1
|
Sabbagh Q, Haghshenas S, Piard J, Trouvé C, Amiel J, Attié-Bitach T, Balci T, Barat-Houari M, Belonis A, Boute O, Brightman DS, Bruel AL, Caraffi SG, Chatron N, Collet C, Dufour W, Edery P, Fong CT, Fusco C, Gatinois V, Gouy E, Guerrot AM, Heide S, Joshi A, Karp N, Keren B, Lesieur-Sebellin M, Levy J, Levy MA, Lozano C, Lyonnet S, Margot H, Marzin P, McConkey H, Michaud V, Nicolas G, Nizard M, Paulet A, Peluso F, Pernin V, Perrin L, Philippe C, Prasad C, Prasad M, Relator R, Rio M, Rondeau S, Ruault V, Ruiz-Pallares N, Sanchez E, Shears D, Siu VM, Sorlin A, Tedder M, Tharreau M, Mau-Them FT, van der Laan L, Van Gils J, Verloes A, Whalen S, Willems M, Yauy K, Zuntini R, Kerkhof J, Sadikovic B, Geneviève D. Clinico-biological refinement of BCL11B-related disorder and identification of an episignature: A series of 20 unreported individuals. Genet Med 2024; 26:101007. [PMID: 37860968 DOI: 10.1016/j.gim.2023.101007] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023] Open
Abstract
PURPOSE BCL11B-related disorder (BCL11B-RD) arises from rare genetic variants within the BCL11B gene, resulting in a distinctive clinical spectrum encompassing syndromic neurodevelopmental disorder, with or without intellectual disability, associated with facial features and impaired immune function. This study presents an in-depth clinico-biological analysis of 20 newly reported individuals with BCL11B-RD, coupled with a characterization of genome-wide DNA methylation patterns of this genetic condition. METHODS Through an international collaboration, clinical and molecular data from 20 individuals were systematically gathered, and a comparative analysis was conducted between this series and existing literature. We further scrutinized peripheral blood DNA methylation profile of individuals with BCL11B-RD, contrasting them with healthy controls and other neurodevelopmental disorders marked by established episignature. RESULTS Our findings unveil rarely documented clinical manifestations, notably including Rubinstein-Taybi-like facial features, craniosynostosis, and autoimmune disorders, all manifesting within the realm of BCL11B-RD. We refine the intricacies of T cell compartment alterations of BCL11B-RD, revealing decreased levels naive CD4+ T cells and recent thymic emigrants while concurrently observing an elevated proportion of effector-memory expressing CD45RA CD8+ T cells (TEMRA). Finally, a distinct DNA methylation episignature exclusive to BCL11B-RD is unveiled. CONCLUSION This study serves to enrich our comprehension of the clinico-biological landscape of BCL11B-RD, potentially furnishing a more precise framework for diagnosis and follow-up of individuals carrying pathogenic BCL11B variant. Moreover, the identification of a unique DNA methylation episignature offers a valuable diagnosis tool for BCL11B-RD, thereby facilitating routine clinical practice by empowering physicians to reevaluate variants of uncertain significance within the BCL11B gene.
Collapse
Affiliation(s)
- Quentin Sabbagh
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Juliette Piard
- University Hospital of Besançon, Department of Clinical Genetics, Besançon, France
| | - Chloé Trouvé
- University Hospital of Besançon, Department of Clinical Genetics, Besançon, France
| | - Jeanne Amiel
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Tania Attié-Bitach
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Tugce Balci
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Mouna Barat-Houari
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Alyce Belonis
- Cincinnati Children's Hospital Medical Center, Division of Human Genetics, Cincinnati, OH; University of Cincinnati College of Medicine, Department of Pediatrics, Cincinnati, OH
| | - Odile Boute
- University Hospital of Lille, Department of Clinical Genetics, Lille, France
| | - Diana S Brightman
- Cincinnati Children's Hospital Medical Center, Division of Human Genetics, Cincinnati, OH
| | - Ange-Line Bruel
- University Hospital of Dijon, Laboratory of Molecular Genetics and Cytogenetics, Inserm UMR 1231 GAD, Dijon, France
| | | | - Nicolas Chatron
- University Hospital of Lyon, Laboratory of Medical Genetics, AURAGEN Platform, Lyon, France
| | - Corinne Collet
- Robert Debré University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - William Dufour
- University Hospital of Lille, Department of Clinical Genetics, Lille, France
| | - Patrick Edery
- University Hospital of Lyon, Department of Clinical Genetics, Lyon, France
| | - Chin-To Fong
- University of Rochester, Department of Genetics, Rochester, NY
| | - Carlo Fusco
- Azienda USL-IRCCS di Reggio Emilia, Child Neurology and Psychiatry Unit, 42123 Reggio Emilia, Italy
| | - Vincent Gatinois
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Evan Gouy
- University Hospital of Lyon, Department of Clinical Genetics, Lyon, France
| | - Anne-Marie Guerrot
- Rouen-Normandie University, University Hospital of Rouen, Department of Genetics, Reference Center for Developmental Disorders, Inserm UMR1245, F-76000 Rouen, France
| | - Solveig Heide
- Pitié-Salpêtrière University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Aakash Joshi
- Churchill Hospital, Department of Clinical Genetics, ERN-ITHACA, Oxford, United Kingdom
| | - Natalya Karp
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Boris Keren
- Pitié-Salpêtrière University Hospital, Laboratory of Molecular Genetics and Cytogenetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Marion Lesieur-Sebellin
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Jonathan Levy
- Robert Debré University Hospital, Laboratory of Cytogenetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Claire Lozano
- University Hospital of Montpellier, Department of Immunology, Montpellier, France
| | - Stanislas Lyonnet
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Henri Margot
- University of Bordeaux, University Hospital of Bordeaux, Department of Medical Genetics, MRGM Inserm UMR1211, F-33000 Bordeaux, France
| | - Pauline Marzin
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Vincent Michaud
- University of Bordeaux, University Hospital of Bordeaux, Department of Medical Genetics, MRGM Inserm UMR1211, F-33000 Bordeaux, France
| | - Gaël Nicolas
- Rouen-Normandie University, University Hospital of Rouen, Department of Genetics, Reference Center for Developmental Disorders, Inserm UMR1245, F-76000 Rouen, France
| | - Mevyn Nizard
- Necker-Enfants Malades University Hospital, Department of Pediatric Endocrinology, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Alix Paulet
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Francesca Peluso
- Azienda USL-IRCCS di Reggio Emilia, Medical Genetics Unit, 42123 Reggio Emilia, Italy
| | - Vincent Pernin
- University of Montpellier, Department of Nephrology, Montpellier, France
| | - Laurence Perrin
- Robert Debré University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Christophe Philippe
- University Hospital of Dijon, Laboratory of Molecular Genetics and Cytogenetics, Inserm UMR 1231 GAD, Dijon, France; Hospital of Metz-Thionville, Mercy Hospital, Laboratory of Genetics, Metz, France
| | - Chitra Prasad
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Madhavi Prasad
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Marlène Rio
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Sophie Rondeau
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Valentin Ruault
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France
| | - Nathalie Ruiz-Pallares
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Elodie Sanchez
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Debbie Shears
- Churchill Hospital, Department of Clinical Genetics, ERN-ITHACA, Oxford, United Kingdom
| | - Victoria Mok Siu
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Arthur Sorlin
- University Hospital of Dijon, Laboratory of Molecular Genetics and Cytogenetics, Inserm UMR 1231 GAD, Dijon, France
| | | | - Mylène Tharreau
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Frédéric Tran Mau-Them
- University Hospital of Dijon, Laboratory of Molecular Genetics and Cytogenetics, Inserm UMR 1231 GAD, Dijon, France
| | - Liselot van der Laan
- University of Amsterdam, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, AUMC Department of Human Genetics, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Julien Van Gils
- University of Bordeaux, University Hospital of Bordeaux, Department of Medical Genetics, MRGM Inserm UMR1211, F-33000 Bordeaux, France
| | - Alain Verloes
- Robert Debré University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Sandra Whalen
- Pitié-Salpêtrière University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Marjolaine Willems
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France
| | - Kévin Yauy
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France
| | - Roberta Zuntini
- Azienda USL-IRCCS di Reggio Emilia, Medical Genetics Unit, 42123 Reggio Emilia, Italy
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - David Geneviève
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France.
| |
Collapse
|
2
|
de Boer E, Ockeloen CW, Kampen RA, Hampstead JE, Dingemans AJM, Rots D, Lütje L, Ashraf T, Baker R, Barat-Houari M, Angle B, Chatron N, Denommé-Pichon AS, Devinsky O, Dubourg C, Elmslie F, Elloumi HZ, Faivre L, Fitzgerald-Butt S, Geneviève D, Goos JAC, Helm BM, Kini U, Lasa-Aranzasti A, Lesca G, Lynch SA, Mathijssen IMJ, McGowan R, Monaghan KG, Odent S, Pfundt R, Putoux A, van Reeuwijk J, Santen GWE, Sasaki E, Sorlin A, van der Spek PJ, Stegmann APA, Swagemakers SMA, Valenzuela I, Viora-Dupont E, Vitobello A, Ware SM, Wéber M, Gilissen C, Low KJ, Fisher SE, Vissers LELM, Wong MMK, Kleefstra T. Missense variants in ANKRD11 cause KBG syndrome by impairment of stability or transcriptional activity of the encoded protein. Genet Med 2023; 25:100962. [PMID: 37658852 DOI: 10.1016/j.gim.2023.100962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023] Open
Affiliation(s)
- Elke de Boer
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | | | - Rosalie A Kampen
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Juliet E Hampstead
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Alexander J M Dingemans
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Dmitrijs Rots
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Lukas Lütje
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Tazeen Ashraf
- Department of Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom; Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | | | - Mouna Barat-Houari
- Genetic Laboratory of Rare and Autoinflammatory Diseases, Department of Medical Genetics, Rare Diseases and Personalized Medicine, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Brad Angle
- Advocate Children's Hospital, Park Ridge, IL
| | - Nicolas Chatron
- Service de Génétique, Hospices Civils de Lyon, Bron, France; Institut NeuroMyoGene, CNRS UMR5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Anne-Sophie Denommé-Pichon
- Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR1231-Inserm, Dijon, France; Laboratoire de Génétique Chromosomique et Moléculaire, UF6254 Innovation en Diagnostic Génomique des Maladies Rares, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Orrin Devinsky
- Department of Neurology, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Christèle Dubourg
- Service de Génétique Moléculaire et Génomique Médicale, CHU de Rennes, Rennes, France; University of Rennes, CNRS, IGDR, UMR 6290, Rennes, France
| | - Frances Elmslie
- South West Thames Regional Clinical Genetics Service, St George's Hospital, University of London, London, United Kingdom
| | | | - Laurence Faivre
- Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR1231-Inserm, Dijon, France; Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France; Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Sarah Fitzgerald-Butt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indiana University, Indianapolis, IN
| | - David Geneviève
- Medical Genetic Department, Rare Diseases and Personalized Medicine, Montpellier University, Inserm U1183, CHU Montpellier, Montpellier, France
| | - Jacqueline A C Goos
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Dutch Craniofacial Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Benjamin M Helm
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indiana University, Indianapolis, IN; Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Amaia Lasa-Aranzasti
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital and Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Gaetan Lesca
- Service de Génétique, Hospices Civils de Lyon, Bron, France; Institut NeuroMyoGene, CNRS UMR5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Sally A Lynch
- Department of Clinical Genetics, Children's Health Ireland at Crumlin and Temple Street, Dublin, Ireland
| | - Irene M J Mathijssen
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Dutch Craniofacial Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ruth McGowan
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Scottish Genomes Partnership, Glasgow, United Kingdom
| | | | - Sylvie Odent
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, ERN ITHACA, Hôpital Sud, Rennes, France
| | - Rolph Pfundt
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
| | - Audrey Putoux
- Service de Génétique - Centre de Référence Anomalies du Développement, Hospices Civils de Lyon, Bron, France; Équipe GENDEV, Centre de Recherche en Neurosciences de Lyon, INSERM U1028 CNRS UMR5292, Université Claude Bernard Lyon 1, Lyon, France
| | - Jeroen van Reeuwijk
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Erina Sasaki
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Arthur Sorlin
- Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR1231-Inserm, Dijon, France; Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Peter J van der Spek
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Department of Clinical Genetics, Maastricht University Medical Center+, Maastricht University, Maastricht, The Netherlands
| | - Sigrid M A Swagemakers
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital and Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Eléonore Viora-Dupont
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Antonio Vitobello
- Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR1231-Inserm, Dijon, France; Laboratoire de Génétique Chromosomique et Moléculaire, UF6254 Innovation en Diagnostic Génomique des Maladies Rares, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Stephanie M Ware
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indiana University, Indianapolis, IN; Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
| | - Mathys Wéber
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Christian Gilissen
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Karen J Low
- Department of Clinical Genetics, University Hospital Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
| | - Simon E Fisher
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands; Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Maggie M K Wong
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands; Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, The Netherlands
| |
Collapse
|
3
|
de Boer E, Ockeloen CW, Kampen RA, Hampstead JE, Dingemans AJM, Rots D, Lütje L, Ashraf T, Baker R, Barat-Houari M, Angle B, Chatron N, Denommé-Pichon AS, Devinsky O, Dubourg C, Elmslie F, Elloumi HZ, Faivre L, Fitzgerald-Butt S, Geneviève D, Goos JAC, Helm BM, Kini U, Lasa-Aranzasti A, Lesca G, Lynch SA, Mathijssen IMJ, McGowan R, Monaghan KG, Odent S, Pfundt R, Putoux A, van Reeuwijk J, Santen GWE, Sasaki E, Sorlin A, van der Spek PJ, Stegmann APA, Swagemakers SMA, Valenzuela I, Viora-Dupont E, Vitobello A, Ware SM, Wéber M, Gilissen C, Low KJ, Fisher SE, Vissers LELM, Wong MMK, Kleefstra T. Missense variants in ANKRD11 cause KBG syndrome by impairment of stability or transcriptional activity of the encoded protein. Genet Med 2022; 24:2051-2064. [PMID: 35833929 DOI: 10.1016/j.gim.2022.06.007] [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] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 12/01/2022] Open
Abstract
PURPOSE Although haploinsufficiency of ANKRD11 is among the most common genetic causes of neurodevelopmental disorders, the role of rare ANKRD11 missense variation remains unclear. We characterized clinical, molecular, and functional spectra of ANKRD11 missense variants. METHODS We collected clinical information of individuals with ANKRD11 missense variants and evaluated phenotypic fit to KBG syndrome. We assessed pathogenicity of variants through in silico analyses and cell-based experiments. RESULTS We identified 20 unique, mostly de novo, ANKRD11 missense variants in 29 individuals, presenting with syndromic neurodevelopmental disorders similar to KBG syndrome caused by ANKRD11 protein truncating variants or 16q24.3 microdeletions. Missense variants significantly clustered in repression domain 2 at the ANKRD11 C-terminus. Of the 10 functionally studied missense variants, 6 reduced ANKRD11 stability. One variant caused decreased proteasome degradation and loss of ANKRD11 transcriptional activity. CONCLUSION Our study indicates that pathogenic heterozygous ANKRD11 missense variants cause the clinically recognizable KBG syndrome. Disrupted transrepression capacity and reduced protein stability each independently lead to ANKRD11 loss-of-function, consistent with haploinsufficiency. This highlights the diagnostic relevance of ANKRD11 missense variants, but also poses diagnostic challenges because the KBG-associated phenotype may be mild and inherited pathogenic ANKRD11 (missense) variants are increasingly observed, warranting stringent variant classification and careful phenotyping.
Collapse
Affiliation(s)
- Elke de Boer
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | | | - Rosalie A Kampen
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Juliet E Hampstead
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Alexander J M Dingemans
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Dmitrijs Rots
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Lukas Lütje
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Tazeen Ashraf
- Department of Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom; Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | | | - Mouna Barat-Houari
- Genetic Laboratory of Rare and Autoinflammatory Diseases, Department of Medical Genetics, Rare Diseases and Personalized Medicine, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Brad Angle
- Advocate Children's Hospital, Park Ridge, IL
| | - Nicolas Chatron
- Service de Génétique, Hospices Civils de Lyon, Bron, France; Institut NeuroMyoGene, CNRS UMR5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Anne-Sophie Denommé-Pichon
- Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR1231-Inserm, Dijon, France; Laboratoire de Génétique Chromosomique et Moléculaire, UF6254 Innovation en Diagnostic Génomique des Maladies Rares, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Orrin Devinsky
- Department of Neurology, NYU Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Christèle Dubourg
- Service de Génétique Moléculaire et Génomique Médicale, CHU de Rennes, Rennes, France; University of Rennes, CNRS, IGDR, UMR 6290, Rennes, France
| | - Frances Elmslie
- South West Thames Regional Clinical Genetics Service, St George's Hospital, University of London, London, United Kingdom
| | | | - Laurence Faivre
- Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR1231-Inserm, Dijon, France; Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France; Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Sarah Fitzgerald-Butt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indiana University, Indianapolis, IN
| | - David Geneviève
- Medical Genetic Department, Rare Diseases and Personalized Medicine, Montpellier University, Inserm U1183, CHU Montpellier, Montpellier, France
| | - Jacqueline A C Goos
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Dutch Craniofacial Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Benjamin M Helm
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indiana University, Indianapolis, IN; Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Amaia Lasa-Aranzasti
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital and Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Gaetan Lesca
- Service de Génétique, Hospices Civils de Lyon, Bron, France; Institut NeuroMyoGene, CNRS UMR5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Sally A Lynch
- Department of Clinical Genetics, Children's Health Ireland at Crumlin and Temple Street, Dublin, Ireland
| | - Irene M J Mathijssen
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Dutch Craniofacial Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ruth McGowan
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Scottish Genomes Partnership, Glasgow, United Kingdom
| | | | - Sylvie Odent
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, ERN ITHACA, Hôpital Sud, Rennes, France
| | - Rolph Pfundt
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
| | - Audrey Putoux
- Service de Génétique - Centre de Référence Anomalies du Développement, Hospices Civils de Lyon, Bron, France; Équipe GENDEV, Centre de Recherche en Neurosciences de Lyon, INSERM U1028 CNRS UMR5292, Université Claude Bernard Lyon 1, Lyon, France
| | - Jeroen van Reeuwijk
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Erina Sasaki
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Arthur Sorlin
- Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR1231-Inserm, Dijon, France; Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Peter J van der Spek
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Department of Clinical Genetics, Maastricht University Medical Center+, Maastricht University, Maastricht, The Netherlands
| | - Sigrid M A Swagemakers
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital and Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Eléonore Viora-Dupont
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Antonio Vitobello
- Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR1231-Inserm, Dijon, France; Laboratoire de Génétique Chromosomique et Moléculaire, UF6254 Innovation en Diagnostic Génomique des Maladies Rares, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Stephanie M Ware
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indiana University, Indianapolis, IN; Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
| | - Mathys Wéber
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Christian Gilissen
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Karen J Low
- Department of Clinical Genetics, University Hospital Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
| | - Simon E Fisher
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands; Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Maggie M K Wong
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands; Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, The Netherlands
| |
Collapse
|
4
|
Wells CF, Boursier G, Yauy K, Ruiz-Pallares N, Mechin D, Ruault V, Tharreau M, Blanchet P, Pinson L, Coubes C, Fila M, Baleine J, Pidoux O, Badr M, Milesi C, Cambonie G, Mesnage R, Dereure M, Ardouin O, Guignard T, Geneviève D, Barat-Houari M, Willems M. Rapid exome sequencing in critically ill infants: implementation in routine care from French regional hospital's perspective. Eur J Hum Genet 2022; 30:1076-1082. [PMID: 35729264 PMCID: PMC9436918 DOI: 10.1038/s41431-022-01133-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/18/2022] [Accepted: 06/09/2022] [Indexed: 01/15/2023] Open
Abstract
This monocentric study included fifteen children under a year old in intensive care with suspected monogenic conditions for rapid trio exome sequencing (rES) between April 2019 and April 2021. The primary outcome was the time from blood sampling to rapid exome sequencing report to parents. All results were available within 16 days and were reported to parents in or under 16 days in 13 of the 15 individuals (86%). Six individuals (40%) received a diagnosis with rES, two had a genetic condition not diagnosed by rES. Eight individuals had their care impacted by their rES results, four were discharged or died before the results. This small-scale study shows that rES can be implemented in a regional University hospital with rapid impactful diagnosis to improve care in critically ill infants.
Collapse
Affiliation(s)
- Constance F Wells
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Guilaine Boursier
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Kevin Yauy
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
- Institute of Advanced Biosciences, Centre de recherche UGA, Inserm U 1209, CNRS UMR 5309, Grenoble, France
- SeqOne Genomics, Montpellier, France
| | - Nathalie Ruiz-Pallares
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Déborah Mechin
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Valentin Ruault
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Mylène Tharreau
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Patricia Blanchet
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Lucile Pinson
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Christine Coubes
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Marc Fila
- Pediatric Nephrology department, Montpellier university hospital, Univ, Montpellier, France
| | - Julien Baleine
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Odile Pidoux
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Maliha Badr
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Christophe Milesi
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Gilles Cambonie
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Renaud Mesnage
- Department of Neonatal Medicine and Pediatric Intensive Care, Montpellier university Hospital, Univ, Montpellier, France
| | - Maëlle Dereure
- Clinical research and epidemiology department, Montpellier university hospital, Univ, Montpellier, France
| | - Olivier Ardouin
- Molecular medicine and genomics platform, Montpellier university hospital, Montpellier, France
| | - Thomas Guignard
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Montpellier university hospital, Univ, Montpellier, France
| | - David Geneviève
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Mouna Barat-Houari
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Marjolaine Willems
- Department of Medical Genetics, Rare diseases and Personalized medicine, CHU Montpellier, Univ Montpellier, Montpellier, France.
- Inserm U1298, INM, CHU Montpellier, Univ. Montpellier, Montpellier, France.
- Reference Centre AD SOOR, AnDDI-RARE, Competence Centre for Rare Skeletal Disorders, OSCAR Network, Montpellier, France.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Rouxel F, Relator R, Kerkhof J, McConkey H, Levy M, Dias P, Barat-Houari M, Bednarek N, Boute O, Chatron N, Cherik F, Delahaye-Duriez A, Doco-Fenzy M, Faivre L, Gauthier LW, Heron D, Hildebrand MS, Lesca G, Lespinasse J, Mazel B, Menke LA, Morgan AT, Pinson L, Quelin C, Rossi M, Ruiz-Pallares N, Tran-Mau-Them F, Van Kessel IN, Vincent M, Weber M, Willems M, Leguyader G, Sadikovic B, Genevieve D. CDK13-related disorder: Report of a series of 18 previously unpublished individuals and description of an epigenetic signature. Genet Med 2022; 24:1096-1107. [PMID: 35063350 DOI: 10.1016/j.gim.2021.12.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 01/02/2023] Open
Abstract
PURPOSE Rare genetic variants in CDK13 are responsible for CDK13-related disorder (CDK13-RD), with main clinical features being developmental delay or intellectual disability, facial features, behavioral problems, congenital heart defect, and seizures. In this paper, we report 18 novel individuals with CDK13-RD and provide characterization of genome-wide DNA methylation. METHODS We obtained clinical phenotype and neuropsychological data for 18 and 10 individuals, respectively, and compared this series with the literature. We also compared peripheral blood DNA methylation profiles in individuals with CDK13-RD, controls, and other neurodevelopmental disorders episignatures. Finally, we developed a support vector machine-based classifier distinguishing CDK13-RD and non-CDK13-RD samples. RESULTS We reported health and developmental parameters, clinical data, and neuropsychological profile of individuals with CDK13-RD. Genome-wide differential methylation analysis revealed a global hypomethylated profile in individuals with CDK13-RD in a highly sensitive and specific model that could aid in reclassifying variants of uncertain significance. CONCLUSION We describe the novel features such as anxiety disorder, cryptorchidism, and disrupted sleep in CDK13-RD. We define a CDK13-RD DNA methylation episignature as a diagnostic tool and a defining functional feature of the evolving clinical presentation of this disorder. We also show overlap of the CDK13 DNA methylation profile in an individual with a functionally and clinically related CCNK-related disorder.
Collapse
Affiliation(s)
- Flavien Rouxel
- Génétique clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, INSERM U1183, ERN ITHACA, Montpellier, France
| | - Raissa Relator
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer Kerkhof
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Haley McConkey
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Michael Levy
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Patricia Dias
- Genetics Department, Hospital Center of Lisbon North, ERN ITHACA, Lisbon, Portugal
| | - Mouna Barat-Houari
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique des Maladies Rares et Auto-Inflammatoires, CHU Montpellier, Université de Montpellier, Montpellier, France
| | - Nathalie Bednarek
- Genetics Department, CHU Reims, Medical school IFR53, EA3801, Reims, France
| | - Odile Boute
- Genetics Department, Guy Fontaine Medical Center, CLAD Nord de France, Jeanne de Flandre Hospital, CHRU Lille, Lille, France
| | - Nicolas Chatron
- Genetics Department, Lyon University Hospital, and Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Claude Bernard Lyon 1 University, Lyon, France
| | - Florian Cherik
- Genetics Department, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Andrée Delahaye-Duriez
- Department of Histology Embryology and Cytogenetics, Jean Verdier Hospital; Paris 13 University, Sorbonne Paris Cité, UFR SMBH Bobigny; PROTECT, INSERM, Paris Diderot University, Paris, France
| | - Martine Doco-Fenzy
- Genetics Department, CHU Reims, Medical school IFR53, EA3801, Reims, France
| | - Laurence Faivre
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, CHU Dijon, Dijon, France; Genetics of Developmental Disorders, INSERM - Bourgogne Franche-Comté University, UMR 1231 GAD Team, Dijon, France
| | - Lucas W Gauthier
- Genetics Department, Lyon University Hospital, and Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Claude Bernard Lyon 1 University, Lyon, France
| | - Delphine Heron
- Genetics Department, University Hospital Pitié-Salpétrière, Paris, France
| | - Michael S Hildebrand
- Epilepsy Research Center, Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, Victoria, Australia; Murdoch Children's Research Institute, Department of Audiology and Speech Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Gaëtan Lesca
- Genetics Department, Lyon University Hospital, and Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Claude Bernard Lyon 1 University, Lyon, France
| | | | - Benoit Mazel
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, CHU Dijon, Dijon, France
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, ERN ITHACA, Amsterdam, Netherlands
| | - Angela T Morgan
- Department of Audiology and Speech Pathology, Melbourne School of Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Lucile Pinson
- Génétique clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, INSERM U1183, ERN ITHACA, Montpellier, France
| | - Chloe Quelin
- Department of Clinical Genetics, CLAD Ouest, CHU de Rennes, Hôpital Sud, Rennes, France
| | - Massimiliano Rossi
- Genetics Department, Lyon University Hospital, and Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Claude Bernard Lyon 1 University, Lyon, France; Genetics Department, Referral Centre for Developmental Abnormalities, Lyon University Hospital Lyon, France; INSERM U1028, CNRS UMR5292, Lyon Neuroscience Research Centre, GENDEV Team, Claude Bernard Lyon 1 University, Lyon, France
| | - Nathalie Ruiz-Pallares
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique des Maladies Rares et Auto-Inflammatoires, CHU Montpellier, Université de Montpellier, Montpellier, France
| | - Frederic Tran-Mau-Them
- Genetics of Developmental Disorders, INSERM - Bourgogne Franche-Comté University, UMR 1231 GAD Team, Dijon, France; Functional Unit 6254 Innovation in Genomic Diagnosis of Rare Diseases, CHU Dijon Bourgogne, Dijon, France
| | - Imke N Van Kessel
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, ERN ITHACA, Amsterdam, Netherlands
| | | | - Mathys Weber
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, CHU Dijon, Dijon, France
| | - Marjolaine Willems
- Génétique clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, INSERM U1183, ERN ITHACA, Montpellier, France
| | - Gwenael Leguyader
- Genetics Department, CHU de Poitiers, Poitiers University Hospital, Poitiers, France
| | - Bekim Sadikovic
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
| | - David Genevieve
- Génétique clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, INSERM U1183, ERN ITHACA, Montpellier, France.
| |
Collapse
|
7
|
Cherik F, Reilly J, Kerkhof J, Levy M, McConkey H, Barat-Houari M, Butler KM, Coubes C, Lee JA, Le Guyader G, Louie RJ, Patterson WG, Tedder ML, Bak M, Hammer TB, Craigen W, Démurger F, Dubourg C, Fradin M, Franciskovich R, Frengen E, Friedman J, Palares NR, Iascone M, Misceo D, Monin P, Odent S, Philippe C, Rouxel F, Saletti V, Strømme P, Thulin PC, Sadikovic B, Genevieve D. DNA methylation episignature in Gabriele-de Vries syndrome. Genet Med 2022; 24:905-914. [PMID: 35027293 DOI: 10.1016/j.gim.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE Gabriele-de Vries syndrome (GADEVS) is a rare genetic disorder characterized by developmental delay and/or intellectual disability, hypotonia, feeding difficulties, and distinct facial features. To refine the phenotype and to better understand the molecular basis of the syndrome, we analyzed clinical data and performed genome-wide DNA methylation analysis of a series of individuals carrying a YY1 variant. METHODS Clinical data were collected for 13 individuals not yet reported through an international call for collaboration. DNA was collected for 11 of these individuals and 2 previously reported individuals in an attempt to delineate a specific DNA methylation signature in GADEVS. RESULTS Phenotype in most individuals overlapped with the previously described features. We described 1 individual with atypical phenotype, heterozygous for a missense variant in a domain usually not involved in individuals with YY1 pathogenic missense variations. We also described a specific peripheral blood DNA methylation profile associated with YY1 variants. CONCLUSION We reported a distinct DNA methylation episignature in GADEVS. We expanded the clinical profile of GADEVS to include thin/sparse hair and cryptorchidism. We also highlighted the utility of DNA methylation episignature analysis for classification of variants of unknown clinical significance.
Collapse
Affiliation(s)
- Florian Cherik
- Department of Medical Genetics, Reference Centre for Rare Diseases, Developmental Anomalies and Malformation Syndromes Sud-Est, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Jennifer Kerkhof
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph's Healthcare, London, Ontario, Canada
| | - Michael Levy
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph's Healthcare, London, Ontario, Canada
| | - Haley McConkey
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph's Healthcare, London, Ontario, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Kameryn M Butler
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Christine Coubes
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Montpellier University Hospital, Montpellier, France
| | - Jennifer A Lee
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Gwenael Le Guyader
- Clinical Genetics Department, Poitiers University Hospital, Poitiers, France
| | - Raymond J Louie
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Wesley G Patterson
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Matthew L Tedder
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Mads Bak
- Clinical genetic department, Righospitalet, Copenhagen, Denmark
| | - Trine Bjørg Hammer
- Clinical genetic department, Righospitalet, Copenhagen, Denmark; Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - William Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Florence Démurger
- Medical Genetics Department, Bretagne-Atlantique Hospital, Vannes, France
| | - Christèle Dubourg
- Department of Molecular Genetics and Genomics, Rennes University Hospital, Rennes, France; Univ Rennes, CNRS, IGDR, UMR 6290, Rennes, France
| | - Mélanie Fradin
- Department of Clinical Genetics, Reference Centre for Rare Diseases, CLAD Ouest, Rennes University Hospital, Rennes, France
| | - Rachel Franciskovich
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospitals and University of Oslo, Oslo, Norway
| | - Jennifer Friedman
- Departments of Neurosciences and Pediatrics, University of California San Diego, San Diego, CA; Division of Neurology, Rady Children's Hospital, San Diego, CA; Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA
| | - Nathalie Ruiz Palares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Maria Iascone
- Medical Genetics Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Doriana Misceo
- Department of Medical Genetics, Oslo University Hospitals and University of Oslo, Oslo, Norway
| | - Pauline Monin
- Department of Medical Genetics, Women Mother Children Hospital, Hospices Civils de Lyon, Lyon, France
| | - Sylvie Odent
- Department of Medical Genetics, Reference Center for Developmental Anomalies, CLAD Ouest, Rennes University Hospital, ERN ITHACA, CNRS UMR 6290, Genetics and Development Institute, Rennes University, Rennes, France
| | - Christophe Philippe
- Functional Unit of Innovative Diagnosis for Rare Diseases, Dijon Bourgogne University Hospital, Dijon, France
| | - Flavien Rouxel
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Montpellier University Hospital, Montpellier, France
| | - Veronica Saletti
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Petter Strømme
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, and University of Oslo, Oslo, Norway
| | | | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph's Healthcare, London, Ontario, Canada.
| | - David Genevieve
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Montpellier University Hospital, Montpellier, France.
| |
Collapse
|
8
|
Willems M, Amouroux C, Barat-Houari M, Salles JP, Edouard T. Exploring the genetic causes of isolated short stature. What has happened to idiopathic short stature? Arch Pediatr 2022; 28:8S27-8S32. [PMID: 37870530 DOI: 10.1016/s0929-693x(22)00040-9] [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] [Indexed: 11/25/2022]
Abstract
Statural growth is underpinned by development of the growth plate during the process of endochondral ossification, which is strongly regulated by numerous local factors (intracellular, paracrine and extracellular matrix factors) and systemic factors (nutrition, hormones, proinflammatory cytokines and extracellular fluids). This explains why growth retardation can be associated with numerous pathologies, particularly genetic syndromes, hormonal or inflammatory conditions, or gastrointestinal disorders having a nutritional impact. However, in most cases (80%), no specific aetiology is found after clinical investigation and conventional additional tests have been carried out. In such cases, "idiopathic" short stature is diagnosed, which includes patients presenting with constitutional delay of growth and development and familial short stature, but also patients with very subtle constitutional skeletal dysplasia which are not easily identifiable. In recent years, new methods of genetic investigation (e.g. gene panels, exome or genome sequencing) have made it possible to identify many genetic variants associated with apparently isolated short stature. Indeed, it is still difficult to estimate the proportion of patients presenting with idiopathic short stature for which a molecular diagnosis of monogenic conditions could be made. This estimate varies hugely depending on the thoroughness of the clinical, laboratory and radiological assessments performed prior to molecular analysis, since retrospective analysis of positive cases usually reveals subtle signs of underlying syndromes or rare skeletal disorders. Molecular diagnosis in children is important to be able to offer genetic counselling and to organise patient management. Moreover, improved understanding of the molecular basis of these cases of short stature opens up numerous possibilities for more specific treatments targeting the growth plate. © 2022 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.
Collapse
Affiliation(s)
- M Willems
- Medical Genetic Department for Rare Diseases and Personalised Medicine, Reference Centre AD SOOR, AnDDI-RARE, Competence Centre for Rare Skeletal Disorders, OSCAR Network, Inserm U1298, INM, Arnaud de Villeneuve Hospital and University of Montpellier, Montpellier, France
| | - C Amouroux
- Paediatric Endocrine Unit, Competence Centre for Rare Diseases of Calcium and Phosphate Metabolism, OSCAR Network, Arnaud de Villeneuve Hospital and University of Montpellier, Montpellier, France
| | - M Barat-Houari
- Molecular Biology Unit, Competence Centre for Rare Skeletal Disorders, OSCAR Network, Arnaud de Villeneuve Hospital and University of Montpellier, Montpellier, France
| | - J-P Salles
- Endocrine, Bone Diseases and Genetics Unit, Reference Centre for Rare Diseases of Calcium and Phosphate Metabolism and Competence Centre for Rare Skeletal Disorders, ERN BOND, OSCAR Network, Children's Hospital, Toulouse University Hospital, Toulouse, France
| | - T Edouard
- Endocrine, Bone Diseases and Genetics Unit, Reference Centre for Rare Diseases of Calcium and Phosphate Metabolism and Competence Centre for Rare Skeletal Disorders, ERN BOND, OSCAR Network, Children's Hospital, Toulouse University Hospital, Toulouse, France.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Rouxel F, Yauy K, Boursier G, Gatinois V, Barat-Houari M, Sanchez E, Lacombe D, Arpin S, Giuliano F, Haye D, Rio M, Toutain A, Dieterich K, Brischoux-Boucher E, Julia S, Nizon M, Afenjar A, Keren B, Jacquette A, Moutton S, Jacquemont ML, Duflos C, Capri Y, Amiel J, Blanchet P, Lyonnet S, Sanlaville D, Genevieve D. Using deep-neural-network-driven facial recognition to identify distinct Kabuki syndrome 1 and 2 gestalt. Eur J Hum Genet 2021; 30:682-686. [PMID: 34803161 DOI: 10.1038/s41431-021-00994-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 10/06/2021] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
Kabuki syndrome (KS) is a rare genetic disorder caused by mutations in two major genes, KMT2D and KDM6A, that are responsible for Kabuki syndrome 1 (KS1, OMIM147920) and Kabuki syndrome 2 (KS2, OMIM300867), respectively. We lack a description of clinical signs to distinguish KS1 and KS2. We used facial morphology analysis to detect any facial morphological differences between the two KS types. We used a facial-recognition algorithm to explore any facial morphologic differences between the two types of KS. We compared several image series of KS1 and KS2 individuals, then compared images of those of Caucasian origin only (12 individuals for each gene) because this was the main ethnicity in this series. We also collected 32 images from the literature to amass a large series. We externally validated results obtained by the algorithm with evaluations by trained clinical geneticists using the same set of pictures. Use of the algorithm revealed a statistically significant difference between each group for our series of images, demonstrating a different facial morphotype between KS1 and KS2 individuals (mean area under the receiver operating characteristic curve = 0.85 [p = 0.027] between KS1 and KS2). The algorithm was better at discriminating between the two types of KS with images from our series than those from the literature (p = 0.0007). Clinical geneticists trained to distinguished KS1 and KS2 significantly recognised a unique facial morphotype, which validated algorithm findings (p = 1.6e-11). Our deep-neural-network-driven facial-recognition algorithm can reveal specific composite gestalt images for KS1 and KS2 individuals.
Collapse
Affiliation(s)
- Flavien Rouxel
- Montpellier University, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Centre de référence anomalies du développement SOOR, INSERM U1183, Montpellier, France
| | - Kevin Yauy
- Montpellier University, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Centre de référence anomalies du développement SOOR, INSERM U1183, Montpellier, France
| | - Guilaine Boursier
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique des Maladies Rares et Auto-inflammatoires, CHU Montpellier, Université de Montpellier, Montpellier, France
| | - Vincent Gatinois
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, laboratoire de génétique chromosomique, CHU Montpellier, Université de Montpellier, Montpellier, France
| | - Mouna Barat-Houari
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique des Maladies Rares et Auto-inflammatoires, CHU Montpellier, Université de Montpellier, Montpellier, France
| | - Elodie Sanchez
- Montpellier University, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Centre de référence anomalies du développement SOOR, INSERM U1183, Montpellier, France
| | - Didier Lacombe
- Service de génétique médicale, Centre de référence anomalies du développement SOOR, CHU Bordeaux, INSERM U1211, Université de Bordeaux, Bordeaux, France
| | - Stéphanie Arpin
- Service de Génétique, CHU Tours, UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - Fabienne Giuliano
- Service de Médecine Génétique, CHUV, Université de Lausanne, Lausanne, France
| | - Damien Haye
- Génétique médicale, Hôpital Robert Debré, APHP, Paris, France.,Génétique médicale, Hôpital Pitié-Salpétrière, APHP, Paris, France
| | - Marlène Rio
- Fédération de génétique, et Institut Imagine, UMR-1163, Hôpital Universitaire Necker-Enfants Malades, APHP, Paris, France
| | - Annick Toutain
- Service de Génétique, CHU Tours, UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - Klaus Dieterich
- Service de Génétique Médicale, CHU Grenoble Alpes, Univ. Grenoble Alpes, Inserm, U1216, GIN, 38000, Grenoble, France
| | | | - Sophie Julia
- Service de génétique clinique, CHU Toulouse, Toulouse, France
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes, CEDEX 1, France
| | - Alexandra Afenjar
- APHP, Département de génétique, Sorbonne Université, GRC n°19, ConCer-LD, Centre de Référence déficiences intellectuelles de causes rares, Hôpital Armand Trousseau, F-75012, Paris, France
| | - Boris Keren
- Génétique médicale, Hôpital Pitié-Salpétrière, APHP, Paris, France
| | | | - Sebastien Moutton
- Centre Pluridisciplinaire de Diagnostic PréNatal, Pôle mère enfant, Maison de Santé Protestante Bordeaux Bagatelle, 33400, Talence, France
| | | | - Claire Duflos
- Département d'information médicale, CHU de Montpellier, Montpellier, France
| | - Yline Capri
- Génétique médicale, Hôpital Robert Debré, APHP, Paris, France
| | - Jeanne Amiel
- Fédération de génétique, et Institut Imagine, UMR-1163, Hôpital Universitaire Necker-Enfants Malades, APHP, Paris, France
| | - Patricia Blanchet
- Montpellier University, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Centre de référence anomalies du développement SOOR, INSERM U1183, Montpellier, France
| | - Stanislas Lyonnet
- Fédération de génétique, et Institut Imagine, UMR-1163, Hôpital Universitaire Necker-Enfants Malades, APHP, Paris, France
| | | | - David Genevieve
- Montpellier University, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Centre de référence anomalies du développement SOOR, INSERM U1183, Montpellier, France.
| |
Collapse
|
11
|
Aref-Eshghi E, Kerkhof J, Pedro VP, France GDI, Barat-Houari M, Ruiz-Pallares N, Andrau JC, Lacombe D, Van-Gils J, Fergelot P, Dubourg C, Cormier-Daire V, Rondeau S, Lecoquierre F, Saugier-Veber P, Nicolas G, Lesca G, Chatron N, Sanlaville D, Vitobello A, Faivre L, Thauvin-Robinet C, Laumonnier F, Raynaud M, Alders M, Mannens M, Henneman P, Hennekam RC, Velasco G, Francastel C, Ulveling D, Ciolfi A, Pizzi S, Tartaglia M, Heide S, Héron D, Mignot C, Keren B, Whalen S, Afenjar A, Bienvenu T, Campeau PM, Rousseau J, Levy MA, Brick L, Kozenko M, Balci TB, Siu VM, Stuart A, Kadour M, Masters J, Takano K, Kleefstra T, de Leeuw N, Field M, Shaw M, Gecz J, Ainsworth PJ, Lin H, Rodenhiser DI, Friez MJ, Tedder M, Lee JA, DuPont BR, Stevenson RE, Skinner SA, Schwartz CE, Genevieve D, Sadikovic B. Evaluation of DNA Methylation Episignatures for Diagnosis and Phenotype Correlations in 42 Mendelian Neurodevelopmental Disorders. Am J Hum Genet 2021; 108:1161-1163. [PMID: 34087165 DOI: 10.1016/j.ajhg.2021.04.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
|
12
|
Ruault V, Yauy K, Fabre A, Fradin M, Van-Gils J, Angelini C, Baujat G, Blanchet P, Cuinat S, Isidor B, Jorgensen C, Lacombe D, Moutton S, Odent S, Sanchez E, Sigaudy S, Touitou I, Willems M, Apparailly F, Geneviève D, Barat-Houari M. Clinical and Molecular Spectrum of Nonsyndromic Early-Onset Osteoarthritis. Arthritis Rheumatol 2020; 72:1689-1693. [PMID: 32510848 DOI: 10.1002/art.41387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Osteoarthritis (OA) is the most common joint disease worldwide. The etiology of OA is varied, ranging from multifactorial to environmental to monogenic. In a condition called early-onset OA, OA occurs at an earlier age than is typical in the general population. To our knowledge, there have been no large-scale genetic studies of individuals with early-onset OA. The present study was undertaken to investigate causes of monogenic OA in individuals with nonsyndromic early-onset OA. METHODS The study probands were 45 patients with nonsyndromic early-onset OA who were referred to our skeletal disease center by skeletal dysplasia experts between 2013 and 2019. Criteria for early-onset OA included radiographic evidence, body mass index ≤30 kg/m2 , age at onset ≤50 years, and involvement of ≥1 joint site. Molecular analysis was performed with a next-generation sequencing panel. RESULTS We identified a genetic variant in 13 probands (29%); the affected gene was COL2A1 in 11, ACAN in 1, and SLC26A2 in 1. After familial segregation analysis, 20 additional individuals were identified. The mean ± SD age at onset of joint pain was 19.5 ± 3.9 years (95% confidence interval 3-47). Eighteen of 33 subjects (55%) with nonsyndromic early-onset OA and a genetic variant had had at least 1 joint replacement (mean ± SD age at first joint replacement 41 ± 4.2 years; mean number of joint replacements 2.6 per individual), and 21 (45%) of the joint replacement surgeries were performed when the patient was <45 years old. Of the 20 patients age >40 years, 17 (85%) had had at least 1 joint replacement. CONCLUSION We confirmed that COL2A1 is the main monogenic cause of nonsyndromic early-onset OA. However, on the basis of genetic heterogeneity of early-onset OA, we recommend next-generation sequencing for all individuals who undergo joint replacement prior to the age of 45 years. Lifestyle recommendations for prevention should be implemented.
Collapse
Affiliation(s)
- Valentin Ruault
- Université de Montpellier, Centre Hospitalier Universitaire Montpellier, CLAD Sud Languedoc-Roussillon, Montpellier, France
| | - Kevin Yauy
- Université de Montpellier, Centre Hospitalier Universitaire Montpellier, CLAD Sud Languedoc-Roussillon and SeqOne, Montpellier, France, and Institute of Advanced Biosciences, Université Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Grenoble, France
| | - Aurélie Fabre
- Université de Montpellier, Centre Hospitalier Universitaire Montpellier, CLAD Sud Languedoc-Roussillon, Montpellier, France
| | - Mélanie Fradin
- Centre Hospitalier Universitaire Hôpital Sud, CLAD Ouest, CNRS UMR 6290, Université de Rennes, Rennes, France
| | | | | | | | - Patricia Blanchet
- Université de Montpellier, Centre Hospitalier Universitaire Montpellier, CLAD Sud Languedoc-Roussillon, Montpellier, France
| | - Silvestre Cuinat
- Centre Hospitalier Universitaire Nantes, CLAD Ouest, Nantes, France
| | - Bertrand Isidor
- Centre Hospitalier Universitaire Nantes, CLAD Ouest, Nantes, France
| | - Christian Jorgensen
- Université de Montpellier, Centre Hospitalier Universitaire Montpellier, INSERM, Montpellier, France
| | | | - Sébastien Moutton
- Centre Pluridisciplinaire de Diagnostic Prénatal, Pôle Mère-Enfant, Maison de Santé Protestante de Bordeaux-Bagatelle, Talence, France
| | - Sylvie Odent
- Centre Hospitalier Universitaire Hôpital Sud, CLAD Ouest, CNRS UMR 6290, Université de Rennes, Rennes, France
| | - Elodie Sanchez
- Université de Montpellier, Centre Hospitalier Universitaire Montpellier, CLAD Sud Languedoc-Roussillon, INSERM, Montpellier, France
| | - Sabine Sigaudy
- Centre Hospitalier Universitaire de Marseille, Hôpital de la Timone, Marseille, France
| | - Isabelle Touitou
- Université de Montpellier, Centre Hospitalier Universitaire Montpellier, CLAD Sud Languedoc-Roussillon, INSERM, Montpellier, France
| | - Marjolaine Willems
- Université de Montpellier, Centre Hospitalier Universitaire Montpellier, CLAD Sud Languedoc-Roussillon, Montpellier, France
| | - Florence Apparailly
- Université de Montpellier, Centre Hospitalier Universitaire Montpellier, CLAD Sud Languedoc-Roussillon, INSERM, Montpellier, France
| | - David Geneviève
- Université de Montpellier, Centre Hospitalier Universitaire Montpellier, CLAD Sud Languedoc-Roussillon, INSERM, Montpellier, France
| | - Mouna Barat-Houari
- Université de Montpellier, Centre Hospitalier Universitaire Montpellier, CLAD Sud Languedoc-Roussillon, Montpellier, France
| |
Collapse
|
13
|
Aref-Eshghi E, Kerkhof J, Pedro VP, Barat-Houari M, Ruiz-Pallares N, Andrau JC, Lacombe D, Van-Gils J, Fergelot P, Dubourg C, Cormier-Daire V, Rondeau S, Lecoquierre F, Saugier-Veber P, Nicolas G, Lesca G, Chatron N, Sanlaville D, Vitobello A, Faivre L, Thauvin-Robinet C, Laumonnier F, Raynaud M, Alders M, Mannens M, Henneman P, Hennekam RC, Velasco G, Francastel C, Ulveling D, Ciolfi A, Pizzi S, Tartaglia M, Heide S, Héron D, Mignot C, Keren B, Whalen S, Afenjar A, Bienvenu T, Campeau PM, Rousseau J, Levy MA, Brick L, Kozenko M, Balci TB, Siu VM, Stuart A, Kadour M, Masters J, Takano K, Kleefstra T, de Leeuw N, Field M, Shaw M, Gecz J, Ainsworth PJ, Lin H, Rodenhiser DI, Friez MJ, Tedder M, Lee JA, DuPont BR, Stevenson RE, Skinner SA, Schwartz CE, Genevieve D, Sadikovic B, Sadikovic B. Evaluation of DNA Methylation Episignatures for Diagnosis and Phenotype Correlations in 42 Mendelian Neurodevelopmental Disorders. Am J Hum Genet 2020; 106:356-370. [PMID: 32109418 DOI: 10.1016/j.ajhg.2020.01.019] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [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: 11/08/2019] [Accepted: 01/27/2020] [Indexed: 01/24/2023] Open
Abstract
Genetic syndromes frequently present with overlapping clinical features and inconclusive or ambiguous genetic findings which can confound accurate diagnosis and clinical management. An expanding number of genetic syndromes have been shown to have unique genomic DNA methylation patterns (called "episignatures"). Peripheral blood episignatures can be used for diagnostic testing as well as for the interpretation of ambiguous genetic test results. We present here an approach to episignature mapping in 42 genetic syndromes, which has allowed the identification of 34 robust disease-specific episignatures. We examine emerging patterns of overlap, as well as similarities and hierarchical relationships across these episignatures, to highlight their key features as they are related to genetic heterogeneity, dosage effect, unaffected carrier status, and incomplete penetrance. We demonstrate the necessity of multiclass modeling for accurate genetic variant classification and show how disease classification using a single episignature at a time can sometimes lead to classification errors in closely related episignatures. We demonstrate the utility of this tool in resolving ambiguous clinical cases and identification of previously undiagnosed cases through mass screening of a large cohort of subjects with developmental delays and congenital anomalies. This study more than doubles the number of published syndromes with DNA methylation episignatures and, most significantly, opens new avenues for accurate diagnosis and clinical assessment in individuals affected by these disorders.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bekim 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.
| |
Collapse
|
14
|
Ruault V, Corsini C, Duflos C, Akouete S, Georgescu V, Abaji M, Alembick Y, Alix E, Amiel J, Amouroux C, Barat-Houari M, Baumann C, Bonnard A, Boursier G, Boute O, Burglen L, Busa T, Cordier MP, Cormier-Daire V, Delrue MA, Doray B, Faivre L, Fradin M, Gilbert-Dussardier B, Giuliano F, Goldenberg A, Gorokhova S, Héron D, Isidor B, Jacquemont ML, Jacquette A, Jeandel C, Lacombe D, Le Merrer M, Sang KHLQ, Lyonnet S, Manouvrier S, Michot C, Moncla A, Moutton S, Odent S, Pelet A, Philip N, Pinson L, Reversat J, Roume J, Sanchez E, Sanlaville D, Sarda P, Schaefer E, Till M, Touitou I, Toutain A, Willems M, Gatinois V, Geneviève D. Growth charts in Kabuki syndrome 1. Am J Med Genet A 2019; 182:446-453. [PMID: 31876365 DOI: 10.1002/ajmg.a.61462] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 09/11/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 11/08/2022]
Abstract
Kabuki syndrome (KS, KS1: OMIM 147920 and KS2: OMIM 300867) is caused by pathogenic variations in KMT2D or KDM6A. KS is characterized by multiple congenital anomalies and neurodevelopmental disorders. Growth restriction is frequently reported. Here we aimed to create specific growth charts for individuals with KS1, identify parameters used for size prognosis and investigate the impact of growth hormone therapy on adult height. Growth parameters and parental size were obtained for 95 KS1 individuals (41 females). Growth charts for height, weight, body mass index (BMI) and occipitofrontal circumference were generated in standard deviation values for the first time in KS1. Statural growth of KS1 individuals was compared to parental target size. According to the charts, height, weight, BMI, and occipitofrontal circumference were lower for KS1 individuals than the normative French population. For males and females, the mean growth of KS1 individuals was -2 and -1.8 SD of their parental target size, respectively. Growth hormone therapy did not increase size beyond the predicted size. This study, from the largest cohort available, proposes growth charts for widespread use in the management of KS1, especially for size prognosis and screening of other diseases responsible for growth impairment beyond a calculated specific target size.
Collapse
Affiliation(s)
- Valentin Ruault
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Univer Montpellier, CHU de Montpellier, CLAD ASOOR Montpellier, France
| | - Carole Corsini
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Univer Montpellier, CHU de Montpellier, CLAD ASOOR Montpellier, France
| | - Claire Duflos
- Clinical Research and Epidemiolgy Unit, Département de l'Information Médicale, CHU, University Montpellier, Montpellier, France
| | - Sandrine Akouete
- Clinical Research and Epidemiolgy Unit, Département de l'Information Médicale, CHU, University Montpellier, Montpellier, France
| | - Véra Georgescu
- Clinical Research and Epidemiolgy Unit, Département de l'Information Médicale, CHU, University Montpellier, Montpellier, France
| | - Mario Abaji
- Département de Génétique Médicale, Hôpital de la Timone, CLAD Sud-PACA, Marseille, France
| | - Yves Alembick
- Service de Génétique, Hôpital de Hautepierre, CHU Strasbourg, CLAD Est, Strasbourg, France
| | - Eudeline Alix
- Département de Cytogénétique, Hospices civil de Lyon, Centre des neurosciences, Tiger, Université Claude Bernard Lyon 1, Lyon, France
| | - Jeanne Amiel
- Département de Génétique, Unité Inserm U781, Institut Imagine, Hôpital Necker enfants Malades, CLAD Ile de France, Paris, France
| | - Cyril Amouroux
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Univer Montpellier, CHU de Montpellier, CLAD ASOOR Montpellier, France
| | - Mouna Barat-Houari
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Univer Montpellier, CHU de Montpellier, CLAD ASOOR Montpellier, France
| | - Clarisse Baumann
- Département de Génétique, Hôpital Robert Debré, CLAD Ile de France, Paris, France
| | - Adeline Bonnard
- Département de Génétique, Unité Inserm U781, Institut Imagine, Hôpital Necker enfants Malades, CLAD Ile de France, Paris, France
| | - Guilaine Boursier
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Univer Montpellier, CHU de Montpellier, CLAD ASOOR Montpellier, France
| | - Odile Boute
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, CLAD Nord, Lille, France
| | - Lydie Burglen
- Service de Génétique, CHU Trousseau, CLAD Ile de France, Paris, France
| | - Tiffany Busa
- Département de Génétique Médicale, Hôpital de la Timone, CLAD Sud-PACA, Marseille, France
| | - Marie-Pierre Cordier
- Département de Cytogénétique, Hospices civil de Lyon, Centre des neurosciences, Tiger, Université Claude Bernard Lyon 1, Lyon, France
| | - Valérie Cormier-Daire
- Département de Génétique, Unité Inserm U781, Institut Imagine, Hôpital Necker enfants Malades, CLAD Ile de France, Paris, France
| | - Marie-Ange Delrue
- Service de Génétique, Hôpital Pellegrin, CLAD Sud-Ouest, Bordeaux, France
| | - Bérénice Doray
- Service de Génétique, Hôpital de Hautepierre, CHU Strasbourg, CLAD Est, Strasbourg, France
| | - Laurence Faivre
- Centre de Génétique, Hôpital d'enfant, CLAD Est, Dijon, France
| | - Mélanie Fradin
- Service de Génétique médicale, Hôpital Sud, CLAD Ouest, Rennes, France
| | | | | | | | - Svetlana Gorokhova
- Département de Génétique Médicale, Hôpital de la Timone, CLAD Sud-PACA, Marseille, France
| | - Delphine Héron
- Département de Génétique, CHU La Pitié-Salpêtrière, CLAD Ile de France, Paris, France
| | - Bertrand Isidor
- Service de Génétique, CHU Nantes, CLAD Ouest, Nantes, France
| | - Marie-Line Jacquemont
- Service de Génétique, Hôpital Saint Pierre, GH Sud Réunion, Ile de la Réunion, Saint Pierre, France
| | - Aurélia Jacquette
- Département de Génétique, CHU La Pitié-Salpêtrière, CLAD Ile de France, Paris, France
| | - Claire Jeandel
- Service de Pédiatrie, CHU de Montpellier, Montpellier, France
| | - Didier Lacombe
- Service de Génétique, Hôpital Pellegrin, CLAD Sud-Ouest, Bordeaux, France
| | - Martine Le Merrer
- Département de Génétique, Unité Inserm U781, Institut Imagine, Hôpital Necker enfants Malades, CLAD Ile de France, Paris, France
| | - Kim Hanh Le Quan Sang
- Département de Génétique, Unité Inserm U781, Institut Imagine, Hôpital Necker enfants Malades, CLAD Ile de France, Paris, France
| | - Stanislas Lyonnet
- Département de Génétique, Unité Inserm U781, Institut Imagine, Hôpital Necker enfants Malades, CLAD Ile de France, Paris, France
| | - Sylvie Manouvrier
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, CLAD Nord, Lille, France
| | - Caroline Michot
- Département de Génétique, Unité Inserm U781, Institut Imagine, Hôpital Necker enfants Malades, CLAD Ile de France, Paris, France
| | - Anne Moncla
- Département de Génétique Médicale, Hôpital de la Timone, CLAD Sud-PACA, Marseille, France
| | - Sébastien Moutton
- Service de Génétique, Hôpital Pellegrin, CLAD Sud-Ouest, Bordeaux, France
| | - Sylvie Odent
- Service de Génétique médicale, Hôpital Sud, CLAD Ouest, Rennes, France
| | - Anna Pelet
- Département de Génétique, Unité Inserm U781, Institut Imagine, Hôpital Necker enfants Malades, CLAD Ile de France, Paris, France
| | - Nicole Philip
- Département de Génétique Médicale, Hôpital de la Timone, CLAD Sud-PACA, Marseille, France
| | - Lucile Pinson
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Univer Montpellier, CHU de Montpellier, CLAD ASOOR Montpellier, France
| | - Julie Reversat
- Département de Cytogénétique, Hospices civil de Lyon, Centre des neurosciences, Tiger, Université Claude Bernard Lyon 1, Lyon, France
| | - Joëlle Roume
- Service de Génétique, Hôpital Poissy-saint Germain, Poissy, France
| | - Elodie Sanchez
- Département de Génétique, Unité Inserm U781, Institut Imagine, Hôpital Necker enfants Malades, CLAD Ile de France, Paris, France
| | - Damien Sanlaville
- Département de Cytogénétique, Hospices civil de Lyon, Centre des neurosciences, Tiger, Université Claude Bernard Lyon 1, Lyon, France
| | - Pierre Sarda
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Univer Montpellier, CHU de Montpellier, CLAD ASOOR Montpellier, France
| | - Elise Schaefer
- Service de Génétique, Hôpital de Hautepierre, CHU Strasbourg, CLAD Est, Strasbourg, France
| | - Marianne Till
- Département de Cytogénétique, Hospices civil de Lyon, Centre des neurosciences, Tiger, Université Claude Bernard Lyon 1, Lyon, France
| | - Isabelle Touitou
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Univer Montpellier, CHU de Montpellier, CLAD ASOOR Montpellier, France
| | - Annick Toutain
- Service de Génétique, Hôpital Bretonneau, CLAD Ouest, Tours, France
| | - Marjolaine Willems
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Univer Montpellier, CHU de Montpellier, CLAD ASOOR Montpellier, France
| | - Vincent Gatinois
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Univer Montpellier, CHU de Montpellier, CLAD ASOOR Montpellier, France
| | - David Geneviève
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Univer Montpellier, CHU de Montpellier, CLAD ASOOR Montpellier, France
| |
Collapse
|
15
|
Bögershausen N, Gatinois V, Riehmer V, Kayserili H, Becker J, Thoenes M, Simsek-Kiper PÖ, Barat-Houari M, Elcioglu NH, Wieczorek D, Tinschert S, Sarrabay G, Strom TM, Fabre A, Baynam G, Sanchez E, Nürnberg G, Altunoglu U, Capri Y, Isidor B, Lacombe D, Corsini C, Cormier-Daire V, Sanlaville D, Giuliano F, Le Quan Sang KH, Kayirangwa H, Nürnberg P, Meitinger T, Boduroglu K, Zoll B, Lyonnet S, Tzschach A, Verloes A, Di Donato N, Touitou I, Netzer C, Li Y, Geneviève D, Yigit G, Wollnik B. Mutation Update for Kabuki Syndrome GenesKMT2DandKDM6Aand Further Delineation of X-Linked Kabuki Syndrome Subtype 2. Hum Mutat 2016; 37:847-64. [DOI: 10.1002/humu.23026] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/26/2016] [Indexed: 12/29/2022]
|
16
|
Barat-Houari M, Dumont B, Fabre A, Them FT, Alembik Y, Alessandri JL, Amiel J, Audebert S, Baumann-Morel C, Blanchet P, Bieth E, Brechard M, Busa T, Calvas P, Capri Y, Cartault F, Chassaing N, Ciorca V, Coubes C, David A, Delezoide AL, Dupin-Deguine D, El Chehadeh S, Faivre L, Giuliano F, Goldenberg A, Isidor B, Jacquemont ML, Julia S, Kaplan J, Lacombe D, Lebrun M, Marlin S, Martin-Coignard D, Martinovic J, Masurel A, Melki J, Mozelle-Nivoix M, Nguyen K, Odent S, Philip N, Pinson L, Plessis G, Quélin C, Shaeffer E, Sigaudy S, Thauvin C, Till M, Touraine R, Vigneron J, Baujat G, Cormier-Daire V, Le Merrer M, Geneviève D, Touitou I. The expanding spectrum of COL2A1 gene variants IN 136 patients with a skeletal dysplasia phenotype. Eur J Hum Genet 2015; 24:992-1000. [PMID: 26626311 DOI: 10.1038/ejhg.2015.250] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 08/21/2015] [Accepted: 10/29/2015] [Indexed: 11/09/2022] Open
Abstract
Heterozygous COL2A1 variants cause a wide spectrum of skeletal dysplasia termed type II collagenopathies. We assessed the impact of this gene in our French series. A decision tree was applied to select 136 probands (71 Stickler cases, 21 Spondyloepiphyseal dysplasia congenita cases, 11 Kniest dysplasia cases, and 34 other dysplasia cases) before molecular diagnosis by Sanger sequencing. We identified 66 different variants among the 71 positive patients. Among those patients, 18 belonged to multiplex families and 53 were sporadic. Most variants (38/44, 86%) were located in the triple helical domain of the collagen chain and glycine substitutions were mainly observed in severe phenotypes, whereas arginine to cysteine changes were more often encountered in moderate phenotypes. This series of skeletal dysplasia is one of the largest reported so far, adding 44 novel variants (15%) to published data. We have confirmed that about half of our Stickler patients (46%) carried a COL2A1 variant, and that the molecular spectrum was different across the phenotypes. To further address the question of genotype-phenotype correlation, we plan to screen our patients for other candidate genes using a targeted next-generation sequencing approach.
Collapse
Affiliation(s)
- Mouna Barat-Houari
- Laboratoire de génétique des maladies rares et auto-inflammatoires, CHRU, Montpellier, France.,Génétique des Maladies Auto-inflammatoires et des Ostéo-arthropathies chroniques, INSERM U1183, Montpellier, France
| | - Bruno Dumont
- Laboratoire de génétique des maladies rares et auto-inflammatoires, CHRU, Montpellier, France
| | - Aurélie Fabre
- Laboratoire de génétique des maladies rares et auto-inflammatoires, CHRU, Montpellier, France
| | - Frédéric Tm Them
- Département de Génétique Médicale, Centre de référence des anomalies du développement, Centre de compétence des Maladies Osseuses Constitutionnelles, CHRU, Montpellier, France
| | - Yves Alembik
- Génétique Médicale, Hôpital Hautepierre, Strasbourg, France
| | | | - Jeanne Amiel
- Département de Génétique et INSERM U781, Université Paris Descartes-Sorbonne Paris Cité, Fondation Imagine, Hôpital Necker-Enfants malades, AP-HP, Paris, France
| | - Séverine Audebert
- Pédiatrie et Génétique Médicale, CHU de Brest - Hôpital Auguste Morvan, Brest, France
| | | | - Patricia Blanchet
- Département de Génétique Médicale, Centre de référence des anomalies du développement, Centre de compétence des Maladies Osseuses Constitutionnelles, CHRU, Montpellier, France
| | - Eric Bieth
- Département de Génétique Médicale, institut Fédératif de Biologie, Hôpital Purpan, Toulouse, France
| | - Marie Brechard
- Unité de consultations externes, Hôpital Saint Joseph, Marseille, France
| | - Tiffany Busa
- Unité de Génétique Clinique, Hôpital d'Enfants de la Timone, Marseille, France
| | - Patrick Calvas
- Département de Génétique Médicale, institut Fédératif de Biologie, Hôpital Purpan, Toulouse, France
| | - Yline Capri
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | - François Cartault
- Service de Génétique, CHU Félix Guyon, Saint-Denis, La Réunion, France
| | - Nicolas Chassaing
- Département de Génétique Médicale, institut Fédératif de Biologie, Hôpital Purpan, Toulouse, France
| | | | - Christine Coubes
- Département de Génétique Médicale, Centre de référence des anomalies du développement, Centre de compétence des Maladies Osseuses Constitutionnelles, CHRU, Montpellier, France
| | | | | | - Delphine Dupin-Deguine
- Département de Génétique Médicale, institut Fédératif de Biologie, Hôpital Purpan, Toulouse, France
| | | | - Laurence Faivre
- Centre de Génétique, CHU Dijon - Hôpital d'Enfants, Dijon, France
| | - Fabienne Giuliano
- Département de Génétique Médicale, CHU de Nice - Hôpital de l'Archet II, Nice, France
| | - Alice Goldenberg
- Unité de Génétique Clinique, CHU de Rouen - Hôpital Charles Nicolle, Rouen, France
| | | | | | - Sophie Julia
- Département de Génétique Médicale, institut Fédératif de Biologie, Hôpital Purpan, Toulouse, France
| | - Josseline Kaplan
- Département de Génétique et INSERM U781, Université Paris Descartes-Sorbonne Paris Cité, Fondation Imagine, Hôpital Necker-Enfants malades, AP-HP, Paris, France
| | - Didier Lacombe
- Département de Génétique Médicale, Groupe Hospitalier Pellegrin, Bordeaux, France
| | - Marine Lebrun
- Génétique Clinique, Chromosomique et Moléculaire, CHU Hôpital Nord, St Pirest en Jarez, France
| | - Sandrine Marlin
- Génétique et Embryologie Médicales, Hôpital Armand Trousseau, Paris, France
| | | | | | - Alice Masurel
- Centre de Génétique, CHU Dijon - Hôpital d'Enfants, Dijon, France
| | - Judith Melki
- Pôle Neurosciences Tête et Cou (NTC), GHU Paris-Sud - Hôpital de Bicêtre, Le Kremlin Bicêtre, France
| | | | - Karine Nguyen
- Unité de Génétique Clinique, Hôpital d'Enfants de la Timone, Marseille, France
| | - Sylvie Odent
- Service de Génétique Clinique, numéro 9, CHU, Rennes, France
| | - Nicole Philip
- Unité de Génétique Clinique, Hôpital d'Enfants de la Timone, Marseille, France
| | - Lucile Pinson
- Département de Génétique Médicale, Centre de référence des anomalies du développement, Centre de compétence des Maladies Osseuses Constitutionnelles, CHRU, Montpellier, France
| | | | - Chloé Quélin
- Service de Génétique Clinique, numéro 9, CHU, Rennes, France
| | - Elise Shaeffer
- Génétique Médicale, Hôpital Hautepierre, Strasbourg, France
| | - Sabine Sigaudy
- Unité de Génétique Clinique, Hôpital d'Enfants de la Timone, Marseille, France
| | - Christel Thauvin
- Centre de Génétique, CHU Dijon - Hôpital d'Enfants, Dijon, France
| | - Marianne Till
- Service de Cytogénétique Constitutionnelle, Groupement Hospitalier Est - Hôpitaux de Lyon, Bron, France
| | - Renaud Touraine
- Génétique Clinique, Chromosomique et Moléculaire, CHU Hôpital Nord, St Pirest en Jarez, France
| | | | - Geneviève Baujat
- Département de Génétique et INSERM U781, Université Paris Descartes-Sorbonne Paris Cité, Fondation Imagine, Hôpital Necker-Enfants malades, AP-HP, Paris, France
| | - Valérie Cormier-Daire
- Département de Génétique et INSERM U781, Université Paris Descartes-Sorbonne Paris Cité, Fondation Imagine, Hôpital Necker-Enfants malades, AP-HP, Paris, France
| | - Martine Le Merrer
- Département de Génétique et INSERM U781, Université Paris Descartes-Sorbonne Paris Cité, Fondation Imagine, Hôpital Necker-Enfants malades, AP-HP, Paris, France
| | - David Geneviève
- Département de Génétique Médicale, Centre de référence des anomalies du développement, Centre de compétence des Maladies Osseuses Constitutionnelles, CHRU, Montpellier, France.,Génétique des Maladies Auto-inflammatoires et des Ostéo-arthropathies chroniques, INSERM U1183, Montpellier, France.,Université de Montpellier, Montpellier, France
| | - Isabelle Touitou
- Laboratoire de génétique des maladies rares et auto-inflammatoires, CHRU, Montpellier, France.,Génétique des Maladies Auto-inflammatoires et des Ostéo-arthropathies chroniques, INSERM U1183, Montpellier, France.,Université de Montpellier, Montpellier, France
| |
Collapse
|
17
|
Barat-Houari M, Sarrabay G, Gatinois V, Fabre A, Dumont B, Genevieve D, Touitou I. Mutation Update for COL2A1 Gene Variants Associated with Type II Collagenopathies. Hum Mutat 2015; 37:7-15. [PMID: 26443184 DOI: 10.1002/humu.22915] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [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: 05/07/2015] [Accepted: 09/23/2015] [Indexed: 12/19/2022]
Abstract
Mutations in the COL2A1 gene cause a spectrum of rare autosomal-dominant conditions characterized by skeletal dysplasia, short stature, and sensorial defects. An early diagnosis is critical to providing relevant patient care and follow-up, and genetic counseling to affected families. There are no recent exhaustive descriptions of the causal mutations in the literature. Here, we provide a review of COL2A1 mutations extracted from the Leiden Open Variation Database (LOVD) that we updated with data from PubMed and our own patients. Over 700 patients were recorded, harboring 415 different mutations. One-third of the mutations are dominant-negative mutations that affect the glycine residue in the G-X-Y repeats of the alpha 1 chain. These mutations disrupt the collagen triple helix and are common in achondrogenesis type II and hypochondrogenesis. The mutations resulting in a premature stop codon are found in less severe phenotypes such as Stickler syndrome. The p.(Arg275Cys) substitution is found in all patients with COL2A1-associated Czech dysplasia. LOVD-COL2A1 provides support and potential collaborative material for scientific and clinical projects aimed at elucidating phenotype-genotype correlation and differential diagnosis in patients with type II collagenopathies.
Collapse
Affiliation(s)
- Mouna Barat-Houari
- Laboratory of Rare and Autoinflammatory Diseases, CHRU, Montpellier, France.,Genetics & Immunopathology of Inflammatory Osteoarticular Diseases, INSERM UMR1183, Montpellier, France
| | - Guillaume Sarrabay
- Laboratory of Rare and Autoinflammatory Diseases, CHRU, Montpellier, France.,Genetics & Immunopathology of Inflammatory Osteoarticular Diseases, INSERM UMR1183, Montpellier, France
| | - Vincent Gatinois
- Laboratory of Rare and Autoinflammatory Diseases, CHRU, Montpellier, France.,University of Montpellier, Montpellier, France
| | - Aurélie Fabre
- Laboratory of Rare and Autoinflammatory Diseases, CHRU, Montpellier, France
| | - Bruno Dumont
- Laboratory of Rare and Autoinflammatory Diseases, CHRU, Montpellier, France
| | - David Genevieve
- Genetics & Immunopathology of Inflammatory Osteoarticular Diseases, INSERM UMR1183, Montpellier, France.,University of Montpellier, Montpellier, France.,Department of Medical Genetics, Reference Center for Developmental Abnormalities and Constitutional Bone Diseases, CHRU, Montpellier, France
| | - Isabelle Touitou
- Laboratory of Rare and Autoinflammatory Diseases, CHRU, Montpellier, France.,Genetics & Immunopathology of Inflammatory Osteoarticular Diseases, INSERM UMR1183, Montpellier, France.,University of Montpellier, Montpellier, France
| |
Collapse
|
18
|
Barat-Houari M, Baujat G, Tran Mau Them F, Fabre A, Geneviève D, Touitou I. Confirmation of autosomal recessive inheritance ofCOL2A1mutations in spondyloepiphyseal dysplasia congenita: Lessons for genetic counseling. Am J Med Genet A 2015; 170A:263-5. [DOI: 10.1002/ajmg.a.37374] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 08/31/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Mouna Barat-Houari
- Laboratoire de génétique des maladies rares et auto-inflammatoires; CHRU; Montpellier France
- Génétique des Maladies Auto-inflammatoires et des Ostéo-arthropathies chroniques; INSERM U1183; Montpellier France
| | - Geneviève Baujat
- Département de Génétique et INSERM U781; Université Paris Descartes-Sorbonne Paris Cité; Fondation Imagine; Hôpital Necker-Enfants malades; AP-HP; Paris France
| | - Frédéric Tran Mau Them
- Département de Génétique Médicale; Centre de référence des anomalies du développement; Centre de compétence des Maladies Osseuses Constitutionnelles; CHRU; Montpellier France
| | - Aurélie Fabre
- Laboratoire de génétique des maladies rares et auto-inflammatoires; CHRU; Montpellier France
| | - David Geneviève
- Génétique des Maladies Auto-inflammatoires et des Ostéo-arthropathies chroniques; INSERM U1183; Montpellier France
- Département de Génétique Médicale; Centre de référence des anomalies du développement; Centre de compétence des Maladies Osseuses Constitutionnelles; CHRU; Montpellier France
- Université de Montpellier; Montpellier France
| | - Isabelle Touitou
- Laboratoire de génétique des maladies rares et auto-inflammatoires; CHRU; Montpellier France
- Génétique des Maladies Auto-inflammatoires et des Ostéo-arthropathies chroniques; INSERM U1183; Montpellier France
- Université de Montpellier; Montpellier France
| |
Collapse
|
19
|
Sarrabay G, Barat-Houari M, Annakib S, Touitou I. The autoinflammatory diseases: a fashion with blurred boundaries! Semin Immunopathol 2015; 37:359-62. [DOI: 10.1007/s00281-015-0495-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/05/2015] [Indexed: 01/05/2023]
|
20
|
Tran TA, Pariente D, Guitton C, Delwail A, Barat-Houari M, Meinzer U. Treatment of Erdheim–Chester disease with canakinumab. Rheumatology (Oxford) 2014; 53:2312-4. [DOI: 10.1093/rheumatology/keu344] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
21
|
Tran Mau-Them F, Boualam A, Barat-Houari M, Jeandel C, Cottalorda J, Cormier-Daire V, Fabre A, Dumont B, Lefort G, Baujat G, Le Merrer M, Jorgensen C, Touitou I, Geneviève D. Dysspondyloenchondromatosis withoutCOL2A1mutation: Possible genetic heterogeneity. Am J Med Genet A 2013; 164A:769-73. [DOI: 10.1002/ajmg.a.36331] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/13/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Frédéric Tran Mau-Them
- Département de Génétique Médicale; Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, CHRU Montpellier, Faculté de Médecine Université Montpellier 1; Montpellier France
| | - Aurélia Boualam
- Département de Génétique Médicale; Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, CHRU Montpellier, Faculté de Médecine Université Montpellier 1; Montpellier France
| | - Mouna Barat-Houari
- Laboratoire des maladies rares et auto-inflammatoire; CHRU Montpellier; Montpellier France
| | - Claire Jeandel
- Endocrinologie pédiatrique; CHRU Montpellier; Montpellier France
| | - Jérôme Cottalorda
- Chirurgie orthopédique et plastique infantile; CHRU Montpellier; Montpellier France
| | - Valérie Cormier-Daire
- Centre de référence Maladies Osseuses Constitutionnelles, Département de Génétique, Unité Inserm U781; Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Hôpital Necker Enfants Malades; Paris France
| | - Aurélie Fabre
- Laboratoire des maladies rares et auto-inflammatoire; CHRU Montpellier; Montpellier France
| | - Bruno Dumont
- Laboratoire des maladies rares et auto-inflammatoire; CHRU Montpellier; Montpellier France
| | - Geneviève Lefort
- Département de Génétique Médicale; Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, CHRU Montpellier, Faculté de Médecine Université Montpellier 1; Montpellier France
| | - Geneviève Baujat
- Centre de référence Maladies Osseuses Constitutionnelles, Département de Génétique, Unité Inserm U781; Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Hôpital Necker Enfants Malades; Paris France
| | - Martine Le Merrer
- Centre de référence Maladies Osseuses Constitutionnelles, Département de Génétique, Unité Inserm U781; Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Hôpital Necker Enfants Malades; Paris France
| | - Christian Jorgensen
- Unité Inserm U844; CHRU Montpellier; Montpellier France
- Faculté de Médecine Université de Montpellier 1, UM1; Montpellier France
| | - Isabelle Touitou
- Laboratoire des maladies rares et auto-inflammatoire; CHRU Montpellier; Montpellier France
- Unité Inserm U844; CHRU Montpellier; Montpellier France
- Faculté de Médecine Université de Montpellier 1, UM1; Montpellier France
| | - David Geneviève
- Département de Génétique Médicale; Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, CHRU Montpellier, Faculté de Médecine Université Montpellier 1; Montpellier France
- Unité Inserm U844; CHRU Montpellier; Montpellier France
- Faculté de Médecine Université de Montpellier 1, UM1; Montpellier France
| |
Collapse
|
22
|
Khaib Dit Naib O, Aribi M, Idder A, Chiali A, Sairi H, Touitou I, Lefranc G, Barat-Houari M. P03-010 - IL10 SNPs associated with BD in Western Algeria. Pediatr Rheumatol Online J 2013. [PMCID: PMC3953154 DOI: 10.1186/1546-0096-11-s1-a205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
23
|
Zhou Q, Laxer R, Pelletier M, Ramaswamy M, Wang HY, Chin D, Gül A, Sibley C, Barat-Houari M, Siegel R, Kastner DL, Aksentijevich I. OR9-001 - Exome sequencing in monogenic Behçet-like disease. Pediatr Rheumatol Online J 2013. [PMCID: PMC3953183 DOI: 10.1186/1546-0096-11-s1-a184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
24
|
Khaib Dit Naib O, Aribi M, Idder A, Chiali A, Sairi H, Touitou I, Lefranc G, Barat-Houari M. Association Analysis of IL10, TNF-α, and IL23R-IL12RB2 SNPs with Behçet's Disease Risk in Western Algeria. Front Immunol 2013; 4:342. [PMID: 24151497 PMCID: PMC3801160 DOI: 10.3389/fimmu.2013.00342] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [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: 07/27/2013] [Accepted: 10/06/2013] [Indexed: 12/29/2022] Open
Abstract
Objective: We have conducted the first study of the association of interleukin (IL)-10, tumor necrosis factor alpha (TNF-α), and IL23R-IL12RB2 region single nucleotide polymorphisms (SNPs) with Behçet’s disease (BD) in Western Algeria. Methods: A total of 51 BD patients and 96 unrelated controls from West region of Algeria were genotyped by direct sequencing for 11 SNPs including 2 SNPs from the IL10 promoter [c.-819T > C (rs1800871), c.-592A > C (rs1800872)], 6 SNPs from the TNF-α promoter [c.-1211T > C (rs1799964), c.-1043C > A (rs1800630), c.-1037C > T (rs1799724), c.-556G > A (rs1800750), c.-488G > A (rs1800629), and c.-418G > A (rs361525)], and 3 SNPs from the IL23R-IL12RB2 region [g.67747415A > C (rs12119179), g.67740092G > A (rs11209032), and g.67760140T > C (rs924080)]. Results: The minor alleles c.-819T and c.-592A were significantly associated with BD [odds ratio (OR) = 2.18; 95% confidence interval (CI) 1.28–3.73, p = 0.003]; whereas, there was weaker association between TNF-α promoter SNPs or IL23R-IL12RB2 region and disease risk. Conclusion: Unlike the TNF-α and the IL23R-IL12RB2 region SNPs, the two IL10 SNPs were strongly associated with BD. The -819T, and -592A alleles and the -819TT, -819CT, and -592AA and -592CA genotypes seem to be highly involved in the risk of developing of BD in the population of Western Algeria.
Collapse
Affiliation(s)
- Ouahiba Khaib Dit Naib
- Laboratory of Applied Molecular Biology and Immunology. Department of Biology, Abou-Bekr Belkaïd University , Tlemcen , Algeria
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Rittore C, Sanchez E, Soler S, Barat-Houari M, Albers M, Obici L, McDermott MF, Touitou I, Grandemange S. Identification of a new exon 2-skipped TNFR1 transcript: regulation by three functional polymorphisms of the TNFR-associated periodic syndrome (TRAPS) gene. Ann Rheum Dis 2013; 73:290-7. [PMID: 23505244 DOI: 10.1136/annrheumdis-2012-203023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Mutations in the TNFRSF1A gene encoding the tumour necrosis factor α cell surface receptor, TNFR1, cause TNFR-associated periodic syndrome (TRAPS) and polymorphisms in TNFRSF1A, including rs4149570, rs767455 and rs1800692, are associated with inflammatory diseases. OBJECTIVES To describe a new exon 2-spliced transcript-TNFR1-d2-and the impact of these three single nucleotide polymorphisms on exon 2 splicing, transcriptional activity of TNFRSF1A and TRAPS phenotype. METHODS Expression of TNFRSF1A transcripts was performed by reverse-transcription-PCR in a range of human cells and tissues. Exon 2 splicing and transcriptional activity were analysed in HEK293T and SW480 cells by in vitro alternative splicing and luciferase assays, respectively. We constructed haplotypes containing rs4149570, rs767455 and rs1800692 in controls (n=72), patients with TRAPS (n=111) and in TRAPS-like patients (n=450) to compare their distribution and association with clinical features of TRAPS. RESULTS TNFR1-d2 was expressed in a tissue-specific manner, whereas TNFR1 expression was ubiquitous. Alternative splicing assays showed that the T-A-T haplotype at rs4149570-rs767455-rs1800692 had a significantly higher expression of exon 2-skipping product (p=0.02) compared with the G-G-C haplotype. Transcriptional activity from the T-T haplotype at rs4149570-rs1800692 was increased compared with the G-C haplotype (p=0.03). In patients with TRAPS, rs1800692 T/T homozygotes were excessively rare (p<10(-4)) and TRAPS-like patients with this genotype experienced less fever. CONCLUSIONS Our study provides a new mechanism of TNFRSF1A regulation whereby three polymorphisms in the promoter, exon 1 and intron 4 have a functional and combined effect on exon 2 splicing, via a coupling mechanism between transcription and splicing. These polymorphisms may affect the phenotype of TRAPS and TRAPS-like patients.
Collapse
Affiliation(s)
- Cécile Rittore
- Génétique des maladies Autoinflammatoires et des ostéoarthropathies chroniques, INSERM U844, Hôpital Saint Eloi, Bâtiment INM, , Montpellier, France
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Ben-Chetrit E, Touitou I, Fellig Y, Barat-Houari M. Kimura's disease and Behcet's syndrome in the same family--are they associated? Joint Bone Spine 2012; 80:44-7. [PMID: 22749664 DOI: 10.1016/j.jbspin.2012.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 04/10/2012] [Indexed: 11/25/2022]
Abstract
BACKGROUND Behcet's disease (BD) and Kimura's disease (KD) are two inflammatory diseases commonly found in Japan. In Israel, both diseases are quite rare. Recently, we encountered a family whose three siblings suffer from BD and an additional brother suffers from KD. This observation raised the question as to whether both diseases have a common underlying genetic basis. AIM OF THE STUDY To describe this unique family and to search for possible common alleles in the IL10 gene between BD and KD, as several SNPs in this gene are known to be associated with BD. METHODS Three BD siblings and their brother with KD were interviewed and examined. Genomic DNA was prepared from blood samples taken from all nine members of the family. The DNA was genotyped for sequence variations of six SNPs on the IL10 gene. RESULTS The IL10 SNPs did not segregate with BD and KD suggesting that there was no association between the IL10 gene and these diseases in this family. CONCLUSIONS SNPs in the IL10 gene shown to be susceptibility factors in adult BD were not associated with BD in this family. The question regarding a possible common genetic basis for KD and BD requires further investigation.
Collapse
Affiliation(s)
- Eldad Ben-Chetrit
- Department of Medicine, Rheumatology Unit, Hadassah-Hebrew University Medical Center Head, POB 12000, Jerusalem, Israel.
| | | | | | | |
Collapse
|
27
|
Radouane A, Oudghiri M, Chakib A, Bennani S, Touitou I, Barat-Houari M. SNPs in the TNF- gene promoter associated with Behcet's disease in Moroccan patients. Rheumatology (Oxford) 2012; 51:1595-9. [DOI: 10.1093/rheumatology/kes141] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
28
|
Barat-Houari M, Nguyen K, Bernard R, Fernandez C, Vovan C, Bareil C, Khau Van Kien P, Thorel D, Tuffery-Giraud S, Vasseur F, Attarian S, Pouget J, Girardet A, Lévy N, Claustres M. New multiplex PCR-based protocol allowing indirect diagnosis of FSHD on single cells: can PGD be offered despite high risk of recombination? Eur J Hum Genet 2010; 18:533-8. [PMID: 19935833 PMCID: PMC2987324 DOI: 10.1038/ejhg.2009.207] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 10/01/2009] [Accepted: 10/14/2009] [Indexed: 01/23/2023] Open
Abstract
Molecular pathophysiology of facioscapulohumeral muscular dystrophy (FSHD) involves the heterozygous contraction of the number of tandemly repeated D4Z4 units at chromosome 4q35.2. FSHD is associated with a range of 1-10 D4Z4 units instead of 11-150 in normal controls. Several factors complicate FSHD molecular diagnosis, especially the cis-segregation of D4Z4 contraction with a 4qA allele, whereas D4Z4 shortening is silent both on alleles 4qB and 10q. Discrimination of pathogenic 4q-D4Z4 alleles from highly homologous 10q-D4Z4 arrays requires the use of the conventional Southern blot, which is not suitable at the single-cell level. Preimplantation genetic diagnosis (PGD) is a frequent request from FSHD families with several affected relatives. We aimed to develop a rapid and sensitive PCR-based multiplex approach on single cells to perform an indirect familial segregation study of pathogenic alleles. Among several available polymorphic markers at 4q35.2, the four most proximal (D4S2390, D4S1652, D4S2930 and D4S1523, <1.23 Mb) showing the highest heterozygote frequencies (67-91%) were selected. Five recombination events in the D4S2390-D4S1523 interval were observed among 144 meioses. In the D4S2390-D4Z4 interval, no recombination event occurred among 28 FSHD meioses. Instead, a particular haplotype segregated with both clinical and molecular status, allowing the characterization of an at-risk allele in each tested FSHD family (maximal LOD score 2.98 for theta=0.0). This indirect protocol can easily complement conventional techniques in prenatal diagnosis. Although our multiplex PCR-based approach technically fulfils guidelines for single-cell analysis, the relatively high recombination risk hampers its application to PGD.
Collapse
Affiliation(s)
- Mouna Barat-Houari
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Vasseur F, Caeyseele T, Barat-Houari M, Lobbens S, Meirhaeghe A, Meyre D, Froguel P, Amouyel P, Helbecque N. Concordance of two multiple analytical approaches demonstrate that interaction between BMI and ADIPOQ haplotypes is a determinant of LDL cholesterol in a general French population. J Hum Genet 2010; 55:227-31. [PMID: 20186155 DOI: 10.1038/jhg.2010.10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic and environmental factors are involved in insulin resistance (IR). IR and dyslipidemia associate with increased risk of cardiovascular diseases. Plasma low-density lipoprotein cholesterol (LDL-C) level is a marker of cardiovascular risk. In a Caucasian general population we aimed at determining the multifactorial components of LDL-C levels using 10 genes and 3 phenotypes. In the PPARG, UCP3, ADIPOQ, TNF, LIPC, CARTPT, PCSK9, SCAP, SCARB1 and ENPP1 genes known to be associated with IR or dyslipidemia we genotyped 19 single nucleotide polymorphisms (SNPs) in 846 subjects. When several SNPs were genotyped for a given gene we constructed haplotypes. Including genetic and environmental variables (gender, body mass index (BMI) and adiponectin level) we used (1) the multifactor dimensionality reduction method to explain clusters of high and low LDL-C, and (2) the restricted partition method to explain LDL-C levels. Both methods showed that BMI and haplotypes at the ADIPOQ adiponectin encoding gene but not adiponectin level itself, were discriminant regarding to LDL-C. Subjects bearing an at-risk combination of BMI and ADIPOQ genotypes were prone to have a higher LDL-C (OR=3.13, 95% CI=2.20-4.46, P<0.0001). Our results suggest that in interaction with BMI, ADIPOQ haplotypes capture genetic variation(s) from neighboring gene(s) that would modulate LDL-C level.
Collapse
Affiliation(s)
- Francis Vasseur
- Biostatistics Department EA2694, University Hospital, University Lille Nord de France, UDSL, Lille cedex, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Vasseur F, Guérardel A, Barat-Houari M, Cottel D, Amouyel P, Froguel P, Helbecque N. Impact of a CART promoter genetic variation on plasma lipid profile in a general population. Mol Genet Metab 2007; 90:199-204. [PMID: 17008116 DOI: 10.1016/j.ymgme.2006.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Accepted: 08/17/2006] [Indexed: 11/20/2022]
Abstract
The cocaine and amphetamine regulated transcript (CART), an anorexigenic peptide responding to leptin, is expressed in various areas of the hypothalamus. The role of CART in humans and its potential contribution to abnormalities in feeding control are mostly unknown. Since CART plays an important role in the hypothalamic regulation of energy balance by reducing food intake and increasing lipid substrate utilization, it might affect cholesterol metabolism as Neuropeptide Y or pro-opiomelanocortin do. In the present work, we studied the potential effects of three SNPs of the CART promoter in a WHO-MONICA general population from North of France (n=840), untreated for hypercholesterolemia, hypertension, or diabetes mellitus since any treatment is likely to interfere with lipoprotein/lipid variables. Our results show associations between these SNPs and plasma LDL-cholesterol level and the LDL/HDL ratio, a marker of atherogenicity. A haplotypic study suggests that these effects are mainly attributable to the functional SNP -3608C>T. Subjects bearing the -3608 C allele present a plasma lipid profile protective against atherogenesis: decrease of plasma LDL-cholesterol level (p=0.001) and of the LDL/HDL ratio (p=0.0003). This result offers new evidences for a potential implication of the CART gene in lipid metabolism and in atherogenesis.
Collapse
Affiliation(s)
- Francis Vasseur
- CNRS UMR 8090, Institut de Biologie de Lille, Institut Pasteur de Lille, 1 rue du Professeur Calmette, BP 245, 59019 Lille Cedex, France
| | | | | | | | | | | | | |
Collapse
|
31
|
Barat-Houari M, Hilliou F, Jousset FX, Sofer L, Deleury E, Rocher J, Ravallec M, Galibert L, Delobel P, Feyereisen R, Fournier P, Volkoff AN. Gene expression profiling of Spodoptera frugiperda hemocytes and fat body using cDNA microarray reveals polydnavirus-associated variations in lepidopteran host genes transcript levels. BMC Genomics 2006; 7:160. [PMID: 16790040 PMCID: PMC1559612 DOI: 10.1186/1471-2164-7-160] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Accepted: 06/21/2006] [Indexed: 01/12/2023] Open
Abstract
Background Genomic approaches provide unique opportunities to study interactions of insects with their pathogens. We developed a cDNA microarray to analyze the gene transcription profile of the lepidopteran pest Spodoptera frugiperda in response to injection of the polydnavirus HdIV associated with the ichneumonid wasp Hyposoter didymator. Polydnaviruses are associated with parasitic ichneumonoid wasps and are required for their development within the lepidopteran host, in which they act as potent immunosuppressive pathogens. In this study, we analyzed transcriptional variations in the two main effectors of the insect immune response, the hemocytes and the fat body, after injection of filter-purified HdIV. Results Results show that 24 hours post-injection, about 4% of the 1750 arrayed host genes display changes in their transcript levels with a large proportion (76%) showing a decrease. As a comparison, in S. frugiperda fat body, after injection of the pathogenic JcDNV densovirus, 8 genes display significant changes in their transcript level. They differ from the 7 affected by HdIV and, as opposed to HdIV injection, are all up-regulated. Interestingly, several of the genes that are modulated by HdIV injection have been shown to be involved in lepidopteran innate immunity. Levels of transcripts related to calreticulin, prophenoloxidase-activating enzyme, immulectin-2 and a novel lepidopteran scavenger receptor are decreased in hemocytes of HdIV-injected caterpillars. This was confirmed by quantitative RT-PCR analysis but not observed after injection of heat-inactivated HdIV. Conversely, an increased level of transcripts was found for a galactose-binding lectin and, surprisingly, for the prophenoloxidase subunits. The results obtained suggest that HdIV injection affects transcript levels of genes encoding different components of the host immune response (non-self recognition, humoral and cellular responses). Conclusion This analysis of the host-polydnavirus interactions by a microarray approach indicates that the presence of HdIV induces, directly or indirectly, variations in transcript levels of specific host genes, changes that could be responsible in part for the alterations observed in the parasitized host physiology. Development of such global approaches will allow a better understanding of the strategies employed by parasites to manipulate their host physiology, and will permit the identification of potential targets of the immunosuppressive polydnaviruses.
Collapse
Affiliation(s)
- M Barat-Houari
- UMR 1231 Biologie Intégrative et Virologie des Insectes. INRA – Université de Montpellier II. Place Eugène Bataillon, Case Courrier 101, 34 095 Montpellier Cedex, France
| | - F Hilliou
- UMR 1112 R.O.S.E. INRA – Université de Nice-Sophia Antipolis, Laboratoire de Génomique Fonctionnelle des Insectes, 400 route des Chappes, BP 167, 06 903 Sophia Antipolis Cedex, France
| | - F-X Jousset
- UMR 1231 Biologie Intégrative et Virologie des Insectes. INRA – Université de Montpellier II. Place Eugène Bataillon, Case Courrier 101, 34 095 Montpellier Cedex, France
| | - L Sofer
- UMR 1112 R.O.S.E. INRA – Université de Nice-Sophia Antipolis, Laboratoire de Génomique Fonctionnelle des Insectes, 400 route des Chappes, BP 167, 06 903 Sophia Antipolis Cedex, France
| | - E Deleury
- UMR 1112 R.O.S.E. INRA – Université de Nice-Sophia Antipolis, Laboratoire de Génomique Fonctionnelle des Insectes, 400 route des Chappes, BP 167, 06 903 Sophia Antipolis Cedex, France
| | - J Rocher
- UMR 1231 Biologie Intégrative et Virologie des Insectes. INRA – Université de Montpellier II. Place Eugène Bataillon, Case Courrier 101, 34 095 Montpellier Cedex, France
| | - M Ravallec
- UMR 1231 Biologie Intégrative et Virologie des Insectes. INRA – Université de Montpellier II. Place Eugène Bataillon, Case Courrier 101, 34 095 Montpellier Cedex, France
| | - L Galibert
- UMR 1231 Biologie Intégrative et Virologie des Insectes. INRA – Université de Montpellier II. Place Eugène Bataillon, Case Courrier 101, 34 095 Montpellier Cedex, France
| | - P Delobel
- INRA U.M.R. Sciences pour l'Oenologie, Equipe Microbiologie – Bât 28, 2, place Viala, 34 060 Montpellier Cedex 01, France
| | - R Feyereisen
- UMR 1112 R.O.S.E. INRA – Université de Nice-Sophia Antipolis, Laboratoire de Génomique Fonctionnelle des Insectes, 400 route des Chappes, BP 167, 06 903 Sophia Antipolis Cedex, France
| | - P Fournier
- UMR 1231 Biologie Intégrative et Virologie des Insectes. INRA – Université de Montpellier II. Place Eugène Bataillon, Case Courrier 101, 34 095 Montpellier Cedex, France
| | - A-N Volkoff
- UMR 1231 Biologie Intégrative et Virologie des Insectes. INRA – Université de Montpellier II. Place Eugène Bataillon, Case Courrier 101, 34 095 Montpellier Cedex, France
| |
Collapse
|
32
|
Galibert L, Devauchelle G, Cousserans F, Rocher J, Cérutti P, Barat-Houari M, Fournier P, Volkoff AN. Members of the Hyposoter didymator Ichnovirus repeat element gene family are differentially expressed in Spodoptera frugiperda. Virol J 2006; 3:48. [PMID: 16784535 PMCID: PMC1539012 DOI: 10.1186/1743-422x-3-48] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Accepted: 06/19/2006] [Indexed: 11/10/2022] Open
Abstract
Background The abundance and the conservation of the repeated element (rep) genes in Ichnoviruses genomes suggest that this gene family plays an important role in viral cycles. In the Ichnovirus associated with the wasp Hyposoter didymator, named HdIV, 10 rep genes were identified to date. In this work, we report a relative quantitative transcription study of these HdIV rep genes in several tissues of the lepidopteran host Spodoptera frugiperda as well as in the H. didymator wasps. Results The data obtained in this work indicate that, in the early phases of infection (24 hours), HdIV rep genes each display different levels of transcripts in parasitized 2nd instar or HdIV-injected last instar S. frugiperda larvae. Only one, rep1, is significantly transcribed in female wasps. Transcript levels of the HdIV rep genes were found as not correlated to their copy number in HdIV genome. Our results also show that HdIV rep genes display different tissue specificity, and that they are primarily transcribed in S. frugiperda fat body and cuticular epithelium. Conclusion This work is the first quantitative analysis of transcription of the ichnovirus rep gene family, and the first investigation on a correlation between transcript levels and gene copy numbers in Ichnoviruses. Our data indicate that, despite similar gene copy numbers, not all the members of this gene family are significantly transcribed 24 hours after infection in lepidopteran larvae. Additionally, our data show that, as opposed to other described HdIV genes, rep genes are little transcribed in hemocytes, thus suggesting that they are not directly associated with the disruption of the immune response but rather involved in other physiological alterations of the infected lepidopteran larva.
Collapse
Affiliation(s)
- L Galibert
- UMR1231 INRA-UMII Biologie Intégrative et Virologie des Insectes (BIVI), Place Eugène Bataillon, Case Courrier 101, 34 095 Montpellier Cédex5, France
| | - G Devauchelle
- UMR 5160 CNRS-UMI Baculovirus et Thérapie, 30 380 Saint Christol-lez-Alès, France
| | - F Cousserans
- UMR1231 INRA-UMII Biologie Intégrative et Virologie des Insectes (BIVI), Place Eugène Bataillon, Case Courrier 101, 34 095 Montpellier Cédex5, France
| | - J Rocher
- UMR1231 INRA-UMII Biologie Intégrative et Virologie des Insectes (BIVI), Place Eugène Bataillon, Case Courrier 101, 34 095 Montpellier Cédex5, France
| | - P Cérutti
- UMR 5160 CNRS-UMI Baculovirus et Thérapie, 30 380 Saint Christol-lez-Alès, France
| | - M Barat-Houari
- UMR1231 INRA-UMII Biologie Intégrative et Virologie des Insectes (BIVI), Place Eugène Bataillon, Case Courrier 101, 34 095 Montpellier Cédex5, France
| | - P Fournier
- UMR1231 INRA-UMII Biologie Intégrative et Virologie des Insectes (BIVI), Place Eugène Bataillon, Case Courrier 101, 34 095 Montpellier Cédex5, France
| | - AN Volkoff
- UMR1231 INRA-UMII Biologie Intégrative et Virologie des Insectes (BIVI), Place Eugène Bataillon, Case Courrier 101, 34 095 Montpellier Cédex5, France
| |
Collapse
|
33
|
Guérardel A, Barat-Houari M, Vasseur F, Dina C, Vatin V, Clément K, Eberlé D, Vasseur-Delannoy V, Bell CG, Galan P, Hercberg S, Helbecque N, Potoczna N, Horber FF, Boutin P, Froguel P. Analysis of sequence variability in the CART gene in relation to obesity in a Caucasian population. BMC Genet 2005; 6:19. [PMID: 15823203 PMCID: PMC1087839 DOI: 10.1186/1471-2156-6-19] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Accepted: 04/11/2005] [Indexed: 11/30/2022] Open
Abstract
Background Cocaine and amphetamine regulated transcript (CART) is an anorectic neuropeptide located principally in hypothalamus. CART has been shown to be involved in control of feeding behavior, but a direct relationship with obesity has not been established. The aim of this study was to evaluate the effect of polymorphisms within the CART gene with regards to a possible association with obesity in a Caucasian population. Results Screening of the entire gene as well as a 3.7 kb region of 5' upstream sequence revealed 31 SNPs and 3 rare variants ; 14 of which were subsequently genotyped in 292 French morbidly obese subjects and 368 controls. Haplotype analysis suggested an association with obesity which was found to be mainly due to SNP-3608T>C (rs7379701) (p = 0.009). Genotyping additional cases and controls also of European Caucasian origin supported further this possible association between the CART SNP -3608T>C T allele and obesity (global p-value = 0.0005). Functional studies also suggested that the SNP -3608T>C could modulate nuclear protein binding. Conclusion CART SNP -3608T>C may possibly contribute to the genetic risk for obesity in the Caucasian population. However confirmation of the importance of the role of the CART gene in energy homeostasis and obesity will require investigation and replication in further populations.
Collapse
Affiliation(s)
- Audrey Guérardel
- Institute of Biology-CNRS UMR 8090, Pasteur Institute, Lille, France
| | | | - Francis Vasseur
- Institute of Biology-CNRS UMR 8090, Pasteur Institute, Lille, France
- University Hospital, Lille, France
| | - Christian Dina
- Institute of Biology-CNRS UMR 8090, Pasteur Institute, Lille, France
| | - Vincent Vatin
- Institute of Biology-CNRS UMR 8090, Pasteur Institute, Lille, France
| | - Karine Clément
- Department of Nutrition-EA3502, Paris VI University, INSERM "Avenir" Hôtel-Dieu, Paris, France
| | - Delphine Eberlé
- Department of Nutrition-EA3502, Paris VI University, INSERM "Avenir" Hôtel-Dieu, Paris, France
| | | | - Christopher G Bell
- Imperial College genome Centre and Genomic Medicine, Hammersmith Campus, Imperial College London, UK
| | - Pilar Galan
- Scientific and Technical Institute of Nutrition and Food (ISTNA-CNAM), INSERM U557, INRA U1125, Paris, France
| | - Serge Hercberg
- Scientific and Technical Institute of Nutrition and Food (ISTNA-CNAM), INSERM U557, INRA U1125, Paris, France
| | - Nicole Helbecque
- Service d'Epidémiologie et de Santé Publique-INSERM U.508, Pasteur Institute, Lille, France
| | - Natascha Potoczna
- Dr. Horber Adipositas Stiftung, Hornbachstrasse 50, 8034, Zürich, Switzerland
| | - Fritz F Horber
- Dr. Horber Adipositas Stiftung, Hornbachstrasse 50, 8034, Zürich, Switzerland
| | - Philippe Boutin
- Institute of Biology-CNRS UMR 8090, Pasteur Institute, Lille, France
| | - Philippe Froguel
- Imperial College genome Centre and Genomic Medicine, Hammersmith Campus, Imperial College London, UK
| |
Collapse
|
34
|
Barat-Houari M, Clément K, Vatin V, Dina C, Bonhomme G, Vasseur F, Guy-Grand B, Froguel P. Positional candidate gene analysis of Lim domain homeobox gene (Isl-1) on chromosome 5q11-q13 in a French morbidly obese population suggests indication for association with type 2 diabetes. Diabetes 2002; 51:1640-3. [PMID: 11978668 DOI: 10.2337/diabetes.51.5.1640] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Lim domain homeobox gene (Isl-1) is a positional candidate gene for obesity that maps on chromosome 5q11-q13, a locus linked to BMI and leptin levels in French Caucasians. Isl-1 might be involved in body weight regulation and glucose homeostasis via the activation of proglucagon gene expression, which encodes for glucagon and glucagon-like peptides. By mutation screening of 72 obese subjects, we identified three single-nucleotide polymorphisms (SNPs) in the Isl1 gene. The allele frequencies in the morbidly obese group did not differ from that of the control group. In the obese group, the -47G allele was associated with a decreased risk of type 2 diabetes (odds ratio 0.41, P = 0.019). The AG bearers displayed a higher maximal BMI than the AA bearers in the whole obese group (P = 0.026) as well as in the type 2 diabetic obese subgroup (P = 0.014). In obese families, this allele was not preferentially transmitted from heterozygous parents to their obese siblings, indicating that Isl-1 does not contribute to the linkage with obesity on 5cen-q. However, in French Caucasian morbidly obese subjects, the Isl1-47A-->G SNP may modulate the risk for type 2 diabetes and may increase body weight in diabetic morbidly obese subjects.
Collapse
Affiliation(s)
- Mouna Barat-Houari
- Institute of Biology, Centre National de la Recherche Scientifique (CNRS) 80-90, Lille, France
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Delplanque J, Barat-Houari M, Dina C, Gallina P, Clément K, Guy-Grand B, Vasseur F, Boutin P, Froguel P. Linkage and association studies between the proopiomelanocortin (POMC) gene and obesity in caucasian families. Diabetologia 2000; 43:1554-7. [PMID: 11151766 DOI: 10.1007/s001250051568] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
AIMS/HYPOTHESIS The region 2p21-23, containing the proopiomelanocortin gene (POMC), was reported to be linked to leptin concentrations in Mexican-American, French and African-American cohorts. A polyhormone peptide, POMC is expressed in brain, gut, placenta and pancreas. The POMC mutations are responsible for rare cases of early-onset obesity. Thus we examined the contribution of the POMC locus to obesity in French families. METHODS Single and multipoint linkage studies were done between obesity, obesity associated-phenotypes (leptin values and z-score of the body mass index) and three newly mapped markers surrounding POMC in 264 affected sib-pairs from French obese families. Mutation screening of the exons and intron/exon junctions of the POMC gene was realised by direct sequencing. Association studies were done in 379 unrelated obese patients and 370 non-obese non-diabetic subjects. RESULTS Linkage analysis confirmed the trend towards linkage between polymorphic markers around POMC and variations of leptin concentrations and z-score (maximum lod score at D2S2337 = 2.03). Mutation screening of the POMC gene in the French Caucasian cohort identified two previously reported polymorphisms. None of these variants was associated with obesity, diabetes or serum leptin and lipid concentrations. CONCLUSION/INTERPRETATION Our results indicate that mutations in the POMC gene do not contribute to the variance of obesity associated phenotypes, at least in French Caucasians. Given the replicated evidence of linkage between leptin values and the chromosome 2p21-23 region in different populations, it is likely that functional variant(s) in the POMC regulating sequences or in an unknown gene in this region explains this linkage.
Collapse
Affiliation(s)
- J Delplanque
- Institute of Biology-CNRS 8090, Pasteur Institute of Lille, CHRU of Lille, Lille, France
| | | | | | | | | | | | | | | | | |
Collapse
|