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Kerkhof J, Rastin C, Levy MA, Relator R, McConkey H, Demain L, Dominguez-Garrido E, Kaat LD, Houge SD, DuPont BR, Fee T, Fletcher RS, Gokhale D, Haukanes BI, Henneman P, Hilton S, Hilton BA, Jenkinson S, Lee JA, Louie RJ, Motazacker MM, Rzasa J, Stevenson RE, Plomp A, van der Laan L, van der Smagt J, Walden KK, Banka S, Mannens M, Skinner SA, Friez MJ, Campbell C, Tedder ML, Alders M, Sadikovic B. Diagnostic utility and reporting recommendations for clinical DNA methylation episignature testing in genetically undiagnosed rare diseases. Genet Med 2024; 26:101075. [PMID: 38251460 DOI: 10.1016/j.gim.2024.101075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
PURPOSE This study aims to assess the diagnostic utility and provide reporting recommendations for clinical DNA methylation episignature testing based on the cohort of patients tested through the EpiSign Clinical Testing Network. METHODS The EpiSign assay utilized unsupervised clustering techniques and a support vector machine-based classification algorithm to compare each patient's genome-wide DNA methylation profile with the EpiSign Knowledge Database, yielding the result that was reported. An international working group, representing distinct EpiSign Clinical Testing Network health jurisdictions, collaborated to establish recommendations for interpretation and reporting of episignature testing. RESULTS Among 2399 cases analyzed, 1667 cases underwent a comprehensive screen of validated episignatures, imprinting, and promoter regions, resulting in 18.7% (312/1667) positive reports. The remaining 732 referrals underwent targeted episignature analysis for assessment of sequence or copy-number variants (CNVs) of uncertain significance or for assessment of clinical diagnoses without confirmed molecular findings, and 32.4% (237/732) were positive. Cases with detailed clinical information were highlighted to describe various utility scenarios for episignature testing. CONCLUSION Clinical DNA methylation testing including episignatures, imprinting, and promoter analysis provided by an integrated network of clinical laboratories enables test standardization and demonstrates significant diagnostic yield and clinical utility beyond DNA sequence analysis in rare diseases.
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Affiliation(s)
- Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Cassandra Rastin
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Leigh Demain
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Laura Donker Kaat
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sofia Douzgou Houge
- Haukeland University Hospital, Centre for Medical Genetics and Molecular Medicine, Bergen, Norway
| | | | | | | | - David Gokhale
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Bjørn Ivar Haukanes
- Haukeland University Hospital, Centre for Medical Genetics and Molecular Medicine, Bergen, Norway
| | - Peter Henneman
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Sarah Hilton
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Sarah Jenkinson
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | | | - M Mahdi Motazacker
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jessica Rzasa
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | | | - Astrid Plomp
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands
| | - Liselot van der Laan
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jasper van der Smagt
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | | | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Marcel Mannens
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | - Christopher Campbell
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
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2
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Bhat S, Rousseau J, Michaud C, Lourenço CM, Stoler JM, Louie RJ, Clarkson LK, Lichty A, Koboldt DC, Reshmi SC, Sisodiya SM, Hoytema van Konijnenburg EMM, Koop K, van Hasselt PM, Démurger F, Dubourg C, Sullivan BR, Hughes SS, Thiffault I, Tremblay ES, Accogli A, Srour M, Blunck R, Campeau PM. Mono-allelic KCNB2 variants lead to a neurodevelopmental syndrome caused by altered channel inactivation. Am J Hum Genet 2024; 111:761-777. [PMID: 38503299 PMCID: PMC11023922 DOI: 10.1016/j.ajhg.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/21/2024] Open
Abstract
Ion channels mediate voltage fluxes or action potentials that are central to the functioning of excitable cells such as neurons. The KCNB family of voltage-gated potassium channels (Kv) consists of two members (KCNB1 and KCNB2) encoded by KCNB1 and KCNB2, respectively. These channels are major contributors to delayed rectifier potassium currents arising from the neuronal soma which modulate overall excitability of neurons. In this study, we identified several mono-allelic pathogenic missense variants in KCNB2, in individuals with a neurodevelopmental syndrome with epilepsy and autism in some individuals. Recurrent dysmorphisms included a broad forehead, synophrys, and digital anomalies. Additionally, we selected three variants where genetic transmission has not been assessed, from two epilepsy studies, for inclusion in our experiments. We characterized channel properties of these variants by expressing them in oocytes of Xenopus laevis and conducting cut-open oocyte voltage clamp electrophysiology. Our datasets indicate no significant change in absolute conductance and conductance-voltage relationships of most disease variants as compared to wild type (WT), when expressed either alone or co-expressed with WT-KCNB2. However, variants c.1141A>G (p.Thr381Ala) and c.641C>T (p.Thr214Met) show complete abrogation of currents when expressed alone with the former exhibiting a left shift in activation midpoint when expressed alone or with WT-KCNB2. The variants we studied, nevertheless, show collective features of increased inactivation shifted to hyperpolarized potentials. We suggest that the effects of the variants on channel inactivation result in hyper-excitability of neurons, which contributes to disease manifestations.
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Affiliation(s)
- Shreyas Bhat
- Center for Interdisciplinary Research on Brain and Learning (CIRCA), Department of Physics and Department of Pharmacology and Physiology, Université de Montréal, Montréal, QC, Canada
| | - Justine Rousseau
- Centre de Recherche Du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Coralie Michaud
- Centre de Recherche Du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | | | - Joan M Stoler
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | | | | | - Angie Lichty
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Daniel C Koboldt
- Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, OH, USA
| | - Shalini C Reshmi
- Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, OH, USA; Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | | | - Klaas Koop
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter M van Hasselt
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Christèle Dubourg
- Department of Molecular Genetics and Genomics, Rennes University Hospital, Rennes, France; Université de Rennes, CNRS, IGDR, UMR 6290 Rennes, France
| | - Bonnie R Sullivan
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Susan S Hughes
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Isabelle Thiffault
- Departments of Pediatrics and of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Elisabeth Simard Tremblay
- Department of Neurology and Neurosurgery, McGill University Health Centre, Montréal, QC, Canada; Department of Pediatrics, Division of Pediatric Neurology, McGill University, Montréal, QC, Canada
| | - Andrea Accogli
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montréal, QC, Canada; Department of Human Genetics, Faculty of Medicine, McGill University, Montral, QC H3A 1B1, Canada
| | - Myriam Srour
- Department of Pediatrics, Division of Pediatric Neurology, McGill University, Montréal, QC, Canada; Department of Human Genetics, Faculty of Medicine, McGill University, Montral, QC H3A 1B1, Canada
| | - Rikard Blunck
- Center for Interdisciplinary Research on Brain and Learning (CIRCA), Department of Physics and Department of Pharmacology and Physiology, Université de Montréal, Montréal, QC, Canada.
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3
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Werren EA, LaForce GR, Srivastava A, Perillo DR, Li S, Johnson K, Baris S, Berger B, Regan SL, Pfennig CD, de Munnik S, Pfundt R, Hebbar M, Jimenez-Heredia R, Karakoc-Aydiner E, Ozen A, Dmytrus J, Krolo A, Corning K, Prijoles EJ, Louie RJ, Lebel RR, Le TL, Amiel J, Gordon CT, Boztug K, Girisha KM, Shukla A, Bielas SL, Schaffer AE. TREX tetramer disruption alters RNA processing necessary for corticogenesis in THOC6 Intellectual Disability Syndrome. Nat Commun 2024; 15:1640. [PMID: 38388531 PMCID: PMC10884030 DOI: 10.1038/s41467-024-45948-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
THOC6 variants are the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 is critical for mammalian Transcription Export complex (TREX) tetramer formation, which is composed of four six-subunit THO monomers. The TREX tetramer facilitates mammalian RNA processing, in addition to the nuclear mRNA export functions of the TREX dimer conserved through yeast. Human and mouse TIDS model systems revealed novel THOC6-dependent, species-specific TREX tetramer functions. Germline biallelic Thoc6 loss-of-function (LOF) variants result in mouse embryonic lethality. Biallelic THOC6 LOF variants reduce the binding affinity of ALYREF to THOC5 without affecting the protein expression of TREX members, implicating impaired TREX tetramer formation. Defects in RNA nuclear export functions were not detected in biallelic THOC6 LOF human neural cells. Instead, mis-splicing was detected in human and mouse neural tissue, revealing novel THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for key signaling pathways known to regulate the transition from proliferative to neurogenic divisions during human corticogenesis. Together, these findings implicate altered RNA processing in the developmental biology of TIDS neuropathology.
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Affiliation(s)
- Elizabeth A Werren
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Anshika Srivastava
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
| | - Delia R Perillo
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Shaokun Li
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Katherine Johnson
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Safa Baris
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Brandon Berger
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Samantha L Regan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Christian D Pfennig
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sonja de Munnik
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, 6524, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, 6524, the Netherlands
| | - Malavika Hebbar
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 98195, Seattle, WA, USA
| | - Raúl Jimenez-Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
| | - Elif Karakoc-Aydiner
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Ahmet Ozen
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Jasmin Dmytrus
- Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Ana Krolo
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
| | - Ken Corning
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - E J Prijoles
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | | | - Robert Roger Lebel
- Section of Medical Genetics, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Thuy-Linh Le
- Imagine Institute, INSERM U1163, Paris Cité University, Paris, 75015, France
| | - Jeanne Amiel
- Imagine Institute, INSERM U1163, Paris Cité University, Paris, 75015, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, 75015, France
| | | | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
- Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, 1090, Austria
- St. Anna Children's Hospital and Children's Cancer Research Institute, Department of Pediatrics, Medical University of Vienna, Vienna, 1090, Austria
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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4
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Dohrn MF, Beijer D, Lone MA, Bayraktar E, Oflazer P, Orbach R, Donkervoort S, Foley AR, Rose A, Lyons M, Louie RJ, Gable K, Dunn T, Chen S, Danzi MC, Synofzik M, Bönnemann CG, Nazlı Başak A, Hornemann T, Zuchner S. Recurrent de-novo gain-of-function mutation in SPTLC2 confirms dysregulated sphingolipid production to cause juvenile amyotrophic lateral sclerosis. J Neurol Neurosurg Psychiatry 2024; 95:201-205. [PMID: 38041684 PMCID: PMC10922288 DOI: 10.1136/jnnp-2023-332130] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/27/2023] [Indexed: 12/03/2023]
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) leads to paralysis and death by progressive degeneration of motor neurons. Recently, specific gain-of-function mutations in SPTLC1 were identified in patients with juvenile form of ALS. SPTLC2 encodes the second catalytic subunit of the serine-palmitoyltransferase (SPT) complex. METHODS We used the GENESIS platform to screen 700 ALS whole-genome and whole-exome data sets for variants in SPTLC2. The de-novo status was confirmed by Sanger sequencing. Sphingolipidomics was performed using liquid chromatography and high-resolution mass spectrometry. RESULTS Two unrelated patients presented with early-onset progressive proximal and distal muscle weakness, oral fasciculations, and pyramidal signs. Both patients carried the novel de-novo SPTLC2 mutation, c.203T>G, p.Met68Arg. This variant lies within a single short transmembrane domain of SPTLC2, suggesting that the mutation renders the SPT complex irresponsive to regulation through ORMDL3. Confirming this hypothesis, ceramide and complex sphingolipid levels were significantly increased in patient plasma. Accordingly, excessive sphingolipid production was shown in mutant-expressing human embryonic kindney (HEK) cells. CONCLUSIONS Specific gain-of-function mutations in both core subunits affect the homoeostatic control of SPT. SPTLC2 represents a new Mendelian ALS gene, highlighting a key role of dysregulated sphingolipid synthesis in the pathogenesis of juvenile ALS. Given the direct interaction of SPTLC1 and SPTLC2, this knowledge might open new therapeutic avenues for motor neuron diseases.
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Affiliation(s)
- Maike F Dohrn
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida, USA
- Department of Neurology, Medical Faculty RWTH Aachen University, Aachen, Germany
| | - Danique Beijer
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida, USA
- Translational Genomics of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Museer A Lone
- Institute of Clinical Chemistry, University Hospital Zürich, Zürich, Switzerland
| | - Elif Bayraktar
- Koç University, School of Medicine, Translational Medicine Research Center- NDAL, Istanbul, Turkey
| | - Piraye Oflazer
- Koç University, School of Medicine, Department of Neurology, Istanbul, Turkey
| | - Rotem Orbach
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institutes of Health, Bethesda, Maryland, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institutes of Health, Bethesda, Maryland, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institutes of Health, Bethesda, Maryland, USA
| | - Aubrey Rose
- Greenwood Genetic Center Foundation, Greenwood, South Carolina, USA
| | - Michael Lyons
- Greenwood Genetic Center Foundation, Greenwood, South Carolina, USA
| | - Raymond J Louie
- Greenwood Genetic Center Foundation, Greenwood, South Carolina, USA
| | - Kenneth Gable
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, Maryland, USA
| | - Teresa Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, Maryland, USA
| | - Sitong Chen
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Matt C Danzi
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Matthis Synofzik
- Translational Genomics of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institutes of Health, Bethesda, Maryland, USA
| | - A Nazlı Başak
- Koç University, School of Medicine, Translational Medicine Research Center- NDAL, Istanbul, Turkey
| | - Thorsten Hornemann
- Institute of Clinical Chemistry, University Hospital Zürich, Zürich, Switzerland
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida, USA
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5
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Claus LR, Chen C, Stallworth J, Turner JL, Slaats GG, Hawks AL, Mabillard H, Senum SR, Srikanth S, Flanagan-Steet H, Louie RJ, Silver J, Lerner-Ellis J, Morel C, Mighton C, Sleutels F, van Slegtenhorst M, van Ham T, Brooks AS, Dorresteijn EM, Barakat TS, Dahan K, Demoulin N, Goffin EJ, Olinger E, Larsen M, Hertz JM, Lilien MR, Obeidová L, Seeman T, Stone HK, Kerecuk L, Gurgu M, Yousef Yengej FA, Ammerlaan CME, Rookmaaker MB, Hanna C, Rogers RC, Duran K, Peters E, Sayer JA, van Haaften G, Harris PC, Ling K, Mason JM, van Eerde AM, Steet R. Certain heterozygous variants in the kinase domain of the serine/threonine kinase NEK8 can cause an autosomal dominant form of polycystic kidney disease. Kidney Int 2023; 104:995-1007. [PMID: 37598857 PMCID: PMC10592035 DOI: 10.1016/j.kint.2023.07.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/22/2023]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) resulting from pathogenic variants in PKD1 and PKD2 is the most common form of PKD, but other genetic causes tied to primary cilia function have been identified. Biallelic pathogenic variants in the serine/threonine kinase NEK8 cause a syndromic ciliopathy with extra-kidney manifestations. Here we identify NEK8 as a disease gene for ADPKD in 12 families. Clinical evaluation was combined with functional studies using fibroblasts and tubuloids from affected individuals. Nek8 knockout mouse kidney epithelial (IMCD3) cells transfected with wild type or variant NEK8 were further used to study ciliogenesis, ciliary trafficking, kinase function, and DNA damage responses. Twenty-one affected monoallelic individuals uniformly exhibited cystic kidney disease (mostly neonatal) without consistent extra-kidney manifestations. Recurrent de novo mutations of the NEK8 missense variant p.Arg45Trp, including mosaicism, were seen in ten families. Missense variants elsewhere within the kinase domain (p.Ile150Met and p.Lys157Gln) were also identified. Functional studies demonstrated normal localization of the NEK8 protein to the proximal cilium and no consistent cilia formation defects in patient-derived cells. NEK8-wild type protein and all variant forms of the protein expressed in Nek8 knockout IMCD3 cells were localized to cilia and supported ciliogenesis. However, Nek8 knockout IMCD3 cells expressing NEK8-p.Arg45Trp and NEK8-p.Lys157Gln showed significantly decreased polycystin-2 but normal ANKS6 localization in cilia. Moreover, p.Arg45Trp NEK8 exhibited reduced kinase activity in vitro. In patient derived tubuloids and IMCD3 cells expressing NEK8-p.Arg45Trp, DNA damage signaling was increased compared to healthy passage-matched controls. Thus, we propose a dominant-negative effect for specific heterozygous missense variants in the NEK8 kinase domain as a new cause of PKD.
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Affiliation(s)
- Laura R Claus
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Chuan Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Joshua L Turner
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Gisela G Slaats
- Department of Nephrology and Hypertension, Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alexandra L Hawks
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Holly Mabillard
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Sarah R Senum
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Sujata Srikanth
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | | | - Raymond J Louie
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Josh Silver
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Chantal Morel
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Frank Sleutels
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Tjakko van Ham
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Eiske M Dorresteijn
- Department of Pediatric Nephrology, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Karin Dahan
- Institute Pathology and Genetic, Center of Human Genetics, Charleroi, Belgium
| | - Nathalie Demoulin
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
| | - Eric Jean Goffin
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
| | - Eric Olinger
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Martin Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jens Michael Hertz
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Marc R Lilien
- Department of Pediatric Nephrology, Wilhelmina Children's Hospital, Utrecht, the Netherlands
| | - Lena Obeidová
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Tomas Seeman
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic; Department of Pediatrics, University Hospital Ostrava, Ostrava, Czech Republic; Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Hillarey K Stone
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Larissa Kerecuk
- Birmingham Women's and Children's National Health Services (NHS) Foundation Trust, National Institute for Health Care and Research (NIHR) Clinical Research Network (CRN) West Midlands, Birmingham, UK
| | - Mihai Gurgu
- Fundeni Clinical Institute, Bucharest, Romania
| | - Fjodor A Yousef Yengej
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands; Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW, Utrecht, the Netherlands
| | - Carola M E Ammerlaan
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands; Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW, Utrecht, the Netherlands
| | - Maarten B Rookmaaker
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Christian Hanna
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA; Division of Pediatric Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - R Curtis Rogers
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Karen Duran
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Edith Peters
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - John A Sayer
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK; Renal Services, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK; National Institute for Health and Care Research (NIHR) Biomedical Research Centre, Newcastle, UK
| | - Gijs van Haaften
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter C Harris
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA.
| | - Jennifer M Mason
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA.
| | - Albertien M van Eerde
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Richard Steet
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA.
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6
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Rots D, Jakub TE, Keung C, Jackson A, Banka S, Pfundt R, de Vries BBA, van Jaarsveld RH, Hopman SMJ, van Binsbergen E, Valenzuela I, Hempel M, Bierhals T, Kortüm F, Lecoquierre F, Goldenberg A, Hertz JM, Andersen CB, Kibæk M, Prijoles EJ, Stevenson RE, Everman DB, Patterson WG, Meng L, Gijavanekar C, De Dios K, Lakhani S, Levy T, Wagner M, Wieczorek D, Benke PJ, Lopez Garcia MS, Perrier R, Sousa SB, Almeida PM, Simões MJ, Isidor B, Deb W, Schmanski AA, Abdul-Rahman O, Philippe C, Bruel AL, Faivre L, Vitobello A, Thauvin C, Smits JJ, Garavelli L, Caraffi SG, Peluso F, Davis-Keppen L, Platt D, Royer E, Leeuwen L, Sinnema M, Stegmann APA, Stumpel CTRM, Tiller GE, Bosch DGM, Potgieter ST, Joss S, Splitt M, Holden S, Prapa M, Foulds N, Douzgou S, Puura K, Waltes R, Chiocchetti AG, Freitag CM, Satterstrom FK, De Rubeis S, Buxbaum J, Gelb BD, Branko A, Kushima I, Howe J, Scherer SW, Arado A, Baldo C, Patat O, Bénédicte D, Lopergolo D, Santorelli FM, Haack TB, Dufke A, Bertrand M, Falb RJ, Rieß A, Krieg P, Spranger S, Bedeschi MF, Iascone M, Josephi-Taylor S, Roscioli T, Buckley MF, Liebelt J, Dagli AI, Aten E, Hurst ACE, Hicks A, Suri M, Aliu E, Naik S, Sidlow R, Coursimault J, Nicolas G, Küpper H, Petit F, Ibrahim V, Top D, Di Cara F, Louie RJ, Stolerman E, Brunner HG, Vissers LELM, Kramer JM, Kleefstra T. The clinical and molecular spectrum of the KDM6B-related neurodevelopmental disorder. Am J Hum Genet 2023; 110:963-978. [PMID: 37196654 PMCID: PMC10257005 DOI: 10.1016/j.ajhg.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
De novo variants are a leading cause of neurodevelopmental disorders (NDDs), but because every monogenic NDD is different and usually extremely rare, it remains a major challenge to understand the complete phenotype and genotype spectrum of any morbid gene. According to OMIM, heterozygous variants in KDM6B cause "neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities." Here, by examining the molecular and clinical spectrum of 85 reported individuals with mostly de novo (likely) pathogenic KDM6B variants, we demonstrate that this description is inaccurate and potentially misleading. Cognitive deficits are seen consistently in all individuals, but the overall phenotype is highly variable. Notably, coarse facies and distal skeletal anomalies, as defined by OMIM, are rare in this expanded cohort while other features are unexpectedly common (e.g., hypotonia, psychosis, etc.). Using 3D protein structure analysis and an innovative dual Drosophila gain-of-function assay, we demonstrated a disruptive effect of 11 missense/in-frame indels located in or near the enzymatic JmJC or Zn-containing domain of KDM6B. Consistent with the role of KDM6B in human cognition, we demonstrated a role for the Drosophila KDM6B ortholog in memory and behavior. Taken together, we accurately define the broad clinical spectrum of the KDM6B-related NDD, introduce an innovative functional testing paradigm for the assessment of KDM6B variants, and demonstrate a conserved role for KDM6B in cognition and behavior. Our study demonstrates the critical importance of international collaboration, sharing of clinical data, and rigorous functional analysis of genetic variants to ensure correct disease diagnosis for rare disorders.
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Affiliation(s)
- Dmitrijs Rots
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | - Taryn E Jakub
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada
| | - Crystal Keung
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada
| | - Adam Jackson
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Rolph Pfundt
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | | | | | - Saskia M J Hopman
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Irene Valenzuela
- Hospital Universitari Vall D'Hebron, Clinical and Molecular Genetics Unit, Barcelona, Catalonia, Spain
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Francois Lecoquierre
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Alice Goldenberg
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Jens Michael Hertz
- Odense University Hospital, Department of Clinical Genetics, Odense, Denmark; University of Southern Denmark, Department of Clinical Research, Odense, Denmark
| | | | - Maria Kibæk
- Department of Pediatrics, Odense University Hospital, Odense, Denmark
| | | | | | | | | | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Charul Gijavanekar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Karl De Dios
- Division of Medical Genetics, Dayton Children's Hospital, Dayton, OH, USA
| | - Shenela Lakhani
- Center for Neurogenetics, Weill Cornell Medicine, Brain and Mind Research Institute, New York, NY, USA
| | - Tess Levy
- Center for Neurogenetics, Weill Cornell Medicine, Brain and Mind Research Institute, New York, NY, USA
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technical University Munich, Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany; Division of Pediatric Neurology, Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital, Munich, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Paul J Benke
- Division of Genetics, Joe DiMaggio Children's Hospital, Hollywood, FL, USA
| | | | - Renee Perrier
- Department of Medical Genetics, Alberta Children's Hospital and Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Sergio B Sousa
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Pedro M Almeida
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Maria José Simões
- CBR Genomics, Cantanhede, Portugal; Genoinseq, Next-Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France; Université de Nantes, CHU Nantes, CNRS, INSERM, l'Institut du Thorax, 44007 Nantes, France
| | - Wallid Deb
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France; Université de Nantes, CHU Nantes, CNRS, INSERM, l'Institut du Thorax, 44007 Nantes, France
| | - Andrew A Schmanski
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Omar Abdul-Rahman
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Ange-Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Laurence Faivre
- Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France; Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Génétique, FHU-TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Christel Thauvin
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Jeroen J Smits
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Stefano G Caraffi
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Francesca Peluso
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Laura Davis-Keppen
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Dylan Platt
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Erin Royer
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Lisette Leeuwen
- University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Margje Sinnema
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | - Alexander P A Stegmann
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | - Constance T R M Stumpel
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands; Department of Clinical Genetics and GROW-School for Oncology and Reproduction, Maastricht, the Netherlands
| | - George E Tiller
- Kaiser Permanente, Department of Genetics, Los Angeles, CA, USA
| | | | | | - Shelagh Joss
- West of Scotland Regional Genetics Service, Laboratory Medicine Building, Queen Elizabeth University Hospital, Glasgow, UK
| | - Miranda Splitt
- Northern Genetics Service, Institute of Genetic Medicine, International Centre for Life, Newcastle Upon Tyne NE1 3BZ, UK
| | - Simon Holden
- Department of Clinical Genetics, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Matina Prapa
- Department of Clinical Genetics, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Nicola Foulds
- Wessex Clinical Genetics Services, University Hospital Southampton NHS Foundation Trust, Southampton SO16 5YA, UK
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Kaija Puura
- Department of Child Psychiatry, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Regina Waltes
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - Andreas G Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - F Kyle Satterstrom
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Silvia De Rubeis
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph Buxbaum
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksic Branko
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan; Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Jennifer Howe
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Alessia Arado
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Chiara Baldo
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Olivier Patat
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Demeer Bénédicte
- Service de Génétique Clinique, Centre de référence maladies rares, CHU d'Amiens-site Sud, Amiens, France
| | - Diego Lopergolo
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy; UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 2, 53100 Siena, Italy; IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Pisa, Italy
| | - Filippo M Santorelli
- IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Pisa, Italy
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Ruth J Falb
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Angelika Rieß
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Peter Krieg
- Department of Pediatrics, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | | | | | - Maria Iascone
- Laboratory of Medical Genetics, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Sarah Josephi-Taylor
- Department of Clinical Genetics, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Tony Roscioli
- Neuroscience Research Australia, University of New South Wales, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics Laboratory, Sydney, NSW, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW 2031, Australia; Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2031, Australia
| | - Michael F Buckley
- New South Wales Health Pathology Randwick Genomics Laboratory, Sydney, NSW, Australia
| | - Jan Liebelt
- South Australian Clinical Genetics Service, Women's and Children's Hospital, Adelaide, SA, Australia
| | - Aditi I Dagli
- Orlando Health Arnold Palmer Hospital for Children, Division of Genetics, Orlando, FL, USA
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alesha Hicks
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, City Hospital Campus, Nottingham, UK
| | - Ermal Aliu
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Sunil Naik
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Richard Sidlow
- Valley Children's Hospital, Valley Children's Place, Madera, CA 93636, USA
| | - Juliette Coursimault
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Gaël Nicolas
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Hanna Küpper
- Neuropediatric Department, University Hospital Tübingen, Tübingen, Germany
| | - Florence Petit
- Centre Hospitalier Universitaire de Lille, Clinique de Génétique Guy Fontaine, Lille, France
| | - Veyan Ibrahim
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada; Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Deniz Top
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada; Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Francesca Di Cara
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | | | | | - Han G Brunner
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands; Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | | | - Jamie M Kramer
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada.
| | - Tjitske Kleefstra
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands; Center for Neuropsychiatry, Vincent van Gogh, Venray, the Netherlands; Department of Clinical Genetics, ErasmusMC, Rotterdam, the Netherlands.
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7
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Bogaert E, Garde A, Gautier T, Rooney K, Duffourd Y, LeBlanc P, van Reempts E, Tran Mau-Them F, Wentzensen IM, Au KS, Richardson K, Northrup H, Gatinois V, Geneviève D, Louie RJ, Lyons MJ, Laulund LW, Brasch-Andersen C, Maxel Juul T, El It F, Marle N, Callier P, Relator R, Haghshenas S, McConkey H, Kerkhof J, Cesario C, Novelli A, Brunetti-Pierri N, Pinelli M, Pennamen P, Naudion S, Legendre M, Courdier C, Trimouille A, Fenzy MD, Pais L, Yeung A, Nugent K, Roeder ER, Mitani T, Posey JE, Calame D, Yonath H, Rosenfeld JA, Musante L, Faletra F, Montanari F, Sartor G, Vancini A, Seri M, Besmond C, Poirier K, Hubert L, Hemelsoet D, Munnich A, Lupski JR, Philippe C, Thauvin-Robinet C, Faivre L, Sadikovic B, Govin J, Dermaut B, Vitobello A. SRSF1 haploinsufficiency is responsible for a syndromic developmental disorder associated with intellectual disability. Am J Hum Genet 2023; 110:790-808. [PMID: 37071997 PMCID: PMC10183470 DOI: 10.1016/j.ajhg.2023.03.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/23/2023] [Indexed: 04/20/2023] Open
Abstract
SRSF1 (also known as ASF/SF2) is a non-small nuclear ribonucleoprotein (non-snRNP) that belongs to the arginine/serine (R/S) domain family. It recognizes and binds to mRNA, regulating both constitutive and alternative splicing. The complete loss of this proto-oncogene in mice is embryonically lethal. Through international data sharing, we identified 17 individuals (10 females and 7 males) with a neurodevelopmental disorder (NDD) with heterozygous germline SRSF1 variants, mostly de novo, including three frameshift variants, three nonsense variants, seven missense variants, and two microdeletions within region 17q22 encompassing SRSF1. Only in one family, the de novo origin could not be established. All individuals featured a recurrent phenotype including developmental delay and intellectual disability (DD/ID), hypotonia, neurobehavioral problems, with variable skeletal (66.7%) and cardiac (46%) anomalies. To investigate the functional consequences of SRSF1 variants, we performed in silico structural modeling, developed an in vivo splicing assay in Drosophila, and carried out episignature analysis in blood-derived DNA from affected individuals. We found that all loss-of-function and 5 out of 7 missense variants were pathogenic, leading to a loss of SRSF1 splicing activity in Drosophila, correlating with a detectable and specific DNA methylation episignature. In addition, our orthogonal in silico, in vivo, and epigenetics analyses enabled the separation of clearly pathogenic missense variants from those with uncertain significance. Overall, these results indicated that haploinsufficiency of SRSF1 is responsible for a syndromic NDD with ID due to a partial loss of SRSF1-mediated splicing activity.
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Affiliation(s)
- Elke Bogaert
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Aurore Garde
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs", Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Thierry Gautier
- University Grenoble Alpes, Inserm U1209, CNRS UMR 5309, Institute for Advanced Biosciences (IAB), 38000 Grenoble, France
| | - Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Yannis Duffourd
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Pontus LeBlanc
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Emma van Reempts
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Frederic Tran Mau-Them
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | | | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Kate Richardson
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Vincent Gatinois
- Unité de Génétique Chromosomique, CHU Montpellier, Montpellier, France
| | - David Geneviève
- Montpellier University, Inserm U1183, Montpellier, France; Reference center for rare disease developmental anomaly malformative syndrome, Department of Medical Genetics, Montpellier Hospital, Montpellier, France
| | | | | | | | - Charlotte Brasch-Andersen
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark; Human Genetics, Department of Clinical Research, Health Faculty, University of Southern Denmark, 5000 Odense, Denmark
| | - Trine Maxel Juul
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Fatima El It
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France
| | - Nathalie Marle
- Laboratoire de Génétique Chromosomique et Moléculaire, Pôle de Biologie, CHU de Dijon, Dijon, France
| | - Patrick Callier
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Laboratoire de Génétique Chromosomique et Moléculaire, Pôle de Biologie, CHU de Dijon, Dijon, France
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Claudia Cesario
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | | | - Sophie Naudion
- Medical Genetics Department, CHU Bordeaux, Bordeaux, France
| | | | | | - Aurelien Trimouille
- INSERM U1211, Laboratoire MRGM, Bordeaux University, Bordeaux, France; Pathology Department, CHU Bordeaux, Bordeaux, France
| | - Martine Doco Fenzy
- Service de génétique, CHU de Reims, Reims, France; Service de génétique médicale, CHU de Nantes, Nantes, France; L'institut du thorax, INSERM, CNRS, UNIV Nantes, CHU de Nantes, Nantes, France
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Kimberly Nugent
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Daniel Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Hagith Yonath
- Internal Medicine A, Danek Gertner Institute of Human Genetics, Sheba Medical Center, Ramat Gan, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics Laboratories, Houston, TX, USA
| | - Luciana Musante
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Francesca Montanari
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanna Sartor
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Marco Seri
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Claude Besmond
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Karine Poirier
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Laurence Hubert
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Dimitri Hemelsoet
- Department of Neurology, Ghent University Hospital, 9000 Ghent, Belgium
| | - Arnold Munnich
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Christophe Philippe
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Christel Thauvin-Robinet
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France; Centre de Référence Maladies Rares « Déficiences intellectuelles de causes rares », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Laurence Faivre
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs", Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Jérôme Govin
- University Grenoble Alpes, Inserm U1209, CNRS UMR 5309, Institute for Advanced Biosciences (IAB), 38000 Grenoble, France
| | - Bart Dermaut
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium.
| | - Antonio Vitobello
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France.
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8
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Batkovskyte D, McKenzie F, Taylan F, Simsek-Kiper PO, Nikkel SM, Ohashi H, Stevenson RE, Ha T, Cavalcanti DP, Miyahara H, Skinner SA, Aguirre MA, Akçören Z, Utine GE, Chiu T, Shimizu K, Hammarsjö A, Boduroglu K, Moore HW, Louie RJ, Arts P, Merrihew AN, Babic M, Jackson MR, Papadogiannakis N, Lindstrand A, Nordgren A, Barnett CP, Scott HS, Chagin AS, Nishimura G, Grigelioniene G. Al-Gazali skeletal dysplasia constitutes the lethal end of ADAMTSL2-related disorders. J Bone Miner Res 2023; 38:692-706. [PMID: 36896612 DOI: 10.1002/jbmr.4799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023]
Abstract
Lethal short-limb skeletal dysplasia Al-Gazali type (OMIM %601356) is an ultra-rare disorder previously reported in only three unrelated individuals. The genetic etiology for Al-Gazali skeletal dysplasia has up until now been unknown. Through international collaborative efforts involving seven clinical centers worldwide, a cohort of nine patients with clinical and radiographic features consistent with short-limb skeletal dysplasia Al-Gazali type was collected. The affected individuals presented with moderate intrauterine growth restriction, relative macrocephaly, hypertrichosis, large anterior fontanelle, short neck, short and stiff limbs with small hands and feet, severe brachydactyly, and generalized bone sclerosis with mild platyspondyly. Biallelic disease-causing variants in ADAMTSL2 were detected using massively parallel sequencing (MPS) and Sanger sequencing techniques. Six individuals were compound heterozygous and one individual was homozygous for pathogenic variants in ADAMTSL2. In one of the families pathogenic variants were detected in parental samples only. Overall, this study sheds light on the genetic cause of Al-Gazali skeletal dysplasia and identifies it as a semi-lethal part of the spectrum of ADAMTSL2-related disorders. Furthermore, we highlight the importance of meticulous analysis of the pseudogene region of ADAMTSL2 where disease-causing variants might be located.
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Affiliation(s)
- Dominyka Batkovskyte
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Fiona McKenzie
- Genetic Services of Western Australia, Perth, WA, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Pelin Ozlem Simsek-Kiper
- Division of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine, Hacettepe University, 06100, Sihhiye, Ankara, Turkey
| | - Sarah M Nikkel
- Provincial Medical Genetics Program, BC Women's Hospital, Vancouver, British Columbia, Canada.,University of British Columbia, Vancouver, British Columbia, Canada
| | - Hirofumi Ohashi
- Division of Medical Genetics, Saitama Children's Medical Center, Saitama, Japan
| | | | - Thuong Ha
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia.,UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | - Denise P Cavalcanti
- Skeletal Dysplasias Group, Department of Translational Medicine, Medical Genetics, University of Campinas (UNICAMP), Campinas, Brazil
| | - Hiroyuki Miyahara
- Division of Neonatology, Kawaguchi City Medical Center, Kawaguchi, Japan
| | | | - Miguel A Aguirre
- Centro Nacional de Genética Médica (CENAGEM), A.N.L.I.S "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Zühal Akçören
- Division of Pediatric Pathology, Department of Pediatrics, Faculty of Medicine, Hacettepe University, 06100, Sihhiye, Ankara, Turkey
| | - Gulen Eda Utine
- Division of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine, Hacettepe University, 06100, Sihhiye, Ankara, Turkey
| | - Tillie Chiu
- CHEO Genetics Clinic, Regional Genetics Program, Ottawa, ON, Canada
| | - Kenji Shimizu
- Division of Medical Genetics, Saitama Children's Medical Center, Saitama, Japan
| | - Anna Hammarsjö
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Koray Boduroglu
- Division of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine, Hacettepe University, 06100, Sihhiye, Ankara, Turkey
| | - Hannah W Moore
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | | | - Peer Arts
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia.,UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | | | - Milena Babic
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia.,Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
| | - Matilda R Jackson
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia.,Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia.,Australian Genomics Health Alliance, Melbourne, VIC, Australia
| | - Nikos Papadogiannakis
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden.,Institute of Biomedicine, Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Christopher P Barnett
- Paediatric and Reproductive Genetics Unit, South Australian Clinical Genetics Service, Women's and Children's Hospital, North Adelaide, SA, Australia.,Adelaide Medical School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Hamish S Scott
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia.,UniSA Clinical and Health Sciences, University of South Australia, Adelaide, Australia.,Paediatric and Reproductive Genetics Unit, South Australian Clinical Genetics Service, Women's and Children's Hospital, North Adelaide, SA, Australia.,Adelaide Medical School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Andrei S Chagin
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.,Institute of Medicine, Gothenburg University, Gothenburg, Sweden
| | - Gen Nishimura
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Radiology, Musashino-Yowakai Hospital, Tokyo, Japan
| | - Giedre Grigelioniene
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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9
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Schwartz CE, Louie RJ, Toutain A, Skinner C, Friez MJ, Stevenson RE. X-Linked intellectual disability update 2022. Am J Med Genet A 2023; 191:144-159. [PMID: 36300573 DOI: 10.1002/ajmg.a.63008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 07/28/2022] [Accepted: 09/29/2022] [Indexed: 12/14/2022]
Abstract
Genes that are involved in the transcription process, mitochondrial function, glycoprotein metabolism, and ubiquitination dominate the list of 21 new genes associated with X-linked intellectual disability since the last update in 2017. The new genes were identified by sequencing of candidate genes (2), the entire X-chromosome (2), the whole exome (15), or the whole genome (2). With these additions, 42 (21%) of the 199 named XLID syndromes and 27 (25%) of the 108 numbered nonsyndromic XLID families remain to be resolved at the molecular level. Although the pace of discovery of new XLID genes has slowed during the past 5 years, the density of genes on the X chromosome that cause intellectual disability still appears to be twice the density of intellectual disability genes on the autosomes.
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Affiliation(s)
| | | | - Annick Toutain
- Department of Medical Genetics, Centre Hospitalier Universitaire, Tours, France
| | - Cindy Skinner
- Greenwood Genetic Center, Greenwood, South Carolina, USA
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10
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Cooley Coleman JA, Gass JM, Srikanth S, Pauly R, Ziats CA, Everman DB, Skinner SA, Bell S, Louie RJ, Cascio L, Patterson WG, Jones JR, Di Donato N, Stevenson RE, Boccuto L. Clinical and functional characterization of germline PIK3CA variants in patients with PIK3CA-related overgrowth Spectrum disorders. Hum Mol Genet 2022; 32:1457-1465. [PMID: 36458889 DOI: 10.1093/hmg/ddac296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Abstract
Mosaic variants in the PIK3CA gene, encoding the catalytic subunit of phosphatidylinositol 3-kinase (PI3K), produce constitutive PI3K activation which causes PIK3CA-related overgrowth spectrum (PROS) disorders. To date, fewer than 20 patients have been described with germline alterations in PIK3CA. In this study, we describe three unrelated individuals with overgrowth and germline PIK3CA variants. These variants were discovered through whole-exome sequencing and confirmed as germline by testing multiple tissue types, when available. Functional analysis using Patient 1’s fibroblast cell line and two previously reported patients’ cell lines showed increased phosphorylation of AKT during cellular starvation revealing constitutive activation of the PI3K/AKT/mTOR pathway. Alternatively, stimulation of the cells by fetal bovine serum produced a reduced response, indicating an activated status of the PI3K complex reducing the pathway response to further external stimulation. Additional studies utilizing Biolog Phenotype Microarray technology indicated reduced energy production when cells were exposed to growth factors stimulating the PI3K/AKT/mTOR pathway, confirming the trend observed in the AKT phosphorylation test after stimulation. Furthermore, treatment with inhibitors of the PI3K/AKT/mTOR pathway rescued the normal energy response in the patients’ cells. Collectively, these data demonstrate that disease-causing germline PIK3CA variants have a functional consequence, similar to mosaic variants in the PI3K/AKT/mTOR pathway.
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Affiliation(s)
| | - Jennifer M Gass
- Greenwood Genetic Center , Greenwood, South Carolina, 29646 USA
- Florida Cancer Specialist , Fort Myers, Florida 33916 USA
| | - Sujata Srikanth
- Greenwood Genetic Center , Greenwood, South Carolina, 29646 USA
- REDDILAB , Clemson University, Clemson, South Carolina, 29634 USA
| | - Rini Pauly
- Greenwood Genetic Center , Greenwood, South Carolina, 29646 USA
| | - Catherine A Ziats
- Greenwood Genetic Center , Greenwood, South Carolina, 29646 USA
- Division of Medical Genetics , Department of Pediatrics, Dell Medical School at the University of Texas, Austin, Texas, 78712 USA
| | - David B Everman
- Greenwood Genetic Center , Greenwood, South Carolina, 29646 USA
| | | | - Shannon Bell
- Greenwood Genetic Center , Greenwood, South Carolina, 29646 USA
| | - Raymond J Louie
- Greenwood Genetic Center , Greenwood, South Carolina, 29646 USA
| | - Lauren Cascio
- Greenwood Genetic Center , Greenwood, South Carolina, 29646 USA
- REDDILAB , Clemson University, Clemson, South Carolina, 29634 USA
| | | | - Julie R Jones
- Greenwood Genetic Center , Greenwood, South Carolina, 29646 USA
| | - Nataliya Di Donato
- Institute for Clinical Genetics , University Hospital, TU Dresden, Dresden , Germany
| | | | - Luigi Boccuto
- Greenwood Genetic Center , Greenwood, South Carolina, 29646 USA
- School of Nursing , College of Behavioral, Social and Health Sciences, Clemson University, Clemson, South Carolina, 29634 USA
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11
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Schalk A, Cousin MA, Dsouza NR, Challman TD, Wain KE, Powis Z, Minks K, Trimouille A, Lasseaux E, Lacombe D, Angelini C, Michaud V, Van-Gils J, Spataro N, Ruiz A, Gabau E, Stolerman E, Washington C, Louie RJ, Lanpher BC, Kemppainen JL, Innes AM, Kooy RF, Meuwissen M, Goldenberg A, Lecoquierre F, Vera G, Diderich KEM, Sheidley BR, Achkar CME, Park M, Hamdan FF, Michaud JL, Lewis AJ, Zweier C, Reis A, Wagner M, Weigand H, Journel H, Keren B, Passemard S, Mignot C, van Gassen KL, Brilstra EH, Itzikowitz G, O’Heir E, Allen J, Donald KA, Korf BR, Skelton T, Thompson ML, Robin NH, Rudy N, Dobyns WB, Foss K, Zarate YA, Bosanko KA, Alembik Y, Durand B, Mau-Them FT, Ranza E, Blanc X, Antonarakis SE, McWalter K, Torti E, Millan F, Dameron A, Tokita MJ, Zimmermann MT, Klee EW, Piton A, Gerard B. De novo coding variants in the AGO1 gene cause a neurodevelopmental disorder with intellectual disability. J Med Genet 2022; 59:965-975. [PMID: 34930816 PMCID: PMC9241146 DOI: 10.1136/jmedgenet-2021-107751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 11/09/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND High-impact pathogenic variants in more than a thousand genes are involved in Mendelian forms of neurodevelopmental disorders (NDD). METHODS This study describes the molecular and clinical characterisation of 28 probands with NDD harbouring heterozygous AGO1 coding variants, occurring de novo for all those whose transmission could have been verified (26/28). RESULTS A total of 15 unique variants leading to amino acid changes or deletions were identified: 12 missense variants, two in-frame deletions of one codon, and one canonical splice variant leading to a deletion of two amino acid residues. Recurrently identified variants were present in several unrelated individuals: p.(Phe180del), p.(Leu190Pro), p.(Leu190Arg), p.(Gly199Ser), p.(Val254Ile) and p.(Glu376del). AGO1 encodes the Argonaute 1 protein, which functions in gene-silencing pathways mediated by small non-coding RNAs. Three-dimensional protein structure predictions suggest that these variants might alter the flexibility of the AGO1 linker domains, which likely would impair its function in mRNA processing. Affected individuals present with intellectual disability of varying severity, as well as speech and motor delay, autistic behaviour and additional behavioural manifestations. CONCLUSION Our study establishes that de novo coding variants in AGO1 are involved in a novel monogenic form of NDD, highly similar to the recently reported AGO2-related NDD.
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Affiliation(s)
- Audrey Schalk
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
| | - Margot A. Cousin
- Department of Health Sciences Research, Mayo Clinic,
Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
| | - Nikita R. Dsouza
- Bioinformatics Research and Development Laboratory,
Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin,
Milwaukee, WI 53226, USA
| | - Thomas D. Challman
- Autism & Developmental Medicine Institute, Geisinger,
Lewisburg, Pennsylvania, PA 17837, United States
| | - Karen E. Wain
- Autism & Developmental Medicine Institute, Geisinger,
Lewisburg, Pennsylvania, PA 17837, United States
| | - Zöe Powis
- Department of Clinical Genomics, Ambry Genetics, Aliso
Viejo, California, CA 92656, United States
| | - Kelly Minks
- Department of Clinical Genomics, Ambry Genetics, Aliso
Viejo, California, CA 92656, United States
| | - Aurélien Trimouille
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
- Maladies rares: Génétique et
Métabolisme (MRGM), INSERM U1211, Université de Bordeaux,
Bordeaux
| | - Eulalie Lasseaux
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
| | - Didier Lacombe
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
| | - Chloé Angelini
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
- Maladies rares: Génétique et
Métabolisme (MRGM), INSERM U1211, Université de Bordeaux,
Bordeaux
| | - Vincent Michaud
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
- Maladies rares: Génétique et
Métabolisme (MRGM), INSERM U1211, Université de Bordeaux,
Bordeaux
| | - Julien Van-Gils
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
| | - Nino Spataro
- Genetics Laboratory, UDIAT-Centre Diagnòstic. Parc
Taulí Hospital Universitari. Institut d’Investigació i
Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona.
Sabadell, Spain
| | - Anna Ruiz
- Genetics Laboratory, UDIAT-Centre Diagnòstic. Parc
Taulí Hospital Universitari. Institut d’Investigació i
Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona.
Sabadell, Spain
| | - Elizabeth Gabau
- Paediatric Unit. ParcTaulí Hospital Universitari.
Institut d’Investigació i Innovació Parc Taulí I3PT.
Universitat Autònoma de Barcelona. Sabadell, Spain
| | - Elliot Stolerman
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Camerun Washington
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Raymond J. Louie
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester,
Minnesota, MN 55905, United States
| | - Jennifer L. Kemppainen
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester,
Minnesota, MN 55905, United States
| | - A. Micheil Innes
- Department of Medical Genetics and Alberta
Children’s Hospital Research Institute, Cumming School of Medicine,
University of Calgary, Calgary, AB, Canada
| | - R. Frank Kooy
- Department of Medical Genetics, University and University
Hospital Antwerp, Antwerp, Belgium
| | - Marije Meuwissen
- Department of Medical Genetics, University and University
Hospital Antwerp, Antwerp, Belgium
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen
University Hospital, Department of Genetics and Reference Center for Developmental
Disorders, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen,
France
| | - François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen
University Hospital, Department of Genetics and Reference Center for Developmental
Disorders, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen,
France
| | - Gabriella Vera
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen
University Hospital, Department of Genetics and Reference Center for Developmental
Disorders, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen,
France
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus Medical Center,
Rotterdam, The Netherlands
| | - Beth Rosen Sheidley
- Division of Epilepsy and Clinical Neurophysiology,
Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts,
MA 02115, United States
| | - Christelle Moufawad El Achkar
- Division of Epilepsy and Clinical Neurophysiology,
Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts,
MA 02115, United States
| | - Meredith Park
- Division of Epilepsy and Clinical Neurophysiology,
Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts,
MA 02115, United States
| | - Fadi F. Hamdan
- Division of Medical Genetics, Department of Pediatrics,
CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Jacques L. Michaud
- Division of Medical Genetics, Department of Pediatrics,
CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Ann J. Lewis
- Pediatric Neurology, Kaiser Permanente Santa Clara
Homestead, Santa Clara, United States
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern
University Hospital, University of Bern, Bern, Switzerland
- Institute of Human Genetics,
Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen,
Germany
| | - André Reis
- Department of Human Genetics, Inselspital, Bern
University Hospital, University of Bern, Bern, Switzerland
- Institute of Human Genetics,
Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen,
Germany
| | - Matias Wagner
- Institute of Human Genetics, Technical University Munich,
Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum
München, Neuherberg, Germany
| | - Heike Weigand
- Department of Pediatric Neurology, Developmental Medicine
and Social Pediatrics, Dr. von Hauner’s Children’s Hospital,
University of Munich, Munich, Germany
| | - Hubert Journel
- Service de Génétique Médicale,
Hôpital Chubert, Vannes, France
| | - Boris Keren
- Département de Génétique et de
Cytogénétique, Centre de Reference Déficience Intellectuelle de
Causes Rares, GRC UPMC « Déficience Intellectuelle et Autisme
», Hôpital Pitié-Salpêtrière, AP-HP, Paris,
France
- INSERM U 1127, CNRS UMR 7225, Sorbonne
Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la
Moelle épinière, ICM, Paris, France
| | | | - Cyril Mignot
- Département de Génétique et de
Cytogénétique, Centre de Reference Déficience Intellectuelle de
Causes Rares, GRC UPMC « Déficience Intellectuelle et Autisme
», Hôpital Pitié-Salpêtrière, AP-HP, Paris,
France
- INSERM U 1127, CNRS UMR 7225, Sorbonne
Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la
Moelle épinière, ICM, Paris, France
| | | | - Eva H. Brilstra
- Department of Genetics, Center for Molecular Medicine,
University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gina Itzikowitz
- Department of Paediatrics and Child Health, Red Cross War
Memorial Children’s Hospital, University of Cape Town, SA
| | - Emily O’Heir
- Center for Mendelian Genomics and Program in Medical and
Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston
Children’s Hospital, Boston, MA, USA
| | - Jake Allen
- Stanley Center for Psychiatric Research, Broad Institute
of MIT and Harvard, Cambridge, MA, USA
| | - Kirsten A. Donald
- Department of Paediatrics and Child Health, Red Cross War
Memorial Children’s Hospital, University of Cape Town, SA
- Neuroscience Institute, University of Cape Town, SA
| | - Bruce R. Korf
- Department of Genetics, University of Alabama at
Birmingham, Birmingham, AL 35294, USA
| | - Tammi Skelton
- Department of Genetics, University of Alabama at
Birmingham, Birmingham, AL 35294, USA
| | - Michelle L Thompson
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
- HudsonAlpha Institute for Biotechnology, Huntsville,
Alabama, USA
| | - Nathaniel H. Robin
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - Natasha Rudy
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - William B. Dobyns
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - Kimberly Foss
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - Yuri A Zarate
- Section of Genetics and Metabolism, University of
Arkansas for Medical Sciences, Little Rock, USA
| | - Katherine A. Bosanko
- Section of Genetics and Metabolism, University of
Arkansas for Medical Sciences, Little Rock, USA
| | - Yves Alembik
- Service de Génétique Médicale,
Institut de génétique médicale d’Alsace (IGMA),
Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Benjamin Durand
- Service de Génétique Médicale,
Institut de génétique médicale d’Alsace (IGMA),
Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Frédéric Tran Mau-Them
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, 1207
Geneva, Switzerland
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, 1207
Geneva, Switzerland
| | | | | | | | | | | | | | - Michael T. Zimmermann
- Bioinformatics Research and Development Laboratory,
Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin,
Milwaukee, WI 53226, USA
- Clinical and Translational Sciences Institute, Medical
College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biochemistry, Medical College of Wisconsin,
Milwaukee, WI 53226, USA
| | - Eric W. Klee
- Department of Health Sciences Research, Mayo Clinic,
Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Amélie Piton
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
- Institut de Genetique et de Biologie Moleculaire et
Cellulaire, Illkirch 67400, France
| | - Bénédicte Gerard
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
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12
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Küry S, Zhang J, Besnard T, Caro-Llopis A, Zeng X, Robert SM, Josiah SS, Kiziltug E, Denommé-Pichon AS, Cogné B, Kundishora AJ, Hao LT, Li H, Stevenson RE, Louie RJ, Deb W, Torti E, Vignard V, McWalter K, Raymond FL, Rajabi F, Ranza E, Grozeva D, Coury SA, Blanc X, Brischoux-Boucher E, Keren B, Õunap K, Reinson K, Ilves P, Wentzensen IM, Barr EE, Guihard SH, Charles P, Seaby EG, Monaghan KG, Rio M, van Bever Y, van Slegtenhorst M, Chung WK, Wilson A, Quinquis D, Bréhéret F, Retterer K, Lindenbaum P, Scalais E, Rhodes L, Stouffs K, Pereira EM, Berger SM, Milla SS, Jaykumar AB, Cobb MH, Panchagnula S, Duy PQ, Vincent M, Mercier S, Gilbert-Dussardier B, Le Guillou X, Audebert-Bellanger S, Odent S, Schmitt S, Boisseau P, Bonneau D, Toutain A, Colin E, Pasquier L, Redon R, Bouman A, Rosenfeld JA, Friez MJ, Pérez-Peña H, Akhtar Rizvi SR, Haider S, Antonarakis SE, Schwartz CE, Martínez F, Bézieau S, Kahle KT, Isidor B. Rare pathogenic variants in WNK3 cause X-linked intellectual disability. Genet Med 2022; 24:1941-1951. [PMID: 35678782 DOI: 10.1016/j.gim.2022.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 02/08/2023] Open
Abstract
PURPOSE WNK3 kinase (PRKWNK3) has been implicated in the development and function of the brain via its regulation of the cation-chloride cotransporters, but the role of WNK3 in human development is unknown. METHOD We ascertained exome or genome sequences of individuals with rare familial or sporadic forms of intellectual disability (ID). RESULTS We identified a total of 6 different maternally-inherited, hemizygous, 3 loss-of-function or 3 pathogenic missense variants (p.Pro204Arg, p.Leu300Ser, p.Glu607Val) in WNK3 in 14 male individuals from 6 unrelated families. Affected individuals had ID with variable presence of epilepsy and structural brain defects. WNK3 variants cosegregated with the disease in 3 different families with multiple affected individuals. This included 1 large family previously diagnosed with X-linked Prieto syndrome. WNK3 pathogenic missense variants localize to the catalytic domain and impede the inhibitory phosphorylation of the neuronal-specific chloride cotransporter KCC2 at threonine 1007, a site critically regulated during the development of synaptic inhibition. CONCLUSION Pathogenic WNK3 variants cause a rare form of human X-linked ID with variable epilepsy and structural brain abnormalities and implicate impaired phospho-regulation of KCC2 as a pathogenic mechanism.
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Affiliation(s)
- Sébastien Küry
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France.
| | - Jinwei Zhang
- Hatherly Laboratories, The Institute of Biomedical and Clinical Sciences, College of Medicine and Health, University of Exeter, Exeter, United Kingdom; Department of Neurosurgery, Yale School of Medicine, Yale University, New Haven, CT; State Key Laboratory of Bio-Organic and Natural Products Chemistry, Research Center of Chemical Kinomics, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Thomas Besnard
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Alfonso Caro-Llopis
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Xue Zeng
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT
| | - Stephanie M Robert
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT
| | - Sunday S Josiah
- Hatherly Laboratories, The Institute of Biomedical and Clinical Sciences, College of Medicine and Health, University of Exeter, Exeter, United Kingdom
| | - Emre Kiziltug
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT
| | - Anne-Sophie Denommé-Pichon
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire Angers, Angers, France; UMR CNRS 6214, INSERM 1083, Université d'Angers, Angers, France
| | - Benjamin Cogné
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Adam J Kundishora
- Department of Neurosurgery, Yale School of Medicine, Yale University, New Haven, CT
| | - Le T Hao
- Department of Neurosurgery, Yale School of Medicine, Yale University, New Haven, CT
| | - Hong Li
- Departments of Human Genetics and Pediatrics, School of Medicine, Emory University, Atlanta, GA
| | | | | | - Wallid Deb
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | | | - Virginie Vignard
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | | | - F Lucy Raymond
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Biomedical Campus Cambridge, Cambridge, United Kingdom
| | - Farrah Rajabi
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Detelina Grozeva
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Biomedical Campus Cambridge, Cambridge, United Kingdom; Centre for Trials Research, Cardiff University, Cardiff, United Kingdom
| | - Stephanie A Coury
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Elise Brischoux-Boucher
- Centre de Génétique Humaine, CHU de Besançon, Université de Bourgogne Franche-Comté, Besançon, France
| | - Boris Keren
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Karit Reinson
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Pilvi Ilves
- Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia; Department of Radiology, Tartu University Hospital, Tartu, Estonia
| | | | - Eileen E Barr
- Departments of Human Genetics and Pediatrics, School of Medicine, Emory University, Atlanta, GA
| | - Solveig Heide Guihard
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Groupe de Recherche Clinique, Déficience Intellectuelle et Autisme, Sorbonne University, Paris, France
| | - Perrine Charles
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Eleanor G Seaby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Genomic Informatics Group, University of Southampton, Southampton, United Kingdom
| | | | - Marlène Rio
- Developmental Brain Disorders laboratory, INSERM UMR 1163, Imagine Institute, University of Paris, Paris, France; Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Necker Enfants Malades Hospital, APHP, Paris, France
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, Columbia University New York, NY
| | - Ashley Wilson
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Delphine Quinquis
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Flora Bréhéret
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France
| | | | - Pierre Lindenbaum
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Emmanuel Scalais
- Division of Pediatric Neurology, Department of Pediatrics, Centre Hospitalier de Luxembourg, Luxembourg City, Luxembourg
| | | | - Katrien Stouffs
- Neurogenetics Research Group, Reproduction and Genetics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan, Brussels, Belgium
| | - Elaine M Pereira
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Sara M Berger
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Sarah S Milla
- Department of Radiology and Imaging Sciences, School of Medicine, Emory University, Atlanta, GA
| | - Ankita B Jaykumar
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX
| | - Melanie H Cobb
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX
| | - Shreyas Panchagnula
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Phan Q Duy
- Department of Neurosurgery, Yale School of Medicine, Yale University, New Haven, CT
| | - Marie Vincent
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Sandra Mercier
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | | | | | | | - Sylvie Odent
- Service de Génétique Clinique, ERN ITHACA, CHU Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, IGDR UMR 6290 CNRS, INSERM, IGDR Univ Rennes, Rennes, France
| | - Sébastien Schmitt
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Pierre Boisseau
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Dominique Bonneau
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire Angers, Angers, France; UMR CNRS 6214, INSERM 1083, Université d'Angers, Angers, France
| | - Annick Toutain
- Unité de Génétique Médicale, Centre Hospitalier Régional Universitaire de Tours, France; Unité Mixte de Recherche 1253, iBrain, Université de Tours, Institut National de la Santé et de la Recherche Médicale, Tours, France
| | - Estelle Colin
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire Angers, Angers, France; UMR CNRS 6214, INSERM 1083, Université d'Angers, Angers, France
| | - Laurent Pasquier
- Service de Génétique Clinique, ERN ITHACA, CHU Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, IGDR UMR 6290 CNRS, INSERM, IGDR Univ Rennes, Rennes, France
| | - Richard Redon
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | - Helena Pérez-Peña
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, University College London, London, United Kingdom
| | - Syed Raza Akhtar Rizvi
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, University College London, London, United Kingdom
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, University College London, London, United Kingdom; Centre for Advanced Research Computing, University College London, London, United Kingdom
| | - Stylianos E Antonarakis
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland; Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland; iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, Geneva, Switzerland
| | | | - Francisco Martínez
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Stéphane Bézieau
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale School of Medicine, Yale University, New Haven, CT; Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT; NIH-Yale Centers for Mendelian Genomics, Yale School of Medicine, Yale University, New Haven, CT; Yale Stem Cell Center, Yale School of Medicine, Yale University, New Haven, CT.
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
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13
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Levy MA, Relator R, McConkey H, Pranckeviciene E, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Ferilli M, Fletcher RS, Cherick F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Plomp AS, Poulton C, Reilly J, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, John MS, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci TB, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Campion D, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Heron D, Husson T, Kernohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vincent M, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders. Hum Mutat 2022; 43:1609-1628. [PMID: 35904121 DOI: 10.1002/humu.24446] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/30/2022] [Accepted: 07/27/2022] [Indexed: 11/10/2022]
Abstract
An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes which can share significant overlap amongst different conditions. In this study we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Erinija Pranckeviciene
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | | | - Mariet W Elting
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Marco Ferilli
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Florian Cherick
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, The Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000, Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | | | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | | | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Delphine Heron
- AP-HP, Département de Génétique Médicale, Groupe Hospitalier Pitié Salpétrière, Paris, France
| | - Thomas Husson
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, UK, and Sheffield Children's Hospital NHS Foundation Trust
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Dept of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Marie Vincent
- Service de génétique Médicale, CHU Nantes, France.,Institut du thorax, INSERM, CNRS, UNIV Nantes, 44007, Nantes, France
| | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
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14
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Sohn YB, Rogers C, Stallworth J, Cooley Coleman JA, Buch L, Jozwiak E, Johnson JA, Wood T, Harmatz P, Pollard L, Louie RJ. RNA analysis of the GALNS transcript reveals novel pathogenic mechanisms associated with Morquio syndrome A. Mol Genet Metab Rep 2022; 31:100875. [PMID: 35782621 PMCID: PMC9248232 DOI: 10.1016/j.ymgmr.2022.100875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 11/29/2022] Open
Abstract
Morquio syndrome A (Mucopolysaccharidosis IVA, MPS IVA) is an autosomal recessive lysosomal storage disorder caused by deficiency of N-acetyl-galactosamine-6-sulfatase (GALNS) which catabolizes the glycosaminoglycans (GAG), keratan sulfate and chondroitin-6-sulfate. Homozygous or compound heterozygous pathogenic variants in the GALNS result in the deficiency of the enzyme and consequent GAG accumulations. DNA sequence and copy number analysis of the GALNS coding region fails to identify biallelic causative pathogenic variants in up to 15% of patients with Morquio syndrome A. RNA transcript analysis was performed to identify pathogenic alterations in two unrelated families with Morquio syndrome A in whom a single heterozygous or no pathogenic alteration was detected by standard analysis of the GALNS gene. RNA sequencing and quantitative expression analysis identified the overabundance of an aberrant GALNS transcript isoform and a reduction of the clinically relevant isoform (NM_000512.4) in the Morquio syndrome A patients from both families. The aberrant isoform (ENST00000568613.1) was produced by alternative splicing and contained intronic sequence that was likely a cryptic exon predicted to result in a reading frame shift and generation of a premature termination codon. These findings indicated that the aberrant splicing is likely the novel molecular defect in our patients. RNA transcript analysis could be useful to identify pathogenic alterations and increase the yield of molecular diagnosis in patients with Morquio syndrome A whose genetic variants are not found by standard sequencing or gene dosage analysis.
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Affiliation(s)
- Young Bae Sohn
- Department of Medical Genetics, Ajou University Hospital, Ajou University School of Medicine, Suwon, Republic of Korea
- Corresponding author at: Department of Medical Genetics, Ajou University Hospital, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea.
| | | | | | | | - Laura Buch
- Greenwood Genetic Center, Greenwood, SC, USA
| | - Erin Jozwiak
- UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
| | - Jo Ann Johnson
- UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
| | - Tim Wood
- Section of Genetics and Metabolism, University of Colorado/Children's Hospital of Colorado, Aurora, CO, USA
| | - Paul Harmatz
- UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
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15
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Tedder ML, DuPont BR, Lee JA, Louie RJ, Kerkhof J, Sadikovic B, Friez MJ. 30. The application of DNA methylation episignatures to resolve variants of uncertain clinical significance. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.05.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Cordovado A, Schaettin M, Jeanne M, Panasenkava V, Denommé-Pichon AS, Keren B, Mignot C, Doco-Fenzy M, Rodan L, Ramsey K, Narayanan V, Jones JR, Prijoles EJ, Mitchell WG, Ozmore JR, Juliette K, Torti E, Normand EA, Granger L, Petersen AK, Au MG, Matheny JP, Phornphutkul C, Chambers MK, Fernández-Ramos JA, López-Laso E, Kruer MC, Bakhtiari S, Zollino M, Morleo M, Marangi G, Mei D, Pisano T, Guerrini R, Louie RJ, Childers A, Everman DB, Isidor B, Audebert-Bellanger S, Odent S, Bonneau D, Gilbert-Dussardier B, Redon R, Bézieau S, Laumonnier F, Stoeckli ET, Toutain A, Vuillaume ML. SEMA6B variants cause intellectual disability and alter dendritic spine density and axon guidance. Hum Mol Genet 2022; 31:3325-3340. [PMID: 35604360 DOI: 10.1093/hmg/ddac114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/25/2022] [Accepted: 05/12/2022] [Indexed: 11/14/2022] Open
Abstract
Intellectual disability is a neurodevelopmental disorder frequently caused by monogenic defects. In this study, we collected 14 SEMA6B heterozygous variants in 16 unrelated patients referred for intellectual disability to different centres. Whereas until now SEMA6B variants have mainly been reported in patients with progressive myoclonic epilepsy, our study indicates that the clinical spectrum is wider, and also includes non-syndromic intellectual disability without epilepsy or myoclonus. To assess the pathogenicity of these variants, selected mutated forms of Sema6b were overexpressed in HEK293T cells and in primary neuronal cultures. shRNAs targeting Sema6b were also used in neuronal cultures to measure the impact of the decreased Sema6b expression on morphogenesis and synaptogenesis. The overexpression of some variants leads to a subcellular mislocalisation of SEMA6B protein in HEK293T cells and to a reduced spine density due to loss of mature spines in neuronal cultures. Sema6b knock-down also impairs spine density and spine maturation. In addition, we conducted in vivo rescue experiments in chicken embryos with the selected mutated forms of Sema6b expressed in commissural neurons after knock-down of endogenous SEMA6B. We observed that expression of these variants in commissural neurons fails to rescue the normal axon pathway. In conclusion, identification of SEMA6B variants in patients presenting with an overlapping phenotype with intellectual disability, and functional studies highlight the important role of SEMA6B in neuronal development, notably in spine formation and maturation, and in axon guidance. This study adds SEMA6B to the list of intellectual disability-related genes.
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Affiliation(s)
- Amélie Cordovado
- UMR 1253, iBrain, University of Tours, Inserm, 37032 Tours, France
| | - Martina Schaettin
- Department of Molecular Life Sciences and Neuroscience Center Zurich, University of Zurich, Zurich 8057, Switzerland
| | - Médéric Jeanne
- UMR 1253, iBrain, University of Tours, Inserm, 37032 Tours, France.,Genetics Department, University Hospital of Tours, 37044 Tours, France
| | | | - Anne-Sophie Denommé-Pichon
- Functional Unit in Innovative Genomic Diagnosis of Rare Diseases, FHU-TRANSLAD, Dijon-Bourgogne University Hospital, Dijon, France.,UMR1231 GAD, Inserm - Bourgogne-Franche Comté University, Dijon, France
| | - Boris Keren
- Genetics Department, Pitié-Salpêtrière Hospital, AP-HP. Sorbonne University, 75651 Paris, France
| | - Cyril Mignot
- Genetics Department, Pitié-Salpêtrière Hospital, AP-HP. Sorbonne University, 75651 Paris, France
| | - Martine Doco-Fenzy
- University Hospital Reims, AMH2, Genetics Division, SFR CAP santé EA3801, Reims, France
| | - Lance Rodan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.,Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Julie R Jones
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, SC, USA
| | | | - Wendy G Mitchell
- Neurology Division, Keck School of Medicine, University of Southern California, Children's Hospital Los Angeles, USA
| | | | - Kali Juliette
- Gillette Children's Specialty Healthcare: Neurology Department, St Paul, MN 55101, USA
| | | | | | - Leslie Granger
- Genetics Division, Department of Pediatric Development and Rehabilitation, Randall Children's Hospital, Portland, OR 97227, USA
| | - Andrea K Petersen
- Genetics Division, Department of Pediatric Development and Rehabilitation, Randall Children's Hospital, Portland, OR 97227, USA
| | - Margaret G Au
- University of Kentucky: Department of Genetics and Metabolism, Lexington, KY 40536, USA
| | - Juliann P Matheny
- University of Kentucky: Department of Genetics and Metabolism, Lexington, KY 40536, USA
| | - Chanika Phornphutkul
- Division of Human Genetics, Department of Pediatrics, Warren Alpert Medical School of Brown University, Hasbro Children's Hospital, Providence, RI 02903, USA
| | - Mary-Kathryn Chambers
- Division of Genetics, Rhode Island Hospital, Hasbro Children's Hospital, Providence, RI 02903, USA
| | | | - Eduardo López-Laso
- Pediatric Neurology Unit, department of Pediatrics, University Hospital Reina Sofía, IMIBIC and CIBERER, Córdoba, Spain
| | - Michael C Kruer
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA.,Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA.,Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Marcella Zollino
- Università Cattolica Sacro Cuore, Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Roma, Italy.,Fondazione Policlinico A. Gemelli IRCCS, U. O. C. Genetica Medica, Roma, Italy
| | - Manuela Morleo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy.,Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples 80138, Italy
| | - Giuseppe Marangi
- Università Cattolica Sacro Cuore, Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Roma, Italy.,Fondazione Policlinico A. Gemelli IRCCS, U. O. C. Genetica Medica, Roma, Italy
| | - Davide Mei
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children's Hospital, Member of ERN Epicare, University of Florence, Florence, Italy
| | - Tiziana Pisano
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children's Hospital, Member of ERN Epicare, University of Florence, Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children's Hospital, Member of ERN Epicare, University of Florence, Florence, Italy
| | - Raymond J Louie
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, SC, USA
| | - Anna Childers
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, SC, USA
| | - David B Everman
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, SC, USA
| | - Betrand Isidor
- Medical Genetics Service, Clinical Genetics Unit, University Hospital of Nantes, Hôtel Dieu, 44093 Nantes, France
| | | | - Sylvie Odent
- Clinical Genetics Service, University Hospital, Genetic and Development Institute of Rennes IGDR, UMR 6290 University of Rennes, ITHACA ERN, 35203 Rennes, France
| | - Dominique Bonneau
- Department of Medical Genetics, University Hospital of Angers and Mitovasc INSERM 1083, CNRS 6015, 49000 Angers, France
| | | | - Richard Redon
- INSERM, CNRS, UNIV Nantes, Thorax Institute, 44007 Nantes, France
| | - Stéphane Bézieau
- INSERM, CNRS, UNIV Nantes, Thorax Institute, 44007 Nantes, France.,University Hospital of Nantes, Medical Genetics Service 44093 Nantes, France
| | | | - Esther T Stoeckli
- Department of Molecular Life Sciences and Neuroscience Center Zurich, University of Zurich, Zurich 8057, Switzerland
| | - Annick Toutain
- UMR 1253, iBrain, University of Tours, Inserm, 37032 Tours, France.,Genetics Department, University Hospital of Tours, 37044 Tours, France
| | - Marie-Laure Vuillaume
- UMR 1253, iBrain, University of Tours, Inserm, 37032 Tours, France.,Genetics Department, University Hospital of Tours, 37044 Tours, France
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17
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Cherik F, Reilly J, Kerkhof J, Levy M, McConkey H, Barat-Houari M, Butler KM, Coubes C, Lee JA, Le Guyader G, Louie RJ, Patterson WG, Tedder ML, Bak M, Hammer TB, Craigen W, Démurger F, Dubourg C, Fradin M, Franciskovich R, Frengen E, Friedman J, Palares NR, Iascone M, Misceo D, Monin P, Odent S, Philippe C, Rouxel F, Saletti V, Strømme P, Thulin PC, Sadikovic B, Genevieve D. DNA methylation episignature in Gabriele-de Vries syndrome. Genet Med 2022; 24:905-914. [PMID: 35027293 DOI: 10.1016/j.gim.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE Gabriele-de Vries syndrome (GADEVS) is a rare genetic disorder characterized by developmental delay and/or intellectual disability, hypotonia, feeding difficulties, and distinct facial features. To refine the phenotype and to better understand the molecular basis of the syndrome, we analyzed clinical data and performed genome-wide DNA methylation analysis of a series of individuals carrying a YY1 variant. METHODS Clinical data were collected for 13 individuals not yet reported through an international call for collaboration. DNA was collected for 11 of these individuals and 2 previously reported individuals in an attempt to delineate a specific DNA methylation signature in GADEVS. RESULTS Phenotype in most individuals overlapped with the previously described features. We described 1 individual with atypical phenotype, heterozygous for a missense variant in a domain usually not involved in individuals with YY1 pathogenic missense variations. We also described a specific peripheral blood DNA methylation profile associated with YY1 variants. CONCLUSION We reported a distinct DNA methylation episignature in GADEVS. We expanded the clinical profile of GADEVS to include thin/sparse hair and cryptorchidism. We also highlighted the utility of DNA methylation episignature analysis for classification of variants of unknown clinical significance.
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Affiliation(s)
- Florian Cherik
- Department of Medical Genetics, Reference Centre for Rare Diseases, Developmental Anomalies and Malformation Syndromes Sud-Est, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Jennifer Kerkhof
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph's Healthcare, London, Ontario, Canada
| | - Michael Levy
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph's Healthcare, London, Ontario, Canada
| | - Haley McConkey
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph's Healthcare, London, Ontario, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Kameryn M Butler
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Christine Coubes
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Montpellier University Hospital, Montpellier, France
| | - Jennifer A Lee
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Gwenael Le Guyader
- Clinical Genetics Department, Poitiers University Hospital, Poitiers, France
| | - Raymond J Louie
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Wesley G Patterson
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Matthew L Tedder
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Mads Bak
- Clinical genetic department, Righospitalet, Copenhagen, Denmark
| | - Trine Bjørg Hammer
- Clinical genetic department, Righospitalet, Copenhagen, Denmark; Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - William Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Florence Démurger
- Medical Genetics Department, Bretagne-Atlantique Hospital, Vannes, France
| | - Christèle Dubourg
- Department of Molecular Genetics and Genomics, Rennes University Hospital, Rennes, France; Univ Rennes, CNRS, IGDR, UMR 6290, Rennes, France
| | - Mélanie Fradin
- Department of Clinical Genetics, Reference Centre for Rare Diseases, CLAD Ouest, Rennes University Hospital, Rennes, France
| | - Rachel Franciskovich
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospitals and University of Oslo, Oslo, Norway
| | - Jennifer Friedman
- Departments of Neurosciences and Pediatrics, University of California San Diego, San Diego, CA; Division of Neurology, Rady Children's Hospital, San Diego, CA; Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA
| | - Nathalie Ruiz Palares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Maria Iascone
- Medical Genetics Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Doriana Misceo
- Department of Medical Genetics, Oslo University Hospitals and University of Oslo, Oslo, Norway
| | - Pauline Monin
- Department of Medical Genetics, Women Mother Children Hospital, Hospices Civils de Lyon, Lyon, France
| | - Sylvie Odent
- Department of Medical Genetics, Reference Center for Developmental Anomalies, CLAD Ouest, Rennes University Hospital, ERN ITHACA, CNRS UMR 6290, Genetics and Development Institute, Rennes University, Rennes, France
| | - Christophe Philippe
- Functional Unit of Innovative Diagnosis for Rare Diseases, Dijon Bourgogne University Hospital, Dijon, France
| | - Flavien Rouxel
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Montpellier University Hospital, Montpellier, France
| | - Veronica Saletti
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Petter Strømme
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, and University of Oslo, Oslo, Norway
| | | | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph's Healthcare, London, Ontario, Canada.
| | - David Genevieve
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Montpellier University Hospital, Montpellier, France.
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18
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Gooch C, Souder JP, Tedder ML, Kerkhof J, Lee JA, Louie RJ, Sadikovic B, Fletcher RS, Robin NH. Near complete deletion of KMT2D in a college student. Am J Med Genet A 2022; 188:1550-1555. [PMID: 35040536 PMCID: PMC8995339 DOI: 10.1002/ajmg.a.62652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/09/2022]
Abstract
Pathogenic variants in KMT2D are typically associated with Kabuki syndrome (KS), a rare multisystem disorder. KS is characterized by facial dysmorphisms, intellectual disability, skeletal and dermatoglyphic differences, and poor growth. Seventy percent of individuals with clinically diagnosed KS have a confirmed pathogenic variant in KMT2D or less commonly KDM6A. The majority of mutations found in KMT2D are de novo nonsense or frameshift, with deletions and duplications rarely reported in the literature. Here, we present the case of near complete deletion of KMT2D in a college student with normal intelligence discovered via exome sequencing and EpiSign methylation testing. This case provides evidence that large deletions in KMT2D are compatible with normal intelligence and presents EpiSign as a method for discovering molecular causes of KS not identified by traditional molecular testing.
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Affiliation(s)
- Catherine Gooch
- Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jaclyn Paige Souder
- Medical Scientist Training Program, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer A Lee
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | | | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | | | - Nathaniel H Robin
- Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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19
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Levy MA, McConkey H, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Fletcher RS, Cherik F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Pizzi S, Plomp AS, Poulton C, Reilly J, Relator R, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, St John M, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci T, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Kerrnohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders. HGG Adv 2022; 3:100075. [PMID: 35047860 PMCID: PMC8756545 DOI: 10.1016/j.xhgg.2021.100075] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, UK
| | | | - Mariet W Elting
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | - Florian Cherik
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, the Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Kristin D Kerrnohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Department of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
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20
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Stolz JR, Foote KM, Veenstra-Knol HE, Pfundt R, ten Broeke SW, de Leeuw N, Roht L, Pajusalu S, Part R, Rebane I, Õunap K, Stark Z, Kirk EP, Lawson JA, Lunke S, Christodoulou J, Louie RJ, Rogers RC, Davis JM, Innes AM, Wei XC, Keren B, Mignot C, Lebel RR, Sperber SM, Sakonju A, Dosa N, Barge-Schaapveld DQ, Peeters-Scholte CM, Ruivenkamp CA, van Bon BW, Kennedy J, Low KJ, Ellard S, Pang L, Junewick JJ, Mark PR, Carvill GL, Swanson GT. Clustered mutations in the GRIK2 kainate receptor subunit gene underlie diverse neurodevelopmental disorders. Am J Hum Genet 2021; 108:2206. [PMID: 34739836 DOI: 10.1016/j.ajhg.2021.09.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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21
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Burns W, Bird LM, Heron D, Keren B, Ramachandra D, Thiffault I, Del Viso F, Amudhavalli S, Engleman K, Parenti I, Kaiser FJ, Wierzba J, Riedhammer KM, Liptay S, Zadeh N, Porrmann J, Fischer A, Gößwein S, McLaughlin HM, Telegrafi A, Langley KG, Steet R, Louie RJ, Lyons MJ. Syndromic neurodevelopmental disorder associated with de novo variants in DDX23. Am J Med Genet A 2021; 185:2863-2872. [PMID: 34050707 DOI: 10.1002/ajmg.a.62359] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/17/2021] [Accepted: 04/24/2021] [Indexed: 02/05/2023]
Abstract
The DEAD/DEAH box RNA helicases are a superfamily of proteins involved in the processing and transportation of RNA within the cell. A growing literature supports this family of proteins as contributing to various types of human disorders from neurodevelopmental disorders to syndromes with multiple congenital anomalies. This article presents a cohort of nine unrelated individuals with de novo missense alterations in DDX23 (Dead-Box Helicase 23). The gene is ubiquitously expressed and functions in RNA splicing, maintenance of genome stability, and the sensing of double-stranded RNA. Our cohort of patients, gathered through GeneMatcher, exhibited features including tone abnormalities, global developmental delay, facial dysmorphism, autism spectrum disorder, and seizures. Additionally, there were a variety of other findings in the skeletal, renal, ocular, and cardiac systems. The missense alterations all occurred within a highly conserved RecA-like domain of the protein, and are located within or proximal to the DEAD box sequence. The individuals presented in this article provide evidence of a syndrome related to alterations in DDX23 characterized predominantly by atypical neurodevelopment.
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Affiliation(s)
- William Burns
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Lynne M Bird
- San Diego - Department of Pediatrics, University of California, San Diego, California, USA
- Division of Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, California, USA
| | - Delphine Heron
- Département de Génétique, Pitié-Salpêtrière Hospital, APHP.Sorbonne Université, Paris, France
| | - Boris Keren
- Département de Génétique, Pitié-Salpêtrière Hospital, APHP.Sorbonne Université, Paris, France
| | - Divya Ramachandra
- Division of Genetics, Advocate Hope Children's Hospital, Oak Lawn, Illinois, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Florencia Del Viso
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | | | - Kendra Engleman
- Department of Pediatics, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Ilaria Parenti
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Frank J Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Jolanta Wierzba
- Department of Pediatric and Internal Medicine Nursing, Medical University of Gdańsk, Poland
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Susanne Liptay
- Department of Pediatrics, Kinderklinik München Schwabing, School of Medicine, Technical University of Munich, Munich, Germany
| | - Neda Zadeh
- Genetics Center, Orange, California, USA
- Division of Medical Genetics, CHOC Children's Hospital, Orange, California, USA
| | - Joseph Porrmann
- Faculty of Medicine Carl Gustav Carus, TU Dresden, Fetscherstr. 74, Institute for Clinical Genetics, Dresden, Germany
| | - Andrea Fischer
- Faculty of Medicine Carl Gustav Carus, TU Dresden, Fetscherstr. 74, Institute for Clinical Genetics, Dresden, Germany
| | - Sophie Gößwein
- Faculty of Medicine Carl Gustav Carus, TU Dresden, Fetscherstr. 74, Institute for Clinical Genetics, Dresden, Germany
| | | | | | | | - Richard Steet
- Greenwood Genetic Center, Greenwood, South Carolina, USA
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22
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Stolz JR, Foote KM, Veenstra-Knol HE, Pfundt R, Ten Broeke SW, de Leeuw N, Roht L, Pajusalu S, Part R, Rebane I, Õunap K, Stark Z, Kirk EP, Lawson JA, Lunke S, Christodoulou J, Louie RJ, Rogers RC, Davis JM, Innes AM, Wei XC, Keren B, Mignot C, Lebel RR, Sperber SM, Sakonju A, Dosa N, Barge-Schaapveld DQCM, Peeters-Scholte CMPCD, Ruivenkamp CAL, van Bon BW, Kennedy J, Low KJ, Ellard S, Pang L, Junewick JJ, Mark PR, Carvill GL, Swanson GT. Clustered mutations in the GRIK2 kainate receptor subunit gene underlie diverse neurodevelopmental disorders. Am J Hum Genet 2021; 108:1692-1709. [PMID: 34375587 PMCID: PMC8456161 DOI: 10.1016/j.ajhg.2021.07.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/15/2021] [Indexed: 12/14/2022] Open
Abstract
Kainate receptors (KARs) are glutamate-gated cation channels with diverse roles in the central nervous system. Bi-allelic loss of function of the KAR-encoding gene GRIK2 causes a nonsyndromic neurodevelopmental disorder (NDD) with intellectual disability and developmental delay as core features. The extent to which mono-allelic variants in GRIK2 also underlie NDDs is less understood because only a single individual has been reported previously. Here, we describe an additional eleven individuals with heterozygous de novo variants in GRIK2 causative for neurodevelopmental deficits that include intellectual disability. Five children harbored recurrent de novo variants (three encoding p.Thr660Lys and two p.Thr660Arg), and four children and one adult were homozygous for a previously reported variant (c.1969G>A [p.Ala657Thr]). Individuals with shared variants had some overlapping behavioral and neurological dysfunction, suggesting that the GRIK2 variants are likely pathogenic. Analogous mutations introduced into recombinant GluK2 KAR subunits at sites within the M3 transmembrane domain (encoding p.Ala657Thr, p.Thr660Lys, and p.Thr660Arg) and the M3-S2 linker domain (encoding p.Ile668Thr) had complex effects on functional properties and membrane localization of homomeric and heteromeric KARs. Both p.Thr660Lys and p.Thr660Arg mutant KARs exhibited markedly slowed gating kinetics, similar to p.Ala657Thr-containing receptors. Moreover, we observed emerging genotype-phenotype correlations, including the presence of severe epilepsy in individuals with the p.Thr660Lys variant and hypomyelination in individuals with either the p.Thr660Lys or p.Thr660Arg variant. Collectively, these results demonstrate that human GRIK2 variants predicted to alter channel function are causative for early childhood development disorders and further emphasize the importance of clarifying the role of KARs in early nervous system development.
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Affiliation(s)
- Jacob R Stolz
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kendall M Foote
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Hermine E Veenstra-Knol
- Department of Genetics, University Medical Center Groningen, Groningen 9700, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen 6525, the Netherlands
| | - Sanne W Ten Broeke
- Department of Genetics, University Medical Center Groningen, Groningen 9700, the Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen 6525, the Netherlands
| | - Laura Roht
- Department of Clinical Genetics, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, Tartu University, Tartu 51003, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, Tartu University, Tartu 51003, Estonia
| | - Reelika Part
- Department of Neonatal and Infant Medicine, Tallinn Children's Hospital, Tallinn 13419, Estonia
| | - Ionella Rebane
- Department of Neonatal and Infant Medicine, Tallinn Children's Hospital, Tallinn 13419, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, Tartu University, Tartu 51003, Estonia
| | - Zornitza Stark
- Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Edwin P Kirk
- School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - John A Lawson
- Department of Neurology, Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Sebastian Lunke
- Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | - John Christodoulou
- Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | | | | | | | - A Micheil Innes
- Departments of Medical Genetics and Pediatrics, Cumming School of Medicine, University of Calgary, Alberta T2N 4N1, Canada
| | - Xing-Chang Wei
- Department of Diagnostic Imaging, Cumming School of Medicine, University of Calgary, AB T2N 4N1, Canada
| | - Boris Keren
- Département de Génétique, Hôpital Pitié-Salpêtrière, Paris 75013, France
| | - Cyril Mignot
- Département de Génétique, Hôpital Pitié-Salpêtrière, Paris 75013, France
| | - Robert Roger Lebel
- Division of Development, Behavior, and Genetics, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Steven M Sperber
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Ai Sakonju
- Department of Neurology, Upstate Health Care Center, Syracuse, NY 13210, USA
| | - Nienke Dosa
- Division of Development, Behavior, and Genetics, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | | | | | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Bregje W van Bon
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen 6525, the Netherlands
| | - Joanna Kennedy
- University Hospital Bristol, NHS Foundation Trust, Bristol BS1 3NU, UK
| | - Karen J Low
- University Hospital Bristol, NHS Foundation Trust, Bristol BS1 3NU, UK
| | - Sian Ellard
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Lewis Pang
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Joseph J Junewick
- Department of Radiology, Helen DeVos Children's Hospital, Grand Rapids, MI 49503, USA
| | - Paul R Mark
- Spectrum Health Medical Genetics, Grand Rapids, MI 49503, USA
| | - Gemma L Carvill
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Geoffrey T Swanson
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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Ortega V, Louie RJ, Jones MA, Chaubey A, DuPont BR, Britt A, Ray J, McLean SD, Littlejohn RO, Velagaleti G. Copy neutral absence of heterozygosity on chromosome 15 distal long arm: A surrogate marker for Prader-Willi/Angelman syndromes? Mol Cytogenet 2021; 14:37. [PMID: 34261519 PMCID: PMC8278679 DOI: 10.1186/s13039-021-00558-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/06/2021] [Indexed: 11/25/2022] Open
Abstract
Background Copy-neutral absence of heterozygosity (CN-AOH) observed on a single chromosome or part of a chromosome may be indicative of uniparental disomy (UPD) and may require additional testing when such chromosomes or chromosome regions are known to harbor imprinted genes. Case presentation Here we report 2 cases of neonates that presented to clinic with hypotonia, poor oral skills including inability to feed by mouth, weak cry, no response to noxious stimulation and vertical plantar creases (case 1) and hypotonia and respiratory distress (case 2). A preliminary chromosome analysis showed normal karyotypes in both cases while the high-resolution single nucleotide polymorphism (SNP) microarray showed copy neutral absence of heterozygosity involving chromosome 15 distal long arm. In case 1, the CN-AOH involved a 28.7 Mb block from genomic coordinates 73703619_102429049. In case 2, the CN-AOH involved a 15.3 Mb block from genomic coordinates 54729197_70057534. In both cases, methylation-specific PCR did not detect an unmethylated allele for the SNRPN gene suggesting either a deletion of paternal allele or maternal UPD for chromosome 15. Since microarray analysis did not show any copy number alterations on chromosome 15, a microdeletion was ruled out. Conclusions Based on our cases, we suggest that CN-AOH on chromosome 15, even if it does not involve the critical region of 15q12q13, should warrant additional studies for diagnosis of Prader–Willi/Angelman syndromes.
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Affiliation(s)
- Veronica Ortega
- Department of Pathology, University of Texas Health, San Antonio, TX, USA
| | | | | | | | | | - Allison Britt
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Joseph Ray
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott D McLean
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rebecca O Littlejohn
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Gopalrao Velagaleti
- Department of Pathology, University of Texas Health, San Antonio, TX, USA. .,Department of Pathology and Laboratory Medicine, University of Texas Health Science Center Mail Code, Mail Code 7750, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
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24
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Yu SH, Wang T, Wiggins K, Louie RJ, Merino EF, Skinner C, Cassera MB, Meagher K, Goldberg P, Rismanchi N, Chen D, Lyons MJ, Flanagan-Steet H, Steet R. Lysosomal cholesterol accumulation contributes to the movement phenotypes associated with NUS1 haploinsufficiency. Genet Med 2021; 23:1305-1314. [PMID: 33731878 PMCID: PMC8263489 DOI: 10.1038/s41436-021-01137-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 11/30/2022] Open
Abstract
PURPOSE Variants in NUS1 are associated with a congenital disorder of glycosylation, developmental and epileptic encephalopathies, and are possible contributors to Parkinson disease pathogenesis. How the diverse functions of the NUS1-encoded Nogo B receptor (NgBR) relate to these different phenotypes is largely unknown. We present three patients with de novo heterozygous variants in NUS1 that cause a complex movement disorder, define pathogenic mechanisms in cells and zebrafish, and identify possible therapy. METHODS Comprehensive functional studies were performed using patient fibroblasts, and a zebrafish model mimicking NUS1 haploinsufficiency. RESULTS We show that de novo NUS1 variants reduce NgBR and Niemann-Pick type C2 (NPC2) protein amount, impair dolichol biosynthesis, and cause lysosomal cholesterol accumulation. Reducing nus1 expression 50% in zebrafish embryos causes abnormal swim behaviors, cholesterol accumulation in the nervous system, and impaired turnover of lysosomal membrane proteins. Reduction of cholesterol buildup with 2-hydroxypropyl-ß-cyclodextrin significantly alleviates lysosomal proteolysis and motility defects. CONCLUSION Our results demonstrate that these NUS1 variants cause multiple lysosomal phenotypes in cells. We show that the movement deficits associated with nus1 reduction in zebrafish arise in part from defective efflux of cholesterol from lysosomes, suggesting that treatments targeting cholesterol accumulation could be therapeutic.
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Affiliation(s)
- Seok-Ho Yu
- Greenwood Genetic Center, Greenwood, SC, USA
| | - Tong Wang
- Greenwood Genetic Center, Greenwood, SC, USA
| | | | | | - Emilio F Merino
- Department of Biochemistry and Molecular Biology, and Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Athens, GA, USA
| | | | - Maria B Cassera
- Department of Biochemistry and Molecular Biology, and Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Athens, GA, USA
| | - Kirsten Meagher
- Department of Medical Genetics, British Columbia Women's Hospital and Health Centre, Vancouver, BC, Canada
| | - Paul Goldberg
- Department of Medical Genetics, British Columbia Women's Hospital and Health Centre, Vancouver, BC, Canada
| | - Neggy Rismanchi
- Department of Neuroscience at the University of California, San Diego, San Diego, CA, USA
- Division of Neurology, Rady Children's Hospital San Diego, San Diego, CA, USA
| | - Dillon Chen
- Department of Neuroscience at the University of California, San Diego, San Diego, CA, USA
- Division of Neurology, Rady Children's Hospital San Diego, San Diego, CA, USA
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25
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Parenti I, Lehalle D, Nava C, Torti E, Leitão E, Person R, Mizuguchi T, Matsumoto N, Kato M, Nakamura K, de Man SA, Cope H, Shashi V, Friedman J, Joset P, Steindl K, Rauch A, Muffels I, van Hasselt PM, Petit F, Smol T, Le Guyader G, Bilan F, Sorlin A, Vitobello A, Philippe C, van de Laar IMBH, van Slegtenhorst MA, Campeau PM, Au PYB, Nakashima M, Saitsu H, Yamamoto T, Nomura Y, Louie RJ, Lyons MJ, Dobson A, Plomp AS, Motazacker MM, Kaiser FJ, Timberlake AT, Fuchs SA, Depienne C, Mignot C. Missense and truncating variants in CHD5 in a dominant neurodevelopmental disorder with intellectual disability, behavioral disturbances, and epilepsy. Hum Genet 2021; 140:1109-1120. [PMID: 33944996 PMCID: PMC8197709 DOI: 10.1007/s00439-021-02283-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/15/2021] [Indexed: 12/27/2022]
Abstract
Located in the critical 1p36 microdeletion region, the chromodomain helicase DNA-binding protein 5 (CHD5) gene encodes a subunit of the nucleosome remodeling and deacetylation (NuRD) complex required for neuronal development. Pathogenic variants in six of nine chromodomain (CHD) genes cause autosomal dominant neurodevelopmental disorders, while CHD5-related disorders are still unknown. Thanks to GeneMatcher and international collaborations, we assembled a cohort of 16 unrelated individuals harboring heterozygous CHD5 variants, all identified by exome sequencing. Twelve patients had de novo CHD5 variants, including ten missense and two splice site variants. Three familial cases had nonsense or missense variants segregating with speech delay, learning disabilities, and/or craniosynostosis. One patient carried a frameshift variant of unknown inheritance due to unavailability of the father. The most common clinical features included language deficits (81%), behavioral symptoms (69%), intellectual disability (64%), epilepsy (62%), and motor delay (56%). Epilepsy types were variable, with West syndrome observed in three patients, generalized tonic-clonic seizures in two, and other subtypes observed in one individual each. Our findings suggest that, in line with other CHD-related disorders, heterozygous CHD5 variants are associated with a variable neurodevelopmental syndrome that includes intellectual disability with speech delay, epilepsy, and behavioral problems as main features.
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Affiliation(s)
- Ilaria Parenti
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Daphné Lehalle
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière and Hôpital Trousseau, APHP, Sorbonne Université, Paris, France
| | - Caroline Nava
- Institut du Cerveau (ICM), UMR S 1127, Inserm U1127, CNRS UMR 7225, Sorbonne Université, 75013, Paris, France
| | | | - Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | | | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, 142-8666, Japan
| | - Kazuyuki Nakamura
- Department of Pediatrics, Yamagata University Faculty of Medicine, Yamagata, 990-9585, Japan
| | - Stella A de Man
- Department of Pediatrics, Amphia Hospital, Breda, The Netherlands
| | - Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jennifer Friedman
- Departments of Neuroscience and Pediatrics, Division of Neurology, Rady Children's Hospital, UCSD, San Diego and Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
- Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases University of Zurich, 8032, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
- Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases University of Zurich, 8032, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
- Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases University of Zurich, 8032, Zurich, Switzerland
| | - Irena Muffels
- Department of Metabolic Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Peter M van Hasselt
- Department of Metabolic Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Thomas Smol
- Institut de Génétique Médicale, CHRU Lille, Université de Lille, Lille, France
| | - Gwenaël Le Guyader
- Service de Génétique Médicale, CHU de Poitiers, Poitiers, France
- EA3808 NEUVACOD, University of Poitiers, Poitiers, France
| | - Frédéric Bilan
- Service de Génétique Médicale, CHU de Poitiers, Poitiers, France
- EA3808 NEUVACOD, University of Poitiers, Poitiers, France
| | - Arthur Sorlin
- Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France
- Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marjon A van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, Montreal, QC, H3T 1C5, Canada
- Sainte-Justine Hospital, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | - Ping Yee Billie Au
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - Tatsuya Yamamoto
- Department of Pediatrics, Hirosaki University Graduate School of Medicine and School of Medicine, Hirosaki, 036-8562, Japan
| | - Yumiko Nomura
- Department of Pediatrics, Hirosaki National Hospital, Hirosaki, 036-8545, Japan
- Aomori City Health Center, Aomori, 030-0962, Japan
| | | | | | - Amy Dobson
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Astrid S Plomp
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - M Mahdi Motazacker
- Laboratory of Genome Diagnostics, Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Frank J Kaiser
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, NYU Langone Health, New York, NY, USA
| | - Sabine A Fuchs
- Department of Metabolic Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
- Institut du Cerveau (ICM), UMR S 1127, Inserm U1127, CNRS UMR 7225, Sorbonne Université, 75013, Paris, France.
| | - Cyril Mignot
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière and Hôpital Trousseau, APHP, Sorbonne Université, Paris, France.
- Institut du Cerveau (ICM), UMR S 1127, Inserm U1127, CNRS UMR 7225, Sorbonne Université, 75013, Paris, France.
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26
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Latypova X, Vincent M, Mollé A, Adebambo OA, Fourgeux C, Khan TN, Caro A, Rosello M, Orellana C, Niyazov D, Lederer D, Deprez M, Capri Y, Kannu P, Tabet AC, Levy J, Aten E, den Hollander N, Splitt M, Walia J, Immken LL, Stankiewicz P, McWalter K, Suchy S, Louie RJ, Bell S, Stevenson RE, Rousseau J, Willem C, Retiere C, Yang XJ, Campeau PM, Martinez F, Rosenfeld JA, Le Caignec C, Küry S, Mercier S, Moradkhani K, Conrad S, Besnard T, Cogné B, Katsanis N, Bézieau S, Poschmann J, Davis EE, Isidor B. Haploinsufficiency of the Sin3/HDAC corepressor complex member SIN3B causes a syndromic intellectual disability/autism spectrum disorder. Am J Hum Genet 2021; 108:929-941. [PMID: 33811806 DOI: 10.1016/j.ajhg.2021.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/18/2021] [Indexed: 11/28/2022] Open
Abstract
Proteins involved in transcriptional regulation harbor a demonstrated enrichment of mutations in neurodevelopmental disorders. The Sin3 (Swi-independent 3)/histone deacetylase (HDAC) complex plays a central role in histone deacetylation and transcriptional repression. Among the two vertebrate paralogs encoding the Sin3 complex, SIN3A variants cause syndromic intellectual disability, but the clinical consequences of SIN3B haploinsufficiency in humans are uncharacterized. Here, we describe a syndrome hallmarked by intellectual disability, developmental delay, and dysmorphic facial features with variably penetrant autism spectrum disorder, congenital malformations, corpus callosum defects, and impaired growth caused by disruptive SIN3B variants. Using chromosomal microarray or exome sequencing, and through international data sharing efforts, we identified nine individuals with heterozygous SIN3B deletion or single-nucleotide variants. Five individuals harbor heterozygous deletions encompassing SIN3B that reside within a ∼230 kb minimal region of overlap on 19p13.11, two individuals have a rare nonsynonymous substitution, and two individuals have a single-nucleotide deletion that results in a frameshift and predicted premature termination codon. To test the relevance of SIN3B impairment to measurable aspects of the human phenotype, we disrupted the orthologous zebrafish locus by genome editing and transient suppression. The mutant and morphant larvae display altered craniofacial patterning, commissural axon defects, and reduced body length supportive of an essential role for Sin3 function in growth and patterning of anterior structures. To investigate further the molecular consequences of SIN3B variants, we quantified genome-wide enhancer and promoter activity states by using H3K27ac ChIP-seq. We show that, similar to SIN3A mutations, SIN3B disruption causes hyperacetylation of a subset of enhancers and promoters in peripheral blood mononuclear cells. Together, these data demonstrate that SIN3B haploinsufficiency leads to a hitherto unknown intellectual disability/autism syndrome, uncover a crucial role of SIN3B in the central nervous system, and define the epigenetic landscape associated with Sin3 complex impairment.
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Affiliation(s)
- Xenia Latypova
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Alice Mollé
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France
| | | | - Cynthia Fourgeux
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France
| | - Tahir N Khan
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA; Department of Biological Sciences, National University of Medical Sciences, 46000 Rawalpindi, Pakistan
| | - Alfonso Caro
- Unidad de Genética, Grupo de Investigación Traslacional en Genética, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Monica Rosello
- Unidad de Genética, Grupo de Investigación Traslacional en Genética, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Carmen Orellana
- Unidad de Genética, Grupo de Investigación Traslacional en Genética, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Dmitriy Niyazov
- Department of Pediatrics, Ochsner Clinic, New Orleans, LA 70128, USA
| | - Damien Lederer
- Centre de Génétique Humaine, IPG, 6041 Gosselies, Belgium
| | - Marie Deprez
- Service de Neuropédiatrie, Clinique Saint Elizabeth, 5000 Namur, Belgium
| | - Yline Capri
- Service de Génétique Médicale, Hôpital Robert Debré, 75019 Paris, France
| | - Peter Kannu
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | | | - Jonathan Levy
- Service de Cytogénétique, Hôpital Robert Debré, 75019 Paris, France
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Nicolette den Hollander
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Miranda Splitt
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle Upon Tyne NE1 3BZ, UK
| | - Jagdeep Walia
- Kingston General Hospital Research Institute, 76 Stuart Street, Kingston, ON K7L 2V7, Canada
| | - Ladonna L Immken
- Clinical Genetics, Dell Children's Medical Group, Austin, TX 78731, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Sharon Suchy
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Raymond J Louie
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Shannon Bell
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Roger E Stevenson
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Justine Rousseau
- Sainte-Justine Hospital, 3175, Cote-Sainte-Catherine, Montreal, QC, Canada
| | | | - Christelle Retiere
- Etablissement Français du Sang, 44000 Nantes, France; CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, 44000 Nantes, France; LabEx IGO, Nantes 44000, France
| | - Xiang-Jiao Yang
- Rosalind & Morris Goodman Cancer Research Center and Department of Medicine, McGill University, Montreal, QC H3A 1A3, Canada
| | - Philippe M Campeau
- Sainte-Justine Hospital, 3175, Cote-Sainte-Catherine, Montreal, QC, Canada
| | - Francisco Martinez
- Unidad de Genética, Grupo de Investigación Traslacional en Genética, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cédric Le Caignec
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Sandra Mercier
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Kamran Moradkhani
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France
| | - Solène Conrad
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France
| | - Thomas Besnard
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA; Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Jeremie Poschmann
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France.
| | - Erica E Davis
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France.
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27
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Gass JM, Louie RJ, Merrihew A, Hilton BA, DuPont BR, Lyons M. 19. De novo homozygous variant due to uniparental isodisomy results in a recessive disorder. Cancer Genet 2021. [DOI: 10.1016/j.cancergen.2021.01.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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28
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Sadikovic B, Levy MA, Kerkhof J, Aref-Eshghi E, Schenkel L, Stuart A, McConkey H, Henneman P, Venema A, Schwartz CE, Stevenson RE, Skinner SA, DuPont BR, Fletcher RS, Balci TB, Siu VM, Granadillo JL, Masters J, Kadour M, Friez MJ, van Haelst MM, Mannens MMAM, Louie RJ, Lee JA, Tedder ML, Alders M. Correction: Clinical epigenomics: genome-wide DNA methylation analysis for the diagnosis of Mendelian disorders. Genet Med 2021; 23:2228. [PMID: 33637969 PMCID: PMC9119201 DOI: 10.1038/s41436-021-01130-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Laila Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Haley McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Peter Henneman
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Andrea Venema
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Victoria Mok Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Jennefer Masters
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Mike Kadour
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | | | - Mieke M van Haelst
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
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29
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Sadikovic B, Levy MA, Kerkhof J, Aref-Eshghi E, Schenkel L, Stuart A, McConkey H, Henneman P, Venema A, Schwartz CE, Stevenson RE, Skinner SA, DuPont BR, Fletcher RS, Balci TB, Siu VM, Granadillo JL, Masters J, Kadour M, Friez MJ, van Haelst MM, Mannens MMAM, Louie RJ, Lee JA, Tedder ML, Alders M. Clinical epigenomics: genome-wide DNA methylation analysis for the diagnosis of Mendelian disorders. Genet Med 2021; 23:1065-1074. [PMID: 33547396 PMCID: PMC8187150 DOI: 10.1038/s41436-020-01096-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 01/23/2023] Open
Abstract
Purpose We describe the clinical implementation of genome-wide DNA methylation analysis in rare disorders across the EpiSign diagnostic laboratory network and the assessment of results and clinical impact in the first subjects tested. Methods We outline the logistics and data flow between an integrated network of clinical diagnostics laboratories in Europe, the United States, and Canada. We describe the clinical validation of EpiSign using 211 specimens and assess the test performance and diagnostic yield in the first 207 subjects tested involving two patient subgroups: the targeted cohort (subjects with previous ambiguous/inconclusive genetic findings including genetic variants of unknown clinical significance) and the screening cohort (subjects with clinical findings consistent with hereditary neurodevelopmental syndromes and no previous conclusive genetic findings). Results Among the 207 subjects tested, 57 (27.6%) were positive for a diagnostic episignature including 48/136 (35.3%) in the targeted cohort and 8/71 (11.3%) in the screening cohort, with 4/207 (1.9%) remaining inconclusive after EpiSign analysis. Conclusion This study describes the implementation of diagnostic clinical genomic DNA methylation testing in patients with rare disorders. It provides strong evidence of clinical utility of EpiSign analysis, including the ability to provide conclusive findings in the majority of subjects tested.
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Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Laila Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Haley McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Peter Henneman
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Andrea Venema
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Victoria Mok Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Jennefer Masters
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Mike Kadour
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | | | - Mieke M van Haelst
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
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30
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El Hayek L, Tuncay IO, Nijem N, Russell J, Ludwig S, Kaur K, Li X, Anderton P, Tang M, Gerard A, Heinze A, Zacher P, Alsaif HS, Rad A, Hassanpour K, Abbaszadegan MR, Washington C, DuPont BR, Louie RJ, Couse M, Faden M, Rogers RC, Abou Jamra R, Elias ER, Maroofian R, Houlden H, Lehman A, Beutler B, Chahrour MH. KDM5A mutations identified in autism spectrum disorder using forward genetics. eLife 2020; 9:56883. [PMID: 33350388 PMCID: PMC7755391 DOI: 10.7554/elife.56883] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/06/2020] [Indexed: 12/29/2022] Open
Abstract
Autism spectrum disorder (ASD) is a constellation of neurodevelopmental disorders with high phenotypic and genetic heterogeneity, complicating the discovery of causative genes. Through a forward genetics approach selecting for defective vocalization in mice, we identified Kdm5a as a candidate ASD gene. To validate our discovery, we generated a Kdm5a knockout mouse model (Kdm5a-/-) and confirmed that inactivating Kdm5a disrupts vocalization. In addition, Kdm5a-/- mice displayed repetitive behaviors, sociability deficits, cognitive dysfunction, and abnormal dendritic morphogenesis. Loss of KDM5A also resulted in dysregulation of the hippocampal transcriptome. To determine if KDM5A mutations cause ASD in humans, we screened whole exome sequencing and microarray data from a clinical cohort. We identified pathogenic KDM5A variants in nine patients with ASD and lack of speech. Our findings illustrate the power and efficacy of forward genetics in identifying ASD genes and highlight the importance of KDM5A in normal brain development and function.
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Affiliation(s)
- Lauretta El Hayek
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
| | - Islam Oguz Tuncay
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nadine Nijem
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Kiran Kaur
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Priscilla Anderton
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Texas Children's Hospital, Houston, United States
| | - Anja Heinze
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Pia Zacher
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.,The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Aboulfazl Rad
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Islamic Republic of Iran
| | - Kazem Hassanpour
- Non-Communicable Diseases Research Center, Sabzevar University of Medical Sciences, Sabzevar, Islamic Republic of Iran
| | - Mohammad Reza Abbaszadegan
- Pardis Clinical and Genetics Laboratory, Mashhad, Islamic Republic of Iran.,Division of Human Genetics, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Islamic Republic of Iran
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- Department of Medical Genetics, University of British Columbia, British Columbia Children's and Women's Hospital Research Institute, Vancouver, Canada
| | - Madeline Couse
- Department of Medical Genetics, University of British Columbia, British Columbia Children's and Women's Hospital Research Institute, Vancouver, Canada
| | - Maha Faden
- Department of Genetics, King Saud Medical City, Riyadh, Saudi Arabia
| | | | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Ellen R Elias
- Department of Pediatrics and Genetics, University of Colorado School of Medicine, Aurora, United States
| | - Reza Maroofian
- Department of Neuromuscular Diseases, University College London, Queen Square Institute of Neurology, London, United Kingdom
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College London, Queen Square Institute of Neurology, London, United Kingdom
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, British Columbia Children's and Women's Hospital Research Institute, Vancouver, Canada
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Maria H Chahrour
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States.,Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, United States.,Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
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31
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Barish S, Barakat TS, Michel BC, Mashtalir N, Phillips JB, Valencia AM, Ugur B, Wegner J, Scott TM, Bostwick B, Murdock DR, Dai H, Perenthaler E, Nikoncuk A, van Slegtenhorst M, Brooks AS, Keren B, Nava C, Mignot C, Douglas J, Rodan L, Nowak C, Ellard S, Stals K, Lynch SA, Faoucher M, Lesca G, Edery P, Engleman KL, Zhou D, Thiffault I, Herriges J, Gass J, Louie RJ, Stolerman E, Washington C, Vetrini F, Otsubo A, Pratt VM, Conboy E, Treat K, Shannon N, Camacho J, Wakeling E, Yuan B, Chen CA, Rosenfeld JA, Westerfield M, Wangler M, Yamamoto S, Kadoch C, Scott DA, Bellen HJ. BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms. Am J Hum Genet 2020; 107:1096-1112. [PMID: 33232675 PMCID: PMC7820627 DOI: 10.1016/j.ajhg.2020.11.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/03/2020] [Indexed: 12/30/2022] Open
Abstract
SWI/SNF-related intellectual disability disorders (SSRIDDs) are rare neurodevelopmental disorders characterized by developmental disability, coarse facial features, and fifth digit/nail hypoplasia that are caused by pathogenic variants in genes that encode for members of the SWI/SNF (or BAF) family of chromatin remodeling complexes. We have identified 12 individuals with rare variants (10 loss-of-function, 2 missense) in the BICRA (BRD4 interacting chromatin remodeling complex-associated protein) gene, also known as GLTSCR1, which encodes a subunit of the non-canonical BAF (ncBAF) complex. These individuals exhibited neurodevelopmental phenotypes that include developmental delay, intellectual disability, autism spectrum disorder, and behavioral abnormalities as well as dysmorphic features. Notably, the majority of individuals lack the fifth digit/nail hypoplasia phenotype, a hallmark of most SSRIDDs. To confirm the role of BICRA in the development of these phenotypes, we performed functional characterization of the zebrafish and Drosophila orthologs of BICRA. In zebrafish, a mutation of bicra that mimics one of the loss-of-function variants leads to craniofacial defects possibly akin to the dysmorphic facial features seen in individuals harboring putatively pathogenic BICRA variants. We further show that Bicra physically binds to other non-canonical ncBAF complex members, including the BRD9/7 ortholog, CG7154, and is the defining member of the ncBAF complex in flies. Like other SWI/SNF complex members, loss of Bicra function in flies acts as a dominant enhancer of position effect variegation but in a more context-specific manner. We conclude that haploinsufficiency of BICRA leads to a unique SSRIDD in humans whose phenotypes overlap with those previously reported.
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Affiliation(s)
- Scott Barish
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Brittany C Michel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nazar Mashtalir
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Alfredo M Valencia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology Program, Harvard University, Cambridge, MA 02138, USA
| | - Berrak Ugur
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeremy Wegner
- Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Tiana M Scott
- Department of Microbiology and Molecular Biology, College of Life Science, Brigham Young University, Provo, UT 84602, USA
| | - Brett Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David R Murdock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - Elena Perenthaler
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Anita Nikoncuk
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Boris Keren
- APHP Sorbonne Université, Département de Génétique and Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière, 75006 Paris, France
| | - Caroline Nava
- APHP Sorbonne Université, Département de Génétique and Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière, 75006 Paris, France
| | - Cyril Mignot
- APHP Sorbonne Université, Département de Génétique and Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière, 75006 Paris, France
| | - Jessica Douglas
- Department of Pediatrics, Boston Children's at Waltham, Waltham, MA 02453, USA
| | - Lance Rodan
- Department of Pediatrics, Boston Children's at Waltham, Waltham, MA 02453, USA
| | - Catherine Nowak
- Department of Pediatrics, Boston Children's at Waltham, Waltham, MA 02453, USA
| | - Sian Ellard
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Karen Stals
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK; Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter EX4 4PY, UK
| | - Sally Ann Lynch
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin D12 N512, Ireland
| | - Marie Faoucher
- Department of Medical Genetics, Lyon University Hospital, Université Claude bernard Lyon 1, Lyon 69100, France
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University Hospital, Université Claude bernard Lyon 1, Lyon 69100, France
| | - Patrick Edery
- Department of Medical Genetics, Lyon University Hospital, Université Claude bernard Lyon 1, Lyon 69100, France
| | - Kendra L Engleman
- Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Dihong Zhou
- Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Isabelle Thiffault
- Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - John Herriges
- Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Jennifer Gass
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Raymond J Louie
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Elliot Stolerman
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Camerun Washington
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Francesco Vetrini
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Aiko Otsubo
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Victoria M Pratt
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Erin Conboy
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Kayla Treat
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Nora Shannon
- Regional Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham NG5 1PB, UK
| | - Jose Camacho
- Pediatric Genetics and Metabolism, Loma Linda University Children's Hospital, Loma Linda, CA 92354, USA
| | - Emma Wakeling
- Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - Monte Westerfield
- Department of Biology, University of Oregon, Eugene, OR 97403, USA; Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Michael Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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32
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Mochel F, Rastetter A, Ceulemans B, Platzer K, Yang S, Shinde DN, Helbig KL, Lopergolo D, Mari F, Renieri A, Benetti E, Canitano R, Waisfisz Q, Plomp AS, Huisman SA, Wilson GN, Cathey SS, Louie RJ, Gaudio DD, Waggoner D, Kacker S, Nugent KM, Roeder ER, Bruel AL, Thevenon J, Ehmke N, Horn D, Holtgrewe M, Kaiser FJ, Kamphausen SB, Abou Jamra R, Weckhuysen S, Dalle C, Depienne C. Variants in the SK2 channel gene (KCNN2) lead to dominant neurodevelopmental movement disorders. Brain 2020; 143:3564-3573. [PMID: 33242881 DOI: 10.1093/brain/awaa346] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/17/2020] [Accepted: 09/08/2020] [Indexed: 11/14/2022] Open
Abstract
KCNN2 encodes the small conductance calcium-activated potassium channel 2 (SK2). Rodent models with spontaneous Kcnn2 mutations show abnormal gait and locomotor activity, tremor and memory deficits, but human disorders related to KCNN2 variants are largely unknown. Using exome sequencing, we identified a de novo KCNN2 frameshift deletion in a patient with learning disabilities, cerebellar ataxia and white matter abnormalities on brain MRI. This discovery prompted us to collect data from nine additional patients with de novo KCNN2 variants (one nonsense, one splice site, six missense variants and one in-frame deletion) and one family with a missense variant inherited from the affected mother. We investigated the functional impact of six selected variants on SK2 channel function using the patch-clamp technique. All variants tested but one, which was reclassified to uncertain significance, led to a loss-of-function of SK2 channels. Patients with KCNN2 variants had motor and language developmental delay, intellectual disability often associated with early-onset movement disorders comprising cerebellar ataxia and/or extrapyramidal symptoms. Altogether, our findings provide evidence that heterozygous variants, likely causing a haploinsufficiency of the KCNN2 gene, lead to novel autosomal dominant neurodevelopmental movement disorders mirroring phenotypes previously described in rodents.
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Affiliation(s)
- Fanny Mochel
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013 Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique and Centre de Référence Neurométabolique Adulte, F-75013, Paris, France
| | - Agnès Rastetter
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013 Paris, France
| | - Berten Ceulemans
- Division of Paediatric Neurology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Deepali N Shinde
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,The Epilepsy Neurogenetics Initiative, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Diego Lopergolo
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Elisa Benetti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Roberto Canitano
- Division of Child and Adolescent Neuropsychiatry, University Hospital of Siena, Siena, Italy
| | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Astrid S Plomp
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sylvia A Huisman
- Department of Pediatrics, Amsterdam UMC, Amsterdam, The Netherlands.,Prinsenstichting, Purmerend, The Netherlands
| | - Golder N Wilson
- Department of Pediatrics, Texas Tech University Health Science Center, Lubbock, Texas, USA
| | - Sara S Cathey
- Greenwood Genetic Center, Greenwood, South Carolina, 29646, USA
| | - Raymond J Louie
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Daniela Del Gaudio
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Darrel Waggoner
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Shawn Kacker
- Department of Pediatrics, Section of Child Neurology, University of Chicago, Chicago, IL, 60637, USA
| | - Kimberly M Nugent
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ange-Line Bruel
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de référence maladies rares 'déficiences intellectuelles de causes rares', Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Julien Thevenon
- Service de Génétique, Génomique, et Procréation, Centre Hospitalier Universitaire Grenoble Alpes, 38700 La Tronche, France.,INSERM 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Université Grenoble Alpes, 38706 Grenoble, France
| | - Nadja Ehmke
- Institute for Human Genetics and Medical Genetics, Charité - Universitaetsmedizin Berlin, Berlin, Germany
| | - Denise Horn
- Institute for Human Genetics and Medical Genetics, Charité - Universitaetsmedizin Berlin, Berlin, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics - CUBI, Berlin Institute of Health (BIH), Berlin, Germany
| | - Frank J Kaiser
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany
| | | | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Sarah Weckhuysen
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium.,Department of Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Carine Dalle
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013 Paris, France
| | - Christel Depienne
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013 Paris, France.,Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany
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33
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Bryant L, Li D, Cox SG, Marchione D, Joiner EF, Wilson K, Janssen K, Lee P, March ME, Nair D, Sherr E, Fregeau B, Wierenga KJ, Wadley A, Mancini GMS, Powell-Hamilton N, van de Kamp J, Grebe T, Dean J, Ross A, Crawford HP, Powis Z, Cho MT, Willing MC, Manwaring L, Schot R, Nava C, Afenjar A, Lessel D, Wagner M, Klopstock T, Winkelmann J, Catarino CB, Retterer K, Schuette JL, Innis JW, Pizzino A, Lüttgen S, Denecke J, Strom TM, Monaghan KG, Yuan ZF, Dubbs H, Bend R, Lee JA, Lyons MJ, Hoefele J, Günthner R, Reutter H, Keren B, Radtke K, Sherbini O, Mrokse C, Helbig KL, Odent S, Cogne B, Mercier S, Bezieau S, Besnard T, Kury S, Redon R, Reinson K, Wojcik MH, Õunap K, Ilves P, Innes AM, Kernohan KD, Costain G, Meyn MS, Chitayat D, Zackai E, Lehman A, Kitson H, Martin MG, Martinez-Agosto JA, Nelson SF, Palmer CGS, Papp JC, Parker NH, Sinsheimer JS, Vilain E, Wan J, Yoon AJ, Zheng A, Brimble E, Ferrero GB, Radio FC, Carli D, Barresi S, Brusco A, Tartaglia M, Thomas JM, Umana L, Weiss MM, Gotway G, Stuurman KE, Thompson ML, McWalter K, Stumpel CTRM, Stevens SJC, Stegmann APA, Tveten K, Vøllo A, Prescott T, Fagerberg C, Laulund LW, Larsen MJ, Byler M, Lebel RR, Hurst AC, Dean J, Schrier Vergano SA, Norman J, Mercimek-Andrews S, Neira J, Van Allen MI, Longo N, Sellars E, Louie RJ, Cathey SS, Brokamp E, Heron D, Snyder M, Vanderver A, Simon C, de la Cruz X, Padilla N, Crump JG, Chung W, Garcia B, Hakonarson HH, Bhoj EJ. Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients. Sci Adv 2020; 6:eabc9207. [PMID: 33268356 PMCID: PMC7821880 DOI: 10.1126/sciadv.abc9207] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/19/2020] [Indexed: 05/07/2023]
Abstract
Although somatic mutations in Histone 3.3 (H3.3) are well-studied drivers of oncogenesis, the role of germline mutations remains unreported. We analyze 46 patients bearing de novo germline mutations in histone 3 family 3A (H3F3A) or H3F3B with progressive neurologic dysfunction and congenital anomalies without malignancies. Molecular modeling of all 37 variants demonstrated clear disruptions in interactions with DNA, other histones, and histone chaperone proteins. Patient histone posttranslational modifications (PTMs) analysis revealed notably aberrant local PTM patterns distinct from the somatic lysine mutations that cause global PTM dysregulation. RNA sequencing on patient cells demonstrated up-regulated gene expression related to mitosis and cell division, and cellular assays confirmed an increased proliferative capacity. A zebrafish model showed craniofacial anomalies and a defect in Foxd3-derived glia. These data suggest that the mechanism of germline mutations are distinct from cancer-associated somatic histone mutations but may converge on control of cell proliferation.
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Affiliation(s)
- Laura Bryant
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Samuel G Cox
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, CA 90033, USA
| | - Dylan Marchione
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Evan F Joiner
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Khadija Wilson
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin Janssen
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pearl Lee
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael E March
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Divya Nair
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elliott Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brieana Fregeau
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Klaas J Wierenga
- Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Alexandrea Wadley
- Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, Netherlands
| | - Nina Powell-Hamilton
- Department of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, DE 19810, USA
| | | | - Theresa Grebe
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | - John Dean
- Department of Medical Genetics, Aberdeen Royal Infirmary, Aberdeen, Scotland, UK
| | - Alison Ross
- Department of Medical Genetics, Aberdeen Royal Infirmary, Aberdeen, Scotland, UK
| | - Heather P Crawford
- Clinical and Metabolic Genetics, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Zoe Powis
- Department of Emerging Genetic Medicine, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Megan T Cho
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Marcia C Willing
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Linda Manwaring
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Rachel Schot
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, Netherlands
| | - Caroline Nava
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, Paris, France
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013 Paris, France
| | - Alexandra Afenjar
- Service de génétique, CRMR des malformations et maladies congénitales du cervelet et CRMR déficience intellectuelle, hôpital Trousseau, AP-HP, France
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Undiagnosed Disease Program at the University Medical Center Hamburg-Eppendorf (UDP-UKE), Martinistrasse 52, 20246 Hamburg, Germany
| | - Matias Wagner
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Technische Universität München, Munich, Germany
| | - Thomas Klopstock
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians University, Ziemssenstr. 1a, 80336 Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Juliane Winkelmann
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
- Klinik und Poliklinik für Neurologie, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Claudia B Catarino
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians University, Ziemssenstr. 1a, 80336 Munich, Germany
| | - Kyle Retterer
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Jane L Schuette
- Division of Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey W Innis
- Division of Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amy Pizzino
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Sabine Lüttgen
- Department of Pediatrics, University Medical Center Eppendorf, 20246 Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, 20246 Hamburg, Germany
| | - Tim M Strom
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Technische Universität München, Munich, Germany
| | | | - Zuo-Fei Yuan
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Holly Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Renee Bend
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | | | - Julia Hoefele
- Institut für Humangenetik, Technische Universität München, Munich, Germany
| | - Roman Günthner
- Department of Nephrology, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
| | - Heiko Reutter
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University Hospital Bonn & Institute of Human Genetics, University Hospital Bonn, Bonn, Germany
| | - Boris Keren
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013 Paris, France
| | - Kelly Radtke
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Omar Sherbini
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Cameron Mrokse
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Katherine L Helbig
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sylvie Odent
- CHU Rennes, Service de Génétique Clinique, CNRS UMR6290, University Rennes1, Rennes, France
| | - Benjamin Cogne
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Stephane Bezieau
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Thomas Besnard
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Sebastien Kury
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Richard Redon
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Karit Reinson
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Monica H Wojcik
- Division of Genetics and Genomics and Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute, Cambridge, MA 02142, USA
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Pilvi Ilves
- Radiology Department of Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - A Micheil Innes
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H8L1, Canada
- Newborn Screening Ontario (NSO), Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - M Stephen Meyn
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Center for Human Genomics and Precision Medicine, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, Wisconsin 53705, USA
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Hilary Kitson
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
| | - Martin G Martin
- Division of Gastroenterology and Nutrition, Department of Pediatrics, Mattel Children's Hospital, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research and the David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Stan F Nelson
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Christina G S Palmer
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Institute for Society and Genetics, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jeanette C Papp
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Neil H Parker
- David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Janet S Sinsheimer
- Institute for Society and Genetics, Departments of Human Genetics, Biomathematics, and Biostatistics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - Jijun Wan
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Amanda J Yoon
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Allison Zheng
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Elise Brimble
- Department of Neurology and Neurological Sciences, Stanford Medicine, Stanford, CA 94305, USA
| | | | | | - Diana Carli
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Jennifer Muncy Thomas
- Pediatrics and Neurology and Neurotherapeutics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luis Umana
- Genetics and Metabolism, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marjan M Weiss
- Department of Clinical Genetics, VU Medical Center, Amsterdam, Netherlands
| | - Garrett Gotway
- Genetics and Metabolism, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - K E Stuurman
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, Netherlands
| | | | | | - Constance T R M Stumpel
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Arve Vøllo
- Department of Pediatrics, Hospital of Østfold, 1714 Grålum, Norway
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Melissa Byler
- SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | | | - Anna C Hurst
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joy Dean
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk VA 23507, USA
| | | | - Saadet Mercimek-Andrews
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Juanita Neira
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Margot I Van Allen
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Medical Genetics Programs, Provincial Health Shared Services BC and Vancouver Island Health Shared Services BC, Canada
| | - Nicola Longo
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT 84112, USA
| | - Elizabeth Sellars
- University of Arkansas for Medical Sciences, Little Rock, AR 72701, USA
| | | | | | | | - Delphine Heron
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013 Paris, France
| | - Molly Snyder
- Child Neurology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Celeste Simon
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Xavier de la Cruz
- Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Natália Padilla
- Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, CA 90033, USA
| | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Garcia
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, CA 90033, USA
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hakon H Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elizabeth J Bhoj
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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34
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Louie RJ, Collins DL, Friez MJ, Skinner C, Schwartz CE, Stevenson RE. Schimke XLID syndrome results from a deletion in BCAP31. Am J Med Genet A 2020; 182:2168-2174. [PMID: 32681719 DOI: 10.1002/ajmg.a.61755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 05/31/2020] [Indexed: 12/13/2022]
Abstract
A family with three affected males and a second family with a single affected male with intellectual disability, microcephaly, ophthalmoplegia, deafness, and Involuntary limb movements were reported by Schimke and Associates in 1984. The affected males with Schimke X-linked intellectual disability (XLID) syndrome (OMIM# 312840) had a similar facial appearance with deep-set eyes, downslanting palpebral fissures, hypotelorism, narrow nose and alae nasi, cupped ears and spacing of the teeth. Two mothers had mild hearing loss but no other manifestations of the disorder. The authors considered the disorder to be distinctive and likely X-linked. Whole genome sequencing in the single affected male available and the three carrier females from one of the families with Schimke XLID syndrome identified a 2 bp deletion in the BCAP31 gene. During the past decade, pathogenic alterations of the BCAP31 gene have been associated with deafness, dystonia, and central hypomyelination, an XLID condition given the eponym DDCH syndrome. A comparison of clinical findings in Schimke XLID syndrome and DDCH syndrome shows them to be the same clinical entity. The BCAP31 protein functions in endoplasmic reticulum-associated degradation to promote ubiquitination and destruction of misfolded proteins.
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Affiliation(s)
| | | | | | - Cindy Skinner
- Greenwood Genetic Center, Greenwood, South Carolina, USA
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35
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Gass JM, Head BB, Shields SM, Stevenson RE, Louie RJ. Hydrocephaly associated with compound heterozygous alterations in TRAPPC12. Birth Defects Res 2020; 112:1028-1034. [PMID: 32347653 DOI: 10.1002/bdr2.1699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 11/06/2022]
Abstract
BACKGROUND Hydrocephalus is characterized by increased cerebrospinal fluid within the brain, a causally heterogeneous disorder estimated to affect 1 per 1,000 live births, with the most severe cases often leading to fetal demise. The large number of known genetic and environmental factors that contribute to hydrocephalus makes the differential diagnosis challenging. CASES Three consecutive pregnancies of an unrelated couple were found by ultrasound to carry fetuses with hydrocephaly. DNA from two affected fetuses and the parents were subjected to whole exome sequencing. Heterozygous alterations in the TRAPPC12 gene were identified in the parents and compound heterozygous alterations were present in the two affected fetuses. The variant from the father (c.954del) leads to a premature termination of the transcript; the variant from the mother (c.1677+5G>A) affects a splice site which leads to aberrant splicing of the TRAPPC12 transcript. CONCLUSION Compound heterozygous variants in TRAPPC12, which encodes a protein involved in Golgi trafficking and mitosis, may disrupt normal brain embryogenesis leading to hydrocephalus and recurrent pregnancy loss.
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Affiliation(s)
- Jennifer M Gass
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Barbara B Head
- Maternal-Fetal Medicine Division, Department of Obstetrics and Gynecology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Sally M Shields
- Maternal-Fetal Medicine Division, Department of Obstetrics and Gynecology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Roger E Stevenson
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Raymond J Louie
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina, USA
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36
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Beck DB, Petracovici A, He C, Moore HW, Louie RJ, Ansar M, Douzgou S, Sithambaram S, Cottrell T, Santos-Cortez RLP, Prijoles EJ, Bend R, Keren B, Mignot C, Nougues MC, Õunap K, Reimand T, Pajusalu S, Zahid M, Saqib MAN, Buratti J, Seaby EG, McWalter K, Telegrafi A, Baldridge D, Shinawi M, Leal SM, Schaefer GB, Stevenson RE, Banka S, Bonasio R, Fahrner JA. Delineation of a Human Mendelian Disorder of the DNA Demethylation Machinery: TET3 Deficiency. Am J Hum Genet 2020; 106:234-245. [PMID: 31928709 DOI: 10.1016/j.ajhg.2019.12.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
Germline pathogenic variants in chromatin-modifying enzymes are a common cause of pediatric developmental disorders. These enzymes catalyze reactions that regulate epigenetic inheritance via histone post-translational modifications and DNA methylation. Cytosine methylation (5-methylcytosine [5mC]) of DNA is the quintessential epigenetic mark, yet no human Mendelian disorder of DNA demethylation has yet been delineated. Here, we describe in detail a Mendelian disorder caused by the disruption of DNA demethylation. TET3 is a methylcytosine dioxygenase that initiates DNA demethylation during early zygote formation, embryogenesis, and neuronal differentiation and is intolerant to haploinsufficiency in mice and humans. We identify and characterize 11 cases of human TET3 deficiency in eight families with the common phenotypic features of intellectual disability and/or global developmental delay; hypotonia; autistic traits; movement disorders; growth abnormalities; and facial dysmorphism. Mono-allelic frameshift and nonsense variants in TET3 occur throughout the coding region. Mono-allelic and bi-allelic missense variants localize to conserved residues; all but one such variant occur within the catalytic domain, and most display hypomorphic function in an assay of catalytic activity. TET3 deficiency and other Mendelian disorders of the epigenetic machinery show substantial phenotypic overlap, including features of intellectual disability and abnormal growth, underscoring shared disease mechanisms.
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Affiliation(s)
- David B Beck
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ana Petracovici
- Graduate Group in Genetics and Epigenetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Chongsheng He
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Current address: Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082 Hunan, P.R. China
| | | | | | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan
| | - Sofia Douzgou
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Sivagamy Sithambaram
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Trudie Cottrell
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | | | | | - Renee Bend
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Boris Keren
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France
| | - Cyril Mignot
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris 75013, France
| | - Marie-Christine Nougues
- Assistance Publique-Hôpitaux de Paris, Armand Trousseau Hospital, Department of Neuropediatrics, Paris 75012, France
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia; Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50406, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia; Yale University School of Medicine, Department of Genetics, New Haven, CT 06510, USA
| | - Muhammad Zahid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan
| | | | - Julien Buratti
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France
| | - Eleanor G Seaby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - Dustin Baldridge
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Taub Institute for Alzheimer's D disease and the Aging Brain, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY 10032, USA
| | | | | | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Roberto Bonasio
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jill A Fahrner
- Department of Pediatrics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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37
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Louie RJ, Friez MJ, Skinner C, Baraitser M, Clark RD, Schwartz CE, Stevenson RE. Clark-Baraitser syndrome is associated with a nonsense alteration in the autosomal gene TRIP12. Am J Med Genet A 2019; 182:595-596. [PMID: 31814248 DOI: 10.1002/ajmg.a.61443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/22/2019] [Accepted: 11/26/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Raymond J Louie
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Michael J Friez
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Cindy Skinner
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Michael Baraitser
- Department of Clinical Genetics, Hospital for Sick Children, London, UK
| | - Robin D Clark
- Division of Medical Genetics, Loma Linda University School of Medicine, Loma Linda, California
| | - Charles E Schwartz
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Roger E Stevenson
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
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38
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Kruszka P, Berger SI, Casa V, Dekker MR, Gaesser J, Weiss K, Martinez AF, Murdock DR, Louie RJ, Prijoles EJ, Lichty AW, Brouwer OF, Zonneveld-Huijssoon E, Stephan MJ, Hogue J, Hu P, Tanima-Nagai M, Everson JL, Prasad C, Cereda A, Iascone M, Schreiber A, Zurcher V, Corsten-Janssen N, Escobar L, Clegg NJ, Delgado MR, Hajirnis O, Balasubramanian M, Kayserili H, Deardorff M, Poot RA, Wendt KS, Lipinski RJ, Muenke M. Cohesin complex-associated holoprosencephaly. Brain 2019; 142:2631-2643. [PMID: 31334757 PMCID: PMC7245359 DOI: 10.1093/brain/awz210] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/15/2019] [Accepted: 05/22/2019] [Indexed: 12/16/2022] Open
Abstract
Marked by incomplete division of the embryonic forebrain, holoprosencephaly is one of the most common human developmental disorders. Despite decades of phenotype-driven research, 80-90% of aneuploidy-negative holoprosencephaly individuals with a probable genetic aetiology do not have a genetic diagnosis. Here we report holoprosencephaly associated with variants in the two X-linked cohesin complex genes, STAG2 and SMC1A, with loss-of-function variants in 10 individuals and a missense variant in one. Additionally, we report four individuals with variants in the cohesin complex genes that are not X-linked, SMC3 and RAD21. Using whole mount in situ hybridization, we show that STAG2 and SMC1A are expressed in the prosencephalic neural folds during primary neurulation in the mouse, consistent with forebrain morphogenesis and holoprosencephaly pathogenesis. Finally, we found that shRNA knockdown of STAG2 and SMC1A causes aberrant expression of HPE-associated genes ZIC2, GLI2, SMAD3 and FGFR1 in human neural stem cells. These findings show the cohesin complex as an important regulator of median forebrain development and X-linked inheritance patterns in holoprosencephaly.
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Affiliation(s)
- Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Seth I Berger
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Valentina Casa
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Mike R Dekker
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Jenna Gaesser
- Department of Pediatrics, Division of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Karin Weiss
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ariel F Martinez
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David R Murdock
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raymond J Louie
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC, USA
| | - Eloise J Prijoles
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC, USA
| | - Angie W Lichty
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC, USA
| | - Oebele F Brouwer
- Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mark J Stephan
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Jacob Hogue
- Division of Clinical Genetics, Department of Pediatrics, Madigan Army Hospital, Tacoma, WA, USA
| | - Ping Hu
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Momoko Tanima-Nagai
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joshua L Everson
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Environmental Toxicology Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Chitra Prasad
- Children’s Health Research Institute, London, ON, Canada
| | - Anna Cereda
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | | | - Vickie Zurcher
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Nicole Corsten-Janssen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Luis Escobar
- Peyton Manning Children’s Hospital at St. Vincent, Medical Genetics and Neurodevelopment Center, Indianapolis, IN, USA
| | - Nancy J Clegg
- Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Mauricio R Delgado
- Texas Scottish Rite Hospital for Children, Dallas, TX, USA
- Department of Neurology and Neurotherapeutics UT Southwestern Medical Center Dallas, TX, USA
| | - Omkar Hajirnis
- Pediatric Neurology, Synapses Child Neurology and Development Centre, Thane, Maharashtra, India
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children’s, NHS Foundation Trust, Sheffield, UK
- Academic Unit of Child Health, University of Sheffield, Sheffield, UK
| | - Hülya Kayserili
- Medical Genetics, Medical Faculty, Koç University, Istanbul, Turkey
| | - Matthew Deardorff
- The Division of Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- The Department of Pediatrics, The Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Raymond A Poot
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Robert J Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Environmental Toxicology Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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39
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Stolerman ES, Francisco E, Stallworth JL, Jones JR, Monaghan KG, Keller-Ramey J, Person R, Wentzensen IM, McWalter K, Keren B, Heron B, Nava C, Heron D, Kim K, Burton B, Al-Musafri F, O'Grady L, Sahai I, Escobar LF, Meuwissen M, Reyniers E, Kooy F, Lacassie Y, Gunay-Aygun M, Schatz KS, Hochstenbach R, Zwijnenburg PJG, Waisfisz Q, van Slegtenhorst M, Mancini GMS, Louie RJ. Genetic variants in the KDM6B gene are associated with neurodevelopmental delays and dysmorphic features. Am J Med Genet A 2019; 179:1276-1286. [PMID: 31124279 DOI: 10.1002/ajmg.a.61173] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/29/2022]
Abstract
Lysine-specific demethylase 6B (KDM6B) demethylates trimethylated lysine-27 on histone H3. The methylation and demethylation of histone proteins affects gene expression during development. Pathogenic alterations in histone lysine methylation and demethylation genes have been associated with multiple neurodevelopmental disorders. We have identified a number of de novo alterations in the KDM6B gene via whole exome sequencing (WES) in a cohort of 12 unrelated patients with developmental delay, intellectual disability, dysmorphic facial features, and other clinical findings. Our findings will allow for further investigation in to the role of the KDM6B gene in human neurodevelopmental disorders.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Boris Keren
- APHP, Hôpital Armand Trousseau, Paris, France
| | | | | | | | - Katherine Kim
- Division of Genetics, Birth Defects and Metabolism, Ann and Robert H. Lurie Children's Hospital, Chicago, Illinois.,Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Barbara Burton
- Division of Genetics, Birth Defects and Metabolism, Ann and Robert H. Lurie Children's Hospital, Chicago, Illinois.,Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | | | | | | | - Luis F Escobar
- Medical Genetics and Neurodevelopmental Center, Peyton Manning Children's, Hospital at St. Vincent, Indianapolis, Indiana
| | | | - Edwin Reyniers
- Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Frank Kooy
- Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Yves Lacassie
- Children's Hospital New Orleans, New Orleans, Louisiana.,Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Meral Gunay-Aygun
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | | | - Ron Hochstenbach
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Petra J G Zwijnenburg
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
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40
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Snijders Blok L, Rousseau J, Twist J, Ehresmann S, Takaku M, Venselaar H, Rodan LH, Nowak CB, Douglas J, Swoboda KJ, Steeves MA, Sahai I, Stumpel CTRM, Stegmann APA, Wheeler P, Willing M, Fiala E, Kochhar A, Gibson WT, Cohen ASA, Agbahovbe R, Innes AM, Au PYB, Rankin J, Anderson IJ, Skinner SA, Louie RJ, Warren HE, Afenjar A, Keren B, Nava C, Buratti J, Isapof A, Rodriguez D, Lewandowski R, Propst J, van Essen T, Choi M, Lee S, Chae JH, Price S, Schnur RE, Douglas G, Wentzensen IM, Zweier C, Reis A, Bialer MG, Moore C, Koopmans M, Brilstra EH, Monroe GR, van Gassen KLI, van Binsbergen E, Newbury-Ecob R, Bownass L, Bader I, Mayr JA, Wortmann SB, Jakielski KJ, Strand EA, Kloth K, Bierhals T, Roberts JD, Petrovich RM, Machida S, Kurumizaka H, Lelieveld S, Pfundt R, Jansen S, Deriziotis P, Faivre L, Thevenon J, Assoum M, Shriberg L, Kleefstra T, Brunner HG, Wade PA, Fisher SE, Campeau PM. Author Correction: CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language. Nat Commun 2019; 10:2079. [PMID: 31048695 PMCID: PMC6497626 DOI: 10.1038/s41467-019-10161-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Lot Snijders Blok
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500HB, The Netherlands.,Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, 6500AH, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, 6500HE, The Netherlands
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Joanna Twist
- National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Sophie Ehresmann
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Motoki Takaku
- National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500HB, The Netherlands
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Catherine B Nowak
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jessica Douglas
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kathryn J Swoboda
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Marcie A Steeves
- Department of Medical Genetics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Inderneel Sahai
- Department of Medical Genetics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Connie T R M Stumpel
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, 6202AZ, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, 6202AZ, The Netherlands
| | | | - Marcia Willing
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elise Fiala
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - William T Gibson
- British Columbia Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Ana S A Cohen
- British Columbia Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Ruky Agbahovbe
- British Columbia Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - P Y Billie Au
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Julia Rankin
- Department of Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust (Heavitree), Exeter, EX2 5DW, UK
| | - Ilse J Anderson
- Division of Genetics, Department of Medicine, University of Tennessee Medical Center, Knoxville, TN 37920, USA
| | | | | | | | - Alexandra Afenjar
- GRC ConCer-LD, Sorbonne Universités, UPMC Univ Paris ; Department of Medical Genetics and Centre de Référence Malformations et maladies congénitales du cervelet et déficiences intellectuelles de causes rares, Armand Trousseau Hospital, GHUEP, AP-HP, Paris, 75012, France
| | - Boris Keren
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, 75013, France.,Groupe de Recherche Clinique (GRC) 'déficience intellectuelle et autisme' UPMC, Paris, 75005, France
| | - Caroline Nava
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, 75013, France.,Groupe de Recherche Clinique (GRC) 'déficience intellectuelle et autisme' UPMC, Paris, 75005, France.,INSERM, U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, 75013, Paris, France
| | - Julien Buratti
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, 75013, France
| | - Arnaud Isapof
- GRC ConCer-LD, Sorbonne Universités, UPMC Univ Paris 06; Department Child Neurology and Reference Center for Neuromuscular Diseases "Nord/Est/Ile-de-France", FILNEMUS, Armand Trousseau Hospital, GHUEP, AP-HP, Paris, 75012, France
| | - Diana Rodriguez
- GRC ConCer-LD, Sorbonne Universités, UPMC Univ Paris 06; Department of Child Neurology and National Reference Center for Neurogenetic Disorders, Armand Trousseau Hospital, GHUEP, AP-HP, INSERM U1141, 75012, Paris, France
| | - Raymond Lewandowski
- Clinical Genetics Division, Virginia Commonwealth University Health System, Richmond, VA 23298, USA
| | - Jennifer Propst
- Clinical Genetics Division, Virginia Commonwealth University Health System, Richmond, VA 23298, USA
| | - Ton van Essen
- Clinical Genetics Department, University Medical Center Groningen, Groningen, 9700RB, The Netherlands
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 08826, Republic of Korea
| | - Sangmoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 08826, Republic of Korea
| | - Jong H Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, 08826, Republic of Korea
| | - Susan Price
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7HE, UK
| | | | | | | | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Martin G Bialer
- Northwell Health, Division of Medical Genetics and Genomics, Great Neck, NY 11021, USA
| | - Christine Moore
- Northwell Health, Division of Medical Genetics and Genomics, Great Neck, NY 11021, USA
| | - Marije Koopmans
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, 3508AB, The Netherlands
| | - Eva H Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, 3508AB, The Netherlands
| | - Glen R Monroe
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, 3508AB, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, 3508AB, The Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, 3508AB, The Netherlands
| | - Ruth Newbury-Ecob
- University Hospitals Bristol, Department of Clinical Genetics, St Michael's Hospital, Bristol, BS2 8EG, UK
| | - Lucy Bownass
- University Hospitals Bristol, Department of Clinical Genetics, St Michael's Hospital, Bristol, BS2 8EG, UK
| | - Ingrid Bader
- Department of Clinical Genetics, University Children's Hospital, Paracelsus Medical University, Salzburg, A-5020, Austria
| | - Johannes A Mayr
- Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University, Salzburg, A-5020, Austria
| | - Saskia B Wortmann
- Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University, Salzburg, A-5020, Austria.,Institute of Human Genetics, Technische Universität München, Munich, 81675, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, 85764, Germany
| | - Kathy J Jakielski
- Communication Sciences and Disorders, Augustana College, Rock Island, IL 61201, USA
| | - Edythe A Strand
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Katja Kloth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | | | - John D Roberts
- National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Robert M Petrovich
- National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | | | | | - Stefan Lelieveld
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500HB, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500HB, The Netherlands
| | - Sandra Jansen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500HB, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, 6500HE, The Netherlands
| | - Pelagia Deriziotis
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, 6500AH, The Netherlands
| | - Laurence Faivre
- Equipe Génétique des Anomalies du Développement, Université de Bourgogne-Franche Comté, Dijon, 21070, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon et Université de Bourgogne, Dijon, 21079, France
| | - Julien Thevenon
- Equipe Génétique des Anomalies du Développement, Université de Bourgogne-Franche Comté, Dijon, 21070, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon et Université de Bourgogne, Dijon, 21079, France
| | - Mirna Assoum
- Equipe Génétique des Anomalies du Développement, Université de Bourgogne-Franche Comté, Dijon, 21070, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon et Université de Bourgogne, Dijon, 21079, France
| | | | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500HB, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, 6500HE, The Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500HB, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, 6500HE, The Netherlands.,Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, 6202AZ, The Netherlands
| | - Paul A Wade
- National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, 6500AH, The Netherlands. .,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, 6500HE, The Netherlands.
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada. .,Sainte-Justine Hospital, University of Montreal, Montreal, QC H3T 1C5, Canada.
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41
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Blok LS, Rousseau J, Twist J, Ehresmann S, Takaku M, Venselaar H, Rodan LH, Nowak CB, Douglas J, Swoboda KJ, Steeves MA, Sahai I, Stumpel CTRM, Stegmann APA, Wheeler P, Willing M, Fiala E, Kochhar A, Gibson WT, Cohen ASA, Agbahovbe R, Innes AM, Au PYB, Rankin J, Anderson IJ, Skinner SA, Louie RJ, Warren HE, Afenjar A, Keren B, Nava C, Buratti J, Isapof A, Rodriguez D, Lewandowski R, Propst J, van Essen T, Choi M, Lee S, Chae JH, Price S, Schnur RE, Douglas G, Wentzensen IM, Zweier C, Reis A, Bialer MG, Moore C, Koopmans M, Brilstra EH, Monroe GR, van Gassen KLI, van Binsbergen E, Newbury-Ecob R, Bownass L, Bader I, Mayr JA, Wortmann SB, Jakielski KJ, Strand EA, Kloth K, Bierhals T, Roberts JD, Petrovich RM, Machida S, Kurumizaka H, Lelieveld S, Pfundt R, Jansen S, Deriziotis P, Faivre L, Thevenon J, Assoum M, Shriberg L, Kleefstra T, Brunner HG, Wade PA, Fisher SE, Campeau PM. Author Correction: CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language. Nat Commun 2019; 10:883. [PMID: 30770872 PMCID: PMC6377600 DOI: 10.1038/s41467-019-08800-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Lot Snijders Blok
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500HB, The Netherlands.,Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, 6500AH, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, 6500HE, The Netherlands
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, Montreal, QC, H3T 1C5, Canada
| | - Joanna Twist
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Sophie Ehresmann
- CHU Sainte-Justine Research Center, Montreal, QC, H3T 1C5, Canada
| | - Motoki Takaku
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500HB, The Netherlands
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Catherine B Nowak
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Jessica Douglas
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Kathryn J Swoboda
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Marcie A Steeves
- Department of Medical Genetics, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Inderneel Sahai
- Department of Medical Genetics, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Connie T R M Stumpel
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, 6202AZ, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, 6202AZ, The Netherlands
| | | | - Marcia Willing
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Elise Fiala
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - William T Gibson
- British Columbia Children's Hospital Research Institute, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Ana S A Cohen
- British Columbia Children's Hospital Research Institute, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Ruky Agbahovbe
- British Columbia Children's Hospital Research Institute, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - P Y Billie Au
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Julia Rankin
- Department of Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust (Heavitree), Exeter, EX2 5DW, UK
| | - Ilse J Anderson
- Division of Genetics, Department of Medicine, University of Tennessee Medical Center, Knoxville, TN, 37920, USA
| | | | | | | | - Alexandra Afenjar
- GRC ConCer-LD, Sorbonne Universités, UPMC Univ Paris ; Department of Medical Genetics and Centre de Référence Malformations et maladies congénitales du cervelet et déficiences intellectuelles de causes rares, Armand Trousseau Hospital, GHUEP, AP-HP, Paris, 75012, France
| | - Boris Keren
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, 75013, France.,Groupe de Recherche Clinique (GRC) 'déficience intellectuelle et autisme' UPMC, Paris, 75005, France
| | - Caroline Nava
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, 75013, France.,Groupe de Recherche Clinique (GRC) 'déficience intellectuelle et autisme' UPMC, Paris, 75005, France.,INSERM, U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, 75013, Paris, France
| | - Julien Buratti
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, 75013, France
| | - Arnaud Isapof
- GRC ConCer-LD, Sorbonne Universités, UPMC Univ Paris 06; Department Child Neurology and Reference Center for Neuromuscular Diseases "Nord/Est/Ile-de-France", FILNEMUS, Armand Trousseau Hospital, GHUEP, AP-HP, Paris, 75012, France
| | - Diana Rodriguez
- GRC ConCer-LD, Sorbonne Universités, UPMC Univ Paris 06; Department of Child Neurology and National Reference Center for Neurogenetic Disorders, Armand Trousseau Hospital, GHUEP, AP-HP, INSERM U1141, 75012, Paris, France
| | - Raymond Lewandowski
- Clinical Genetics Division, Virginia Commonwealth University Health System, Richmond, VA, 23298, USA
| | - Jennifer Propst
- Clinical Genetics Division, Virginia Commonwealth University Health System, Richmond, VA, 23298, USA
| | - Ton van Essen
- Clinical Genetics Department, University Medical Center Groningen, Groningen, 9700RB, The Netherlands
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 08826, Republic of Korea
| | - Sangmoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 08826, Republic of Korea
| | - Jong H Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, 08826, Republic of Korea
| | - Susan Price
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7HE, UK
| | | | | | | | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Martin G Bialer
- Northwell Health, Division of Medical Genetics and Genomics, Great Neck NY, 11021, USA
| | - Christine Moore
- Northwell Health, Division of Medical Genetics and Genomics, Great Neck NY, 11021, USA
| | - Marije Koopmans
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, 3508AB, The Netherlands
| | - Eva H Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, 3508AB, The Netherlands
| | - Glen R Monroe
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, 3508AB, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, 3508AB, The Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, 3508AB, The Netherlands
| | - Ruth Newbury-Ecob
- University Hospitals Bristol, Department of Clinical Genetics, St Michael's Hospital, Bristol, BS2 8EG, UK
| | - Lucy Bownass
- University Hospitals Bristol, Department of Clinical Genetics, St Michael's Hospital, Bristol, BS2 8EG, UK
| | - Ingrid Bader
- Department of Clinical Genetics, University Children's Hospital, Paracelsus Medical University, Salzburg, A-5020, Austria
| | - Johannes A Mayr
- Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University, Salzburg, A-5020, Austria
| | - Saskia B Wortmann
- Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University, Salzburg, A-5020, Austria.,Institute of Human Genetics, Technische Universität München, Munich, 81675, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, 85764, Germany
| | - Kathy J Jakielski
- Communication Sciences and Disorders, Augustana College, Rock Island, IL, 61201, USA
| | - Edythe A Strand
- Department of Neurology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Katja Kloth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | | | - John D Roberts
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Robert M Petrovich
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | | | | | - Stefan Lelieveld
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500HB, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500HB, The Netherlands
| | - Sandra Jansen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500HB, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, 6500HE, The Netherlands
| | - Pelagia Deriziotis
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, 6500AH, The Netherlands
| | - Laurence Faivre
- Equipe Génétique des Anomalies du Développement, Université de Bourgogne- Franche Comté, Dijon, 21070, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon et Université de Bourgogne, Dijon, 21079, France
| | - Julien Thevenon
- Equipe Génétique des Anomalies du Développement, Université de Bourgogne- Franche Comté, Dijon, 21070, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon et Université de Bourgogne, Dijon, 21079, France
| | - Mirna Assoum
- Equipe Génétique des Anomalies du Développement, Université de Bourgogne- Franche Comté, Dijon, 21070, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon et Université de Bourgogne, Dijon, 21079, France
| | | | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500HB, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, 6500HE, The Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500HB, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, 6500HE, The Netherlands.,Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, 6202AZ, The Netherlands
| | - Paul A Wade
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, 6500AH, The Netherlands. .,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, 6500HE, The Netherlands.
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, Montreal, QC, H3T 1C5, Canada. .,Sainte-Justine Hospital, University of Montreal, Montreal, QC, H3T 1C5, Canada.
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42
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Warren HE, Louie RJ, Friez MJ, Frías JL, Leroy JG, Spranger JW, Skinner SA, Champaigne NL. Two unrelated patients with autosomal dominant omodysplasia and FRIZZLED2 mutations. Clin Case Rep 2018; 6:2252-2255. [PMID: 30455931 PMCID: PMC6230601 DOI: 10.1002/ccr3.1818] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/26/2018] [Accepted: 08/20/2018] [Indexed: 11/08/2022] Open
Abstract
Presented are two patients with autosomal dominant omodysplasia and mutations in the FZD2 gene. The mutations identified have been recently reported, suggesting the possibility of recurrent mutations. The phenotypes of these patients overlap with what has been previously reported, though intellectual disability as seen in our patient is not typical.
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Affiliation(s)
| | | | | | - Jaime L. Frías
- Department of PediatricsUniversity of South FloridaTampaFlorida
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43
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Lessel D, Gehbauer C, Bramswig NC, Schluth-Bolard C, Venkataramanappa S, van Gassen KLI, Hempel M, Haack TB, Baresic A, Genetti CA, Funari MFA, Lessel I, Kuhlmann L, Simon R, Liu P, Denecke J, Kuechler A, de Kruijff I, Shoukier M, Lek M, Mullen T, Lüdecke HJ, Lerario AM, Kobbe R, Krieger T, Demeer B, Lebrun M, Keren B, Nava C, Buratti J, Afenjar A, Shinawi M, Guillen Sacoto MJ, Gauthier J, Hamdan FF, Laberge AM, Campeau PM, Louie RJ, Cathey SS, Prinz I, Jorge AAL, Terhal PA, Lenhard B, Wieczorek D, Strom TM, Agrawal PB, Britsch S, Tolosa E, Kubisch C. BCL11B mutations in patients affected by a neurodevelopmental disorder with reduced type 2 innate lymphoid cells. Brain 2018; 141:2299-2311. [PMID: 29985992 PMCID: PMC6061686 DOI: 10.1093/brain/awy173] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/09/2018] [Accepted: 05/08/2018] [Indexed: 12/16/2022] Open
Abstract
The transcription factor BCL11B is essential for development of the nervous and the immune system, and Bcl11b deficiency results in structural brain defects, reduced learning capacity, and impaired immune cell development in mice. However, the precise role of BCL11B in humans is largely unexplored, except for a single patient with a BCL11B missense mutation, affected by multisystem anomalies and profound immune deficiency. Using massively parallel sequencing we identified 13 patients bearing heterozygous germline alterations in BCL11B. Notably, all of them are affected by global developmental delay with speech impairment and intellectual disability; however, none displayed overt clinical signs of immune deficiency. Six frameshift mutations, two nonsense mutations, one missense mutation, and two chromosomal rearrangements resulting in diminished BCL11B expression, arose de novo. A further frameshift mutation was transmitted from a similarly affected mother. Interestingly, the most severely affected patient harbours a missense mutation within a zinc-finger domain of BCL11B, probably affecting the DNA-binding structural interface, similar to the recently published patient. Furthermore, the most C-terminally located premature termination codon mutation fails to rescue the progenitor cell proliferation defect in hippocampal slice cultures from Bcl11b-deficient mice. Concerning the role of BCL11B in the immune system, extensive immune phenotyping of our patients revealed alterations in the T cell compartment and lack of peripheral type 2 innate lymphoid cells (ILC2s), consistent with the findings described in Bcl11b-deficient mice. Unsupervised analysis of 102 T lymphocyte subpopulations showed that the patients clearly cluster apart from healthy children, further supporting the common aetiology of the disorder. Taken together, we show here that mutations leading either to BCL11B haploinsufficiency or to a truncated BCL11B protein clinically cause a non-syndromic neurodevelopmental delay. In addition, we suggest that missense mutations affecting specific sites within zinc-finger domains might result in distinct and more severe clinical outcomes.
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Affiliation(s)
- Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christina Gehbauer
- Department of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nuria C Bramswig
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Caroline Schluth-Bolard
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Lyon Neuroscience Research Center, Inserm U1028 - CNRS UMR5292 - UCBLyon1, GENDEV Team, Bron, France
| | | | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Haack
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Anja Baresic
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, London, UK
| | - Casie A Genetti
- Divisions of Genetics and Genomics and Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital and Harvard Medical School, Boston, USA
| | - Mariana F A Funari
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular (LIM42), Hospital das Clinicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Ivana Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leonie Kuhlmann
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Ruth Simon
- Institute of Molecular and Cellular Anatomy, Ulm University, Ulm, Germany
| | - Pentao Liu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, Hamburg, Germany
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Ineke de Kruijff
- Department of Pediatrics, St. Antonius Hospital, Nieuwegein, The Netherlands
| | | | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Thomas Mullen
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Hermann-Josef Lüdecke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- Institute of Human Genetics, University Clinic, Heinrich-Heine University, Düsseldorf, Germany
| | - Antonio M Lerario
- Unidade de Endocrinologia Genetica (LIM25), Hospital das Clinicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brazil
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, USA
| | - Robin Kobbe
- Department of Pediatrics, University Medical Center Eppendorf, Hamburg, Germany
| | - Thorsten Krieger
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benedicte Demeer
- Unité de Génétique Clinique, CLAD Nord de France, CHU Amiens-Picardie, Amiens, France
| | - Marine Lebrun
- Service de Génétique Clinique, Chromosomique et Moléculaire, CHU Hôpital Nord, Saint-Etienne, France
| | - Boris Keren
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Caroline Nava
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Julien Buratti
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Alexandra Afenjar
- Département de génétique médicale, Sorbonne Université, GRC n°19, pathologies Congénitales du Cervelet-LeucoDystrophies, AP-HP, Centre de Référence déficiences intellectuelles de causes rares, Hôpital Armand Trousseau, F-75012 Paris, France
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicin, St. Louis, MO, USA
| | | | - Julie Gauthier
- Molecular Diagnostic Laboratory and Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Canada
| | - Fadi F Hamdan
- Molecular Diagnostic Laboratory and Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Canada
| | - Anne-Marie Laberge
- Division of Medical Genetics and Research Center, CHU Sainte-Justine and Department of Pediatrics, Université de Montréal, Montreal, Canada
| | - Philippe M Campeau
- Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, Canada
| | | | - Sara S Cathey
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Immo Prinz
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Alexander A L Jorge
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular (LIM42), Hospital das Clinicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brazil
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, USA
| | - Paulien A Terhal
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Boris Lenhard
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Dagmar Wieczorek
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- Institute of Human Genetics, University Clinic, Heinrich-Heine University, Düsseldorf, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Pankaj B Agrawal
- Divisions of Genetics and Genomics and Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital and Harvard Medical School, Boston, USA
| | - Stefan Britsch
- Institute of Molecular and Cellular Anatomy, Ulm University, Ulm, Germany
| | - Eva Tolosa
- Department of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Padró M, Louie RJ, Lananna BV, Krieg AJ, Timmerman LA, Chan DA. Genome-independent hypoxic repression of estrogen receptor alpha in breast cancer cells. BMC Cancer 2017; 17:203. [PMID: 28320353 PMCID: PMC5358051 DOI: 10.1186/s12885-017-3140-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 02/15/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND About 75-80% of breast tumors express the estrogen receptor alpha (ER-α) and are treated with endocrine-target therapeutics, making this the premier therapeutic modality in the breast cancer clinic. However, acquired resistance is common and about 20% of resistant tumors loose ER-α expression via unknown mechanisms. Inhibition of ER-α loss could improve endocrine therapeutic efficacy, benefiting a significant number of patients. Here we test whether tumor hypoxia might commonly produce ER-α loss. METHODS Using standard molecular and cellular biological assays and a work station/incubator with controllable oxygen levels, we analyze the effects of hypoxia on ER-α protein, mRNA, and transcriptional activity in a panel of independently-derived ER-α positive cell lines. These lines were chosen to represent the diverse genetic backgrounds and mutations commonly present in ER-α positive tumors. Using shRNA-mediated knockdown and overexpression studies we also elucidate the role of hypoxia-inducible factor 1-alpha (HIF-1α) in the hypoxia-induced decrease in ER-α abundance. RESULTS We present the first comprehensive overview of the effects of bona fide low environmental oxygen (hypoxia) and HIF-1α activity on ER-α abundance and transcriptional activity. We find that stabilized HIF-1α induces rapid loss of ER-α protein in all members of our diverse panel of breast cancer cell lines, which involves proteolysis rather than transcriptional repression. Reduced ER-α severely attenuates ER-α directed transcription, and inhibits cell proliferation without overt signs of cell death in the cell lines tested, despite their varying genomic backgrounds. CONCLUSIONS These studies reveal a common hypoxia response that produces reduced ER-α expression and cell cycle stalling, and demonstrate a common role for HIF-1α in ER-α loss. We hypothesize that inhibitors of HIF-1α or the proteasome might stabilize ER-α expression in breast tumors in vivo, and work in combination with endocrine therapies to reduce resistance. Our data also suggests that disease re-occurrence in patients with ER-α positive tumors may arise from tumor cells chronically resident in hypoxic environments. We hypothesize that these non-proliferating cells may survive undetected until conditions change to oxygenate the environment, or cells eventually switch to proliferation via other signaling pathways.
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Affiliation(s)
- Mercè Padró
- Department of Radiation Oncology, University of California, San Francisco, CA, 94115, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, UCSF Mail stop 0875, 2340 Sutter Street, Room N361, San Francisco, CA, 94115, USA
| | - Raymond J Louie
- Department of Radiation Oncology, University of California, San Francisco, CA, 94115, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, UCSF Mail stop 0875, 2340 Sutter Street, Room N361, San Francisco, CA, 94115, USA
| | - Brian V Lananna
- Department of Radiation Oncology, University of California, San Francisco, CA, 94115, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, UCSF Mail stop 0875, 2340 Sutter Street, Room N361, San Francisco, CA, 94115, USA
| | - Adam J Krieg
- Department of Obstetrics and Gynecology, Kansas University Medical Center, Kansas City, KS, 66160, USA
| | - Luika A Timmerman
- Helen Diller Family Comprehensive Cancer Center, University of California, UCSF Mail stop 0875, 2340 Sutter Street, Room N361, San Francisco, CA, 94115, USA.
| | - Denise A Chan
- Department of Radiation Oncology, University of California, San Francisco, CA, 94115, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, UCSF Mail stop 0875, 2340 Sutter Street, Room N361, San Francisco, CA, 94115, USA
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Louie RJ, Tan QKG, Gilner JB, Rogers RC, Younge N, Wechsler SB, McDonald MT, Gordon B, Saski CA, Jones JR, Chapman SJ, Stevenson RE, Sleasman JW, Friez MJ. Novel pathogenic variants in FOXP3 in fetuses with echogenic bowel and skin desquamation identified by ultrasound. Am J Med Genet A 2017; 173:1219-1225. [PMID: 28317311 DOI: 10.1002/ajmg.a.38144] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 12/05/2016] [Accepted: 12/30/2016] [Indexed: 11/12/2022]
Abstract
Immunodysregulation, Polyendocrinopathy, Enteropathy, X-linked (IPEX) syndrome is a rare, X-linked recessive disease that affects regulatory T cells (Tregs) resulting in diarrhea, enteropathy, eczema, and insulin-dependent diabetes mellitus. IPEX syndrome is caused by pathogenic alterations in FOXP3 located at Xp11.23. FOXP3 encodes a transcription factor that interacts with several partners, including NFAT and NF-κB, and is necessary for the proper cellular differentiation of Tregs. Although variable, the vast majority of IPEX syndrome patients have onset of disease during infancy with severe enteropathy. Only five families with prenatal presentation of IPEX syndrome have been reported. Here, we present two additional prenatal onset cases with novel inherited frameshift pathogenic variants in FOXP3 that generate premature stop codons. Ultrasound findings in the first patient identified echogenic bowel, echogenic debris, scalp edema, and hydrops. In the second patient, ultrasound findings included polyhydramnios with echogenic debris, prominent fluid-filled loops of bowel, and echogenic bowel. These cases further broaden the phenotypic spectrum of IPEX syndrome by describing previously unappreciated prenatal ultrasound findings associated with the disease.
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Affiliation(s)
| | | | | | | | - Noelle Younge
- Duke University School of Medicine, Durham, North Carolina
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Humtsoe JO, Pham E, Louie RJ, Chan DA, Kramer RH. ErbB3 upregulation by the HNSCC 3D microenvironment modulates cell survival and growth. Oncogene 2015; 35:1554-64. [PMID: 26073080 DOI: 10.1038/onc.2015.220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/06/2015] [Accepted: 04/20/2015] [Indexed: 12/11/2022]
Abstract
Head and neck squamous carcinomas (HNSCC) present as dense epithelioid three-dimensional (3D) tumor nests that can mediate signals via the human epidermal growth factor receptor (ErbB) tyrosine kinase family to promote intratumoral survival and growth. We examined the role of the tumor microenvironment on ErbB receptor family expression and found that the status of intercellular organization altered the receptor profile. We showed that HNSCC cells forced into tumor island-like 3D aggregates strongly upregulated ErbB3 at the level of transcription. Not only was the elevated ErbB3 responsive to HRG-β1-induced enhanced signaling mechanism, but also analysis by siRNA-knockdown and kinase inhibitor strategies revealed that the ErbB3/AKT signaling pathway was sufficient to enhance tumor cell survival and growth potential. Elevated ErbB3 expression in the high-density 3D culture system was strongly associated with hypoxia-induced HIF-1α. Hypoxia-regulated ErbB3 expression was mediated by the HIF-1α-binding consensus sequence in the ErbB3 proximal promoter. The findings show that the local 3D tumor microenvironment can trigger reprograming and switching of ErbB family members and thereby influence ErbB3-driven tumor growth.
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Affiliation(s)
- J O Humtsoe
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - E Pham
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - R J Louie
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - D A Chan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - R H Kramer
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
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Bakhoum SF, Kabeche L, Wood MD, Laucius CD, Qu D, Laughney AM, Reynolds GE, Louie RJ, Phillips J, Chan DA, Zaki BI, Murnane JP, Petritsch C, Compton DA. Numerical chromosomal instability mediates susceptibility to radiation treatment. Nat Commun 2015; 6:5990. [PMID: 25606712 DOI: 10.1038/ncomms6990] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/01/2014] [Indexed: 01/05/2023] Open
Abstract
The exquisite sensitivity of mitotic cancer cells to ionizing radiation (IR) underlies an important rationale for the widely used fractionated radiation therapy. However, the mechanism for this cell cycle-dependent vulnerability is unknown. Here we show that treatment with IR leads to mitotic chromosome segregation errors in vivo and long-lasting aneuploidy in tumour-derived cell lines. These mitotic errors generate an abundance of micronuclei that predispose chromosomes to subsequent catastrophic pulverization thereby independently amplifying radiation-induced genome damage. Experimentally suppressing whole-chromosome missegregation reduces downstream chromosomal defects and significantly increases the viability of irradiated mitotic cells. Further, orthotopically transplanted human glioblastoma tumours in which chromosome missegregation rates have been reduced are rendered markedly more resistant to IR, exhibiting diminished markers of cell death in response to treatment. This work identifies a novel mitotic pathway for radiation-induced genome damage, which occurs outside of the primary nucleus and augments chromosomal breaks. This relationship between radiation treatment and whole-chromosome missegregation can be exploited to modulate therapeutic response in a clinically relevant manner.
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Affiliation(s)
- Samuel F Bakhoum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Lilian Kabeche
- 1] Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA [2] Norris-Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756, USA
| | - Matthew D Wood
- Department of Pathology, University of California San Francisco, San Francisco, California 94143, USA
| | - Christopher D Laucius
- 1] Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA [2] Norris-Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756, USA
| | - Dian Qu
- 1] Department of Neurological Surgery and the Brain Tumor Research Center, University of California San Francisco, San Francisco, California 94143, USA [2] Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94143, USA
| | - Ashley M Laughney
- Department of Radiology, Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Gloria E Reynolds
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California 94143, USA
| | - Raymond J Louie
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California 94143, USA
| | - Joanna Phillips
- 1] Department of Neurological Surgery and the Brain Tumor Research Center, University of California San Francisco, San Francisco, California 94143, USA [2] Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94143, USA
| | - Denise A Chan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California 94143, USA
| | - Bassem I Zaki
- Section of Radiation Oncology, Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756, USA
| | - John P Murnane
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California 94143, USA
| | - Claudia Petritsch
- 1] Department of Neurological Surgery and the Brain Tumor Research Center, University of California San Francisco, San Francisco, California 94143, USA [2] Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94143, USA
| | - Duane A Compton
- 1] Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA [2] Norris-Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756, USA
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Timmerman LA, Holton T, Yuneva M, Louie RJ, Padró M, Daemen A, Hu M, Chan DA, Ethier SP, van 't Veer LJ, Polyak K, McCormick F, Gray JW. Glutamine sensitivity analysis identifies the xCT antiporter as a common triple-negative breast tumor therapeutic target. Cancer Cell 2013; 24:450-65. [PMID: 24094812 PMCID: PMC3931310 DOI: 10.1016/j.ccr.2013.08.020] [Citation(s) in RCA: 407] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Revised: 03/21/2013] [Accepted: 08/23/2013] [Indexed: 01/18/2023]
Abstract
A handful of tumor-derived cell lines form the mainstay of cancer therapeutic development, yielding drugs with an impact typically measured as months to disease progression. To develop more effective breast cancer therapeutics and more readily understand their clinical impact, we constructed a functional metabolic portrait of 46 independently derived breast cell lines. Our analysis of glutamine uptake and dependence identified a subset of triple-negative samples that are glutamine auxotrophs. Ambient glutamine indirectly supports environmental cystine acquisition via the xCT antiporter, which is expressed on one-third of triple-negative tumors in vivo. xCT inhibition with the clinically approved anti-inflammatory sulfasalazine decreases tumor growth, revealing a therapeutic target in breast tumors of poorest prognosis and a lead compound for rapid, effective drug development.
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Affiliation(s)
- Luika A Timmerman
- UCSF/Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA.
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Louie RJ, Guo J, Rodgers JW, White R, Shah N, Pagant S, Kim P, Livstone M, Dolinski K, McKinney BA, Hong J, Sorscher EJ, Bryan J, Miller EA, Hartman JL. A yeast phenomic model for the gene interaction network modulating CFTR-ΔF508 protein biogenesis. Genome Med 2012; 4:103. [PMID: 23270647 PMCID: PMC3906889 DOI: 10.1186/gm404] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 12/27/2012] [Indexed: 01/20/2023] Open
Abstract
Background The overall influence of gene interaction in human disease is unknown. In cystic fibrosis (CF) a single allele of the cystic fibrosis transmembrane conductance regulator (CFTR-ΔF508) accounts for most of the disease. In cell models, CFTR-ΔF508 exhibits defective protein biogenesis and degradation rather than proper trafficking to the plasma membrane where CFTR normally functions. Numerous genes function in the biogenesis of CFTR and influence the fate of CFTR-ΔF508. However it is not known whether genetic variation in such genes contributes to disease severity in patients. Nor is there an easy way to study how numerous gene interactions involving CFTR-ΔF would manifest phenotypically. Methods To gain insight into the function and evolutionary conservation of a gene interaction network that regulates biogenesis of a misfolded ABC transporter, we employed yeast genetics to develop a 'phenomic' model, in which the CFTR-ΔF508-equivalent residue of a yeast homolog is mutated (Yor1-ΔF670), and where the genome is scanned quantitatively for interaction. We first confirmed that Yor1-ΔF undergoes protein misfolding and has reduced half-life, analogous to CFTR-ΔF. Gene interaction was then assessed quantitatively by growth curves for approximately 5,000 double mutants, based on alteration in the dose response to growth inhibition by oligomycin, a toxin extruded from the cell at the plasma membrane by Yor1. Results From a comparative genomic perspective, yeast gene interactions influencing Yor1-ΔF biogenesis were representative of human homologs previously found to modulate processing of CFTR-ΔF in mammalian cells. Additional evolutionarily conserved pathways were implicated by the study, and a ΔF-specific pro-biogenesis function of the recently discovered ER membrane complex (EMC) was evident from the yeast screen. This novel function was validated biochemically by siRNA of an EMC ortholog in a human cell line expressing CFTR-ΔF508. The precision and accuracy of quantitative high throughput cell array phenotyping (Q-HTCP), which captures tens of thousands of growth curves simultaneously, provided powerful resolution to measure gene interaction on a phenomic scale, based on discrete cell proliferation parameters. Conclusion We propose phenomic analysis of Yor1-ΔF as a model for investigating gene interaction networks that can modulate cystic fibrosis disease severity. Although the clinical relevance of the Yor1-ΔF gene interaction network for cystic fibrosis remains to be defined, the model appears to be informative with respect to human cell models of CFTR-ΔF. Moreover, the general strategy of yeast phenomics can be employed in a systematic manner to model gene interaction for other diseases relating to pathologies that result from protein misfolding or potentially any disease involving evolutionarily conserved genetic pathways.
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Louie RJ, Pagant S, Youn JY, Halliday JJ, Huyer G, Michaelis S, Miller EA. Functional rescue of a misfolded eukaryotic ATP-binding cassette transporter by domain replacement. J Biol Chem 2010; 285:36225-34. [PMID: 20843810 DOI: 10.1074/jbc.m110.160523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP-binding cassette (ABC) transporters are integral membrane proteins that couple ATP binding/hydrolysis with the transport of hydrophilic substrates across lipid barriers. Deletion of Phe-670 in the first nucleotide-binding domain (NBD1) of the yeast ABC transporter, Yor1p, perturbs interdomain associations, reduces functionality, and hinders proper transport to the plasma membrane. Functionality of Yor1p-ΔF was restored upon co-expression of a peptide containing wild-type NBD1. To gain insight into the biogenesis of this important class of proteins, we defined the requirements for this rescue. We show that a misfolding lesion in NBD1 of the full-length protein is a prerequisite for functional rescue by exogenous NBD1, which is mediated by physical replacement of the dysfunctional domain by the soluble NBD1. This association does not restore trafficking of Yor1p-ΔF but instead confers catalytic activity to the small population of Yor1p-ΔF that escapes to the plasma membrane. An important coupling between the exogenous NBD1 and ICL4 within full-length aberrant Yor1p-ΔF is required for functional rescue but not for the physical interaction between the two polypeptides. Together, our genetic and biochemical data reveal that it is possible to modulate activity of ABC transporters by physically replacing dysfunctional domains.
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Affiliation(s)
- Raymond J Louie
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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