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Choufani S, Cytrynbaum C, Chung BHY, Turinsky AL, Grafodatskaya D, Chen YA, Cohen ASA, Dupuis L, Butcher DT, Siu MT, Luk HM, Lo IFM, Lam STS, Caluseriu O, Stavropoulos DJ, Reardon W, Mendoza-Londono R, Brudno M, Gibson WT, Chitayat D, Weksberg R. NSD1 mutations generate a genome-wide DNA methylation signature. Nat Commun 2015; 6:10207. [PMID: 26690673 PMCID: PMC4703864 DOI: 10.1038/ncomms10207] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 11/13/2015] [Indexed: 01/07/2023] Open
Abstract
Sotos syndrome (SS) represents an important human model system for the study of epigenetic regulation; it is an overgrowth/intellectual disability syndrome caused by mutations in a histone methyltransferase, NSD1. As layered epigenetic modifications are often interdependent, we propose that pathogenic NSD1 mutations have a genome-wide impact on the most stable epigenetic mark, DNA methylation (DNAm). By interrogating DNAm in SS patients, we identify a genome-wide, highly significant NSD1+/−-specific signature that differentiates pathogenic NSD1 mutations from controls, benign NSD1 variants and the clinically overlapping Weaver syndrome. Validation studies of independent cohorts of SS and controls assigned 100% of these samples correctly. This highly specific and sensitive NSD1+/− signature encompasses genes that function in cellular morphogenesis and neuronal differentiation, reflecting cardinal features of the SS phenotype. The identification of SS-specific genome-wide DNAm alterations will facilitate both the elucidation of the molecular pathophysiology of SS and the development of improved diagnostic testing. Sotos syndrome is an growth syndrome characterized by advanced growth in childhood, characteristic facial appearance and intellectual disability. Here the authors identify a genome-wide DNA methylation signature that accurately diagnoses Sotos Syndrome and distinguishes it from similar conditions.
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Affiliation(s)
- S Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
| | - C Cytrynbaum
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Department of Molecular Genetics, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
| | - B H Y Chung
- Department of Pediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, 6/F, William MW Mong Block, 21 Sassoon Road, Pokfulam, Hong Kong
| | - A L Turinsky
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Centre for Computational Medicine, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
| | - D Grafodatskaya
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
| | - Y A Chen
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Institute of Medical Science, School of Graduate Studies, University of Toronto, 2374-1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - A S A Cohen
- Department of Medical Genetics, UBC, Child and Family Research Institute, 950W 28th Avenue, Vancouver, British Columbia V5Z 4H4, USA
| | - L Dupuis
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Department of Molecular Genetics, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
| | - D T Butcher
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
| | - M T Siu
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
| | - H M Luk
- Clinical Genetics Service, Department of Health, Cheung Sha Wan Jockey Club Clinic, 1/F-3/F, 2 Kwong Lee Road, Sham Shui Po, Kowloon, Hong Kong
| | - I F M Lo
- Clinical Genetics Service, Department of Health, Cheung Sha Wan Jockey Club Clinic, 1/F-3/F, 2 Kwong Lee Road, Sham Shui Po, Kowloon, Hong Kong
| | - S T S Lam
- Clinical Genetics Service, Department of Health, Cheung Sha Wan Jockey Club Clinic, 1/F-3/F, 2 Kwong Lee Road, Sham Shui Po, Kowloon, Hong Kong
| | - O Caluseriu
- Department of Medical Genetics, University of Alberta, 116 Street and 85 Avenue, Edmonton, Alberta, Canada T6G 2R3
| | - D J Stavropoulos
- Pediatric Laboratory Medicine, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Laboratory Medicine and Pathobiology, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
| | - W Reardon
- Our Lady's Hospital for Sick Children, Crumlin D12 N512 Ireland
| | - R Mendoza-Londono
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Department of Pediatrics, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
| | - M Brudno
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Centre for Computational Medicine, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Department of Computer Science, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
| | - W T Gibson
- Department of Medical Genetics, UBC, Child and Family Research Institute, 950W 28th Avenue, Vancouver, British Columbia V5Z 4H4, USA
| | - D Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Department of Molecular Genetics, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1.,Department of Pediatrics, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1.,Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5
| | - R Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Department of Molecular Genetics, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1.,Institute of Medical Science, School of Graduate Studies, University of Toronto, 2374-1 King's College Circle, Toronto, Ontario, Canada M5S 1A8.,Department of Pediatrics, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
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