1
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Mullegama SV, Kiernan KA, Torti E, Pavlovsky E, Tilton N, Sekula A, Gao H, Alaimo JT, Engleman K, Rush ET, Blocker K, Dipple KM, Fettig VM, Hare H, Glass I, Grange DK, Griffin M, Phornphutkul C, Massingham L, Mehta L, Miller DE, Thies J, Merritt JL, Muller E, Osmond M, Sawyer SL, Slaugh R, Hickey RE, Wolf B, Choudhary S, Simonović M, Zhang Y, Palculict TB, Telegrafi A, Carere DA, Wentzensen IM, Morrow MM, Monaghan KG, Yang J, Juusola J. De novo missense variants in exon 9 of SEPHS1 cause a neurodevelopmental condition with developmental delay, poor growth, hypotonia, and dysmorphic features. Am J Hum Genet 2024; 111:778-790. [PMID: 38531365 PMCID: PMC11023921 DOI: 10.1016/j.ajhg.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024] Open
Abstract
Selenophosphate synthetase (SEPHS) plays an essential role in selenium metabolism. Two mammalian SEPHS paralogues, SEPHS1 and SEPHS2, share high sequence identity and structural homology with SEPHS. Here, we report nine individuals from eight families with developmental delay, growth and feeding problems, hypotonia, and dysmorphic features, all with heterozygous missense variants in SEPHS1. Eight of these individuals had a recurrent variant at amino acid position 371 of SEPHS1 (p.Arg371Trp, p.Arg371Gln, and p.Arg371Gly); seven of these variants were known to be de novo. Structural modeling and biochemical assays were used to understand the effect of these variants on SEPHS1 function. We found that a variant at residue Trp352 results in local structural changes of the C-terminal region of SEPHS1 that decrease the overall thermal stability of the enzyme. In contrast, variants of a solvent-exposed residue Arg371 do not impact enzyme stability and folding but could modulate direct protein-protein interactions of SEPSH1 with cellular factors in promoting cell proliferation and development. In neuronal SH-SY5Y cells, we assessed the impact of SEPHS1 variants on cell proliferation and ROS production and investigated the mRNA expression levels of genes encoding stress-related selenoproteins. Our findings provided evidence that the identified SEPHS1 variants enhance cell proliferation by modulating ROS homeostasis. Our study supports the hypothesis that SEPHS1 plays a critical role during human development and provides a basis for further investigation into the molecular mechanisms employed by SEPHS1. Furthermore, our data suggest that variants in SEPHS1 are associated with a neurodevelopmental disorder.
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Affiliation(s)
- Sureni V Mullegama
- GeneDx, Gaithersburg, MD 20877, USA; Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA.
| | - Kaitlyn A Kiernan
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | | | - Ethan Pavlovsky
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Nicholas Tilton
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Austin Sekula
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Hua Gao
- GeneDx, Gaithersburg, MD 20877, USA
| | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, USA; Department of Pediatrics, University of Missouri Kansas City, School of Medicine, Kansas City, MO, USA; Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | - Kendra Engleman
- Department of Pediatrics, University of Missouri Kansas City, School of Medicine, Kansas City, MO, USA; Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA
| | - Eric T Rush
- Department of Pediatrics, University of Missouri Kansas City, School of Medicine, Kansas City, MO, USA; Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA; Department of Internal Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Karli Blocker
- Division of Clinical Genetics, Stanford Children's Health, San Francisco, CA, USA
| | - Katrina M Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Veronica M Fettig
- Center for Inherited Cardiovascular Disease, Cardiovascular Genetics Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Heather Hare
- Northeastern Ontario Medical Genetics Program, Health Sciences, North Sudbury, ON, Canada
| | - Ian Glass
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael Griffin
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Chanika Phornphutkul
- Division of Genetics, Department of Pediatrics, Alpert School of Medicine at Brown University, Providence, RI, USA
| | - Lauren Massingham
- Division of Genetics, Department of Pediatrics, Alpert School of Medicine at Brown University, Providence, RI, USA
| | - Lakshmi Mehta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Jenny Thies
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, USA
| | - J Lawrence Merritt
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Eric Muller
- Division of Clinical Genetics, Stanford Children's Health, San Francisco, CA, USA
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Sarah L Sawyer
- Department of Pediatrics, University of Ottawa, Ottawa, ON, Canada
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel E Hickey
- Department of Pediatrics, Division of Genetics, Birth Defects and Metabolism, Anne & Robert H. Lurie Children's Hospital, Chicago, IL, USA
| | - Barry Wolf
- Department of Pediatrics, Division of Genetics, Birth Defects and Metabolism, Anne & Robert H. Lurie Children's Hospital, Chicago, IL, USA
| | - Sanjeev Choudhary
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Miljan Simonović
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Yueqing Zhang
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | | | | | | | | | | | - Jun Yang
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.
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Szot JO, Cuny H, Martin EM, Sheng DZ, Iyer K, Portelli S, Nguyen V, Gereis JM, Alankarage D, Chitayat D, Chong K, Wentzensen IM, Vincent-Delormé C, Lermine A, Burkitt-Wright E, Ji W, Jeffries L, Pais LS, Tan TY, Pitt J, Wise CA, Wright H, Andrews ID, Pruniski B, Grebe TA, Corsten-Janssen N, Bouman K, Poulton C, Prakash S, Keren B, Brown NJ, Hunter MF, Heath O, Lakhani SA, McDermott JH, Ascher DB, Chapman G, Bozon K, Dunwoodie SL. A metabolic signature for NADSYN1-dependent congenital NAD deficiency disorder. J Clin Invest 2024; 134:e174824. [PMID: 38357931 PMCID: PMC10866660 DOI: 10.1172/jci174824] [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: 09/06/2023] [Accepted: 12/20/2023] [Indexed: 02/16/2024] Open
Abstract
Nicotinamide adenine dinucleotide (NAD) is essential for embryonic development. To date, biallelic loss-of-function variants in 3 genes encoding nonredundant enzymes of the NAD de novo synthesis pathway - KYNU, HAAO, and NADSYN1 - have been identified in humans with congenital malformations defined as congenital NAD deficiency disorder (CNDD). Here, we identified 13 further individuals with biallelic NADSYN1 variants predicted to be damaging, and phenotypes ranging from multiple severe malformations to the complete absence of malformation. Enzymatic assessment of variant deleteriousness in vitro revealed protein domain-specific perturbation, complemented by protein structure modeling in silico. We reproduced NADSYN1-dependent CNDD in mice and assessed various maternal NAD precursor supplementation strategies to prevent adverse pregnancy outcomes. While for Nadsyn1+/- mothers, any B3 vitamer was suitable to raise NAD, preventing embryo loss and malformation, Nadsyn1-/- mothers required supplementation with amidated NAD precursors (nicotinamide or nicotinamide mononucleotide) bypassing their metabolic block. The circulatory NAD metabolome in mice and humans before and after NAD precursor supplementation revealed a consistent metabolic signature with utility for patient identification. Our data collectively improve clinical diagnostics of NADSYN1-dependent CNDD, provide guidance for the therapeutic prevention of CNDD, and suggest an ongoing need to maintain NAD levels via amidated NAD precursor supplementation after birth.
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Affiliation(s)
- Justin O. Szot
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, New South Wales, Australia
| | - Hartmut Cuny
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Ella M.M.A. Martin
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, New South Wales, Australia
| | - Delicia Z. Sheng
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, New South Wales, Australia
| | - Kavitha Iyer
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, New South Wales, Australia
| | - Stephanie Portelli
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Vivien Nguyen
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, New South Wales, Australia
| | - Jessica M. Gereis
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, New South Wales, Australia
| | - Dimuthu Alankarage
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, New South Wales, Australia
| | - David Chitayat
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, and
- Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Karen Chong
- Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Alban Lermine
- Laboratoire de Biologie Médicale Multisites SeqOIA, FMG2025, Paris, France
| | - Emma Burkitt-Wright
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Weizhen Ji
- Yale University School of Medicine, Pediatric Genomics Discovery Program, New Haven, Connecticut, USA
| | - Lauren Jeffries
- Yale University School of Medicine, Pediatric Genomics Discovery Program, New Haven, Connecticut, USA
| | - Lynn S. Pais
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Tiong Y. Tan
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - James Pitt
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Metabolic Laboratory, Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Cheryl A. Wise
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Nedlands, Perth, Western Australia, Australia
| | - Helen Wright
- General Paediatric Department, Perth Children’s Hospital, Perth, Western Australia, Australia
- Rural Clinical School, University of Western Australia, Perth, Western Australia, Australia
| | | | - Brianna Pruniski
- Division of Genetics and Metabolism, Phoenix Children’s Hospital, Phoenix, Arizona, USA
| | - Theresa A. Grebe
- Division of Genetics and Metabolism, Phoenix Children’s Hospital, Phoenix, Arizona, USA
| | - Nicole Corsten-Janssen
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Katelijne Bouman
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Cathryn Poulton
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia, Australia
| | - Supraja Prakash
- Division of Genetics and Metabolism, Phoenix Children’s Hospital, Phoenix, Arizona, USA
| | - Boris Keren
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique – Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Natasha J. Brown
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Matthew F. Hunter
- Monash Genetics, Monash Health, Clayton, Victoria, Australia
- Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Oliver Heath
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Metabolic Medicine, The Royal Children’s Hospital, Melbourne, Victoria, Australia
| | - Saquib A. Lakhani
- Yale University School of Medicine, Pediatric Genomics Discovery Program, New Haven, Connecticut, USA
| | - John H. McDermott
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - David B. Ascher
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Gavin Chapman
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Kayleigh Bozon
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, New South Wales, Australia
| | - Sally L. Dunwoodie
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, Sydney, New South Wales, Australia
- Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
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3
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Rigter PMF, de Konink C, Dunn MJ, Proietti Onori M, Humberson JB, Thomas M, Barnes C, Prada CE, Weaver KN, Ryan TD, Caluseriu O, Conway J, Calamaro E, Fong CT, Wuyts W, Meuwissen M, Hordijk E, Jonkers CN, Anderson L, Yuseinova B, Polonia S, Beysen D, Stark Z, Savva E, Poulton C, McKenzie F, Bhoj E, Bupp CP, Bézieau S, Mercier S, Blevins A, Wentzensen IM, Xia F, Rosenfeld JA, Hsieh TC, Krawitz PM, Elbracht M, Veenma DCM, Schulman H, Stratton MM, Küry S, van Woerden GM. Role of CAMK2D in neurodevelopment and associated conditions. Am J Hum Genet 2024; 111:364-382. [PMID: 38272033 PMCID: PMC10870144 DOI: 10.1016/j.ajhg.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
The calcium/calmodulin-dependent protein kinase type 2 (CAMK2) family consists of four different isozymes, encoded by four different genes-CAMK2A, CAMK2B, CAMK2G, and CAMK2D-of which the first three have been associated recently with neurodevelopmental disorders. CAMK2D is one of the major CAMK2 proteins expressed in the heart and has been associated with cardiac anomalies. Although this CAMK2 isoform is also known to be one of the major CAMK2 subtypes expressed during early brain development, it has never been linked with neurodevelopmental disorders until now. Here we show that CAMK2D plays an important role in neurodevelopment not only in mice but also in humans. We identified eight individuals harboring heterozygous variants in CAMK2D who display symptoms of intellectual disability, delayed speech, behavioral problems, and dilated cardiomyopathy. The majority of the variants tested lead to a gain of function (GoF), which appears to cause both neurological problems and dilated cardiomyopathy. In contrast, loss-of-function (LoF) variants appear to induce only neurological symptoms. Together, we describe a cohort of individuals with neurodevelopmental disorders and cardiac anomalies, harboring pathogenic variants in CAMK2D, confirming an important role for the CAMK2D isozyme in both heart and brain function.
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Affiliation(s)
- Pomme M F Rigter
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands; ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands
| | - Charlotte de Konink
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands; Department of Neuroscience, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands
| | - Matthew J Dunn
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Martina Proietti Onori
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands; Department of Neuroscience, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands
| | - Jennifer B Humberson
- Pediatric Specialty Care, University of Virginia Health, Charlottesville, VA 22903, USA
| | - Matthew Thomas
- Division of Genetics, Department of Pediatrics, University of Virginia Children's, Charlottesville, VA 22903, USA
| | - Caitlin Barnes
- Division of Genetics, Department of Pediatrics, University of Virginia Children's, Charlottesville, VA 22903, USA
| | - Carlos E Prada
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Division of Genetics, Genomics, and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Fundacion Cardiovascular de Colombia, Bucaramanga, Colombia
| | - K Nicole Weaver
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Thomas D Ryan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada; Stollery Children's Hospital, Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2B7, Canada
| | - Jennifer Conway
- Stollery Children's Hospital, Department of Pediatrics, Division of Pediatric Cardiology, University of Alberta, Edmonton, AB T6G 2B7, Canada
| | - Emily Calamaro
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Chin-To Fong
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Wim Wuyts
- Department of Medical Genetics, University of Antwerp and University Hospital of Antwerp, 2650 Edegem, Belgium
| | - Marije Meuwissen
- Department of Medical Genetics, University of Antwerp and University Hospital of Antwerp, 2650 Edegem, Belgium
| | - Eva Hordijk
- Department of Neuroscience, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands
| | - Carsten N Jonkers
- Department of Neuroscience, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands
| | - Lucas Anderson
- Department of Neuroscience, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands
| | - Berfin Yuseinova
- Department of Neuroscience, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands
| | - Sarah Polonia
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands
| | - Diane Beysen
- Department of Paediatric Neurology, University Hospital of Antwerp, 2650 Edegem, Belgium; Department of Translational Neurosciences, University of Antwerp, 2650 Edegem, Belgium
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Australian Genomics, Melbourne, VIC 3052, Australia
| | - Elena Savva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Cathryn Poulton
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia
| | - Fiona McKenzie
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia; School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6009, Australia
| | - Elizabeth Bhoj
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Caleb P Bupp
- Corewell Health & Helen DeVos Children's Hospital, Grand Rapids, MI 49503, USA
| | - Stéphane Bézieau
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, 44000 Nantes, France
| | - Sandra Mercier
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France; Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, 44000 Nantes, France
| | | | - Ingrid M Wentzensen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fan Xia
- 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 Laboratories, Houston, TX 77021, USA
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, 53127 Bonn, Germany
| | - Peter M Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, 53127 Bonn, Germany
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, 52074 Aachen, Germany
| | - Danielle C M Veenma
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands; Sophia Children's Hospital, Erasmus Medical Center, Rotterdam 3015 CN, the Netherlands
| | - Howard Schulman
- Department of Neurobiology, Stanford University, School of Medicine, Stanford, CA 94305, USA; Panorama Research Institute, Sunnyvale, CA 94089, USA
| | - Margaret M Stratton
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Sébastien Küry
- Corewell Health & Helen DeVos Children's Hospital, Grand Rapids, MI 49503, USA; Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000 Nantes, France.
| | - Geeske M van Woerden
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands; ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands; Department of Neuroscience, Erasmus Medical Center, Rotterdam 3015 GD, the Netherlands.
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4
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Lin SJ, Vona B, Lau T, Huang K, Zaki MS, Aldeen HS, Karimiani EG, Rocca C, Noureldeen MM, Saad AK, Petree C, Bartolomaeus T, Abou Jamra R, Zifarelli G, Gotkhindikar A, Wentzensen IM, Liao M, Cork EE, Varshney P, Hashemi N, Mohammadi MH, Rad A, Neira J, Toosi MB, Knopp C, Kurth I, Challman TD, Smith R, Abdalla A, Haaf T, Suri M, Joshi M, Chung WK, Moreno-De-Luca A, Houlden H, Maroofian R, Varshney GK. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Med 2023; 15:102. [PMID: 38031187 PMCID: PMC10688095 DOI: 10.1186/s13073-023-01258-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship. METHODS Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity. RESULTS A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy. CONCLUSIONS Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as "OGDHL-related disorders".
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Affiliation(s)
- Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Barbara Vona
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
- Department of Otolaryngology-Head and Neck Surgery, Tübingen Hearing Research Center, Eberhard Karls University, Tübingen, 72076, Germany
| | - Tracy Lau
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Kevin Huang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Huda Shujaa Aldeen
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace London, London, UK
| | - Clarissa Rocca
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Mahmoud M Noureldeen
- Department of Pediatrics, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Ahmed K Saad
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Cassidy Petree
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Tobias Bartolomaeus
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | | | | | | | - Emalyn Elise Cork
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pratishtha Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Narges Hashemi
- Department of Pediatrics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Aboulfazl Rad
- Department of Otolaryngology-Head and Neck Surgery, Tübingen Hearing Research Center, Eberhard Karls University, Tübingen, 72076, Germany
| | - Juanita Neira
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Mehran Beiraghi Toosi
- Department of Pediatrics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Cordula Knopp
- Institute for Human Genetics and Genomic Medicine, RWTH Aachen University, Pauwelsstr. 30, Aachen, 52074, Germany
| | - Ingo Kurth
- Institute for Human Genetics and Genomic Medicine, RWTH Aachen University, Pauwelsstr. 30, Aachen, 52074, Germany
| | - Thomas D Challman
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Rebecca Smith
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Asmahan Abdalla
- Department of Pediatric Endocrinology, Gaafar Ibn Auf Children's Tertiary Hospital, Khartoum, Sudan
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Manali Joshi
- Bioinformatics Centre, S. P. Pune University, Pune, India
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospitaland, Harvard Medical School , Boston, MA, USA
| | - Andres Moreno-De-Luca
- Department of Diagnostic Radiology, Kingston Health Sciences Centre, Queen's University, Kingston, ON, Canada
| | - Henry Houlden
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK.
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA.
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5
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Ahmad N, Fazeli W, Schließke S, Lesca G, Gokce-Samar Z, Mekbib KY, Jin SC, Burton J, Hoganson G, Petersen A, Gracie S, Granger L, Bartels E, Oppermann H, Kundishora A, Till M, Milleret-Pignot C, Dangerfield S, Viskochil D, Anderson KJ, Palculict TB, Schnur RE, Wentzensen IM, Tiller GE, Kahle KT, Kunz WS, Burkart S, Simons M, Sticht H, Abou Jamra R, Neuser S. De Novo Variants in RAB11B Cause Various Degrees of Global Developmental Delay and Intellectual Disability in Children. Pediatr Neurol 2023; 148:164-171. [PMID: 37734130 DOI: 10.1016/j.pediatrneurol.2023.08.023] [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: 05/16/2023] [Revised: 07/20/2023] [Accepted: 08/15/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND RAB11B was described previously once with a severe form of intellectual disability. We aim at validation and delineation of the role of RAB11B in neurodevelopmental disorders. METHODS We present seven novel individuals with disease-associated variants in RAB11B when compared with the six cases described in the literature. We performed a cross-sectional analysis to identify the clinical spectrum and the core phenotype. Additionally, structural effects of the variants were assessed by molecular modeling. RESULTS Seven distinct de novo missense variants were identified, three of them recurrent (p.(Gly21Arg), p.(Val22Met), and p.(Ala68Thr)). Molecular modeling suggests that those variants either affect the nucleotide binding (at amino acid positions 21, 22, 33, 68) or the interaction with effector molecules (at positions 72 and 75). Our data confirmed the main manifestations as neurodevelopmental disorder with intellectual disability (85%), muscular hypotonia (83%), structural brain anomalies (77%), and visual impairment (70%). Combined analysis indicates a genotype-phenotype correlation; variants impacting the nucleotide binding cause a severe phenotype with intellectual disability, and variants outside the binding pocket lead to a milder phenotype with epilepsy. CONCLUSIONS We confirm that disease-associated missense variants in RAB11B cause a neurodevelopmental disorder and suggest a genotype-phenotype correlation based on the impact on nucleotide binding functionality of RAB11B.
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Affiliation(s)
- Natalie Ahmad
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Walid Fazeli
- Department of Pediatric Neurology, University Hospital Bonn, Bonn, Germany
| | - Sophia Schließke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University Hospital, University of Lyon, UCB1, Lyon, France
| | | | - Kedous Y Mekbib
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut; Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Jennifer Burton
- University of Illinois College of Medicine, Peoria, Illinois
| | - George Hoganson
- University of Illinois College of Medicine, Peoria, Illinois
| | - Andrea Petersen
- Department of Genetics and Metabolism, Randall Children's Hospital, Portland, Oregon
| | - Sara Gracie
- Department of Genetics and Metabolism, Randall Children's Hospital, Portland, Oregon
| | - Leslie Granger
- Department of Genetics and Metabolism, Randall Children's Hospital, Portland, Oregon
| | - Enrika Bartels
- Institute of Clinical Genetics and Tumor Genetics, Bonn, Germany
| | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Adam Kundishora
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Marianne Till
- Department of Medical Genetics, Lyon University Hospital, University of Lyon, UCB1, Lyon, France
| | | | | | | | - Katherine J Anderson
- University of Utah, Salt Lake City, Utah; Department of Pediatrics, University of Vermont Medical Center, Burlington, Vermont
| | | | | | | | - George E Tiller
- Department of Genetics, Kaiser Permanente, Los Angeles, California
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Wolfram S Kunz
- Department of Epileptology, University Hospital Bonn, Bonn, Germany
| | - Sebastian Burkart
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Matias Simons
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Sonja Neuser
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
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6
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Saffari A, Lau T, Tajsharghi H, Karimiani EG, Kariminejad A, Efthymiou S, Zifarelli G, Sultan T, Toosi MB, Sedighzadeh S, Siu VM, Ortigoza-Escobar JD, AlShamsi AM, Ibrahim S, Al-Sannaa NA, Al-Hertani W, Sandra W, Tarnopolsky M, Alavi S, Li C, Day-Salvatore DL, Martínez-González MJ, Levandoski KM, Bedoukian E, Madan-Khetarpal S, Idleburg MJ, Menezes MJ, Siddharth A, Platzer K, Oppermann H, Smitka M, Collins F, Lek M, Shahrooei M, Ghavideldarestani M, Herman I, Rendu J, Faure J, Baker J, Bhambhani V, Calderwood L, Akhondian J, Imannezhad S, Mirzadeh HS, Hashemi N, Doosti M, Safi M, Ahangari N, Torbati PN, Abedini S, Salpietro V, Gulec EY, Eshaghian S, Ghazavi M, Pascher MT, Vogel M, Abicht A, Moutton S, Bruel AL, Rieubland C, Gallati S, Strom TM, Lochmüller H, Mohammadi MH, Alvi JR, Zackai EH, Keena BA, Skraban CM, Berger SI, Andrew EH, Rahimian E, Morrow MM, Wentzensen IM, Millan F, Henderson LB, Dafsari HS, Jungbluth H, Gomez-Ospina N, McRae A, Peter M, Veltra D, Marinakis NM, Sofocleous C, Ashrafzadeh F, Pehlivan D, Lemke JR, Melki J, Benezit A, Bauer P, Weis D, Lupski JR, Senderek J, Christodoulou J, Chung WK, Goodchild R, Offiah AC, Moreno-De-Luca A, Suri M, Ebrahimi-Fakhari D, Houlden H, Maroofian R. The clinical and genetic spectrum of autosomal-recessive TOR1A-related disorders. Brain 2023; 146:3273-3288. [PMID: 36757831 PMCID: PMC10393417 DOI: 10.1093/brain/awad039] [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: 08/26/2022] [Revised: 12/20/2022] [Accepted: 01/23/2023] [Indexed: 02/10/2023] Open
Abstract
In the field of rare diseases, progress in molecular diagnostics led to the recognition that variants linked to autosomal-dominant neurodegenerative diseases of later onset can, in the context of biallelic inheritance, cause devastating neurodevelopmental disorders and infantile or childhood-onset neurodegeneration. TOR1A-associated arthrogryposis multiplex congenita 5 (AMC5) is a rare neurodevelopmental disorder arising from biallelic variants in TOR1A, a gene that in the heterozygous state is associated with torsion dystonia-1 (DYT1 or DYT-TOR1A), an early-onset dystonia with reduced penetrance. While 15 individuals with AMC5-TOR1A have been reported (less than 10 in detail), a systematic investigation of the full disease-associated spectrum has not been conducted. Here, we assess the clinical, radiological and molecular characteristics of 57 individuals from 40 families with biallelic variants in TOR1A. Median age at last follow-up was 3 years (0-24 years). Most individuals presented with severe congenital flexion contractures (95%) and variable developmental delay (79%). Motor symptoms were reported in 79% and included lower limb spasticity and pyramidal signs, as well as gait disturbances. Facial dysmorphism was an integral part of the phenotype, with key features being a broad/full nasal tip, narrowing of the forehead and full cheeks. Analysis of disease-associated manifestations delineated a phenotypic spectrum ranging from normal cognition and mild gait disturbance to congenital arthrogryposis, global developmental delay, intellectual disability, absent speech and inability to walk. In a subset, the presentation was consistent with foetal akinesia deformation sequence with severe intrauterine abnormalities. Survival was 71%, with higher mortality in males. Death occurred at a median age of 1.2 months (1 week-9 years), due to respiratory failure, cardiac arrest or sepsis. Analysis of brain MRI studies identified non-specific neuroimaging features, including a hypoplastic corpus callosum (72%), foci of signal abnormality in the subcortical and periventricular white matter (55%), diffuse white matter volume loss (45%), mega cisterna magna (36%) and arachnoid cysts (27%). The molecular spectrum included 22 distinct variants, defining a mutational hotspot in the C-terminal domain of the Torsin-1A protein. Genotype-phenotype analysis revealed an association of missense variants in the 3-helix bundle domain to an attenuated phenotype, while missense variants near the Walker A/B motif as well as biallelic truncating variants were linked to early death. In summary, this systematic cross-sectional analysis of a large cohort of individuals with biallelic TOR1A variants across a wide age-range delineates the clinical and genetic spectrum of TOR1A-related autosomal-recessive disease and highlights potential predictors for disease severity and survival.
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Affiliation(s)
- Afshin Saffari
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Child Neurology and Inherited Metabolic Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Tracy Lau
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
| | - Homa Tajsharghi
- School of Health Sciences, Division of Biomedicine, University of Skovde, Skovde, Sweden
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London, UK
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | | | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
| | | | - Tipu Sultan
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
| | - Mehran Beiraghi Toosi
- Department of Pediatrics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Neuroscience Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sahar Sedighzadeh
- Department of Biological Sciences, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- KaryoGen, Isfahan, Iran
| | - Victoria Mok Siu
- Division of Medical Genetics, Department of Pediatrics, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Juan Darío Ortigoza-Escobar
- Movement Disorders Unit, Pediatric Neurology Department, Institut de Recerca, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - Aisha M AlShamsi
- Genetic Division, Pediatrics Department, Tawam Hospital, Al Ain, UAE
| | - Shahnaz Ibrahim
- Department of pediatrics and child Health, Aga Khan University, Karachi, Pakistan
| | | | - Walla Al-Hertani
- Harvard Medical School, Boston Children's Hospital, Department of Pediatrics, Division of Genetics and Genomics, Boston, MA, USA
| | - Whalen Sandra
- APHP UF de Génétique Clinique, Centre de Référence des Anomalies du Développement et Syndromes Malformatifs, APHP, Hôpital Armand Trousseau, ERN ITHACA, Sorbonne Université, Paris, France
| | - Mark Tarnopolsky
- Department of Pediatrics (MT – Neuromuscular and Neurometabolics, CL – Medical Genetics), McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Shahryar Alavi
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
| | - Chumei Li
- Department of Pediatrics (MT – Neuromuscular and Neurometabolics, CL – Medical Genetics), McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Debra-Lynn Day-Salvatore
- The Department of Medical Genetics and Genomic Medicine at Saint Peter's University Hospital, New Brunswick, NJ, USA
| | | | - Kristin M Levandoski
- The Department of Medical Genetics and Genomic Medicine at Saint Peter's University Hospital, New Brunswick, NJ, USA
| | - Emma Bedoukian
- Roberts Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Suneeta Madan-Khetarpal
- Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michaela J Idleburg
- Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Minal Juliet Menezes
- Department of Anaesthesia, the Children's Hospital at Westmead, Sydney, NSW, Australia
- Discipline of Child and Adolescent Health, and Specialty of Genomic Medicine, Sydney Medical School, Sydney University, Sydney, NSW, Australia
| | - Aishwarya Siddharth
- Harvard Medical School, Boston Children's Hospital, Department of Pediatrics, Division of Genetics and Genomics, Boston, MA, USA
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Martin Smitka
- Department of Neuropediatrics, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Felicity Collins
- Discipline of Child and Adolescent Health, and Specialty of Genomic Medicine, Sydney Medical School, Sydney University, Sydney, NSW, Australia
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Mohmmad Shahrooei
- Medical Laboratory of Dr. Shahrooei, Tehran, Iran
- Department of Microbiology and Immunology, Clinical and Diagnostic Immunology, KU Leuven, Leuven, Belgium
| | | | - Isabella Herman
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
- Division of Pediatric Neuroscience, Boys Town National Research Hospital, Boys Town, NE, USA
| | - John Rendu
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut Neurosciences, Grenoble, France
| | - Julien Faure
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut Neurosciences, Grenoble, France
| | - Janice Baker
- Division of Genetics and Genomic Medicine, Children's Hospital and Clinics of Minnesota, Minneapolis, Minnesota, USA
| | - Vikas Bhambhani
- Division of Genetics and Genomic Medicine, Children's Hospital and Clinics of Minnesota, Minneapolis, Minnesota, USA
| | - Laurel Calderwood
- Lucile Packard Children's Hospital Stanford, Palo Alto, CA, USA
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Javad Akhondian
- Pediatric Neurology Department, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shima Imannezhad
- Department of Pediatric Neurology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hanieh Sadat Mirzadeh
- Department of Pediatric Neurology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Narges Hashemi
- Department of Pediatrics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Doosti
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Mojtaba Safi
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Najmeh Ahangari
- Innovative medical research centre, Mashhad branch, Islamic Azad University, Mashhad, Iran
| | | | - Soheila Abedini
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
| | - Vincenzo Salpietro
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
| | - Elif Yilmaz Gulec
- Istanbul Medeniyet University Medical School, Department of Medical Genetics, Istanbul, Turkey
| | | | - Mohammadreza Ghazavi
- Department of Pediatric Neurology, Imam Hossein Children's Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Michael T Pascher
- Friedrich-Baur-Institute at the Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Marina Vogel
- Friedrich-Baur-Institute at the Department of Neurology, University Hospital, LMU Munich, Munich, Germany
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Angela Abicht
- Friedrich-Baur-Institute at the Department of Neurology, University Hospital, LMU Munich, Munich, Germany
- Medizinisch Genetisches Zentrum, Munich, German
| | - Sébastien Moutton
- Multidisciplinary Center for Prenatal Diagnosis, Pôle Mère Enfant, Maison de Santé Protestante Bordeaux Bagatelle, Talence, France
| | - Ange-Line Bruel
- Équipe Génétique des Anomalies du Développement (GAD), INSERM UMR1231, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Claudine Rieubland
- Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Switzerland
| | - Sabina Gallati
- Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Switzerland
| | - Tim M Strom
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
| | | | - Javeria Raza Alvi
- Department of Pediatric Neurology, The Children's Hospital and the University of Child Health Sciences, Lahore, Pakistan
| | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Beth A Keena
- Division of Human Genetics, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Cara M Skraban
- Division of Human Genetics, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Seth I Berger
- Children's National Research Institute, Washington DC, USA
| | - Erin H Andrew
- Children's National Research Institute, Washington DC, USA
| | | | | | | | | | | | - Hormos Salimi Dafsari
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Max-Planck-Institute for Biology of Ageing and CECAD, Cologne, Germany
- Department of Paediatric Neurology - Neuromuscular Service, Evelina London Children's Hospital, Guy's & St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Heinz Jungbluth
- Department of Paediatric Neurology - Neuromuscular Service, Evelina London Children's Hospital, Guy's & St Thomas' Hospital NHS Foundation Trust, London, UK
- Randall Centre for Cell and Molecular Biophysics, Muscle Signalling Section, Faculty of Life Sciences and Medicine (FoLSM), King's College London, London, UK
| | | | - Anne McRae
- Division of Genetics, Genomics, and Metabolism, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, USA
| | - Merlene Peter
- Division of Genetics, Genomics, and Metabolism, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, USA
| | - Danai Veltra
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia's Children's Hospital, Athens, Greece
| | - Nikolaos M Marinakis
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia's Children's Hospital, Athens, Greece
| | - Christalena Sofocleous
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia's Children's Hospital, Athens, Greece
| | - Farah Ashrafzadeh
- Department of Pediatric Neurology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Judith Melki
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR-1195, Université Paris Saclay, Le Kremlin Bicêtre, 94276, Paris, France
| | - Audrey Benezit
- Neurologie et réanimation pédiatrique, Hôpital Raymond Poincaré, APHP, Garches, France
| | - Peter Bauer
- CENTOGENE GmbH, Am Strande 7, 18055 Rostock, Germany
| | - Denisa Weis
- Department of Medical Genetics, Kepler University Hospital, Johann Kepler University, Linz, Austria
| | - James R Lupski
- 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
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jan Senderek
- Friedrich-Baur-Institute at the Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - John Christodoulou
- Discipline of Child and Adolescent Health, and Specialty of Genomic Medicine, Sydney Medical School, Sydney University, Sydney, NSW, Australia
- Murdoch Children's Research Institute, Melbourne and Department of Paediatrics, Melbourne Medical School, University of Melbourne, Melbourne, VIC, Australia
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University New York, NY, USA
| | - Rose Goodchild
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
- VIB-KU Leuven Center for Brain and Disease Research, Laboratory for Dystonia Research, Leuven, Belgium
| | - Amaka C Offiah
- Department of Oncology & Metabolism, University of Sheffield, UK
| | - Andres Moreno-De-Luca
- Autism & Developmental Medicine Institute, Genomic Medicine Institute, Department of Radiology, Diagnostic Medicine Institute, Geisinger, Danville, PA, USA
| | - Mohnish Suri
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Darius Ebrahimi-Fakhari
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Movement Disorders Program, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
- Intellectual and Developmental Disabilities Research Center, Boston Children's Hospital, Boston, MA, USA
| | - Henry Houlden
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
| | - Reza Maroofian
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
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7
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Pagnamenta AT, Belles RS, Salbert BA, Wentzensen IM, Guillen Sacoto MJ, Santos FJR, Caffo A, Ferla M, Banos‐Pinero B, Pawliczak K, Makvand M, Najmabadi H, Maroofian R, Lester T, Yanez‐Felix AL, Villarroel‐Cortes CE, Xia F, Al Fayez K, Al Hashem A, Shears D, Irving M, Offiah AC, Kariminejad A, Taylor JC. The prevalence and phenotypic range associated with biallelic PKDCC variants. Clin Genet 2023; 104:121-126. [PMID: 36896672 PMCID: PMC10952701 DOI: 10.1111/cge.14324] [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: 11/30/2022] [Revised: 02/08/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023]
Abstract
PKDCC encodes a component of Hedgehog signalling required for normal chondrogenesis and skeletal development. Although biallelic PKDCC variants have been implicated in rhizomelic shortening of limbs with variable dysmorphic features, this association was based on just two patients. In this study, data from the 100 000 Genomes Project was used in conjunction with exome sequencing and panel-testing results accessed via international collaboration to assemble a cohort of eight individuals from seven independent families with biallelic PKDCC variants. The allelic series included six frameshifts, a previously described splice-donor site variant and a likely pathogenic missense variant observed in two families that was supported by in silico structural modelling. Database queries suggested that the prevalence of this condition is between 1 of 127 and 1 of 721 in clinical cohorts with skeletal dysplasia of unknown aetiology. Clinical assessments, combined with data from previously published cases, indicate a predominantly upper limb involvement. Micrognathia, hypertelorism and hearing loss appear to be commonly co-occurring features. In conclusion, this study strengthens the link between biallelic inactivation of PKDCC and rhizomelic limb-shortening and will enable clinical testing laboratories to better interpret variants in this gene.
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Affiliation(s)
- Alistair T. Pagnamenta
- NIHR Biomedical Research Centre, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | | | | | | | | | - Francis Jeshira Reynoso Santos
- Joe DiMaggio Children's HospitalHollywoodFloridaUSA
- Division of Human GeneticsChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Alesky Caffo
- Joe DiMaggio Children's HospitalHollywoodFloridaUSA
| | - Matteo Ferla
- NIHR Biomedical Research Centre, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Benito Banos‐Pinero
- Oxford Genetics LaboratoriesOxford University Hospitals NHS Foundation Trust, The Churchill HospitalOxfordUK
| | | | - Mina Makvand
- Kariminejad‐Najmabadi Pathology & Genetics CenterTehranIran
| | - Hossein Najmabadi
- Kariminejad‐Najmabadi Pathology & Genetics CenterTehranIran
- Genetics Research CenterUniversity of Social Welfare & Rehabilitation ScienceTehranIran
| | | | - Reza Maroofian
- Department of Neuromuscular DiseasesUCL Queen Square Institute of Neurology, University College LondonLondonUK
| | - Tracy Lester
- Oxford Genetics LaboratoriesOxford University Hospitals NHS Foundation Trust, The Churchill HospitalOxfordUK
| | | | | | - Fan Xia
- Baylor GeneticsHoustonTexasUSA
| | - Khowla Al Fayez
- Department of Pediatrics, Division of Clinical Genetic and Metabolic MedicinePrince Sultan Medical Military CityRiyadhSaudi Arabia
| | - Amal Al Hashem
- Department of Pediatrics, Division of Clinical Genetic and Metabolic MedicinePrince Sultan Medical Military CityRiyadhSaudi Arabia
| | - Deborah Shears
- Oxford Centre for Genomic MedicineOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Melita Irving
- Department of Clinical GeneticsGuy's and St Thomas' NHS Foundation TrustLondonUK
| | - Amaka C. Offiah
- Department of Oncology & MetabolismUniversity of SheffieldSheffieldUK
| | | | - Jenny C. Taylor
- NIHR Biomedical Research Centre, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
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8
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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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9
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Thomas-Wilson A, Schacht JP, Chitayat D, Blaser S, Santos FJR, Glaser K, Caffo A, Wentzensen IM, Henderson LB, Zhang F, Zhu Y, Di Corleto E, da Silva Costa F, Vink R, Alkhunaizi E, Russell L, Buckley MF, Roscioli T, Pereira EM, Ganapathi M. Biallelic variants in TUBGCP6 result in microcephaly and chorioretinopathy 1: Report of four cases and a literature review. Am J Med Genet A 2023. [PMID: 37031378 DOI: 10.1002/ajmg.a.63203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/10/2023]
Abstract
Autosomal recessive microcephaly and chorioretinopathy-1 (MCCRP1) is a rare Mendelian disorder resulting from biallelic loss of function variants in Tubulin-Gamma Complex Associated Protein 6 (TUBGCP6, MIM#610053). Clinical features of this disorder include microcephaly, cognitive impairment, dysmorphic features, and variable ophthalmological anomalies including chorioretinopathy. Microcephaly can be recognized prenatally and visual impairment becomes evident during the first year of life. The clinical presentation resembles the findings in some acquired conditions such as congenital toxoplasmosis and cytomegalovirus infections; thus, it is important to recognize and diagnose this syndrome in view of its impact on patient health management and familial reproductive plans. To date, only seven molecularly confirmed patients from five unrelated families have been reported. We report an additional four unrelated patients with TUBGCP6 variants including one prenatal diagnosis and review the clinical phenotypes and genotypes of all the known cases. This report expands the molecular and phenotypic spectrum of TUBGCP6 and includes additional prenatal findings associated with MCCRP1.
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Affiliation(s)
- Amanda Thomas-Wilson
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - John P Schacht
- Department of Pediatrics, Division of Clinical Genetics, Columbia University Irving Medical Center, New York, New York, USA
| | - David Chitayat
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Susan Blaser
- Department of Diagnostic Imaging, Division of Pediatric Neuroradiology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | | | - Kimberly Glaser
- Department of Clinical Genetics, Joe DiMaggio Children's Hospital, Hollywood, Florida, USA
| | - Alesky Caffo
- Department of Clinical Genetics, Joe DiMaggio Children's Hospital, Hollywood, Florida, USA
| | | | | | - Futao Zhang
- New South Wales Health Pathology, Randwick Genomics Laboratory, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Ying Zhu
- New South Wales Health Pathology, Randwick Genomics Laboratory, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Ellen Di Corleto
- Maternal Fetal Medicine Unit, Gold Coast University Hospital, Gold Coast, Queensland, Australia
| | - Fabricio da Silva Costa
- Maternal Fetal Medicine Unit, Gold Coast University Hospital, Gold Coast, Queensland, Australia
- School of Medicine and Dentistry, Griffith University, Gold Coast, Queensland, Australia
| | - Rebecca Vink
- Neuroscience Research Australia (NeuRA), Sydney, New South Wales, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | - Ebba Alkhunaizi
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Genetics, McGill University Health Centre, Montreal, Quebec, Canada
| | - Laura Russell
- Department of Medical Genetics, McGill University Health Centre, Montreal, Quebec, Canada
| | - Michael F Buckley
- New South Wales Health Pathology, Randwick Genomics Laboratory, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Tony Roscioli
- New South Wales Health Pathology, Randwick Genomics Laboratory, Prince of Wales Hospital, Sydney, New South Wales, Australia
- Neuroscience Research Australia (NeuRA), Sydney, New South Wales, Australia
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Elaine Maria Pereira
- Department of Pediatrics, Division of Clinical Genetics, Columbia University Irving Medical Center, New York, New York, USA
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
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10
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Holtz AM, VanCoillie R, Vansickle EA, Carere DA, Withrow K, Torti E, Juusola J, Millan F, Person R, Guillen Sacoto MJ, Si Y, Wentzensen IM, Pugh J, Vasileiou G, Rieger M, Reis A, Argilli E, Sherr EH, Aldinger KA, Dobyns WB, Brunet T, Hoefele J, Wagner M, Haber B, Kotzaeridou U, Keren B, Heron D, Mignot C, Heide S, Courtin T, Buratti J, Murugasen S, Donald KA, O'Heir E, Moody S, Kim KH, Burton BK, Yoon G, Campo MD, Masser-Frye D, Kozenko M, Parkinson C, Sell SL, Gordon PL, Prokop JW, Karaa A, Bupp C, Raby BA. Heterozygous variants in MYH10 associated with neurodevelopmental disorders and congenital anomalies with evidence for primary cilia-dependent defects in Hedgehog signaling. Genet Med 2022; 24:2065-2078. [PMID: 35980381 PMCID: PMC10765599 DOI: 10.1016/j.gim.2022.07.005] [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: 12/02/2021] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 10/15/2022] Open
Abstract
PURPOSE Nonmuscle myosin II complexes are master regulators of actin dynamics that play essential roles during embryogenesis with vertebrates possessing 3 nonmuscle myosin II heavy chain genes, MYH9, MYH10, and MYH14. As opposed to MYH9 and MYH14, no recognizable disorder has been associated with MYH10. We sought to define the clinical characteristics and molecular mechanism of a novel autosomal dominant disorder related to MYH10. METHODS An international collaboration identified the patient cohort. CAS9-mediated knockout cell models were used to explore the mechanism of disease pathogenesis. RESULTS We identified a cohort of 16 individuals with heterozygous MYH10 variants presenting with a broad spectrum of neurodevelopmental disorders and variable congenital anomalies that affect most organ systems and were recapitulated in animal models of altered MYH10 activity. Variants were typically de novo missense changes with clustering observed in the motor domain. MYH10 knockout cells showed defects in primary ciliogenesis and reduced ciliary length with impaired Hedgehog signaling. MYH10 variant overexpression produced a dominant-negative effect on ciliary length. CONCLUSION These data presented a novel genetic cause of isolated and syndromic neurodevelopmental disorders related to heterozygous variants in the MYH10 gene with implications for disrupted primary cilia length control and altered Hedgehog signaling in disease pathogenesis.
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Affiliation(s)
- Alexander M Holtz
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA.
| | - Rachel VanCoillie
- Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, MI
| | - Elizabeth A Vansickle
- Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, MI
| | | | | | | | | | | | | | | | | | | | - Jada Pugh
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD; Department of Health, Behavior and Society, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Georgia Vasileiou
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Melissa Rieger
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Emanuela Argilli
- Brain Development Research Program, Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Elliott H Sherr
- Brain Development Research Program, Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA
| | - William B Dobyns
- Division of Pediatric Genetics and Metabolism, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Theresa Brunet
- Institute of Human Genetics, Technical University Munich School of Medicine, Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Technical University Munich School of Medicine, Munich, Germany
| | - Matias Wagner
- Institute of Human Genetics, Technical University Munich School of Medicine, 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
| | - Benjamin Haber
- Division of Child Neurology and Inherited Metabolic Diseases, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Urania Kotzaeridou
- Division of Child Neurology and Inherited Metabolic Diseases, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Boris Keren
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne University, Paris, France
| | - Delphine Heron
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne University, Paris, France
| | - Cyril Mignot
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne University, Paris, France
| | - Solveig Heide
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne University, Paris, France
| | - Thomas Courtin
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne University, Paris, France
| | - Julien Buratti
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne University, Paris, France
| | - Serini Murugasen
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Rondebosch, South Africa
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Rondebosch, South Africa
| | - Emily O'Heir
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Shade Moody
- Division of Child and Adolescent Neurology, The University of Texas Health Science Center, Houston, TX
| | - Katherine H Kim
- Division of Genetics, Birth Defects, and Metabolism, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Barbara K Burton
- Division of Genetics, Birth Defects, and Metabolism, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Grace Yoon
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Miguel Del Campo
- Division of Dysmorphology & Teratology, Department of Pediatrics, University of California San Diego, San Diego, CA
| | - Diane Masser-Frye
- Division of Genetics/ Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA
| | - Mariya Kozenko
- Division of Genetics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Christina Parkinson
- Division of Genetics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Susan L Sell
- Department of Pediatrics, Penn State Health Children's Hospital, Hershey, PA
| | - Patricia L Gordon
- Department of Pediatrics, Penn State Health Children's Hospital, Hershey, PA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI
| | - Amel Karaa
- Division of Genetics and Genomics, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Caleb Bupp
- Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, MI.
| | - Benjamin A Raby
- Division of Pulmonary Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA.
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11
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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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12
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Guerrini R, Mei D, Kerti-Szigeti K, Pepe S, Koenig MK, Von Allmen G, Cho MT, McDonald K, Baker J, Bhambhani V, Powis Z, Rodan L, Nabbout R, Barcia G, Rosenfeld JA, Bacino CA, Mignot C, Power LH, Harris CJ, Marjanovic D, Møller RS, Hammer TB, Keski Filppula R, Vieira P, Hildebrandt C, Sacharow S, Maragliano L, Benfenati F, Lachlan K, Benneche A, Petit F, de Sainte Agathe JM, Hallinan B, Si Y, Wentzensen IM, Zou F, Narayanan V, Matsumoto N, Boncristiano A, la Marca G, Kato M, Anderson K, Barba C, Sturiale L, Garozzo D, Bei R, Masuelli L, Conti V, Novarino G, Fassio A. Phenotypic and genetic spectrum of ATP6V1A encephalopathy: a disorder of lysosomal homeostasis. Brain 2022; 145:2687-2703. [PMID: 35675510 PMCID: PMC10893886 DOI: 10.1093/brain/awac145] [Citation(s) in RCA: 6] [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: 07/15/2021] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 11/30/2023] Open
Abstract
Vacuolar-type H+-ATPase (V-ATPase) is a multimeric complex present in a variety of cellular membranes that acts as an ATP-dependent proton pump and plays a key role in pH homeostasis and intracellular signalling pathways. In humans, 22 autosomal genes encode for a redundant set of subunits allowing the composition of diverse V-ATPase complexes with specific properties and expression. Sixteen subunits have been linked to human disease. Here we describe 26 patients harbouring 20 distinct pathogenic de novo missense ATP6V1A variants, mainly clustering within the ATP synthase α/β family-nucleotide-binding domain. At a mean age of 7 years (extremes: 6 weeks, youngest deceased patient to 22 years, oldest patient) clinical pictures included early lethal encephalopathies with rapidly progressive massive brain atrophy, severe developmental epileptic encephalopathies and static intellectual disability with epilepsy. The first clinical manifestation was early hypotonia, in 70%; 81% developed epilepsy, manifested as developmental epileptic encephalopathies in 58% of the cohort and with infantile spasms in 62%; 63% of developmental epileptic encephalopathies failed to achieve any developmental, communicative or motor skills. Less severe outcomes were observed in 23% of patients who, at a mean age of 10 years and 6 months, exhibited moderate intellectual disability, with independent walking and variable epilepsy. None of the patients developed communicative language. Microcephaly (38%) and amelogenesis imperfecta/enamel dysplasia (42%) were additional clinical features. Brain MRI demonstrated hypomyelination and generalized atrophy in 68%. Atrophy was progressive in all eight individuals undergoing repeated MRIs. Fibroblasts of two patients with developmental epileptic encephalopathies showed decreased LAMP1 expression, Lysotracker staining and increased organelle pH, consistent with lysosomal impairment and loss of V-ATPase function. Fibroblasts of two patients with milder disease, exhibited a different phenotype with increased Lysotracker staining, decreased organelle pH and no significant modification in LAMP1 expression. Quantification of substrates for lysosomal enzymes in cellular extracts from four patients revealed discrete accumulation. Transmission electron microscopy of fibroblasts of four patients with variable severity and of induced pluripotent stem cell-derived neurons from two patients with developmental epileptic encephalopathies showed electron-dense inclusions, lipid droplets, osmiophilic material and lamellated membrane structures resembling phospholipids. Quantitative assessment in induced pluripotent stem cell-derived neurons identified significantly smaller lysosomes. ATP6V1A-related encephalopathy represents a new paradigm among lysosomal disorders. It results from a dysfunctional endo-lysosomal membrane protein causing altered pH homeostasis. Its pathophysiology implies intracellular accumulation of substrates whose composition remains unclear, and a combination of developmental brain abnormalities and neurodegenerative changes established during prenatal and early postanal development, whose severity is variably determined by specific pathogenic variants.
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Affiliation(s)
- Renzo Guerrini
- Neuroscience Department, Children's Hospital Meyer, University of Florence, Florence, Italy
| | - Davide Mei
- Neuroscience Department, Children's Hospital Meyer, University of Florence, Florence, Italy
| | | | - Sara Pepe
- Department of Experimental Medicine, University of Genoa, Italy
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - Mary Kay Koenig
- Department of Pediatrics, Division of Child and Adolescent Neurology, The University of Texas McGovern Medical School, Houston, TX, USA
| | - Gretchen Von Allmen
- Department of Pediatrics, Division of Child and Adolescent Neurology, The University of Texas McGovern Medical School, Houston, TX, USA
| | | | - Kimberly McDonald
- Pediatric Neurology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Janice Baker
- Genetics and Genomics, Children's Minnesota, Minneapolis, MN, USA
| | - Vikas Bhambhani
- Genetics and Genomics, Children's Minnesota, Minneapolis, MN, USA
| | - Zöe Powis
- Ambry Genetics, Aliso Viejo, CA, USA
| | - Lance Rodan
- Division of Genetics and Genomics and Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Rima Nabbout
- Reference Centre for Rare Epilepsies, Department of Genetics, Necker Enfants Malades Hospital, APHP, member of ERN EpiCARE, Université de Paris, Paris, France
| | - Giulia Barcia
- Reference Centre for Rare Epilepsies, Department of Genetics, Necker Enfants Malades Hospital, APHP, member of ERN EpiCARE, Université de Paris, Paris, France
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Cyril Mignot
- APHP, Sorbonne Université, Départément de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
- Institut du Cerveau (ICM), UMR S 1127, Inserm U1127, CNRS UMR 7225, Sorbonne Université, 75013 Paris, France
| | - Lillian H Power
- Pediatric Neurology, Stead Family Department of Pediatrics, University of Iowa Stead Family Children’s Hospital, Iowa City, IA, USA
| | - Catharine J Harris
- Department of Pediatric Genetics, University of Missouri Medical Center, Columbia, MO 65212, USA
| | - Dragan Marjanovic
- Danish Epilepsy Centre Filadelfia, Adult Neurology, Dianalund, Denmark
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Treatment, Danish Epilepsy Center Filadelfia, Dianalund, Denmark
- Department of Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Trine B Hammer
- Department of Epilepsy Genetics and Personalized Treatment, Danish Epilepsy Center Filadelfia, Dianalund, Denmark
| | - The DDD Study
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Riikka Keski Filppula
- Department of Clinical Genetics, Oulu University Hospital, Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - Päivi Vieira
- Clinic for Children and Adolescents, Oulu University Hospital, Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - Clara Hildebrandt
- Division of Genetics and Genomics, Metabolism Program, Boston Children's Hospital, Boston, MA, USA
| | | | | | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Katherine Lachlan
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Human Development and Health, Faculty of Medicine University of Southampton, Southampton, UK
| | - Andreas Benneche
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | | | - Jean Madeleine de Sainte Agathe
- Laboratoire de Biologie Médicale Multi Sites SeqOIA, Laboratoire de Médecine Génomique, APHP. Sorbonne Université, Paris, France
| | - Barbara Hallinan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Child Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yue Si
- GeneDx, Gaithersburg, MD 20877, USA
| | | | | | - Vinodh Narayanan
- Neurogenomics Division, Center for Rare Childhood Disorders, Translational Genomics Research Institute (TGen), Phoenix, AZ 85012, USA
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | | | - Giancarlo la Marca
- Newborn Screening, Clinical Chemistry and Pharmacology Laboratory, Meyer Children’s University Hospital, Florence, Italy
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine and Epilepsy Medical Center, Showa University Hospital, Tokyo, Japan
| | | | - Carmen Barba
- Neuroscience Department, Children's Hospital Meyer, University of Florence, Florence, Italy
| | - Luisa Sturiale
- CNR, Institute for Polymers, Composites and Biomaterials, IPCB, 95126 Catania, Italy
| | - Domenico Garozzo
- CNR, Institute for Polymers, Composites and Biomaterials, IPCB, 95126 Catania, Italy
| | - Roberto Bei
- Department of Clinical Sciences and Translational Medicine, University of Rome ‘Tor Vergata', Rome, Italy
| | | | - Laura Masuelli
- Department of Experimental Medicine, University of Rome ‘Sapienza', Rome, Italy
| | - Valerio Conti
- Neuroscience Department, Children's Hospital Meyer, University of Florence, Florence, Italy
| | - Gaia Novarino
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Anna Fassio
- Department of Experimental Medicine, University of Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
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13
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Stephenson SE, Costain G, Blok LE, Silk MA, Nguyen TB, Dong X, Alhuzaimi DE, Dowling JJ, Walker S, Amburgey K, Hayeems RZ, Rodan LH, Schwartz MA, Picker J, Lynch SA, Gupta A, Rasmussen KJ, Schimmenti LA, Klee EW, Niu Z, Agre KE, Chilton I, Chung WK, Revah-Politi A, Au PB, Griffith C, Racobaldo M, Raas-Rothschild A, Ben Zeev B, Barel O, Moutton S, Morice-Picard F, Carmignac V, Cornaton J, Marle N, Devinsky O, Stimach C, Wechsler SB, Hainline BE, Sapp K, Willems M, Bruel AL, Dias KR, Evans CA, Roscioli T, Sachdev R, Temple SE, Zhu Y, Baker JJ, Scheffer IE, Gardiner FJ, Schneider AL, Muir AM, Mefford HC, Crunk A, Heise EM, Millan F, Monaghan KG, Person R, Rhodes L, Richards S, Wentzensen IM, Cogné B, Isidor B, Nizon M, Vincent M, Besnard T, Piton A, Marcelis C, Kato K, Koyama N, Ogi T, Goh ESY, Richmond C, Amor DJ, Boyce JO, Morgan AT, Hildebrand MS, Kaspi A, Bahlo M, Friðriksdóttir R, Katrínardóttir H, Sulem P, Stefánsson K, Björnsson HT, Mandelstam S, Morleo M, Mariani M, Scala M, Accogli A, Torella A, Capra V, Wallis M, Jansen S, Waisfisz Q, de Haan H, Sadedin S, Lim SC, White SM, Ascher DB, Schenck A, Lockhart PJ, Christodoulou J, Tan TY, Christodoulou J, Tan TY. Germline variants in tumor suppressor FBXW7 lead to impaired ubiquitination and a neurodevelopmental syndrome. Am J Hum Genet 2022; 109:601-617. [PMID: 35395208 DOI: 10.1016/j.ajhg.2022.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 10/28/2021] [Accepted: 02/28/2022] [Indexed: 11/01/2022] Open
Abstract
Neurodevelopmental disorders are highly heterogenous conditions resulting from abnormalities of brain architecture and/or function. FBXW7 (F-box and WD-repeat-domain-containing 7), a recognized developmental regulator and tumor suppressor, has been shown to regulate cell-cycle progression and cell growth and survival by targeting substrates including CYCLIN E1/2 and NOTCH for degradation via the ubiquitin proteasome system. We used a genotype-first approach and global data-sharing platforms to identify 35 individuals harboring de novo and inherited FBXW7 germline monoallelic chromosomal deletions and nonsense, frameshift, splice-site, and missense variants associated with a neurodevelopmental syndrome. The FBXW7 neurodevelopmental syndrome is distinguished by global developmental delay, borderline to severe intellectual disability, hypotonia, and gastrointestinal issues. Brain imaging detailed variable underlying structural abnormalities affecting the cerebellum, corpus collosum, and white matter. A crystal-structure model of FBXW7 predicted that missense variants were clustered at the substrate-binding surface of the WD40 domain and that these might reduce FBXW7 substrate binding affinity. Expression of recombinant FBXW7 missense variants in cultured cells demonstrated impaired CYCLIN E1 and CYCLIN E2 turnover. Pan-neuronal knockdown of the Drosophila ortholog, archipelago, impaired learning and neuronal function. Collectively, the data presented herein provide compelling evidence of an F-Box protein-related, phenotypically variable neurodevelopmental disorder associated with monoallelic variants in FBXW7.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - John Christodoulou
- Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia; Victorian Clinical Genetics Services, Melbourne, VIC 3052, Australia
| | - Tiong Yang Tan
- Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia; Victorian Clinical Genetics Services, Melbourne, VIC 3052, Australia.
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14
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Fasham J, Lin S, Ghosh P, Radio FC, Farrow EG, Thiffault I, Kussman J, Zhou D, Hemming R, Zahka K, Chioza BA, Rawlins LE, Wenger OK, Gunning AC, Pizzi S, Onesimo R, Zampino G, Barker E, Osawa N, Rodriguez MC, Neuhann TM, Zackai EH, Keena B, Capasso J, Levin AV, Bhoj E, Li D, Hakonarson H, Wentzensen IM, Jackson A, Chandler KE, Coban-Akdemir ZH, Posey JE, Banka S, Lupski JR, Sheppard SE, Tartaglia M, Triggs-Raine B, Crosby AH, Baple EL. Elucidating the clinical spectrum and molecular basis of HYAL2 deficiency. Genet Med 2022; 24:631-644. [PMID: 34906488 PMCID: PMC9933146 DOI: 10.1016/j.gim.2021.10.014] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/03/2021] [Accepted: 10/21/2021] [Indexed: 11/25/2022] Open
Abstract
PURPOSE We previously defined biallelic HYAL2 variants causing a novel disorder in 2 families, involving orofacial clefting, facial dysmorphism, congenital heart disease, and ocular abnormalities, with Hyal2 knockout mice displaying similar phenotypes. In this study, we better define the phenotype and pathologic disease mechanism. METHODS Clinical and genomic investigations were undertaken alongside molecular studies, including immunoblotting and immunofluorescence analyses of variant/wild-type human HYAL2 expressed in mouse fibroblasts, and in silico modeling of putative pathogenic variants. RESULTS Ten newly identified individuals with this condition were investigated, and they were associated with 9 novel pathogenic variants. Clinical studies defined genotype-phenotype correlations and confirmed a recognizable craniofacial phenotype in addition to myopia, cleft lip/palate, and congenital cardiac anomalies as the most consistent manifestations of the condition. In silico modeling of missense variants identified likely deleterious effects on protein folding. Consistent with this, functional studies indicated that these variants cause protein instability and a concomitant cell surface absence of HYAL2 protein. CONCLUSION These studies confirm an association between HYAL2 alterations and syndromic cleft lip/palate, provide experimental evidence for the pathogenicity of missense alleles, enable further insights into the pathomolecular basis of the disease, and delineate the core and variable clinical outcomes of the condition.
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Affiliation(s)
- James Fasham
- Medical Research, Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom; Peninsula Clinical Genetics Service, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Siying Lin
- Medical Research, Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Promita Ghosh
- Department of Biochemistry and Medical Genetics, Rax Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù (Bambino Gesù Pediatric Hospital), IRCCS, Rome, Italy
| | - Emily G Farrow
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO
| | | | - Jennifer Kussman
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO
| | - Dihong Zhou
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO
| | - Rick Hemming
- Department of Biochemistry and Medical Genetics, Rax Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kenneth Zahka
- Pediatric Cardiology, Cleveland Clinic, Cleveland, OH
| | - Barry A Chioza
- Medical Research, Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Lettie E Rawlins
- Medical Research, Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom; Peninsula Clinical Genetics Service, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Olivia K Wenger
- New Leaf Center, Clinic for Special Children, Mount Eaton, OH
| | - Adam C Gunning
- Medical Research, Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù (Bambino Gesù Pediatric Hospital), IRCCS, Rome, Italy
| | - Roberta Onesimo
- Center for Rare Disease and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli (Gemelli University Hospital), IRCCS, Rome, Italy
| | - Giuseppe Zampino
- Center for Rare Disease and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli (Gemelli University Hospital), IRCCS, Rome, Italy
| | - Emily Barker
- Department of Biochemistry and Medical Genetics, Rax Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Natasha Osawa
- Department of Biochemistry and Medical Genetics, Rax Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Megan Christine Rodriguez
- Department of Biochemistry and Medical Genetics, Rax Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Beth Keena
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jenina Capasso
- Golisano Children's Hospital and Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY
| | - Alex V Levin
- Golisano Children's Hospital and Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY
| | - Elizabeth Bhoj
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Dong Li
- Golisano Children's Hospital and Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY
| | - Hakon Hakonarson
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Adam Jackson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Kate E Chandler
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | | | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX
| | - Sarah E Sheppard
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù (Bambino Gesù Pediatric Hospital), IRCCS, Rome, Italy.
| | - Barbara Triggs-Raine
- Department of Biochemistry and Medical Genetics, Rax Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Andrew H Crosby
- Medical Research, Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom.
| | - Emma L Baple
- Medical Research, Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom; Peninsula Clinical Genetics Service, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom.
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15
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Küry S, Ebstein F, Mollé A, Besnard T, Lee MK, Vignard V, Hery T, Nizon M, Mancini GM, Giltay JC, Cogné B, McWalter K, Deb W, Mor-Shaked H, Li H, Schnur RE, Wentzensen IM, Denommé-Pichon AS, Fourgeux C, Verheijen FW, Faurie E, Schot R, Stevens CA, Smits DJ, Barr E, Sheffer R, Bernstein JA, Stimach CL, Kovitch E, Shashi V, Schoch K, Smith W, van Jaarsveld RH, Hurst AC, Smith K, Baugh EH, Bohm SG, Vyhnálková E, Ryba L, Delnatte C, Neira J, Bonneau D, Toutain A, Rosenfeld JA, Audebert-Bellanger S, Gilbert-Dussardier B, Odent S, Laumonnier F, Berger SI, Smith AC, Bourdeaut F, Stern MH, Redon R, Krüger E, Margueron R, Bézieau S, Poschmann J, Isidor B, Isidor B. Rare germline heterozygous missense variants in BRCA1-associated protein 1, BAP1, cause a syndromic neurodevelopmental disorder. Am J Hum Genet 2022; 109:361-372. [PMID: 35051358 DOI: 10.1016/j.ajhg.2021.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/14/2021] [Indexed: 12/23/2022] Open
Abstract
Nuclear deubiquitinase BAP1 (BRCA1-associated protein 1) is a core component of multiprotein complexes that promote transcription by reversing the ubiquitination of histone 2A (H2A). BAP1 is a tumor suppressor whose germline loss-of-function variants predispose to cancer. To our knowledge, there are very rare examples of different germline variants in the same gene causing either a neurodevelopmental disorder (NDD) or a tumor predisposition syndrome. Here, we report a series of 11 de novo germline heterozygous missense BAP1 variants associated with a rare syndromic NDD. Functional analysis showed that most of the variants cannot rescue the consequences of BAP1 inactivation, suggesting a loss-of-function mechanism. In T cells isolated from two affected children, H2A deubiquitination was impaired. In matching peripheral blood mononuclear cells, histone H3 K27 acetylation ChIP-seq indicated that these BAP1 variants induced genome-wide chromatin state alterations, with enrichment for regulatory regions surrounding genes of the ubiquitin-proteasome system (UPS). Altogether, these results define a clinical syndrome caused by rare germline missense BAP1 variants that alter chromatin remodeling through abnormal histone ubiquitination and lead to transcriptional dysregulation of developmental genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France; Université de Nantes, CHU Nantes, CNRS, INSERM, l'Institut du Thorax, 44007 Nantes, France.
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16
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Laboy Cintron D, Muir AM, Scott A, McDonald M, Monaghan KG, Santiago-Sim T, Wentzensen IM, De Luca C, Brancati F, Harris DJ, Goueli C, Stottmann R, Prada CE, Biderman Waberski M, Mefford HC. A recurrent, de novo pathogenic variant in ARPC4 disrupts actin filament formation and causes microcephaly and speech delay. Human Genetics and Genomics Advances 2022; 3:100072. [PMID: 35047857 PMCID: PMC8756495 DOI: 10.1016/j.xhgg.2021.100072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/17/2021] [Indexed: 11/18/2022] Open
Abstract
We report seven affected individuals from six families with a recurrent, de novo variant in the ARPC4 gene (c.472C>T [p.Arg158Cys (GenBank: NM_005718.4)]). Core features in affected individuals include microcephaly, mild motor delays, and significant speech impairment. ARPC4 is a core subunit of the actin-related protein (ARP2/3) complex, which catalyzes the formation of F-actin networks. We show that the recurrent ARPC4 missense change is associated with a decreased amount of F-actin in cells from two affected individuals. Taken together, our results implicate heterozygous ARPC4 missense variants as a cause of neurodevelopmental disorders and microcephaly.
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Affiliation(s)
- Dianne Laboy Cintron
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA
| | - Alison M Muir
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA
| | - Abbey Scott
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, USA
| | - Marie McDonald
- Department of Pediatrics, Duke University, Durham, NC, USA
| | | | | | | | - Chiara De Luca
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | | | - Francesco Brancati
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy.,IRCCS San Raffaele Roma, 00163 Roma, Italy
| | - David J Harris
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Cecilia Goueli
- Department of Pediatrics, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | | | - Carlos E Prada
- Department of Pediatrics, Cincinnati Children's Hospital, Cincinnati, OH, USA.,Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.,Department of Pediatrics, Feinberg School of Medicine of Northwestern University, Chicago, IL 60611, USA
| | | | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA.,Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, USA
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17
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Acharya A, Kavus H, Dunn P, Nasir A, Folk L, Withrow K, Wentzensen IM, Ruzhnikov MRZ, Fallot C, Smol T, Rama M, Brown K, Whalen S, Ziegler A, Barth M, Chassevent A, Smith-Hicks C, Afenjar A, Courtin T, Heide S, Font-Montgomery E, Heid C, Hamm JA, Love DR, Thabet F, Misra VK, Cunningham M, Leal SM, Jarvela I, Normand EA, Zou F, Helal M, Keren B, Torti E, Chung WK, Schrauwen I. Delineating the genotypic and phenotypic spectrum of HECW2-related neurodevelopmental disorders. J Med Genet 2021; 59:669-677. [PMID: 34321324 DOI: 10.1136/jmedgenet-2021-107871] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/06/2021] [Indexed: 11/03/2022]
Abstract
BACKGROUND Variants in HECW2 have recently been reported to cause a neurodevelopmental disorder with hypotonia, seizures and impaired language; however, only six variants have been reported and the clinical characteristics have only broadly been defined. METHODS Molecular and clinical data were collected from clinical and research cohorts. Massive parallel sequencing was performed and identified individuals with a HECW2-related neurodevelopmental disorder. RESULTS We identified 13 novel missense variants in HECW2 in 22 unpublished cases, of which 18 were confirmed to have a de novo variant. In addition, we reviewed the genotypes and phenotypes of previously reported and new cases with HECW2 variants (n=35 cases). All variants identified are missense, and the majority of likely pathogenic and pathogenic variants are located in or near the C-terminal HECT domain (88.2%). We identified several clustered variants and four recurrent variants (p.(Arg1191Gln);p.(Asn1199Lys);p.(Phe1327Ser);p.(Arg1330Trp)). Two variants, (p.(Arg1191Gln);p.(Arg1330Trp)), accounted for 22.9% and 20% of cases, respectively. Clinical characterisation suggests complete penetrance for hypotonia with or without spasticity (100%), developmental delay/intellectual disability (100%) and developmental language disorder (100%). Other common features are behavioural problems (88.9%), vision problems (83.9%), motor coordination/movement (75%) and gastrointestinal issues (70%). Seizures were present in 61.3% of individuals. Genotype-phenotype analysis shows that HECT domain variants are more frequently associated with cortical visual impairment and gastrointestinal issues. Seizures were only observed in individuals with variants in or near the HECT domain. CONCLUSION We provide a comprehensive review and expansion of the genotypic and phenotypic spectrum of HECW2 disorders, aiding future molecular and clinical diagnosis and management.
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Affiliation(s)
- Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Haluk Kavus
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Patrick Dunn
- The George Washington University, Washington, District of Columbia, USA
| | - Abdul Nasir
- Department of Molecular Science and Technology, Ajou University, Suwon, The Republic of Korea
| | | | | | | | - Maura R Z Ruzhnikov
- Neurology and Neurological Sciences, Pediatrics, Division of Medical Genetics, Stanford University and Lucile Packard Children's Hospital, Palo Alto, California, USA
| | | | - Thomas Smol
- Institut de Génétique, Univ Lille, EA7364 RADEME, CHU Lille, Lille, France
| | | | - Kathleen Brown
- Pediatrics-Clinical Genetics and Metabolism, School of Medicine, University of Colorado-Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sandra Whalen
- UF de génétique Clinique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Assistance Publique-Hôpitaux de Paris (APHP) Sorbonne Université, Hôpital Armand Trousseau, ERN-ITHACA, Paris, France
| | - Alban Ziegler
- Department of Genetics, Angers University Hospital, Angers, France
| | - Magali Barth
- Department of Genetics, Angers University Hospital, Angers, France
| | - Anna Chassevent
- Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Constance Smith-Hicks
- Division of Neurogenetics, Kennedy Krieger Institute, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alexandra Afenjar
- Assistance Publique-Hôpitaux de Paris (APHP) Sorbonne Université, Centre de Référence Malformations et maladies congénitales du cervelet et déficiences intellectuelles de causes rares, département de génétique et embryologie médicale, Hôpital Trousseau, Paris, France
| | - Thomas Courtin
- Département de génétique, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Solveig Heide
- Department of Genetics, Pitié-Salpêtrière Hospital, Referral Center for Intellectual Disabilities of Rare Causes, Assistance Publique-Hôpitaux de Paris (APHP) Sorbonne Université, Paris, France
| | | | - Caleb Heid
- University Hospital Medical Genetics Clinic, University of Missouri, Columbia, Missouri, USA
| | - J Austin Hamm
- Pediatric Genetics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA
| | | | - Farouq Thabet
- Pediatric Neurology Division, Sidra Medicine, Doha, Qatar
| | - Vinod K Misra
- Department of Pediatrics, Division of Genetic, Genomic, and Metabolic Disorders, Children's Hospital of Michigan, Detroit, Michigan, USA.,Discipline of Pediatrics, Central Michigan University, Mount Pleasant, Michigan, USA
| | - Mitch Cunningham
- Department of Pediatrics, Division of Genetic, Genomic, and Metabolic Disorders, Children's Hospital of Michigan, Detroit, Michigan, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center and the Department of Neurology, Columbia University Medical Center, New York, New York, USA.,Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, New York, USA
| | - Irma Jarvela
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | | | | | - Mayada Helal
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Boris Keren
- Département de génétique, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | | | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, New York, USA .,Department of Medicine, Columbia University, New York, New York, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
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18
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Palmer EE, Whitton C, Hashem MO, Clark RD, Ramanathan S, Starr LJ, Velasco D, De Dios JK, Singh E, Cormier-Daire V, Chopra M, Rodan LH, Nellaker C, Lakhani S, Mallack EJ, Panzer K, Sidhu A, Wentzensen IM, Lacombe D, Michaud V, Alkuraya FS. CHEDDA syndrome is an underrecognized neurodevelopmental disorder with a highly restricted ATN1 mutation spectrum. Clin Genet 2021; 100:468-477. [PMID: 34212383 DOI: 10.1111/cge.14022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/08/2021] [Accepted: 06/12/2021] [Indexed: 11/28/2022]
Abstract
We describe the clinical features of nine unrelated individuals with rare de novo missense or in-frame deletions/duplications within the "HX motif" of exon 7 of ATN1. We previously proposed that individuals with such variants should be considered as being affected by the syndromic condition of congenital hypotonia, epilepsy, developmental delay, and digital anomalies (CHEDDA), distinct from dentatorubral-pallidoluysian atrophy (DRPLA) secondary to expansion variants in exon 5 of ATN1. We confirm that the universal phenotypic features of CHEDDA are distinctive facial features and global developmental delay. Infantile hypotonia and minor hand and feet differences are common and can present as arthrogryposis. Common comorbidities include severe feeding difficulties, often requiring gastrostomy support, as well as visual and hearing impairments. Epilepsy and congenital malformations of the brain, heart, and genitourinary systems are frequent but not universal. Our study confirms the clinical entity of CHEDDA secondary to a mutational signature restricted to exon 7 of ATN1. We propose a clinical schedule for assessment upon diagnosis, surveillance, and early intervention including the potential of neuroimaging for prognostication.
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Affiliation(s)
- Elizabeth E Palmer
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales, Randwick, New South Wales, Australia
| | - Chloe Whitton
- Faculty of Medicine, University of New South Wales, Randwick, New South Wales, Australia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Robin D Clark
- Division of Medical Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Subhadra Ramanathan
- Division of Medical Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Lois J Starr
- Division of Medical Genetics, Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska, USA, Omaha, Nebraska, USA
| | - Danita Velasco
- Division of Medical Genetics, Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska, USA, Omaha, Nebraska, USA
| | - John Karl De Dios
- Division of Medical Genetics, Department of Pediatrics, Dayton Children's Hospital, Dayton, Ohio, USA
| | - Emily Singh
- Division of Genetics, Medical College of Wisconsin with Children's Wisconsin, Milwaukee, Wisconsin, USA
| | - Valerie Cormier-Daire
- Service de Génétique Clinique, INSERM UMR 1163, Hôpital Necker-Enfants Malades, Institut IMAGINE, Université de Paris, Paris, France
| | - Maya Chopra
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Lance H Rodan
- Department of Neurology, Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Christoffer Nellaker
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford, UK.,Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK.,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Shenela Lakhani
- Centre for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Eric J Mallack
- Centre for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Karin Panzer
- Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Alpa Sidhu
- Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | | | - Didier Lacombe
- Service de Génétique Médicale, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, CHU de Bordeaux, Bordeaux, France.,Maladies Rares, Génétique et Métabolisme (MRGM), U 1211 INSERM/Université de Bordeaux, Bordeaux, France
| | - Vincent Michaud
- Service de Génétique Médicale, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, CHU de Bordeaux, Bordeaux, France.,Maladies Rares, Génétique et Métabolisme (MRGM), U 1211 INSERM/Université de Bordeaux, Bordeaux, France
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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19
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Bowles B, Ferrer A, Nishimura CJ, Pinto E Vairo F, Rey T, Leheup B, Sullivan J, Schoch K, Stong N, Agolini E, Cocciadiferro D, Williams A, Cummings A, Loddo S, Genovese S, Roadhouse C, McWalter K, Wentzensen IM, Li C, Babovic-Vuksanovic D, Lanpher BC, Dentici ML, Ankala A, Hamm JA, Dallapiccola B, Radio FC, Shashi V, Gérard B, Bloch-Zupan A, Smith RJ, Klee EW. TSPEAR variants are primarily associated with ectodermal dysplasia and tooth agenesis but not hearing loss: A novel cohort study. Am J Med Genet A 2021; 185:2417-2433. [PMID: 34042254 PMCID: PMC8361973 DOI: 10.1002/ajmg.a.62347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 12/30/2022]
Abstract
Biallelic loss‐of‐function variants in the thrombospondin‐type laminin G domain and epilepsy‐associated repeats (TSPEAR) gene have recently been associated with ectodermal dysplasia and hearing loss. The first reports describing a TSPEAR disease association identified this gene is a cause of nonsyndromic hearing loss, but subsequent reports involving additional affected families have questioned this evidence and suggested a stronger association with ectodermal dysplasia. To clarify genotype–phenotype associations for TSPEAR variants, we characterized 13 individuals with biallelic TSPEAR variants. Individuals underwent either exome sequencing or panel‐based genetic testing. Nearly all of these newly reported individuals (11/13) have phenotypes that include tooth agenesis or ectodermal dysplasia, while three newly reported individuals have hearing loss. Of the individuals displaying hearing loss, all have additional variants in other hearing‐loss‐associated genes, specifically TMPRSS3, GJB2, and GJB6, that present competing candidates for their hearing loss phenotype. When presented alongside previous reports, the overall evidence supports the association of TSPEAR variants with ectodermal dysplasia and tooth agenesis features but creates significant doubt as to whether TSPEAR variants are a monogenic cause of hearing loss. Further functional evidence is needed to evaluate this phenotypic association.
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Affiliation(s)
- Bradley Bowles
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Alejandro Ferrer
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Carla J Nishimura
- Molecular Otolaryngology and Renal Research Laboratories, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Tristan Rey
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France.,Laboratoires de Diagnostic génétique, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Illkirch, France
| | - Bruno Leheup
- Département de Médecine Infantile, CHRU de Nancy, Nancy, France
| | - Jennifer Sullivan
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Kelly Schoch
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA.,Brystol Myers Squibb, New York, New York, USA
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Dario Cocciadiferro
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Abigail Williams
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA
| | - Alex Cummings
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA.,University of Wisconsin Hospitals and Clinics, Madison, Wisconsin, USA
| | - Sara Loddo
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chelsea Roadhouse
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | | | | | - Chumei Li
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Arun Ankala
- EGL Genetics LLC, Tucker, Georgia, USA.,Emory University School of Medicine, Atlanta, Georgia, USA
| | - J Austin Hamm
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Benedicte Gérard
- Laboratoires de Diagnostic génétique, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France
| | - Agnes Bloch-Zupan
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France.,Centre de référence des maladies rares orales et dentaires O-Rares, Filière Santé Maladies rares TETE COU, European Reference Network CRANIO, Pôle de Médecine et Chirurgie Bucco-dentaires, Hôpital Civil, Hôpitaux Universitaires de Strasbourg (HUS), Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Illkirch, France
| | - Richard J Smith
- Molecular Otolaryngology and Renal Research Laboratories, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
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20
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Schnur RE, Yousaf S, Liu J, Chung WK, Rhodes L, Marble M, Zambrano RM, Sobreira N, Jayakar P, Pierpont ME, Schultz MJ, Pichurin PN, Olson RJ, Graham GE, Osmond M, Contreras-García GA, Campo-Neira KA, Peñaloza-Mantilla CA, Flage M, Kuppa S, Navarro K, Sacoto MJG, Wentzensen IM, Scarano MI, Juusola J, Prada CE, Hufnagel RB. UBA2 variants underlie a recognizable syndrome with variable aplasia cutis congenita and ectrodactyly. Genet Med 2021; 23:1624-1635. [PMID: 34040189 PMCID: PMC8463496 DOI: 10.1038/s41436-021-01182-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 02/10/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/17/2022] Open
Abstract
Purpose: The human chromosome 19q13.11 deletion syndrome is associated with a variable phenotype that includes aplasia cutis congenita (ACC) and ectrodactyly as specific features. UBA2 (ubiquitin-like modifier-activating enzyme 2) lies adjacent to the minimal deletion overlap region. We aim to define the UBA2-related phenotypic spectrum in humans and zebrafish due to sequence variants and to establish the mechanism of disease. Methods: Exome Sequencing was used to detect UBA2 sequence variants in 16 subjects in 7 unrelated families. uba2 loss-of-function was modeled in zebrafish. Effects of human missense variants were assessed in zebrafish rescue experiments. Results: 7 human UBA2 loss-of-function and missense sequence variants were detected. UBA2-phenotypes included ACC, ectrodactyly, neurodevelopmental abnormalities, ectodermal, skeletal, craniofacial, cardiac, renal, and genital anomalies. uba2 was expressed in zebrafish eye, brain, and pectoral fins; uba2-null fish showed deficient growth, microcephaly, microphthalmia, mandibular hypoplasia, and abnormal fins. uba2-mRNAs with human missense variants failed to rescue nullizygous zebrafish phenotypes. Conclusion: UBA2 variants cause a recognizable syndrome with a wide phenotypic spectrum. Our data suggest that loss of UBA2 function underlies the human UBA2 monogenic disorder and highlights the importance of SUMOylation in the development of affected tissues.
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Affiliation(s)
- Rhonda E Schnur
- Clinical Genomics Program, GeneDx, Gaithersburg, MD, USA. .,Division of Genetics, Department of Pediatrics, Cooper Medical School of Rowan University, Cooper University Health Care, Camden, NJ, USA.
| | - Sairah Yousaf
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - James Liu
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wendy K Chung
- Division of Clinical Genetics, Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Lindsay Rhodes
- Clinical Genomics Program, GeneDx, Gaithersburg, MD, USA
| | - Michael Marble
- Department of Pediatrics, Division of Pediatric Genetics, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Regina M Zambrano
- Department of Pediatrics, Division of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL, USA
| | - Mary Ella Pierpont
- Departments of Pediatrics and Ophthalmology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Matthew J Schultz
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Gail E Graham
- Division of Genetics, Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Gustavo A Contreras-García
- Division de Genética Médica, Departamento de Pediatría-Hospital Universitario de Santander, Departamento de Ciencias Básicas, Grupo de Investigación en Genética Humana UIS, Facultad de Salud, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Karina A Campo-Neira
- Semillero de Investigación en Genética Humana SIGENH, Escuela de Medicina, Facultad de Salud, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Camilo A Peñaloza-Mantilla
- Semillero de Investigación en Genética Humana SIGENH, Escuela de Medicina, Facultad de Salud, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Mark Flage
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Srikar Kuppa
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Karina Navarro
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Maria I Scarano
- Division of Genetics, Department of Pediatrics, Cooper Medical School of Rowan University, Cooper University Health Care, Camden, NJ, USA
| | - Jane Juusola
- Clinical Genomics Program, GeneDx, Gaithersburg, MD, USA
| | - Carlos E Prada
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Robert B Hufnagel
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
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21
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Gripp KW, Smithson SF, Scurr IJ, Baptista J, Majumdar A, Pierre G, Williams M, Henderson LB, Wentzensen IM, McLaughlin H, Leeuwen L, Simon MEH, van Binsbergen E, Dinulos MBP, Kaplan JD, McRae A, Superti-Furga A, Good JM, Kutsche K. Syndromic disorders caused by gain-of-function variants in KCNH1, KCNK4, and KCNN3-a subgroup of K + channelopathies. Eur J Hum Genet 2021; 29:1384-1395. [PMID: 33594261 PMCID: PMC8440610 DOI: 10.1038/s41431-021-00818-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 11/09/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 12/13/2022] Open
Abstract
Decreased or increased activity of potassium channels caused by loss-of-function and gain-of-function (GOF) variants in the corresponding genes, respectively, underlies a broad spectrum of human disorders affecting the central nervous system, heart, kidney, and other organs. While the association of epilepsy and intellectual disability (ID) with variants affecting function in genes encoding potassium channels is well known, GOF missense variants in K+ channel encoding genes in individuals with syndromic developmental disorders have only recently been recognized. These syndromic phenotypes include Zimmermann–Laband and Temple–Baraitser syndromes, caused by dominant variants in KCNH1, FHEIG syndrome due to dominant variants in KCNK4, and the clinical picture associated with dominant variants in KCNN3. Here we review the presentation of these individuals, including five newly reported with variants in KCNH1 and three additional individuals with KCNN3 variants, all variants likely affecting function. There is notable overlap in the phenotypic findings of these syndromes associated with dominant KCNN3, KCNH1, and KCNK4 variants, sharing developmental delay and/or ID, coarse facial features, gingival enlargement, distal digital hypoplasia, and hypertrichosis. We suggest to combine the phenotypes and define a new subgroup of potassium channelopathies caused by increased K+ conductance, referred to as syndromic neurodevelopmental K+ channelopathies due to dominant variants in KCNH1, KCNK4, or KCNN3.
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Affiliation(s)
- Karen W Gripp
- Division of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Sarah F Smithson
- Department of Clinical Genetics, University Hospitals Bristol and Weston, Bristol, UK
| | - Ingrid J Scurr
- Department of Clinical Genetics, University Hospitals Bristol and Weston, Bristol, UK
| | - Julia Baptista
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK.,College of Medicine and Health, University of Exeter, Exeter, UK
| | - Anirban Majumdar
- Department of Paediatric Neurology, Bristol Royal Hospital for Children, Bristol, UK
| | - Germaine Pierre
- Department of Paediatric Metabolic Medicine, Bristol Royal Hospital for Children, Bristol, UK
| | - Maggie Williams
- Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | | | | | | | - Lisette Leeuwen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marleen E H Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mary Beth P Dinulos
- Section of Genetics and Child Development, Children's Hospital at Dartmouth, Lebanon, NH, USA
| | - Julie D Kaplan
- Division of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Anne McRae
- Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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22
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Muir AM, Gardner JF, van Jaarsveld RH, de Lange IM, van der Smagt JJ, Wilson GN, Dubbs H, Goldberg EM, Zitano L, Bupp C, Martinez J, Srour M, Accogli A, Alhakeem A, Meltzer M, Gropman A, Brewer C, Caswell RC, Montgomery T, McKenna C, McKee S, Powell C, Vasudevan PC, Brady AF, Joss S, Tysoe C, Noh G, Tarnopolsky M, Brady L, Zafar M, Schrier Vergano SA, Murray B, Sawyer L, Hainline BE, Sapp K, DeMarzo D, Huismann DJ, Wentzensen IM, Schnur RE, Monaghan KG, Juusola J, Rhodes L, Dobyns WB, Lecoquierre F, Goldenberg A, Polster T, Axer-Schaefer S, Platzer K, Klöckner C, Hoffman TL, MacArthur DG, O'Leary MC, VanNoy GE, England E, Varghese VC, Mefford HC. Variants in GNAI1 cause a syndrome associated with variable features including developmental delay, seizures, and hypotonia. Genet Med 2021; 23:881-887. [PMID: 33473207 PMCID: PMC8107131 DOI: 10.1038/s41436-020-01076-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 09/25/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Neurodevelopmental disorders (NDDs) encompass a spectrum of genetically heterogeneous disorders with features that commonly include developmental delay, intellectual disability, and autism spectrum disorders. We sought to delineate the molecular and phenotypic spectrum of a novel neurodevelopmental disorder caused by variants in the GNAI1 gene. METHODS Through large cohort trio-based exome sequencing and international data-sharing, we identified 24 unrelated individuals with NDD phenotypes and a variant in GNAI1, which encodes the inhibitory Gαi1 subunit of heterotrimeric G-proteins. We collected detailed genotype and phenotype information for each affected individual. RESULTS We identified 16 unique variants in GNAI1 in 24 affected individuals; 23 occurred de novo and 1 was inherited from a mosaic parent. Most affected individuals have a severe neurodevelopmental disorder. Core features include global developmental delay, intellectual disability, hypotonia, and epilepsy. CONCLUSION This collaboration establishes GNAI1 variants as a cause of NDDs. GNAI1-related NDD is most often characterized by severe to profound delays, hypotonia, epilepsy that ranges from self-limiting to intractable, behavior problems, and variable mild dysmorphic features.
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Affiliation(s)
- Alison M Muir
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA
| | | | | | - Iris M de Lange
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Golder N Wilson
- Texas Tech Health Science Center, Lubbock and KinderGenome Medical Genetics, Dallas, TX, USA
| | - Holly Dubbs
- Department of Pediatrics, Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ethan M Goldberg
- Department of Pediatrics, Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lia Zitano
- Spectrum Health Medical Genetics, Grand Rapids, MI, USA
| | - Caleb Bupp
- Spectrum Health Medical Genetics, Grand Rapids, MI, USA
| | - Jose Martinez
- Department of Pediatrics and Adolescent Medicine, Division of Genetics, University of South Alabama, Mobile, AL, USA
| | - Myriam Srour
- Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre, Montreal, QC, USA
| | - Andrea Accogli
- Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre, Montreal, QC, USA
| | - Afnan Alhakeem
- Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre, Montreal, QC, USA
| | - Meira Meltzer
- Department of Neurology, Children's National Hospital, Washington, DC, USA
| | - Andrea Gropman
- Department of Neurology, Children's National Hospital, Washington, DC, USA
| | - Carole Brewer
- Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Richard C Caswell
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK.,Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Tara Montgomery
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Washington, USA
| | | | - Shane McKee
- Northern Ireland Regional Genetics Service, Exeter, UK
| | - Corinna Powell
- University Hospitals of Leicester NHS Trust Leicester Royal Infirmary Leicester, Exeter, UK
| | - Pradeep C Vasudevan
- University Hospitals of Leicester NHS Trust Leicester Royal Infirmary Leicester, Exeter, UK
| | - Angela F Brady
- North West Thames Regional Genetics Service, Northwick Park and St. Mark's Hospitals, Harrow, UK
| | | | - Carolyn Tysoe
- Royal Devon and Exeter NHS Foundation Trust, Scotland, UK
| | - Grace Noh
- Department of Genetics, Southern California Kaiser Permanente Medical Group, Pasadena, CA, USA
| | - Mark Tarnopolsky
- Department of Pediatrics, Division of Neuromuscular and Neurometabolic Disorders, McMaster Children's Hospital, Hamilton, ON, Canada
| | - Lauren Brady
- Department of Pediatrics, Division of Neuromuscular and Neurometabolic Disorders, McMaster Children's Hospital, Hamilton, ON, Canada
| | | | | | - Brianna Murray
- Children's Hospital of The King's Daughters, Norfolk, Virginia, USA
| | - Lindsey Sawyer
- Children's Hospital of The King's Daughters, Norfolk, Virginia, USA
| | - Bryan E Hainline
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Katherine Sapp
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Danielle DeMarzo
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Darcy J Huismann
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | | | | | | | | | | | - William B Dobyns
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA.,Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, USA
| | - Francois Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Alice Goldenberg
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Tilman Polster
- Paediatric Epileptology Krankenhaus Mara Bethel Epilepsy Centre Bielefeld, Bielefeld, Germany
| | - Susanne Axer-Schaefer
- Paediatric Epileptology Krankenhaus Mara Bethel Epilepsy Centre Bielefeld, Bielefeld, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Chiara Klöckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Trevor L Hoffman
- Department of Genetics, Southern California Kaiser Permanente Medical Group, Pasadena, CA, USA
| | - Daniel G MacArthur
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Centre for Population Genomics, Garvan Institute of Medical Research, and University of New South Wales Sydney, Sydney, Australia.,Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Melanie C O'Leary
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace E VanNoy
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eleina England
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA.
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23
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Schmidt L, Wain KE, Hajek C, Estrada-Veras JI, Guillen Sacoto MJ, Wentzensen IM, Malhotra A, Clause A, Perry D, Moreno-De-Luca A, Bell M. Expanding the Phenotype of TUBB2A-Related Tubulinopathy: Three Cases of a Novel, Heterozygous TUBB2A Pathogenic Variant p.Gly98Arg. Mol Syndromol 2020; 12:33-40. [PMID: 33776625 DOI: 10.1159/000512160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/08/2020] [Indexed: 01/22/2023] Open
Abstract
Tubulinopathies are a group of conditions caused by variants in 6 tubulin genes that present with a spectrum of brain malformations. One of these conditions is TUBB2A-related tubulinopathy. Currently, there are 9 reported individuals with pathogenic variants within the TUBB2A gene, with common manifestations including, but not limited to, global developmental delay, seizures, cortical dysplasia, and dysmorphic corpus callosum. We report 3 patients identified by exome and genome sequencing to have a novel, pathogenic, missense variant in TUBB2A (p.Gly98Arg). They presented similarly with intellectual disability, hypotonia, and global developmental delay and varied with respect to the type of cortical brain malformation, seizure history, diagnosis of autism spectrum disorder, and other features. This case series expands the natural history of TUBB2A-related tubulinopathy while describing the presentation of a novel, pathogenic, missense variant in 3 patients.
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Affiliation(s)
- Lindsey Schmidt
- Sanford Health, Augustana-Sanford Genetic Counseling Program, Sioux Falls, South Dakota, USA
| | - Karen E Wain
- Geisinger Autism & Developmental Medicine Institute, Lewisburg, Pennsylvania, USA
| | | | - Juvianee I Estrada-Veras
- Henry M Jackson Foundation for the Advancement of Military Medicine and Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | | | | | - Alka Malhotra
- Illumina Clinical Services Laboratory, San Diego, California, USA
| | - Amanda Clause
- Illumina Clinical Services Laboratory, San Diego, California, USA
| | - Denise Perry
- Illumina Clinical Services Laboratory, San Diego, California, USA
| | - Andres Moreno-De-Luca
- Department of Radiology, Geisinger Autism & Developmental Medicine Institute, Genomic Medicine Institute, Lewisburg, Pennsylvania, USA
| | - Megan Bell
- Sanford Health, Sioux Falls, South Dakota, USA
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24
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Brunet T, McWalter K, Mayerhanser K, Anbouba GM, Armstrong-Javors A, Bader I, Baugh E, Begtrup A, Bupp CP, Callewaert BL, Cereda A, Cousin MA, Del Rey Jimenez JC, Demmer L, Dsouza NR, Fleischer N, Gavrilova RH, Ghate S, Graf E, Green A, Green SR, Iascone M, Kdissa A, Klee D, Klee EW, Lancaster E, Lindstrom K, Mayr JA, McEntagart M, Meeks NJL, Mittag D, Moore H, Olsen AK, Ortiz D, Parsons G, Pena LDM, Person RE, Punj S, Ramos-Rivera GA, Sacoto MJG, Bradley Schaefer G, Schnur RE, Scott TM, Scott DA, Serbinski CR, Shashi V, Siu VM, Stadheim BF, Sullivan JA, Švantnerová J, Velsher L, Wargowski DS, Wentzensen IM, Wieczorek D, Winkelmann J, Yap P, Zech M, Zimmermann MT, Meitinger T, Distelmaier F, Wagner M. Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder. Genet Med 2020; 23:384-395. [PMID: 33173220 PMCID: PMC7862064 DOI: 10.1038/s41436-020-00993-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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/23/2020] [Indexed: 12/01/2022] Open
Abstract
Purpose We sought to delineate the genotypic and phenotypic spectrum of female and male individuals with X-linked, MSL3-related disorder (Basilicata–Akhtar syndrome). Methods Twenty-five individuals (15 males, 10 females) with causative variants in MSL3 were ascertained through exome or genome sequencing at ten different sequencing centers. Results We identified multiple variant types in MSL3 (ten nonsense, six frameshift, four splice site, three missense, one in-frame-deletion, one multi-exon deletion), most proven to be de novo, and clustering in the terminal eight exons suggesting that truncating variants in the first five exons might be compensated by an alternative MSL3 transcript. Three-dimensional modeling of missense and splice variants indicated that these have a deleterious effect. The main clinical findings comprised developmental delay and intellectual disability ranging from mild to severe. Autism spectrum disorder, muscle tone abnormalities, and macrocephaly were common as well as hearing impairment and gastrointestinal problems. Hypoplasia of the cerebellar vermis emerged as a consistent magnetic resonance image (MRI) finding. Females and males were equally affected. Using facial analysis technology, a recognizable facial gestalt was determined. Conclusion Our aggregated data illustrate the genotypic and phenotypic spectrum of X-linked, MSL3-related disorder (Basilicata–Akhtar syndrome). Our cohort improves the understanding of disease related morbidity and allows us to propose detailed surveillance guidelines for affected individuals.
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Affiliation(s)
- Theresa Brunet
- Institute of Human Genetics, Technical University Munich, Munich, Germany.
| | | | | | - Grace M Anbouba
- Division of Genetics and Metabolism, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Amy Armstrong-Javors
- Department of Pediatric Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Ingrid Bader
- Department of Clinical Genetics, University Children's Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Evan Baugh
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | | | - Caleb P Bupp
- Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, MI, USA.,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Bert L Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Anna Cereda
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Laurie Demmer
- Medical Genetics, Atrium Health Levine Children's Hospital, Charlotte, NC, USA
| | - Nikita R Dsouza
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Ralitza H Gavrilova
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Sumedha Ghate
- St Vincent Hospital Medical Genetics Clinic, Green Bay, WI, USA
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Andrew Green
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Sarah R Green
- University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Springdale, AR, USA
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | | | - Dirk Klee
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Emily Lancaster
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Johannes A Mayr
- Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University, Salzburg, Austria
| | - Meriel McEntagart
- Medical Genetics, St George's University Hospitals NHS FT, London, UK
| | - Naomi J L Meeks
- Department of Pediatrics, Section of Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dana Mittag
- Medical Genetics, Atrium Health Levine Children's Hospital, Charlotte, NC, USA
| | - Harrison Moore
- INTEGRIS Pediatric Specialties/Medical Genetics, Oklahoma City, OK, USA
| | - Anne K Olsen
- Department of Pediatric, Soerlandet Sykehus Kristiansand, Kristiansand, Norway
| | - Damara Ortiz
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Gretchen Parsons
- Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Loren D M Pena
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | | | | | | | - G Bradley Schaefer
- University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Springdale, AR, USA
| | | | - Tiana M Scott
- Texas Children's Hospital, Houston, TX, USA.,Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Daryl A Scott
- Texas Children's Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Carolyn R Serbinski
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - Victoria M Siu
- Department of Pediatrics, Western University, London, ON, Canada
| | | | - Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - Jana Švantnerová
- Second Department of Neurology, Faculty of Medicine, Comenius University, University Hospital Bratislava, Bratislava, Slovakia
| | - Lea Velsher
- Genetics Program, North York General Hospital, Toronto, ON, Canada
| | - David S Wargowski
- Division of Genetics and Metabolism, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,St Vincent Hospital Medical Genetics Clinic, Green Bay, WI, USA
| | | | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,Neurogenetics, Technische Universität München, Munich, Germany
| | - Patrick Yap
- Genetic Health Service New Zealand (Northern Hub), Auckland, New Zealand.,Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Michael Zech
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Thomas Meitinger
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Matias Wagner
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
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25
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Guo H, Zhang Q, Dai R, Yu B, Hoekzema K, Tan J, Tan S, Jia X, Chung WK, Hernan R, Alkuraya FS, Alsulaiman A, Al-Muhaizea MA, Lesca G, Pons L, Labalme A, Laux L, Bryant E, Brown NJ, Savva E, Ayres S, Eratne D, Peeters H, Bilan F, Letienne-Cejudo L, Gilbert-Dussardier B, Ruiz-Arana IL, Merlini JM, Boizot A, Bartoloni L, Santoni F, Karlowicz D, McDonald M, Wu H, Hu Z, Chen G, Ou J, Brasch-Andersen C, Fagerberg CR, Dreyer I, Chun-Hui Tsai A, Slegesky V, McGee RB, Daniels B, Sellars EA, Carpenter LA, Schaefer B, Sacoto MJG, Begtrup A, Schnur RE, Punj S, Wentzensen IM, Rhodes L, Pan Q, Bernier RA, Chen C, Eichler EE, Xia K. NCKAP1 Disruptive Variants Lead to a Neurodevelopmental Disorder with Core Features of Autism. Am J Hum Genet 2020; 107:963-976. [PMID: 33157009 PMCID: PMC7674997 DOI: 10.1016/j.ajhg.2020.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 07/31/2020] [Accepted: 10/12/2020] [Indexed: 12/27/2022] Open
Abstract
NCKAP1/NAP1 regulates neuronal cytoskeletal dynamics and is essential for neuronal differentiation in the developing brain. Deleterious variants in NCKAP1 have been identified in individuals with autism spectrum disorder (ASD) and intellectual disability; however, its clinical significance remains unclear. To determine its significance, we assemble genotype and phenotype data for 21 affected individuals from 20 unrelated families with predicted deleterious variants in NCKAP1. This includes 16 individuals with de novo (n = 8), transmitted (n = 6), or inheritance unknown (n = 2) truncating variants, two individuals with structural variants, and three with potentially disruptive de novo missense variants. We report a de novo and ultra-rare deleterious variant burden of NCKAP1 in individuals with neurodevelopmental disorders which needs further replication. ASD or autistic features, language and motor delay, and variable expression of intellectual or learning disability are common clinical features. Among inherited cases, there is evidence of deleterious variants segregating with neuropsychiatric disorders. Based on available human brain transcriptomic data, we show that NCKAP1 is broadly and highly expressed in both prenatal and postnatal periods and demostrate enriched expression in excitatory neurons and radial glias but depleted expression in inhibitory neurons. Mouse in utero electroporation experiments reveal that Nckap1 loss of function promotes neuronal migration during early cortical development. Combined, these data support a role for disruptive NCKAP1 variants in neurodevelopmental delay/autism, possibly by interfering with neuronal migration early in cortical development.
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Affiliation(s)
- Hui Guo
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
| | - Qiumeng Zhang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Rujia Dai
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China; Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Bin Yu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jieqiong Tan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Senwei Tan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Xiangbin Jia
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University, New York, NY 10027, USA
| | - Rebecca Hernan
- Department of Pediatrics and Medicine, Columbia University, New York, NY 10027, USA
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Ahood Alsulaiman
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Mohammad A Al-Muhaizea
- Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University Hospital, Lyon 69000, France
| | - Linda Pons
- Department of Medical Genetics, Lyon University Hospital, Lyon 69000, France
| | - Audrey Labalme
- Department of Medical Genetics, Lyon University Hospital, Lyon 69000, France
| | - Linda Laux
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Emily Bryant
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Natasha J Brown
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3010, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
| | - Elena Savva
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3010, Australia
| | - Samantha Ayres
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia; Melbourne Genomics Health Alliance, Melbourne, VIC 3010, Australia
| | - Dhamidhu Eratne
- Melbourne Genomics Health Alliance, Melbourne, VIC 3010, Australia; Neuropsychiatry, Royal Melbourne Hospital, Melbourne, VIC 3010, Australia
| | - Hilde Peeters
- Centre for Human Genetics, KU Leuven and Leuven Autism Research (LAuRes), Leuven 3000, Belgium
| | - Frédéric Bilan
- Service de Génétique, CHU de Poitiers, Poitiers 86000, France
| | | | | | - Inge-Lore Ruiz-Arana
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Jenny Meylan Merlini
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Alexia Boizot
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Lucia Bartoloni
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Federico Santoni
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland; Faculty of Biology and Medicine, University of Lausanne, Lausanne 1005, Switzerland
| | - Danielle Karlowicz
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
| | - Marie McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
| | - Huidan Wu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Zhengmao Hu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Guodong Chen
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Jianjun Ou
- Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, Hunan 410078, China
| | | | | | - Inken Dreyer
- Department of Pediatrics, Hospital Sønderjylland, Aabenraa 6200, Denmark
| | - Anne Chun-Hui Tsai
- Department of Pediatrics/Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma, OK 73019, USA; Section of Genetics and Metabolism, Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, Aurora, CO 80045, USA
| | - Valerie Slegesky
- Section of Genetics and Metabolism, Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, Aurora, CO 80045, USA
| | - Rose B McGee
- Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brina Daniels
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR 72701, USA
| | - Elizabeth A Sellars
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR 72701, USA
| | - Lori A Carpenter
- Saint Francis Health System, Inc. St Francis Health Systems, Tulsa, OK 74101, USA
| | | | | | | | | | | | | | | | - Qian Pan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Raphael A Bernier
- Department of Psychiatry, University of Washington, Seattle, WA 98195, USA
| | - Chao Chen
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Kun Xia
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China; Hunan Key Laboratory of Animal Models for Human Diseases, Changsha, Hunan 410078, China; CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Chinese Academy of Sciences, Shanghai 200000, China.
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26
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Connaughton DM, Dai R, Owen DJ, Marquez J, Mann N, Graham-Paquin AL, Nakayama M, Coyaud E, Laurent EMN, St-Germain JR, Blok LS, Vino A, Klämbt V, Deutsch K, Wu CHW, Kolvenbach CM, Kause F, Ottlewski I, Schneider R, Kitzler TM, Majmundar AJ, Buerger F, Onuchic-Whitford AC, Youying M, Kolb A, Salmanullah D, Chen E, van der Ven AT, Rao J, Ityel H, Seltzsam S, Rieke JM, Chen J, Vivante A, Hwang DY, Kohl S, Dworschak GC, Hermle T, Alders M, Bartolomaeus T, Bauer SB, Baum MA, Brilstra EH, Challman TD, Zyskind J, Costin CE, Dipple KM, Duijkers FA, Ferguson M, Fitzpatrick DR, Fick R, Glass IA, Hulick PJ, Kline AD, Krey I, Kumar S, Lu W, Marco EJ, Wentzensen IM, Mefford HC, Platzer K, Povolotskaya IS, Savatt JM, Shcherbakova NV, Senguttuvan P, Squire AE, Stein DR, Thiffault I, Voinova VY, Somers MJG, Ferguson MA, Traum AZ, Daouk GH, Daga A, Rodig NM, Terhal PA, van Binsbergen E, Eid LA, Tasic V, Rasouly HM, Lim TY, Ahram DF, Gharavi AG, Reutter HM, Rehm HL, MacArthur DG, Lek M, Laricchia KM, Lifton RP, Xu H, Mane SM, Sanna-Cherchi S, Sharrocks AD, Raught B, Fisher SE, Bouchard M, Khokha MK, Shril S, Hildebrandt F. Mutations of the Transcriptional Corepressor ZMYM2 Cause Syndromic Urinary Tract Malformations. Am J Hum Genet 2020; 107:727-742. [PMID: 32891193 PMCID: PMC7536580 DOI: 10.1016/j.ajhg.2020.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 04/02/2020] [Accepted: 08/14/2020] [Indexed: 01/10/2023] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) constitute one of the most frequent birth defects and represent the most common cause of chronic kidney disease in the first three decades of life. Despite the discovery of dozens of monogenic causes of CAKUT, most pathogenic pathways remain elusive. We performed whole-exome sequencing (WES) in 551 individuals with CAKUT and identified a heterozygous de novo stop-gain variant in ZMYM2 in two different families with CAKUT. Through collaboration, we identified in total 14 different heterozygous loss-of-function mutations in ZMYM2 in 15 unrelated families. Most mutations occurred de novo, indicating possible interference with reproductive function. Human disease features are replicated in X. tropicalis larvae with morpholino knockdowns, in which expression of truncated ZMYM2 proteins, based on individual mutations, failed to rescue renal and craniofacial defects. Moreover, heterozygous Zmym2-deficient mice recapitulated features of CAKUT with high penetrance. The ZMYM2 protein is a component of a transcriptional corepressor complex recently linked to the silencing of developmentally regulated endogenous retrovirus elements. Using protein-protein interaction assays, we show that ZMYM2 interacts with additional epigenetic silencing complexes, as well as confirming that it binds to FOXP1, a transcription factor that has also been linked to CAKUT. In summary, our findings establish that loss-of-function mutations of ZMYM2, and potentially that of other proteins in its interactome, as causes of human CAKUT, offering new routes for studying the pathogenesis of the disorder.
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Affiliation(s)
- Dervla M Connaughton
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Nephrology, Department of Medicine, University Hospital - London Health Sciences Centre, Schulich School of Medicine & Dentistry, Western University, 339 Windermere Road, London, ON N6A 5A5, Canada
| | - Rufeng Dai
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Nephrology, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Danielle J Owen
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Jonathan Marquez
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nina Mann
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Adda L Graham-Paquin
- Rosalind & Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montréal, QC H3A 1A3, Canada
| | - Makiko Nakayama
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Estelle M N Laurent
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Jonathan R St-Germain
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Lot Snijders Blok
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500HE Nijmegen, the Netherlands; Human Genetics Department, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Arianna Vino
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands
| | - Verena Klämbt
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Konstantin Deutsch
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chen-Han Wilfred Wu
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Caroline M Kolvenbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Franziska Kause
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Isabel Ottlewski
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ronen Schneider
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas M Kitzler
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amar J Majmundar
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Florian Buerger
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ana C Onuchic-Whitford
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mao Youying
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amy Kolb
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daanya Salmanullah
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Evan Chen
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amelie T van der Ven
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jia Rao
- Department of Nephrology, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Hadas Ityel
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Steve Seltzsam
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Johanna M Rieke
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jing Chen
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Asaf Vivante
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Tel Aviv University, Faculty of Medicine, Tel Aviv-Yafo 6997801, Israel
| | - Daw-Yang Hwang
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stefan Kohl
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gabriel C Dworschak
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Tobias Hermle
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mariëlle Alders
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Meibergdreef 9, 1105 Amsterdam, Netherlands
| | - Tobias Bartolomaeus
- Institute of Human Genetics, University of Leipzig Medical Center, Philipp-Rosenthal- Straße 55, 04103 Leipzig, Germany
| | - Stuart B Bauer
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle A Baum
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eva H Brilstra
- Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Thomas D Challman
- Geisinger, Autism & Developmental Medicine Institute, 100 N Academy Avenue, Danville, PA 17822, USA
| | - Jacob Zyskind
- Department of Clinical Genomics, GeneDx, 207 Perry Pkwy, Gaithersburg, MD 20877, USA
| | - Carrie E Costin
- Department of Clinical Genetics, Akron Children's Hospital, One Perkins Square, Akron, OH 44308, USA
| | - Katrina M Dipple
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Floor A Duijkers
- Department of Clinical Genetics, University of Amsterdam, 1012 WX Amsterdam, the Netherlands
| | - Marcia Ferguson
- Department of Clinical Genetics, Harvey Institute for Human Genetics, 6701 Charles St, Towson, MD 21204, USA
| | - David R Fitzpatrick
- MRC Institute of Genetics & Molecular Medicine, Royal Hospital for Sick Children, The University of Edinburgh, 2XU, Crewe Rd S, Edinburgh EH4 2XU, UK
| | - Roger Fick
- Mary Bridge Childrens Hospital, 316 Martin Luther King JR Way, Tacoma, WA 98405, USA
| | - Ian A Glass
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, 1000 Central Street, Suite 610, Evanston, IL 60201, USA
| | - Antonie D Kline
- Department of Clinical Genetics, Harvey Institute for Human Genetics, 6701 Charles St, Towson, MD 21204, USA
| | - Ilona Krey
- Institute of Human Genetics, University of Leipzig Medical Center, Philipp-Rosenthal- Straße 55, 04103 Leipzig, Germany; Swiss Epilepsy Center, Klinik Lengg, Bleulerstrasse 60, 8000 Zürich, Switzerland
| | - Selvin Kumar
- Department of Pediatric Nephrology, Institute of Child Health and Hospital for Children, Tamil Salai, Egmore, Chennai, Tamil Nadu 600008, India
| | - Weining Lu
- Renal Section, Department of Medicine, Boston University Medical Center, 650 Albany Street, Boston, MA 02118, USA
| | - Elysa J Marco
- Cortica Healthcare, 4000 Civic Center Drive, Ste 100, San Rafael, CA 94939, USA
| | - Ingrid M Wentzensen
- Department of Clinical Genomics, GeneDx, 207 Perry Pkwy, Gaithersburg, MD 20877, USA
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Philipp-Rosenthal- Straße 55, 04103 Leipzig, Germany
| | - Inna S Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow 117997, Russia
| | - Juliann M Savatt
- Geisinger, Autism & Developmental Medicine Institute, 100 N Academy Avenue, Danville, PA 17822, USA
| | - Natalia V Shcherbakova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow 117997, Russia
| | - Prabha Senguttuvan
- Department of Pediatric Nephrology, Dr. Mehta's Multi-Specialty Hospital, No.2, Mc Nichols Rd, Chetpet, Chennai, Tamil Nadu 600031, India
| | - Audrey E Squire
- Seattle Children's Hospital, Department of Genetic Medicine, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Deborah R Stein
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, 2401 Gillham Rd, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO 64108, USA; University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, 5000 Holmes St, Kansas City, MO 64110, USA
| | - Victoria Y Voinova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow 117997, Russia
| | - Michael J G Somers
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael A Ferguson
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Avram Z Traum
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ghaleb H Daouk
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ankana Daga
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nancy M Rodig
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Paulien A Terhal
- Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Loai A Eid
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje 1000, North Macedonia
| | - Hila Milo Rasouly
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Tze Y Lim
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Dina F Ahram
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Ali G Gharavi
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Heiko M Reutter
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany; Section of Neonatology and Pediatric Intensive Care, Clinic for Pediatrics, University Hospital Bonn, Adenauerallee 119, 53313 Bonn, Germany
| | - Heidi L Rehm
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Kristen M Laricchia
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Richard P Lifton
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Hong Xu
- Department of Nephrology, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06510, USA
| | - Simone Sanna-Cherchi
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500HE Nijmegen, the Netherlands
| | - Maxime Bouchard
- Rosalind & Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montréal, QC H3A 1A3, Canada
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shirlee Shril
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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27
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Motta M, Pannone L, Pantaleoni F, Bocchinfuso G, Radio FC, Cecchetti S, Ciolfi A, Di Rocco M, Elting MW, Brilstra EH, Boni S, Mazzanti L, Tamburrino F, Walsh L, Payne K, Fernández-Jaén A, Ganapathi M, Chung WK, Grange DK, Dave-Wala A, Reshmi SC, Bartholomew DW, Mouhlas D, Carpentieri G, Bruselles A, Pizzi S, Bellacchio E, Piceci-Sparascio F, Lißewski C, Brinkmann J, Waclaw RR, Waisfisz Q, van Gassen K, Wentzensen IM, Morrow MM, Álvarez S, Martínez-García M, De Luca A, Memo L, Zampino G, Rossi C, Seri M, Gelb BD, Zenker M, Dallapiccola B, Stella L, Prada CE, Martinelli S, Flex E, Tartaglia M. Enhanced MAPK1 Function Causes a Neurodevelopmental Disorder within the RASopathy Clinical Spectrum. Am J Hum Genet 2020; 107:499-513. [PMID: 32721402 DOI: 10.1016/j.ajhg.2020.06.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/24/2020] [Indexed: 12/23/2022] Open
Abstract
Signal transduction through the RAF-MEK-ERK pathway, the first described mitogen-associated protein kinase (MAPK) cascade, mediates multiple cellular processes and participates in early and late developmental programs. Aberrant signaling through this cascade contributes to oncogenesis and underlies the RASopathies, a family of cancer-prone disorders. Here, we report that de novo missense variants in MAPK1, encoding the mitogen-activated protein kinase 1 (i.e., extracellular signal-regulated protein kinase 2, ERK2), cause a neurodevelopmental disease within the RASopathy phenotypic spectrum, reminiscent of Noonan syndrome in some subjects. Pathogenic variants promote increased phosphorylation of the kinase, which enhances translocation to the nucleus and boosts MAPK signaling in vitro and in vivo. Two variant classes are identified, one of which directly disrupts binding to MKP3, a dual-specificity protein phosphatase negatively regulating ERK function. Importantly, signal dysregulation driven by pathogenic MAPK1 variants is stimulus reliant and retains dependence on MEK activity. Our data support a model in which the identified pathogenic variants operate with counteracting effects on MAPK1 function by differentially impacting the ability of the kinase to interact with regulators and substrates, which likely explains the minor role of these variants as driver events contributing to oncogenesis. After nearly 20 years from the discovery of the first gene implicated in Noonan syndrome, PTPN11, the last tier of the MAPK cascade joins the group of genes mutated in RASopathies.
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28
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Mak CCY, Doherty D, Lin AE, Vegas N, Cho MT, Viot G, Dimartino C, Weisfeld-Adams JD, Lessel D, Joss S, Li C, Gonzaga-Jauregui C, Zarate YA, Ehmke N, Horn D, Troyer C, Kant SG, Lee Y, Ishak GE, Leung G, Barone Pritchard A, Yang S, Bend EG, Filippini F, Roadhouse C, Lebrun N, Mehaffey MG, Martin PM, Apple B, Millan F, Puk O, Hoffer MJV, Henderson LB, McGowan R, Wentzensen IM, Pei S, Zahir FR, Yu M, Gibson WT, Seman A, Steeves M, Murrell JR, Luettgen S, Francisco E, Strom TM, Amlie-Wolf L, Kaindl AM, Wilson WG, Halbach S, Basel-Salmon L, Lev-El N, Denecke J, Vissers LELM, Radtke K, Chelly J, Zackai E, Friedman JM, Bamshad MJ, Nickerson DA, Reid RR, Devriendt K, Chae JH, Stolerman E, McDougall C, Powis Z, Bienvenu T, Tan TY, Orenstein N, Dobyns WB, Shieh JT, Choi M, Waggoner D, Gripp KW, Parker MJ, Stoler J, Lyonnet S, Cormier-Daire V, Viskochil D, Hoffman TL, Amiel J, Chung BHY, Gordon CT. MN1 C-terminal truncation syndrome is a novel neurodevelopmental and craniofacial disorder with partial rhombencephalosynapsis. Brain 2020; 143:55-68. [PMID: 31834374 DOI: 10.1093/brain/awz379] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/02/2019] [Accepted: 10/15/2019] [Indexed: 11/12/2022] Open
Abstract
MN1 encodes a transcriptional co-regulator without homology to other proteins, previously implicated in acute myeloid leukaemia and development of the palate. Large deletions encompassing MN1 have been reported in individuals with variable neurodevelopmental anomalies and non-specific facial features. We identified a cluster of de novo truncating mutations in MN1 in a cohort of 23 individuals with strikingly similar dysmorphic facial features, especially midface hypoplasia, and intellectual disability with severe expressive language delay. Imaging revealed an atypical form of rhombencephalosynapsis, a distinctive brain malformation characterized by partial or complete loss of the cerebellar vermis with fusion of the cerebellar hemispheres, in 8/10 individuals. Rhombencephalosynapsis has no previously known definitive genetic or environmental causes. Other frequent features included perisylvian polymicrogyria, abnormal posterior clinoid processes and persistent trigeminal artery. MN1 is encoded by only two exons. All mutations, including the recurrent variant p.Arg1295* observed in 8/21 probands, fall in the terminal exon or the extreme 3' region of exon 1, and are therefore predicted to result in escape from nonsense-mediated mRNA decay. This was confirmed in fibroblasts from three individuals. We propose that the condition described here, MN1 C-terminal truncation (MCTT) syndrome, is not due to MN1 haploinsufficiency but rather is the result of dominantly acting C-terminally truncated MN1 protein. Our data show that MN1 plays a critical role in human craniofacial and brain development, and opens the door to understanding the biological mechanisms underlying rhombencephalosynapsis.
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Affiliation(s)
- Christopher C Y Mak
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Angela E Lin
- Medical Genetics, MassGeneral Hospital for Children, Boston, MA, USA
| | - Nancy Vegas
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | | | - Géraldine Viot
- Gynécologie Obstétrique, Hôpital Cochin, Hôpitaux Universitaires Paris Centre (HUPC), Assistance Publique Hôpitaux de Paris (AP-HP), Paris, France
| | - Clémantine Dimartino
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - James D Weisfeld-Adams
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado-Denver School of Medicine, Aurora, CO, USA
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shelagh Joss
- West of Scotland Regional Genetics Service, Queen Elizabeth University Hospital, Glasgow, UK
| | - Chumei Li
- McMaster University Medical Center, Hamilton, Ontario, Canada
| | | | - Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Little Rock, AR, USA
| | - Nadja Ehmke
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Denise Horn
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Caitlin Troyer
- Pediatrics and Medical Genetics, University of Virginia Health System, Charlottesville, VA, USA
| | - Sarina G Kant
- Department of Clinical Genetics, Leiden University Medical Center, RC Leiden, The Netherlands
| | - Youngha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Gisele E Ishak
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Radiology, University of Washington, Seattle, WA, USA
| | - Gordon Leung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | | | | | - Eric G Bend
- Greenwood Genetic Center, Greenwood, SC, USA.,PreventionGenetics, Marshfield, WI, USA
| | - Francesca Filippini
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | | | - Nicolas Lebrun
- Institut Cochin, INSERM U1016, CNRS UMR, Paris Descartes University, Paris, France
| | | | - Pierre-Marie Martin
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Benjamin Apple
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado-Denver School of Medicine, Aurora, CO, USA
| | | | - Oliver Puk
- Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Mariette J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, RC Leiden, The Netherlands
| | | | - Ruth McGowan
- West of Scotland Regional Genetics Service, Queen Elizabeth University Hospital, Glasgow, UK
| | | | - Steven Pei
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Farah R Zahir
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Mullin Yu
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Ann Seman
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Marcie Steeves
- Medical Genetics, MassGeneral Hospital for Children, Boston, MA, USA
| | - Jill R Murrell
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sabine Luettgen
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Louise Amlie-Wolf
- Division of Medical Genetics, A I duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Angela M Kaindl
- Charité - Universitätsmedizin Berlin, Institute of Neuroanatomy and Cell Biology, Department of Pediatric Neurology and Center for Chronically Sick Children, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - William G Wilson
- Pediatrics and Medical Genetics, University of Virginia Health System, Charlottesville, VA, USA
| | - Sara Halbach
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Lina Basel-Salmon
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel.,Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Noa Lev-El
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, HB Nijmegen, The Netherlands
| | - Kelly Radtke
- Clinical Genomics Department, Ambry Genetics, Aliso Viejo, CA, USA
| | - Jamel Chelly
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Nouvel Hôpital Civil, Strasbourg, France.,Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, 67000 Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA.,University of Washington Center for Mendelian Genomics, Seattle, WA, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,University of Washington Center for Mendelian Genomics, Seattle, WA, USA
| | | | - Russell R Reid
- Department of Surgery, Section of Plastic Surgery, University of Chicago, Chicago, IL, USA
| | - Koenraad Devriendt
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | - Carey McDougall
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zöe Powis
- Clinical Genomics Department, Ambry Genetics, Aliso Viejo, CA, USA
| | - Thierry Bienvenu
- Institut Cochin, INSERM U1016, CNRS UMR, Paris Descartes University, Paris, France.,Laboratoire de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, AP-HP, 75014 Paris, France
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Department of Paediatrics, University of Melbourne, Melbourne, 3052, Australia
| | - Naama Orenstein
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - William B Dobyns
- Department of Pediatrics, University of Washington, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Neurology, University of Washington, Seattle, WA, USA
| | - Joseph T Shieh
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Darrel Waggoner
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Karen W Gripp
- Division of Medical Genetics, A I duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Sheffield S10 2TH, UK
| | - Joan Stoler
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Valérie Cormier-Daire
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France.,Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, Institut Imagine, 75015 Paris, France
| | - David Viskochil
- Division of Medical Genetics, University of Utah, Salt Lake City, UT, USA
| | - Trevor L Hoffman
- Southern California Kaiser Permanente Medical Group, Anaheim, CA, USA
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
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29
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Manole A, Efthymiou S, O'Connor E, Mendes MI, Jennings M, Maroofian R, Davagnanam I, Mankad K, Lopez MR, Salpietro V, Harripaul R, Badalato L, Walia J, Francklyn CS, Athanasiou-Fragkouli A, Sullivan R, Desai S, Baranano K, Zafar F, Rana N, Ilyas M, Horga A, Kara M, Mattioli F, Goldenberg A, Griffin H, Piton A, Henderson LB, Kara B, Aslanger AD, Raaphorst J, Pfundt R, Portier R, Shinawi M, Kirby A, Christensen KM, Wang L, Rosti RO, Paracha SA, Sarwar MT, Jenkins D, Ahmed J, Santoni FA, Ranza E, Iwaszkiewicz J, Cytrynbaum C, Weksberg R, Wentzensen IM, Guillen Sacoto MJ, Si Y, Telegrafi A, Andrews MV, Baldridge D, Gabriel H, Mohr J, Oehl-Jaschkowitz B, Debard S, Senger B, Fischer F, van Ravenwaaij C, Fock AJM, Stevens SJC, Bähler J, Nasar A, Mantovani JF, Manzur A, Sarkozy A, Smith DEC, Salomons GS, Ahmed ZM, Riazuddin S, Riazuddin S, Usmani MA, Seibt A, Ansar M, Antonarakis SE, Vincent JB, Ayub M, Grimmel M, Jelsig AM, Hjortshøj TD, Karstensen HG, Hummel M, Haack TB, Jamshidi Y, Distelmaier F, Horvath R, Gleeson JG, Becker H, Mandel JL, Koolen DA, Houlden H. De Novo and Bi-allelic Pathogenic Variants in NARS1 Cause Neurodevelopmental Delay Due to Toxic Gain-of-Function and Partial Loss-of-Function Effects. Am J Hum Genet 2020; 107:311-324. [PMID: 32738225 PMCID: PMC7413890 DOI: 10.1016/j.ajhg.2020.06.016] [Citation(s) in RCA: 24] [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: 02/25/2020] [Accepted: 06/23/2020] [Indexed: 12/19/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are ubiquitous, ancient enzymes that charge amino acids to cognate tRNA molecules, the essential first step of protein translation. Here, we describe 32 individuals from 21 families, presenting with microcephaly, neurodevelopmental delay, seizures, peripheral neuropathy, and ataxia, with de novo heterozygous and bi-allelic mutations in asparaginyl-tRNA synthetase (NARS1). We demonstrate a reduction in NARS1 mRNA expression as well as in NARS1 enzyme levels and activity in both individual fibroblasts and induced neural progenitor cells (iNPCs). Molecular modeling of the recessive c.1633C>T (p.Arg545Cys) variant shows weaker spatial positioning and tRNA selectivity. We conclude that de novo and bi-allelic mutations in NARS1 are a significant cause of neurodevelopmental disease, where the mechanism for de novo variants could be toxic gain-of-function and for recessive variants, partial loss-of-function.
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Affiliation(s)
- Andreea Manole
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Emer O'Connor
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Marisa I Mendes
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam Gastroenterology and Metabolism, Amsterdam, 1081 the Netherlands
| | - Matthew Jennings
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Indran Davagnanam
- Department of Brain Repair and Rehabilitation, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Kshitij Mankad
- Department of Neuroradiology, Great Ormond Street Hospital for Children, London, WC1N 3JH, UK
| | - Maria Rodriguez Lopez
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London (UCL), London, WC1E 6BT, UK
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Ricardo Harripaul
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, ON, M5T 1R8, Canada; Institute of Medical Science and Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Lauren Badalato
- Department of Pediatrics, Queen's University, Kingston, ON, K7L 2V7, Canada
| | - Jagdeep Walia
- Department of Pediatrics, Queen's University, Kingston, ON, K7L 2V7, Canada
| | - Christopher S Francklyn
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Alkyoni Athanasiou-Fragkouli
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Roisin Sullivan
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Sonal Desai
- Department of Neurology and Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Kristin Baranano
- Department of Neurology and Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Faisal Zafar
- Department of Pediatrics, Multan Hospital, Multan, 60000, Pakistan
| | - Nuzhat Rana
- Department of Pediatrics, Multan Hospital, Multan, 60000, Pakistan
| | | | - Alejandro Horga
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Majdi Kara
- Department of Pediatrics, Tripoli Children's Hospital, Tripoli, Libya
| | - Francesca Mattioli
- Institute for Genetics and Molecular and Cellular Biology (IGBMC), University of Strasbourg, CNRS UMR7104, INSERM U1258, Illkirch, 67404, France
| | - Alice Goldenberg
- Département de Génétique, centre de référence anomalies du développement et syndromes malformatifs, CHU de Rouen, Inserm U1245, UNIROUEN, Normandie Université, Centre Normand de Génomique et de Médecine Personnalisée, Rouen, 76031, France
| | - Helen Griffin
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Amelie Piton
- Institute for Genetics and Molecular and Cellular Biology (IGBMC), University of Strasbourg, CNRS UMR7104, INSERM U1258, Illkirch, 67404, France
| | | | | | | | - Joost Raaphorst
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Department of Neurology, Amsterdam Neuroscience Institute, Amsterdam University Medical Center, 1105AZ Amsterdam, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Ruben Portier
- Department of Neurology, Medisch Spectrum Twente, 7512KZ Enschede, the Netherlands
| | - Marwan Shinawi
- Department of Pediatrics, Divisions of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Amelia Kirby
- Division of Medical Genetics, SSM Health Cardinal Glennon Children's Hospital, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Katherine M Christensen
- Division of Medical Genetics, SSM Health Cardinal Glennon Children's Hospital, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Lu Wang
- Howard Hughes Medical Institute, University of California San Diego and Rady Children's Hospital, La Jolla, CA 92130, USA
| | - Rasim O Rosti
- Howard Hughes Medical Institute, University of California San Diego and Rady Children's Hospital, La Jolla, CA 92130, USA
| | - Sohail A Paracha
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Muhammad T Sarwar
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Dagan Jenkins
- Institute of Child Health, Guilford Street and Dubowitz Neuromuscular Centre, Great Ormond Street Hospital for Children, London, WC1N 3JH, UK
| | - Jawad Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Department of Endocrinology, Diabetes, and Metabolism, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland; Medigenome, The Swiss Institute of Genomic Medicine, Geneva, CH-1207, Switzerland
| | - Justyna Iwaszkiewicz
- Swiss Institute of Bioinformatics, Molecular Modeling Group, Batiment Genopode, Unil Sorge, Lausanne, CH-1015, Switzerland
| | - Cheryl Cytrynbaum
- Hospital for Sick Children, Division of Clinical and Metabolic Genetics, 555 University Ave., Toronto, M5G 1X8, Canada
| | - Rosanna Weksberg
- Hospital for Sick Children, Division of Clinical and Metabolic Genetics, 555 University Ave., Toronto, M5G 1X8, Canada
| | | | | | - Yue Si
- GeneDx, 207 Perry Parkway Gaithersburg, MD 20877, USA
| | | | - Marisa V Andrews
- Department of Pediatrics, Divisions of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Dustin Baldridge
- Department of Pediatrics, Divisions of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Heinz Gabriel
- CeGaT GmbH and Praxis für Humangenetik Tuebingen, Tuebingen, 72076, Germany
| | - Julia Mohr
- CeGaT GmbH and Praxis für Humangenetik Tuebingen, Tuebingen, 72076, Germany
| | | | - Sylvain Debard
- University of Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, 67083, France
| | - Bruno Senger
- University of Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, 67083, France
| | - Frédéric Fischer
- University of Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, 67083, France
| | - Conny van Ravenwaaij
- University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, 9713, the Netherlands
| | - Annemarie J M Fock
- University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, 9713, the Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, 6211, the Netherlands
| | - Jürg Bähler
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London (UCL), London, WC1E 6BT, UK
| | - Amina Nasar
- Department of Pediatrics, Queen's University, Kingston, ON, K7L 2V7, Canada
| | - John F Mantovani
- Division of Child Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Adnan Manzur
- Institute of Child Health, Guilford Street and Dubowitz Neuromuscular Centre, Great Ormond Street Hospital for Children, London, WC1N 3JH, UK
| | - Anna Sarkozy
- Institute of Child Health, Guilford Street and Dubowitz Neuromuscular Centre, Great Ormond Street Hospital for Children, London, WC1N 3JH, UK
| | - Desirée E C Smith
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam Gastroenterology and Metabolism, Amsterdam, 1081 the Netherlands
| | - Gajja S Salomons
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam Gastroenterology and Metabolism, Amsterdam, 1081 the Netherlands
| | - Zubair M Ahmed
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Shaikh Riazuddin
- Jinnah Burn and Reconstructive Surgery Center, Allama Iqbal Medical College, University of Health Sciences, Lahore 54550, Pakistan
| | - Saima Riazuddin
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Muhammad A Usmani
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Annette Seibt
- Department of General Pediatrics, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Institute of Molecular and Clinical Ophthalmology Basel, Basel Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland; iGE3 Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland
| | - John B Vincent
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, ON, M5T 1R8, Canada; Institute of Medical Science and Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Muhammad Ayub
- Department of Pediatrics, Queen's University, Kingston, ON, K7L 2V7, Canada
| | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany
| | - Anne Marie Jelsig
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, 2100, Denmark
| | - Tina Duelund Hjortshøj
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, 2100, Denmark
| | - Helena Gásdal Karstensen
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, 2100, Denmark
| | - Marybeth Hummel
- Department of Pediatrics, Section of Medical Genetics, West Virginia University, Morgantown, WV 26506-9600, USA
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany; Centre for Rare Diseases, University of Tuebingen, 72076 Tübingen, Germany
| | - Yalda Jamshidi
- Genetics Centre, Molecular and Clinical Sciences Institute, St George's University of London, London, SW17 0RE, UK
| | - Felix Distelmaier
- Department of General Pediatrics, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Joseph G Gleeson
- Howard Hughes Medical Institute, University of California San Diego and Rady Children's Hospital, La Jolla, CA 92130, USA
| | - Hubert Becker
- University of Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, 67083, France
| | - Jean-Louis Mandel
- Institute for Genetics and Molecular and Cellular Biology (IGBMC), University of Strasbourg, CNRS UMR7104, INSERM U1258, Illkirch, 67404, France
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Henry Houlden
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
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30
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Rabin R, Radmanesh A, Glass IA, Dobyns WB, Aldinger KA, Shieh JT, Romoser S, Bombei H, Dowsett L, Trapane P, Bernat JA, Baker J, Mendelsohn NJ, Popp B, Siekmeyer M, Sorge I, Sansbury FH, Watts P, Foulds NC, Burton J, Hoganson G, Hurst JA, Menzies L, Osio D, Kerecuk L, Cobben JM, Jizi K, Jacquemont S, Bélanger SA, Löhner K, Veenstra-Knol HE, Lemmink HH, Keller-Ramey J, Wentzensen IM, Punj S, McWalter K, Lenberg J, Ellsworth KA, Radtke K, Akbarian S, Pappas J. Genotype-phenotype correlation at codon 1740 of SETD2. Am J Med Genet A 2020; 182:2037-2048. [PMID: 32710489 DOI: 10.1002/ajmg.a.61724] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 10/24/2019] [Revised: 03/10/2020] [Accepted: 05/08/2020] [Indexed: 11/06/2022]
Abstract
The SET domain containing 2, histone lysine methyltransferase encoded by SETD2 is a dual-function methyltransferase for histones and microtubules and plays an important role for transcriptional regulation, genomic stability, and cytoskeletal functions. Specifically, SETD2 is associated with trimethylation of histone H3 at lysine 36 (H3K36me3) and methylation of α-tubulin at lysine 40. Heterozygous loss of function and missense variants have previously been described with Luscan-Lumish syndrome (LLS), which is characterized by overgrowth, neurodevelopmental features, and absence of overt congenital anomalies. We have identified 15 individuals with de novo variants in codon 1740 of SETD2 whose features differ from those with LLS. Group 1 consists of 12 individuals with heterozygous variant c.5218C>T p.(Arg1740Trp) and Group 2 consists of 3 individuals with heterozygous variant c.5219G>A p.(Arg1740Gln). The phenotype of Group 1 includes microcephaly, profound intellectual disability, congenital anomalies affecting several organ systems, and similar facial features. Individuals in Group 2 had moderate to severe intellectual disability, low normal head circumference, and absence of additional major congenital anomalies. While LLS is likely due to loss of function of SETD2, the clinical features seen in individuals with variants affecting codon 1740 are more severe suggesting an alternative mechanism, such as gain of function, effects on epigenetic regulation, or posttranslational modification of the cytoskeleton. Our report is a prime example of different mutations in the same gene causing diverging phenotypes and the features observed in Group 1 suggest a new clinically recognizable syndrome uniquely associated with the heterozygous variant c.5218C>T p.(Arg1740Trp) in SETD2.
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Affiliation(s)
- Rachel Rabin
- Clinical Genetic Services, Department of Pediatrics, NYU School of Medicine, New York, New York, USA
| | - Alireza Radmanesh
- Division of Pediatric Neuroradiology, Department of Radiology, NYU School of Medicine, New York, New York, USA
| | - Ian A Glass
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - William B Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, Division of Medical Genetics, University of Washington, Seattle, Washington, USA.,Department of Neurology, University of Washington, Seattle, Washington, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Joseph T Shieh
- Institute for Human Genetics, Division of Medical Genetics, Department of Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, California, USA
| | - Shelby Romoser
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals, Iowa City, Iowa, USA
| | - Hannah Bombei
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals, Iowa City, Iowa, USA
| | - Leah Dowsett
- Kapi'olani Medical Specialists and Department of Pediatrics, University of Hawai'i John A. Burns School of Medicine, Honolulu, Hawaii, USA
| | - Pamela Trapane
- Division of Pediatric Genetics, Department of Pediatrics, University of Florida College of Medicine-Jacksonville, Jacksonville, Florida, USA
| | - John A Bernat
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals, Iowa City, Iowa, USA
| | - Janice Baker
- Genomic Medicine, Children's Minnesota, Minneapolis, Minnesota, USA
| | | | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Manuela Siekmeyer
- Department of Pediatrics Hospital for Children and Adolescents, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Ina Sorge
- Department of Pediatric Radiology, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Francis Hugh Sansbury
- All Wales Medical Genomics Service, Institute of Medical Genetics, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - Patrick Watts
- Department of Ophthalmology, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - Nicola C Foulds
- Wessex Clinical Genetics Services, Southampton University Hospital NHS Foundation Trust, Southampton, UK
| | - Jennifer Burton
- University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - George Hoganson
- University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - Jane A Hurst
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Lara Menzies
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Deborah Osio
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Larissa Kerecuk
- Renal Department, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Jan M Cobben
- North West Thames Regional Genetic Services, Northwick Park Hospitals NHS Foundation Trust, London, UK.,Emma Children Hospital, Amsterdam, The Netherlands
| | - Khadijé Jizi
- CHU Sainte-Justine Hospital, Montreal, Quebec, Canada
| | - Sebastien Jacquemont
- CHU Sainte-Justine Research Centre, Montreal, Quebec, Canada.,Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Stacey A Bélanger
- Development Clinic, CHU Sainte-Justine Hospital, Montreal, Quebec, Canada.,Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Katharina Löhner
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Hermine E Veenstra-Knol
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Henny H Lemmink
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | | | | | | | | | - Jerica Lenberg
- Rady Children's Hospital Institute for Genomic Medicine, San Diego, California, USA
| | | | - Kelly Radtke
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California, USA
| | - Schahram Akbarian
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John Pappas
- Clinical Genetic Services, Department of Pediatrics, NYU School of Medicine, New York, New York, USA.,Clinical Genetics, NYU Orthopedic Hospital, New York, New York, USA
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31
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Lindsay F, Anderson I, Wentzensen IM, Suhrbier D, Stevens CA. Genetic evaluation including exome sequencing of two patients with Gomez-Lopez-Hernandez syndrome: Case reports and review of the literature. Am J Med Genet A 2020; 182:623-627. [PMID: 32003537 DOI: 10.1002/ajmg.a.61496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 08/31/2019] [Revised: 01/04/2020] [Accepted: 01/12/2020] [Indexed: 11/06/2022]
Abstract
Rhombencephalosynapsis (RES) is a rare congenital anomaly of the hindbrain characterized by fusion of the cerebellar hemispheres, cerebellar peduncles, and dentate nuclei with vermian absence or hypogenesis. This anomaly can be isolated or part of a larger spectrum of cerebral abnormalities. At least 90 cases are described in the literature and it has been associated with VACTERL and Gomez-Lopez-Hernandez syndrome (GLHS). The most common congenital syndrome associated with RES is GLHS, a rare presumed genetic disorder with over 30 cases thus far described in the literature. No genetic cause has been identified for RES or GLHS. We report two probands diagnosed with GLHS based on clinical criteria. Each proband had RES and bi-parietal scalp alopecia as well as neurologic findings and phenotypic features including trigeminal anesthesia, borderline hypertelorism, midface retrusion, and motor delay. Oliginucleotide-SNP microarray on the male proband revealed a 1.05 Mb copy duplication of uncertain clinical significance at 15q21.3 while oligonucleotide-SNP microarray for the female proband did not reveal any abnormalities. Exome sequencing (ES) was performed on both patients and did not identify any variants that could explain the GLHS phenotype. To our knowledge, these are the first two patients with GLHS described in the literature to undergo ES. Both patients had mild neurologic manifestations requiring physical therapy in early life without known diagnostic cause. Patients found to have scalp alopecia or trigeminal anesthesia with gross motor delay should be evaluated for RES or GLHS as well as screened for associated syndromes and have a complete neurodevelopmental evaluation.
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Affiliation(s)
- Faith Lindsay
- Department of Pediatrics, University of Tennessee College of Medicine, Chattanooga, Tennessee
| | - Ilse Anderson
- Division of Medical Genetics, Department of Medicine, University of Tennessee College of Medicine, Knoxville, Tennessee
| | | | - David Suhrbier
- Department of Pediatrics, University of Tennessee College of Medicine, Chattanooga, Tennessee
| | - Cathy A Stevens
- Department of Pediatrics, University of Tennessee College of Medicine, Chattanooga, Tennessee
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32
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Assoum M, Bruel AL, Crenshaw ML, Delanne J, Wentzensen IM, McWalter K, Dent KM, Vitobello A, Kuentz P, Thevenon J, Duffourd Y, Thauvin-Robinet C, Faivre L. Novel KIAA1033/WASHC4 mutations in three patients with syndromic intellectual disability and a review of the literature. Am J Med Genet A 2020; 182:792-797. [PMID: 31953988 DOI: 10.1002/ajmg.a.61487] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/13/2019] [Accepted: 12/12/2019] [Indexed: 11/09/2022]
Abstract
In 2011, KIAA1033/WASHC4 was associated with autosomal recessive intellectual disability (ARID) in a large consanguineous family comprising seven affected individuals with moderate ID and short stature. Since then, no other cases of KIAA1033 variants have been reported. Here we describe three additional patients (from two unrelated families) with syndromic ID due to compound heterozygous KIAA1033 variants ascertained by exome sequencing (ES). Two sisters, aged 4 and 5.5 years, had a stop-gain and a missense variants, each inherited from one parent (p.(Gln442*) and p.(Asp1048Gly)). Both had learning disabilities, macrocephaly, dysmorphic features, skeletal anomalies, and subependymal heterotopic nodules. In addition, the younger sibling had a congenital absence of the right internal carotid and bilateral sensorineural hearing loss. The third patient was aged 34 years and had two missense variants, one inherited from each parent (p.(Lys1079Arg) and p.(His503Arg)). This patient presented with mild ID, short stature, and microcephaly. KIAA1033 encodes a large protein (WASHC4), which is part of the WASH complex. The WASH complex is involved in the regulation of the fission of tubules that serve as transport intermediates during endosome sorting. Another member of the WASH complex, KIAA0196/WASHC5, has already been implicated in ARID with brain and cardiac malformations, under the designation of 3C or Ritscher-Schinzel syndrome (MIM#20210). ES has proved efficient for finding replications of genes with insufficient data in the literature to be defined as new OMIM genes. We conclude that KIAA1033 is responsible for a heterogeneous ARID phenotype, and additional description will be needed to refine the clinical phenotype.
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Affiliation(s)
- Mirna Assoum
- UMR-Inserm 1231 GAD team, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France
| | - Ange-Line Bruel
- UMR-Inserm 1231 GAD team, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France.,Laboratoire de Génétique chromosomique et moléculaire, UF Innovation en diagnostic génomique des maladies rares, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Melissa L Crenshaw
- Division of Genetics, Johns Hopkins All Children's Hospital, Johns Hopkins University School of Medicine, St. Petersburg, Florida
| | - Julian Delanne
- UMR-Inserm 1231 GAD team, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
| | | | | | - Karin M Dent
- Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Antonio Vitobello
- UMR-Inserm 1231 GAD team, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France.,Laboratoire de Génétique chromosomique et moléculaire, UF Innovation en diagnostic génomique des maladies rares, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Paul Kuentz
- UMR-Inserm 1231 GAD team, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France.,Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Julien Thevenon
- UMR-Inserm 1231 GAD team, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Yannis Duffourd
- UMR-Inserm 1231 GAD team, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France.,Laboratoire de Génétique chromosomique et moléculaire, UF Innovation en diagnostic génomique des maladies rares, Centre Hospitalier Universitaire de Dijon, Dijon, France.,Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Christel Thauvin-Robinet
- UMR-Inserm 1231 GAD team, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France.,Laboratoire de Génétique chromosomique et moléculaire, UF Innovation en diagnostic génomique des maladies rares, Centre Hospitalier Universitaire de Dijon, Dijon, France.,Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Laurence Faivre
- UMR-Inserm 1231 GAD team, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France.,Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
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33
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Balak C, Benard M, Schaefer E, Iqbal S, Ramsey K, Ernoult-Lange M, Mattioli F, Llaci L, Geoffroy V, Courel M, Naymik M, Bachman KK, Pfundt R, Rump P, Ter Beest J, Wentzensen IM, Monaghan KG, McWalter K, Richholt R, Le Béchec A, Jepsen W, De Both M, Belnap N, Boland A, Piras IS, Deleuze JF, Szelinger S, Dollfus H, Chelly J, Muller J, Campbell A, Lal D, Rangasamy S, Mandel JL, Narayanan V, Huentelman M, Weil D, Piton A. Rare De Novo Missense Variants in RNA Helicase DDX6 Cause Intellectual Disability and Dysmorphic Features and Lead to P-Body Defects and RNA Dysregulation. Am J Hum Genet 2019; 105:509-525. [PMID: 31422817 PMCID: PMC6731366 DOI: 10.1016/j.ajhg.2019.07.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/17/2019] [Indexed: 01/13/2023] Open
Abstract
The human RNA helicase DDX6 is an essential component of membrane-less organelles called processing bodies (PBs). PBs are involved in mRNA metabolic processes including translational repression via coordinated storage of mRNAs. Previous studies in human cell lines have implicated altered DDX6 in molecular and cellular dysfunction, but clinical consequences and pathogenesis in humans have yet to be described. Here, we report the identification of five rare de novo missense variants in DDX6 in probands presenting with intellectual disability, developmental delay, and similar dysmorphic features including telecanthus, epicanthus, arched eyebrows, and low-set ears. All five missense variants (p.His372Arg, p.Arg373Gln, p.Cys390Arg, p.Thr391Ile, and p.Thr391Pro) are located in two conserved motifs of the RecA-2 domain of DDX6 involved in RNA binding, helicase activity, and protein-partner binding. We use functional studies to demonstrate that the first variants identified (p.Arg373Gln and p.Cys390Arg) cause significant defects in PB assembly in primary fibroblast and model human cell lines. These variants' interactions with several protein partners were also disrupted in immunoprecipitation assays. Further investigation via complementation assays included the additional variants p.Thr391Ile and p.Thr391Pro, both of which, similarly to p.Arg373Gln and p.Cys390Arg, demonstrated significant defects in P-body assembly. Complementing these molecular findings, modeling of the variants on solved protein structures showed distinct spatial clustering near known protein binding regions. Collectively, our clinical and molecular data describe a neurodevelopmental syndrome associated with pathogenic missense variants in DDX6. Additionally, we suggest DDX6 join the DExD/H-box genes DDX3X and DHX30 in an emerging class of neurodevelopmental disorders involving RNA helicases.
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Affiliation(s)
- Chris Balak
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA.
| | - Marianne Benard
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire de Biologie du Développement, F-75005 Paris, France
| | - Elise Schaefer
- Medical Genetics Department, University Hospitals of Strasbourg, the Institute of Medical Genetics of Alsace, 67000 Strasbourg, France; Laboratoire de Génétique Médicale, Institut de Génétique Médicale d'Alsace, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, 67081 Strasbourg, France
| | - Sumaiya Iqbal
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Keri Ramsey
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Michèle Ernoult-Lange
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire de Biologie du Développement, F-75005 Paris, France
| | - Francesca Mattioli
- Institute of Genetics and Molecular and Cellular Biology, Illkirch, France; French National Center for Scientific Research, UMR7104, 67400 Illkirch, France; National Institute of Health and Medical Research U964, 67400 Illkirch, France; University of Strasbourg, 67081 Illkirch, France
| | - Lorida Llaci
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Véronique Geoffroy
- Laboratoire de Génétique Médicale, Institut de Génétique Médicale d'Alsace, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, 67081 Strasbourg, France
| | - Maité Courel
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire de Biologie du Développement, F-75005 Paris, France
| | - Marcus Naymik
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | | | - Rolph Pfundt
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands
| | - Patrick Rump
- Radboud University Nijmegen Medical Center, Department of Human Genetics, Division of Genome Diagnostics, 6525 GA Nijmegen, the Netherlands
| | - Johanna Ter Beest
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands
| | | | | | | | - Ryan Richholt
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA
| | - Antony Le Béchec
- Medical Bioinformatics Unit, UF7363, Strasbourg University Hospital, 67000 Strasbourg, France
| | - Wayne Jepsen
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Matt De Both
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Newell Belnap
- Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, F-91057, Evry, France
| | - Ignazio S Piras
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, F-91057, Evry, France
| | - Szabolcs Szelinger
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Hélène Dollfus
- Medical Genetics Department, University Hospitals of Strasbourg, the Institute of Medical Genetics of Alsace, 67000 Strasbourg, France; Laboratoire de Génétique Médicale, Institut de Génétique Médicale d'Alsace, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, 67081 Strasbourg, France
| | - Jamel Chelly
- Institute of Genetics and Molecular and Cellular Biology, Illkirch, France; French National Center for Scientific Research, UMR7104, 67400 Illkirch, France; National Institute of Health and Medical Research U964, 67400 Illkirch, France; University of Strasbourg, 67081 Illkirch, France; Molecular Genetics Unit, Strasbourg University Hospital, 67000 Strasbourg, France
| | - Jean Muller
- Laboratoire de Génétique Médicale, Institut de Génétique Médicale d'Alsace, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, 67081 Strasbourg, France; Molecular Genetics Unit, Strasbourg University Hospital, 67000 Strasbourg, France
| | - Arthur Campbell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dennis Lal
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute Cleveland Clinic, Cleveland, OH 44195, USA; Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Sampathkumar Rangasamy
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Jean-Louis Mandel
- Institute of Genetics and Molecular and Cellular Biology, Illkirch, France; French National Center for Scientific Research, UMR7104, 67400 Illkirch, France; National Institute of Health and Medical Research U964, 67400 Illkirch, France; University of Strasbourg, 67081 Illkirch, France; University of Strasbourg Institute of Advanced Studies, 67081 Strasbourg, France
| | - Vinodh Narayanan
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Matt Huentelman
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA; Translational Genomics Research Institute's Center for Rare Childhood Disorders, Phoenix, AZ 85012, USA
| | - Dominique Weil
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire de Biologie du Développement, F-75005 Paris, France
| | - Amélie Piton
- Institute of Genetics and Molecular and Cellular Biology, Illkirch, France; French National Center for Scientific Research, UMR7104, 67400 Illkirch, France; National Institute of Health and Medical Research U964, 67400 Illkirch, France; University of Strasbourg, 67081 Illkirch, France; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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34
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O'Donnell-Luria AH, Pais LS, Faundes V, Wood JC, Sveden A, Luria V, Abou Jamra R, Accogli A, Amburgey K, Anderlid BM, Azzarello-Burri S, Basinger AA, Bianchini C, Bird LM, Buchert R, Carre W, Ceulemans S, Charles P, Cox H, Culliton L, Currò A, Demurger F, Dowling JJ, Duban-Bedu B, Dubourg C, Eiset SE, Escobar LF, Ferrarini A, Haack TB, Hashim M, Heide S, Helbig KL, Helbig I, Heredia R, Héron D, Isidor B, Jonasson AR, Joset P, Keren B, Kok F, Kroes HY, Lavillaureix A, Lu X, Maas SM, Maegawa GHB, Marcelis CLM, Mark PR, Masruha MR, McLaughlin HM, McWalter K, Melchinger EU, Mercimek-Andrews S, Nava C, Pendziwiat M, Person R, Ramelli GP, Ramos LLP, Rauch A, Reavey C, Renieri A, Rieß A, Sanchez-Valle A, Sattar S, Saunders C, Schwarz N, Smol T, Srour M, Steindl K, Syrbe S, Taylor JC, Telegrafi A, Thiffault I, Trauner DA, van der Linden H, van Koningsbruggen S, Villard L, Vogel I, Vogt J, Weber YG, Wentzensen IM, Widjaja E, Zak J, Baxter S, Banka S, Rodan LH. Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy. Am J Hum Genet 2019; 104:1210-1222. [PMID: 31079897 PMCID: PMC6556837 DOI: 10.1016/j.ajhg.2019.03.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 12/20/2018] [Accepted: 03/21/2019] [Indexed: 01/22/2023] Open
Abstract
We delineate a KMT2E-related neurodevelopmental disorder on the basis of 38 individuals in 36 families. This study includes 31 distinct heterozygous variants in KMT2E (28 ascertained from Matchmaker Exchange and three previously reported), and four individuals with chromosome 7q22.2-22.23 microdeletions encompassing KMT2E (one previously reported). Almost all variants occurred de novo, and most were truncating. Most affected individuals with protein-truncating variants presented with mild intellectual disability. One-quarter of individuals met criteria for autism. Additional common features include macrocephaly, hypotonia, functional gastrointestinal abnormalities, and a subtle facial gestalt. Epilepsy was present in about one-fifth of individuals with truncating variants and was responsive to treatment with anti-epileptic medications in almost all. More than 70% of the individuals were male, and expressivity was variable by sex; epilepsy was more common in females and autism more common in males. The four individuals with microdeletions encompassing KMT2E generally presented similarly to those with truncating variants, but the degree of developmental delay was greater. The group of four individuals with missense variants in KMT2E presented with the most severe developmental delays. Epilepsy was present in all individuals with missense variants, often manifesting as treatment-resistant infantile epileptic encephalopathy. Microcephaly was also common in this group. Haploinsufficiency versus gain-of-function or dominant-negative effects specific to these missense variants in KMT2E might explain this divergence in phenotype, but requires independent validation. Disruptive variants in KMT2E are an under-recognized cause of neurodevelopmental abnormalities.
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Affiliation(s)
- Anne H O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Lynn S Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Víctor Faundes
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Jordan C Wood
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Abigail Sveden
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Victor Luria
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
| | - Andrea Accogli
- Department of Pediatrics, Department of Neurology and Neurosurgery, McGill University, Montreal, QC H4A 3J1, Quebec, Canada; Dipartimento di Neuroscienze, Riabilitazione, Oftalmologia, Genetica Scienze Materno-Infantili, Università degli studi di Genova, 16126 Genova, Italy; IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Kimberly Amburgey
- Division of Neurology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto M5G 1X8, ON, Canada
| | - Britt Marie Anderlid
- Department of Molecular Medicine and Surgery, Centre for Molecular Medicine, Karolinska Institutet, Stockholm 17176, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Silvia Azzarello-Burri
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich CH-8952, Switzerland; Neuroscience Center Zurich, University of Zurich and Eidgenössische Technische Hochschule, Zurich 8057, Switzerland
| | - Alice A Basinger
- Genetics, Cook Children's Physician Network, Fort Worth, TX 76104, USA
| | - Claudia Bianchini
- Pediatric Neurology, Neurogenetics, and Neurobiology Unit and Laboratories, Neuroscience Department, Meyer Children's Hospital, University of Florence, 50139 Florence, Italy
| | - Lynne M Bird
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA; Division of Genetics, Rady Children's Hospital of San Diego, San Diego, CA 92123, USA
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen 72076, Germany
| | - Wilfrid Carre
- Laboratoire de Génétique Moléculaire et Génomique, Centre Hospitalier Universitaire de Rennes, Rennes 35033, France
| | - Sophia Ceulemans
- Division of Genetics, Rady Children's Hospital of San Diego, San Diego, CA 92123, USA
| | - Perrine Charles
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris 75013, France; Groupe de Recherche Clinique Déficience Intellectuelle et Autisme, Sorbonne University, Paris 75006, France
| | - Helen Cox
- West Midlands Regional Clinical Genetics Service, Birmingham Women's and Children's Hospital, National Health Service Foundation Trust, Birmingham B15 2TG, UK; Birmingham Health Partners, Birmingham Women's and Children's Hospital, National Health Service Foundation Trust, Birmingham B15 2TG, UK
| | - Lisa Culliton
- Department of Neurology, Children's Mercy Hospital and Clinics, Kansas City, MO 64108, USA
| | - Aurora Currò
- Medical Genetics, University of Siena, 53100 Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy
| | - Florence Demurger
- Service de Génétique Clinique, Centre de Référence Maladies Rares Centre Labellisé Anomalies du Développement-Ouest, Centre Hospitalier Universitaire de Rennes, 35033 Rennes, France
| | - James J Dowling
- Division of Neurology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto M5G 1X8, ON, Canada
| | - Benedicte Duban-Bedu
- Centre de Génétique Chromosomique, Groupement des Hôpitaux de l'Institut Catholique de Lille Hôpital Saint Vincent de Paul, 59020 Lille, France; Faculté de médecine de l'Université Catholoique de Lille, 59800 Lille, France
| | - Christèle Dubourg
- Laboratoire de Génétique Moléculaire et Génomique, Centre Hospitalier Universitaire de Rennes, Rennes 35033, France
| | - Saga Elise Eiset
- Department of Clinical Genetics, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Luis F Escobar
- St. Vincent's Children's Hospital, Indianapolis, IN 46260, USA
| | - Alessandra Ferrarini
- Medical Genetic Unit, Italian Hospital of Lugano, Lugano, Switzerland; Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen 72076, Germany
| | - Mona Hashim
- Oxford National Institute for Health Research Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Solveig Heide
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris 75013, France; Groupe de Recherche Clinique Déficience Intellectuelle et Autisme, Sorbonne University, Paris 75006, France
| | - Katherine L Helbig
- Division of Neurology and Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ingo Helbig
- Division of Neurology and Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA; Department of Neuropediatrics, University Medical Center, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | | | - Delphine Héron
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris 75013, France; Groupe de Recherche Clinique Déficience Intellectuelle et Autisme, Sorbonne University, Paris 75006, France
| | - Bertrand Isidor
- Service de Génétique Médicale, Hôpital Hôtel-Dieu, Centre Hospitalier Universitaire de Nantes, 44093 Nantes, France
| | - Amy R Jonasson
- Division of Genetics and Metabolism, Department of Pediatrics, University of Florida, FL 32610, USA
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich CH-8952, Switzerland; Neuroscience Center Zurich, University of Zurich and Eidgenössische Technische Hochschule, Zurich 8057, Switzerland
| | - Boris Keren
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris 75013, France; Groupe de Recherche Clinique Déficience Intellectuelle et Autisme, Sorbonne University, Paris 75006, France
| | - Fernando Kok
- Mendelics Genomic Analysis, Sao Paulo 04013, Brazil
| | - Hester Y Kroes
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands
| | - Alinoë Lavillaureix
- Service de Génétique Clinique, Centre de Référence Maladies Rares Centre Labellisé Anomalies du Développement-Ouest, Centre Hospitalier Universitaire de Rennes, 35033 Rennes, France
| | - Xin Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Saskia M Maas
- Department of Clinical Genetics, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Gustavo H B Maegawa
- Division of Genetics and Metabolism, Department of Pediatrics, University of Florida, FL 32610, USA
| | - Carlo L M Marcelis
- Department of Clinical Genetics, Radboud University Medical Centre, 6525 GA Nijmegen, the Netherlands
| | - Paul R Mark
- Division of Medical Genetics and Genomics, Spectrum Health, Grand Rapids, MI 49544, USA
| | - Marcelo R Masruha
- Department of Neurology and Neurosurgery, Universidade de Federal de São Paulo, São Paulo 04023, Brazil
| | | | | | - Esther U Melchinger
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen 72076, Germany
| | - Saadet Mercimek-Andrews
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Caroline Nava
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris 75013, France; Groupe de Recherche Clinique Déficience Intellectuelle et Autisme, Sorbonne University, Paris 75006, France
| | - Manuela Pendziwiat
- Department of Neuropediatrics, University Medical Center, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | | | - Gian Paolo Ramelli
- Neuropediatric Unit, Pediatric Department of Southern Switzerland, San Giovanni Hospital, 6500 Bellinzona, Switzerland
| | | | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich CH-8952, Switzerland; Neuroscience Center Zurich, University of Zurich and Eidgenössische Technische Hochschule, Zurich 8057, Switzerland; Rare Disease Initiative Zürich, Clinical Research Priority Program for Rare Diseases, University of Zurich, CH-8006 Zurich, Switzerland
| | | | - Alessandra Renieri
- Medical Genetics, University of Siena, 53100 Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy
| | - Angelika Rieß
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen 72076, Germany
| | - Amarilis Sanchez-Valle
- Department of Pediatrics, Division of Genetics and Metabolism, University of South Florida, Tampa, FL 33606, USA
| | - Shifteh Sattar
- Section of Pediatric Neurology, Rady Children's Hospital, San Diego, CA 92123, USA; Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Carol Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, Kansas City, MO 64108, USA; School of Medicine, University of Missouri, Kansas City, MO 64108, USA
| | - Niklas Schwarz
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | - Thomas Smol
- EA7364 Rares du Developpement Embryonnaire et du Metabolisme, Institut de Genetique Medicale, Centre Hospitalier Universitaire de Lille, University of Lille, F-59000 Lille, France
| | - Myriam Srour
- Department of Pediatrics, Department of Neurology and Neurosurgery, McGill University, Montreal, QC H4A 3J1, Quebec, Canada
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich CH-8952, Switzerland; Neuroscience Center Zurich, University of Zurich and Eidgenössische Technische Hochschule, Zurich 8057, Switzerland
| | - Steffen Syrbe
- Division of Child Neurology and Inherited Metabolic Diseases, Department of General Paediatrics, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Jenny C Taylor
- Oxford National Institute for Health Research Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | - Isabelle Thiffault
- School of Medicine, University of Missouri, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Hospital and Clinics, Kansas City, MO 64108, USA
| | - Doris A Trauner
- Section of Pediatric Neurology, Rady Children's Hospital, San Diego, CA 92123, USA; Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Helio van der Linden
- Pediatric Neurology and Neurophysiology, Instituto de Neurologia de Goiania, Goiania 74210, Brazil
| | - Silvana van Koningsbruggen
- Department of Clinical Genetics, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Laurent Villard
- Department of Medical Genetics, Assistance Publique - Hôpitaux de Marseille, Hôpital d'Enfants de La Timone, 13005 Marseille, France; Marseille Medical Genetics Center, Aix Marseille Univ, Inserm, U1251, Marseille, France
| | - Ida Vogel
- Department of Clinical Genetics, Aarhus University Hospital, 8200 Aarhus, Denmark; Center for Fetal Diagnostics, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Julie Vogt
- West Midlands Regional Clinical Genetics Service, Birmingham Women's and Children's Hospital, National Health Service Foundation Trust, Birmingham B15 2TG, UK; Birmingham Health Partners, Birmingham Women's and Children's Hospital, National Health Service Foundation Trust, Birmingham B15 2TG, UK
| | - Yvonne G Weber
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany; Department for Neurosurgery, University of Tübingen, 72076 Tübingen, Germany
| | | | - Elysa Widjaja
- Department of Diagnostic Imaging, Hospital for Sick Children, University of Toronto, Toronto, M5G 1X8, ON, Canada
| | - Jaroslav Zak
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Samantha Baxter
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, 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 National Health Service Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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35
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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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36
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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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37
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Bell S, Rousseau J, Peng H, Aouabed Z, Priam P, Theroux JF, Jefri M, Tanti A, Wu H, Kolobova I, Silviera H, Manzano-Vargas K, Ehresmann S, Hamdan FF, Hettige N, Zhang X, Antonyan L, Nassif C, Ghaloul-Gonzalez L, Sebastian J, Vockley J, Begtrup AG, Wentzensen IM, Crunk A, Nicholls RD, Herman KC, Deignan JL, Al-Hertani W, Efthymiou S, Salpietro V, Miyake N, Makita Y, Matsumoto N, Østern R, Houge G, Hafström M, Fassi E, Houlden H, Klein Wassink-Ruiter JS, Nelson D, Goldstein A, Dabir T, van Gils J, Bourgeron T, Delorme R, Cooper GM, Martinez JE, Finnila CR, Carmant L, Lortie A, Oegema R, van Gassen K, Mehta SG, Huhle D, Abou Jamra R, Martin S, Brunner HG, Lindhout D, Au M, Graham JM, Coubes C, Turecki G, Gravel S, Mechawar N, Rossignol E, Michaud JL, Lessard J, Ernst C, Campeau PM. Mutations in ACTL6B Cause Neurodevelopmental Deficits and Epilepsy and Lead to Loss of Dendrites in Human Neurons. Am J Hum Genet 2019; 104:815-834. [PMID: 31031012 PMCID: PMC6507050 DOI: 10.1016/j.ajhg.2019.03.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [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: 08/13/2018] [Accepted: 03/01/2019] [Indexed: 02/04/2023] Open
Abstract
We identified individuals with variations in ACTL6B, a component of the chromatin remodeling machinery including the BAF complex. Ten individuals harbored bi-allelic mutations and presented with global developmental delay, epileptic encephalopathy, and spasticity, and ten individuals with de novo heterozygous mutations displayed intellectual disability, ambulation deficits, severe language impairment, hypotonia, Rett-like stereotypies, and minor facial dysmorphisms (wide mouth, diastema, bulbous nose). Nine of these ten unrelated individuals had the identical de novo c.1027G>A (p.Gly343Arg) mutation. Human-derived neurons were generated that recaptured ACTL6B expression patterns in development from progenitor cell to post-mitotic neuron, validating the use of this model. Engineered knock-out of ACTL6B in wild-type human neurons resulted in profound deficits in dendrite development, a result recapitulated in two individuals with different bi-allelic mutations, and reversed on clonal genetic repair or exogenous expression of ACTL6B. Whole-transcriptome analyses and whole-genomic profiling of the BAF complex in wild-type and bi-allelic mutant ACTL6B neural progenitor cells and neurons revealed increased genomic binding of the BAF complex in ACTL6B mutants, with corresponding transcriptional changes in several genes including TPPP and FSCN1, suggesting that altered regulation of some cytoskeletal genes contribute to altered dendrite development. Assessment of bi-alleic and heterozygous ACTL6B mutations on an ACTL6B knock-out human background demonstrated that bi-allelic mutations mimic engineered deletion deficits while heterozygous mutations do not, suggesting that the former are loss of function and the latter are gain of function. These results reveal a role for ACTL6B in neurodevelopment and implicate another component of chromatin remodeling machinery in brain disease.
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Affiliation(s)
- Scott Bell
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Justine Rousseau
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Huashan Peng
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Zahia Aouabed
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Pierre Priam
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Jean-Francois Theroux
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Malvin Jefri
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Arnaud Tanti
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Hanrong Wu
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Ilaria Kolobova
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Heika Silviera
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Karla Manzano-Vargas
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Sophie Ehresmann
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Fadi F Hamdan
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Nuwan Hettige
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Xin Zhang
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Lilit Antonyan
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Christina Nassif
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Lina Ghaloul-Gonzalez
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Jessica Sebastian
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Jerry Vockley
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | | | | | | | - Robert D Nicholls
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Kristin C Herman
- University of California at Davis Medical Center, Section of Medical Genomics, Sacramento, CA 95817, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Walla Al-Hertani
- Departments of Medical Genetics and Paediatrics, Cumming School of Medicine, Alberta Children's Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Stephanie Efthymiou
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Vincenzo Salpietro
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yoshio Makita
- Education Center, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Rune Østern
- Department of Pediatrics, St. Olav's Hospital, Trondheim University Hospital, Postbox 3250, Sluppen 7006 Trondheim, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Maria Hafström
- Department of Pediatrics, St. Olav's Hospital, Trondheim University Hospital, Postbox 3250, Sluppen 7006 Trondheim, Norway
| | - Emily Fassi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Jolien S Klein Wassink-Ruiter
- Department of Genetics, University of Groningen and University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Dominic Nelson
- McGill University, Department of Human Genetics, Montreal, QC H3G 0B1, Canada
| | - Amy Goldstein
- Division of Child Neurology, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Tabib Dabir
- Northern Ireland Regional Genetics Centre, Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast BT9 7AB, UK
| | - Julien van Gils
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, University Paris Diderot, Paris 75015, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, University Paris Diderot, Paris 75015, France
| | - Richard Delorme
- Assistance Publique Hôpitaux de Paris (APHP), Robert Debré Hospital, Child and Adolescent Psychiatry Department, Paris, France
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - Lionel Carmant
- Children's Rehabilitation Service, Mobile, AL 36604, USA
| | - Anne Lortie
- Department of Neurology, University of Montreal, Montreal, QC, Canada
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Sarju G Mehta
- Department of Clinical Genetics, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Dagmar Huhle
- Department of Clinical Genetics, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Rami Abou Jamra
- Institute of Human Genetics, University Medical Center Leipzig, 04103 Leipzig, Germany
| | - Sonja Martin
- Institute of Human Genetics, University Medical Center Leipzig, 04103 Leipzig, Germany
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen 6500 GA, the Netherlands; Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ Maastricht, the Netherlands
| | - Dick Lindhout
- Department of Genetics, University Medical Center Utrecht, Utrecht & Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, the Netherlands
| | - Margaret Au
- Medical Genetics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - John M Graham
- Medical Genetics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Christine Coubes
- Service de génétique clinique, Département de génétique médicale, Maladies rares et médecine personnalisée, Centre de Référence Anomalies du développement et Syndromes malformatifs du Sud-Ouest Occitanie Réunion, CHU de Montpellier, 34295 Montpellier Cedex 5, France
| | - Gustavo Turecki
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Simon Gravel
- Department of Genetics, University of Groningen and University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Naguib Mechawar
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Elsa Rossignol
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Jacques L Michaud
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Julie Lessard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Carl Ernst
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada.
| | - Philippe M Campeau
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada.
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Hiatt SM, Thompson ML, Prokop JW, Lawlor JMJ, Gray DE, Bebin EM, Rinne T, Kempers M, Pfundt R, van Bon BW, Mignot C, Nava C, Depienne C, Kalsner L, Rauch A, Joset P, Bachmann-Gagescu R, Wentzensen IM, McWalter K, Cooper GM. Deleterious Variation in BRSK2 Associates with a Neurodevelopmental Disorder. Am J Hum Genet 2019; 104:701-708. [PMID: 30879638 PMCID: PMC6451696 DOI: 10.1016/j.ajhg.2019.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 11/28/2018] [Accepted: 02/01/2019] [Indexed: 01/08/2023] Open
Abstract
Developmental delay and intellectual disability (DD and ID) are heterogeneous phenotypes that arise in many rare monogenic disorders. Because of this rarity, developing cohorts with enough individuals to robustly identify disease-associated genes is challenging. Social-media platforms that facilitate data sharing among sequencing labs can help to address this challenge. Through one such tool, GeneMatcher, we identified nine DD- and/or ID-affected probands with a rare, heterozygous variant in the gene encoding the serine/threonine-protein kinase BRSK2. All probands have a speech delay, and most present with intellectual disability, motor delay, behavioral issues, and autism. Six of the nine variants are predicted to result in loss of function, and computational modeling predicts that the remaining three missense variants are damaging to BRSK2 structure and function. All nine variants are absent from large variant databases, and BRSK2 is, in general, relatively intolerant to protein-altering variation among humans. In all six probands for whom parents were available, the mutations were found to have arisen de novo. Five of these de novo variants were from cohorts with at least 400 sequenced probands; collectively, the cohorts span 3,429 probands, and the observed rate of de novo variation in these cohorts is significantly higher than the estimated background-mutation rate (p = 2.46 × 10-6). We also find that exome sequencing provides lower coverage and appears less sensitive to rare variation in BRSK2 than does genome sequencing; this fact most likely reduces BRSK2's visibility in many clinical and research sequencing efforts. Altogether, our results implicate damaging variation in BRSK2 as a source of neurodevelopmental disease.
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Affiliation(s)
- Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Jeremy W Prokop
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824, USA
| | - James M J Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - David E Gray
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - E Martina Bebin
- Department of Neurology, University of Alabama Birmingham, Birmingham, AL 35294, USA
| | - Tuula Rinne
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Marlies Kempers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Bregje W van Bon
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Cyril Mignot
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris 75013, France; Centres de Référence Maladies Rares, Déficiences Intellectuelles de Causes Rares, Paris 75013, France; Groupes de Recherche Clinique Paris Sorbonne Déficience Intellectuelle et Autisme, Paris 75013, France
| | - Caroline Nava
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris 75013, France; Faculté de Médecine, Institut du Cerveau et de la Moelle épinière, Sorbonne Université, Paris 75013, France
| | - Christel Depienne
- Faculté de Médecine, Institut du Cerveau et de la Moelle épinière, Sorbonne Université, Paris 75013, France; Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen 45147, Germany
| | - Louisa Kalsner
- Connecticut Children's Medical Center, Farmington, CT 06032, USA
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren 8952, Switzerland; Radiz-Rare Disease Initiative Zurich, Clinical Research Priority Program, University of Zurich, Zurich 8032, Switzerland
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren 8952, Switzerland
| | | | | | | | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
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39
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Cogné B, Ehresmann S, Beauregard-Lacroix E, Rousseau J, Besnard T, Garcia T, Petrovski S, Avni S, McWalter K, Blackburn PR, Sanders SJ, Uguen K, Harris J, Cohen JS, Blyth M, Lehman A, Berg J, Li MH, Kini U, Joss S, von der Lippe C, Gordon CT, Humberson JB, Robak L, Scott DA, Sutton VR, Skraban CM, Johnston JJ, Poduri A, Nordenskjöld M, Shashi V, Gerkes EH, Bongers EM, Gilissen C, Zarate YA, Kvarnung M, Lally KP, Kulch PA, Daniels B, Hernandez-Garcia A, Stong N, McGaughran J, Retterer K, Tveten K, Sullivan J, Geisheker MR, Stray-Pedersen A, Tarpinian JM, Klee EW, Sapp JC, Zyskind J, Holla ØL, Bedoukian E, Filippini F, Guimier A, Picard A, Busk ØL, Punetha J, Pfundt R, Lindstrand A, Nordgren A, Kalb F, Desai M, Ebanks AH, Jhangiani SN, Dewan T, Coban Akdemir ZH, Telegrafi A, Zackai EH, Begtrup A, Song X, Toutain A, Wentzensen IM, Odent S, Bonneau D, Latypova X, Deb W, Redon S, Bilan F, Legendre M, Troyer C, Whitlock K, Caluseriu O, Murphree MI, Pichurin PN, Agre K, Gavrilova R, Rinne T, Park M, Shain C, Heinzen EL, Xiao R, Amiel J, Lyonnet S, Isidor B, Biesecker LG, Lowenstein D, Posey JE, Denommé-Pichon AS, Férec C, Yang XJ, Rosenfeld JA, Gilbert-Dussardier B, Audebert-Bellanger S, Redon R, Stessman HA, Nellaker C, Yang Y, Lupski JR, Goldstein DB, Eichler EE, Bolduc F, Bézieau S, Küry S, Campeau PM, Küry S, Campeau PM. Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability. Am J Hum Genet 2019; 104:530-541. [PMID: 30827496 DOI: 10.1016/j.ajhg.2019.01.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 07/16/2018] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
Acetylation of the lysine residues in histones and other DNA-binding proteins plays a major role in regulation of eukaryotic gene expression. This process is controlled by histone acetyltransferases (HATs/KATs) found in multiprotein complexes that are recruited to chromatin by the scaffolding subunit transformation/transcription domain-associated protein (TRRAP). TRRAP is evolutionarily conserved and is among the top five genes intolerant to missense variation. Through an international collaboration, 17 distinct de novo or apparently de novo variants were identified in TRRAP in 24 individuals. A strong genotype-phenotype correlation was observed with two distinct clinical spectra. The first is a complex, multi-systemic syndrome associated with various malformations of the brain, heart, kidneys, and genitourinary system and characterized by a wide range of intellectual functioning; a number of affected individuals have intellectual disability (ID) and markedly impaired basic life functions. Individuals with this phenotype had missense variants clustering around the c.3127G>A p.(Ala1043Thr) variant identified in five individuals. The second spectrum manifested with autism spectrum disorder (ASD) and/or ID and epilepsy. Facial dysmorphism was seen in both groups and included upslanted palpebral fissures, epicanthus, telecanthus, a wide nasal bridge and ridge, a broad and smooth philtrum, and a thin upper lip. RNA sequencing analysis of skin fibroblasts derived from affected individuals skin fibroblasts showed significant changes in the expression of several genes implicated in neuronal function and ion transport. Thus, we describe here the clinical spectrum associated with TRRAP pathogenic missense variants, and we suggest a genotype-phenotype correlation useful for clinical evaluation of the pathogenicity of the variants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Sébastien Küry
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France; INSERM, CNRS, UNIV Nantes, l'institut du thorax, 44007 Nantes, France.
| | - Philippe M Campeau
- Centre Hospitalier Universitaire Sainte-Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, University of Montreal, Montreal, QC H3T1J4, Canada.
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40
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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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41
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Carapito R, Ivanova EL, Morlon A, Meng L, Molitor A, Erdmann E, Kieffer B, Pichot A, Naegely L, Kolmer A, Paul N, Hanauer A, Tran Mau-Them F, Jean-Marçais N, Hiatt SM, Cooper GM, Tvrdik T, Muir AM, Dimartino C, Chopra M, Amiel J, Gordon CT, Dutreux F, Garde A, Thauvin-Robinet C, Wang X, Leduc MS, Phillips M, Crawford HP, Kukolich MK, Hunt D, Harrison V, Kharbanda M, Smigiel R, Gold N, Hung CY, Viskochil DH, Dugan SL, Bayrak-Toydemir P, Joly-Helas G, Guerrot AM, Schluth-Bolard C, Rio M, Wentzensen IM, McWalter K, Schnur RE, Lewis AM, Lalani SR, Mensah-Bonsu N, Céraline J, Sun Z, Ploski R, Bacino CA, Mefford HC, Faivre L, Bodamer O, Chelly J, Isidor B, Bahram S, Isidor B, Bahram S. ZMIZ1 Variants Cause a Syndromic Neurodevelopmental Disorder. Am J Hum Genet 2019; 104:319-330. [PMID: 30639322 DOI: 10.1016/j.ajhg.2018.12.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/10/2018] [Indexed: 12/01/2022] Open
Abstract
ZMIZ1 is a coactivator of several transcription factors, including p53, the androgen receptor, and NOTCH1. Here, we report 19 subjects with intellectual disability and developmental delay carrying variants in ZMIZ1. The associated features include growth failure, feeding difficulties, microcephaly, facial dysmorphism, and various other congenital malformations. Of these 19, 14 unrelated subjects carried de novo heterozygous single-nucleotide variants (SNVs) or single-base insertions/deletions, 3 siblings harbored a heterozygous single-base insertion, and 2 subjects had a balanced translocation disrupting ZMIZ1 or involving a regulatory region of ZMIZ1. In total, we identified 13 point mutations that affect key protein regions, including a SUMO acceptor site, a central disordered alanine-rich motif, a proline-rich domain, and a transactivation domain. All identified variants were absent from all available exome and genome databases. In vitro, ZMIZ1 showed impaired coactivation of the androgen receptor. In vivo, overexpression of ZMIZ1 mutant alleles in developing mouse brains using in utero electroporation resulted in abnormal pyramidal neuron morphology, polarization, and positioning, underscoring the importance of ZMIZ1 in neural development and supporting mutations in ZMIZ1 as the cause of a rare neurodevelopmental syndrome.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bertrand Isidor
- Service de Génétique Médicale, Hôpital Hôtel-Dieu, CHU de Nantes, 44093 Nantes, France
| | - Seiamak Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), LabEx TRANSPLANTEX, Université de Strasbourg, 4 rue Kirschleger, 67085 Strasbourg, France; Service d'Immunologie Biologique, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, 1 place de l'Hôpital, 67091 Strasbourg, France.
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42
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Fountain MD, Oleson DS, Rech ME, Segebrecht L, Hunter JV, McCarthy JM, Lupo PJ, Holtgrewe M, Moran R, Rosenfeld JA, Isidor B, Le Caignec C, Saenz MS, Pedersen RC, Morgan TM, Pfotenhauer JP, Xia F, Bi W, Kang SHL, Patel A, Krantz ID, Raible SE, Smith W, Cristian I, Torti E, Juusola J, Millan F, Wentzensen IM, Person RE, Küry S, Bézieau S, Uguen K, Férec C, Munnich A, van Haelst M, Lichtenbelt KD, van Gassen K, Hagelstrom T, Chawla A, Perry DL, Taft RJ, Jones M, Masser-Frye D, Dyment D, Venkateswaran S, Li C, Escobar LF, Horn D, Spillmann RC, Peña L, Wierzba J, Strom TM, Parenti I, Kaiser FJ, Ehmke N, Schaaf CP. Pathogenic variants in USP7 cause a neurodevelopmental disorder with speech delays, altered behavior, and neurologic anomalies. Genet Med 2019; 21:1797-1807. [PMID: 30679821 PMCID: PMC6752677 DOI: 10.1038/s41436-019-0433-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/02/2019] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Haploinsufficiency of USP7, located at chromosome 16p13.2, has recently been reported in seven individuals with neurodevelopmental phenotypes, including developmental delay/intellectual disability (DD/ID), autism spectrum disorder (ASD), seizures, and hypogonadism. Further, USP7 was identified to critically incorporate into the MAGEL2-USP7-TRIM27 (MUST), such that pathogenic variants in USP7 lead to altered endosomal F-actin polymerization and dysregulated protein recycling. METHODS We report 16 newly identified individuals with heterozygous USP7 variants, identified by genome or exome sequencing or by chromosome microarray analysis. Clinical features were evaluated by review of medical records. Additional clinical information was obtained on the seven previously reported individuals to fully elucidate the phenotypic expression associated with USP7 haploinsufficiency. RESULTS The clinical manifestations of these 23 individuals suggest a syndrome characterized by DD/ID, hypotonia, eye anomalies,feeding difficulties, GERD, behavioral anomalies, and ASD, and more specific phenotypes of speech delays including a nonverbal phenotype and abnormal brain magnetic resonance image findings including white matter changes based on neuroradiologic examination. CONCLUSION The consistency of clinical features among all individuals presented regardless of de novo USP7 variant type supports haploinsufficiency as a mechanism for pathogenesis and refines the clinical impact faced by affected individuals and caregivers.
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Affiliation(s)
- Michael D Fountain
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David S Oleson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Megan E Rech
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lara Segebrecht
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Jill V Hunter
- Department of Radiology, Texas Children's Hospital, Houston, TX, USA
| | - John M McCarthy
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Philip J Lupo
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Manuel Holtgrewe
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
| | - Rocio Moran
- Department of Genetics, Cleveland Clinic Children's, Cleveland, OH, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Bertrand Isidor
- CHU Nantes, Service de Génétique Médicale, Nantes, France.,l'institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | | | - Margarita S Saenz
- Clinical Genetics and Metabolism, Children's Hospital Colorado, Aurora, CO, USA
| | - Robert C Pedersen
- Department of Pediatrics, Tripler Army Medical Center, Honolulu, HI, USA
| | - Thomas M Morgan
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jean P Pfotenhauer
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sung-Hae L Kang
- Department of Pathology & Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Ian D Krantz
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah E Raible
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wendy Smith
- Department of Pediatrics, The Barbara Bush Children's Hospital, Maine Medical Center, Portland, ME, USA
| | - Ingrid Cristian
- Division of Genetics, Department of Pediatrics, Arnold Palmer Hospital, Orlando, FL, USA
| | | | | | | | | | | | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, Nantes, France.,l'institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Stéphane Bézieau
- CHU Nantes, Service de Génétique Médicale, Nantes, France.,l'institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Kévin Uguen
- Service de Génétique Médicale, CHRU de Brest, INSERM, Brest, France
| | - Claude Férec
- Service de Génétique Médicale, CHRU de Brest, INSERM, Brest, France
| | - Arnold Munnich
- UMR1163, Université Paris Descartes, Sorbonne Paris Cité, Institut IMAGINE, Paris, France
| | - Mieke van Haelst
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.,Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Klaske D Lichtenbelt
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Aditi Chawla
- Illumina Clinical Services Laboratory, Illumina, San Diego, CA, USA
| | - Denise L Perry
- Illumina Clinical Services Laboratory, Illumina, San Diego, CA, USA
| | - Ryan J Taft
- Illumina Clinical Services Laboratory, Illumina, San Diego, CA, USA
| | - Marilyn Jones
- Division of Genetics, Department of Pediatrics, UC San Diego School of Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Diane Masser-Frye
- Division of Genetics, Department of Pediatrics, UC San Diego School of Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - David Dyment
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada.,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Sunita Venkateswaran
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Division of Neurology, Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Chumei Li
- McMaster University Medical Center, Hamilton, ON, Canada
| | - Luis F Escobar
- Medical Genetics and Neurodevelopment Center, St Vincent Children's Hospital, Indianapolis, IN, USA
| | - Denise Horn
- Charité-Universtitätsmedizin Berlin, Institute for Medical Genetics and Human Genetics, Berlin, Germany
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC, USA
| | - Loren Peña
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jolanta Wierzba
- Department of General Nursery, Medical University of Gdańsk, Gdańsk, Poland
| | - Tim M Strom
- Institute of Human Genetics, Technische Universität München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ilaria Parenti
- Section for Functional Genetics, Institute for Human Genetics, University of Lübeck, Lübeck, Germany
| | - Frank J Kaiser
- Section for Functional Genetics, Institute for Human Genetics, University of Lübeck, Lübeck, Germany
| | - Nadja Ehmke
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Christian P Schaaf
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Institute of Human Genetics, University Hospital Cologne, Cologne, Germany. .,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany. .,Center for Rare Diseases, University Hospital Cologne, Cologne, Germany.
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43
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Shashi V, Magiera MM, Klein D, Zaki M, Schoch K, Rudnik-Schöneborn S, Norman A, Lopes Abath Neto O, Dusl M, Yuan X, Bartesaghi L, De Marco P, Alfares AA, Marom R, Arold ST, Guzmán-Vega FJ, Pena LD, Smith EC, Steinlin M, Babiker MO, Mohassel P, Foley AR, Donkervoort S, Kaur R, Ghosh PS, Stanley V, Musaev D, Nava C, Mignot C, Keren B, Scala M, Tassano E, Picco P, Doneda P, Fiorillo C, Issa MY, Alassiri A, Alahmad A, Gerard A, Liu P, Yang Y, Ertl-Wagner B, Kranz PG, Wentzensen IM, Stucka R, Stong N, Allen AS, Goldstein DB, Schoser B, Rösler KM, Alfadhel M, Capra V, Chrast R, Strom TM, Kamsteeg EJ, Bönnemann CG, Gleeson JG, Martini R, Janke C, Senderek J. Loss of tubulin deglutamylase CCP1 causes infantile-onset neurodegeneration. EMBO J 2018; 37:e100540. [PMID: 30420557 PMCID: PMC6276871 DOI: 10.15252/embj.2018100540] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [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: 08/22/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 11/09/2022] Open
Abstract
A set of glutamylases and deglutamylases controls levels of tubulin polyglutamylation, a prominent post-translational modification of neuronal microtubules. Defective tubulin polyglutamylation was first linked to neurodegeneration in the Purkinje cell degeneration (pcd) mouse, which lacks deglutamylase CCP1, displays massive cerebellar atrophy, and accumulates abnormally glutamylated tubulin in degenerating neurons. We found biallelic rare and damaging variants in the gene encoding CCP1 in 13 individuals with infantile-onset neurodegeneration and confirmed the absence of functional CCP1 along with dysregulated tubulin polyglutamylation. The human disease mainly affected the cerebellum, spinal motor neurons, and peripheral nerves. We also demonstrate previously unrecognized peripheral nerve and spinal motor neuron degeneration in pcd mice, which thus recapitulated key features of the human disease. Our findings link human neurodegeneration to tubulin polyglutamylation, entailing this post-translational modification as a potential target for drug development for neurodegenerative disorders.
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Affiliation(s)
- Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Maria M Magiera
- Institut Curie, CNRS UMR3348, PSL Research University, Orsay, France
- CNRS UMR3348, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Dennis Klein
- Department of Neurology, Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Maha Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | | | - Andrew Norman
- Department of Clinical Genetics, St. Michael's Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Osorio Lopes Abath Neto
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Marina Dusl
- Friedrich Baur Institute at the Department of Neurology, Friedrich Baur Institute, University Hospital, LMU Munich, Munich, Germany
| | - Xidi Yuan
- Department of Neurology, Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Luca Bartesaghi
- Department of Neuroscience and Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | - Ahmed A Alfares
- Department of Pediatrics, College of Medicine, Qassim University, Qassim, Saudi Arabia
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Stefan T Arold
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Francisco J Guzmán-Vega
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Loren Dm Pena
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Edward C Smith
- Division of Neurology, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Maja Steinlin
- Division of Neuropaediatrics, Development and Rehabilitation, University Children's Hospital, Inselspital, University of Bern, Bern, Switzerland
| | | | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Rupleen Kaur
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Partha S Ghosh
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Valentina Stanley
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, CA, USA
| | - Damir Musaev
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, CA, USA
| | - Caroline Nava
- Department of Genetics, Assistance Publique des Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
- Institut du Cerveau et de la Moelle épinière, Sorbonne Universités, Inserm U1127, CNRS, UMR 7225, UPMC Univ Paris 06, Paris, France
| | - Cyril Mignot
- Department of Genetics, Assistance Publique des Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
- Institut du Cerveau et de la Moelle épinière, Sorbonne Universités, Inserm U1127, CNRS, UMR 7225, UPMC Univ Paris 06, Paris, France
| | - Boris Keren
- Department of Genetics, Assistance Publique des Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
- Institut du Cerveau et de la Moelle épinière, Sorbonne Universités, Inserm U1127, CNRS, UMR 7225, UPMC Univ Paris 06, Paris, France
| | | | | | - Paolo Picco
- IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Paola Doneda
- Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | - Chiara Fiorillo
- IRCCS Istituto Giannina Gaslini, Genova, Italy
- Università degli Studi di Genova, Genova, Italy
| | - Mahmoud Y Issa
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Ali Alassiri
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ahmed Alahmad
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Birgit Ertl-Wagner
- Department of Diagnostic Imaging, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Peter G Kranz
- Division of Neuroradiology, Department of Radiology, Duke University Medical Center, Durham, NC, USA
| | | | - Rolf Stucka
- Friedrich Baur Institute at the Department of Neurology, Friedrich Baur Institute, University Hospital, LMU Munich, Munich, Germany
| | - Nicholas Stong
- Institute of Genomic Medicine, Columbia University, New York, NY, USA
| | - Andrew S Allen
- Center for Statistical Genetics and Genomics, Duke University Medical Center, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - David B Goldstein
- Institute of Genomic Medicine, Columbia University, New York, NY, USA
| | - Benedikt Schoser
- Friedrich Baur Institute at the Department of Neurology, Friedrich Baur Institute, University Hospital, LMU Munich, Munich, Germany
| | - Kai M Rösler
- Neuromuscular Centre, University Department of Neurology, Inselspital, Bern, Switzerland
| | - Majid Alfadhel
- Genetics Division, Department of Pediatrics, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | | | - Roman Chrast
- Department of Neuroscience and Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Donders Centre for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Joseph G Gleeson
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, CA, USA
| | - Rudolf Martini
- Department of Neurology, Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Carsten Janke
- Institut Curie, CNRS UMR3348, PSL Research University, Orsay, France
- CNRS UMR3348, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Jan Senderek
- Friedrich Baur Institute at the Department of Neurology, Friedrich Baur Institute, University Hospital, LMU Munich, Munich, Germany
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44
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Hiatt SM, Neu MB, Ramaker RC, Hardigan AA, Prokop JW, Hancarova M, Prchalova D, Havlovicova M, Prchal J, Stranecky V, Yim DKC, Powis Z, Keren B, Nava C, Mignot C, Rio M, Revah-Politi A, Hemati P, Stong N, Iglesias AD, Suchy SF, Willaert R, Wentzensen IM, Wheeler PG, Brick L, Kozenko M, Hurst ACE, Wheless JW, Lacassie Y, Myers RM, Barsh GS, Sedlacek Z, Cooper GM. De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay. PLoS Genet 2018; 14:e1007671. [PMID: 30500825 PMCID: PMC6291162 DOI: 10.1371/journal.pgen.1007671] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/12/2018] [Accepted: 08/30/2018] [Indexed: 01/22/2023] Open
Abstract
Mutations that alter signaling of RAS/MAPK-family proteins give rise to a group of Mendelian diseases known as RASopathies. However, among RASopathies, the matrix of genotype-phenotype relationships is still incomplete, in part because there are many RAS-related proteins and in part because the phenotypic consequences may be variable and/or pleiotropic. Here, we describe a cohort of ten cases, drawn from six clinical sites and over 16,000 sequenced probands, with de novo protein-altering variation in RALA, a RAS-like small GTPase. All probands present with speech and motor delays, and most have intellectual disability, low weight, short stature, and facial dysmorphism. The observed rate of de novo RALA variants in affected probands is significantly higher (p = 4.93 x 10−11) than expected from the estimated random mutation rate. Further, all de novo variants described here affect residues within the GTP/GDP-binding region of RALA; in fact, six alleles arose at only two codons, Val25 and Lys128. The affected residues are highly conserved across both RAL- and RAS-family genes, are devoid of variation in large human population datasets, and several are homologous to positions at which disease-associated variants have been observed in other GTPase genes. We directly assayed GTP hydrolysis and RALA effector-protein binding of the observed variants, and found that all but one tested variant significantly reduced both activities compared to wild-type. The one exception, S157A, reduced GTP hydrolysis but significantly increased RALA-effector binding, an observation similar to that seen for oncogenic RAS variants. These results show the power of data sharing for the interpretation and analysis of rare variation, expand the spectrum of molecular causes of developmental disability to include RALA, and provide additional insight into the pathogenesis of human disease caused by mutations in small GTPases. While many causes of developmental disabilities have been identified, a large number of affected children cannot be diagnosed despite extensive medical testing. Previously unknown genetic factors are likely to be the culprits in many of these cases. Using DNA sequencing, and by sharing information among many doctors and researchers, we have identified a set of individuals with developmental problems who all have changes to the same gene, RALA. The affected individuals all have similar symptoms, including intellectual disability, speech delay (or no speech), and problems with motor skills like walking. In nearly all of these cases (10 of 11), the genetic change found in the child was not inherited from either parent. The locations and biological properties of these changes suggest that they are likely to disrupt the normal functions of RALA. Functional experiments also show that the genetic changes found in these individuals alter two key functions of RALA. Together, we have provided evidence that genetic changes in RALA can cause developmental disabilities. These results will allow doctors and researchers to identify additional children with the same condition, providing a clinical diagnosis to these families and leading to new research opportunities.
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Affiliation(s)
- Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Matthew B. Neu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Andrew A. Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI, United States of America
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Darina Prchalova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Marketa Havlovicova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Jan Prchal
- Laboratory of NMR Spectroscopy, University of Chemistry and Technology, Prague, Czech Republic
| | - Viktor Stranecky
- Department of Pediatrics and Adolescent Medicine, Diagnostic and Research Unit for Rare Diseases, Charles University 1st Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Dwight K. C. Yim
- Kaiser Permanente-Hawaii, Honolulu, HI, United States of America
| | - Zöe Powis
- Department of Emerging Genetic Medicine, Ambry Genetics, Aliso Viejo, CA, United States of America
| | - Boris Keren
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Caroline Nava
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Cyril Mignot
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
- Groupe de Recherche Clinique UPMC "Déficience Intellectuelle et Autisme", Paris, France
| | - Marlene Rio
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
- Assistance Publique-Hôpitaux de Paris, service de Génétique, Hôpital Necker-Enfants-Malades, Paris, France
| | - Anya Revah-Politi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Parisa Hemati
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Alejandro D. Iglesias
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, United States of America
| | | | | | | | - Patricia G. Wheeler
- Arnold Palmer Hospital, Division of Genetics, Orlando, FL, United States of America
| | - Lauren Brick
- Department of Genetics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Mariya Kozenko
- Department of Genetics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Anna C. E. Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - James W. Wheless
- Division of Pediatric Neurology, University of Tennessee Health Science Center, Neuroscience Institute & Le Bonheur Comprehensive Epilepsy Program, Memphis, TN, United States of America
- Le Bonheur Children’s Hospital, Memphis, TN, United States of America
| | - Yves Lacassie
- Division of Clinical Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States of America
- Department of Genetics, Children's Hospital, New Orleans, LA, United States of America
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Zdenek Sedlacek
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Gregory M. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- * E-mail:
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45
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Pilarowski GO, Vernon HJ, Applegate CD, Boukas L, Cho MT, Gurnett CA, Benke PJ, Beaver E, Heeley JM, Medne L, Krantz ID, Azage M, Niyazov D, Henderson LB, Wentzensen IM, Baskin B, Sacoto MJG, Bowman GD, Bjornsson HT. Missense variants in the chromatin remodeler CHD1 are associated with neurodevelopmental disability. J Med Genet 2017; 55:561-566. [PMID: 28866611 DOI: 10.1136/jmedgenet-2017-104759] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 04/27/2017] [Revised: 07/07/2017] [Accepted: 08/04/2017] [Indexed: 11/04/2022]
Abstract
BACKGROUND The list of Mendelian disorders of the epigenetic machinery has expanded rapidly during the last 5 years. A few missense variants in the chromatin remodeler CHD1 have been found in several large-scale sequencing efforts focused on uncovering the genetic aetiology of autism. OBJECTIVES To explore whether variants in CHD1 are associated with a human phenotype. METHODS We used GeneMatcher to identify other physicians caring for patients with variants in CHD1. We also explored the epigenetic consequences of one of these variants in cultured fibroblasts. RESULTS Here we describe six CHD1 heterozygous missense variants in a cohort of patients with autism, speech apraxia, developmental delay and facial dysmorphic features. Importantly, three of these variants occurred de novo. We also report on a subject with a de novo deletion covering a large fraction of the CHD1 gene without any obvious neurological phenotype. Finally, we demonstrate increased levels of the closed chromatin modification H3K27me3 in fibroblasts from a subject carrying a de novo variant in CHD1. CONCLUSIONS Our results suggest that variants in CHD1 can lead to diverse phenotypic outcomes; however, the neurodevelopmental phenotype appears to be limited to patients with missense variants, which is compatible with a dominant negative mechanism of disease.
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Affiliation(s)
- Genay O Pilarowski
- Predoctoral Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hilary J Vernon
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Carolyn D Applegate
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Leandros Boukas
- Predoctoral Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Christina A Gurnett
- Department of Neurology, Division of Pediatric Neurology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Paul J Benke
- Joe DiMaggio Children's Hospital, Florida Atlantic School of Medicine, Hollywood, Florida, USA
| | - Erin Beaver
- Mercy Kids Genetics, Mercy Hospital, Saint Louis, Missouri, USA
| | | | - Livija Medne
- Division of Human Genetics, Department of Pediatrics, Individualized Medical Genetics Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ian D Krantz
- Division of Human Genetics, Department of Pediatrics, Individualized Medical Genetics Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Meron Azage
- Department of Pediatrics, Ochsner Clinic, New Orleans, Louisiana, USA
| | - Dmitriy Niyazov
- Department of Pediatrics, Ochsner Clinic, New Orleans, Louisiana, USA
| | | | | | | | | | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hans T Bjornsson
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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46
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Johnston JJ, Lee C, Wentzensen IM, Parisi MA, Crenshaw MM, Sapp JC, Gross JM, Wallingford JB, Biesecker LG. Compound heterozygous alterations in intraflagellar transport protein CLUAP1 in a child with a novel Joubert and oral-facial-digital overlap syndrome. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a001321. [PMID: 28679688 PMCID: PMC5495032 DOI: 10.1101/mcs.a001321] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/05/2016] [Indexed: 12/17/2022] Open
Abstract
Disruption of normal ciliary function results in a range of diseases collectively referred to as ciliopathies. Here we report a child with a phenotype that overlapped with Joubert, oral–facial–digital, and Pallister–Hall syndromes including brain, limb, and craniofacial anomalies. We performed exome-sequence analysis on a proband and both parents, filtered for putative causative variants, and Sanger-verified variants of interest. Identified variants in CLUAP1 were functionally analyzed in a Xenopus system to determine their effect on ciliary function. Two variants in CLUAP1 were identified through exome-sequence analysis, Chr16:g.3558407T>G, c.338T>G, p.(Met113Arg) and Chr16:g.3570011C>T, c.688C>T, p.(Arg230Ter). These variants were rare in the Exome Aggregation Consortium (ExAC) data set of 65,000 individuals (one and two occurrences, respectively). Transfection of mutant CLUAP1 constructs into Xenopus embryos showed reduced protein levels p.(Arg230Ter) and reduced intraflagellar transport p.(Met113Arg). The genetic data show that these variants are present in an affected child, are rare in the population, and result in reduced, but not absent, intraflagellar transport. We conclude that biallelic mutations in CLUAP1 resulted in this novel ciliopathy syndrome in the proband.
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Affiliation(s)
- Jennifer J Johnston
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-4472, USA
| | - Chanjae Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78705, USA
| | - Ingrid M Wentzensen
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-4472, USA
| | - Melissa A Parisi
- Intellectual and Developmental Disabilities Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Molly M Crenshaw
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-4472, USA
| | - Julie C Sapp
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-4472, USA
| | - Jeffrey M Gross
- Departments of Ophthalmology and Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - John B Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78705, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892-4472, USA
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47
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Vivero M, Cho MT, Begtrup A, Wentzensen IM, Walsh L, Payne K, Zarate YA, Bosanko K, Schaefer GB, DeBrosse S, Pollack L, Mason K, Retterer K, DeWard S, Juusola J, Chung WK. Additional de novo missense genetic variants in NALCN associated with CLIFAHDD syndrome. Clin Genet 2017; 91:929-931. [PMID: 28133733 DOI: 10.1111/cge.12899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/17/2016] [Accepted: 10/17/2016] [Indexed: 11/27/2022]
Affiliation(s)
- M Vivero
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - M T Cho
- GeneDx, Gaithersburg, MD, USA
| | | | | | - L Walsh
- Department of Child Neurology, Riley Hospital for Children, Indianapolis, IN, USA
| | - K Payne
- Department of Child Neurology, Riley Hospital for Children, Indianapolis, IN, USA
| | - Y A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Little Rock, AR, USA
| | - K Bosanko
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Little Rock, AR, USA
| | - G B Schaefer
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Little Rock, AR, USA
| | - S DeBrosse
- Center for Human Genetics, University Hospitals Case Medical Center and Case Western Reserve University, Cleveland, OH, USA
| | - L Pollack
- Division of Genetics, Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - K Mason
- Division of Genetics, Arnold Palmer Hospital for Children, Orlando, FL, USA
| | | | | | | | - W K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
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48
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Stern D, Cho MT, Chikarmane R, Willaert R, Retterer K, Kendall F, Deardorff M, Hopkins S, Bedoukian E, Slavotinek A, Schrier Vergano S, Spangler B, McDonald M, McConkie-Rosell A, Burton BK, Kim KH, Oundjian N, Kronn D, Chandy N, Baskin B, Guillen Sacoto MJ, Wentzensen IM, McLaughlin HM, McKnight D, Chung WK. Association of the missense variant p.Arg203Trp in PACS1 as a cause of intellectual disability and seizures. Clin Genet 2017; 92:221-223. [PMID: 28111752 DOI: 10.1111/cge.12956] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/05/2016] [Accepted: 12/06/2016] [Indexed: 02/04/2023]
Abstract
Graphical abstract key: ADHD, attention deficit hyperactivity disorder; ASD, atrial septal defect; DD, developmental delay; EEG, electroencephalogram; Ht, height; ID, intellectual disability; OCD, obsessive-compulsive disorder; OFC, open fontanelle; PDA, patent ductus arteriosis; PFO, patent foramen ovale; VSD, ventricular septal defect; Wt, weight.
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Affiliation(s)
- D Stern
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - M T Cho
- GeneDx, Gaithersburg, MD, USA
| | | | | | | | - F Kendall
- VMP Genetics, Roswell, GA, USA.,Department of Kinesiology, University of Georgia, Athens, GA, USA
| | - M Deardorff
- Department of Pediatrics, Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - S Hopkins
- Division of Neurology, The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - E Bedoukian
- Individualized Medical Genetics Center, Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - A Slavotinek
- Department of Pediatrics, UCSF Benioff Children's Hospital, University of California, San Francisco, CA, USA
| | - S Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA
| | - B Spangler
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA
| | - M McDonald
- Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - A McConkie-Rosell
- Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - B K Burton
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - K H Kim
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | | | - D Kronn
- New York Medical College, Valhalla, NY, USA
| | - N Chandy
- New York Medical College, Valhalla, NY, USA
| | | | | | | | | | | | - W K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.,Department of Medicine, Columbia University Medical Center, New York, NY, USA
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49
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Ma L, Bayram Y, McLaughlin HM, Cho MT, Krokosky A, Turner CE, Lindstrom K, Bupp CP, Mayberry K, Mu W, Bodurtha J, Weinstein V, Zadeh N, Alcaraz W, Powis Z, Shao Y, Scott DA, Lewis AM, White JJ, Jhangiani SN, Gulec EY, Lalani SR, Lupski JR, Retterer K, Schnur RE, Wentzensen IM, Bale S, Chung WK. De novo missense variants in PPP1CB are associated with intellectual disability and congenital heart disease. Hum Genet 2016; 135:1399-1409. [PMID: 27681385 DOI: 10.1007/s00439-016-1731-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/19/2016] [Indexed: 10/20/2022]
Abstract
Intellectual disabilities are genetically heterogeneous and can be associated with congenital anomalies. Using whole-exome sequencing (WES), we identified five different de novo missense variants in the protein phosphatase-1 catalytic subunit beta (PPP1CB) gene in eight unrelated individuals who share an overlapping phenotype of dysmorphic features, macrocephaly, developmental delay or intellectual disability (ID), congenital heart disease, short stature, and skeletal and connective tissue abnormalities. Protein phosphatase-1 (PP1) is a serine/threonine-specific protein phosphatase involved in the dephosphorylation of a variety of proteins. The PPP1CB gene encodes a PP1 subunit that regulates the level of protein phosphorylation. All five altered amino acids we observed are highly conserved among the PP1 subunit family, and all are predicted to disrupt PP1 subunit binding and impair dephosphorylation. Our data suggest that our heterozygous de novo PPP1CB pathogenic variants are associated with syndromic intellectual disability.
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Affiliation(s)
- Lijiang Ma
- Department of Pediatrics, Columbia University Medical Center, 1150 St. Nicholas Avenue, New York, NY, 10032, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Alyson Krokosky
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | | | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | | | | | - Weiyi Mu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Joann Bodurtha
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Veronique Weinstein
- Division of Genetics and Metabolism, Children's National Medical Center, Washington, DC, USA
| | | | | | - Zöe Powis
- Ambry Genetics, Aliso Viejo, CA, USA
| | - Yunru Shao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shalani N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Elif Yilmaz Gulec
- Medical Genetics Section, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, 1150 St. Nicholas Avenue, New York, NY, 10032, USA.
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50
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Ngoh A, McTague A, Wentzensen IM, Meyer E, Applegate C, Kossoff EH, Batista DA, Wang T, Kurian MA. Severe infantile epileptic encephalopathy due to mutations in PLCB1: expansion of the genotypic and phenotypic disease spectrum. Dev Med Child Neurol 2014; 56:1124-8. [PMID: 24684524 PMCID: PMC4230412 DOI: 10.1111/dmcn.12450] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/06/2014] [Indexed: 11/28/2022]
Abstract
Homozygous deletions of chromosome 20p12.3, disrupting the promoter region and first three coding exons of the phospholipase C β1 gene (PLCB1), have previously been described in two reports of early infantile epileptic encephalopathy (EIEE). Both children were born to consanguineous parents, one presented with infantile spasms, the other with migrating partial seizures of infancy. We describe an infant presenting with severe intractable epilepsy (without a specific EIEE electroclinical syndrome diagnosis) and neurodevelopmental delay associated with compound heterozygous mutations in PLCB1. A case note review and molecular genetic investigations were performed for a child, approximately 10 months of age, admitted to Johns Hopkins University Hospital for developmental delay and new-onset seizures. The patient presented at 6 months of age with developmental delay, followed by the onset of intractable, focal, and generalized seizures associated with developmental regression from 10 months of age. Presently, at 2 years of age, the child has severe motor and cognitive delays. Diagnostic microarray revealed a heterozygous 476kb deletion of 20p12.3 (encompassing PLCB1), which was also detected in the mother. The genomic breakpoints for the heterozygous deletion were determined. In order to investigate the presence of a second PLCB1 mutation, direct Sanger sequencing of the coding region and flanking intronic regions was undertaken, revealing a novel heterozygous intron 1 splice site variant (c.99+1G>A) in both the index individual and the father. Advances in molecular genetic testing have greatly improved diagnostic rates in EIEE, and this report further confirms the important role of microarray investigation in this group of disorders. PLCB1-EIEE is now reported in a number of different EIEE phenotypes and our report provides further evidence for phenotypic pleiotropy encountered in early infantile epilepsy syndromes.
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Affiliation(s)
- Adeline Ngoh
- Neurosciences Unit, Developmental Neurosciences, University College London, Institute of Child HealthLondon, UK,Department of Neurology, Great Ormond Street HospitalLondon, UK
| | - Amy McTague
- Neurosciences Unit, Developmental Neurosciences, University College London, Institute of Child HealthLondon, UK,Department of Neurology, Great Ormond Street HospitalLondon, UK
| | - Ingrid M Wentzensen
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | - Esther Meyer
- Neurosciences Unit, Developmental Neurosciences, University College London, Institute of Child HealthLondon, UK
| | - Carolyn Applegate
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | - Eric H Kossoff
- Department of Pediatrics, Johns Hopkins University School of MedicineBaltimore, MD, USA,Department of Neurology, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | - Denise A Batista
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of MedicineBaltimore, MD, USA,Department of Pathology, Johns Hopkins University School of MedicineBaltimore, MD, USA,Kennedy Krieger InstituteBaltimore, MD, USA
| | - Tao Wang
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of MedicineBaltimore, MD, USA,Department of Pediatrics, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | - Manju A Kurian
- Neurosciences Unit, Developmental Neurosciences, University College London, Institute of Child HealthLondon, UK,Department of Neurology, Great Ormond Street HospitalLondon, UK
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