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Schenkel LC, Aref-Eshghi E, Rooney K, Kerkhof J, Levy MA, McConkey H, Rogers RC, Phelan K, Sarasua SM, Jain L, Pauly R, Boccuto L, DuPont B, Cappuccio G, Brunetti-Pierri N, Schwartz CE, Sadikovic B. DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome. Clin Epigenetics 2021; 13:2. [PMID: 33407854 PMCID: PMC7789817 DOI: 10.1186/s13148-020-00990-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 07/17/2020] [Accepted: 12/09/2020] [Indexed: 12/31/2022] Open
Abstract
Background Phelan-McDermid syndrome is characterized by a range of neurodevelopmental phenotypes with incomplete penetrance and variable expressivity. It is caused by a variable size and breakpoint microdeletions in the distal long arm of chromosome 22, referred to as 22q13.3 deletion syndrome, including the SHANK3 gene. Genetic defects in a growing number of neurodevelopmental genes have been shown to cause genome-wide disruptions in epigenomic profiles referred to as epi-signatures in affected individuals. Results In this study we assessed genome-wide DNA methylation profiles in a cohort of 22 individuals with Phelan-McDermid syndrome, including 11 individuals with large (2 to 5.8 Mb) 22q13.3 deletions, 10 with small deletions (< 1 Mb) or intragenic variants in SHANK3 and one mosaic case. We describe a novel genome-wide DNA methylation epi-signature in a subset of individuals with Phelan-McDermid syndrome. Conclusion We identified the critical region including the BRD1 gene as responsible for the Phelan-McDermid syndrome epi-signature. Metabolomic profiles of individuals with the DNA methylation epi-signature showed significantly different metabolomic profiles indicating evidence of two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome.
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Affiliation(s)
- L C Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A3K7, Canada
| | - E Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - K Rooney
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - J Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - M A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - H McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - R C Rogers
- Greenville Office, Greenwood Genetic Center, Greenville, SC, 29605, USA
| | - K Phelan
- Genetics Laboratory, Florida Cancer Specialists and Research Institute, Fort Myers, FL, 33816, USA
| | | | - L Jain
- Greenwood Genetic Center, Greenwood, SC, 29646, USA.,Clemson University, Clemson, SC, 29634, USA
| | - R Pauly
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - L Boccuto
- Greenwood Genetic Center, Greenwood, SC, 29646, USA.,Clemson University, Clemson, SC, 29634, USA
| | - B DuPont
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - G Cappuccio
- Department of Translational Medicine, University Federico II, 80131, Naples, NA, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, NA, Italy
| | - N Brunetti-Pierri
- Department of Translational Medicine, University Federico II, 80131, Naples, NA, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, NA, Italy
| | - C E Schwartz
- Greenwood Genetic Center, Greenwood, SC, 29646, USA.
| | - B Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A3K7, Canada.
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Sciancalepore AG, Sallustio F, Girardo S, Passione LG, Camposeo A, Mele E, Di Lorenzo M, Costantino V, Schena FP, Pisignano D, Casino FG, Mostacci SD, Di Carlo M, Sabato A, Procida C, Creput C, Vanholder R, Stolear JC, Lefrancois G, Hanoy M, Nortier J, Potier J, Sereni L, Ferraresi M, Pereno A, Nazha M, Barbero S, Piccoli GB, Ficheux A, Gayrard N, Duranton F, Guzman C, Szwarc I, Bismuth -Mondolfo J, Brunet P, Servel MF, Argiles A, Bernardo A, Demers J, Hutchcraft A, Marbury TC, Minkus M, Muller M, Stallard R, Culleton B, Krieter DH, Korner T, Devine E, Ruth M, Jankowski J, Wanner C, Lemke HD, Surace A, Rovatti P, Steckiph D, Mancini E, Santoro A, Leypoldt JK, Agar BU, Bernardo A, Culleton BF, Vankova S, Havlin J, Klomp DJ, Van Beijnum F, Day JPR, Wieringa FP, Kooman JP, Gremmels H, Hazenbrink DH, Simonis F, Otten ML, Wester M, Boer WH, Joles JA, Gerritsen KG, Umimoto K, Shimamoto Y, Mastushima K, Miyata M, Muller M, Naik A, Pokropinski S, Bairstow S, Svatek J, Young S, Johnson R, Bernardo A, Rikker C, Juhasz E, Gaspar R, Rosivall L, Rusu E, Zilisteanu D, Balanica S, Achim C, Atasie T, Carstea F, Voiculescu M, Monzon Vazquez T, Saiz Garcia S, Mathani V, Escamilla Cabrera B, Cornelis T, Van Der Sande FM, Eloot S, Cardinaels E, Bekers O, Damoiseaux J, Leunissen KM, Kooman J, Baamonde Laborda E, Bosch Benitez-Parodi E, Perez Suarez G, Anton Perez G, Batista Garcia F, Lago Alonso M, Garcia Canton C, Hashimoto S, Seki M, Tomochika M, Yamamoto R, Okamoto N, Nishikawa A, Koike T, Ravagli E, Maldini L, Badiali F, Perazzini C, Lanciotti G, Steckiph D, Surace A, Rovatti P, Severi S, Rigotti A, McFarlane P, Marticorena R, Dacouris N, Pauly R, Nikitin S, Amdahl M, Bernardo A, Culleton B, Calabrese G, Mancuso D, Mazzotta A, Vagelli G, Balenzano C, Steckiph D, Bertucci A, Della Volpe M, Gonella M, Uchida T, Ando K, Kofuji M, Higuchi T, Momose N, Ito K, Ueda Y, Miyazawa H, Kaku Y, Nabata A, Hoshino T, Mori H, Yoshida I, Ookawara S, Tabei K, Umimoto K, Suyama M, Shimamoto Y, Miyata M, Kamada A, Sakai R, Minakawa A, Fukudome K, Hisanaga S, Ishihara T, Yamada K, Fukunaga S, Inagaki H, Tanaka C, Sato Y, Fujimoto S, Potier J, Bouet J, Queffeulou G, Bell R, Nolin L, Pichette V, Provencher H, Lamarche C, Nadeau-Fredette AC, Ouellet G, Leblanc M, Bezzaoucha S, Kouidmir Y, Kassis J, Alonso ML, Lafrance JP, Vallee M, Fils J, Mailley P, Cantaluppi V, Medica D, Quercia AD, Dellepiane S, Ferrario S, Gai M, Leonardi G, Guarena C, Caiazzo M, Biancone L, Enos M, Culleton B, Wiebenson D, Potier J, Hanoy M, Duquennoy S, Tingli W, Ling Z, Yunying S, Ping F, Dolley-Hitze T, Hamel D, Lombart ML, Leypoldt JK, Bernardo A, Hutchcraft AM, Vanholder R, Culleton BF, Movilli E, Camerini C, Gaggia P, Zubani R, Feller P, Pola A, Carli O, Salviani C, Manenti C, Cancarini G, Bozzoli L, Colombini E, Ricchiuti G, Pisanu G, Gargani L, Donadio C, Sidoti A, Lusini ML, Biagioli M, Ghezzi PM, Sereni L, Caiazzo M, Palladino G, Tomo T, Ishida K, Nakata T, Hamel D, Dolley-Hitze T. HAEMODIALYSIS TECHNIQUES AND ADEQUACY 1. Nephrol Dial Transplant 2014. [DOI: 10.1093/ndt/gfu153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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