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Ciolfi A, Aref-Eshghi E, Pizzi S, Pedace L, Miele E, Kerkhof J, Flex E, Martinelli S, Radio FC, Ruivenkamp CAL, Santen GWE, Bijlsma E, Barge-Schaapveld D, Ounap K, Siu VM, Kooy RF, Dallapiccola B, Sadikovic B, Tartaglia M. Frameshift mutations at the C-terminus of HIST1H1E result in a specific DNA hypomethylation signature. Clin Epigenetics 2020; 12:7. [PMID: 31910894 PMCID: PMC6947958 DOI: 10.1186/s13148-019-0804-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/26/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND We previously associated HIST1H1E mutations causing Rahman syndrome with a specific genome-wide methylation pattern. RESULTS Methylome analysis from peripheral blood samples of six affected subjects led us to identify a specific hypomethylated profile. This "episignature" was enriched for genes involved in neuronal system development and function. A computational classifier yielded full sensitivity and specificity in detecting subjects with Rahman syndrome. Applying this model to a cohort of undiagnosed probands allowed us to reach diagnosis in one subject. CONCLUSIONS We demonstrate an epigenetic signature in subjects with Rahman syndrome that can be used to reach molecular diagnosis.
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Affiliation(s)
- Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, London, N6A 5C1, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, N6A 5W9, Canada
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Lucia Pedace
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Evelina Miele
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Jennifer Kerkhof
- Department of Pathology and Laboratory Medicine, Western University, London, N6A 5C1, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, N6A 5W9, Canada
| | - Elisabetta Flex
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Simone Martinelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300, The Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300, The Netherlands
| | - Emilia Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300, The Netherlands
| | - Daniela Barge-Schaapveld
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300, The Netherlands
| | - Katrin Ounap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, 50406, Tartu, Estonia.,Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia
| | - Victoria Mok Siu
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, 2650, Antwerp, Belgium
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, N6A 5C1, Canada. .,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, N6A 5W9, Canada.
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy.
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Tatton-Brown K, Zachariou A, Loveday C, Renwick A, Mahamdallie S, Aksglaede L, Baralle D, Barge-Schaapveld D, Blyth M, Bouma M, Breckpot J, Crabb B, Dabir T, Cormier-Daire V, Fauth C, Fisher R, Gener B, Goudie D, Homfray T, Hunter M, Jorgensen A, Kant SG, Kirally-Borri C, Koolen D, Kumar A, Labilloy A, Lees M, Marcelis C, Mercer C, Mignot C, Miller K, Neas K, Newbury-Ecob R, Pilz DT, Posmyk R, Prada C, Ramsey K, Randolph LM, Selicorni A, Shears D, Suri M, Temple IK, Turnpenny P, Val Maldergem L, Varghese V, Veenstra-Knol HE, Yachelevich N, Yates L, Rahman N. The Tatton-Brown-Rahman Syndrome: A clinical study of 55 individuals with de novo constitutive DNMT3A variants. Wellcome Open Res 2018; 3:46. [PMID: 29900417 PMCID: PMC5964628 DOI: 10.12688/wellcomeopenres.14430.1] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2018] [Indexed: 01/11/2023] Open
Abstract
Tatton-Brown-Rahman syndrome (TBRS; OMIM 615879), also known as the DNMT3A-overgrowth syndrome, is an overgrowth intellectual disability syndrome first described in 2014 with a report of 13 individuals with constitutive heterozygous
DNMT3A variants. Here we have undertaken a detailed clinical study of 55 individuals with
de novoDNMT3A variants, including the 13 previously reported individuals. An intellectual disability and overgrowth were reported in >80% of individuals with TBRS and were designated major clinical associations. Additional frequent clinical associations (reported in 20-80% individuals) included an evolving facial appearance with low-set, heavy, horizontal eyebrows and prominent upper central incisors; joint hypermobility (74%); obesity (weight ³2SD, 67%); hypotonia (54%); behavioural/psychiatric issues (most frequently autistic spectrum disorder, 51%); kyphoscoliosis (33%) and afebrile seizures (22%). One individual was diagnosed with acute myeloid leukaemia in teenage years. Based upon the results from this study, we present our current management for individuals with TBRS
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Affiliation(s)
- Katrina Tatton-Brown
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.,South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK.,St George's University of London, London, UK
| | - Anna Zachariou
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Chey Loveday
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Anthony Renwick
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Shazia Mahamdallie
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Lise Aksglaede
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
| | - Diana Baralle
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southhampton, UK
| | | | - Moira Blyth
- Department of Clinical Genetics, Chapel Allerton Hospital, Leeds, UK
| | - Mieke Bouma
- Elver Intellectual Disability Centre, Nieuw Wehl, Netherlands
| | - Jeroen Breckpot
- Center for Human Genetics, University Hospitals and KU Leuven, Leuven, Belgium
| | - Beau Crabb
- Genetics Department, Children's Hospitals and Clinics of Minneapolis, Minneapolis, MN, USA
| | - Tabib Dabir
- Northern Ireland Regional Genetics Centre, Clinical Genetics Service, Belfast City Hospital, Belfast, UK
| | | | - Christine Fauth
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Richard Fisher
- Teesside Genetics Unit, The James Cook University Hospital, Middlesbrough, UK
| | - Blanca Gener
- Department of Genetics, Cruces University Hospital, Biocruces Health Research Institute, centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), Basque Country, Spain
| | - David Goudie
- Department of Human Genetics, Ninewells Hospital and Medical School, Dundee, UK
| | - Tessa Homfray
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK.,St George's University of London, London, UK
| | - Matthew Hunter
- Monash Genetics, Monash Health, Melbourne, Australia.,Department of Paediatrics, Monash University, Melbourne, Australia
| | - Agnete Jorgensen
- Division of Child and Adolescent Health, Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
| | - Sarina G Kant
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - Cathy Kirally-Borri
- Department of Health, Genetic Services of Western Australia, Subiaco, Australia
| | - David Koolen
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ajith Kumar
- North East Thames Regional Genetics Service and Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Anatalia Labilloy
- Department of Pediatrics, University of Cincinnati, College of Medicine, Division of Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Hospital Internacional de Colombia, Floridablanca, Colombia
| | - Melissa Lees
- North East Thames Regional Genetics Service and Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Carlo Marcelis
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Catherine Mercer
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southhampton, UK
| | - Cyril Mignot
- Département de Génétique and Centre de Référence Déficiences Intellectuelles de Causes Rares, Assistance Publique - Hôpitaux de Paris , Paris, France
| | | | - Katherine Neas
- Genetic Health Service New Zealand, Wellington, New Zealand
| | - Ruth Newbury-Ecob
- University Hospitals Bristol NHS Trust/University of Bristol, Bristol, UK
| | - Daniela T Pilz
- West of Scotland Clinical Genetics Service, Queen Elizabeth University Hospital,, Glasgow, UK
| | - Renata Posmyk
- Department of Clinical Genetics, Podlaskie Medical Center, Bialystok, Poland.,Department of Perinatology and Obstetrics, Medical University in Bialystok, Bialystok, Poland
| | - Carlos Prada
- Department of Pediatrics, University of Cincinnati, College of Medicine, Division of Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Hospital Internacional de Colombia, Floridablanca, Colombia
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Linda M Randolph
- Division of Medical Genetics, Children's Hospital Los Angeles, University of Southern California/ Keck School of Medicine, Los Angeles, CA, USA
| | | | - Deborah Shears
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southhampton, UK
| | - Peter Turnpenny
- Peninsula Clinical Genetics, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - Lionel Val Maldergem
- Centre de Génétique Humaine and Integrative and Cognitive Neuroscience Research Unit EA481, Besançon, Besançon, France
| | - Vinod Varghese
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Hermine E Veenstra-Knol
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Naomi Yachelevich
- Clinical Genetics Services, New York University Hospitals Center, New York University, New York, NY, USA
| | - Laura Yates
- Teesside Genetics Unit, The James Cook University Hospital, Middlesbrough, UK
| | | | | | - Nazneen Rahman
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.,Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
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