1
|
Kim N, Byun S, Um SJ. Additional Sex Combs-like Family Associated with Epigenetic Regulation. Int J Mol Sci 2024; 25:5119. [PMID: 38791157 PMCID: PMC11121404 DOI: 10.3390/ijms25105119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The additional sex combs-like (ASXL) family, a mammalian homolog of the additional sex combs (Asx) of Drosophila, has been implicated in transcriptional regulation via chromatin modifications. Abnormal expression of ASXL family genes leads to myelodysplastic syndromes and various types of leukemia. De novo mutation of these genes also causes developmental disorders. Genes in this family and their neighbor genes are evolutionary conserved in humans and mice. This review provides a comprehensive summary of epigenetic regulations associated with ASXL family genes. Their expression is commonly regulated by DNA methylation at CpG islands preceding transcription starting sites. Their proteins primarily engage in histone tail modifications through interactions with chromatin regulators (PRC2, TrxG, PR-DUB, SRC1, HP1α, and BET proteins) and with transcription factors, including nuclear hormone receptors (RAR, PPAR, ER, and LXR). Histone modifications associated with these factors include histone H3K9 acetylation and methylation, H3K4 methylation, H3K27 methylation, and H2AK119 deubiquitination. Recently, non-coding RNAs have been identified following mutations in the ASXL1 or ASXL3 gene, along with circular ASXLs and microRNAs that regulate ASXL1 expression. The diverse epigenetic regulations linked to ASXL family genes collectively contribute to tumor suppression and developmental processes. Our understanding of ASXL-regulated epigenetics may provide insights into the development of therapeutic epigenetic drugs.
Collapse
Affiliation(s)
| | | | - Soo-Jong Um
- Department of Integrative Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Gwangjin-Gu, Seoul 05006, Republic of Korea; (N.K.)
| |
Collapse
|
2
|
Lomeli C. S, Kristin B. A. Epigenetic regulation of craniofacial development and disease. Birth Defects Res 2024; 116:e2271. [PMID: 37964651 PMCID: PMC10872612 DOI: 10.1002/bdr2.2271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND The formation of the craniofacial complex relies on proper neural crest development. The gene regulatory networks (GRNs) and signaling pathways orchestrating this process have been extensively studied. These GRNs and signaling cascades are tightly regulated as alterations to any stage of neural crest development can lead to common congenital birth defects, including multiple syndromes affecting facial morphology as well as nonsyndromic facial defects, such as cleft lip with or without cleft palate. Epigenetic factors add a hierarchy to the regulation of transcriptional networks and influence the spatiotemporal activation or repression of specific gene regulatory cascades; however less is known about their exact mechanisms in controlling precise gene regulation. AIMS In this review, we discuss the role of epigenetic factors during neural crest development, specifically during craniofacial development and how compromised activities of these regulators contribute to congenital defects that affect the craniofacial complex.
Collapse
Affiliation(s)
- Shull Lomeli C.
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Artinger Kristin B.
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN, USA
| |
Collapse
|
3
|
Guerra M, Medici V, Weatheritt R, Corvino V, Palacios D, Geloso MC, Farini D, Sette C. Fetal exposure to valproic acid dysregulates the expression of autism-linked genes in the developing cerebellum. Transl Psychiatry 2023; 13:114. [PMID: 37019889 PMCID: PMC10076313 DOI: 10.1038/s41398-023-02391-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 04/07/2023] Open
Abstract
Autism spectrum disorder (ASD) includes a set of highly heritable neurodevelopmental syndromes characterized by social and communication impairment, repetitive behaviour, and intellectual disability. Although mutations in multiple genes have been associated to ASD, most patients lack detectable genetic alterations. For this reason, environmental factors are commonly thought to also contribute to ASD aetiology. Transcriptome analyses have revealed that autistic brains possess distinct gene expression signatures, whose elucidation can provide insights about the mechanisms underlying the effects of ASD-causing genetic and environmental factors. Herein, we have identified a coordinated and temporally regulated programme of gene expression in the post-natal development of cerebellum, a brain area whose defects are strongly associated with ASD. Notably, this cerebellar developmental programme is significantly enriched in ASD-linked genes. Clustering analyses highlighted six different patterns of gene expression modulated during cerebellar development, with most of them being enriched in functional processes that are frequently dysregulated in ASD. By using the valproic acid mouse model of ASD, we found that ASD-linked genes are dysregulated in the developing cerebellum of ASD-like mice, a defect that correlates with impaired social behaviour and altered cerebellar cortical morphology. Moreover, changes in transcript levels were reflected in aberrant protein expression, indicating the functional relevance of these alterations. Thus, our work uncovers a complex ASD-related transcriptional programme regulated during cerebellar development and highlight genes whose expression is dysregulated in this brain area of an ASD mouse model.
Collapse
Affiliation(s)
- Marika Guerra
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, Rome, Italy
- GSTeP-Organoids Research Core Facility, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Vanessa Medici
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, Rome, Italy
| | - Robert Weatheritt
- Garvan Institute of Medical Research, EMBL Australia, Darlinghurst, NSW, Australia
| | - Valentina Corvino
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, Rome, Italy
| | - Daniela Palacios
- Department of Life Science and Public Health, Section of Biology, Catholic University of the Sacred Hearth, Rome, Italy
| | - Maria Concetta Geloso
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, Rome, Italy
- GSTeP-Organoids Research Core Facility, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Donatella Farini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, Rome, Italy.
- GSTeP-Organoids Research Core Facility, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy.
| |
Collapse
|
4
|
Asif M, Abdullah U, Nürnberg P, Tinschert S, Hussain MS. Congenital Microcephaly: A Debate on Diagnostic Challenges and Etiological Paradigm of the Shift from Isolated/Non-Syndromic to Syndromic Microcephaly. Cells 2023; 12:cells12040642. [PMID: 36831309 PMCID: PMC9954724 DOI: 10.3390/cells12040642] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Congenital microcephaly (CM) exhibits broad clinical and genetic heterogeneity and is thus categorized into several subtypes. However, the recent bloom of disease-gene discoveries has revealed more overlaps than differences in the underlying genetic architecture for these clinical sub-categories, complicating the differential diagnosis. Moreover, the mechanism of the paradigm shift from a brain-restricted to a multi-organ phenotype is only vaguely understood. This review article highlights the critical factors considered while defining CM subtypes. It also presents possible arguments on long-standing questions of the brain-specific nature of CM caused by a dysfunction of the ubiquitously expressed proteins. We argue that brain-specific splicing events and organ-restricted protein expression may contribute in part to disparate clinical manifestations. We also highlight the role of genetic modifiers and de novo variants in the multi-organ phenotype of CM and emphasize their consideration in molecular characterization. This review thus attempts to expand our understanding of the phenotypic and etiological variability in CM and invites the development of more comprehensive guidelines.
Collapse
Affiliation(s)
- Maria Asif
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Uzma Abdullah
- University Institute of Biochemistry and Biotechnology (UIBB), PMAS-Arid Agriculture University, Rawalpindi, Rawalpindi 46300, Pakistan
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Sigrid Tinschert
- Zentrum Medizinische Genetik, Medizinische Universität, 6020 Innsbruck, Austria
| | - Muhammad Sajid Hussain
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Correspondence:
| |
Collapse
|
5
|
Schirwani S, Woods E, Koolen DA, Ockeloen CW, Lynch SA, Kavanagh K, Graham JM, Grand K, Pierson TM, Chung JM, Balasubramanian M. Familial Bainbridge-Ropers syndrome: Report of familial ASXL3 inheritance and a milder phenotype. Am J Med Genet A 2023; 191:29-36. [PMID: 36177608 PMCID: PMC10087684 DOI: 10.1002/ajmg.a.62981] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/22/2022] [Accepted: 09/08/2022] [Indexed: 12/14/2022]
Abstract
De novo truncating and splicing pathogenic variants in the Additional Sex Combs-Like 3 (ASXL3) gene are known to cause neurodevelopmental delay, intellectual disability, behavioral difficulties, hypotonia, feeding problems and characteristic facial features. We previously reported 45 patients with ASXL3-related disorder including three individuals with a familial variant. Here we report the detailed clinical and molecular characteristics of these three families with inherited ASXL3-related disorder. First, a father and son with c.2791_2792del p.Gln931fs pathogenic variant. The second, a mother, daughter and son with c.4534C > T, p.Gln1512Ter pathogenic variant. The third, a mother and her daughter with c.4441dup, p.Leu1481fs maternally inherited pathogenic variant. This report demonstrates intrafamilial phenotypic heterogeneity and confirms heritability of ASXL3-related disorder.
Collapse
Affiliation(s)
- Schaida Schirwani
- Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK.,Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Emily Woods
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Charlotte W Ockeloen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sally Ann Lynch
- Department of Clinical Genetics, Children's Health Ireland, Dublin, Ireland
| | - Karl Kavanagh
- Department of Clinical Genetics, Children's Health Ireland, Dublin, Ireland
| | - John M Graham
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Katheryn Grand
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Tyler Mark Pierson
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Cedars-Sinai Center for the Undiagnosed Patient, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jeffrey M Chung
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Meena Balasubramanian
- Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK.,Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| |
Collapse
|
6
|
Švantnerová J, Minár M, Radová S, Kolníková M, Vlkovič P, Zech M. ASXL3 De Novo Variant-Related Neurodevelopmental Disorder Presenting as Dystonic Cerebral Palsy. Neuropediatrics 2022; 53:361-365. [PMID: 35863334 DOI: 10.1055/s-0042-1750721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
ASXL3 loss-of-function variants represent a well-established cause of Bainbridge-Ropers syndrome, a syndromic neurodevelopmental disorder with intellectual and motor disabilities. Although a recent large-scale genomics-based study has suggested an association between ASXL3 variation and cerebral palsy, there have been no detailed case descriptions. We report, here, a female individual with a de novo pathogenic c.1210C > T, p.Gln404* nonsense variant in ASXL3, identified within the frame of an ongoing research project applying trio whole-exome sequencing to the diagnosis of dystonic cerebral palsy. The patient presented with a mixture of infantile-onset limb/trunk dystonic postures and secondarily evolving distal spastic contractures, in addition to more typical features of ASXL3-related diseases such as severe feeding issues, intellectual disability, speech impairment, and facial dysmorphic abnormalities. Our case study confirms a role for ASXL3 pathogenic variants in the etiology of cerebral-palsy phenotypes and indicates that dystonic features can be part of the clinical spectrum in Bainbridge-Ropers syndrome. ASXL3 should be added to target-gene lists used for molecular evaluation of cerebral palsy.
Collapse
Affiliation(s)
- Jana Švantnerová
- Second Department of Neurology, Faculty of Medicine, Comenius University, University Hospital Bratislava, Bratislava, Slovakia
| | - Michal Minár
- Second Department of Neurology, Faculty of Medicine, Comenius University, University Hospital Bratislava, Bratislava, Slovakia
| | - Silvia Radová
- Department of Pediatric Neurology, Faculty of Medicine, Comenius University, University Hospital Bratislava National Institute of Children's Diseases, Bratislava, Slovakia
| | - Miriam Kolníková
- Department of Pediatric Neurology, Faculty of Medicine, Comenius University, University Hospital Bratislava National Institute of Children's Diseases, Bratislava, Slovakia
| | - Peter Vlkovič
- Second Department of Neurology, Faculty of Medicine, Comenius University, University Hospital Bratislava, Bratislava, Slovakia
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany.,Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| |
Collapse
|
7
|
Germline Abnormalities in DNA Methylation and Histone Modification and Associated Cancer Risk. Curr Hematol Malig Rep 2022; 17:82-93. [PMID: 35653077 DOI: 10.1007/s11899-022-00665-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE OF REVIEW Somatic mutations in DNA methyltransferases and other DNA methylation associated genes have been found in a wide variety of cancers. Germline mutations in these genes have been associated with several rare hereditary disorders. Among the described germline/congenital disorders, neurological dysfunction and/or growth abnormalities appear to be a common phenotype. Here, we outline known germline abnormalities and examine the cancer risks associated with these mutations. RECENT FINDINGS The increased use and availability of sequencing techniques in the clinical setting has expanded the identification of germline abnormalities involving DNA methylation machinery. This has provided additional cases to study these rare hereditary disorders and their predisposition to cancer. Studying these syndromes may offer an opportunity to better understand the contribution of these genes in cancer development.
Collapse
|
8
|
Wang Q, Zhang J, Jiang N, Xie J, Yang J, Zhao X. De novo nonsense variant in ASXL3 in a Chinese girl causing Bainbridge-Ropers syndrome: A case report and review of literature. Mol Genet Genomic Med 2022; 10:e1924. [PMID: 35276034 PMCID: PMC9034677 DOI: 10.1002/mgg3.1924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/18/2022] [Accepted: 02/28/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Bainbridge-Ropers syndrome (BRPS, OMIM #615485) was first identified in 2013 by Bainbridge et al. and is a neurodevelopment disorder characterized by failure to thrive, facial dysmorphism and severe developmental delay. BRPS is caused by heterozygous loss-of-function (LOF) variants in the additional sex combs-like 3 (ASXL3) gene. Due to the limited specific recognizable features and overlapping symptoms with Bohring-Opitz syndrome (BOS, OMIM #612990), clinical diagnosis of BRPS is challenging. METHODS In this study, a 2-year-8-month-old Chinese girl was referred for genetic evaluation of severe developmental delay. The reduced fetal movement was found during the antenatal period and bilateral varus deformity of feet was observed at birth. Whole-exome sequencing and Sanger sequencing were used to detect and confirm the variant. RESULTS A novel nonsense variant c.1063G>T (p.E355*) in the ASXL3 gene (NM_030632.3) was identified in the proband and the clinical symptoms were compatible with BRPS. The parents were physical and genetic normal and prenatal diagnosis was requested for her pregnant mother with a negative Sanger sequencing result. CONCLUSION The study revealed a de novo LOF variant in the ASXL3 gene and expanded the mutation spectrum for this clinical condition. By performing a literature review, we summarized genetic results and the clinical phenotypes of all BPRSs reported so far. More cases study may help to elucidate the function of the ASXL3 gene may be critical to understand the genetic aetiology of this syndrome and assist in accurate genetic counselling, informed decision making and prenatal diagnosis.
Collapse
Affiliation(s)
- Qin Wang
- Affiliated Shenzhen Maternity & Child Healthcare HospitalSouthern Medical UniversityShenzhenChina
| | - Jianming Zhang
- Affiliated Shenzhen Maternity & Child Healthcare HospitalSouthern Medical UniversityShenzhenChina
| | - Nan Jiang
- Affiliated Shenzhen Maternity & Child Healthcare HospitalSouthern Medical UniversityShenzhenChina
| | - Jiansheng Xie
- Affiliated Shenzhen Maternity & Child Healthcare HospitalSouthern Medical UniversityShenzhenChina
- The University of Hong Kong‐Shenzhen Hospital ShenzhenShenzhenChina
| | - Jingxin Yang
- Affiliated Shenzhen Maternity & Child Healthcare HospitalSouthern Medical UniversityShenzhenChina
| | - Xiaoshan Zhao
- Affiliated Shenzhen Maternity & Child Healthcare HospitalSouthern Medical UniversityShenzhenChina
| |
Collapse
|
9
|
Schirwani S, Albaba S, Carere DA, Guillen Sacoto MJ, Milan Zamora F, Si Y, Rabin R, Pappas J, Renaud DL, Hauser N, Reid E, Blanchet P, Foulds N, Dixit A, Fisher R, Armstrong R, Isidor B, Cogne B, Schrier Vergano S, Demirdas S, Dykzeul N, Cohen JS, Grand K, Morel D, Slavotinek A, Albassam HF, Naik S, Dean J, Ragge N, Costa C, Tedesco MG, Harrison RE, Bouman A, Palen E, Challman TD, Willemsen MH, Vogt J, Cunniff C, Bergstrom K, Walia JS, Bruel AL, Kini U, Alkuraya FS, Slegesky V, Meeks N, Girotto P, Johnson D, Newbury-Ecob R, Ockeloen CW, Prontera P, Lynch SA, Li D, Graham JM, Pierson TM, Balasubramanian M. Expanding the phenotype of ASXL3-related syndrome: A comprehensive description of 45 unpublished individuals with inherited and de novo pathogenic variants in ASXL3. Am J Med Genet A 2021; 185:3446-3458. [PMID: 34436830 DOI: 10.1002/ajmg.a.62465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/10/2021] [Accepted: 07/08/2021] [Indexed: 12/15/2022]
Abstract
The study aimed at widening the clinical and genetic spectrum of ASXL3-related syndrome, a neurodevelopmental disorder, caused by truncating variants in the ASXL3 gene. In this international collaborative study, we have undertaken a detailed clinical and molecular analysis of 45 previously unpublished individuals with ASXL3-related syndrome, as well as a review of all previously published individuals. We have reviewed the rather limited functional characterization of pathogenic variants in ASXL3 and discuss current understanding of the consequences of the different ASXL3 variants. In this comprehensive analysis of ASXL3-related syndrome, we define its natural history and clinical evolution occurring with age. We report familial ASXL3 pathogenic variants, characterize the phenotype in mildly affected individuals and discuss nonpenetrance. We also discuss the role of missense variants in ASXL3. We delineate a variable but consistent phenotype. The most characteristic features are neurodevelopmental delay with consistently limited speech, significant neuro-behavioral issues, hypotonia, and feeding difficulties. Distinctive features include downslanting palpebral fissures, hypertelorism, tubular nose with a prominent nasal bridge, and low-hanging columella. The presented data will inform clinical management of individuals with ASXL3-related syndrome and improve interpretation of new ASXL3 sequence variants.
Collapse
Affiliation(s)
- Schaida Schirwani
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
- Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK
| | - Shadi Albaba
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | | | | | | | - Yue Si
- GeneDx, Inc, Gaithersburg, Maryland, USA
| | - Rachel Rabin
- Department of Pediatrics, New York University School of Medicine, New York, New York, USA
| | - John Pappas
- Department of Pediatrics, New York University School of Medicine, New York, New York, USA
| | - Deborah L Renaud
- Division of Child and Adolescent Neurology, Departments of Neurology and Pediatrics, Mayo Clinic, Rochester, Minnesota, USA
| | - Natalie Hauser
- Department of Pediatrics, Division of Medical Genomics, Inova Health System, Falls Church, Virginia, USA
| | - Evan Reid
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Patricia Blanchet
- Département de Génétique Médicale, CHU de Montpellier, Montpellier, France
| | - Nichola Foulds
- Wessex Clinical Genetics Services, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Abhijit Dixit
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Richard Fisher
- Teesside Genetics Unit, The James Cook University Hospital, Middlesbrough, UK
| | - Ruth Armstrong
- Departments of Medical Genetics and Paediatric Neurology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Benjamin Cogne
- Service de génétique médicale, CHU Nantes, Nantes, France
| | - Samantha Schrier Vergano
- Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Serwet Demirdas
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Natalie Dykzeul
- Lucile Packard Children's Hospital, Stanford Children's Health, Palo Alto, California, USA
| | - Julie S Cohen
- Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katheryn Grand
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dayna Morel
- University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Anne Slavotinek
- Department of Pediatrics, Division of Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Hessa F Albassam
- Department of Pediatrics, Care National Hospital, Riyadh, Saudi Arabia
| | - Swati Naik
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - John Dean
- Clinical Genetics Service, NHS Grampian, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Nicola Ragge
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Cinzia Costa
- Neurology Clinic, Department of Medicine, Santa Maria della Misericordia Hospital, University of Perugia, Perugia, Italy
| | - Maria Giovanna Tedesco
- Medical Genetics Unit, Santa Maria della Misericordia Hospital, University of Perugia, Perugia, Italy
- Genetics Unit, "Mauro Baschirotto" Institute for Rare Diseases (B.I.R.D.), Costozza di Longare, Vicenza, Italy
| | - Rachel E Harrison
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Emily Palen
- Autism & Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Thomas D Challman
- Autism & Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Christopher Cunniff
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medical College, New York, New York, USA
| | - Katherine Bergstrom
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medical College, New York, New York, USA
| | - Jagdeep S Walia
- Divsion of Medical Genetics, Departments of Pediatrics, Queen's University, Kingston, Ontario, Canada
| | - Ange-Line Bruel
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD Génétique des Anomalies du Développement, FHU-TRANSLAD, Dijon, France
| | - Usha Kini
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Valerie Slegesky
- University of Colorado & Children's Hospital Colorado, Denver, Colorado, USA
| | - Naomi Meeks
- University of Colorado & Children's Hospital Colorado, Denver, Colorado, USA
| | - Paula Girotto
- Division of Child Neurology, Department of Pediatrics, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
| | - Diana Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
- EDS National Diagnostic Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Ruth Newbury-Ecob
- Bristol Regional Genetics Service, St Michael's Hospital, Bristol, UK
| | - Charlotte W Ockeloen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paolo Prontera
- Medical Genetics Unit, Santa Maria della Misericordia Hospital, University of Perugia, Perugia, Italy
| | - Sally Ann Lynch
- Department of Clinical Genetics, Temple Street Children's Hospital, Dublin, Ireland
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - John M Graham
- Cedars-Sinai Medical Center, Harbor-UCLA Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Tyler Mark Pierson
- Departments of Pediatrics, Neurology, Cedars-Sinai Center for the Undiagnosed Patient, and Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles CA, USA
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
- Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK
| |
Collapse
|
10
|
Cuddapah VA, Dubbs HA, Adang L, Kugler SL, McCormick EM, Zolkipli-Cunningham Z, Ortiz-González XR, McCormack S, Zackai E, Licht DJ, Falk MJ, Marsh ED. Understanding the phenotypic spectrum of ASXL-related disease: Ten cases and a review of the literature. Am J Med Genet A 2021; 185:1700-1711. [PMID: 33751773 DOI: 10.1002/ajmg.a.62156] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 02/10/2021] [Accepted: 02/22/2021] [Indexed: 01/11/2023]
Abstract
Over the past decade, pathogenic variants in all members of the ASXL family of genes, ASXL1, ASXL2, and ASXL3, have been found to lead to clinically distinct but overlapping syndromes. Bohring-Opitz syndrome (BOPS) was first described as a clinical syndrome and later found to be associated with pathogenic variants in ASXL1. This syndrome is characterized by developmental delay, microcephaly, characteristic facies, hypotonia, and feeding difficulties. Subsequently, pathogenic variants in ASXL2 were found to lead to Shashi-Pena syndrome (SHAPNS) and in ASXL3 to lead to Bainbridge-Ropers syndrome (BRPS). While SHAPNS and BRPS share many core features with BOPS, there also seem to be emerging clear differences. Here, we present five cases of BOPS, one case of SHAPNS, and four cases of BRPS. By adding our cohort to the limited number of previously published patients, we review the overlapping features of ASXL-related diseases that bind them together, while focusing on the characteristics that make each neurodevelopmental syndrome unique. This will assist in diagnosis of these overlapping conditions and allow clinicians to more comprehensively counsel affected families.
Collapse
Affiliation(s)
- Vishnu Anand Cuddapah
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Holly A Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Departments of Neurology and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,The Epilepsy Neurogenetics Initiative, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Laura Adang
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Steven L Kugler
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Zarazuela Zolkipli-Cunningham
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Departments of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xilma R Ortiz-González
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Departments of Neurology and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,The Epilepsy Neurogenetics Initiative, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Shana McCormack
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elaine Zackai
- Departments of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Daniel J Licht
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marni J Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Departments of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eric D Marsh
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Departments of Neurology and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,The Epilepsy Neurogenetics Initiative, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| |
Collapse
|
11
|
Yu KPT, Luk HM, Fung JLF, Chung BHY, Lo IFM. Further expanding the clinical phenotype in Bainbridge-Ropers syndrome and dissecting genotype-phenotype correlation in the ASXL3 mutational cluster regions. Eur J Med Genet 2020; 64:104107. [PMID: 33242595 DOI: 10.1016/j.ejmg.2020.104107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/22/2020] [Accepted: 11/15/2020] [Indexed: 11/30/2022]
Abstract
Bainbridge-Ropers syndrome (BRPS) [OMIM#615485] is a neurodevelopmental disorder, characterized by delayed psychomotor development with generalized hypotonia, intellectual disability with poor or absent speech, feeding difficulties, growth failure, specific craniofacial and minor skeletal features. It was firstly reported in 2013 by Bainbridge et al., who observed a group of individuals sharing overlapping features with Bohring-Opitz syndrome which were caused by pathogenic variant in ASXL1, who indeed carried truncating mutations in ASXL3. To date, 33 cases were described in the literature. BRPS is caused by loss-of-function mutations in ASXL3 which are mostly located in two mutational cluster regions (MCR). The exact molecular mechanism of these mutations resulting in the disease phenotype is still uncertain due to the observation of LOF mutations in healthy population. Here, we report four individuals with BRPS carrying de novo LOF mutations in ASXL3, comparing and summarizing the clinical phenotype of all BRPS reported so far. Furthermore, we try to dissect the genotype-phenotype correlation among the two well reported MCRs in all BRPS from the literature.
Collapse
Affiliation(s)
- Kris Pui-Tak Yu
- Clinical Genetic Service, Department of Health, University of Hong Kong, HKSAR, Hong Kong.
| | - Ho-Ming Luk
- Clinical Genetic Service, Department of Health, University of Hong Kong, HKSAR, Hong Kong
| | - Jasmine L F Fung
- Department of Paediatrics and Adolescent Medicine, University of Hong Kong, HKSAR, Hong Kong
| | - Brian Hon-Yin Chung
- Department of Paediatrics and Adolescent Medicine, University of Hong Kong, HKSAR, Hong Kong
| | - Ivan Fai-Man Lo
- Clinical Genetic Service, Department of Health, University of Hong Kong, HKSAR, Hong Kong
| |
Collapse
|
12
|
Schirwani S, Hauser N, Platt A, Punj S, Prescott K, Canham N, Study DDD, Mansour S, Balasubramanian M. Mosaicism in ASXL3-related syndrome: Description of five patients from three families. Eur J Med Genet 2020; 63:103925. [PMID: 32240826 DOI: 10.1016/j.ejmg.2020.103925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/20/2020] [Accepted: 03/29/2020] [Indexed: 01/30/2023]
Abstract
De novo pathogenic variants in the additional sex combs-like 3 (ASXL3) gene cause a rare multi-systemic neurodevelopmental disorder. There is growing evidence that germline and somatic mosaicism are more common and play a greater role in genetic disorders than previously acknowledged. There is one previous report of ASXL3-related syndrome caused by de novo pathogenic variants in two siblings suggesting gonadal mosaicism. In this report, we present five patients with ASXL3-related syndrome, describing two families comprising two non-twin siblings harbouring apparent de novo pathogenic variants in ASXL3. Parents were clinically unaffected and there was no evidence of mosaicism from genomic DNA on exome-trio data, suggesting germline mosaicism in one of the parents. We also describe clinical details of a patient with typical features of ASXL3-related syndrome and mosaic de novo pathogenic variant in ASXL3 in 30-35% of both blood and saliva sample on trio-exome sequencing. We expand the known genetic basis of ASXL3-related syndromes and discuss mosaicism as a disease mechanism in five patients from three unrelated families. The findings of this report highlight the importance of taking gonadal mosaicism into consideration when counselling families regarding recurrence risk. We also discuss postzygotic mosaicism as a cause of fully penetrant ASXL3-related syndrome.
Collapse
Affiliation(s)
- Schaida Schirwani
- Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, UK; Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, UK.
| | - Natalie Hauser
- Inova Health System, (or Inova Fairfax Hospital) Department of Paediatrics, Division of Medical Genomics, Falls Church, VA, USA
| | - Anna Platt
- Inova Health System, (or Inova Fairfax Hospital) Department of Paediatrics, Division of Medical Genomics, Falls Church, VA, USA
| | | | - Katrina Prescott
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Natalie Canham
- Cheshire & Merseyside Regional Genetics Service, Liverpool Women's Hospital, Liverpool, UK
| | - D D D Study
- DDD Study, Welcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | - Meena Balasubramanian
- Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, UK; Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, UK
| |
Collapse
|
13
|
Lichtig H, Artamonov A, Polevoy H, Reid CD, Bielas SL, Frank D. Modeling Bainbridge-Ropers Syndrome in Xenopus laevis Embryos. Front Physiol 2020; 11:75. [PMID: 32132929 PMCID: PMC7040374 DOI: 10.3389/fphys.2020.00075] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 01/23/2020] [Indexed: 12/14/2022] Open
Abstract
The Additional sex combs-like (ASXL1-3) genes are linked to human neurodevelopmental disorders. The de novo truncating variants in ASXL1-3 proteins serve as the genetic basis for severe neurodevelopmental diseases such as Bohring-Opitz, Shashi-Pena, and Bainbridge-Ropers syndromes, respectively. The phenotypes of these syndromes are similar but not identical, and include dramatic craniofacial defects, microcephaly, developmental delay, and severe intellectual disability, with a loss of speech and language. Bainbridge-Ropers syndrome resulting from ASXL3 gene mutations also includes features of autism spectrum disorder. Human genomic studies also identified missense ASXL3 variants associated with autism spectrum disorder, but lacking more severe Bainbridge-Ropers syndromic features. While these findings strongly implicate ASXL3 in mammalian brain development, its functions are not clearly understood. ASXL3 protein is a component of the polycomb deubiquitinase complex that removes mono-ubiquitin from Histone H2A. Dynamic chromatin modifications play important roles in the specification of cell fates during early neural patterning and development. In this study, we utilize the frog, Xenopus laevis as a simpler and more accessible vertebrate neurodevelopmental model system to understand the embryological cause of Bainbridge-Ropers syndrome. We have found that ASXL3 protein knockdown during early embryo development highly perturbs neural cell fate specification, potentially resembling the Bainbridge-Ropers syndrome phenotype in humans. Thus, the frog embryo is a powerful tool for understanding the etiology of Bainbridge-Ropers syndrome in humans.
Collapse
Affiliation(s)
- Hava Lichtig
- Department of Biochemistry, Faculty of Medicine, The Rappaport Family Institute for Research in the Medical Sciences, Technion - Israel Institute of Technology, Haifa, Israel
| | - Artyom Artamonov
- Department of Biochemistry, Faculty of Medicine, The Rappaport Family Institute for Research in the Medical Sciences, Technion - Israel Institute of Technology, Haifa, Israel
| | - Hanna Polevoy
- Department of Biochemistry, Faculty of Medicine, The Rappaport Family Institute for Research in the Medical Sciences, Technion - Israel Institute of Technology, Haifa, Israel
| | - Christine D Reid
- Department of Genetics, Stanford University, Stanford, CA, United States
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Dale Frank
- Department of Biochemistry, Faculty of Medicine, The Rappaport Family Institute for Research in the Medical Sciences, Technion - Israel Institute of Technology, Haifa, Israel
| |
Collapse
|
14
|
Powis Z, Farwell Hagman KD, Blanco K, Au M, Graham JM, Singh K, Gallant N, Randolph LM, Towne M, Hunter J, Shinde DN, Palmaer E, Schoenfeld B, Tang S. When moments matter: Finding answers with rapid exome sequencing. Mol Genet Genomic Med 2019; 8:e1027. [PMID: 31872981 PMCID: PMC7005623 DOI: 10.1002/mgg3.1027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/03/2019] [Accepted: 09/18/2019] [Indexed: 01/17/2023] Open
Abstract
Background When time is of the essence in critical care cases, a fast molecular diagnosis is often necessary to help health care providers quickly determine best next steps for treatments, prognosis, and counseling of their patients. In this paper, we present the diagnostic rates and improved quality of life for patients undergoing clinical rapid exome sequencing. Methods The clinical histories and results of 41 patients undergoing rapid exome sequencing were retrospectively reviewed. Results Clinical rapid exome sequencing identified a definitive diagnosis in 13/41 (31.7%) and other relevant findings in 17 of the patients (41.5%). The average time to verbal report was 7 days; to written report was 11 days. Conclusions Our observations demonstrate the utility and effectiveness of rapid family‐based diagnostic exome sequencing in improving patients care.
Collapse
Affiliation(s)
- Zöe Powis
- Ambry Genetics, Aliso Viejo, CA, USA
| | | | | | - Margaret Au
- Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - John M Graham
- Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Kathryn Singh
- Memorial Care Health System Genetics Clinic, Long Beach, CA, USA
| | - Natalie Gallant
- Memorial Care Health System Genetics Clinic, Long Beach, CA, USA
| | - Linda M Randolph
- Division of Medical Genetics, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | | | | | | | | | | | - Sha Tang
- Ambry Genetics, Aliso Viejo, CA, USA
| |
Collapse
|
15
|
Prenatal Neuropathologies in Autism Spectrum Disorder and Intellectual Disability: The Gestation of a Comprehensive Zebrafish Model. J Dev Biol 2018; 6:jdb6040029. [PMID: 30513623 PMCID: PMC6316217 DOI: 10.3390/jdb6040029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 12/27/2022] Open
Abstract
Autism spectrum disorder (ASD) and intellectual disability (ID) are neurodevelopmental disorders with overlapping diagnostic behaviors and risk factors. These include embryonic exposure to teratogens and mutations in genes that have important functions prenatally. Animal models, including rodents and zebrafish, have been essential in delineating mechanisms of neuropathology and identifying developmental critical periods, when those mechanisms are most sensitive to disruption. This review focuses on how the developmentally accessible zebrafish is contributing to our understanding of prenatal pathologies that set the stage for later ASD-ID behavioral deficits. We discuss the known factors that contribute prenatally to ASD-ID and the recent use of zebrafish to model deficits in brain morphogenesis and circuit development. We conclude by suggesting that a future challenge in zebrafish ASD-ID modeling will be to bridge prenatal anatomical and physiological pathologies to behavioral deficits later in life.
Collapse
|
16
|
Global developmental delay and postnatal microcephaly: Bainbridge-Ropers syndrome with a new mutation in ASXL3. NEUROLOGÍA (ENGLISH EDITION) 2018. [DOI: 10.1016/j.nrleng.2017.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
17
|
Contreras-Capetillo S, Vilchis-Zapata Z, Ribbón-Conde J, Pinto-Escalante D. Retraso global del desarrollo y microcefalia posnatal: síndrome de Bainbridge-Ropers con una nueva variante de novo en ASXL3. Neurologia 2018; 33:484-486. [DOI: 10.1016/j.nrl.2017.01.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/12/2016] [Accepted: 01/31/2017] [Indexed: 10/19/2022] Open
|
18
|
Abstract
Craniosynostosis refers to a condition during early development in which one or more of the fibrous sutures of the skull prematurely fuse by turning into bone, which produces recognizable patterns of cranial shape malformations depending on which suture(s) are affected. In addition to cases with isolated cranial dysmorphologies, craniosynostosis appears in syndromes that include skeletal features of the eyes, nose, palate, hands, and feet as well as impairment of vision, hearing, and intellectual development. Approximately 85% of the cases are nonsyndromic sporadic and emerge after de novo structural genome rearrangements or single nucleotide variation, while the remainders consist of syndromic cases following mendelian inheritance. By karyotyping, genome wide linkage, and CNV analyses as well as by whole exome and whole genome sequencing, numerous candidate genes for craniosynostosis belonging to the FGF, Wnt, BMP, Ras/ERK, ephrin, hedgehog, STAT, and retinoic acid signaling pathways have been identified. Many of the craniosynostosis-related candidate genes form a functional network based upon protein-protein or protein-DNA interactions. Depending on which node of this craniosynostosis-related network is affected by a gene mutation or a change in gene expression pattern, a distinct craniosynostosis syndrome or set of phenotypes ensues. Structural variations may alter the dosage of one or several genes or disrupt the genomic architecture of genes and their regulatory elements within topologically associated chromatin domains. These may exert dominant effects by either haploinsufficiency, dominant negative partial loss of function, gain of function, epistatic interaction, or alteration of levels and patterns of gene expression during development. Molecular mechanisms of dominant modes of action of these mutations may include loss of one or several binding sites for cognate protein partners or transcription factor binding sequences. Such losses affect interactions within functional networks governing development and consequently result in phenotypes such as craniosynostosis. Many of the novel variants identified by genome wide CNV analyses, whole exome and whole genome sequencing are incorporated in recently developed diagnostic algorithms for craniosynostosis.
Collapse
Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| |
Collapse
|
19
|
Koboldt DC, Mihalic Mosher T, Kelly BJ, Sites E, Bartholomew D, Hickey SE, McBride K, Wilson RK, White P. A de novo nonsense mutation in ASXL3 shared by siblings with Bainbridge-Ropers syndrome. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002410. [PMID: 29305346 PMCID: PMC5983172 DOI: 10.1101/mcs.a002410] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/26/2017] [Indexed: 12/31/2022] Open
Abstract
Two sisters (ages 16 yr and 15 yr) have been followed by our clinical genetics team for several years. Both girls have severe intellectual disability, hypotonia, seizures, and distinctive craniofacial features. The parents are healthy and have no other children. Oligo array, fragile X testing, and numerous single-gene tests were negative. All four family members underwent research exome sequencing, which revealed a heterozygous nonsense mutation in ASXL3 (p.R1036X) that segregated with disease. Exome data and independent Sanger sequencing confirmed that the variant is de novo, suggesting possible germline mosaicism in one parent. The p.R1036X variant has never been observed in healthy human populations and has been previously reported as a pathogenic mutation. Truncating de novo mutations in ASXL3 cause Bainbridge–Ropers syndrome (BRPS), a developmental disorder with similarities to Bohring–Opitz syndrome. Fewer than 30 BRPS patients have been described in the literature; to our knowledge, this is the first report of the disorder in two related individuals. Our findings lend further support to intellectual disability, absent speech, autistic traits, hypotonia, and distinctive facial appearance as common emerging features of Bainbridge–Ropers syndrome.
Collapse
Affiliation(s)
- Daniel C Koboldt
- Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43205, USA
| | - Theresa Mihalic Mosher
- Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Benjamin J Kelly
- Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Emily Sites
- Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Dennis Bartholomew
- Department of Pediatrics, The Ohio State University, Columbus, Ohio 43205, USA.,Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Scott E Hickey
- Department of Pediatrics, The Ohio State University, Columbus, Ohio 43205, USA.,Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Kim McBride
- Department of Pediatrics, The Ohio State University, Columbus, Ohio 43205, USA.,Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Center for Cardiovascular and Pulmonary Research, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Richard K Wilson
- Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43205, USA
| | - Peter White
- Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43205, USA
| |
Collapse
|
20
|
Childhood-onset generalized epilepsy in Bainbridge-Ropers syndrome. Epilepsy Res 2018; 140:166-170. [PMID: 29367179 DOI: 10.1016/j.eplepsyres.2018.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 01/30/2023]
Abstract
Bainbridge-Ropers syndrome is a genetic syndrome caused by heterozygous loss-of-function pathogenic variants in ASXL3, which encodes a protein involved in transcriptional regulation. Affected individuals have multiple abnormalities including developmental impairment, hypotonia and characteristic facial features. Seizures are reported in approximately a third of cases; however, the epileptology has not been thoroughly studied. We identified three patients with pathogenic ASXL3 variants and seizures at Austin Health and in the DECIPHER database. These three patients had novel de novo ASXL3 pathogenic variants, two with truncation variants and one with a splice site variant. All three had childhood-onset generalized epilepsy with generalized tonic-clonic seizures, with one also having atypical absence seizures. We also reviewed available clinical data on five published patients with Bainbridge-Ropers syndrome and seizures. Of the five previously published patients, three also had generalized tonic-clonic seizures, one of whom also had possible absence seizures; a fourth patient had absence seizures and possible focal seizures. EEG typically showed features consistent with generalized epilepsy including generalized spike-wave, photoparoxysmal response, and occipital intermittent rhythmic epileptiform activity. Bainbridge-Ropers syndrome is associated with childhood-onset generalized epilepsy with generalized tonic-clonic seizures and/or atypical absence seizures.
Collapse
|
21
|
Bacrot S, Mechler C, Talhi N, Martin-Coignard D, Roth P, Michot C, Ichkou A, Alibeu O, Nitschke P, Thomas S, Vekemans M, Razavi F, Boutaud L, Attie-Bitach T. Whole exome sequencing diagnoses the first fetal case of Bainbridge-Ropers syndrome presenting as pontocerebellar hypoplasia type 1. Birth Defects Res 2018; 110:538-542. [DOI: 10.1002/bdr2.1191] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 11/20/2017] [Accepted: 12/01/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Séverine Bacrot
- Unité d'Embryofœtopathologie, Service d'Histologie Embryologie Cytogénétique, Hôpital Necker-Enfants Malades; Assistance Publique Hôpitaux de Paris (APHP); Paris France
| | - Charlotte Mechler
- Unité d'Embryofœtopathologie, Service d'Histologie Embryologie Cytogénétique, Hôpital Necker-Enfants Malades; Assistance Publique Hôpitaux de Paris (APHP); Paris France
| | - Naima Talhi
- Unité d'Embryofœtopathologie, Service d'Histologie Embryologie Cytogénétique, Hôpital Necker-Enfants Malades; Assistance Publique Hôpitaux de Paris (APHP); Paris France
| | | | - Philippe Roth
- Service de Gynécologie-Obstétrique, Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Caroline Michot
- Institut Imagine; INSERM U1163, Université Paris Descartes, Sorbonne Paris Cite; Paris France
- Service de Génétique Médicale; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Amale Ichkou
- Unité d'Embryofœtopathologie, Service d'Histologie Embryologie Cytogénétique, Hôpital Necker-Enfants Malades; Assistance Publique Hôpitaux de Paris (APHP); Paris France
| | | | | | - Sophie Thomas
- Institut Imagine; INSERM U1163, Université Paris Descartes, Sorbonne Paris Cite; Paris France
| | - Michel Vekemans
- Unité d'Embryofœtopathologie, Service d'Histologie Embryologie Cytogénétique, Hôpital Necker-Enfants Malades; Assistance Publique Hôpitaux de Paris (APHP); Paris France
- Institut Imagine; INSERM U1163, Université Paris Descartes, Sorbonne Paris Cite; Paris France
| | - Férechté Razavi
- Unité d'Embryofœtopathologie, Service d'Histologie Embryologie Cytogénétique, Hôpital Necker-Enfants Malades; Assistance Publique Hôpitaux de Paris (APHP); Paris France
| | - Lucile Boutaud
- Unité d'Embryofœtopathologie, Service d'Histologie Embryologie Cytogénétique, Hôpital Necker-Enfants Malades; Assistance Publique Hôpitaux de Paris (APHP); Paris France
- Institut Imagine; INSERM U1163, Université Paris Descartes, Sorbonne Paris Cite; Paris France
| | - Tania Attie-Bitach
- Unité d'Embryofœtopathologie, Service d'Histologie Embryologie Cytogénétique, Hôpital Necker-Enfants Malades; Assistance Publique Hôpitaux de Paris (APHP); Paris France
- Institut Imagine; INSERM U1163, Université Paris Descartes, Sorbonne Paris Cite; Paris France
| |
Collapse
|
22
|
Verhoeven W, Egger J, Räkers E, van Erkelens A, Pfundt R, Willemsen MH. Phenotypic characterization of an older adult male with late-onset epilepsy and a novel mutation in ASXL3 shows overlap with the associated Bainbridge-Ropers syndrome. Neuropsychiatr Dis Treat 2018; 14:867-870. [PMID: 29628764 PMCID: PMC5877499 DOI: 10.2147/ndt.s153511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The additional sex combs like 3 gene is considered to be causative for the rare Bainbridge-Ropers syndrome (BRPS), which is characterized by severe intellectual disability, neonatal hypotonia, nearly absent development of speech and language as well as several facial dysmorphisms. Apart from disruptive autistiform behaviors, sleep disturbances and epileptic phenomena may be present. Here, a 47-year-old severely intellectually disabled male is described in whom exome sequencing disclosed a novel heterozygous frameshift mutation in the ASXL3 gene leading to a premature stopcodon in the last part of the last exon. Mutations in this very end 3' of the gene have not been reported before in BRPS. The phenotypical presentation of the patient including partially therapy-resistant epilepsy starting in later adulthood shows overlap with BRPS, and it was therefore concluded that the phenotype is likely explained by the identified mutation in ASXL3.
Collapse
Affiliation(s)
- Willem Verhoeven
- Vincent van Gogh Institute for Psychiatry, Centre of Excellence for Neuropsychiatry, Venray, the Netherlands.,Department of Psychiatry, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Jos Egger
- Vincent van Gogh Institute for Psychiatry, Centre of Excellence for Neuropsychiatry, Venray, the Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Emmy Räkers
- ASVZ, Centre for People with Intellectual Disabilities, Sliedrecht, the Netherlands
| | - Arjen van Erkelens
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| |
Collapse
|
23
|
Chinen Y, Nakamura S, Ganaha A, Hayashi S, Inazawa J, Yanagi K, Nakanishi K, Kaname T, Naritomi K. Mild prominence of the Sylvian fissure in a Bainbridge-Ropers syndrome patient with a novel frameshift variant in ASXL3. Clin Case Rep 2017; 6:330-336. [PMID: 29445472 PMCID: PMC5799615 DOI: 10.1002/ccr3.1361] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/27/2017] [Accepted: 12/10/2017] [Indexed: 12/28/2022] Open
Abstract
A Japanese boy aged 7 years with Bainbridge‐Ropers syndrome (BRPS) had a prominent domed forehead without metric ridge, mild prominence of the Sylvian fissure with bitemporal hollowing, and a heterozygous de novo novel variant “p.P1010Lfs*14” in ASXL3 gene in addition to typical findings of BRPS.
Collapse
Affiliation(s)
- Yasutsugu Chinen
- Department of Pediatrics Faculty of Medicine University of the Ryukyus Nishihara Japan
| | - Sadao Nakamura
- Department of Pediatrics Faculty of Medicine University of the Ryukyus Nishihara Japan
| | - Akira Ganaha
- Department of Otorhinolaryngology, Head and Neck Surgery Faculty of Medicine University of the Ryukyus Nishihara Japan
| | - Shin Hayashi
- Department of Molecular Cytogenetics Medical Research Institute Tokyo Medical and Dental University Tokyo Japan.,Hard Tissue Genome Research Center Tokyo Medical and Dental University Tokyo Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics Medical Research Institute Tokyo Medical and Dental University Tokyo Japan.,Hard Tissue Genome Research Center Tokyo Medical and Dental University Tokyo Japan
| | - Kumiko Yanagi
- Department of Genome Medicine National Center for Child Health and Development Tokyo Japan
| | - Koichi Nakanishi
- Department of Pediatrics Faculty of Medicine University of the Ryukyus Nishihara Japan
| | - Tadashi Kaname
- Department of Genome Medicine National Center for Child Health and Development Tokyo Japan
| | - Kenji Naritomi
- Okinawa Nanbu Habilitation and Medical Center Naha Japan
| |
Collapse
|
24
|
Jin ZB, Li Z, Liu Z, Jiang Y, Cai XB, Wu J. Identification of de novo germline mutations and causal genes for sporadic diseases using trio-based whole-exome/genome sequencing. Biol Rev Camb Philos Soc 2017; 93:1014-1031. [PMID: 29154454 DOI: 10.1111/brv.12383] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 09/28/2017] [Accepted: 10/10/2017] [Indexed: 12/14/2022]
Abstract
Whole-genome or whole-exome sequencing (WGS/WES) of the affected proband together with normal parents (trio) is commonly adopted to identify de novo germline mutations (DNMs) underlying sporadic cases of various genetic disorders. However, our current knowledge of the occurrence and functional effects of DNMs remains limited and accurately identifying the disease-causing DNM from a group of irrelevant DNMs is complicated. Herein, we provide a general-purpose discussion of important issues related to pathogenic gene identification based on trio-based WGS/WES data. Specifically, the relevance of DNMs to human sporadic diseases, current knowledge of DNM biogenesis mechanisms, and common strategies or software tools used for DNM detection are reviewed, followed by a discussion of pathogenic gene prioritization. In addition, several key factors that may affect DNM identification accuracy and causal gene prioritization are reviewed. Based on recent major advances, this review both sheds light on how trio-based WGS/WES technologies can play a significant role in the identification of DNMs and causal genes for sporadic diseases, and also discusses existing challenges.
Collapse
Affiliation(s)
- Zi-Bing Jin
- Division of Ophthalmic Genetics, The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China.,State Key Laboratory of Ophthalmology Optometry and Vision Science, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Xue-Bi Cai
- Division of Ophthalmic Genetics, The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China.,State Key Laboratory of Ophthalmology Optometry and Vision Science, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| |
Collapse
|
25
|
Dad R, Walker S, Scherer SW, Hassan MJ, Kang SY, Minassian BA. Hyperventilation-athetosis in ASXL3 deficiency (Bainbridge-Ropers) syndrome. NEUROLOGY-GENETICS 2017; 3:e189. [PMID: 28955728 PMCID: PMC5610043 DOI: 10.1212/nxg.0000000000000189] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/25/2017] [Indexed: 11/18/2022]
Affiliation(s)
- Rubina Dad
- Atta-ur Rahman School of Applied Biosciences (R.D., M.J.H.), National University of Sciences and Technology (NUST), Islamabad, Pakistan; Program in Genetics and Genome Biology (R.D.) and The Centre for Applied Genomics, Genetics and Genome Biology (S.W., S.W.S.), The Hospital for Sick Children, Department of Molecular Genetics (S.W.S.), and McLaughlin Centre (S.W.S.), University of Toronto, Ontario, Canada; Department of Neurolgy (S.Y.K.), Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, Gyeonggi-do, Republic of Korea; Program in Genetics and Genome Biology (B.A.M.), Division of Neurology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Ontario, Canada; and Departments of Pediatrics, Neurology, and Neurotherapeutics (B.A.M.), University of Texas Southwestern, Dallas
| | - Susan Walker
- Atta-ur Rahman School of Applied Biosciences (R.D., M.J.H.), National University of Sciences and Technology (NUST), Islamabad, Pakistan; Program in Genetics and Genome Biology (R.D.) and The Centre for Applied Genomics, Genetics and Genome Biology (S.W., S.W.S.), The Hospital for Sick Children, Department of Molecular Genetics (S.W.S.), and McLaughlin Centre (S.W.S.), University of Toronto, Ontario, Canada; Department of Neurolgy (S.Y.K.), Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, Gyeonggi-do, Republic of Korea; Program in Genetics and Genome Biology (B.A.M.), Division of Neurology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Ontario, Canada; and Departments of Pediatrics, Neurology, and Neurotherapeutics (B.A.M.), University of Texas Southwestern, Dallas
| | - Stephen W Scherer
- Atta-ur Rahman School of Applied Biosciences (R.D., M.J.H.), National University of Sciences and Technology (NUST), Islamabad, Pakistan; Program in Genetics and Genome Biology (R.D.) and The Centre for Applied Genomics, Genetics and Genome Biology (S.W., S.W.S.), The Hospital for Sick Children, Department of Molecular Genetics (S.W.S.), and McLaughlin Centre (S.W.S.), University of Toronto, Ontario, Canada; Department of Neurolgy (S.Y.K.), Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, Gyeonggi-do, Republic of Korea; Program in Genetics and Genome Biology (B.A.M.), Division of Neurology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Ontario, Canada; and Departments of Pediatrics, Neurology, and Neurotherapeutics (B.A.M.), University of Texas Southwestern, Dallas
| | - Muhammad Jawad Hassan
- Atta-ur Rahman School of Applied Biosciences (R.D., M.J.H.), National University of Sciences and Technology (NUST), Islamabad, Pakistan; Program in Genetics and Genome Biology (R.D.) and The Centre for Applied Genomics, Genetics and Genome Biology (S.W., S.W.S.), The Hospital for Sick Children, Department of Molecular Genetics (S.W.S.), and McLaughlin Centre (S.W.S.), University of Toronto, Ontario, Canada; Department of Neurolgy (S.Y.K.), Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, Gyeonggi-do, Republic of Korea; Program in Genetics and Genome Biology (B.A.M.), Division of Neurology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Ontario, Canada; and Departments of Pediatrics, Neurology, and Neurotherapeutics (B.A.M.), University of Texas Southwestern, Dallas
| | - Suk Yun Kang
- Atta-ur Rahman School of Applied Biosciences (R.D., M.J.H.), National University of Sciences and Technology (NUST), Islamabad, Pakistan; Program in Genetics and Genome Biology (R.D.) and The Centre for Applied Genomics, Genetics and Genome Biology (S.W., S.W.S.), The Hospital for Sick Children, Department of Molecular Genetics (S.W.S.), and McLaughlin Centre (S.W.S.), University of Toronto, Ontario, Canada; Department of Neurolgy (S.Y.K.), Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, Gyeonggi-do, Republic of Korea; Program in Genetics and Genome Biology (B.A.M.), Division of Neurology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Ontario, Canada; and Departments of Pediatrics, Neurology, and Neurotherapeutics (B.A.M.), University of Texas Southwestern, Dallas
| | - Berge A Minassian
- Atta-ur Rahman School of Applied Biosciences (R.D., M.J.H.), National University of Sciences and Technology (NUST), Islamabad, Pakistan; Program in Genetics and Genome Biology (R.D.) and The Centre for Applied Genomics, Genetics and Genome Biology (S.W., S.W.S.), The Hospital for Sick Children, Department of Molecular Genetics (S.W.S.), and McLaughlin Centre (S.W.S.), University of Toronto, Ontario, Canada; Department of Neurolgy (S.Y.K.), Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, Gyeonggi-do, Republic of Korea; Program in Genetics and Genome Biology (B.A.M.), Division of Neurology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Ontario, Canada; and Departments of Pediatrics, Neurology, and Neurotherapeutics (B.A.M.), University of Texas Southwestern, Dallas
| |
Collapse
|
26
|
Giri D, Rigden D, Didi M, Peak M, McNamara P, Senniappan S. Novel compound heterozygous ASXL3 mutation causing Bainbridge-ropers like syndrome and primary IGF1 deficiency. INTERNATIONAL JOURNAL OF PEDIATRIC ENDOCRINOLOGY 2017; 2017:8. [PMID: 28785287 PMCID: PMC5544984 DOI: 10.1186/s13633-017-0047-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/27/2017] [Indexed: 01/30/2023]
Abstract
Background De novo truncating and splicing mutations in the additional sex combs-like 3 (ASXL3) gene have been implicated in the development of Bainbridge-Ropers syndrome (BRPS) characterised by severe developmental delay, feeding problems, short stature and characteristic facial features. Case presentation We describe, for the first time, a patient with severe short stature, learning difficulties, feeding difficulties and dysmorphic features with a novel compound heterozygous mutation in ASXL3.Additionally the patient also has primary insulin like growth factor-1 (IGF1) deficiency. The mutations occur in exon 11 and proximal part of exon 12 and are strongly conserved at the protein level across various species. In-silico analyses using PolyPhen-2 and SIFT predict the amino acid substitutions to be potentially deleterious to the protein function. Detailed bioinformatics analysis show that the molecular defects caused by the two compound heterozygous mutations synergistically impact on two points of the molecular interaction network of ASXL3. Conclusion We hypothesise that ASXL3 potentially has a role in transcriptional activation of IGF1 involved in signalling pathways that regulate cell proliferation and growth, which could be contributing to short stature encountered in these patients.
Collapse
Affiliation(s)
- Dinesh Giri
- Institute in the Park, Alder Hey Children's NHS Foundation Trust, University of Liverpool, Eaton Road, Liverpool, UK.,Department of Paediatric Endocrinology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Daniel Rigden
- Institute of Intergrative Biology, University of Liverpool, Liverpool, UK
| | - Mohammed Didi
- Department of Paediatric Endocrinology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Matthew Peak
- Institute in the Park, Alder Hey Children's NHS Foundation Trust, University of Liverpool, Eaton Road, Liverpool, UK.,NIHR Alder Hey Clinical Research Facility for Experimental Medicine, Liverpool, UK
| | - Paul McNamara
- Institute in the Park, Alder Hey Children's NHS Foundation Trust, University of Liverpool, Eaton Road, Liverpool, UK
| | - Senthil Senniappan
- Institute in the Park, Alder Hey Children's NHS Foundation Trust, University of Liverpool, Eaton Road, Liverpool, UK.,Department of Paediatric Endocrinology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| |
Collapse
|
27
|
Hegde M, Santani A, Mao R, Ferreira-Gonzalez A, Weck KE, Voelkerding KV. Development and Validation of Clinical Whole-Exome and Whole-Genome Sequencing for Detection of Germline Variants in Inherited Disease. Arch Pathol Lab Med 2017; 141:798-805. [DOI: 10.5858/arpa.2016-0622-ra] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—
With the decrease in the cost of sequencing, the clinical testing paradigm has shifted from single gene to gene panel and now whole-exome and whole-genome sequencing. Clinical laboratories are rapidly implementing next-generation sequencing–based whole-exome and whole-genome sequencing. Because a large number of targets are covered by whole-exome and whole-genome sequencing, it is critical that a laboratory perform appropriate validation studies, develop a quality assurance and quality control program, and participate in proficiency testing.
Objective.—
To provide recommendations for whole-exome and whole-genome sequencing assay design, validation, and implementation for the detection of germline variants associated in inherited disorders.
Data Sources.—
An example of trio sequencing, filtration and annotation of variants, and phenotypic consideration to arrive at clinical diagnosis is discussed.
Conclusions.—
It is critical that clinical laboratories planning to implement whole-exome and whole-genome sequencing design and validate the assay to specifications and ensure adequate performance prior to implementation. Test design specifications, including variant filtering and annotation, phenotypic consideration, guidance on consenting options, and reporting of incidental findings, are provided. These are important steps a laboratory must take to validate and implement whole-exome and whole-genome sequencing in a clinical setting for germline variants in inherited disorders.
Collapse
Affiliation(s)
| | | | | | | | | | - Karl V. Voelkerding
- From the Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia (Dr Hegde); the Department of Clinical Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia (Dr Santani); the Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (Dr Santani); the Department of Pathology, ARUP
| |
Collapse
|
28
|
Balasubramanian M, Willoughby J, Fry AE, Weber A, Firth HV, Deshpande C, Berg JN, Chandler K, Metcalfe KA, Lam W, Pilz DT, Tomkins S. Delineating the phenotypic spectrum of Bainbridge-Ropers syndrome: 12 new patients with de novo, heterozygous, loss-of-function mutations in ASXL3 and review of published literature. J Med Genet 2017; 54:537-543. [PMID: 28100473 DOI: 10.1136/jmedgenet-2016-104360] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/06/2016] [Accepted: 12/12/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND Bainbridge-Ropers syndrome (BRPS) is a recently described developmental disorder caused by de novo truncating mutations in the additional sex combs like 3 (ASXL3) gene. To date, there have been fewer than 10 reported patients. OBJECTIVES Here, we delineate the BRPS phenotype further by describing a series of 12 previously unreported patients identified by the Deciphering Developmental Disorders study. METHODS Trio-based exome sequencing was performed on all 12 patients included in this study, which found a de novo truncating mutation in ASXL3. Detailed phenotypic information and patient images were collected and summarised as part of this study. RESULTS By obtaining genotype:phenotype data, we have been able to demonstrate a second mutation cluster region within ASXL3. This report expands the phenotype of older patients with BRPS; common emerging features include severe intellectual disability (11/12), poor/ absent speech (12/12), autistic traits (9/12), distinct face (arched eyebrows, prominent forehead, high-arched palate, hypertelorism and downslanting palpebral fissures), (9/12), hypotonia (11/12) and significant feeding difficulties (9/12) when young. DISCUSSION Similarities in the patients reported previously in comparison with this cohort included their distinctive craniofacial features, feeding problems, absent/limited speech and intellectual disability. Shared behavioural phenotypes include autistic traits, hand-flapping, rocking, aggressive behaviour and sleep disturbance. CONCLUSIONS This series expands the phenotypic spectrum of this severe disorder and highlights its surprisingly high frequency. With the advent of advanced genomic screening, we are likely to identify more variants in this gene presenting with a variable phenotype, which this study will explore.
Collapse
Affiliation(s)
- M Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - J Willoughby
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - A E Fry
- Institute of Medial Genetics, University Hospital of Wales, Cardiff, UK.,Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - A Weber
- Clinical Genetics Department, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - H V Firth
- East Anglian Medical Genetics Service, Clinical Genetics, Addenbrooke's Hospital, Cambridge, UK
| | - C Deshpande
- Department of Clinical Genetics, Guy's & St. Thomas' Hospital NHS Trust, London, UK
| | - J N Berg
- Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - K Chandler
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester, UK.,Division of Evolution and Genomic sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - K A Metcalfe
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester, UK.,Division of Evolution and Genomic sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - W Lam
- Clinical Genetics Unit, Western General Hospital, Edinburgh, UK
| | - D T Pilz
- West of Scotland Genetics Service, Glasgow, UK
| | - S Tomkins
- Clinical Genetics Service, University Hospitals of Bristol NHS Foundation Trust, Bristol, UK
| |
Collapse
|
29
|
Kuechler A, Czeschik JC, Graf E, Grasshoff U, Hüffmeier U, Busa T, Beck-Woedl S, Faivre L, Rivière JB, Bader I, Koch J, Reis A, Hehr U, Rittinger O, Sperl W, Haack TB, Wieland T, Engels H, Prokisch H, Strom TM, Lüdecke HJ, Wieczorek D. Bainbridge-Ropers syndrome caused by loss-of-function variants in ASXL3: a recognizable condition. Eur J Hum Genet 2016; 25:183-191. [PMID: 27901041 DOI: 10.1038/ejhg.2016.165] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/29/2016] [Accepted: 10/13/2016] [Indexed: 01/06/2023] Open
Abstract
Truncating ASXL3 mutations were first identified in 2013 by Bainbridge et al. as a cause of syndromic intellectual disability in four children with similar phenotypes using whole-exome sequencing. The clinical features - postulated by Bainbridge et al. to be overlapping with Bohring-Opitz syndrome - were developmental delay, severe feeding difficulties, failure to thrive and neurological abnormalities. This condition was included in OMIM as 'Bainbridge-Ropers syndrome' (BRPS, #615485). To date, a total of nine individuals with BRPS have been published in the literature in four reports (Bainbridge et al., Dinwiddie et al, Srivastava et al. and Hori et al.). In this report, we describe six unrelated patients with newly diagnosed heterozygous de novo loss-of-function variants in ASXL3 and concordant clinical features: severe muscular hypotonia with feeding difficulties in infancy, significant motor delay, profound speech impairment, intellectual disability and a characteristic craniofacial phenotype (long face, arched eyebrows with mild synophrys, downslanting palpebral fissures, prominent columella, small alae nasi, high, narrow palate and relatively little facial expression). The majority of key features characteristic for Bohring-Opitz syndrome were absent in our patients (eg, the typical posture of arms, intrauterine growth retardation, microcephaly, trigonocephaly, typical facial gestalt with nevus flammeus of the forehead and exophthalmos). Therefore we emphasize that BRPS syndrome, caused by ASXL3 loss-of-function variants, is a clinically distinct intellectual disability syndrome with a recognizable phenotype distinguishable from that of Bohring-Opitz syndrome.
Collapse
Affiliation(s)
- Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | | | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ute Grasshoff
- Institut für Medizinische Genetik und Angewandte Genomik, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Ulrike Hüffmeier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Tiffany Busa
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs PACA, Service de génétique Clinique, Hôpital Timone Enfants, Marseille, France
| | - Stefanie Beck-Woedl
- Institut für Medizinische Genetik und Angewandte Genomik, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Laurence Faivre
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs et FHU TRANSLAD, Hôpital d'Enfants, Dijon, France.,EA 4271 GAD, Université de Bourgogne, Dijon, France
| | | | - Ingrid Bader
- Department of Pediatrics, Paracelsus Medical University, Salzburg, Austria
| | - Johannes Koch
- Department of Pediatrics, Paracelsus Medical University, Salzburg, Austria
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Ute Hehr
- Zentrum für Humangenetik, Universitätsklinikum Regensburg, Regensburg, Germany
| | - Olaf Rittinger
- Department of Pediatrics, Paracelsus Medical University, Salzburg, Austria
| | - Wolfgang Sperl
- Department of Pediatrics, Paracelsus Medical University, Salzburg, Austria
| | - Tobias B Haack
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Thomas Wieland
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Hermann-Josef Lüdecke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.,Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Dagmar Wieczorek
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.,Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
30
|
Micol JB, Abdel-Wahab O. The Role of Additional Sex Combs-Like Proteins in Cancer. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026526. [PMID: 27527698 DOI: 10.1101/cshperspect.a026526] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Additional sex combs-like (ASXL) proteins are mammalian homologs of Addition of sex combs (Asx), a protein that regulates the balance of trithorax and Polycomb function in Drosophila. All three ASXL family members (ASXL1, ASXL2, and ASXL3) are affected by somatic or de novo germline mutations in cancer or rare developmental syndromes, respectively. Although Asx is characterized as a catalytic partner for the deubiquitinase Calypso (or BAP1), there are domains of ASXL proteins that are distinct from Asx and the roles and redundancies of ASXL members are not yet well understood. Moreover, it is not yet fully clarified if commonly encountered ASXL1 mutations result in a loss of protein or stable expression of a truncated protein with dominant-negative or gain-of-function properties. This review summarizes our current knowledge of the biological and functional roles of ASXL members in development, cancer, and transcription.
Collapse
Affiliation(s)
- Jean-Baptiste Micol
- Hematology Department, INSERM UMR1170, Gustave Roussy Cancer Campus Grand Paris, Villejuif, France Université Paris-Sud, Faculté de Médecine, Le Kremlin-Bicêtre, Paris, France Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| |
Collapse
|
31
|
Mullins C, Fishell G, Tsien RW. Unifying Views of Autism Spectrum Disorders: A Consideration of Autoregulatory Feedback Loops. Neuron 2016; 89:1131-1156. [PMID: 26985722 DOI: 10.1016/j.neuron.2016.02.017] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2016] [Indexed: 12/31/2022]
Abstract
Understanding the mechanisms underlying autism spectrum disorders (ASDs) is a challenging goal. Here we review recent progress on several fronts, including genetics, proteomics, biochemistry, and electrophysiology, that raise motivation for forming a viable pathophysiological hypothesis. In place of a traditionally unidirectional progression, we put forward a framework that extends homeostatic hypotheses by explicitly emphasizing autoregulatory feedback loops and known synaptic biology. The regulated biological feature can be neuronal electrical activity, the collective strength of synapses onto a dendritic branch, the local concentration of a signaling molecule, or the relative strengths of synaptic excitation and inhibition. The sensor of the biological variable (which we have termed the homeostat) engages mechanisms that operate as negative feedback elements to keep the biological variable tightly confined. We categorize known ASD-associated gene products according to their roles in such feedback loops and provide detailed commentary for exemplar genes within each module.
Collapse
Affiliation(s)
- Caitlin Mullins
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA
| | - Gord Fishell
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA
| | - Richard W Tsien
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA.
| |
Collapse
|
32
|
Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis. Hum Genet 2016; 135:797-811. [DOI: 10.1007/s00439-016-1673-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/17/2016] [Indexed: 01/09/2023]
|
33
|
Hori I, Miya F, Ohashi K, Negishi Y, Hattori A, Ando N, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Saitoh S. Novel splicing mutation in the ASXL3 gene causing Bainbridge-Ropers syndrome. Am J Med Genet A 2016; 170:1863-7. [PMID: 27075689 DOI: 10.1002/ajmg.a.37653] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 03/27/2016] [Indexed: 12/28/2022]
Abstract
Bainbridge-Ropers syndrome (BRPS) is characterized by severe developmental delay, feeding problems, short stature, characteristic facal appearance including arched eyebrows and anteverted nares, and ulnar deviation of the hands. BRPS is caused by a heterozygous mutation in the additional sex combs-like 3 (ASXL3) gene. We describe a patient with severe developmental delay, feeding problems, short stature, autism, and sleep disturbance with a heterozygous de novo splicing mutation in the ASXL3 gene. Reported disease-causing mutations in ASXL3 are located mostly in the first half of exon 11, analogous to ASXL1 mutations of which result in Bohring-Opitz syndrome (BOS). Our findings suggest that the expression of the truncated ASXL3 protein, including ASXN and ASXH domains, give rise to BRPS, which is distinct from but overlaps with BOS. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Ikumi Hori
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Fuyuki Miya
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kei Ohashi
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yutaka Negishi
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Ayako Hattori
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Naoki Ando
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Tatsuhiko Tsunoda
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mami Yamasaki
- Department of Neurosurgery, Takatsuki General Hospital, Osaka, Japan
| | - Yonehiro Kanemura
- Division of Regenerative Medicine, Institute for Clinical Research, Osaka National Hospital, National Hospital Organization, Osaka, Japan.,Department of Neurosurgery, Osaka National Hospital, National Hospital Organization, Osaka, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| |
Collapse
|
34
|
Packer A. Neocortical neurogenesis and the etiology of autism spectrum disorder. Neurosci Biobehav Rev 2016; 64:185-95. [PMID: 26949225 DOI: 10.1016/j.neubiorev.2016.03.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 12/11/2022]
Abstract
Researchers have now identified many highly penetrant genetic risk factors for autism spectrum disorder (ASD). Some of these genes encode synaptic proteins, lending support to the hypothesis that ASD is a disorder of synaptic homeostasis. Less attention, however, has been paid to the genetic risk factors that converge on events that precede synaptogenesis, including the proliferation of neural progenitor cells and the migration of neurons to the appropriate layers of the developing neocortex. Here I review this evidence, focusing on studies of mutant mouse phenotypes, human postmortem data, systems biological analyses, and non-genetic risk factors. These findings highlight embryonic neurogenesis as a potentially important locus of pathology in ASD. In some instances, this pathology may be driven by alterations in chromatin biology and canonical Wnt signaling, which in turn affect fundamental cellular processes such as cell-cycle length and cell migration. This view of ASD suggests the need for a better understanding of the relationship between variation in neuron number, laminar composition, and the neural circuitry most relevant to the disorder.
Collapse
Affiliation(s)
- Alan Packer
- Simons Foundation Autism Research Initiative, 160 Fifth Avenue, New York, NY 10010, USA.
| |
Collapse
|
35
|
Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease. Neuron 2016; 88:499-513. [PMID: 26539891 DOI: 10.1016/j.neuron.2015.09.048] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 09/12/2015] [Accepted: 09/25/2015] [Indexed: 11/23/2022]
Abstract
Development of the human nervous system involves complex interactions among fundamental cellular processes and requires a multitude of genes, many of which remain to be associated with human disease. We applied whole exome sequencing to 128 mostly consanguineous families with neurogenetic disorders that often included brain malformations. Rare variant analyses for both single nucleotide variant (SNV) and copy number variant (CNV) alleles allowed for identification of 45 novel variants in 43 known disease genes, 41 candidate genes, and CNVs in 10 families, with an overall potential molecular cause identified in >85% of families studied. Among the candidate genes identified, we found PRUNE, VARS, and DHX37 in multiple families and homozygous loss-of-function variants in AGBL2, SLC18A2, SMARCA1, UBQLN1, and CPLX1. Neuroimaging and in silico analysis of functional and expression proximity between candidate and known disease genes allowed for further understanding of genetic networks underlying specific types of brain malformations.
Collapse
|
36
|
Srivastava A, Ritesh KC, Tsan YC, Liao R, Su F, Cao X, Hannibal MC, Keegan CE, Chinnaiyan AM, Martin DM, Bielas SL. De novo dominant ASXL3 mutations alter H2A deubiquitination and transcription in Bainbridge-Ropers syndrome. Hum Mol Genet 2015; 25:597-608. [PMID: 26647312 DOI: 10.1093/hmg/ddv499] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/01/2015] [Indexed: 12/22/2022] Open
Abstract
De novo truncating mutations in Additional sex combs-like 3 (ASXL3) have been identified in individuals with Bainbridge-Ropers syndrome (BRS), characterized by failure to thrive, global developmental delay, feeding problems, hypotonia, dysmorphic features, profound speech delays and intellectual disability. We identified three novel de novo heterozygous truncating variants distributed across ASXL3, outside the original cluster of ASXL3 mutations previously described for BRS. Primary skin fibroblasts established from a BRS patient were used to investigate the functional impact of pathogenic variants. ASXL3 mRNA transcripts from the mutated allele are prone to nonsense-mediated decay, and expression of ASXL3 is reduced. We found that ASXL3 interacts with BAP1, a hydrolase that removes mono-ubiquitin from histone H2A lysine 119 (H2AK119Ub1) as a component of the Polycomb repressive deubiquitination (PR-DUB) complex. A significant increase in H2AK119Ub1 was observed in ASXL3 patient fibroblasts, highlighting an important functional role for ASXL3 in PR-DUB mediated deubiquitination. Transcriptomes of ASXL3 patient and control fibroblasts were compared to investigate the impact of chromatin changes on transcriptional regulation. Out of 564 significantly differentially expressed genes (DEGs) in ASXL3 patient fibroblasts, 52% were upregulated and 48% downregulated. DEGs were enriched in molecular processes impacting transcriptional regulation, development and proliferation, consistent with the features of BRS. This is the first single gene disorder linked to defects in deubiquitination of H2AK119Ub1 and suggests an important role for dynamic regulation of H2A mono-ubiquitination in transcriptional regulation and the pathophysiology of BRS.
Collapse
Affiliation(s)
| | | | | | | | - Fengyun Su
- Howard Hughes Medical Institute, Department of Pathology, Departments of Urology, Computational Medicine and Bioinformatics, and
| | - Xuhong Cao
- Howard Hughes Medical Institute, Department of Pathology, Departments of Urology, Computational Medicine and Bioinformatics, and
| | - Mark C Hannibal
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Catherine E Keegan
- Department of Human Genetics, Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Howard Hughes Medical Institute, Department of Pathology, Departments of Urology, Computational Medicine and Bioinformatics, and
| | - Donna M Martin
- Department of Human Genetics, Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | | |
Collapse
|
37
|
Ropers HH, Wienker T. Penetrance of pathogenic mutations in haploinsufficient genes for intellectual disability and related disorders. Eur J Med Genet 2015; 58:715-8. [PMID: 26506440 DOI: 10.1016/j.ejmg.2015.10.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 10/15/2015] [Indexed: 01/08/2023]
Abstract
De novo loss of function (LOF) mutations in the ASXL3 gene cause Bainbridge-Ropers syndrome, a severe form of intellectual disability (ID) and developmental delay, but there is evidence that they also occur in healthy individuals. This has prompted us to look for non-pathogenic LOF variants in other ID genes. Heterozygous LOF mutations in ASXL1, a paralog of ASXL3, are known to cause Bohring-Opitz syndrome (BOS), and benign LOF mutations in this gene have not been published to date. Therefore, we were surprised to find 56 ASXL1 LOF variants in the ExAC database (http://exac.broadinstitute.org), comprising exomes from 60,706 individuals who had been selected to exclude severe genetic childhood disorders. 4 of these variants have been described as disease-causing in patients with BOS, which rules out the possibility that pathogenic and clinically neutral LOF variants in this gene are functionally distinct. Apparently benign LOF variants were also detected in several other genes for ID and related disorders, including CDH15, KATNAL2, DEPDC5, ARID1B and AUTS2, both in the ExAC database and in the 6,500 exomes of the Exome Variant Server (http://evs.gs.washington.edu/EVS/). These observations argue for low penetrance of LOF mutations in ASXL1 and other genes for ID and related disorders, which could have far-reaching implications for genetic counseling and research.
Collapse
Affiliation(s)
- H Hilger Ropers
- Institute for Human Genetics, University Medicine, Langenbeckstrasse 1, Building 601, 55131 Mainz, Germany; Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
| | - Thomas Wienker
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| |
Collapse
|
38
|
Dangiolo SB, Wilson A, Jobanputra V, Anyane-Yeboa K. Bohring-Opitz syndrome (BOS) with a new ASXL1 pathogenic variant: Review of the most prevalent molecular and phenotypic features of the syndrome. Am J Med Genet A 2015; 167A:3161-6. [PMID: 26364555 DOI: 10.1002/ajmg.a.37342] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/10/2015] [Indexed: 01/10/2023]
Abstract
Bohring-Opitz syndrome (BOS) was first described by Bohring et al. [1999]. The authors reported four cases which had several features in common, including a prominent metopic suture, hypertelorism, exophthalmos, cleft lip and palate, limb anomalies, as well as difficulty feeding with severe developmental delays. In almost 50% of cases that meet the clinical criteria for BOS, de novo frameshift and nonsense mutations in the ASXL1 gene have been detected, suggesting that loss of function of this gene is a major cause. We report on the clinical characterization of one young female patient who was evaluated because of severe developmental delays, failure to thrive, and multiple minor anomalies and was clinically diagnosed with BOS. Whole exome sequencing analysis detected one novel disruptive frameshift mutation in the ASXL1 gene and we were also able to confirm the presence of two CFTR mutations associated with her chronic pancreatitis with acute severe breakthrough attacks requiring multiple ICU admissions. This latter complication of pancreatitis further contributed to the complexity of the clinical presentation and represents an independent genetic finding. Our case report emphasizes the importance of highly specific phenotypic characterization of patients with complex phenotypes before proceeding with molecular studies. That approach will lead to more accurate molecular data interpretation and better clinical genetic diagnosis, particularly for those patients with rare, difficult-to-diagnose disorders.
Collapse
Affiliation(s)
| | - Ashley Wilson
- Department of Pediatrics, Columbia University Medical Center, New York
| | | | | |
Collapse
|
39
|
Soden SE, Saunders CJ, Willig LK, Farrow EG, Smith LD, Petrikin JE, LePichon JB, Miller NA, Thiffault I, Dinwiddie DL, Twist G, Noll A, Heese BA, Zellmer L, Atherton AM, Abdelmoity AT, Safina N, Nyp SS, Zuccarelli B, Larson IA, Modrcin A, Herd S, Creed M, Ye Z, Yuan X, Brodsky RA, Kingsmore SF. Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders. Sci Transl Med 2015; 6:265ra168. [PMID: 25473036 DOI: 10.1126/scitranslmed.3010076] [Citation(s) in RCA: 384] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Neurodevelopmental disorders (NDDs) affect more than 3% of children and are attributable to single-gene mutations at more than 1000 loci. Traditional methods yield molecular diagnoses in less than one-half of children with NDD. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) can enable diagnosis of NDD, but their clinical and cost-effectiveness are unknown. One hundred families with 119 children affected by NDD received diagnostic WGS and/or WES of parent-child trios, wherein the sequencing approach was guided by acuity of illness. Forty-five percent received molecular diagnoses. An accelerated sequencing modality, rapid WGS, yielded diagnoses in 73% of families with acutely ill children (11 of 15). Forty percent of families with children with nonacute NDD, followed in ambulatory care clinics (34 of 85), received diagnoses: 33 by WES and 1 by staged WES then WGS. The cost of prior negative tests in the nonacute patients was $19,100 per family, suggesting sequencing to be cost-effective at up to $7640 per family. A change in clinical care or impression of the pathophysiology was reported in 49% of newly diagnosed families. If WES or WGS had been performed at symptom onset, genomic diagnoses may have been made 77 months earlier than occurred in this study. It is suggested that initial diagnostic evaluation of children with NDD should include trio WGS or WES, with extension of accelerated sequencing modalities to high-acuity patients.
Collapse
Affiliation(s)
- Sarah E Soden
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA.
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Laurel K Willig
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Josh E Petrikin
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Jean-Baptiste LePichon
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Darrell L Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA. Clinical and Translational Science Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Greyson Twist
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Aaron Noll
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Bryce A Heese
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Lee Zellmer
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Andrea M Atherton
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Ahmed T Abdelmoity
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Nicole Safina
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Sarah S Nyp
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Britton Zuccarelli
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Ingrid A Larson
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Ann Modrcin
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Suzanne Herd
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Mitchell Creed
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Zhaohui Ye
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Xuan Yuan
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Robert A Brodsky
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| |
Collapse
|
40
|
McGinley AL, Li Y, Deliu Z, Wang QT. Additional sex combs-likefamily genes are required for normal cardiovascular development. Genesis 2014; 52:671-86. [DOI: 10.1002/dvg.22793] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/14/2014] [Accepted: 05/20/2014] [Indexed: 01/23/2023]
Affiliation(s)
- Andrea L. McGinley
- Department of Biological Sciences; University of Illinois at Chicago; Chicago Illinois
| | - Yanyang Li
- Department of Biological Sciences; University of Illinois at Chicago; Chicago Illinois
| | - Zane Deliu
- Department of Biological Sciences; University of Illinois at Chicago; Chicago Illinois
| | - Q. Tian Wang
- Department of Biological Sciences; University of Illinois at Chicago; Chicago Illinois
| |
Collapse
|