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Küry S, Ebstein F, Mollé A, Besnard T, Lee MK, Vignard V, Hery T, Nizon M, Mancini GM, Giltay JC, Cogné B, McWalter K, Deb W, Mor-Shaked H, Li H, Schnur RE, Wentzensen IM, Denommé-Pichon AS, Fourgeux C, Verheijen FW, Faurie E, Schot R, Stevens CA, Smits DJ, Barr E, Sheffer R, Bernstein JA, Stimach CL, Kovitch E, Shashi V, Schoch K, Smith W, van Jaarsveld RH, Hurst AC, Smith K, Baugh EH, Bohm SG, Vyhnálková E, Ryba L, Delnatte C, Neira J, Bonneau D, Toutain A, Rosenfeld JA, Audebert-Bellanger S, Gilbert-Dussardier B, Odent S, Laumonnier F, Berger SI, Smith AC, Bourdeaut F, Stern MH, Redon R, Krüger E, Margueron R, Bézieau S, Poschmann J, Isidor B, Isidor B. Rare germline heterozygous missense variants in BRCA1-associated protein 1, BAP1, cause a syndromic neurodevelopmental disorder. Am J Hum Genet 2022; 109:361-372. [PMID: 35051358 DOI: 10.1016/j.ajhg.2021.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 07/22/2021] [Accepted: 12/14/2021] [Indexed: 12/23/2022] Open
Abstract
Nuclear deubiquitinase BAP1 (BRCA1-associated protein 1) is a core component of multiprotein complexes that promote transcription by reversing the ubiquitination of histone 2A (H2A). BAP1 is a tumor suppressor whose germline loss-of-function variants predispose to cancer. To our knowledge, there are very rare examples of different germline variants in the same gene causing either a neurodevelopmental disorder (NDD) or a tumor predisposition syndrome. Here, we report a series of 11 de novo germline heterozygous missense BAP1 variants associated with a rare syndromic NDD. Functional analysis showed that most of the variants cannot rescue the consequences of BAP1 inactivation, suggesting a loss-of-function mechanism. In T cells isolated from two affected children, H2A deubiquitination was impaired. In matching peripheral blood mononuclear cells, histone H3 K27 acetylation ChIP-seq indicated that these BAP1 variants induced genome-wide chromatin state alterations, with enrichment for regulatory regions surrounding genes of the ubiquitin-proteasome system (UPS). Altogether, these results define a clinical syndrome caused by rare germline missense BAP1 variants that alter chromatin remodeling through abnormal histone ubiquitination and lead to transcriptional dysregulation of developmental genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France; Université de Nantes, CHU Nantes, CNRS, INSERM, l'Institut du Thorax, 44007 Nantes, France.
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Zarate YA, Bosanko KA, Caffrey AR, Bernstein JA, Martin DM, Williams MS, Berry-Kravis EM, Mark PR, Manning MA, Bhambhani V, Vargas M, Seeley AH, Estrada-Veras JI, van Dooren MF, Schwab M, Vanderver A, Melis D, Alsadah A, Sadler L, Van Esch H, Callewaert B, Oostra A, Maclean J, Dentici ML, Orlando V, Lipson M, Sparagana SP, Maarup TJ, Alsters SI, Brautbar A, Kovitch E, Naidu S, Lees M, Smith DM, Turner L, Raggio V, Spangenberg L, Garcia-Miñaúr S, Roeder ER, Littlejohn RO, Grange D, Pfotenhauer J, Jones MC, Balasubramanian M, Martinez-Monseny A, Blok LS, Gavrilova R, Fish JL. Mutation update for the SATB2 gene. Hum Mutat 2019; 40:1013-1029. [PMID: 31021519 DOI: 10.1002/humu.23771] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 02/04/2019] [Revised: 04/10/2019] [Accepted: 04/22/2019] [Indexed: 12/20/2022]
Abstract
SATB2-associated syndrome (SAS) is an autosomal dominant neurodevelopmental disorder caused by alterations in the SATB2 gene. Here we present a review of published pathogenic variants in the SATB2 gene to date and report 38 novel alterations found in 57 additional previously unreported individuals. Overall, we present a compilation of 120 unique variants identified in 155 unrelated families ranging from single nucleotide coding variants to genomic rearrangements distributed throughout the entire coding region of SATB2. Single nucleotide variants predicted to result in the occurrence of a premature stop codon were the most commonly seen (51/120 = 42.5%) followed by missense variants (31/120 = 25.8%). We review the rather limited functional characterization of pathogenic variants and discuss current understanding of the consequences of the different molecular alterations. We present an expansive phenotypic review along with novel genotype-phenotype correlations. Lastly, we discuss current knowledge of animal models and present future prospects. This review should help provide better guidance for the care of individuals diagnosed with SAS.
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Affiliation(s)
- Yuri A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Katherine A Bosanko
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Aisling R Caffrey
- Health Outcomes, College of Pharmacy, Department of Pharmacy Practice, University of Rhode Island, Kingston, Rhode Island
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Donna M Martin
- Departments of Pediatrics and Human Genetics, The University of Michigan, Ann Arbor, Michigan
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Elizabeth M Berry-Kravis
- Departments of Pediatrics, Neurological Sciences, Biochemistry, Rush University Medical Center, Chicago, Illinois
| | - Paul R Mark
- Division of Medical Genetics, Spectrum Health, Grand Rapids, Michigan
| | - Melanie A Manning
- Departments of Pathology and Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Vikas Bhambhani
- Division of Genetics and Genomic Medicine, Children's Hospital and Clinics of Minnesota, Minneapolis, Minnesota
| | - Marcelo Vargas
- Division of Genetics and Genomic Medicine, Children's Hospital and Clinics of Minnesota, Minneapolis, Minnesota
| | - Andrea H Seeley
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Juvianee I Estrada-Veras
- Murtha Cancer Center Research Program, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, Maryland.,Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, Maryland.,Pediatric subspecialty-Medical Genetics Service, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Marieke F van Dooren
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Maria Schwab
- Genetics Division, Joseph Sanzari Children's Hospital, Hackensack University Medical Center, Hackensack, New Jersey
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Daniela Melis
- Department of Translational Medical Science, Section of Pediatrics, Federico II University, Naples, Italy
| | - Adnan Alsadah
- Center for Personalized Genetic Healthcare, Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Laurie Sadler
- Division of Genetics, Oishei Children's Hospital, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, New York
| | - Hilde Van Esch
- Department of Human Genetics, University Hospitals Leuven, KU, Leuven, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Ann Oostra
- Department of Pediatric Neurology, Ghent University Hospital, Ghent, Belgium
| | - Jane Maclean
- Pediatric Neurology, Palo Alto Medical Foundation, San Jose, California
| | - Maria Lisa Dentici
- Medical Genetics, Academic Department of Pediatrics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Valeria Orlando
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Mark Lipson
- Department of Genetics, Kaiser Permanente, Sacramento, California
| | - Steven P Sparagana
- Department of Neurology, Texas Scottish Rite Hospital for Children, Dallas, Texas
| | - Timothy J Maarup
- Department of Genetics, Kaiser Permanente, Los Angeles, California
| | - Suzanne Im Alsters
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ariel Brautbar
- Department of Genetics, Cook Chldren's Medical Center, Fort Worth, Texas
| | | | - Sakkubai Naidu
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland
| | - Melissa Lees
- Department of Clinical Genetics, Great Ormond Street Hospital for Children, London, UK
| | | | - Lesley Turner
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Víctor Raggio
- Departamento de Genética, Facultad de Medicina, Montevideo, Uruguay
| | | | - Sixto Garcia-Miñaúr
- Department of Medical Genetics, Hospital Universitario La Paz, Madrid, Spain
| | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Rebecca O Littlejohn
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Dorothy Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medcine, St Louis, Missouri
| | - Jean Pfotenhauer
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Marilyn C Jones
- Division of Genetics, Department of Pediatrics, University of California, San Diego and Rady Children's Hospital, San Diego, California
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Western Bank, Sheffield, UK
| | - Antonio Martinez-Monseny
- Genetics and Molecular Medicine Department, Rare Disease Pediatric Unit, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Lot Snijders Blok
- Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands.,Language & Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Ralitza Gavrilova
- Departments of Neurology and Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Jennifer L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts
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