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Shangguan H, Wang J, Lin J, Huang X, Zeng Y, Chen R. A study on genotypes and phenotypes of short stature caused by epigenetic modification gene variants. Eur J Pediatr 2024; 183:1403-1414. [PMID: 38170291 DOI: 10.1007/s00431-023-05385-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024]
Abstract
Mendelian disorders of the epigenetic machinery (MDEMs) are caused by genetic mutations, a considerable fraction of which are associated with epigenetic modification. These MDEMs exhibit phenotypic overlap broadly characterized by multiorgan abnormalities. The variant detected in genes associated with epigenetic modification can lead to short stature accompanied with multiple system abnormalities. This study is aimed at presenting and summarizing the diagnostic rate, clinical, and genetic profile of MDEMs-associated short stature. Two hundred and fourteen short-stature patients with multiorgan abnormalities were enrolled. Clinical information and whole exome sequence (WES) were analyzed for these patients. WES identified 33 pathogenic/likely pathogenic variants in 19 epigenetic modulation genes (KMT2A, KMT2D, KDM6A, SETD5, KDM5C, HUWE1, UBE2A, NIPBL, SMC1A, RAD21, CREBBP, CUL4B, BPTF, ANKRD11, CHD7, SRCAP, CTCF, MECP2, UBE3A) in 33 patients (15.4%). Of note, 19 variants had never been reported previously. Furthermore, these 33 variants were associated with 16 different disorders with overlapping clinical features characterized by development delay/intelligence disability (31/33; 93.9%), small hands (14/33; 42.4%), clinodactyly of the 5th finger (14/33; 42.4%), long eyelashes (13/33; 39.4%), and hearing impairment (9/33; 27.3%). Additionally, several associated phenotypes are reported for the first time: clubbing with KMT2A variant, webbed neck with SETD5 variant, retinal detachment with CREBBP variant, sparse lateral eyebrow with HUWE1 variant, and long palpebral fissure with eversion of the lateral third of the low eyelid with SRCAP variant.Conclusions: Our study provided a new conceptual framework for further understanding short stature. Specific clinical findings may indicate that a short-stature patient may have an epigenetic modified gene variant.
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Affiliation(s)
- Huakun Shangguan
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, Fuzhou, 350000, China
| | - Jian Wang
- Department of Medical Genetics, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, Shanghai, 200127, China
| | - Jinduan Lin
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, Fuzhou, 350000, China
| | - Xiaozhen Huang
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, Fuzhou, 350000, China
| | - Yan Zeng
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, Fuzhou, 350000, China
| | - Ruimin Chen
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, Fuzhou, 350000, China.
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van Jaarsveld RH, Reilly J, Cornips MC, Hadders MA, Agolini E, Ahimaz P, Anyane-Yeboa K, Bellanger SA, van Binsbergen E, van den Boogaard MJ, Brischoux-Boucher E, Caylor RC, Ciolfi A, van Essen TAJ, Fontana P, Hopman S, Iascone M, Javier MM, Kamsteeg EJ, Kerkhof J, Kido J, Kim HG, Kleefstra T, Lonardo F, Lai A, Lev D, Levy MA, Lewis MES, Lichty A, Mannens MMAM, Matsumoto N, Maya I, McConkey H, Megarbane A, Michaud V, Miele E, Niceta M, Novelli A, Onesimo R, Pfundt R, Popp B, Prijoles E, Relator R, Redon S, Rots D, Rouault K, Saida K, Schieving J, Tartaglia M, Tenconi R, Uguen K, Verbeek N, Walsh CA, Yosovich K, Yuskaitis CJ, Zampino G, Sadikovic B, Alders M, Oegema R. Delineation of a KDM2B-related neurodevelopmental disorder and its associated DNA methylation signature. Genet Med 2023; 25:49-62. [PMID: 36322151 PMCID: PMC9825659 DOI: 10.1016/j.gim.2022.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 11/05/2022] Open
Abstract
PURPOSE Pathogenic variants in genes involved in the epigenetic machinery are an emerging cause of neurodevelopment disorders (NDDs). Lysine-demethylase 2B (KDM2B) encodes an epigenetic regulator and mouse models suggest an important role during development. We set out to determine whether KDM2B variants are associated with NDD. METHODS Through international collaborations, we collected data on individuals with heterozygous KDM2B variants. We applied methylation arrays on peripheral blood DNA samples to determine a KDM2B associated epigenetic signature. RESULTS We recruited a total of 27 individuals with heterozygous variants in KDM2B. We present evidence, including a shared epigenetic signature, to support a pathogenic classification of 15 KDM2B variants and identify the CxxC domain as a mutational hotspot. Both loss-of-function and CxxC-domain missense variants present with a specific subepisignature. Moreover, the KDM2B episignature was identified in the context of a dual molecular diagnosis in multiple individuals. Our efforts resulted in a cohort of 21 individuals with heterozygous (likely) pathogenic variants. Individuals in this cohort present with developmental delay and/or intellectual disability; autism; attention deficit disorder/attention deficit hyperactivity disorder; congenital organ anomalies mainly of the heart, eyes, and urogenital system; and subtle facial dysmorphism. CONCLUSION Pathogenic heterozygous variants in KDM2B are associated with NDD and a specific epigenetic signature detectable in peripheral blood.
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Affiliation(s)
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Marie-Claire Cornips
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Michael A Hadders
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00165 Rome, Italy
| | - Priyanka Ahimaz
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Kwame Anyane-Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Severine Audebert Bellanger
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Ton A J van Essen
- Department of Medical Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Paolo Fontana
- Medical Genetics Unit, A.O.R.N. San Pio, Benevento, Italy
| | - Saskia Hopman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maria Iascone
- Laboratorio di Genetica Medica - ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Margaret M Javier
- Department of Medical Genetics, BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Jun Kido
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Abbe Lai
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program and Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Dorit Lev
- The Rina Mor Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - M E Suzanne Lewis
- Department of Medical Genetics, BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Idit Maya
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach-Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Andre Megarbane
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon; Institut Jérôme Lejeune, Paris, France
| | - Vincent Michaud
- Department of Medical Genetics, CHU Bordeaux, Bordeaux, France
| | - Evelina Miele
- Department of Pediatric Hematology and Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Rome, Italy
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00165 Rome, Italy
| | - Roberta Onesimo
- Center for Rare Diseases and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany; Center of Functional Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Sylvia Redon
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France; Université de Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Dmitrijs Rots
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Karen Rouault
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France; Université de Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Jolanda Schieving
- Department of Pediatric Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Romano Tenconi
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, Padova, Italy
| | - Kevin Uguen
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France
| | - Nienke Verbeek
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christopher A Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA
| | - Keren Yosovich
- Molecular Genetic Laboratory, Edith Wolfson Medical Center, Holon, Israel
| | - Christopher J Yuskaitis
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Giuseppe Zampino
- Center for Rare Diseases and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Faculty of Medicine and Surgery, Catholic University of Sacred Heart, Rome, Italy
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada.
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.
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