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Keskinen S, Paakkola T, Mattila M, Hietala M, Koillinen H, Laine J, Haanpää MK. Prenatal Coffin-Siris Syndrome: Expanding the Phenotypic and Genotypic Spectrum of the Disease. Pediatr Dev Pathol 2024; 27:181-186. [PMID: 37981638 PMCID: PMC11015708 DOI: 10.1177/10935266231210155] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Coffin-Siris syndrome is an autosomal dominant disorder with neurological, cardiovascular, and gastrointestinal symptoms. Patients with Coffin-Siris syndrome typically have variable degree of developmental delay or intellectual disability, muscular hypotonia, dysmorphic facial features, sparse scalp hair, but otherwise hirsutism and fifth digit nail or distal phalanx hypoplasia or aplasia. Coffin-Siris syndrome is caused by pathogenic variants in 12 different genes including SMARCB1 and ARID1A. Pathogenic SMARCB1 gene variants cause Coffin-Siris syndrome 3 whereas pathogenic ARID1A gene variants cause Coffin-Siris syndrome 2. Here, we present two prenatal Coffin-Siris syndrome cases with autosomal dominant pathogenic variants: SMARCB1 gene c.1066_1067del, p.(Leu356AspfsTer4) variant, and a novel ARID1A gene c.1920+3_1920+6del variant. The prenatal phenotype in Coffin-Siris syndrome has been rarely described. This article widens the phenotypic spectrum of prenatal Coffin-Siris syndrome with severely hypoplastic right ventricle with VSD and truncus arteriosus type III, persisting left superior and inferior caval vein, bilateral olfactory nerve aplasia, and hypoplastic thymus. A detailed clinical description of the patients with ultrasound, MRI, and post mortem pictures of the affected fetuses showing the wide phenotypic spectrum of the disease is presented.
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Affiliation(s)
- Sini Keskinen
- Tyks Laboratories, Genomics, Clinical Genetics, Turku University Hospital, Turku, Finland
| | - Teija Paakkola
- Tyks Laboratories, Genomics, Clinical Genetics, Turku University Hospital, Turku, Finland
- Northern Finland Laboratory Centre NordLab and Oulu University Hospital, Oulu, Finland
| | - Mirjami Mattila
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Marja Hietala
- Department of Clinical Genetics, Turku University Hospital, Turku, Finland
| | - Hannele Koillinen
- Department of Clinical Genetics, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Jukka Laine
- Department of Pathology, Turku University Hospital, Turku, Finland
| | - Maria K. Haanpää
- Tyks Laboratories, Genomics, Clinical Genetics, Turku University Hospital, Turku, Finland
- Department of Clinical Genetics, Turku University Hospital, Turku, Finland
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2
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Bosch E, Popp B, Güse E, Skinner C, van der Sluijs PJ, Maystadt I, Pinto AM, Renieri A, Bruno LP, Granata S, Marcelis C, Baysal Ö, Hartwich D, Holthöfer L, Isidor B, Cogne B, Wieczorek D, Capra V, Scala M, De Marco P, Ognibene M, Jamra RA, Platzer K, Carter LB, Kuismin O, van Haeringen A, Maroofian R, Valenzuela I, Cuscó I, Martinez-Agosto JA, Rabani AM, Mefford HC, Pereira EM, Close C, Anyane-Yeboa K, Wagner M, Hannibal MC, Zacher P, Thiffault I, Beunders G, Umair M, Bhola PT, McGinnis E, Millichap J, van de Kamp JM, Prijoles EJ, Dobson A, Shillington A, Graham BH, Garcia EJ, Galindo MK, Ropers FG, Nibbeling EAR, Hubbard G, Karimov C, Goj G, Bend R, Rath J, Morrow MM, Millan F, Salpietro V, Torella A, Nigro V, Kurki M, Stevenson RE, Santen GWE, Zweier M, Campeau PM, Severino M, Reis A, Accogli A, Vasileiou G. Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals. Genet Med 2023; 25:100950. [PMID: 37551667 DOI: 10.1016/j.gim.2023.100950] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 03/28/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023] Open
Abstract
PURPOSE Coffin-Siris and Nicolaides-Baraitser syndromes are recognizable neurodevelopmental disorders caused by germline variants in BAF complex subunits. The SMARCC2 BAFopathy was recently reported. Herein, we present clinical and molecular data on a large cohort. METHODS Clinical symptoms for 41 novel and 24 previously published affected individuals were analyzed using the Human Phenotype Ontology. For genotype-phenotype correlations, molecular data were standardized and grouped into non-truncating and likely gene-disrupting (LGD) variants. Missense variant protein expression and BAF-subunit interactions were examined using 3D protein modeling, co-immunoprecipitation, and proximity-ligation assays. RESULTS Neurodevelopmental delay with intellectual disability, muscular hypotonia, and behavioral disorders were the major manifestations. Clinical hallmarks of BAFopathies were rare. Clinical presentation differed significantly, with LGD variants being predominantly inherited and associated with mildly reduced or normal cognitive development, whereas non-truncating variants were mostly de novo and presented with severe developmental delay. These distinct manifestations and non-truncating variant clustering in functional domains suggest different pathomechanisms. In vitro testing showed decreased protein expression for N-terminal missense variants similar to LGD. CONCLUSION This study improved SMARCC2 variant classification and identified discernible SMARCC2-associated phenotypes for LGD and non-truncating variants, which were distinct from other BAFopathies. The pathomechanism of most non-truncating variants has yet to be investigated.
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Affiliation(s)
- Elisabeth Bosch
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Bernt Popp
- Berlin Institute of Health at Charitè, Universitätsklinikum Berlin, Centre of Functional Genomics, Berlin, Germany; Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Esther Güse
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | | | - Isabelle Maystadt
- Center for Human Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Anna Maria Pinto
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy; Medical Genetics Unit, University of Siena, Siena, Italy
| | - Lucia Pia Bruno
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Stefania Granata
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy; Medical Genetics Unit, University of Siena, Siena, Italy
| | - Carlo Marcelis
- Human Genetics department, Radboud university medical center, Nijmegen, The Netherlands
| | - Özlem Baysal
- Human Genetics department, Radboud university medical center, Nijmegen, The Netherlands
| | - Dewi Hartwich
- Institute of Human Genetics - University Medical Center of the Johannes Gutenberg University Mainz, Germany
| | - Laura Holthöfer
- Institute of Human Genetics - University Medical Center of the Johannes Gutenberg University Mainz, Germany
| | - Bertrand Isidor
- Nantes Université, CHU de Nantes, Service de Génétique médicale, Nantes, France; Nantes Université, CHU de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Benjamin Cogne
- Nantes Université, CHU de Nantes, Service de Génétique médicale, Nantes, France; Nantes Université, CHU de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Valeria Capra
- Genomics and Clinical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Patrizia De Marco
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marzia Ognibene
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Lauren B Carter
- Department of Pediatrics, Division of Medical Genetics, Levine Children's Hospital, Atrium Health, Charlotte, NC
| | - Outi Kuismin
- Department of Clinical Genetics, Research Unit of Clinical Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, University Hospital Vall d'Hebron, Barcelona, Spain; Medicine Genetics Group, Valle Hebron Research Institute, Barcelona, Spain
| | - Ivon Cuscó
- Department of Clinical and Molecular Genetics, University Hospital Vall d'Hebron, Barcelona, Spain; Medicine Genetics Group, Valle Hebron Research Institute, Barcelona, Spain
| | - Julian A Martinez-Agosto
- Departments of Human Genetics, Pediatrics, and Psychiatry, UCLA David Geffen School of Medicine, Los Angeles, CA
| | - Ahna M Rabani
- Department of Pediatrics & Institute for Precision Health, UCLA David Geffen School of Medicine, Los Angeles, CA
| | - Heather C Mefford
- Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, TN
| | - Elaine M Pereira
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Charlotte Close
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Kwame Anyane-Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Mallory Wagner
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan Health System, University of Michigan, Ann Arbor, MI
| | - Mark C Hannibal
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan Health System, University of Michigan, Ann Arbor, MI
| | - Pia Zacher
- Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Isabelle Thiffault
- Department of Pediatrics and Pathology, Genomic Medicine Center, Children's Mercy Kansas City and Children's Mercy Research Institute, Kansas City, MO
| | - Gea Beunders
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia; Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Priya T Bhola
- Department of Genetics, Children's Hospital of Eastern Ontario (CHEO), Ottawa, Canada
| | - Erin McGinnis
- Division of Neurology, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - John Millichap
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Jiddeke M van de Kamp
- Department of Human Genetics, Amsterdam UMC, location VU Medical Center, Amsterdam, The Netherlands
| | | | | | - Amelle Shillington
- Department of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Brett H Graham
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Evan-Jacob Garcia
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | | | - Fabienne G Ropers
- Willem-Alexander Children's Hospital, Department of Pediatrics, Leiden University Medical Center, The Netherlands
| | - Esther A R Nibbeling
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Gail Hubbard
- Department of Medical Genetics, Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA
| | - Catherine Karimov
- Department of Medical Genetics, Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA
| | - Guido Goj
- Vestische Kinder- und Jugendklinik, Datteln, Germany
| | - Renee Bend
- PreventionGenetics, Part of Exact Sciences, Marshfield, WI
| | - Julie Rath
- PreventionGenetics, Part of Exact Sciences, Marshfield, WI
| | | | | | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, United Kingdom; Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy
| | - Mitja Kurki
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA
| | | | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Markus Zweier
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, Switzerland
| | - Philippe M Campeau
- Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | | | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Centre for Rare Diseases Erlangen (ZSEER), Erlangen, Germany
| | - Andrea Accogli
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre; Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Georgia Vasileiou
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Centre for Rare Diseases Erlangen (ZSEER), Erlangen, Germany.
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Shin D, Lee YJ, Jo YH, Kong J, Lee YJ, Nam SO, Lee BL, Oh SH, Kim YM. Coffin-Siris Syndrome: Case Series of Three Patients and a Novel ARID2 Variant. Ann Clin Lab Sci 2023; 53:959-963. [PMID: 38182156] [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] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
Coffin-Siris syndrome (CSS) is a rare congenital disorder characterized by coarse facial features, intellectual disability or developmental delay, and aplasia or hypoplasia of the tips of the fifth finger and/or toes. Mutations in genes affecting the switch/sucrose non-fermenting ATP-dependent chromatin remodeling complex are reported to cause CSS. Here, we describe three CSS patients. Two girls aged 3 and 2 years old presented with global developmental delay, poor growth, and a dysmorphic face. Whole-exome sequencing (WES) was performed and they were diagnosed with CSS due to heterozygous frameshift variants (c.3443_3444del, p.Lys1148ArgfsTer9 and c.2869_2890del, p.Pro957CysfsTer20) in ARID1B A 2-year-old girl presented with gross motor delay and dysmorphic face. She was diagnosed with CSS due to a novel heterozygous frameshift variant (c.4942_4943del: p.Gln1648GlyfsTer8) in ARID2.
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Affiliation(s)
- Donghyun Shin
- Department of Pediatrics, Pusan National University Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Busan, Korea
| | - Yoo Jung Lee
- Department of Pediatrics, Pusan National University Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Busan, Korea
| | - Yoon Hee Jo
- Department of Pediatrics, Pusan National University Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Busan, Korea
| | - Juhyun Kong
- Department of Pediatrics, Pusan National University Children's Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Yangsan, Korea
| | - Yun-Jin Lee
- Department of Pediatrics, Pusan National University Children's Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Yangsan, Korea
| | - Sang Ook Nam
- Department of Pediatrics, Pusan National University Children's Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Yangsan, Korea
| | - Bo Lyun Lee
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Seung Hwan Oh
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, Korea
| | - Young Mi Kim
- Department of Pediatrics, Pusan National University Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Busan, Korea
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Wu C, Maegawa GHB, Zhang H. Integrating whole-genome sequencing and transcriptomic findings in the diagnosis and management of Coffin-Siris syndrome. Brain Dev 2023; 45:495-504. [PMID: 37302973 DOI: 10.1016/j.braindev.2023.05.006] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/15/2023] [Accepted: 05/28/2023] [Indexed: 06/13/2023]
Abstract
INTRODUCTION Although the whole-exome sequencing (WES) approach has been widely used in clinic, many rare diseases with syndromic and nonsyndromic neurological manifestations remain undiagnosed. Coffin-Siris syndrome (CSS) is a rare autosomal dominant genetic disease characterized by neurodevelopmental delay. A suspected diagnosis can be made based on the typical CSS clinical features; however, molecular genetic testing is necessary for a confirmed diagnosis. OBJECTIVES Three CSS-like patients with negative results in the WES and chromosomal microarray analysis (CMA) were recruited in this study. METHODS We used whole-genome sequencing (WGS) technology to sequence the peripheral blood of the three families. To further explore the possible pathogenesis of CSS, we performed RNA-sequencing (RNA-seq). RESULTS WGS identified the three CSS patients were carrying de novo copy number variants of the ARID1B gene, which have not been reported before. RNA-seq identified 184 differentially expressed genes (DEGs), with 116 up-regulated and 68 down-regulated. Functional annotation of DEGs showed that two biological processes (immune response, chemokine activity) and two signaling pathways (cytokine-cytokine receptor interaction, chemokine activity) were highlighted. We speculated that ARID1B deficiency might trigger abnormal immune responses, which may be involved in the pathophysiologic mechanisms of CSS. CONCLUSION Our research provided further support for WGS application in CSS diagnosis and made an investigational approach for the underlying mechanisms of CSS.
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Affiliation(s)
- Chenchen Wu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Gustavo H B Maegawa
- Department of Pediatrics Columbia, University Irving Medical Center, New York-Presbyterian Morgan Stanley Children's Hospital, 622 West 168th Street, PH 17W/PH 11W, New York, NY 10032, United States
| | - Huiwen Zhang
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China.
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5
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Forwood C, Ashton K, Zhu Y, Zhang F, Dias K, Standen K, Evans C, Carey L, Cardamone M, Shalhoub C, Katf H, Riveros C, Hsieh T, Krawitz P, Robinson PN, Dudding‐Byth T, Sadikovic B, Pinner J, Buckley MF, Roscioli T. Integration of EpiSign, facial phenotyping, and likelihood ratio interpretation of clinical abnormalities in the re-classification of an ARID1B missense variant. Am J Med Genet C Semin Med Genet 2023; 193:e32056. [PMID: 37654076 PMCID: PMC10952833 DOI: 10.1002/ajmg.c.32056] [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] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 09/02/2023]
Abstract
Heterozygous ARID1B variants result in Coffin-Siris syndrome. Features may include hypoplastic nails, slow growth, characteristic facial features, hypotonia, hypertrichosis, and sparse scalp hair. Most reported cases are due to ARID1B loss of function variants. We report a boy with developmental delay, feeding difficulties, aspiration, recurrent respiratory infections, slow growth, and hypotonia without a clinical diagnosis, where a previously unreported ARID1B missense variant was classified as a variant of uncertain significance. The pathogenicity of this variant was refined through combined methodologies including genome-wide methylation signature analysis (EpiSign), Machine Learning (ML) facial phenotyping, and LIRICAL. Trio exome sequencing and EpiSign were performed. ML facial phenotyping compared facial images using FaceMatch and GestaltMatcher to syndrome-specific libraries to prioritize the trio exome bioinformatic pipeline gene list output. Phenotype-driven variant prioritization was performed with LIRICAL. A de novo heterozygous missense variant, ARID1B p.(Tyr1268His), was reported as a variant of uncertain significance. The ACMG classification was refined to likely pathogenic by a supportive methylation signature, ML facial phenotyping, and prioritization through LIRICAL. The ARID1B genotype-phenotype has been expanded through an extended analysis of missense variation through genome-wide methylation signatures, ML facial phenotyping, and likelihood-ratio gene prioritization.
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Affiliation(s)
- Caitlin Forwood
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
- Centre for Clinical GeneticsSydney Children's HospitalRandwickAustralia
- Neuroscience Research Australia (NeuRA)University of New South WalesSydneyAustralia
| | - Katie Ashton
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
| | - Ying Zhu
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
| | - Futao Zhang
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
| | - Kerith‐Rae Dias
- Neuroscience Research Australia (NeuRA)University of New South WalesSydneyAustralia
| | - Krystle Standen
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
| | - Carey‐Anne Evans
- Neuroscience Research Australia (NeuRA)University of New South WalesSydneyAustralia
| | - Louise Carey
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
| | - Michael Cardamone
- Sydney Children's HospitalRandwickAustralia
- School of Women's and Children's HealthUNSWSydneyAustralia
| | - Carolyn Shalhoub
- Centre for Clinical GeneticsSydney Children's HospitalRandwickAustralia
| | - Hala Katf
- Sydney Children's HospitalRandwickAustralia
| | - Carlos Riveros
- Bioinformatics, Hunter Medical Research InstituteNewcastleAustralia
| | - Tzung‐Chien Hsieh
- Institute for Genomic Statistics and BioinformaticsUniversity Hospital BonnBonnGermany
| | - Peter Krawitz
- Institute for Genomic Statistics and BioinformaticsUniversity Hospital BonnBonnGermany
| | - Peter N Robinson
- JAX Center for Precision GeneticsThe JAX Cancer CenterFarmingtonConnecticutUSA
| | | | - Bekim Sadikovic
- London Health Sciences Centre, Verspeeten Clinical Genome CentreWestern UniversityLondonCanada
| | - Jason Pinner
- Centre for Clinical GeneticsSydney Children's HospitalRandwickAustralia
- School of Women's and Children's HealthUNSWSydneyAustralia
| | - Michael F. Buckley
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
| | - Tony Roscioli
- NSW Health Pathology Randwick GenomicsPrince of Wales HospitalSydneyAustralia
- Neuroscience Research Australia (NeuRA)University of New South WalesSydneyAustralia
- School of Clinical MedicineUNSWSydneyAustralia
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6
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Rojananuangnit K, Rojnueangnit K. Microspherophakic Angle Closure Glaucoma in a Patient with Coffin-Siris Syndrome: Case Report. Appl Clin Genet 2023; 16:165-170. [PMID: 37663124 PMCID: PMC10474847 DOI: 10.2147/tacg.s422312] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023] Open
Abstract
Background Bilateral secondary angle closure glaucoma is a presenting symptom of microspherophakia and ectopia lentis. Characterizing the associated syndrome and confirmation by genetic testing can identify associated systemic abnormalities and provide appropriate genetic counseling. Case Presentation A 42-year-old woman with severe intellectual disability presented with light perception visual acuity and glaucoma, with intraocular pressure (IOP) in her right and left eyes of 69 and 70 mmHg, respectively. She underwent two sessions of 270-degree laser diode transscleral cytophotocoagulation treatment at a 6-month interval and was prescribed topical anti-glaucoma medication. Her family noticed a progressive decrease in her vision while on treatment for 2 years. She was diagnosed with apparent Weill-Marchesani syndrome, accompanied by angle closure glaucoma and microspherophakia. Cataract surgery and intraocular lens implantation were successful in both eyes and post-operative IOP was controlled with anti-glaucoma medication but her vision did not improve from severe glaucomatous optic neuropathy. Her underlying syndrome was investigated genetically by whole exome sequencing. Results Sequencing showed a pathogenic variant in ARID1B, c.3955dupC (p.Gln1319Profs*14), diagnostic of Coffin-Siris syndrome. This is the first report of Coffin-Siris syndrome associated with microspherophakia and angle closure glaucoma. Conclusion Bilateral angle closure glaucoma from ectopia lentis in patients with genetic syndromes could be an indicator of microspherophakia in adulthood. Ophthalmological surveillance is important in patients with Coffin-Siris syndrome.
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Affiliation(s)
- Kulawan Rojananuangnit
- Glaucoma Unit, Department of Ophthalmology, Mettapracharak (Wat Rai Khing) Hospital, Nakhon Pathom, Thailand
| | - Kitiwan Rojnueangnit
- Division of Genetics, Department of Pediatrics, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
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7
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MacPherson RA, Shankar V, Anholt RRH, Mackay TFC. Genetic and Genomic Analyses of Drosophila melanogaster Models of Chromatin Modification Disorders. bioRxiv 2023:2023.03.30.534923. [PMID: 37034595 PMCID: PMC10081333 DOI: 10.1101/2023.03.30.534923] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Switch/Sucrose Non-Fermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF (Brahma-Related Gene-1 Associated Factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference in Drosophila melanogaster to reduce expression of six genes (brm, osa, Snr1, SMC1, SMC3, vtd) orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration) and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR < 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, including Bap60, which is orthologous to SMARCD1, a SSRIDD-associated BAF component, k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genes brm, osa, and/or Snr1 recapitulated changes in behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in discovery of drugs that ameliorate deleterious phenotypic effects.
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Affiliation(s)
- Rebecca A. MacPherson
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Vijay Shankar
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Robert R. H. Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Trudy F. C. Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
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Rimoldi M, Rinaldi B, Villa R, Cerasani J, Beltrami B, Iascone M, Silipigni R, Boito S, Gangi S, Colombo L, Porro M, Cesaretti C, Bedeschi MF. Congenital diaphragmatic hernia in Coffin Siris syndrome: Further evidence from two cases. Am J Med Genet A 2023; 191:605-611. [PMID: 36416235 DOI: 10.1002/ajmg.a.63054] [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] [Received: 05/03/2022] [Revised: 08/08/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022]
Abstract
Coffin-Siris Syndrome (CSS) is a rare multi-system dominant condition with a variable clinical presentation mainly characterized by hypoplasia/aplasia of the nail and/or distal phalanx of the fifth digit, coarse facies, hirsutism/hypertrichosis, developmental delay and intellectual disability of variable degree and growth impairment. Congenital anomalies may include cardiac, genitourinary and central nervous system malformations whereas congenital diaphragmatic hernia (CDH) is rarely reported. The genes usually involved in CSS pathogenesis are ARID1B (most frequently), SMARCA4, SMARCB1, ARID1A, SMARCE1, DPF2, and PHF6. Here, we present two cases of CSS presenting with CDH, for whom Whole Exome Sequencing (WES) identified two distinct de novo heterozygous causative variants, one in ARID1B (case 1) and one in SMARCA4 (case 2). Due to the rarity of CDH in CSS, in both cases the occurrence of CDH did not represent a predictive sign of CSS but, on the other hand, prompted genetic testing before (case 1) or independently (case 2) from the clinical hypothesis of CSS. We provide further evidence of the association between CSS and CDH, reviewed previous cases from literature and discuss possible functional links to related conditions.
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Affiliation(s)
- Martina Rimoldi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Berardo Rinaldi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Roberta Villa
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Jacopo Cerasani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit (NICU), Department of Clinical Science and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Benedetta Beltrami
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Maria Iascone
- Ospedale Papa Giovanni XXIII, Laboratory of Medical Genetics, Bergamo, Italy
| | - Rosamaria Silipigni
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Laboratory of Medical Genetics, Milan, Italy
| | - Simona Boito
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Fetal Medicine and Surgery Service, Milan, Italy
| | - Silvana Gangi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit (NICU), Department of Clinical Science and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Lorenzo Colombo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit (NICU), Department of Clinical Science and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Matteo Porro
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Pediatric Physical Medicine and Rehabilitation Unit, Milan, Italy
| | - Claudia Cesaretti
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
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9
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Wang Q, Wu J, Yang J, Huang S, Yuan Y, Dai P. Two SOX11 variants cause Coffin-Siris syndrome with a new feature of sensorineural hearing loss. Am J Med Genet A 2023; 191:183-189. [PMID: 36369738 PMCID: PMC10100107 DOI: 10.1002/ajmg.a.63011] [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] [Received: 08/10/2021] [Revised: 08/24/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022]
Abstract
Coffin-Siris syndrome (CSS, OMIM#135900) is a rare congenital disorder associated with neurodevelopmental and dysmorphic features. The primary cause of CSS is pathogenic variants in any of 9 BAF chromatin-remodeling complex encoding genes or the genes SOX11 and PHF6. Herein, we performed whole-exome sequencing (WES) and a series of analyses of growth-related, auditory, and radiological findings in two probands with syndromic sensorineural hearing loss and inner ear malformations who exhibited distinctive facial features, intellectual disability, growth retardation, and fifth finger malformation. Two de novo variants in the SOX11 gene (c.148A>C:p.Lys50Asn; c.811_814del:p.Asn271Serfs*10) were detected in these probands and were identified as pathogenic variants as per ACMG guidelines. These probands were diagnosed as having CSS based upon clinical and genetic findings. This is the first report of CSS caused by variants in SOX11 gene in Chinese individuals. Deleterious SOX11 variants can result in sensorineural hearing loss with inner ear malformation, potentially extending the array of phenotypes associated with these pathogenic variants. We suggest that both genetic and clinical findings be considered when diagnosing syndromic hearing loss.
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Affiliation(s)
- Qiuquan Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of hearing loss Prevention and Treatment, Beijing, China
| | - Jie Wu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of hearing loss Prevention and Treatment, Beijing, China
| | - Jinyuan Yang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of hearing loss Prevention and Treatment, Beijing, China
| | - Shasha Huang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of hearing loss Prevention and Treatment, Beijing, China
| | - Yongyi Yuan
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of hearing loss Prevention and Treatment, Beijing, China
| | - Pu Dai
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of hearing loss Prevention and Treatment, Beijing, China
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Mouskou S, Leka-Emiri S, Korona A, Mastroyanni S, Manolakos E, Papoulidis I, Sekouris N, Katerelos A, Katsarou-Pectasides E, Voudris K. Growth Hormone Deficiency due to p.(Gln467Argfs*64) Mutation in the ARID1B Gene in a Girl with Coffin-Siris Syndrome. Mol Syndromol 2022; 13:425-432. [PMID: 36588753 PMCID: PMC9801320 DOI: 10.1159/000522532] [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] [Received: 02/23/2021] [Accepted: 02/09/2022] [Indexed: 01/04/2023] Open
Abstract
Introduction Coffin-Siris syndrome (CSS) (MIM #135900) is an extremely rare genetic multisystemic disorder characterized by aplasia or hypoplasia of the upper phalanx of the fifth finger, moderate to severe cognitive and/or developmental delay, and characteristic facial features (thick lashes, hypertrichosis of the trunk, sparse hair). Congenital anomalies of the brain, kidney, and heart have been described but are less consistent across patients. Case presentation We report a case of a 12-year-5-month-old girl with the clinical features of CSS, severe scoliosis, and epilepsy. Growth hormone deficiency was diagnosed at the age of 9 years. Recombinant human growth hormone (rhGH) treatment was started that resulted in a significant improvement of the growth velocity up to 5.4 cm/year (>90-97th centile). Next-generation sequencing identified a mutation in the ARID1B gene. Discusion Despite its phenotypic heterogeneity, key features of CSS have become clearer and along with molecular diagnosis, a further global approach to improve the care of these individuals is enabled. Appropriate therapies for this population are needed to optimize growth and intellectual potentials.
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Affiliation(s)
- Stella Mouskou
- Department of Neurology, ‘P & A Kyriakou’ Children's Hospital, Athens, Greece,*Stella Mouskou,
| | - Sofia Leka-Emiri
- Department of Endocrinology-Growth and Development, ‘P & A Kyriakou’ Children's Hospital, Athens, Greece
| | - Anastasia Korona
- Department of Neurology, ‘P & A Kyriakou’ Children's Hospital, Athens, Greece
| | - Sotiria Mastroyanni
- Department of Neurology, ‘P & A Kyriakou’ Children's Hospital, Athens, Greece
| | | | | | - Nick Sekouris
- Department of Orthopedics, “KAT” General Hospital, Athens, Greece
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Caengprasath N, Buasong A, Ittiwut C, Khongphatthanayothin A, Porntaveetus T, Shotelersuk V. Severe coarctation of the aorta, developmental delay, and multiple dysmorphic features in a child with SMAD6 and SMARCA4 variants. Eur J Med Genet 2022; 65:104601. [PMID: 36049609 DOI: 10.1016/j.ejmg.2022.104601] [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: 04/12/2022] [Revised: 06/18/2022] [Accepted: 08/25/2022] [Indexed: 01/28/2023]
Abstract
Pathogenic variants in SMARCA4 cause Coffin-Siris syndrome (CSS) while those in SMAD6 lead to aortic valve disease and other dysmorphisms. We identified a 6-year-old Thai boy with features of CSS alongside unusual manifestations including, very severe coarctation of the aorta (CoA) requiring coarctectomy in the neonatal period and bilateral radioulnar synostoses. Trio exome sequencing revealed that the patient harbored two de novo variants, a missense c.2475G > T, p.(Trp825Cys) in SMARCA4 and a nonsense c.652C > T, p.(Gln218Ter) in SMAD6. Both of which have never been previously reported. The clinical presentations in our patient are a result of the combinational features of each genetic variant: the SMARCA4 p.(Trp825Cys) variant leads to facial features of Coffin Siris syndrome and Dandy-Walker malformation, while the SMAD6 p.(Gln218Ter) variant underlies radioulnar synostosis. Interestingly, the severity of CoA in the proband is beyond the phenotypic spectra of each genetic variant and may be a result of the synergistic effects of both variants. Here, we report a child with variants in SMARCA4 or SMAD6 with combined features of each plus a severe CoA, possibly due to an additive effect of each variant.
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Affiliation(s)
- Natarin Caengprasath
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Aayalida Buasong
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Chupong Ittiwut
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Apichai Khongphatthanayothin
- Center of Excellence in Arrhythmia Research, Department of Medicine, Chulalongkorn University and Bangkok General Hospital, Bangkok, Thailand
| | - Thantrira Porntaveetus
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
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12
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Bilha SC, Teodoriu L, Velicescu C, Caba L. Pituitary hypoplasia and growth hormone deficiency in a patient with Coffin-Siris syndrome and severe short stature: case report and literature review. Arch Clin Cases 2022; 9:121-125. [PMID: 36176497 PMCID: PMC9512126 DOI: 10.22551/2022.36.0903.10216] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Coffin-Siris syndrome (CSS) is a rare genetic disorder caused by the haploinsufficiency of one of the various genes that are part of the Brahma/BRG1-associated factor (BAF) complex. The BAF complex is one of the chromatin remodeling complexes, involved in embryonic and neural development, and various gene mutations are associated with cognitive impairment. CSS has a highly variable genotype and phenotype expression, thus lacking standardized criteria for diagnosis. It is generally accepted to associate 5th digit/nail hypoplasia, intellectual disability (ID)/developmental delay and specific coarse facial features. CSS patients usually display miscellaneous cardiac, genitourinary and central nervous system (CNS) anomalies. Many patients also associate intrauterine growth restriction, failure to thrive and short stature, with several cases demonstrating growth hormone deficiency (GHD). We report the case of a 4-year-old girl with severe short stature (-3.2 standard deviations) due to pituitary hypoplasia and GHD that associated hypoplastic distal phalanx of the 5th digit in the hands and feet, severe ID, coarse facial features (bushy eyebrows, bulbous nose, flat nasal bridge, dental anomalies, thick lips, dental anomalies, bilateral epicanthal fold) and CNS anomalies (agenesis of the corpus callosum and bilateral hippocampal atrophy), thus meeting clinical criteria for the diagnosis of CSS. Karyotype was 46,XX. The patient was started on GH replacement therapy, with favorable outcomes. Current practical knowledge regarding CSS diagnosis and management from the endocrinological point of view is also reviewed.
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Affiliation(s)
- Stefana Catalina Bilha
- Endocrinology Department, Grigore T. Popa University of Medicine and Pharmacy Iasi, Romania
| | - Laura Teodoriu
- Endocrinology Department, Grigore T. Popa University of Medicine and Pharmacy Iasi, Romania
| | - Cristian Velicescu
- Surgery Department, Grigore T. Popa University of Medicine and Pharmacy Iasi, Romania.,
Corresponding author: Cristian Velicescu, Surgery Department, Grigore T. Popa University of Medicine and Pharmacy, 16 Universitatii str. Iasi 700115, Romania.
| | - Lavinia Caba
- Department of Medical Genetics, Grigore T. Popa University of Medicine and Pharmacy Iasi, Romania
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Gofin Y, Zhao X, Gerard A, Scaglia F, Wangler MF, Vergano SAS, Scott DA. Evidence for an association between Coffin-Siris syndrome and congenital diaphragmatic hernia. Am J Med Genet A 2022; 188:2718-2723. [PMID: 35796094 PMCID: PMC9378577 DOI: 10.1002/ajmg.a.62889] [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: 04/29/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 01/25/2023]
Abstract
Coffin-Siris syndrome (CSS) is an autosomal dominant neurodevelopmental syndrome that can present with a variety of structural birth defects. Pathogenic variants in 12 genes have been shown to cause CSS. Most of these genes encode proteins that are a part of the mammalian switch/sucrose non-fermentable (mSWI/SNF; BAF) complex. An association between genes that cause CSS and congenital diaphragmatic hernia (CDH) has been suggested based on case reports and the analysis of CSS and CDH cohorts. Here, we describe an unpublished individual with CSS and CDH, and we report additional clinical information on four published cases. Data from these individuals, and a review of the literature, provide evidence that deleterious variants in ARID1B, ARID1A, SMARCB1, SMARCA4, SMARCE1, ARID2, DPF2, and SMARCC2, which are associated with CSS types 1-8, respectively, are associated with the development of CDH. This suggests that additional genetic testing to identify a separate cause of CDH in an individual with CSS may be unwarranted, and that comprehensive genetic testing for individuals with non-isolated CDH should include an evaluation of CSS-related genes. These data also suggest that the mSWI/SNF (BAF) complex may play an important role in diaphragm development.
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MESH Headings
- Abnormalities, Multiple/diagnosis
- Abnormalities, Multiple/genetics
- Chromosomal Proteins, Non-Histone
- DNA Helicases/genetics
- DNA-Binding Proteins/genetics
- Face/abnormalities
- Hand Deformities, Congenital/complications
- Hand Deformities, Congenital/diagnosis
- Hand Deformities, Congenital/genetics
- Hernias, Diaphragmatic, Congenital/genetics
- Hernias, Diaphragmatic, Congenital/pathology
- Humans
- Intellectual Disability/pathology
- Micrognathism/genetics
- Micrognathism/pathology
- Neck/abnormalities
- Nuclear Proteins/genetics
- Transcription Factors/genetics
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Affiliation(s)
- Yoel Gofin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics, Houston, TX 77021, USA
| | - Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030
- Joint BCM-CUHK Center of Medical Genetics, Prince of Wales Hospital, ShaTin, Hong Kong SAR
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030
| | - Samantha A. Schrier Vergano
- Division of Medical Genetics and Metabolism, Children’s Hospital of The King’s Daughters, Norfolk, VA 23507, USA
- Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA 23501, USA
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
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Tan Y, Chen J, Li Y, Liu Y, Wang Y, Xia S, Chen L, Wei W, Chen Z. Three Novel ARID1B Variations in Coffin-Siris Syndrome Patients. Neurol India 2022; 70:2174-2179. [PMID: 36352633 DOI: 10.4103/0028-3886.359283] [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] [Indexed: 06/16/2023]
Abstract
Coffin-Siris syndrome (CSS) (OMIM #135900) involves multiple congenital malformations, including hypotonia, short stature, sparse scalp hair, a coarse face, prominent eyebrows, a wide mouth, delayed bone age, and hypoplastic or absent fifth fingers/toes or nails, together with developmental delay. The cause of CSS is suggested to be related to alterations in the BRG- or HRBM-associated factor (BAF) pathway in humans. In this gene family, pathogenic variations in the AT-rich interactive domain-containing protein 1B (ARID1B) gene are revealed to be a significant element causing neurodevelopmental disability in patients with CSS. Herein, we describe the clinical features and gene variations in four Chinese patients with CSS. All the patients shared common features of short fifth fingers/toes or hypoplastic nails, coarse facial features, thick eyebrows, long cilia, a flat nasal bridge, a broad nose, a wide mouth, a high palate, and hypotonia. Besides, they had an intellectual disability, language, and motor developmental delay. Candidate genes were screened for variations using polymerase chain reaction (PCR) and sequencing. The variations were sequenced by next-generation sequencing and confirmed by first-generation sequencing. Exome sequencing suggested four de novo variations in the ARID1B gene in four unrelated patients. These included two frameshift variations (c.3581delC, c.6661_6662insG) and two nonsense variations (c.1936C>T, c.2248C>T). Of the four variations, three variations were novel. The results in our present study broaden the understanding of the disease and further interpret the molecular genetic mechanism of these rare variations in CSS.
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Affiliation(s)
- Yuxia Tan
- Department of Pediatrics, The Affiliated Hospital of Qingdao University, Haier Road; Department of Pediatrics, Zibo City Maternal and Child Health Hospital, Zibo City, Shandong Province, Qingdao, Shandong, 266034, China
| | - Jun Chen
- Department of Neurology and Rehabilitation, Qingdao Women and Children's Hospital, Qingdao University. No. 6 Tongfu Road, Qingdao, Shandong, 266034, China
| | - Yutang Li
- Department of Neurology and Rehabilitation, Qingdao Women and Children's Hospital, Qingdao University. No. 6 Tongfu Road, Qingdao, Shandong, 266034, China
| | - Yedan Liu
- Department of Pediatrics, The Affiliated Hospital of Qingdao University, Haier Road, Qingdao, Shandong, 266034, China
| | - Yu Wang
- Department of Pediatrics, Zibo City Maternal and Child Health Hospital, Zibo City, Shandong Province, China
| | - Shungang Xia
- Department of Pediatrics, Zibo City Maternal and Child Health Hospital, Zibo City, Shandong Province, China
| | - Liping Chen
- Department of Pediatrics, Zibo City Maternal and Child Health Hospital, Zibo City, Shandong Province, China
| | - Wei Wei
- Beijing Kangso Medical Inspection Co., Ltd, Building 10, Zone C, Yiyuan Science and Technology Park Haidian District. No. 65 Xingshikou Road, Beijing, 100195, China
| | - Zongbo Chen
- Department of Pediatrics, The Affiliated Hospital of Qingdao University, Haier Road, Qingdao, Shandong, 266034, China
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15
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Tao DY, Niu HH, Zhang JJ, Zhang HQ, Zeng MH, Cheng SQ. Short stature and melanocytic nevi in a girl with ARID1B-related Coffin-Siris syndrome: a case report. BMC Pediatr 2022; 22:486. [PMID: 35964110 PMCID: PMC9375425 DOI: 10.1186/s12887-022-03535-4] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/02/2022] [Indexed: 11/12/2022] Open
Abstract
Background Coffin-Siris syndrome (CSS) is a rare autosomal dominant disorder characterized by intellectual disability, developmental delay, and characteristic facial features. Few patients with cutaneous phenotype in this rare syndrome have been reported. Case presentation Herein, we describe a 12-year-old Chinese girl diagnosed with CSS, who was referred to our hospital because of intellectual disability and short stature. Prominent characteristics of the cutaneous system were observed: (1) A congenital giant nevus from the left frontal and temporal regions to the entire left scalp; and (2) multiple melanocytic nevi on the face and trunk. Whole exome sequencing revealed a novel heterozygous variant in the ARID1B gene. Recombinant human growth hormone (rhGH) was given for short stature, and resulted in significantly improved height. No enlargement or malignant transformation of nevi occurred within 4 years of follow-up. Conclusion The symptoms in cutaneous system is noteworthy,which may be a neglected phenotype in CSS.The therapeutic response of growth hormone is effective in this patient and no tumor related signs were found. Supplementary Information The online version contains supplementary material available at 10.1186/s12887-022-03535-4.
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Affiliation(s)
- Dong-Ying Tao
- Department of Pediatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, 710032, Shaanxi Province, China
| | - Huan-Hong Niu
- Department of Pediatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, 710032, Shaanxi Province, China
| | - Jing-Jing Zhang
- Department of Pediatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, 710032, Shaanxi Province, China
| | - Hui-Qin Zhang
- Department of Pediatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, 710032, Shaanxi Province, China
| | - Ming-Hua Zeng
- Medical Experiment and Training Center, Hanzhong Vocational and Technical College, Hanzhong, 723002, Shaanxi Province, China
| | - Sheng-Quan Cheng
- Department of Pediatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xincheng District, Xi'an, 710032, Shaanxi Province, China.
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Liu M, Wan L, Wang C, Yuan H, Peng Y, Wan N, Tang Z, Yuan X, Chen D, Long Z, Shi Y, Qiu R, Tang B, Jiang H, Chen Z. Coffin-Siris syndrome in two chinese patients with novel pathogenic variants of ARID1A and SMARCA4. Genes Genomics 2022; 44:1061-1070. [PMID: 35353340 DOI: 10.1007/s13258-022-01231-2] [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: 10/24/2021] [Accepted: 02/05/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Coffin-Siris syndrome (CSS) is a rare congenital syndrome characterized by developmental delay, intellectual disability, microcephaly, coarse face and hypoplastic nail of the fifth digits. Heterozygous variants of different BAF complex-related genes were reported to cause CSS, including ARID1A and SMARCA4. So far, no CSS patients with ARID1A and SMARCA4 variants have been reported in China. OBJECTIVE The aim of the current study was to identify the causes of two Chinese patients with congenital growth deficiency and intellectual disability. METHODS Genomic DNA was extracted from the peripheral venous blood of patients and their family members. Genetic analysis included whole-exome and Sanger sequencing. Pathogenicity assessments of variants were performed according to the guideline of the American College of Medical Genetics and Genomics. The phenotypic characteristics of all CSS subtypes were summarized through literature review. RESULTS We identified two Chinese CSS patients carrying novel variants of ARID1A and SMARCA4 respectively. The cases presented most core symptoms of CSS except for the digits involvement. Additionally, we performed a review of the phenotypic characteristics in CSS, highlighting phenotypic varieties and related potential causes. CONCLUSIONS We reported the first Chinese CSS2 and CSS4 patients with novel variants of ARID1A and SMARCA4. Our study expanded the genetic and phenotypic spectrum of CSS, providing a comprehensive overview of genotype-phenotype correlations of CSS.
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Affiliation(s)
- Mingjie Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Linlin Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chunrong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongyu Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yun Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Na Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhichao Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xinrong Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Daji Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhe Long
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuting Shi
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Rong Qiu
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China
- Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China
- Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
- National International Collaborative Research Center for Medical Metabolomics, Central South University, Changsha, Hunan, China
| | - Zhao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China.
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.
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Slavotinek A, Lefebvre M, Brehin AC, Thauvin C, Patrier S, Sparks TN, Norton M, Yu J, Huang E. Prenatal presentation of multiple anomalies associated with haploinsufficiency for ARID1A. Eur J Med Genet 2022; 65:104407. [PMID: 34942405 PMCID: PMC9162882 DOI: 10.1016/j.ejmg.2021.104407] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 07/24/2021] [Revised: 11/04/2021] [Accepted: 12/14/2021] [Indexed: 02/03/2023]
Abstract
The ARID1A gene is an infrequent cause of Coffin-Siris syndrome (CSS) and has been associated with severe to profound developmental delays and hypotonia in addition to characteristic craniofacial and digital findings. We present three fetuses and a male neonate with ventriculomegaly/hydrocephalus, absence of the corpus callosum (ACC), cerebellar hypoplasia, retinal dysplasia, lung lobulation defects, renal dysplasia, imperforate or anteriorly placed anus, thymus hypoplasia and a single umbilical artery. Facial anomalies included downslanting palpebral fissures, wide-spaced eyes, low-set and posteriorly rotated ears, a small jaw, widely spaced nipples and hypoplastic nails. All fetuses had heterozygous variants predicting premature protein truncation in ARID1A (c.4886dup:p.Val1630Cysfs*18; c.4860dup:p.Pro1621Thrfs*27; and c.175G>T:p.Glu59*) and the baby's microarray demonstrated mosaicism for a deletion at chromosome 1p36.11 (arr[GRCh37] 1p36.11(26,797,508_27,052,080)×1∼2), that contained the first exon of ARID1A. Although malformations, in particular ACC, have been described with CSS caused by pathogenic variants in ARID1A, prenatal presentations associated with this gene are rare. Retinal dysplasia, lung lobulation defects and absent thymus were novel findings in association with ARID1A variants. Studies in cancer have demonstrated that pathogenic ARID1A variants hamper nuclear import of the protein and/or affect interaction with the subunits of SWI/SNF complex, resulting in dysregulation of the PI3K/AKT pathway and perturbed PTEN and PIKC3A signaling. As haploinsufficiency for PTEN and PIKC3A can be associated with ventriculomegaly/hydrocephalus, aberrant expression of these genes is a putative mechanism for the brain malformations demonstrated in patients with ARID1A variants.
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Affiliation(s)
- Anne Slavotinek
- Dept. Pediatrics, University of California San Francisco, San Francisco, CA, 94143, USA, Corresponding author. (A. Slavotinek)
| | - Mathilde Lefebvre
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231, Génétique des Anomalies du Développement, Dijon, France
| | | | - Christel Thauvin
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231, Génétique des Anomalies du Développement, Dijon, France
| | - Sophie Patrier
- Department of Pathology, CHU Rouen, F-76000, Rouen, France
| | - Teresa N. Sparks
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Mary Norton
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Jingwei Yu
- Dept. Cytogenetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Eric Huang
- Dept. Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
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18
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Morota J, Ishige T, Suzuki M, Igarashi Y, Takizawa T. Non-occlusive mesenteric ischemia in a toddler with 6q25 microdeletion syndrome. Pediatr Int 2022; 64:e14751. [PMID: 34813130 DOI: 10.1111/ped.14751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/10/2021] [Accepted: 04/15/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Junichiro Morota
- Department of Pediatrics, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Takashi Ishige
- Department of Pediatrics, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Makoto Suzuki
- Division of Pediatric Surgery, Department of General Surgical Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Yoshiko Igarashi
- Department of Pediatrics, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Takumi Takizawa
- Department of Pediatrics, Gunma University Graduate School of Medicine, Maebashi, Japan
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19
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Lohiya N, Chalipat S, Lohiya N, Malwade S. Neurocognitive, behavioral and socio-adaptive functioning assessment in a case of Coffin-Siris syndrome: A holistic approach/perspective beyond the identification of the disorder. J Pediatr Rehabil Med 2022; 15:529-532. [PMID: 35754295 DOI: 10.3233/prm-210050] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
PURPOSE Coffin-Siris syndrome (CSS) is a rare genetic disorder characterized by the presence of particular facies, congenital malformations, intellectual developmental disorder, behavioral issues, and speech and language impairment. Thorough neuropsychological assessments in the case of CSS have been reported infrequently, and its subdomains are poorly defined. A detailed description of the clinical, neurocognitive, behavioral, socio-adaptive sequelae of the patient with CSS is provided. RESULTS The clinical diagnosis in the patient was confirmed by genetic analysis, which identified the presence of mutation of ARID1B gene; the parents' Sanger sequencing reported normal. The neuropsychological assessments revealed borderline intellectual functioning (IQ-75, verbal > performance) with a mild socio-adaptive deficit score of 64 as suggested by the adaptive scale. The behavioral profile reported that the child had significant difficulties in the attention subdomain with concern in social and thought subdomains. The child met the profile for mild severity of Autism Spectrum Disorder and did not meet the criteria for Attention Deficit Hyperactivity Disorder. In addition, the child had scholastic difficulties in reading and mathematical skills. CONCLUSION Neurocognitive, behavioral, socio-adaptive functioning and comorbidity assessment in order to provide holistic management of such children after thorough evaluation is essential for their overall functioning.
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Affiliation(s)
- Nirali Lohiya
- Dr. D Y Patil Medical College and Hospital, Pune, Maharashtra, India.,Division of Developmental & Behavioral Pediatrics, Silver Lining Pediatric Super speciality center, Nagpur, Maharashtra, India
| | - Shiji Chalipat
- Dr. D Y Patil Medical College and Hospital, Pune, Maharashtra, India
| | - Nikhil Lohiya
- Dr. D Y Patil Medical College and Hospital, Pune, Maharashtra, India.,Division of Growth & Endocrinology, Silver Lining Pediatric Super speciality center, Nagpur, Maharashtra, India
| | - Sudhir Malwade
- Department of Pediatrics, Dr. D Y Patil Medical College and Hospital, Pune, Maharashtra, India
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20
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Abstract
BACKGROUND Coffin-Siris syndrome (CSS) is a multiple congenital anomaly syndrome characterized by coarse facial features, sparse scalp hair, hypertrichosis, and hypo/aplastic digital nails and phalanges. Mutations in the BAF (SWI/SNF)-complex subunits (SMARCE1, SMARCB1, SMARCA4, SMARCA2, ARID1B, and ARID1A) have been shown to cause CSS. People diagnosed with BAF pathway related diseases are increasing, and ARID2 (NM_152641.4) is the least common of these genes. Mutations in the ARID2 gene is the cause for Coffin-Siris syndrome 6 (CSS6). By now only 16 individuals with CSS have been reported to have pathogenic variants in ARID2. CASE PRESENTATION In this article, we introduced two individuals with clinical features consistent with CSS6 (Coffin-Siris syndrome 6). This article increases the number of reported cases, provides better phenotypic information for this rare syndrome, and allows everyone to better understand the disease. CONCLUSION Our observations indicate that ARID2 mutations could have variable phenotypes, even in patients from the same family.
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Affiliation(s)
- Xiaoyan Wang
- Department of Endocrinology, Children's Hospital of Soochow University, Suzhou, China
| | - Haiying Wu
- Department of Endocrinology, Children's Hospital of Soochow University, Suzhou, China
| | - Hui Sun
- Department of Endocrinology, Children's Hospital of Soochow University, Suzhou, China
| | - Lili Wang
- Department of Endocrinology, Children's Hospital of Soochow University, Suzhou, China
| | - Linqi Chen
- Department of Endocrinology, Children's Hospital of Soochow University, Suzhou, China
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21
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Li D, Downes H, Hou C, Hakonarson H, Zackai EH, Schrier Vergano SA, Bhoj EJ. Further supporting SMARCC2-related neurodevelopmental disorder through exome analysis and reanalysis in two patients. Am J Med Genet A 2021; 188:878-882. [PMID: 34881817 DOI: 10.1002/ajmg.a.62597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 08/13/2021] [Revised: 10/20/2021] [Accepted: 11/20/2021] [Indexed: 11/12/2022]
Abstract
BAFopathies are a heterogenous group of neurodevelopmental disorders caused by mutations in genes encoding subunits of the BAF complex, and they exhibit a broad clinical phenotypic spectrum. Pathogenic heterozygous variants in SMARCC2 have been implicated in Coffin-Siris syndrome 8 (MIM 618362) with variable neurodevelopmental presentations. We report here two relatively severely affected patients with two different SMARCC2 variants: one has de novo pathogenic variant, c.1824_1826del, p.(Leu609del), in a suspected hotspot region through reanalysis of previously negative clinical exome data, and the other has a likely pathogenic loss-of-function variant, c.1094_1097delAGAA, p.(Lys365Thrfs*12) through exome analysis in an adopted subject. Regardless of variant type, both patients have severe developmental delays, severe speech delay, short stature, hypotonia, seizures, and craniofacial dysmorphisms, blurring previously speculated genotype-phenotype correlation on missense and loss-of-function variants. This report extends our understanding of the genotypic and phenotypic spectrums of the SMARCC2-related neurodevelopmental disorder.
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Affiliation(s)
- Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Helen Downes
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Cuiping Hou
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elaine H Zackai
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, Virginia, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Elizabeth J Bhoj
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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22
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Qian Y, Zhou Y, Wu B, Chen H, Xu S, Wang Y, Zhang P, Li G, Xu Q, Zhou W, Xu X, Wang H. Novel Variants of the SMARCA4 Gene Associated with Autistic Features Rather Than Typical Coffin-Siris Syndrome in Eight Chinese Pediatric Patients. J Autism Dev Disord 2021; 52:5033-5041. [PMID: 34813034 DOI: 10.1007/s10803-021-05365-2] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2021] [Indexed: 11/29/2022]
Abstract
Autism spectrum disorders (ASDs) are a group of neurodevelopmental-related disorders with a high genetic risk. Recently, chromatin remodeling factors have been found to be related to ASDs. SMARCA4 is such a catalytic subunit of the chromatin-remodeling complex. In this report, we identified seven novel missense variants in the SMARCA4 gene from eight pediatric patients. All eight patients had moderate to severe intellectual disability, and seven showed autistic/likely autistic features. Compared with the patients reported in the literature, our patients were less likely to show craniofacial or finger/toe anomalies. Our findings further supported that SMARCA4 is associated with ASDs. We suggest that individuals with the abovementioned phenotypes should consider genetic testing.
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Affiliation(s)
- Yanyan Qian
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Yuanfeng Zhou
- Neurology Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Bingbing Wu
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Huiyao Chen
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Suzhen Xu
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Yao Wang
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Ping Zhang
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Gang Li
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Qiong Xu
- Department of Child Health Care, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Wenhao Zhou
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Xiu Xu
- Department of Child Health Care, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China.
| | - Huijun Wang
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China.
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23
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Vasko A, Drivas TG, Schrier Vergano SA. Genotype-Phenotype Correlations in 208 Individuals with Coffin-Siris Syndrome. Genes (Basel) 2021; 12. [PMID: 34205270 DOI: 10.3390/genes12060937] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 01/18/2023] Open
Abstract
Coffin-Siris syndrome (CSS, MIM 135900) is a multi-system intellectual disability syndrome characterized by classic dysmorphic features, developmental delays, and organ system anomalies. Genes in the BRG1(BRM)-associated factors (BAF, Brahma associated factor) complex have been shown to be causative, including ARID1A, ARID1B, ARID2, DPF2, SMARCA4, SMARCB1, SMARCC2, SMARCE1, SOX11, and SOX4. In order to describe more robust genotype-phenotype correlations, we collected data from 208 individuals from the CSS/BAF complex registry with pathogenic variants in seven of these genes. Data were organized into cohorts by affected gene, comparing genotype groups across a number of binary and quantitative phenotypes. We determined that, while numerous phenotypes are seen in individuals with variants in the BAF complex, hypotonia, hypertrichosis, sparse scalp hair, and hypoplasia of the distal phalanx are still some of the most common features. It has been previously proposed that individuals with ARID-related variants are thought to have more learning and developmental struggles, and individuals with SMARC-related variants, while they also have developmental delay, tend to have more severe organ-related complications. SOX-related variants also have developmental differences and organ-related complications but are most associated with neurodevelopmental differences. While these generalizations still overall hold true, we have found that all individuals with BAF-related conditions are at risk of many aspects of the phenotype, and management and surveillance should be broad.
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24
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Min Z, Qian C, Ying D. Novel ARID1B variant inherited from somatogonadal mosaic mother in siblings with Coffin-Siris syndrome 1. Exp Ther Med 2021; 21:614. [PMID: 33936271 PMCID: PMC8082577 DOI: 10.3892/etm.2021.10046] [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] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/21/2020] [Indexed: 12/20/2022] Open
Abstract
Coffin-Siris syndrome1 (CSS1; Online Mendelian Inheritance in Man no. 135900) is a multiple malformation syndrome characterized by intellectual and/or developmental delay, and hypoplastic or absent fifth fingernails and/or toenails. AT-rich interaction domain-containing protein 1B (ARID1B) is the most frequently mutated gene in CSS1 and the majority of reported cases have been sporadic. Using whole-exome sequencing, the present study identified two siblings with CSS1 with a novel heterozygous co-segregating pathogenic variant in the ARID1B gene (c.3468_3471del). Additionally, the current study confirmed a 4% somatic ARID1B mosaicism in the patient's mother. The results expanded the spectrum of known ARID1B pathogenic variants. To the best of our knowledge, the present study is the first to provide experimental evidence that an ARID1B pathogenic variant can be inherited from a clinically healthy somatogonadal mosaic mother.
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Affiliation(s)
- Zhong Min
- Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing 400014, P.R. China.,Pediatric Research Institute, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Engineering Research Center of Stem Cell Therapy, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing 400014, P.R. China.,National Clinical Research Center for Child Health and Disorders, Chongqing 400014, P.R. China.,Department of Pediatric, Qianjiang Central Hospital of Chongqing, Chongqing 409000, P.R. China
| | - Cheng Qian
- Pediatric Research Institute, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Engineering Research Center of Stem Cell Therapy, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing 400014, P.R. China.,National Clinical Research Center for Child Health and Disorders, Chongqing 400014, P.R. China.,Department of Primary Child Health Care, Children's Hospital of Chongqing Medical University, Chongqing 400014, P.R. China
| | - Dai Ying
- Pediatric Research Institute, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Engineering Research Center of Stem Cell Therapy, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing 400014, P.R. China.,National Clinical Research Center for Child Health and Disorders, Chongqing 400014, P.R. China.,Department of Primary Child Health Care, Children's Hospital of Chongqing Medical University, Chongqing 400014, P.R. China
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25
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Cheng SSW, Luk HM, Mok MTS, Leung SS, Lo IFM. Genotype and phenotype in 18 Chinese patients with Coffin-Siris syndrome. Am J Med Genet A 2021; 185:2250-2261. [PMID: 33768696 DOI: 10.1002/ajmg.a.62187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 01/04/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 01/28/2023]
Abstract
Coffin-Siris syndrome (CSS, MIM# 1359200) is a multisystem congenital disorder characterized by coarse facial features, hypoplasia of the fifth digits and nails, and intellectual disability. It is a genetically heterogeneous condition caused by pathogenic variants in genes encoding proteins of the BAF (BRG1-associated factors) chromatin modeling complex and its downstream transcriptional factor. To date over 220 CSS individuals with pathogenic variants found have been described in the literature. This case series reported 18 molecularly confirmed Chinese individuals (17 with ARIDIB (OMIM*614556) variants and one with SMARCB1 (OMIM*601607) variant) from 17 unrelated families in Hong Kong. The clinical features of these 18 Chinese CSS patients together with two previously reported Chinese patients with ARID1B variants were reviewed. Among the 19 Chinese patients with ARID1B variants, our data suggested a lower prevalence of feeding problem, autistic features, agenesis of corpus callosum (ACC) or partial/hypoplasia of corpus callosum, and sparse hair when compared with previous reports. There was appearing higher prevalence of digital hypoplasia. Digital hypoplasia was observed to become less noticeable with time in some patients. This report highlighted the age-dependent phenotypic presentation of CSS and ethnicity-related effect on ARID1B-CSS phenotype. Moreover, this series included the first family with molecularly confirmed maternal somatic mosaicism of ARID1B variant leading to familial CSS recurrence.
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Affiliation(s)
- Shirley S W Cheng
- Clinical Genetic Service, Department of Health, HKSAR, Hong Kong, China
| | - Ho-Ming Luk
- Clinical Genetic Service, Department of Health, HKSAR, Hong Kong, China
| | - Myth Tsz-Shun Mok
- Clinical Genetic Service, Department of Health, HKSAR, Hong Kong, China
| | - Sha-Sha Leung
- Clinical Genetic Service, Department of Health, HKSAR, Hong Kong, China
| | - Ivan F M Lo
- Clinical Genetic Service, Department of Health, HKSAR, Hong Kong, China
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26
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Diel H, Ding C, Grehn F, Chronopoulos P, Bartsch O, Hoffmann EM. First observation of secondary childhood glaucoma in Coffin-Siris syndrome: a case report and literature review. BMC Ophthalmol 2021; 21:28. [PMID: 33430815 PMCID: PMC7802219 DOI: 10.1186/s12886-020-01788-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Severe congenital ophthalmological malformations and glaucoma might be an important occasional feature in patients with Coffin-Siris syndrome (CSS), especially Coffin-Siris syndrome 9 (CSS9, OMIM #615866) caused by SOX11 mutation. Recently, primary (open-angle) glaucoma was described in two children with the most common form of Coffin-Siris syndrome, CSS1 (OMIM #135900) by ARID1B (AT-rich interaction domain-containing protein 1B) gene mutation. In this article, we present the first report of glaucoma with Coffin-Siris syndrome 9 as well as the first report of secondary glaucoma with any form of Coffin-Siris syndrome. These findings indicate that secondary glaucoma is an occasional finding in patients with Coffin-Siris syndrome. CASE PRESENTATION A child with secondary childhood glaucoma and additional ocular manifestations was evaluated and treated at the childhood glaucoma centre in Mainz, Germany. Examination under general anaesthesia revealed ocular anterior segment dysgenesis (ASD) (Peters type iridocorneal dysgenesis) in combination with congenital limbal stem cell deficiency (LSCD), aniridia, and cataract. The patient also had multiple other congenital anomalies and severe developmental delay. To explain his combination of anomalies, molecular genetic analysis from peripheral blood was performed in late 2018 and early 2019. Following normal findings with a panel diagnostic of 18 genes associated with congenital glaucoma, whole exome sequencing was performed and revealed a novel likely pathogenic heterozygous variant c.251G>T, p.(Gly84Val) in the SOX11 gene (SRY-related HMG-box gene 11). The variant had occurred de novo. Thus, the multiple congenital anomalies and developmental delay of the patient represented Coffin-Siris syndrome 9 (CSS9, OMIM #615866). CONCLUSIONS When eye diseases occur in combination with other systemic features, genetic analysis can be seminal. Results indicate that glaucoma is an occasional feature of patients with Coffin-Siris syndrome. As early treatment may improve the visual outcome of patients with glaucoma, we suggest that patients with Coffin-Siris syndrome should receive specific ophthalmological screening.
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Affiliation(s)
- Heidi Diel
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, D – 55131 Mainz, Germany
| | - Can Ding
- Institute of Human Genetics, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Franz Grehn
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, D – 55131 Mainz, Germany
| | - Panagiotis Chronopoulos
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, D – 55131 Mainz, Germany
| | - Oliver Bartsch
- Institute of Human Genetics, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Esther M. Hoffmann
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, D – 55131 Mainz, Germany
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Saviola D, De Gaetano K, Galvani R, Bosetti S, Abbati P, Igharo V, De Tanti A. Rehabilitation in a rare case of coffin-siris syndrome with major cognitive and behavioural disorders. J Pediatr Rehabil Med 2021; 14:525-532. [PMID: 34180430 DOI: 10.3233/prm-200785] [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] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Coffin-Siris syndrome is a rare genetic disease with heterozygous variants in the ARID1A, ARID1B, ARID2, DPF2, SMARCA4, SMARCB1, SMARCE1 or SOX11 genes. It may manifest with somatic anomalies, deafness, urogenital malformations, recurrent infections, mental retardation, speech deficit, agenesis of the corpus callosum, convulsions, hypotonia, developmental delay, and scoliosis. CASE REPORT A 14-year-old boy with Coffin-Siris syndrome due to variants in the ARID1A gene was referred to the clinic. His rehabilitation over a 9-year period was described. The problem of assessment and the approach to rehabilitation was discussed, enabling a progressive remodelling of the cognitive-behavioural disorders that most hindered the possibility of his acquiring new skills and achieving social and family integration. CLINICAL REHABILITATION A protracted, customised, multiprofessional rehabilitation approach, centred on realistic functional objectives, implemented with the direct involvement of the family and school, was the only way to achieve the maximum independence and social and family integration permitted by his residual disability.
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Affiliation(s)
- Donatella Saviola
- Cardinal Ferrari Rehabilitation Centre, Santo Stefano Riabilitazione, Fontanellato, Italy
| | - Katia De Gaetano
- Cardinal Ferrari Rehabilitation Centre, Santo Stefano Riabilitazione, Fontanellato, Italy
| | - Romina Galvani
- Cardinal Ferrari Rehabilitation Centre, Santo Stefano Riabilitazione, Fontanellato, Italy
| | - Sara Bosetti
- Cardinal Ferrari Rehabilitation Centre, Santo Stefano Riabilitazione, Fontanellato, Italy
| | - Paola Abbati
- Cardinal Ferrari Rehabilitation Centre, Santo Stefano Riabilitazione, Fontanellato, Italy
| | - Vivian Igharo
- Cardinal Ferrari Rehabilitation Centre, Santo Stefano Riabilitazione, Fontanellato, Italy
| | - Antonio De Tanti
- Cardinal Ferrari Rehabilitation Centre, Santo Stefano Riabilitazione, Fontanellato, Italy
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Fujita T, Ihara Y, Hayashi H, Ishii A, Ideguchi H, Inoue T, Imaizumi T, Yamamoto T, Hirose S. Coffin-Siris syndrome with bilateral macular dysplasia caused by a novel exonic deletion in ARID1B. Congenit Anom (Kyoto) 2020; 60:189-193. [PMID: 32618029 DOI: 10.1111/cga.12383] [Citation(s) in RCA: 2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/06/2020] [Accepted: 06/27/2020] [Indexed: 12/19/2022]
Abstract
Coffin-Siris syndrome (CSS) is a congenital anomaly syndrome characterized by developmental delay, coarse facial features, and hypoplasia of the fifth digit's nail or phalanges. Herein, we report a case of the 8-year-old female patient who showed developmental delay associated with dysplasia in the macular and large toe area. Comprehensive genomic analysis showed no possible candidate variants, but the subsequent genomic copy number analysis revealed a novel exonic deletion in the coding region of AT-rich interactive domain-containing protein 1B (ARID1B), a gene responsible for CSS. Genomic copy number analysis can aid in diagnosing CSS by confirming undiagnosed exonic deletions in ARID1B. Furthermore, this is the first report of CSS associated with bilateral macular dysplasia.
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Affiliation(s)
- Takako Fujita
- Department of Pediatrics, School of Medicine, Fukuoka University, Fukuoka, Japan
| | - Yukiko Ihara
- Department of Pediatrics, School of Medicine, Fukuoka University, Fukuoka, Japan
| | - Hitomi Hayashi
- Department of Pediatrics, School of Medicine, Fukuoka University, Fukuoka, Japan
| | - Atsushi Ishii
- Department of Pediatrics, School of Medicine, Fukuoka University, Fukuoka, Japan
| | - Hiroshi Ideguchi
- Department of Pediatrics, School of Medicine, Fukuoka University, Fukuoka, Japan
| | - Takahito Inoue
- Department of Pediatrics, School of Medicine, Fukuoka University, Fukuoka, Japan
| | - Taichi Imaizumi
- Department of Pediatrics, School of Medicine, St. Marianna Medical University, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Shinichi Hirose
- Department of Pediatrics, School of Medicine, Fukuoka University, Fukuoka, Japan
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Miraldi Utz V, Brightman DS, Sandoval MA, Hufnagel RB, Saal HM. Systemic and ocular manifestations of a patient with mosaic ARID1A-associated Coffin-Siris syndrome and review of select mosaic conditions with ophthalmic manifestations. Am J Med Genet C Semin Med Genet 2020; 184:644-655. [PMID: 32888375 DOI: 10.1002/ajmg.c.31839] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/06/2020] [Accepted: 08/09/2020] [Indexed: 12/16/2022]
Abstract
Mosaic genetic mutations may be somatic, germline, or "gonosomal" and have the potential to cause genetic syndromes, disorders, or malformations. Mutations can occur at any point in embryonic development and the timing determines the extent of distribution of the mutation throughout the body and different tissue types. The eye and visual pathway offer a unique opportunity to study somatic and gonosomal mosaic mutations as the eye consists of tissues derived from all three germ layers allowing disease pathology to be assessed with noninvasive imaging. In this review, we describe systemic and ocular manifestations in a child with mosaic Coffin-Siris syndrome. The patient presented with a significant medical history of accommodative esotropia and hyperopia, macrocephaly, polydactyly, global developmental delay, hypotonia, ureteropelvic junction (UPJ) obstruction, and brain MRI abnormalities. The ophthalmic findings in this patient were nonspecific, however, they are consistent with ocular manifestations reported in other patients with Coffin-Siris syndrome. We also review ophthalmic findings of select mosaic chromosomal and single-gene disorders. Ophthalmic assessment alongside clinical genetic testing may play an important role in diagnosis of genetic syndromes as well as understanding disease pathology, particularly when mosaicism plays a role.
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Affiliation(s)
- Virginia Miraldi Utz
- Abrahamson Pediatric Eye Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Ophthalmology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Diana S Brightman
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Monica A Sandoval
- Abrahamson Pediatric Eye Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Robert B Hufnagel
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Howard M Saal
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
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Li D, Ahrens-Nicklas RC, Baker J, Bhambhani V, Calhoun A, Cohen JS, Deardorff MA, Fernández-Jaén A, Kamien B, Jain M, Mckenzie F, Mintz M, Motter C, Niles K, Ritter A, Rogers C, Roifman M, Townshend S, Ward-Melver C, Schrier Vergano SA. The variability of SMARCA4-related Coffin-Siris syndrome: Do nonsense candidate variants add to milder phenotypes? Am J Med Genet A 2020; 182:2058-2067. [PMID: 32686290 DOI: 10.1002/ajmg.a.61732] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 09/26/2019] [Revised: 05/13/2020] [Accepted: 05/19/2020] [Indexed: 12/25/2022]
Abstract
SMARCA4 encodes a central ATPase subunit in the BRG1-/BRM-associated factors (BAF) or polybromo-associated BAF (PBAF) complex in humans, which is responsible in part for chromatin remodeling and transcriptional regulation. Variants in this and other genes encoding BAF/PBAF complexes have been implicated in Coffin-Siris Syndrome, a multiple congenital anomaly syndrome classically characterized by learning and developmental differences, coarse facial features, hypertrichosis, and underdevelopment of the fifth digits/nails of the hands and feet. Individuals with SMARCA4 variants have been previously reported and appear to display a variable phenotype. We describe here a cohort of 15 unrelated individuals with SMARCA4 variants from the Coffin-Siris syndrome/BAF pathway disorders registry who further display variability in severity and degrees of learning impairment and health issues. Within this cohort, we also report two individuals with novel nonsense variants who appear to have a phenotype of milder learning/behavioral differences and no organ-system involvement.
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Affiliation(s)
- Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rebecca C Ahrens-Nicklas
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Janice Baker
- Genomic Medicine, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Vikas Bhambhani
- Genomic Medicine, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Amy Calhoun
- Division of Medical Genetics and Genomics, University of Iowa Stead Family Children's Hospital, Iowa City, Iowa, USA
| | - Julie S Cohen
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthew A Deardorff
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Alberto Fernández-Jaén
- Department of Neuropediatrics, Hospital Universitario Quirónsalud, Universidad Europea de Madrid, Madrid, Spain
| | - Benjamin Kamien
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, Western Australia, Australia
| | - Mahim Jain
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Fiona Mckenzie
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, Western Australia, Australia
| | - Mark Mintz
- CNNH NeuroHealth and the Clinical Research Center of New Jersey, Voorhees, New Jersey, USA
| | | | - Kirsten Niles
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, Toronto, Canada
| | - Alyssa Ritter
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Curtis Rogers
- Division of Clinical Genetics, Greenwood Genetics Center, Greenville, South Carolina, USA
| | - Maian Roifman
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, Toronto, Canada
| | - Sharron Townshend
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, Western Australia, Australia
| | | | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, Virginia, USA
- Department of Pediatrics, Eastern Virginia Medical School, Norfolk, Virginia, USA
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31
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Lian S, Ting TW, Lai AHM, Tan ES, Wei H, Cham B, Tan EC. Coffin-Siris Syndrome-1: Report of five cases from Asian populations with truncating mutations in the ARID1B gene. J Neurol Sci 2020; 414:116819. [PMID: 32339967 DOI: 10.1016/j.jns.2020.116819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Pathogenic variants of the ARID1B gene are recognized as the most common cause of Coffin-Siris syndrome (CSS) and also one of the most common causes for intellectual disability (ID). Reported ARID1B variants in association with CSS are mostly from patients of European ancestry. METHODS We performed next-generation sequencing to identify pathogenic variants in patients with congenital disorders from the Genetics clinics. The identified variants were validated by Sanger sequencing. Parental samples were tested by Sanger sequencing to determine inheritance status. RESULTS Truncating variants in ARID1B were identified in five unrelated Asian patients (one Malay, two Chinese and two Indian) with features of CSS. One was a nonsense mutation which had been documented in three other reports while the other four were novel variants, including two nonsense substitutions and two small deletions resulting in premature termination of translation. Similar to previous reports, all patients have developmental and speech delay, with additional presentations such as ectodermal/facial abnormalities commonly observed in CSS patients. CONCLUSIONS Our results unveil ARID1B variants in association with CSS in multiple Southeast Asian ethnic groups, and confirm that variants associated with this disorder tend to be of the truncating type. This finding may provide additional insight into the function of the protein and the disease mechanism.
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32
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Lee BL, Oh SH, Jun KR, Hur YJ, Lee JE, Keum C, Chung WY. First Korean Case of Coffin-Siris Syndrome with a Novel Frameshift ARID1B Mutation. Ann Clin Lab Sci 2020; 50:140-145. [PMID: 32161024] [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] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Coffin-Siris Syndrome (CSS) is a rare neurodevelopmental disorder characterized by intellectual disability, coarse facial features, hypoplastic digits/nails, and hypertrichosis. The genes causative of CSS mainly encode the SWI/SNF complex, which contributes to chromatin remodeling and regulates the access of transcriptional factors to specific gene sites. While ARID1B mutations account for a third of all CSS cases, the condition's phenotypic features vary widely. We document the case of a girl with CSS who presented with a variant facial appearance, global developmental delay with speech impairment, agenesis of the corpus callosum, funnel chest, and bilateral renal stones without hypertrichosis or hypoplasia of the fifth fingernail. Genetic analysis revealed that the patient had a novel heterozygous frameshift mutation c.2201dupG (p.Ser736Ilefs*27) on the ARID1B gene.
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Affiliation(s)
- Bo Lyun Lee
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Seung Hwan Oh
- Department of Laboratory Medicine, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Kyung Ran Jun
- Department of Laboratory Medicine, Haeundae Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Yun Jung Hur
- Department of Pediatrics, Haeundae Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Jeong Eun Lee
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
| | | | - Woo Yeong Chung
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
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Valencia AM, Collings CK, Dao HT, St Pierre R, Cheng YC, Huang J, Sun ZY, Seo HS, Mashtalir N, Comstock DE, Bolonduro O, Vangos NE, Yeoh ZC, Dornon MK, Hermawan C, Barrett L, Dhe-Paganon S, Woolf CJ, Muir TW, Kadoch C. Recurrent SMARCB1 Mutations Reveal a Nucleosome Acidic Patch Interaction Site That Potentiates mSWI/SNF Complex Chromatin Remodeling. Cell 2019; 179:1342-1356.e23. [PMID: 31759698 DOI: 10.1016/j.cell.2019.10.044] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/02/2019] [Accepted: 10/30/2019] [Indexed: 12/21/2022]
Abstract
Mammalian switch/sucrose non-fermentable (mSWI/SNF) complexes are multi-component machines that remodel chromatin architecture. Dissection of the subunit- and domain-specific contributions to complex activities is needed to advance mechanistic understanding. Here, we examine the molecular, structural, and genome-wide regulatory consequences of recurrent, single-residue mutations in the putative coiled-coil C-terminal domain (CTD) of the SMARCB1 (BAF47) subunit, which cause the intellectual disability disorder Coffin-Siris syndrome (CSS), and are recurrently found in cancers. We find that the SMARCB1 CTD contains a basic α helix that binds directly to the nucleosome acidic patch and that all CSS-associated mutations disrupt this binding. Furthermore, these mutations abrogate mSWI/SNF-mediated nucleosome remodeling activity and enhancer DNA accessibility without changes in genome-wide complex localization. Finally, heterozygous CSS-associated SMARCB1 mutations result in dominant gene regulatory and morphologic changes during iPSC-neuronal differentiation. These studies unmask an evolutionarily conserved structural role for the SMARCB1 CTD that is perturbed in human disease.
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Kalmbach A, Schröder C, Klein-Hitpass L, Nordström K, Ulz P, Heitzer E, Speicher MR, Rahmann S, Wieczorek D, Horsthemke B, Bramswig NC. Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome. Cytogenet Genome Res 2019; 159:1-11. [PMID: 31658463 DOI: 10.1159/000503266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 01/15/2023] Open
Abstract
The switch/sucrose non-fermenting (SWI/SNF) complex is an ATP-dependent chromatin remodeller that regulates the spacing of nucleosomes and thereby controls gene expression. Heterozygous mutations in genes encoding subunits of the SWI/SNF complex have been reported in individuals with Coffin-Siris syndrome (CSS), with the majority of the mutations in ARID1B. CSS is a rare congenital disorder characterized by facial dysmorphisms, digital anomalies, and variable intellectual disability. We hypothesized that mutations in genes encoding subunits of the ubiquitously expressed SWI/SNF complex may lead to alterations of the nucleosome profiles in different cell types. We performed the first study on CSS-patient samples and investigated the nucleosome landscapes of cell-free DNA (cfDNA) isolated from blood plasma by whole-genome sequencing. In addition, we studied the nucleosome landscapes of CD14+ monocytes from CSS-affected individuals by nucleosome occupancy and methylome-sequencing (NOMe-seq) as well as their expression profiles. In cfDNA of CSS-affected individuals with heterozygous ARID1B mutations, we did not observe major changes in the nucleosome profile around transcription start sites. In CD14+ monocytes, we found few genomic regions with different nucleosome occupancy when compared to controls. RNA-seq analysis of CD14+ monocytes of these individuals detected only few differentially expressed genes, which were not in proximity to any of the identified differential nucleosome-depleted regions. In conclusion, we show that heterozygous mutations in the human SWI/SNF subunit ARID1B do not have a major impact on the nucleosome landscape or gene expression in blood cells. This might be due to functional redundancy, cell-type specificity, or alternative functions of ARID1B.
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Pranckėnienė L, Siavrienė E, Gueneau L, Preikšaitienė E, Mikštienė V, Reymond A, Kučinskas V. De novo splice site variant of ARID1B associated with pathogenesis of Coffin-Siris syndrome. Mol Genet Genomic Med 2019; 7:e1006. [PMID: 31628733 PMCID: PMC6900373 DOI: 10.1002/mgg3.1006] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/06/2019] [Accepted: 09/18/2019] [Indexed: 02/02/2023] Open
Abstract
Background Coffin–Siris syndrome is an extremely rare syndrome associated with developmental and congenital anomalies. It is caused by heterozygous pathogenic variants of ARID1A, ARID1B, SMARCA4, SMARCB1, SMARCE1, and SOX11. Methods This case study presents the whole exome sequencing of a patient with characteristic clinical features of Coffin–Siris syndrome. Analysis included Sanger sequencing of complementary DNA and bioinformatic analysis of the variant. Results Analysis of cDNA Sanger sequencing data revealed that the donor splice site variant led to skipping of exon 19. Further, bioinformatic analysis predicted abnormal splicing in a translational frameshift of 11 amino acids and the creation of a premature termination codon. Results found a novel de novo splice site variant c.5025+2T>C in the ARID1B and truncated 1 633 amino acid protein NP_065783.3:p. (Thr1633Valfs*11). Conclusion Truncated ARID1B resulted in loss of the BAF250 domain, which is part of SWI/SNF‐like ATP‐dependent chromatin remodeling complex. The severe clinical manifestation presented by the proband was attributed to the disappearance of the BAF250 domain in the ARID1B protein. Our finding provides strong evidence that this pathogenic variant of exon 19 caused a frameshift mutation in the ARID1B at the terminal exon, resulting in the expression of a severe phenotype of CSS.
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Affiliation(s)
- Laura Pranckėnienė
- Department of Human and Medical GeneticsInstitute of Biomedical SciencesFaculty of MedicineVilnius UniversityVilniusLithuania
| | - Evelina Siavrienė
- Department of Human and Medical GeneticsInstitute of Biomedical SciencesFaculty of MedicineVilnius UniversityVilniusLithuania
| | - Lucie Gueneau
- Centre for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
| | - Eglė Preikšaitienė
- Department of Human and Medical GeneticsInstitute of Biomedical SciencesFaculty of MedicineVilnius UniversityVilniusLithuania
| | - Violeta Mikštienė
- Department of Human and Medical GeneticsInstitute of Biomedical SciencesFaculty of MedicineVilnius UniversityVilniusLithuania
| | - Alexandre Reymond
- Centre for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
| | - Vaidutis Kučinskas
- Department of Human and Medical GeneticsInstitute of Biomedical SciencesFaculty of MedicineVilnius UniversityVilniusLithuania
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Knapp KM, Poke G, Jenkins D, Truter W, Bicknell LS. Expanding the phenotypic spectrum associated with DPF2: A new case report. Am J Med Genet A 2019; 179:1637-1641. [PMID: 31207137 DOI: 10.1002/ajmg.a.61262] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 11/29/2018] [Revised: 03/26/2019] [Accepted: 06/01/2019] [Indexed: 11/07/2022]
Abstract
Coffin-Siris syndrome (CSS) is a clinically and genetically heterogeneous developmental disorder, linked to disruption of the BAF chromatin-remodeling complex. Recently, de novo missense and truncating variants have been reported in DPF2 in patients sharing some of the common features of CSS. Here we report a further individual harboring a novel de novo missense DPF2 variant, c.1066T>G, p.Cys356Gly. Structural modeling indicated that the predicted amino acid substitution affects a core residue required for zinc ion coordination and would likely alter the PHD2 domain structure of DPF2. The clinical presentation of Pierre Robin sequence and diaphragmatic hernia did not immediately suggest CSS, with the more common CSS features of hypoplastic toenails and characteristic facial features very subtle. This individual further broadens the phenotypic features of DPF2-related CSS, as well as CSS more generally.
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Affiliation(s)
- Karen M Knapp
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Gemma Poke
- Genetic Health Service New Zealand, Wellington, New Zealand
| | - Danielle Jenkins
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Werner Truter
- Department of Child Health, MidCentral District Health Board, Palmerston North, New Zealand
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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Cappuccio G, Brunetti-Pierri R, Torella A, Pinelli M, Castello R, Casari G, Nigro V, Banfi S, Simonelli F, Brunetti-Pierri N. Retinal dystrophy in an individual carrying a de novo missense variant of SMARCA4. Mol Genet Genomic Med 2019; 7:e682. [PMID: 30973214 PMCID: PMC6565552 DOI: 10.1002/mgg3.682] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 02/22/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Coffin-Siris syndrome (CSS) is characterized by intellectual disability, dysmorphic facial features, growth deficiency, microcephaly, and abnormalities of the fifth fingers/toes. CSS is caused by mutations in several genes of the BRG1-associated factor pathway including SMARCA4. METHODS Whole-exome sequencing was performed on a 14-year-old female individual who presented with mild intellectual disability and dysmorphic features, tooth abnormalities, and short stature. She had brachydactyly but no aplasia or hypoplasia of the distal phalanx or nail of the fifth digit. She was also found to have retinal dystrophy that has not been previously reported in CSS. RESULTS The individual presented herein was found to harbor a previously unreported de novo variant in SMARCA4. CONCLUSION This case expands the phenotypic spectrum of CSS manifestations.
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Affiliation(s)
- Gerarda Cappuccio
- Department of Translational Medicine, Federico II University, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Raffaella Brunetti-Pierri
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Michele Pinelli
- Department of Translational Medicine, Federico II University, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | | | - Giorgio Casari
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | | | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
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Khazanchi R, Ronspies CA, Smith SC, Starr LJ. Patient with anomalous skin pigmentation expands the phenotype of ARID2 loss-of-function disorder, a SWI/SNF-related intellectual disability. Am J Med Genet A 2019; 179:808-812. [PMID: 30838730 DOI: 10.1002/ajmg.a.61075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 06/21/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 12/20/2022]
Abstract
ARID2 loss-of-function is associated with a rare genetic disorder characterized in 14 reported patients to date. ARID2 encodes a member of the SWItch/sucrose non-fermentable chromatin remodeling complex. Other genes encoding subunits of this complex, such as ARID1A, ARID1B, and SMARCA2, are mutated in association with Coffin-Siris syndrome (CSS) and Nicolaides Baraitser syndrome (NCBRS) phenotypes. Previously reported ARID2 mutations manifested clinically with a CSS-like phenotype including intellectual disability, coarsened facial features, fifth toenail hypoplasia, and other recognizable dysmorphisms. However, heterogeneity exists between previously reported patients with some patients showing more overlapping features with NCBRS. Herein, we present a patient with a novel disease-causing ARID2 loss-of-function mutation. His clinical features included intellectual disability, coarse and dysmorphic facial features, toenail hypoplasia, ADHD, short stature, and delayed development consistent with prior reports. Our patient also presented with previously unreported clinical findings including ophthalmologic involvement, persistent fetal fingertip and toetip pads, and diffuse hyperpigmentary and hypopigmentary changes sparing his face, palms, and soles. The anomalous skin findings are particularly of interest given prior literature outlining the role of ARID2 in melanocyte homeostasis and melanoma. This clinical report and review of the literature is further affirming of the characteristic symptoms and expands the phenotype of this newly described and rare syndrome.
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Affiliation(s)
- Rohan Khazanchi
- College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Carey A Ronspies
- Munroe-Meyer Institute for Genetics & Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska
| | - Scott C Smith
- Munroe-Meyer Institute for Genetics & Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska
| | - Lois J Starr
- Munroe-Meyer Institute for Genetics & Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska
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Tchanque-Fossuo CN, Dahle SE, Kiuru M, Isseroff RR. Vitiligo and melanocytic nevi: New findings in Coffin-Siris syndrome associated with ARID1 germline mutation. JAAD Case Rep 2018; 5:50-53. [PMID: 30581937 PMCID: PMC6287087 DOI: 10.1016/j.jdcr.2018.08.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Key Words
- ARID1A, AT-rich interactive domain 1A gene
- ARID1B
- ARID1B, AT-rich interactive domain 1B gene
- CDK, cyclin-dependent kinase
- CSS, Coffin-Siris syndrome
- Coffin-Siris syndrome
- MITF, microphthalmia transcription factor
- SMARB1, SWI/SNF–related, matrix-associated, actin-dependent regulator of chromatin subfamily B member 1
- SMARCA4, SWI/SNF–related, matrix-associated, actin-dependent regulator of chromatin subfamily A member 4
- SMARCE1, SWI/SNF–related, matrix-associated, actin-dependent regulator of chromatin subfamily E member 1
- SWI/SNF, switch/sucrose nonfermenting
- melanoma
- nevi
- vitiligo
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Affiliation(s)
- Catherine N. Tchanque-Fossuo
- Department of Dermatology, University of California, Davis, Sacramento, California
- Dermatology Service, VA Northern California, Sacramento VA Medical Center, Mather, California
- Correspondence to: Catherine N. Tchanque-Fossuo, MD, MS, Department of Dermatology, University of California, Davis, School of Medicine, 3301 C St, Ste 1400, Sacramento, CA 95816.
| | - Sara E. Dahle
- Department of Dermatology, University of California, Davis, Sacramento, California
- Podiatry Section, Department of Surgery, VA Northern California, Sacramento VA Medical Center, Mather, California
| | - Maija Kiuru
- Department of Dermatology, University of California, Davis, Sacramento, California
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California
| | - R. Rivkah Isseroff
- Department of Dermatology, University of California, Davis, Sacramento, California
- Dermatology Service, VA Northern California, Sacramento VA Medical Center, Mather, California
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Paulraj P, Palumbos JC, Openshaw A, Carey JC, Toydemir RM. Multiple Congenital Anomalies and Global Developmental Delay in a Patient with Interstitial 6q25.2q26 Deletion: A Diagnostic Odyssey. Cytogenet Genome Res 2018; 156:191-196. [PMID: 30439704 DOI: 10.1159/000494871] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2018] [Indexed: 12/17/2022] Open
Abstract
Interstitial deletions involving 6q25 are rare chromosomal abnormalities associated with distinctive phenotypic features. We describe a 9-year-old boy who was followed from his infancy due to his multiple congenital anomalies and complex medical history. Over the years, a number of diagnoses were considered including Cornelia de Lange syndrome, Rubinstein-Taybi syndrome, as well as "a novel genetic disorder." Various genetic tests, including a BAC-based array-CGH analysis, were reported as normal. Recently, a SNP-based microarray analysis was performed and showed an 11.1-Mb deletion from 6q25.2 to 6q26, including ARID1B and ZDHHC14. Recent literature suggests that the 6q25 deletion syndrome is a recognizable entity characterized by growth delay, developmental disabilities, microcephaly, hearing loss, and variable other malformations including cleft palate. These features overlap with those of Coffin-Siris syndrome, which is caused by deletions and loss-of-function mutations of ARID1B. Retrospectively, this patient has features resembling both Coffin-Siris and 6q25 microdeletion syndromes.
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Mannino EA, Miyawaki H, Santen G, Schrier Vergano SA. First data from a parent-reported registry of 81 individuals with Coffin-Siris syndrome: Natural history and management recommendations. Am J Med Genet A 2018; 176:2250-2258. [PMID: 30276971 DOI: 10.1002/ajmg.a.40471] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/25/2018] [Accepted: 06/21/2018] [Indexed: 11/05/2022]
Abstract
Coffin-Siris syndrome (CSS; MIM 135900) is a multisystem congenital anomaly syndrome caused by mutations in the genes in the Brg-1 associated factors (BAF) complex. Classically, individuals with CSS have been described with hypo- or aplasia of the fifth digit nails or phalanges (hence the term "fifth digit syndrome"). Other physical features seen include growth restriction, coarse facial features, hypertrichosis or hirsutism, sparse scalp hair, dental anomalies, and other organ-system abnormalities. Varying degrees of developmental and intellectual delay are universal. To date, approximately 200 individuals have been described in the literature. With the advent of large-scale genetic testing such as whole-exome sequencing is becoming more available, more individuals are being found to have mutations in this pathway, and the phenotypic spectrum appears to be broadening. We report here a large cohort of 81 individuals with the diagnosis of CSS from the first parent-reported CSS/BAF complex registry in an effort to describe this variation among individuals, the natural history of the syndrome, and draw some gene-phenotype correlations. We propose that changes in the BAF complex may represent a spectrum of disorders, including both ARID1B-related nonsyndromic intellectual disability (ARID1B-ID) and CSS with classic physical features. In addition, we offer surveillance and management recommendations based on the medical issues encountered in this cohort to help guide physicians and patients' families.
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Affiliation(s)
- Elizabeth A Mannino
- Doctor of Medicine Program, Eastern Virginia Medical School, Norfolk, Virginia
| | - Hanae Miyawaki
- Master of Public Health Program, Eastern Virginia Medical School, Old Dominion University, Norfolk, Virginia
| | - Gijs Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, Virginia.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, Virginia
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Bögershausen N, Wollnik B. Mutational Landscapes and Phenotypic Spectrum of SWI/SNF-Related Intellectual Disability Disorders. Front Mol Neurosci 2018; 11:252. [PMID: 30123105 PMCID: PMC6085491 DOI: 10.3389/fnmol.2018.00252] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/03/2018] [Indexed: 12/29/2022] Open
Abstract
Mutations in genes that encode proteins of the SWI/SNF complex, called BAF complex in mammals, cause a spectrum of disorders that ranges from syndromic intellectual disability to Coffin-Siris syndrome (CSS) to Nicolaides-Baraitser syndrome (NCBRS). While NCBRS is known to be a recognizable and restricted phenotype, caused by missense mutations in SMARCA2, the term CSS has been used lately for a more heterogeneous group of phenotypes that are caused by mutations in either of the genes ARID1B, ARID1A, ARID2, SMARCA4, SMARCB1, SMARCE1, SOX11, or DPF2. In this review, we summarize the current knowledge on the phenotypic traits and molecular causes of the above named conditions, consider the question whether a clinical distinction of the phenotypes is still adequate, and suggest the term "SWI/SNF-related intellectual disability disorders" (SSRIDDs). We will also outline important features to identify the ARID1B-related phenotype in the absence of classic CSS features, and discuss distinctive and overlapping features of the SSRIDD subtypes. Moreover, we will briefly review the function of the SWI/SNF complex in development and describe the mutational landscapes of the genes involved in SSRIDD.
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Affiliation(s)
- Nina Bögershausen
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
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Vasileiou G, Vergarajauregui S, Endele S, Popp B, Büttner C, Ekici AB, Gerard M, Bramswig NC, Albrecht B, Clayton-Smith J, Morton J, Tomkins S, Low K, Weber A, Wenzel M, Altmüller J, Li Y, Wollnik B, Hoganson G, Plona MR, Cho MT, Thiel CT, Lüdecke HJ, Strom TM, Calpena E, Wilkie AOM, Wieczorek D, Engel FB, Reis A. Mutations in the BAF-Complex Subunit DPF2 Are Associated with Coffin-Siris Syndrome. Am J Hum Genet 2018; 102:468-479. [PMID: 29429572 DOI: 10.1016/j.ajhg.2018.01.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [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: 10/04/2017] [Accepted: 01/17/2018] [Indexed: 12/31/2022] Open
Abstract
Variants affecting the function of different subunits of the BAF chromatin-remodelling complex lead to various neurodevelopmental syndromes, including Coffin-Siris syndrome. Furthermore, variants in proteins containing PHD fingers, motifs recognizing specific histone tail modifications, have been associated with several neurological and developmental-delay disorders. Here, we report eight heterozygous de novo variants (one frameshift, two splice site, and five missense) in the gene encoding the BAF complex subunit double plant homeodomain finger 2 (DPF2). Affected individuals share common clinical features described in individuals with Coffin-Siris syndrome, including coarse facial features, global developmental delay, intellectual disability, speech impairment, and hypoplasia of fingernails and toenails. All variants occur within the highly conserved PHD1 and PHD2 motifs. Moreover, missense variants are situated close to zinc binding sites and are predicted to disrupt these sites. Pull-down assays of recombinant proteins and histone peptides revealed that a subset of the identified missense variants abolish or impaire DPF2 binding to unmodified and modified H3 histone tails. These results suggest an impairment of PHD finger structural integrity and cohesion and most likely an aberrant recognition of histone modifications. Furthermore, the overexpression of these variants in HEK293 and COS7 cell lines was associated with the formation of nuclear aggregates and the recruitment of both wild-type DPF2 and BRG1 to these aggregates. Expression analysis of truncating variants found in the affected individuals indicated that the aberrant transcripts escape nonsense-mediated decay. Altogether, we provide compelling evidence that de novo variants in DPF2 cause Coffin-Siris syndrome and propose a dominant-negative mechanism of pathogenicity.
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Affiliation(s)
- Georgia Vasileiou
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Silvia Vergarajauregui
- Experimental Renal and Cardiovascular Research, Institute of Pathology, Department of Nephropathology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Sabine Endele
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Bernt Popp
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Christian Büttner
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Marion Gerard
- Génétique Clinique, Centre Hospitalier Universitaire de Caen, Caen 14000, France
| | - Nuria C Bramswig
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45122 Essen, Germany
| | - Beate Albrecht
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45122 Essen, Germany
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Jenny Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's Hospital NHS Foundation Trust, Birmingham B15 2TG, UK
| | - Susan Tomkins
- Clinical Genetics Service, University Hospitals of Bristol NHS Foundation Trust, Bristol BS2 8HW, UK
| | - Karen Low
- Clinical Genetics Service, University Hospitals of Bristol NHS Foundation Trust, Bristol BS2 8HW, UK
| | - Astrid Weber
- Merseyside and Cheshire Clinical Genetics Service, Liverpool Women's NHS Foundation Hospital Trust, Liverpool L8 7SS, UK
| | | | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Yun Li
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - George Hoganson
- Pediatric Genetics, University of Illinois Hospital, Chicago, IL 60612, USA
| | - Maria-Renée Plona
- Pediatric Genetics, University of Illinois Hospital, Chicago, IL 60612, USA
| | | | - Christian T Thiel
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Hermann-Josef Lüdecke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45122 Essen, Germany; Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Dagmar Wieczorek
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45122 Essen, Germany; Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Felix B Engel
- Experimental Renal and Cardiovascular Research, Institute of Pathology, Department of Nephropathology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany.
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Celen C, Chuang JC, Luo X, Nijem N, Walker AK, Chen F, Zhang S, Chung AS, Nguyen LH, Nassour I, Budhipramono A, Sun X, Bok LA, McEntagart M, Gevers EF, Birnbaum SG, Eisch AJ, Powell CM, Ge WP, Santen GW, Chahrour M, Zhu H. Arid1b haploinsufficient mice reveal neuropsychiatric phenotypes and reversible causes of growth impairment. eLife 2017; 6. [PMID: 28695822 PMCID: PMC5515576 DOI: 10.7554/elife.25730] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [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: 02/03/2017] [Accepted: 06/24/2017] [Indexed: 12/17/2022] Open
Abstract
Sequencing studies have implicated haploinsufficiency of ARID1B, a SWI/SNF chromatin-remodeling subunit, in short stature (Yu et al., 2015), autism spectrum disorder (O'Roak et al., 2012), intellectual disability (Deciphering Developmental Disorders Study, 2015), and corpus callosum agenesis (Halgren et al., 2012). In addition, ARID1B is the most common cause of Coffin-Siris syndrome, a developmental delay syndrome characterized by some of the above abnormalities (Santen et al., 2012; Tsurusaki et al., 2012; Wieczorek et al., 2013). We generated Arid1b heterozygous mice, which showed social behavior impairment, altered vocalization, anxiety-like behavior, neuroanatomical abnormalities, and growth impairment. In the brain, Arid1b haploinsufficiency resulted in changes in the expression of SWI/SNF-regulated genes implicated in neuropsychiatric disorders. A focus on reversible mechanisms identified Insulin-like growth factor (IGF1) deficiency with inadequate compensation by Growth hormone-releasing hormone (GHRH) and Growth hormone (GH), underappreciated findings in ARID1B patients. Therapeutically, GH supplementation was able to correct growth retardation and muscle weakness. This model functionally validates the involvement of ARID1B in human disorders, and allows mechanistic dissection of neurodevelopmental diseases linked to chromatin-remodeling. DOI:http://dx.doi.org/10.7554/eLife.25730.001 DNA does not just float freely inside our cells. Instead, it is wound around proteins called histones and packaged tidily into a form called chromatin. This packaging allows genes to be switched on or off by making it easier or harder to access different stretches of the genetic code. A group of proteins called the SWI/SNF chromatin-remodeling complex are responsible for the packing and unpacking of DNA during development, dictating the fate of thousands of genes. Mutations that affect one component of this complex, a protein known ARID1B, are associated with a rare genetic condition called Coffin-Siris syndrome, and may also have a role to play in autism spectrum disorders and intellectual disability. However, there were previously no animal models that can be used to study this mutation in the laboratory. Celen, Chuang et al. have now genetically modified mice to remove one of their two copies of the gene that encodes the mouse equivalent of ARID1B. This change replicates the mutation that is most commonly seen in people with Coffin-Siris syndrome. Celen, Chuang et al. report that the mutant mice with just one working copy of the gene showed many features also seen in Coffin-Siris syndrome, including a smaller size and weaker muscles. The mutant mice also repeated certain behaviors, like grooming themselves, and showed unusual interactions with other mice. Further tests showed that the mutant mice had lower than expected levels of growth hormone in their blood. The mice were then treated with growth hormone supplements to find out if this could reverse any of their symptoms. Indeed, this treatment made the mice larger and stronger, but did not change their behavior. Some doctors are already treating people with Coffin-Siris syndrome with growth hormone, and these new findings suggest that this treatment counteracts defects caused directly by the mutation affecting ARID1B. Moreover, this mouse model will allow the role of ARID1B to be investigated further in the laboratory, and could be used as a tool to discover, develop and test new treatments for Coffin-Siris syndrome. DOI:http://dx.doi.org/10.7554/eLife.25730.002
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Affiliation(s)
- Cemre Celen
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jen-Chieh Chuang
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xin Luo
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nadine Nijem
- Departments of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States.,Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
| | - Angela K Walker
- Departments of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Fei Chen
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Departments of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States.,Departments of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Shuyuan Zhang
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Andrew S Chung
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Liem H Nguyen
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ibrahim Nassour
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Albert Budhipramono
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xuxu Sun
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Levinus A Bok
- Department of Pediatrics, Máxima Medical Center, Veldhoven, The Netherlands
| | - Meriel McEntagart
- Medical Genetics, St George's University Hospitals, NHS Foundation Trust, United Kingdom Caroline Brain, Endocrinology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Evelien F Gevers
- William Harvey Research Institute, Barts and the London, Queen Mary University of London, London, United Kingdom
| | - Shari G Birnbaum
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Amelia J Eisch
- Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia, and Mahoney Institute of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Craig M Powell
- Departments of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Woo-Ping Ge
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Departments of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States.,Departments of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Gijs We Santen
- Department of Clinical genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Maria Chahrour
- Departments of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States.,Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
| | - Hao Zhu
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
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Zweier M, Peippo MM, Pöyhönen M, Kääriäinen H, Begemann A, Joset P, Oneda B, Rauch A. The HHID syndrome of hypertrichosis, hyperkeratosis, abnormal corpus callosum, intellectual disability, and minor anomalies is caused by mutations in ARID1B. Am J Med Genet A 2017; 173:1440-1443. [PMID: 28323383 PMCID: PMC5413807 DOI: 10.1002/ajmg.a.38143] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 11/15/2022]
Affiliation(s)
- Markus Zweier
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | | | - Minna Pöyhönen
- Department of Clinical Genetics, Helsinki University Central Hospital and Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | | | - Anaïs Begemann
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland.,Radiz-Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Zurich, Switzerland
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland.,Radiz-Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
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Takenouchi T, Yoshihashi H, Sakaguchi Y, Uehara T, Honda M, Takahashi T, Kosaki K, Miyama S. Hirschsprung disease as a yet undescribed phenotype in a patient with ARID1B mutation. Am J Med Genet A 2016; 170:3249-3252. [PMID: 27511161 DOI: 10.1002/ajmg.a.37861] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 02/09/2016] [Accepted: 07/08/2016] [Indexed: 01/18/2023]
Abstract
Mutations in the BAF complex (mammalian SWI/SNF complex) are responsible for Coffin-Siris syndrome, which is characterized by developmental delay, distinctive facial features, hirsutism, and hypoplasia/aplasia of the fifth finger/fingernails. Hirschsprung disease is characterized by defective stem cells in the enteric neural system, and the involvement of multiple signaling cascades has been implicated. So far, the roles of the BAF complex in the genesis of Hirschsprung disease have remained unknown. Here, we document a patient with coarse facial features, postnatal growth failure, developmental delay, epilepsy, and hypoplasia of the corpus callosum and cerebellum but without a hypoplastic fifth finger/fingernail. In addition, he had Hirschsprung disease. Exome sequencing with a gene set representing a total of 4,813 genes with known relationships to human diseases revealed a heterozygous frameshift mutation in ARID1B (c.5789delC p.Pro1930Leufs*44). The presence of a congenital cataract and Hirschsprung disease in the presently reported patient further expands the phenotypic spectrum of patients with ARID1B mutations and may suggest the potential role of the BAF complex in the pathogenesis of the enteric neural system. The present observation is in agreement with a recent study of Drosophila neuroblasts showing that the dysregulated BAF complex leads to an abnormal lineage progression of neural stem cell lineages and that Hirschsprung disease is caused by abnormal stem cell lineages in the peripheral neural tissues. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Toshiki Takenouchi
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.,Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Hiroshi Yoshihashi
- Department of Genetics, Tokyo Metropolitan Children's Medical Center, Fuchu, Tokyo, Japan
| | - Yuri Sakaguchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan.,Department of Neurology, Tokyo Metropolitan Children's Medical Center, Fuchu, Tokyo, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Masataka Honda
- Department of Nephrology, Tokyo Metropolitan Children's Medical Center, Fuchu, Tokyo, Japan
| | - Takao Takahashi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Sahoko Miyama
- Department of Neurology, Tokyo Metropolitan Children's Medical Center, Fuchu, Tokyo, Japan
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Sonmez FM, Uctepe E, Gunduz M, Gormez Z, Erpolat S, Oznur M, Sagiroglu MS, Demirci H, Gunduz E. Coffin-Siris syndrome with café-au-lait spots, obesity and hyperinsulinism caused by a mutation in the ARID1B gene. Intractable Rare Dis Res 2016; 5:222-6. [PMID: 27672547 PMCID: PMC4995424 DOI: 10.5582/irdr.2014.01040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Coffin-Siris syndrome (CSS) (MIM 135900) is characterized by developmental delay, severe speech impairment, distinctive facial features, hypertrichosis, aplasia or hypoplasia of the distal phalanx or nail of the fifth digit and agenesis of the corpus callosum. Recently, it was shown that mutations in the ARID1B gene are the main cause of CSS, accounting for 76% of identified mutations. Here, we report a 15 year-old female patient who was admitted to our clinic with seizures, speech problems, dysmorphic features, bilaterally big, large thumb, café-au-lait (CAL) spots, obesity and hyperinsulinism. First, the patient was thought to have an association of neurofibromatosis and Rubinstein Taybi syndrome. Because of the large size of the NF1 gene for neurofibromatosis and CREBBP gene for Rubinstein Taybi syndrome, whole exome sequence analysis (WES) was conducted and a novel ARID1B mutation was identified. The proband WES test identified a novel heterozygous frameshift mutation c.3394_3395insTA in exon 13 of ARID1B (NM_017519.2) predicting a premature stop codon p.(Tyr1132Leufs*67). Sanger sequencing confirmed the heterozygous c.3394_3395insTA mutation in the proband and that it was not present in her parents indicating de novo mutation. Further investigation and new cases will help to understand this phenomenon better.
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Affiliation(s)
- Fatma Mujgan Sonmez
- Department of Child Neurology, Turgut Özal University Faculty of Medicine, Ankara, Turkey
- Address correspondence to: Dr. Fatma Mujgan Sonmez, Department of Child Neurology, Turgut Ozal University Faculty of Medicine, Alparslan Turkes Caddesi No: 57 06510, Ankara, Turkey. E-mail:
| | - Eyyup Uctepe
- Department of Medical Genetics, Health Sciences University, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkey
| | - Mehmet Gunduz
- Department of Medical Genetics, Turgut Özal University Faculty of Medicine, Ankara, Turkey
- Department of Otolaryngology, Turgut Özal University Faculty of Medicine, Ankara, Turkey
| | - Zeliha Gormez
- Advanced Genomics and Bioinformatics Research Center, The Scientific and Technological Research Council of Turkey (TUBITAK-BILGEM), Kocaeli, Turkey
| | - Seval Erpolat
- Department of Dermatology, Turgut Özal University Faculty of Medicine, Ankara, Turkey
| | - Murat Oznur
- Department of Medical Genetics, Turgut Özal University Faculty of Medicine, Ankara, Turkey
| | - Mahmut Samil Sagiroglu
- Advanced Genomics and Bioinformatics Research Center, The Scientific and Technological Research Council of Turkey (TUBITAK-BILGEM), Kocaeli, Turkey
| | - Huseyin Demirci
- Advanced Genomics and Bioinformatics Research Center, The Scientific and Technological Research Council of Turkey (TUBITAK-BILGEM), Kocaeli, Turkey
| | - Esra Gunduz
- Department of Medical Genetics, Turgut Özal University Faculty of Medicine, Ankara, Turkey
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Zarate YA, Bhoj E, Kaylor J, Li D, Tsurusaki Y, Miyake N, Matsumoto N, Phadke S, Escobar L, Irani A, Hakonarson H, Schrier Vergano SA. SMARCE1, a rare cause of Coffin-Siris Syndrome: Clinical description of three additional cases. Am J Med Genet A 2016; 170:1967-73. [PMID: 27264197 PMCID: PMC5870868 DOI: 10.1002/ajmg.a.37722] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/21/2016] [Indexed: 11/06/2022]
Abstract
Coffin-Siris syndrome (CSS, MIM 135900), is a well-described, multiple congenital anomaly syndrome characterized by coarse facial features, hypertrichosis, sparse scalp hair, and hypo/aplastic digital nails and phalanges, typically of the 5th digits. Mutations in the BAF (SWI/SNF)-complex subunits (SMARCA4, SMARCE1, SMARCB1, SMARCA2, ARID1B, and ARID1A) have been shown to cause not only CSS, but also related disorders including Nicolaides-Baraitser (MIM 601358) syndrome and ARID1B-intellectual disability syndrome (MIM 614562). At least 200 individuals with CSS have been found to have a mutation in the BAF pathway. However, to date, only three individuals with CSS have been reported to have pathogenic variants in SMARCE1. We report here three additional individuals with clinical features consistent with CSS and alterations in SMARCE1, one of which is novel. The probands all exhibited dysmorphic facial features, moderate developmental and cognitive delay, poor growth, and hypoplastic digital nails/phalanges, including digits not typically affected in the other genes associated with CSS. Two of the three probands had a variety of different organ system anomalies, including cardiac disease, genitourinary abnormalities, feeding difficulties, and vision abnormalities. The 3rd proband has not had further investigative studies. Although an increasing number of individuals are being diagnosed with disorders in the BAF pathway, SMARCE1 is the least common of these genes. This report doubles the number of probands with these mutations, and allows for better phenotypic information of this rare syndrome. © 2016 Wiley Periodicals, Inc.
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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
| | - Elizabeth Bhoj
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Julie Kaylor
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Yoshinori Tsurusaki
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Shubha Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Science, Lucknow, India
| | - Luis Escobar
- Medical Genetics and Neurodevelopmental Pediatrics, St. Vincent's Peyton Manning Children's Hospital, Indianapolis, Indiana
| | - Afifa Irani
- Medical Genetics and Neurodevelopmental Pediatrics, St. Vincent's Peyton Manning Children's Hospital, Indianapolis, Indiana
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, Virginia
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Chandler RL, Magnuson T. The SWI/SNF BAF-A complex is essential for neural crest development. Dev Biol 2016; 411:15-24. [PMID: 26806701 DOI: 10.1016/j.ydbio.2016.01.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 01/17/2016] [Accepted: 01/20/2016] [Indexed: 10/22/2022]
Abstract
Growing evidence indicates that chromatin remodeler mutations underlie the pathogenesis of human neurocristopathies or disorders that affect neural crest cells (NCCs). However, causal relationships among chromatin remodeler subunit mutations and NCC defects remain poorly understood. Here we show that homozygous loss of ARID1A-containing, SWI/SNF chromatin remodeling complexes (BAF-A) in NCCs results in embryonic lethality in mice, with mutant embryos succumbing to heart defects. Strikingly, monoallelic loss of ARID1A in NCCs led to craniofacial defects in adult mice, including shortened snouts and low set ears, and these defects were more pronounced following homozygous loss of ARID1A, with the ventral cranial bones being greatly reduced in size. Early NCC specification and expression of the BRG1 NCC target gene, PLEXINA2, occurred normally in the absence of ARID1A. Nonetheless, mutant embryos displayed incomplete conotruncal septation of the cardiac outflow tract and defects in the posterior pharyngeal arteries, culminating in persistent truncus arteriosus and agenesis of the ductus arteriosus. Consistent with this, migrating cardiac NCCs underwent apoptosis within the circumpharyngeal ridge. Our data support the notion that multiple, distinct chromatin remodeling complexes govern genetically separable events in NCC development and highlight a potential pathogenic role for NCCs in the human BAF complex disorder, Coffin-Siris Syndrome.
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Affiliation(s)
- Ronald L Chandler
- Department of Genetics, University of North Carolina at Chapel Hill, United States
| | - Terry Magnuson
- Department of Genetics, University of North Carolina at Chapel Hill, United States.
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50
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Abstract
Various biological networks can be constructed, each featuring gene/protein relationships of different meanings (e.g., protein interactions or gene co-expression). However, this diversity is classically not considered and the different interaction categories are usually aggregated in a single network. The multiplex framework, where biological relationships are represented by different network layers reflecting the various nature of interactions, is expected to retain more information. Here we assessed aggregation, consensus and multiplex-modularity approaches to detect communities from multiple network sources. By simulating random networks, we demonstrated that the multiplex-modularity method outperforms the aggregation and consensus approaches when network layers are incomplete or heterogeneous in density. Application to a multiplex biological network containing 4 layers of physical or functional interactions allowed recovering communities more accurately annotated than their aggregated counterparts. Overall, taking into account the multiplexity of biological networks leads to better-defined functional modules. A user-friendly graphical software to detect communities from multiplex networks, and corresponding C source codes, are available at GitHub (https://github.com/gilles-didier/MolTi).
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Affiliation(s)
- Gilles Didier
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373 , Marseille , France
| | - Christine Brun
- Aix Marseille Université, Inserm, TAGC UMR_S1090 , Marseille , France ; CNRS , Marseille , France
| | - Anaïs Baudot
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373 , Marseille , France
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