Anne-Sophie Denommé-Pichon
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon, Bourgogne, Dijon, France
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Anne Dieux
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
| | - Christèle Dubourg
- Service de Génétique Moléculaire et Génomique, CHU Pontchaillou, Rennes, France
- Université de Rennes, IGDR (Institut de Génétique et Développement), CNRS UMR 6290, INSERM ERL 1305, Rennes, France
| | - Patrick Edery
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, Genetics of Neurodevelopment (GENDEV) Team, 69500, Bron, France
| | - Salima El Chehadeh
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Illkirch-Graffenstaden, France
- Laboratoire de Génétique Médicale, UMRS 1112, Institut de Génétique Médicale d'Alsace (IGMA), Université de Strasbourg et INSERM, Strasbourg, France
| | - Laurence Faivre
- Centre de Génétique et Centre de référence « Déficiences intellectuelles de causes rares », FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
| | - Patricia Fergelot
- Department of Medical Genetics, University Hospital of Bordeaux and INSERM U1211, University of Bordeaux, Bordeaux, France
| | - Mélanie Fradin
- Service de Génétique Clinique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Rennes, Rennes, France
| | - Aurore Garde
- Centre de Génétique et Centre de référence « Déficiences intellectuelles de causes rares », FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
| | - David Geneviève
- Université Montpellier, Inserm U1183, Montpellier, France
- Centre de référence anomalies du développement et syndromes malformatifs, Génétique Clinique, CHU Montpellier, Montpellier, France
| | | | - Cyril Goizet
- NRGEN team, Univ. Bordeaux, CNRS, INCIA, UMR 5287, EPHE, F-33000, Bordeaux, France
- Centre de Référence Maladies Rares Neurogénétique, Service de Génétique Médicale, Bordeaux University Hospital (CHU Bordeaux), Bordeaux, France
| | - Alice Goldenberg
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Evan Gouy
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Génétique et neurobiologie de C.elegans, MéLis (CNRS UMR 5284 -INSERM U1314), Institut NeuroMyogene, Université Claude Bernard Lyon 1, Lyon, France
| | - Anne-Marie Guerrot
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Anne Guimier
- Service de médecine génomique des maladies rares - GHU Necker- Enfants malades, Paris, France
| | - Inès Harzalla
- Service de Génétique, CHU Hôpital Nord, Saint Etienne, France
| | - Delphine Héron
- APHP.Sorbonne Université, Département de Génétique, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Bertrand Isidor
- Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- CHU Nantes, Service de Génétique Médicale, Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
| | - Didier Lacombe
- Department of Medical Genetics, University Hospital of Bordeaux and INSERM U1211, University of Bordeaux, Bordeaux, France
| | - Xavier Le Guillou Horn
- CHU de Poitiers, Service de Génétique Médicale, F - 86000, Poitiers, France
- Université de Poitiers, CNRS 7348, LabCom I3M-Dactim mis / LMA, F-86000, Poitiers, France
| | - Boris Keren
- Département de génétique médicale, Hôpital Pitié-Salpêtrière, AP-HP.Sorbonne Université, 75013, Paris, France
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Elodie Lacaze
- Le Havre Hospital, Department of Medical Genetics, F 76600, Le Havre, France
| | - Alinoë Lavillaureix
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du développement, FHU GenOMedS, Univ Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, France
| | - Daphné Lehalle
- APHP.Sorbonne Université, Département de Génétique, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Gaëtan Lesca
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - James Lespinasse
- UF de génétique médicale, Centre Hospitalier Métropole Savoie, BP 31135, 73011, Chambéry, France
| | - Jonathan Levy
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
| | - Stanislas Lyonnet
- Service de médecine génomique des maladies rares, Hôpital Universitaire Necker-Enfants malades, APHP, Paris, France
- Laboratoire embryologie et génétique des malformations, Institut Imagine, UMR-II63, INSERM, Université Paris Cité, GHU Necker- Enfants malades, Paris, France
| | - Godeliève Morel
- Service de Génétique Clinique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Rennes, Rennes, France
| | - Nolwenn Jean-Marçais
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du développement, FHU GenOMedS, Rennes, France
| | - Sandrine Marlin
- Service de médecine génomique des maladies rares - GHU Necker- Enfants malades, Paris, France
| | - Luisa Marsili
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
| | - Cyril Mignot
- APHP.Sorbonne Université, Département de Génétique, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Sophie Nambot
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
| | - Mathilde Nizon
- Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- CHU Nantes, Service de Génétique Médicale, Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Laurent Pasquier
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du développement, FHU GenOMedS, Rennes, France
| | - Laurine Perrin
- Médecine Physique et Réadaptation pédiatrique CHU Saint-Etienne, 42055, Saint-Etienne Cedex 2, France
| | - Florence Petit
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
- Univ. Lille, CHU Lille, ULR 7364 - RADEME - Institut de Génétique Médicale, F-59000, Lille, France
| | - Veronique Pingault
- Service de Médecine Génomique des maladies rares, AP-HP. Centre, Hôpital Necker-Enfants Malades, F-75015, Paris, France
- Université Paris Cité, Institut Imagine, Inserm U1163, F-75015, Paris, France
| | - Amélie Piton
- Laboratoire de diagnostic génétique, IGMA, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Fabienne Prieur
- Service de Génétique, CHU Hôpital Nord, Saint Etienne, France
| | - Audrey Putoux
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, Genetics of Neurodevelopment (GENDEV) Team, 69500, Bron, France
| | - Marc Planes
- Service de Génétique Médicale et Biologie de la Reproduction, CHU de Brest, Brest, France
| | - Sylvie Odent
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du développement, FHU GenOMedS, Univ Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, France
| | - Chloé Quélin
- Service de Génétique Clinique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Rennes, Rennes, France
| | - Sylvia Quemener-Redon
- Service de Génétique Médicale et Biologie de la Reproduction, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France
- Centre de Référence Déficiences Intellectuelles de causes rares, Brest, France
| | - Mélanie Rama
- CHU Lille - Institut de Génétique Médicale, F-59000, Lille, France
| | - Marlène Rio
- Service de médecine génomique des maladies rares - GHU Necker- Enfants malades, Paris, France
| | - Massimiliano Rossi
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, Genetics of Neurodevelopment (GENDEV) Team, 69500, Bron, France
| | - Elise Schaefer
- Service de Génétique Médicale -Institut de Génétique Médicale d'Alsace - CHU Strasbourg, Strasbourg, France
| | - Sophie Rondeau
- Service de médecine génomique des maladies rares - GHU Necker- Enfants malades, Paris, France
| | - Pascale Saugier-Veber
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Thomas Smol
- Univ. Lille, CHU Lille, ULR 7364 - RADEME - Institut de Génétique Médicale, F-59000, Lille, France
- CHU Lille - Institut de Génétique Médicale, F-59000, Lille, France
| | - Sabine Sigaudy
- Aix Marseille Univ, INSERM, MMG, CRMR syndromes malformatifs et anomalies du développement, département de génétique, APHM Hopital Timone, Marseille, France
| | - Renaud Touraine
- Service de Génétique, CHU Hôpital Nord, Saint Etienne, France
| | - Frederic Tran Mau-Them
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon, Bourgogne, Dijon, France
| | - Aurélien Trimouille
- Service de Pathologie, CHU Bordeaux, Bordeaux, France
- Inserm U1211 MRGM, Université de Bordeaux, Bordeaux, France
| | - Julien Van Gils
- Department of Medical Genetics, University Hospital of Bordeaux and INSERM U1211, University of Bordeaux, Bordeaux, France
| | | | - Valérie Vantalon
- Centre d'Excellence InovAND-Service de psychiatrie de l'enfant et de l'adolescent-CHU Robert Debré, Paris, France
| | - Gabriella Vera
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Marie Vincent
- Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- CHU Nantes, Service de Génétique Médicale, Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
| | - Alban Ziegler
- Service de Génétique Médicale, CHU Angers, Angers, France
| | - Olivier Guillin
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Psychiatry, F-76000, Rouen, France
| | - Dominique Campion
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Psychiatry, F-76000, Rouen, France
| | - Camille Charbonnier
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Biostatistics, F-76000, Rouen, France.
| |
Collapse
|
6
|
Zech M, Winkelmann J. Next-generation sequencing and bioinformatics in rare movement disorders. Nat Rev Neurol 2024; 20:114-126. [PMID: 38172289 DOI: 10.1038/s41582-023-00909-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
The ability to sequence entire exomes and genomes has revolutionized molecular testing in rare movement disorders, and genomic sequencing is becoming an integral part of routine diagnostic workflows for these heterogeneous conditions. However, interpretation of the extensive genomic variant information that is being generated presents substantial challenges. In this Perspective, we outline multidimensional strategies for genetic diagnosis in patients with rare movement disorders. We examine bioinformatics tools and computational metrics that have been developed to facilitate accurate prioritization of disease-causing variants. Additionally, we highlight community-driven data-sharing and case-matchmaking platforms, which are designed to foster the discovery of new genotype-phenotype relationships. Finally, we consider how multiomic data integration might optimize diagnostic success by combining genomic, epigenetic, transcriptomic and/or proteomic profiling to enable a more holistic evaluation of variant effects. Together, the approaches that we discuss offer pathways to the improved understanding of the genetic basis of rare movement disorders.
Collapse
Affiliation(s)
- Michael Zech
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany.
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany.
- DZPG, Deutsches Zentrum für Psychische Gesundheit, Munich, Germany.
| |
Collapse
|
7
|
Thomsen M, Lange LM, Zech M, Lohmann K. Genetics and Pathogenesis of Dystonia. ANNUAL REVIEW OF PATHOLOGY 2024; 19:99-131. [PMID: 37738511 DOI: 10.1146/annurev-pathmechdis-051122-110756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Dystonia is a clinically and genetically highly heterogeneous neurological disorder characterized by abnormal movements and postures caused by involuntary sustained or intermittent muscle contractions. A number of groundbreaking genetic and molecular insights have recently been gained. While they enable genetic testing and counseling, their translation into new therapies is still limited. However, we are beginning to understand shared pathophysiological pathways and molecular mechanisms. It has become clear that dystonia results from a dysfunctional network involving the basal ganglia, cerebellum, thalamus, and cortex. On the molecular level, more than a handful of, often intertwined, pathways have been linked to pathogenic variants in dystonia genes, including gene transcription during neurodevelopment (e.g., KMT2B, THAP1), calcium homeostasis (e.g., ANO3, HPCA), striatal dopamine signaling (e.g., GNAL), endoplasmic reticulum stress response (e.g., EIF2AK2, PRKRA, TOR1A), autophagy (e.g., VPS16), and others. Thus, different forms of dystonia can be molecularly grouped, which may facilitate treatment development in the future.
Collapse
Affiliation(s)
- Mirja Thomsen
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
| | - Lara M Lange
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
| |
Collapse
|
8
|
Sugeno N, Hasegawa T, Haginoya K, Kubota T, Ikeda K, Nakamura T, Ishiyama S, Sato K, Yoshida S, Koshimizu E, Uematsu M, Miyatake S, Matsumoto N, Aoki M. Detection of Modified Histones from Oral Mucosa of a Patient with DYT- KMT2B Dystonia. Mol Syndromol 2023; 14:461-468. [PMID: 38108041 PMCID: PMC10722472 DOI: 10.1159/000530625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/07/2023] [Indexed: 12/19/2023] Open
Abstract
Introduction DYT-KMT2B is a rare childhood-onset, hereditary movement disorder typically characterized by lower-limb dystonia and subsequently spreads into the craniocervical and laryngeal muscles. Recently, KMT2B-encoding lysine (K)-specific histone methyltransferase 2B was identified as the causative gene for DYT-KMT2B, also known as DYT28. In addition to the fact that many physicians do not have sufficient experience or knowledge of hereditary dystonia, the clinical features of DYT-KMT2B overlap with those of other hereditary dystonia, and limited clinical biomarkers make the diagnosis difficult. Methods Histone proteins were purified from the oral mucosa of patients with de novo KMT2B mutation causing premature stop codon, and then trimethylated fourth lysine residue of histone H3 (H3K4me3) which was catalyzed by KMT2B was analyzed by immunoblotting with specific antibody. We further analyzed the significance of H3K4me3 in patients with DYT-KMT2B using publicly available datasets. Results H3K4me3 histone mark was markedly lower in the patient than in the control group. Additionally, a reanalysis of publicly available datasets concerning DNA methylation also demonstrated that KMT2B remained inactive in DYT-KMT2B. Discussion Although only one case was studied due to the rarity of the disease, the reduction of H3K4me3 in the patient's biological sample supports the dysfunction of KMT2B in DYT-KMT2B. Together with informatics approaches, our results suggest that KMT2B haploinsufficiency contributes to the DYT-KMT2B pathogenic process.
Collapse
Affiliation(s)
- Naoto Sugeno
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takafumi Hasegawa
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kazuhiro Haginoya
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
- Department of Pediatric Neurology, Miyagi Children’s Hospital, Sendai, Japan
| | - Takafumi Kubota
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kensuke Ikeda
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takaaki Nakamura
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shun Ishiyama
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kazuki Sato
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shun Yoshida
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Mitsugu Uematsu
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Masashi Aoki
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| |
Collapse
|
9
|
Wu MC, Chang YY, Lan MY, Chen YF, Tai CH, Chen SJ, Lin CH. Blood neurofilament light chain as a surrogate marker for dystonia. Eur J Neurol 2023; 30:3098-3104. [PMID: 37422850 DOI: 10.1111/ene.15972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/15/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
BACKGROUND AND PURPOSE Dystonia is a heterogeneous movement disorder, and it remains unclear whether neurodegeneration is involved. Neurofilament light chain (NfL) is a biosignature of neurodegeneration. We aimed to investigate whether plasma NfL levels were elevated and associated with disease severity in patients with dystonia. METHOD We enrolled 231 unrelated dystonia patients (isolated dystonia n = 203; combined dystonia n = 28) and 54 healthy controls from movement disorder clinics. Clinical severity was evaluated using the Fahn Marsden Dystonia Rating Scale, the Unified Dystonia Rating Scale, and the Global Dystonia Rating Scale. Blood NfL levels were measured by single-molecule array. RESULTS Plasma NfL levels were significantly higher in those with generalized dystonia compared to those with focal dystonia (20.1 ± 8.8 vs. 11.7 ± 7.2 pg/mL; p = 0.01) or controls (p < 0.01), while the level was comparable between the focal dystonia group and controls (p = 0.08). Furthermore, the dystonia combined with parkinsonism group had higher NfL levels than the isolated dystonia group (17.4 ± 6.2 vs. 13.5 ± 7.5 pg/mL; p = 0.04). Notably, whole-exome sequencing was performed in 79 patients and two patients were identified as having likely pathogenic variants: one had a heterozygous c.122G>A (p.R41H) variant in THAP1 (DYT6) and the other carried a c.1825G>A (p.D609N) substitution in ATP1A3 (DYT12). No significant correlation was found between plasma NfL levels and dystonia rating scores. CONCLUSION Plasma NfL levels are elevated in patients with generalized dystonia and dystonia combined with parkinsonism, suggesting that neurodegeneration is involved in the disease process of this subgroup of patients.
Collapse
Affiliation(s)
- Meng-Chen Wu
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Geriatrics and Gerontology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yung-Yee Chang
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Center for Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Min-Yu Lan
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Center for Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Ying-Fa Chen
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Center for Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Chun-Hwei Tai
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Szu-Ju Chen
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chin-Hsien Lin
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
10
|
Smirnov D, Konstantinovskiy N, Prokisch H. Integrative omics approaches to advance rare disease diagnostics. J Inherit Metab Dis 2023; 46:824-838. [PMID: 37553850 DOI: 10.1002/jimd.12663] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/10/2023]
Abstract
Over the past decade high-throughput DNA sequencing approaches, namely whole exome and whole genome sequencing became a standard procedure in Mendelian disease diagnostics. Implementation of these technologies greatly facilitated diagnostics and shifted the analysis paradigm from variant identification to prioritisation and evaluation. The diagnostic rates vary widely depending on the cohort size, heterogeneity and disease and range from around 30% to 50% leaving the majority of patients undiagnosed. Advances in omics technologies and computational analysis provide an opportunity to increase these unfavourable rates by providing evidence for disease-causing variant validation and prioritisation. This review aims to provide an overview of the current application of several omics technologies including RNA-sequencing, proteomics, metabolomics and DNA-methylation profiling for diagnostics of rare genetic diseases in general and inborn errors of metabolism in particular.
Collapse
Affiliation(s)
- Dmitrii Smirnov
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
| | - Nikita Konstantinovskiy
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Holger Prokisch
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
| |
Collapse
|
11
|
Dhar D, Holla VV, Kumari R, Sriram N, Saini J, Yadav R, Pandey A, Kamble N, Muthusamy B, Pal PK. KMT2B-Related Dystonia in Indian Patients With Literature Review and Emphasis on Asian Cohort. J Mov Disord 2023; 16:285-294. [PMID: 37309110 PMCID: PMC10548078 DOI: 10.14802/jmd.23035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/12/2023] [Accepted: 05/29/2023] [Indexed: 06/14/2023] Open
Abstract
OBJECTIVE aaMutations in the KMT2B gene have been identified in patients previously diagnosed with idiopathic dystonia. Literature on KMT2B-related dystonia is sparse in the Indian and Asian populations. METHODS aaWe report seven patients with KMT2B-related dystonia studied prospectively from May 2021 to September 2022. Patients underwent deep clinical phenotyping and genetic testing by whole-exome sequencing (WES). A systematic literature search was performed to identify the spectrum of previously published KMT2B-related disorders in the Asian subcontinent. RESULTS aaThe seven identified patients with KMT2B-related dystonia had a median age at onset of four years. The majority experienced onset in the lower limbs (n = 5, 71.4%), with generalization at a median duration of 2 years. All patients except one had complex phenotypes manifesting as facial dysmorphism (n = 4), microcephaly (n = 3), developmental delay (n = 3), and short stature (n = 1). Magnetic resonance imaging (MRI) abnormalities were present in four cases. WES revealed novel mutations in the KMT2B gene in all patients except one. Compared to the largest cohort of patients with KMT2B-related disorders, the Asian cohort, comprising 42 patients, had a lower prevalence of female patients, facial dysmorphism, microcephaly, intellectual disability, and MRI abnormalities. Protein-truncating variants were more prevalent than missense variants. While microcephaly and short stature were more common in patients with missense mutations, facial dysmorphism was more common in patients with truncating variants. Deep brain stimulation, performed in 17 patients, had satisfactory outcomes. CONCLUSION aaThis is the largest series of patients with KMT2B-related disorders from India, further expanding the clinico-genotypic spectrum. The extended Asian cohort emphasizes the unique attributes of this part of the world.
Collapse
Affiliation(s)
- Debjyoti Dhar
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Vikram V Holla
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Riyanka Kumari
- Institute of Bioinformatics, International Technology Park, Bengaluru, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Neeharika Sriram
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Jitender Saini
- Department of Neuroimaging and Intervention Radiology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Ravi Yadav
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Nitish Kamble
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Babylakshmi Muthusamy
- Institute of Bioinformatics, International Technology Park, Bengaluru, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| |
Collapse
|
12
|
Oexle K, Zech M, Stühn LG, Siegert S, Brunet T, Schmidt WM, Wagner M, Schmidt A, Engels H, Tilch E, Monestier O, Destrėe A, Hanker B, Boesch S, Jech R, Berutti R, Kaiser F, Haslinger B, Haack TB, Garavaglia B, Krawitz P, Winkelmann J, Mirza-Schreiber N. Episignature analysis of moderate effects and mosaics. Eur J Hum Genet 2023; 31:1032-1039. [PMID: 37365401 PMCID: PMC10474287 DOI: 10.1038/s41431-023-01406-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/14/2023] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
DNA methylation classifiers ("episignatures") help to determine the pathogenicity of variants of uncertain significance (VUS). However, their sensitivity is limited due to their training on unambiguous cases with strong-effect variants so that the classification of variants with reduced effect size or in mosaic state may fail. Moreover, episignature evaluation of mosaics as a function of their degree of mosaicism has not been developed so far. We improved episignatures with respect to three categories. Applying (i) minimum-redundancy-maximum-relevance feature selection we reduced their length by up to one order of magnitude without loss of accuracy. Performing (ii) repeated re-training of a support vector machine classifier by step-wise inclusion of cases in the training set that reached probability scores larger than 0.5, we increased the sensitivity of the episignature-classifiers by 30%. In the newly diagnosed patients we confirmed the association between DNA methylation aberration and age at onset of KMT2B-deficient dystonia. Moreover, we found evidence for allelic series, including KMT2B-variants with moderate effects and comparatively mild phenotypes such as late-onset focal dystonia. Retrained classifiers also can detect mosaics that previously remained below the 0.5-threshold, as we showed for KMT2D-associated Kabuki syndrome. Conversely, episignature-classifiers are able to revoke erroneous exome calls of mosaicism, as we demonstrated by (iii) comparing presumed mosaic cases with a distribution of artificial in silico-mosaics that represented all the possible variation in degree of mosaicism, variant read sampling and methylation analysis.
Collapse
Affiliation(s)
- Konrad Oexle
- Neurogenetic Systems Analysis Group, Institute of Neurogenomics, Helmholtz Munich, 85764, Neuherberg, Germany.
- Institute of Neurogenomics,Helmholtz Munich, 85764, Neuherberg, Germany.
- Institute of Human Genetics, Technical University of Munich, School of Medicine, 81675, Munich, Germany.
| | - Michael Zech
- Institute of Neurogenomics,Helmholtz Munich, 85764, Neuherberg, Germany
- Institute of Human Genetics, Technical University of Munich, School of Medicine, 81675, Munich, Germany
| | - Lara G Stühn
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076, Tübingen, Germany
- Centre for Rare Diseases, University of Tuebingen, 72076, Tuebingen, Germany
| | - Sandy Siegert
- Department of Pediatric and Adolescent Medicine, Medical University of Vienna, 1090, Wien, Austria
| | - Theresa Brunet
- Institute of Human Genetics, Technical University of Munich, School of Medicine, 81675, Munich, Germany
| | - Wolfgang M Schmidt
- Neuromuscular Research Department, Center for Anatomy and Cell Biology, Medical University of Vienna, 1090, Vienna, Austria
| | - Matias Wagner
- Institute of Human Genetics, Technical University of Munich, School of Medicine, 81675, Munich, Germany
| | - Axel Schmidt
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, 53127, Bonn, Germany
| | - Hartmut Engels
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, 53127, Bonn, Germany
| | - Erik Tilch
- Neurogenetic Systems Analysis Group, Institute of Neurogenomics, Helmholtz Munich, 85764, Neuherberg, Germany
- Institute of Neurogenomics,Helmholtz Munich, 85764, Neuherberg, Germany
| | - Olivier Monestier
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique ASBL, 6041, Gosselies, Belgium
| | - Anne Destrėe
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique ASBL, 6041, Gosselies, Belgium
| | - Britta Hanker
- Institute of Human Genetics, Universitätsklinikum Schleswig-Holstein, 23538, Lübeck, Germany
| | - Sylvia Boesch
- Department of Neurology, Medizinische Universität, 6020, Insbruck, Austria
| | - Robert Jech
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, 12108, Prague, Czech Republic
| | - Riccardo Berutti
- Institute of Neurogenomics,Helmholtz Munich, 85764, Neuherberg, Germany
- Institute of Human Genetics, Technical University of Munich, School of Medicine, 81675, Munich, Germany
| | - Frank Kaiser
- Institute of Human Genetics, Universitätsklinikum Essen, 45122, Essen, Germany
| | - Bernhard Haslinger
- Department of Neurology, Technical University of Munich, School of Medicine, 81675, Munich, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076, Tübingen, Germany
- Centre for Rare Diseases, University of Tuebingen, 72076, Tuebingen, Germany
| | - Barbara Garavaglia
- Fondazione IRCCS, Istituto Neurologico Carlo Besta, 20133, Milano, Italy
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, Universität Bonn, 53127, Bonn, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics,Helmholtz Munich, 85764, Neuherberg, Germany
- Institute of Human Genetics, Technical University of Munich, School of Medicine, 81675, Munich, Germany
- Chair of Neurogenetics, Technical University of Munich, School of Medicine, 81675, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377, Munich, Germany
| | - Nazanin Mirza-Schreiber
- Neurogenetic Systems Analysis Group, Institute of Neurogenomics, Helmholtz Munich, 85764, Neuherberg, Germany
- Institute of Neurogenomics,Helmholtz Munich, 85764, Neuherberg, Germany
| |
Collapse
|
13
|
Di Fonzo A, Jinnah HA, Zech M. Dystonia genes and their biological pathways. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2023; 169:61-103. [PMID: 37482402 DOI: 10.1016/bs.irn.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
High-throughput sequencing has been instrumental in uncovering the spectrum of pathogenic genetic alterations that contribute to the etiology of dystonia. Despite the immense heterogeneity in monogenic causes, studies performed during the past few years have highlighted that many rare deleterious variants associated with dystonic presentations affect genes that have roles in certain conserved pathways in neural physiology. These various gene mutations that appear to converge towards the disruption of interconnected cellular networks were shown to produce a wide range of different dystonic disease phenotypes, including isolated and combined dystonias as well as numerous clinically complex, often neurodevelopmental disorder-related conditions that can manifest with dystonic features in the context of multisystem disturbances. In this chapter, we summarize the manifold dystonia-gene relationships based on their association with a discrete number of unifying pathophysiological mechanisms and molecular cascade abnormalities. The themes on which we focus comprise dopamine signaling, heavy metal accumulation and calcifications in the brain, nuclear envelope function and stress response, gene transcription control, energy homeostasis, lysosomal trafficking, calcium and ion channel-mediated signaling, synaptic transmission beyond dopamine pathways, extra- and intracellular structural organization, and protein synthesis and degradation. Enhancing knowledge about the concept of shared etiological pathways in the pathogenesis of dystonia will motivate clinicians and researchers to find more efficacious treatments that allow to reverse pathologies in patient-specific core molecular networks and connected multipathway loops.
Collapse
Affiliation(s)
- Alessio Di Fonzo
- Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - H A Jinnah
- Departments of Neurology, Human Genetics, and Pediatrics, Atlanta, GA, United States
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
| |
Collapse
|
14
|
Bogaert E, Garde A, Gautier T, Rooney K, Duffourd Y, LeBlanc P, van Reempts E, Tran Mau-Them F, Wentzensen IM, Au KS, Richardson K, Northrup H, Gatinois V, Geneviève D, Louie RJ, Lyons MJ, Laulund LW, Brasch-Andersen C, Maxel Juul T, El It F, Marle N, Callier P, Relator R, Haghshenas S, McConkey H, Kerkhof J, Cesario C, Novelli A, Brunetti-Pierri N, Pinelli M, Pennamen P, Naudion S, Legendre M, Courdier C, Trimouille A, Fenzy MD, Pais L, Yeung A, Nugent K, Roeder ER, Mitani T, Posey JE, Calame D, Yonath H, Rosenfeld JA, Musante L, Faletra F, Montanari F, Sartor G, Vancini A, Seri M, Besmond C, Poirier K, Hubert L, Hemelsoet D, Munnich A, Lupski JR, Philippe C, Thauvin-Robinet C, Faivre L, Sadikovic B, Govin J, Dermaut B, Vitobello A. SRSF1 haploinsufficiency is responsible for a syndromic developmental disorder associated with intellectual disability. Am J Hum Genet 2023; 110:790-808. [PMID: 37071997 PMCID: PMC10183470 DOI: 10.1016/j.ajhg.2023.03.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/23/2023] [Indexed: 04/20/2023] Open
Abstract
SRSF1 (also known as ASF/SF2) is a non-small nuclear ribonucleoprotein (non-snRNP) that belongs to the arginine/serine (R/S) domain family. It recognizes and binds to mRNA, regulating both constitutive and alternative splicing. The complete loss of this proto-oncogene in mice is embryonically lethal. Through international data sharing, we identified 17 individuals (10 females and 7 males) with a neurodevelopmental disorder (NDD) with heterozygous germline SRSF1 variants, mostly de novo, including three frameshift variants, three nonsense variants, seven missense variants, and two microdeletions within region 17q22 encompassing SRSF1. Only in one family, the de novo origin could not be established. All individuals featured a recurrent phenotype including developmental delay and intellectual disability (DD/ID), hypotonia, neurobehavioral problems, with variable skeletal (66.7%) and cardiac (46%) anomalies. To investigate the functional consequences of SRSF1 variants, we performed in silico structural modeling, developed an in vivo splicing assay in Drosophila, and carried out episignature analysis in blood-derived DNA from affected individuals. We found that all loss-of-function and 5 out of 7 missense variants were pathogenic, leading to a loss of SRSF1 splicing activity in Drosophila, correlating with a detectable and specific DNA methylation episignature. In addition, our orthogonal in silico, in vivo, and epigenetics analyses enabled the separation of clearly pathogenic missense variants from those with uncertain significance. Overall, these results indicated that haploinsufficiency of SRSF1 is responsible for a syndromic NDD with ID due to a partial loss of SRSF1-mediated splicing activity.
Collapse
Affiliation(s)
- Elke Bogaert
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Aurore Garde
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs", Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Thierry Gautier
- University Grenoble Alpes, Inserm U1209, CNRS UMR 5309, Institute for Advanced Biosciences (IAB), 38000 Grenoble, France
| | - Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Yannis Duffourd
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Pontus LeBlanc
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Emma van Reempts
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Frederic Tran Mau-Them
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | | | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Kate Richardson
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Vincent Gatinois
- Unité de Génétique Chromosomique, CHU Montpellier, Montpellier, France
| | - David Geneviève
- Montpellier University, Inserm U1183, Montpellier, France; Reference center for rare disease developmental anomaly malformative syndrome, Department of Medical Genetics, Montpellier Hospital, Montpellier, France
| | | | | | | | - Charlotte Brasch-Andersen
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark; Human Genetics, Department of Clinical Research, Health Faculty, University of Southern Denmark, 5000 Odense, Denmark
| | - Trine Maxel Juul
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Fatima El It
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France
| | - Nathalie Marle
- Laboratoire de Génétique Chromosomique et Moléculaire, Pôle de Biologie, CHU de Dijon, Dijon, France
| | - Patrick Callier
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Laboratoire de Génétique Chromosomique et Moléculaire, Pôle de Biologie, CHU de Dijon, Dijon, France
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Claudia Cesario
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | | | - Sophie Naudion
- Medical Genetics Department, CHU Bordeaux, Bordeaux, France
| | | | | | - Aurelien Trimouille
- INSERM U1211, Laboratoire MRGM, Bordeaux University, Bordeaux, France; Pathology Department, CHU Bordeaux, Bordeaux, France
| | - Martine Doco Fenzy
- Service de génétique, CHU de Reims, Reims, France; Service de génétique médicale, CHU de Nantes, Nantes, France; L'institut du thorax, INSERM, CNRS, UNIV Nantes, CHU de Nantes, Nantes, France
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Kimberly Nugent
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Daniel Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Hagith Yonath
- Internal Medicine A, Danek Gertner Institute of Human Genetics, Sheba Medical Center, Ramat Gan, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics Laboratories, Houston, TX, USA
| | - Luciana Musante
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Francesca Montanari
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanna Sartor
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Marco Seri
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Claude Besmond
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Karine Poirier
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Laurence Hubert
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Dimitri Hemelsoet
- Department of Neurology, Ghent University Hospital, 9000 Ghent, Belgium
| | - Arnold Munnich
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Christophe Philippe
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Christel Thauvin-Robinet
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France; Centre de Référence Maladies Rares « Déficiences intellectuelles de causes rares », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Laurence Faivre
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs", Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Jérôme Govin
- University Grenoble Alpes, Inserm U1209, CNRS UMR 5309, Institute for Advanced Biosciences (IAB), 38000 Grenoble, France
| | - Bart Dermaut
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium.
| | - Antonio Vitobello
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France.
| |
Collapse
|
15
|
DNA methylation episignature for Witteveen-Kolk syndrome due to SIN3A haploinsufficiency. Genet Med 2023; 25:63-75. [PMID: 36399132 DOI: 10.1016/j.gim.2022.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/19/2022] Open
Abstract
PURPOSE Witteveen-Kolk syndrome (WITKOS) is a rare, autosomal dominant neurodevelopmental disorder caused by heterozygous loss-of-function alterations in the SIN3A gene. WITKOS has variable expressivity that commonly overlaps with other neurodevelopmental disorders. In this study, we characterized a distinct DNA methylation epigenetic signature (episignature) distinguishing WITKOS from unaffected individuals as well as individuals with other neurodevelopmental disorders with episignatures and described 9 previously unpublished individuals with SIN3A haploinsufficiency. METHODS We studied the phenotypic characteristics and the genome-wide DNA methylation in the peripheral blood samples of 20 individuals with heterozygous alterations in SIN3A. A total of 14 samples were used for the identification of the episignature and building of a predictive diagnostic biomarker, whereas the diagnostic model was used to investigate the methylation pattern of the remaining 6 samples. RESULTS A predominantly hypomethylated DNA methylation profile specific to WITKOS was identified, and the classifier model was able to diagnose a previously unresolved test case. The episignature was sensitive enough to detect individuals with varying degrees of phenotypic severity carrying SIN3A haploinsufficient variants. CONCLUSION We identified a novel, robust episignature in WITKOS due to SIN3A haploinsufficiency. This episignature has the potential to aid identification and diagnosis of individuals with WITKOS.
Collapse
|
16
|
Timmers ER, Plösch T, Smit M, Hof IH, Verkaik-Schakel RN, Tijssen MAJ, de Koning TJ, Niezen-Koning KE. Methylation of the serotonin reuptake transporter gene and non-motor symptoms in dystonia patients. Clin Epigenetics 2022; 14:170. [PMID: 36503539 PMCID: PMC9743677 DOI: 10.1186/s13148-022-01384-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Dystonia is a rare movement disorder, in which patients suffer from involuntary twisting movements or abnormal posturing. Next to these motor symptoms, patients have a high prevalence of psychiatric comorbidity, suggesting a role for serotonin in its pathophysiology. This study investigates the percentage of DNA methylation of the gene encoding for the serotonin reuptake transporter (SLC6A4) in dystonia patients and the associations between methylation levels and presence and severity of psychiatric symptoms. METHODS Patients with cervical dystonia (n = 49), myoclonus dystonia (n = 41) and dopa-responsive dystonia (DRD) (n = 27) and a group of healthy controls (n = 56) were included. Psychiatric comorbidity was evaluated with validated questionnaires. Methylation levels of 20 CpG sites situated 69 to 213 base pairs upstream of the start codon of SLC6A4 were investigated. Methylation in dystonia patients was compared to healthy controls, correcting for age, and correlated with psychiatric comorbidity. RESULTS Bootstrapped quantile regression analysis showed that being a dystonia patient compared to a healthy control significantly explains the methylation level at two CpG sites (CpG 24: pseudo-R2 = 0.05, p = 0.04, CpG 32: pseudo-R2 = 0.14, p = 0.03). Subgroup analysis revealed that being a DRD patient significantly explained a part of the variance of methylation levels at two CpG sites (CpG 21: pseudo-R2 = 0.03, p = 0.00, CpG 24: pseudo-R2 = 0.06, p = 0.03). Regression analysis showed that methylation level at CpG 38 significantly explained a small proportion of the variance of severity score for anxiety (R2 = 0.07, p = 0.04) and having a diagnosis of depression (Nagelkerke R2: 0.11, p = 0.00). Genotype of the 5-HTTLPR polymorphism had no additional effect on these associations. CONCLUSIONS This study showed an association between percentage of methylation at several specific sites of the promoter region of SLCA64 and (dopa-responsive) dystonia patients compared to healthy controls. Furthermore, methylation levels were associated with severity of anxiety and presence of a depressive disorder in the dystonia group. This study suggests alterations in the serotonergic metabolism in dystonia patients, and its relation with the non-motor symptoms.
Collapse
Affiliation(s)
- Elze R. Timmers
- grid.4830.f0000 0004 0407 1981Department of Neurology, University Medical Center Groningen, University of Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands ,grid.4494.d0000 0000 9558 4598Expertise Center Movement Disorders Groningen, University Medical Center Groningen (UMCG), PO Box 30.001, 9700 RB Groningen, The Netherlands
| | - Torsten Plösch
- grid.4830.f0000 0004 0407 1981Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marenka Smit
- grid.4830.f0000 0004 0407 1981Department of Neurology, University Medical Center Groningen, University of Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands ,grid.4494.d0000 0000 9558 4598Expertise Center Movement Disorders Groningen, University Medical Center Groningen (UMCG), PO Box 30.001, 9700 RB Groningen, The Netherlands
| | - Ingrid H. Hof
- grid.4494.d0000 0000 9558 4598Laboratory of Metabolic Diseases, Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands
| | - Rikst Nynke Verkaik-Schakel
- grid.4830.f0000 0004 0407 1981Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marina A. J. Tijssen
- grid.4830.f0000 0004 0407 1981Department of Neurology, University Medical Center Groningen, University of Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands ,grid.4494.d0000 0000 9558 4598Expertise Center Movement Disorders Groningen, University Medical Center Groningen (UMCG), PO Box 30.001, 9700 RB Groningen, The Netherlands
| | - Tom J. de Koning
- grid.4494.d0000 0000 9558 4598Expertise Center Movement Disorders Groningen, University Medical Center Groningen (UMCG), PO Box 30.001, 9700 RB Groningen, The Netherlands ,grid.4514.40000 0001 0930 2361Pediatrics, Department of Clinical Sciences, Lund University, Box 117, 221 00 Lund, Sweden
| | - Klary E. Niezen-Koning
- grid.4494.d0000 0000 9558 4598Expertise Center Movement Disorders Groningen, University Medical Center Groningen (UMCG), PO Box 30.001, 9700 RB Groningen, The Netherlands ,grid.4494.d0000 0000 9558 4598Laboratory of Metabolic Diseases, Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands
| |
Collapse
|
17
|
Dzinovic I, Boesch S, Škorvánek M, Necpál J, Švantnerová J, Pavelekova P, Havránková P, Tsoma E, Indelicato E, Runkel E, Held V, Weise D, Janzarik W, Eckenweiler M, Berweck S, Mall V, Haslinger B, Jech R, Winkelmann J, Zech M. Genetic overlap between dystonia and other neurologic disorders: A study of 1,100 exomes. Parkinsonism Relat Disord 2022; 102:1-6. [PMID: 35872528 DOI: 10.1016/j.parkreldis.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/29/2022] [Accepted: 07/08/2022] [Indexed: 10/17/2022]
Abstract
INTRODUCTION Although shared genetic factors have been previously reported between dystonia and other neurologic conditions, no sequencing study exploring such links is available. In a large dystonic cohort, we aimed at analyzing the proportions of causative variants in genes associated with disease categories other than dystonia. METHODS Gene findings related to whole-exome sequencing-derived diagnoses in 1100 dystonia index cases were compared with expert-curated molecular testing panels for ataxia, parkinsonism, spastic paraplegia, neuropathy, epilepsy, and intellectual disability. RESULTS Among 220 diagnosed patients, 21% had variants in ataxia-linked genes; 15% in parkinsonism-linked genes; 15% in spastic-paraplegia-linked genes; 12% in neuropathy-linked genes; 32% in epilepsy-linked genes; and 65% in intellectual-disability-linked genes. Most diagnosed presentations (80%) were related to genes listed in ≥1 studied panel; 71% of the involved loci were found in the non-dystonia panels but not in an expert-curated gene list for dystonia. CONCLUSIONS Our study indicates a convergence in the genetics of dystonia and other neurologic phenotypes, informing diagnostic evaluation strategies and pathophysiological considerations.
Collapse
Affiliation(s)
- Ivana Dzinovic
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sylvia Boesch
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Matej Škorvánek
- Department of Neurology, P.J. Safarik University, Kosice, Slovak Republic; Department of Neurology, University Hospital of L. Pasteur, Kosice, Slovak Republic
| | - Ján Necpál
- Department of Neurology, Zvolen Hospital, Slovakia
| | - Jana Švantnerová
- Second Department of Neurology, Faculty of Medicine, Comenius University, University Hospital Bratislava, Bratislava, Slovakia
| | - Petra Pavelekova
- Department of Neurology, P.J. Safarik University, Kosice, Slovak Republic; Department of Neurology, University Hospital of L. Pasteur, Kosice, Slovak Republic
| | - Petra Havránková
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Eugenia Tsoma
- Regional Clinical Center of Neurosurgery and Neurology, Department of Family Medicine and Outpatient Care, Uzhhorod National University, Uzhhorod, Ukraine
| | | | - Eva Runkel
- Klinikum Aschaffenburg-Alzenau, Aschaffenburg, Germany
| | - Valentin Held
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - David Weise
- Klinik für Neurologie, Asklepios Fachklinikum Stadtroda, Stadtroda, Germany; Department of Neurology, University of Leipzig, Leipzig, Germany
| | - Wibke Janzarik
- Department of Neuropediatrics and Muscle Disorders, University Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Matthias Eckenweiler
- Department of Neuropediatrics and Muscle Disorders, University Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Steffen Berweck
- Ludwig Maximilian University of Munich, Munich, Germany; Hospital for Neuropediatrics and Neurological Rehabilitation, Centre of Epilepsy for Children and Adolescents, Schoen Klinik Vogtareuth, Vogtareuth, Germany
| | - Volker Mall
- Lehrstuhl für Sozialpädiatrie, Technische Universität München, Munich, Germany; kbo-Kinderzentrum München, Munich, Germany
| | - Bernhard Haslinger
- Department of Neurology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Robert Jech
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Lehrstuhl für Neurogenetik, Technische Universität München, Munich, Germany; Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
| |
Collapse
|
18
|
Thomsen M, Lohmann K. Importance of Methylation Pattern: Episignatures as a Novel Instrument in Diagnostics. Mov Disord 2021; 37:38. [PMID: 34817105 DOI: 10.1002/mds.28877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 11/08/2022] Open
Affiliation(s)
- Mirja Thomsen
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| |
Collapse
|