1
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Popp B, Bienvenu T, Giurgea I, Metreau J, Kraus C, Reis A, Fischer J, Bralo MP, Castano JT, Lapunzina P, Almoguera B, Lopez-Grondona F, Sticht H, Zweier C. The recurrent TCF4 missense variant p.(Arg389Cys) causes a neurodevelopmental disorder overlapping with but not typical for Pitt-Hopkins syndrome. Clin Genet 2022; 102:517-523. [PMID: 35908153 PMCID: PMC10108566 DOI: 10.1111/cge.14206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022]
Abstract
TCF4 haploinsufficiency by deletions, truncating variants or loss-of-function missense variants within the DNA-binding and protein interacting bHLH domain causes Pitt-Hopkins syndrome (PTHS). This neurodevelopmental disorder (NDD) is characterized by severe intellectual disability (ID), epilepsy, hyperbreathing and a typical facial gestalt. Only few aberrations of the N-terminus of TCF4 were associated with milder or atypical phenotypes. By personal communication and searching databases we assembled six cases with the novel, recurrent, de novo missense variant c.1165C > T, p.(Arg389Cys) in TCF4. This variant was identified by diagnostic exome or panel sequencing and is located upstream of the bHLH domain. All six individuals presented with moderate to severe ID with language impairment. Microcephaly occurred in two individuals, epilepsy only in one, and no breathing anomalies or myopia were reported. Facial gestalt showed some aspects of PTHS but was rather non-specific in most individuals. Interestingly, the variant is located within the AD2 activation domain next to a highly conserved coactivator-recruitment motif and might alter interaction with coactivator proteins independently from the bHLH domain. Our findings of a recurrent missense variant outside the bHLH domain in six individuals with an ID phenotype overlapping with but not typical for PTHS delineate a novel genotype-phenotype correlation for TCF4-related NDDs. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Functional Genomics, Berlin, Germany
| | - Thierry Bienvenu
- INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Université de Paris, Paris, France
| | - Irina Giurgea
- Département de Génétique Médicale, INSERM Childhood Genetic Diseases, AP-HP. Sorbonne Université, Hôpital Trousseau, Paris, France
| | - Julia Metreau
- APHP, Service de neurologie pédiatrique, Hôpital Universitaire Bicetre, Le Kremlin-Bicetre, France
| | - Cornelia Kraus
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jan Fischer
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - María Palomares Bralo
- INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, IDIPAZ, Madrid, Spain.,ITHACA European Reference Network, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Jair Tenorio Castano
- INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, IDIPAZ, Madrid, Spain.,ITHACA European Reference Network, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Pablo Lapunzina
- INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, IDIPAZ, Madrid, Spain.,ITHACA European Reference Network, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Berta Almoguera
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Department of Genetics and Genomics, Fundación Jiménez Díaz University Hospital, Madrid, Spain
| | - Fermina Lopez-Grondona
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Department of Genetics and Genomics, Fundación Jiménez Díaz University Hospital, Madrid, Spain
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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2
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Levy MA, Relator R, McConkey H, Pranckeviciene E, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Ferilli M, Fletcher RS, Cherick F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Plomp AS, Poulton C, Reilly J, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, John MS, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci TB, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Campion D, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Heron D, Husson T, Kernohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vincent M, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders. Hum Mutat 2022; 43:1609-1628. [PMID: 35904121 DOI: 10.1002/humu.24446] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/30/2022] [Accepted: 07/27/2022] [Indexed: 11/10/2022]
Abstract
An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes which can share significant overlap amongst different conditions. In this study we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Erinija Pranckeviciene
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | | | - Mariet W Elting
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Marco Ferilli
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Florian Cherick
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, The Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000, Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | | | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | | | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Delphine Heron
- AP-HP, Département de Génétique Médicale, Groupe Hospitalier Pitié Salpétrière, Paris, France
| | - Thomas Husson
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, UK, and Sheffield Children's Hospital NHS Foundation Trust
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Dept of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Marie Vincent
- Service de génétique Médicale, CHU Nantes, France.,Institut du thorax, INSERM, CNRS, UNIV Nantes, 44007, Nantes, France
| | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
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3
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Levy MA, McConkey H, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Fletcher RS, Cherik F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Pizzi S, Plomp AS, Poulton C, Reilly J, Relator R, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, St John M, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci T, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Kerrnohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders. HGG Adv 2022; 3:100075. [PMID: 35047860 PMCID: PMC8756545 DOI: 10.1016/j.xhgg.2021.100075] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, UK
| | | | - Mariet W Elting
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | - Florian Cherik
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, the Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Kristin D Kerrnohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Department of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
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4
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Quintana Castanedo L, Sánchez Orta A, Maseda Pedrero R, Santos Simarro F, Palomares Bralo M, Feito Rodríguez M, de Lucas Laguna R. Skin and nails abnormalities in a patient with ZTTK syndrome and a de novo mutation in SON. Pediatr Dermatol 2020; 37:517-519. [PMID: 32045494 DOI: 10.1111/pde.14113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome is a rare, severe, and recently described multisystem developmental disorder characterized by delayed psychomotor development and intellectual disability, characteristic facial features, hypotonia, poor overall growth, and visual abnormalities. Mucocutaneous manifestations have not been reported so far among individuals with ZTTK syndrome. Herein, we present a patient with ZTTK syndrome due to a de novo mutation in SON gene, who has dental abnormalities and retronychia of the toenails. We suggest that mucocutaneous features may be a part of the phenotype.
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Affiliation(s)
| | - Alba Sánchez Orta
- Department of Dermatology, Hospital Universitario La Paz, Madrid, Spain
| | | | - Fernando Santos Simarro
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPaz, CIBERER, Madrid, Spain
| | - María Palomares Bralo
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPaz, CIBERER, Madrid, Spain
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5
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Vallespín E, Palomares Bralo M, Mori MÁ, Martín R, García-Miñaúr S, Fernández L, de Torres ML, García-Santiago F, Mansilla E, Santos F, M-Montaño VE, Crespo MC, Martín S, Martínez-Glez V, Delicado A, Lapunzina P, Nevado J. Customized high resolution CGH-array for clinical diagnosis reveals additional genomic imbalances in previous well-defined pathological samples. Am J Med Genet A 2013; 161A:1950-60. [DOI: 10.1002/ajmg.a.35960] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 03/03/2013] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Victoria E. M-Montaño
- Section of Functional and Structural Genomics of Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ; Hospital Universitario La Paz; Madrid; Spain
| | - M. Carmen Crespo
- Section of Functional and Structural Genomics of Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ; Hospital Universitario La Paz; Madrid; Spain
| | - Sol Martín
- Section of Functional and Structural Genomics of Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ; Hospital Universitario La Paz; Madrid; Spain
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