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Oddsson A, Sulem P, Sveinbjornsson G, Arnadottir GA, Steinthorsdottir V, Halldorsson GH, Atlason BA, Oskarsson GR, Helgason H, Nielsen HS, Westergaard D, Karjalainen JM, Katrinardottir H, Fridriksdottir R, Jensson BO, Tragante V, Ferkingstad E, Jonsson H, Gudjonsson SA, Beyter D, Moore KHS, Thordardottir HB, Kristmundsdottir S, Stefansson OA, Rantapää-Dahlqvist S, Sonderby IE, Didriksen M, Stridh P, Haavik J, Tryggvadottir L, Frei O, Walters GB, Kockum I, Hjalgrim H, Olafsdottir TA, Selbaek G, Nyegaard M, Erikstrup C, Brodersen T, Saevarsdottir S, Olsson T, Nielsen KR, Haraldsson A, Bruun MT, Hansen TF, Steingrimsdottir T, Jacobsen RL, Lie RT, Djurovic S, Alfredsson L, Lopez de Lapuente Portilla A, Brunak S, Melsted P, Halldorsson BV, Saemundsdottir J, Magnusson OT, Padyukov L, Banasik K, Rafnar T, Askling J, Klareskog L, Pedersen OB, Masson G, Havdahl A, Nilsson B, Andreassen OA, Daly M, Ostrowski SR, Jonsdottir I, Stefansson H, Holm H, Helgason A, Thorsteinsdottir U, Stefansson K, Gudbjartsson DF. Publisher Correction: Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality. Nat Commun 2023; 14:3923. [PMID: 37400429 PMCID: PMC10318025 DOI: 10.1038/s41467-023-39492-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023] Open
Affiliation(s)
| | | | | | - Gudny A Arnadottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | - Henriette Svarre Nielsen
- Deptartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - David Westergaard
- Deptartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Juha M Karjalainen
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | | | | | - Kristjan H S Moore
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Helga B Thordardottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Ida Elken Sonderby
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Maria Didriksen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Pernilla Stridh
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Jan Haavik
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Bergen Center of Brain Plasticity, Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Laufey Tryggvadottir
- Icelandic Cancer Registry, Icelandic Cancer Society, Reykjavik, Iceland
- Faculty of Medicine, BMC, Laeknagardur, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Oleksandr Frei
- NORMENT Centre, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | | | - Ingrid Kockum
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Hjalgrim
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Geir Selbaek
- Norwegian National Centre of Ageing and Health, Vestfold Hospital Trust, Tonsberg, Norway
- Department of Geriatric Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mette Nyegaard
- Deptartment of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Thorsten Brodersen
- Department of Clinical Immunology, Zealand University Hospital, Koge, Denmark
| | - Saedis Saevarsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Kaspar Rene Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Asgeir Haraldsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Children's Hospital Iceland, Landspitali University Hospital, Reykjavik, Iceland
| | - Mie Topholm Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Thora Steingrimsdottir
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Rikke Louise Jacobsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Soren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pall Melsted
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | | | | | - Leonid Padyukov
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Johan Askling
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lars Klareskog
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Ole Birger Pedersen
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Koge, Denmark
| | | | - Alexandra Havdahl
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
| | - Bjorn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund, Sweden
| | - Ole A Andreassen
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Mark Daly
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Deptartment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Hilma Holm
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
| | - Agnar Helgason
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
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52
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Priolo M, Zara E, Radio FC, Ciolfi A, Spadaro F, Bellacchio E, Mancini C, Pantaleoni F, Cordeddu V, Chiriatti L, Niceta M, Africa E, Mammì C, Melis D, Coppola S, Tartaglia M. Clinical profiling of MRD48 and functional characterization of two novel pathogenic RAC1 variants. Eur J Hum Genet 2023; 31:805-814. [PMID: 37059841 PMCID: PMC10326044 DOI: 10.1038/s41431-023-01351-7] [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: 11/21/2022] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 04/16/2023] Open
Abstract
RAC1 is a member of the Rac/Rho GTPase subfamily within the RAS superfamily of small GTP-binding proteins, comprising 3 paralogs playing a critical role in actin cytoskeleton remodeling, cell migration, proliferation and differentiation. De novo missense variants in RAC1 are associated with a rare neurodevelopmental disorder (MRD48) characterized by DD/ID and brain abnormalities coupled with a wide range of additional features. Structural and functional studies have documented either a dominant negative or constitutively active behavior for a subset of mutations. Here, we describe two individuals with previously unreported de novo missense RAC1 variants. We functionally demonstrate their pathogenicity proving a gain-of-function (GoF) effect for both. By reviewing the clinical features of these two individuals and the previously published MRD48 subjects, we further delineate the clinical profile of the disorder, confirming its phenotypic variability. Moreover, we compare the main features of MRD48 with the neurodevelopmental disease caused by GoF variants in the paralog RAC3, highlighting similarities and differences. Finally, we review all previously reported variants in RAC proteins and in the closely related CDC42, providing an updated overview of the spectrum and hotspots of pathogenic variants affecting these functionally related GTPases.
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Affiliation(s)
- Manuela Priolo
- USD Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, 89124, Reggio Calabria, Italy.
| | - Erika Zara
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
- Department of Biology and Biotechnology, Sapienza University, 00185, Rome, Italy
| | | | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Emanuele Bellacchio
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Cecilia Mancini
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Francesca Pantaleoni
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Viviana Cordeddu
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Luigi Chiriatti
- USD Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, 89124, Reggio Calabria, Italy
| | - Marcello Niceta
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Emilio Africa
- USD Neuroradiologia, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, 89124, Reggio Calabria, Italy
| | - Corrado Mammì
- USD Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, 89124, Reggio Calabria, Italy
| | - Daniela Melis
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Università di Salerno, 84084, Salerno, Italy
| | - Simona Coppola
- National Center for Rare Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy.
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53
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Morison LD, van Reyk O, Forbes E, Rouxel F, Faivre L, Bruinsma F, Vincent M, Jacquemont ML, Dykzeul NL, Geneviève D, Amor DJ, Morgan AT. CDK13-related disorder: a deep characterization of speech and language abilities and addition of 33 novel cases. Eur J Hum Genet 2023; 31:793-804. [PMID: 36599938 PMCID: PMC10325997 DOI: 10.1038/s41431-022-01275-8] [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: 09/30/2022] [Revised: 12/01/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023] Open
Abstract
Speech and language impairments are central features of CDK13-related disorder. While pathogenic CDK13 variants have been associated with childhood apraxia of speech (CAS), a systematic characterisation of communication has not been conducted. Here we examined speech, language, non-verbal communication skills, social behaviour and health and development in 41 individuals with CDK13-related disorder from 10 countries (male = 22, median-age 7 years 1 month, range 1-25 years; 33 novel). Most participants used augmentative and alternative communication (AAC) in early childhood (24/41). CAS was common (14/22). Performance varied widely across intellectual ability, social behaviour and expressive language skills, with participants ranging from within average through to the severely impaired range. Receptive language was significantly stronger than expressive language ability. Social motivation was a relative strength. In terms of a broader health phenotype, a quarter had one or more of: renal, urogenital, musculoskeletal, and cardiac malformations, vision impairment, ear infections and/or sleep disturbance. All had gross and fine motor impairments (41/41). Other conditions included mild-moderate intellectual disability (16/22) and autism (7/41). No genotype-phenotype correlations were found. Recognition of CAS, a rare speech disorder, is required to ensure appropriately targeted therapy. The high prevalence of speech and language impairment underscores the importance of tailored speech therapy, particularly early access to AAC supports.
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Affiliation(s)
- Lottie D Morison
- Speech and Language, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Olivia van Reyk
- Speech and Language, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Elana Forbes
- Speech and Language, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Flavien Rouxel
- Génétique Clinique, Départment de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, Montpellier, France
| | - Laurence Faivre
- Centre de Référence Anomalies du Développment et Syndromes Malformatifs, FHU TRANSLAD, CHU Dijon, Dijon, France
- Genetics of Developmental Disorders, INSERM - Bourgogne Franche-Comté Univeristy, Dijon, France
| | | | - Marie Vincent
- Service de génétique médicale, CHU Nantes, 9 quai Moncousu, Nantes, France
| | | | - Natalie L Dykzeul
- Lucile Packard Children's Hospital, Stanford Children's Health, Palo Alto, CA, USA
| | - David Geneviève
- Génétique Clinique, Départment de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, Montpellier, France
| | - David J Amor
- Speech and Language, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- The Royal Children's Hospital, Melbourne, VIC, Australia
| | - Angela T Morgan
- Speech and Language, Murdoch Children's Research Institute, Melbourne, VIC, Australia.
- The Royal Children's Hospital, Melbourne, VIC, Australia.
- Department of Audiology and Speech Pathology, The University of Melbourne, Melbourne, VIC, Australia.
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Lyon GJ, Vedaie M, Beisheim T, Park A, Marchi E, Gottlieb L, Hsieh TC, Klinkhammer H, Sandomirsky K, Cheng H, Starr LJ, Preddy I, Tseng M, Li Q, Hu Y, Wang K, Carvalho A, Martinez F, Caro-Llopis A, Gavin M, Amble K, Krawitz P, Marmorstein R, Herr-Israel E. Expanding the phenotypic spectrum of NAA10-related neurodevelopmental syndrome and NAA15-related neurodevelopmental syndrome. Eur J Hum Genet 2023; 31:824-833. [PMID: 37130971 PMCID: PMC10325952 DOI: 10.1038/s41431-023-01368-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/11/2023] [Accepted: 04/17/2023] [Indexed: 05/04/2023] Open
Abstract
Amino-terminal (Nt-) acetylation (NTA) is a common protein modification, affecting 80% of cytosolic proteins in humans. The human essential gene, NAA10, encodes for the enzyme NAA10, which is the catalytic subunit in the N-terminal acetyltransferase A (NatA) complex, also including the accessory protein, NAA15. The full spectrum of human genetic variation in this pathway is currently unknown. Here we reveal the genetic landscape of variation in NAA10 and NAA15 in humans. Through a genotype-first approach, one clinician interviewed the parents of 56 individuals with NAA10 variants and 19 individuals with NAA15 variants, which were added to all known cases (N = 106 for NAA10 and N = 66 for NAA15). Although there is clinical overlap between the two syndromes, functional assessment demonstrates that the overall level of functioning for the probands with NAA10 variants is significantly lower than the probands with NAA15 variants. The phenotypic spectrum includes variable levels of intellectual disability, delayed milestones, autism spectrum disorder, craniofacial dysmorphology, cardiac anomalies, seizures, and visual abnormalities (including cortical visual impairment and microphthalmia). One female with the p.Arg83Cys variant and one female with an NAA15 frameshift variant both have microphthalmia. The frameshift variants located toward the C-terminal end of NAA10 have much less impact on overall functioning, whereas the females with the p.Arg83Cys missense in NAA10 have substantial impairment. The overall data are consistent with a phenotypic spectrum for these alleles, involving multiple organ systems, thus revealing the widespread effect of alterations of the NTA pathway in humans.
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Affiliation(s)
- Gholson J Lyon
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA.
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA.
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, USA.
| | - Marall Vedaie
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Travis Beisheim
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Agnes Park
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Elaine Marchi
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Leah Gottlieb
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Katherine Sandomirsky
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | | | - Lois J Starr
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Isabelle Preddy
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Marcellus Tseng
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Quan Li
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, M5G2C1, Canada
| | - Yu Hu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Ana Carvalho
- Department of Medical Genetics, Pediatric Hospital, Coimbra Hospital and University Centre, Coimbra, Portugal
| | - Francisco Martinez
- Unidad de Genetica, Hospital Universitario y Politecnico La Fe, 46026, Valencia, Spain
| | - Alfonso Caro-Llopis
- Grupo de Investigacion Traslacional en Genetica, Instituto de Investigacion Sanitaria La Fe, 46026, Valencia, Spain
| | - Maureen Gavin
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Karen Amble
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ellen Herr-Israel
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
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55
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Zanoni P, Steindl K, Sticht H, Oneda B, Joset P, Ivanovski I, Horn AHC, Cabello EM, Laube J, Zweier M, Baumer A, Rauch A, Khan N. The genetic landscape and clinical implication of pediatric Moyamoya angiopathy in an international cohort. Eur J Hum Genet 2023; 31:784-792. [PMID: 37012328 PMCID: PMC10325976 DOI: 10.1038/s41431-023-01320-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 12/16/2022] [Accepted: 02/13/2023] [Indexed: 04/05/2023] Open
Abstract
Pediatric Moyamoya Angiopathy (MMA) is a progressive intracranial occlusive arteriopathy that represents a leading cause of transient ischemic attacks and strokes in childhood. Despite this, up to now no large, exclusively pediatric MMA cohort has been subjected to systematic genetic investigation. In this study, we performed molecular karyotyping, exome sequencing and automated structural assessment of missense variants on a series of 88 pediatric MMA patients and correlated genetic, angiographic and clinical (stroke burden) findings. The two largest subgroups in our cohort consisted of RNF213 and neurofibromatosis type 1 (NF1) patients. While deleterious RNF213 variants were associated with a severe MMA clinical course with early symptom onset, frequent posterior cerebral artery involvement and higher stroke rates in multiple territories, NF1 patients had a similar infarct burden compared to non-NF1 individuals and were often diagnosed incidentally during routine MRIs. Additionally, we found that MMA-associated RNF213 variants have lower predicted functional impact compared to those associated with aortic disease. We also raise the question of MMA as a feature of recurrent as well as rare chromosomal imbalances and further support the possible association of MMA with STAT3 deficiency. In conclusion, we provide a comprehensive characterization at the genetic and clinical level of a large exclusively pediatric MMA population. Due to the clinical differences found across genetic subgroups, we propose genetic testing for risk stratification as part of the routine assessment of pediatric MMA patients.
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Affiliation(s)
- Paolo Zanoni
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland.
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Pascal Joset
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Ivan Ivanovski
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Anselm H C Horn
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Elena M Cabello
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Julia Laube
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, 8952, Switzerland.
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, 8000, Switzerland.
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, 8000, Switzerland.
- Moyamoya Center, University Children's Hospital, University of Zurich, Zurich, 8032, Switzerland.
| | - Nadia Khan
- Moyamoya Center, University Children's Hospital, University of Zurich, Zurich, 8032, Switzerland.
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56
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Hou J, Liang WY, Xiong S, Long P, Yue T, Wen X, Wang T, Deng H. Identification of hub genes and potential ceRNA networks of diabetic cardiomyopathy. Sci Rep 2023; 13:10258. [PMID: 37355664 PMCID: PMC10290640 DOI: 10.1038/s41598-023-37378-5] [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: 01/10/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023] Open
Abstract
Diabetic cardiomyopathy (DCM), a common complication of diabetes, is defined as ventricular dysfunction in the absence of underlying heart disease. Noncoding RNAs (ncRNAs), including long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), play a crucial role in the development of DCM. Weighted Gene Co-Expression Network Analysis (WGCNA) was used to identify key modules in DCM-related pathways. DCM-related miRNA-mRNA network and DCM-related ceRNA network were constructed by miRNA-seq to identify hub genes in these modules. We identified five hub genes that are associated with the onset of DCM, including Troponin C1 (Tnnc1), Phospholamban (Pln), Fatty acid binding proteins 3 (Fabp3), Popeye domain containing 2 (Popdc2), and Tripartite Motif-containing Protein 63 (Trim63). miRNAs that target the hub genes were mainly involved in TGF-β and Wnt signaling pathways. GO BP enrichment analysis found these miRNAs were involved in the signaling of TGF-β and glucose homeostasis. Q-PCR results found the gene expressions of Pln, Fabp3, Trim63, Tnnc1, and Popdc2 were significantly increased in DCM. Our study identified five hub genes (Tnnc1, Pln, Fabp3, Popdc2, Trim63) whose associated ceRNA networks are responsible for the onset of DCM.
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Affiliation(s)
- Jun Hou
- Department of Cardiology, The Third People's Hospital of Chengdu/Affiliated Hospital of Southwest Jiaotong University, Chengdu, Sichuan, China
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Wan Yi Liang
- Department of Microbiology and Immunology, Faculty of Science, University of British Columbia, Vancouver, BC, Canada
| | - Shiqiang Xiong
- Department of Cardiology, The Third People's Hospital of Chengdu/Affiliated Hospital of Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Pan Long
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Tian Yue
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Xudong Wen
- Department of Gastroenterology and Hepatology, Chengdu First People's Hospital, Chengdu, Sichuan, China
| | - Tianchen Wang
- Alfred E. Mann Department of Biomedical Engineering, University of South California, Los Angeles, CA, USA
| | - Haoyu Deng
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada.
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57
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Kobayashi Y, Tohyama J, Akasaka N, Yamada K, Hojo M, Seki E, Miura M, Soma N, Ono T, Kato M, Nakashima M, Saitsu H, Matsumoto N. The HCN1 p.Ser399Pro variant causes epileptic encephalopathy with super-refractory status epilepticus. Hum Genome Var 2023; 10:20. [PMID: 37353494 PMCID: PMC10290089 DOI: 10.1038/s41439-023-00247-8] [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: 04/24/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/25/2023] Open
Abstract
HCN1 is one of four genes encoding hyperpolarization-activated cyclic nucleotide-gated channels. The phenotypic spectrum associated with HCN1 variants ranges from neonatal developmental and epileptic encephalopathy to idiopathic generalized epilepsy. We report a Japanese patient with repetitive focal seizures and super-refractory status epilepticus since early infancy caused by a de novo HCN1 variant, NM_021072.4, c.1195T>C, p.(Ser399Pro). This variant might have a dominant-negative effect on channel function, leading to severe epileptic encephalopathy.
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Affiliation(s)
- Yu Kobayashi
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan
| | - Jun Tohyama
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan.
| | - Noriyuki Akasaka
- Department of Pediatrics, Niigata Prefecture Hamagumi Medical Rehabilitation Center for Disabled Children, Niigata, Japan
| | - Kei Yamada
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan
| | - Moemi Hojo
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan
| | - Eijun Seki
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan
| | - Masaki Miura
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan
| | - Noriko Soma
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan
| | - Takeshi Ono
- Department of Pediatrics, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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58
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Ayers KL, Eggers S, Rollo BN, Smith KR, Davidson NM, Siddall NA, Zhao L, Bowles J, Weiss K, Zanni G, Burglen L, Ben-Shachar S, Rosensaft J, Raas-Rothschild A, Jørgensen A, Schittenhelm RB, Huang C, Robevska G, van den Bergen J, Casagranda F, Cyza J, Pachernegg S, Wright DK, Bahlo M, Oshlack A, O'Brien TJ, Kwan P, Koopman P, Hime GR, Girard N, Hoffmann C, Shilon Y, Zung A, Bertini E, Milh M, Ben Rhouma B, Belguith N, Bashamboo A, McElreavey K, Banne E, Weintrob N, BenZeev B, Sinclair AH. Author Correction: Variants in SART3 cause a spliceosomopathy characterised by failure of testis development and neuronal defects. Nat Commun 2023; 14:3566. [PMID: 37322043 PMCID: PMC10272200 DOI: 10.1038/s41467-023-39372-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Affiliation(s)
- Katie L Ayers
- The Murdoch Children's Research Institute, Melbourne, VIC, Australia.
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia.
| | - Stefanie Eggers
- The Victorian Clinical Genetics Services, Melbourne, VIC, Australia
| | - Ben N Rollo
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, VIC, Australia
| | - Katherine R Smith
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Nadia M Davidson
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- School of BioSciences, Faculty of Science, University of Melbourne, Melbourne, VIC, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Nicole A Siddall
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Liang Zhao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Josephine Bowles
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Institute of Technology, Haifa, Israel
| | - Ginevra Zanni
- Unit of Muscular and Neurodegenerative Disorders and Unit of Developmental Neurology, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lydie Burglen
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Et Laboratoire de Neurogénétique Moléculaire, Département de Génétique et Embryologie Médicale, APHP. Sorbonne Université, Hôpital Trousseau, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Shay Ben-Shachar
- Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Jenny Rosensaft
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Annick Raas-Rothschild
- Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anne Jørgensen
- Department of Growth and Reproduction, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Cheng Huang
- Monash Proteomics and Metabolomics Facility, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Gorjana Robevska
- The Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | | | - Franca Casagranda
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Justyna Cyza
- The Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Svenja Pachernegg
- The Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - David K Wright
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, VIC, Australia
| | - Melanie Bahlo
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Alicia Oshlack
- The Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, Australia
| | - Terrence J O'Brien
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, VIC, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, Australia
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, VIC, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Gary R Hime
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Nadine Girard
- Department of Pediatric Neurology, Aix-Marseille Université, APHM, Timone Hospital, Marseille, France
| | - Chen Hoffmann
- Radiology Department, Sheba medical Centre, Tel Aviv, Israel
| | - Yuval Shilon
- Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Amnon Zung
- Pediatrics Department, Kaplan Medical Center, Rehovot, 76100, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School, Jerusalem, Israel
| | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Disorders and Unit of Developmental Neurology, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Mathieu Milh
- Department of Pediatric Neurology, Aix-Marseille Université, APHM, Timone Hospital, Marseille, France
| | - Bochra Ben Rhouma
- Higher Institute of Nursing Sciences of Gabes, University of Gabes, Gabes, Tunisia
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| | - Neila Belguith
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Anu Bashamboo
- Institut Pasteur, Université de Paris, CNRS UMR3738, Human Developmental Genetics, 75015, Paris, France
| | - Kenneth McElreavey
- Institut Pasteur, Université de Paris, CNRS UMR3738, Human Developmental Genetics, 75015, Paris, France
| | - Ehud Banne
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
- The Rina Mor Genetic Institute, Wolfson Medical Center, Holon, 58100, Israel
| | - Naomi Weintrob
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Pediatric Endocrinology Unit, Dana-Dwek Children's Hospital, Tel Aviv Medical Center, Tel Aviv, Israel
| | | | - Andrew H Sinclair
- The Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
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59
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Oddsson A, Sulem P, Sveinbjornsson G, Arnadottir GA, Steinthorsdottir V, Halldorsson GH, Atlason BA, Oskarsson GR, Helgason H, Nielsen HS, Westergaard D, Karjalainen JM, Katrinardottir H, Fridriksdottir R, Jensson BO, Tragante V, Ferkingstad E, Jonsson H, Gudjonsson SA, Beyter D, Moore KHS, Thordardottir HB, Kristmundsdottir S, Stefansson OA, Rantapää-Dahlqvist S, Sonderby IE, Didriksen M, Stridh P, Haavik J, Tryggvadottir L, Frei O, Walters GB, Kockum I, Hjalgrim H, Olafsdottir TA, Selbaek G, Nyegaard M, Erikstrup C, Brodersen T, Saevarsdottir S, Olsson T, Nielsen KR, Haraldsson A, Bruun MT, Hansen TF, Steingrimsdottir T, Jacobsen RL, Lie RT, Djurovic S, Alfredsson L, Lopez de Lapuente Portilla A, Brunak S, Melsted P, Halldorsson BV, Saemundsdottir J, Magnusson OT, Padyukov L, Banasik K, Rafnar T, Askling J, Klareskog L, Pedersen OB, Masson G, Havdahl A, Nilsson B, Andreassen OA, Daly M, Ostrowski SR, Jonsdottir I, Stefansson H, Holm H, Helgason A, Thorsteinsdottir U, Stefansson K, Gudbjartsson DF. Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality. Nat Commun 2023; 14:3453. [PMID: 37301908 PMCID: PMC10257723 DOI: 10.1038/s41467-023-38951-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Genotypes causing pregnancy loss and perinatal mortality are depleted among living individuals and are therefore difficult to find. To explore genetic causes of recessive lethality, we searched for sequence variants with deficit of homozygosity among 1.52 million individuals from six European populations. In this study, we identified 25 genes harboring protein-altering sequence variants with a strong deficit of homozygosity (10% or less of predicted homozygotes). Sequence variants in 12 of the genes cause Mendelian disease under a recessive mode of inheritance, two under a dominant mode, but variants in the remaining 11 have not been reported to cause disease. Sequence variants with a strong deficit of homozygosity are over-represented among genes essential for growth of human cell lines and genes orthologous to mouse genes known to affect viability. The function of these genes gives insight into the genetics of intrauterine lethality. We also identified 1077 genes with homozygous predicted loss-of-function genotypes not previously described, bringing the total set of genes completely knocked out in humans to 4785.
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Affiliation(s)
| | | | | | - Gudny A Arnadottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | - Henriette Svarre Nielsen
- Deptartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - David Westergaard
- Deptartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Juha M Karjalainen
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | | | | | - Kristjan H S Moore
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Helga B Thordardottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Ida Elken Sonderby
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Maria Didriksen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Pernilla Stridh
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Jan Haavik
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Bergen Center of Brain Plasticity, Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Laufey Tryggvadottir
- Icelandic Cancer Registry, Icelandic Cancer Society, Reykjavik, Iceland
- Faculty of Medicine, BMC, Laeknagardur, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Oleksandr Frei
- NORMENT Centre, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | | | - Ingrid Kockum
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Hjalgrim
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Geir Selbaek
- Norwegian National Centre of Ageing and Health, Vestfold Hospital Trust, Tonsberg, Norway
- Department of Geriatric Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mette Nyegaard
- Deptartment of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Thorsten Brodersen
- Department of Clinical Immunology, Zealand University Hospital, Koge, Denmark
| | - Saedis Saevarsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Kaspar Rene Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Asgeir Haraldsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Children's Hospital Iceland, Landspitali University Hospital, Reykjavik, Iceland
| | - Mie Topholm Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Thora Steingrimsdottir
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Rikke Louise Jacobsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Soren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pall Melsted
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | | | | | - Leonid Padyukov
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Johan Askling
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lars Klareskog
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Ole Birger Pedersen
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Koge, Denmark
| | | | - Alexandra Havdahl
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
| | - Bjorn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund, Sweden
| | - Ole A Andreassen
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Mark Daly
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Deptartment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Hilma Holm
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
| | - Agnar Helgason
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
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60
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Ayers KL, Eggers S, Rollo BN, Smith KR, Davidson NM, Siddall NA, Zhao L, Bowles J, Weiss K, Zanni G, Burglen L, Ben-Shachar S, Rosensaft J, Raas-Rothschild A, Jørgensen A, Schittenhelm RB, Huang C, Robevska G, van den Bergen J, Casagranda F, Cyza J, Pachernegg S, Wright DK, Bahlo M, Oshlack A, O'Brien TJ, Kwan P, Koopman P, Hime GR, Girard N, Hoffmann C, Shilon Y, Zung A, Bertini E, Milh M, Ben Rhouma B, Belguith N, Bashamboo A, McElreavey K, Banne E, Weintrob N, BenZeev B, Sinclair AH. Variants in SART3 cause a spliceosomopathy characterised by failure of testis development and neuronal defects. Nat Commun 2023; 14:3403. [PMID: 37296101 PMCID: PMC10256788 DOI: 10.1038/s41467-023-39040-0] [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: 04/03/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Squamous cell carcinoma antigen recognized by T cells 3 (SART3) is an RNA-binding protein with numerous biological functions including recycling small nuclear RNAs to the spliceosome. Here, we identify recessive variants in SART3 in nine individuals presenting with intellectual disability, global developmental delay and a subset of brain anomalies, together with gonadal dysgenesis in 46,XY individuals. Knockdown of the Drosophila orthologue of SART3 reveals a conserved role in testicular and neuronal development. Human induced pluripotent stem cells carrying patient variants in SART3 show disruption to multiple signalling pathways, upregulation of spliceosome components and demonstrate aberrant gonadal and neuronal differentiation in vitro. Collectively, these findings suggest that bi-allelic SART3 variants underlie a spliceosomopathy which we tentatively propose be termed INDYGON syndrome (Intellectual disability, Neurodevelopmental defects and Developmental delay with 46,XY GONadal dysgenesis). Our findings will enable additional diagnoses and improved outcomes for individuals born with this condition.
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Affiliation(s)
- Katie L Ayers
- The Murdoch Children's Research Institute, Melbourne, Australia.
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia.
| | - Stefanie Eggers
- The Victorian Clinical Genetics Services, Melbourne, Australia
| | - Ben N Rollo
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
| | - Katherine R Smith
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Nadia M Davidson
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- School of BioSciences, Faculty of Science, University of Melbourne, Melbourne, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Nicole A Siddall
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Liang Zhao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Josephine Bowles
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Institute of Technology, Haifa, Israel
| | - Ginevra Zanni
- Unit of Muscular and Neurodegenerative Disorders and Unit of Developmental Neurology, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lydie Burglen
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Et Laboratoire de Neurogénétique Moléculaire, Département de Génétique et Embryologie Médicale, APHP. Sorbonne Université, Hôpital Trousseau, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Shay Ben-Shachar
- Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Jenny Rosensaft
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Annick Raas-Rothschild
- Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anne Jørgensen
- Department of Growth and Reproduction, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Cheng Huang
- Monash Proteomics and Metabolomics Facility, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | | | | | - Franca Casagranda
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Justyna Cyza
- The Murdoch Children's Research Institute, Melbourne, Australia
| | - Svenja Pachernegg
- The Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - David K Wright
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
| | - Melanie Bahlo
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Alicia Oshlack
- The Peter MacCallum Cancer Centre, Melbourne, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Terrence J O'Brien
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, Australia
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Gary R Hime
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Nadine Girard
- Aix-Marseille Université, APHM. Department of Pediatric Neurology, Timone Hospital, Marseille, France
| | - Chen Hoffmann
- Radiology Department, Sheba medical Centre, Tel Aviv, Israel
| | - Yuval Shilon
- Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Amnon Zung
- Pediatrics Department, Kaplan Medical Center, Rehovot, 76100, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School, Jerusalem, Israel
| | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Disorders and Unit of Developmental Neurology, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Mathieu Milh
- Aix-Marseille Université, APHM. Department of Pediatric Neurology, Timone Hospital, Marseille, France
| | - Bochra Ben Rhouma
- Higher Institute of Nursing Sciences of Gabes, University of Gabes, Gabes, Tunisia
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| | - Neila Belguith
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Anu Bashamboo
- Institut Pasteur, Université de Paris, CNRS UMR3738, Human Developmental Genetics, 75015, Paris, France
| | - Kenneth McElreavey
- Institut Pasteur, Université de Paris, CNRS UMR3738, Human Developmental Genetics, 75015, Paris, France
| | - Ehud Banne
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
- The Rina Mor Genetic Institute, Wolfson Medical Center, Holon, 58100, Israel
| | - Naomi Weintrob
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Pediatric Endocrinology Unit, Dana-Dwek Children's Hospital, Tel Aviv Medical Center, Tel Aviv, Israel
| | | | - Andrew H Sinclair
- The Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
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61
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Leggatt G, Cheng G, Narain S, Briseño-Roa L, Annereau JP, Gast C, Gilbert RD, Ennis S. A genotype-to-phenotype approach suggests under-reporting of single nucleotide variants in nephrocystin-1 (NPHP1) related disease (UK 100,000 Genomes Project). Sci Rep 2023; 13:9369. [PMID: 37296294 PMCID: PMC10256716 DOI: 10.1038/s41598-023-32169-4] [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: 08/26/2022] [Accepted: 03/23/2023] [Indexed: 06/12/2023] Open
Abstract
Autosomal recessive whole gene deletions of nephrocystin-1 (NPHP1) result in abnormal structure and function of the primary cilia. These deletions can result in a tubulointerstitial kidney disease known as nephronophthisis and retinal (Senior-Løken syndrome) and neurological (Joubert syndrome) diseases. Nephronophthisis is a common cause of end-stage kidney disease (ESKD) in children and up to 1% of adult onset ESKD. Single nucleotide variants (SNVs) and small insertions and deletions (Indels) have been less well characterised. We used a gene pathogenicity scoring system (GenePy) and a genotype-to-phenotype approach on individuals recruited to the UK Genomics England (GEL) 100,000 Genomes Project (100kGP) (n = 78,050). This approach identified all participants with NPHP1-related diseases reported by NHS Genomics Medical Centres and an additional eight participants. Extreme NPHP1 gene scores, often underpinned by clear recessive inheritance, were observed in patients from diverse recruitment categories, including cancer, suggesting the possibility of a more widespread disease than previously appreciated. In total, ten participants had homozygous CNV deletions with eight homozygous or compound heterozygous with SNVs. Our data also reveals strong in-silico evidence that approximately 44% of NPHP1 related disease may be due to SNVs with AlphaFold structural modelling evidence for a significant impact on protein structure. This study suggests historical under-reporting of SNVS in NPHP1 related diseases compared with CNVs.
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Affiliation(s)
- Gary Leggatt
- University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK.
- Wessex Kidney Centre, Portsmouth Hospitals University NHS Trust, Southwick Hill Road, Cosham, Portsmouth, PO6 3LY, UK.
- University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK.
| | - Guo Cheng
- University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK
| | - Sumit Narain
- University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK
| | - Luis Briseño-Roa
- Medetia, Imagine Institute for Genetic Diseases, 24 Boulevard du Montparnasse, 75015, Paris, France
| | - Jean-Philippe Annereau
- Medetia, Imagine Institute for Genetic Diseases, 24 Boulevard du Montparnasse, 75015, Paris, France
| | - Christine Gast
- University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK
- Wessex Kidney Centre, Portsmouth Hospitals University NHS Trust, Southwick Hill Road, Cosham, Portsmouth, PO6 3LY, UK
| | - Rodney D Gilbert
- University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK
- Southampton Children's Hospital, Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK
| | - Sarah Ennis
- University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road Shirley, Southampton, SO16 6YD, UK
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62
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Imanishi R, Nakau K, Shimada S, Oka H, Takeguchi R, Tanaka R, Sugiyama T, Nii M, Okamoto T, Nagaya K, Makita Y, Yanagi K, Kaname T, Takahashi S. A novel HECW2 variant in an infant with congenital long QT syndrome. Hum Genome Var 2023; 10:17. [PMID: 37280227 PMCID: PMC10244414 DOI: 10.1038/s41439-023-00245-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/04/2023] [Accepted: 05/11/2023] [Indexed: 06/08/2023] Open
Abstract
Pathogenic variants of HECW2 have been reported in cases of neurodevelopmental disorder with hypotonia, seizures, and absent language (NDHSAL; OMIM #617268). A novel HECW2 variant (NM_001348768.2:c.4343 T > C,p.Leu1448Ser) was identified in an NDHSAL infant with severe cardiac comorbidities. The patient presented with fetal tachyarrhythmia and hydrops and was postnatally diagnosed with long QT syndrome. This study provides evidence that HECW2 pathogenic variants can cause long QT syndrome along with neurodevelopmental disorders.
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Affiliation(s)
- Rina Imanishi
- Department of Pediatrics, Asahikawa Medical University, Hokkaido, Japan
| | - Kouichi Nakau
- Department of Pediatrics, Asahikawa Medical University, Hokkaido, Japan
| | - Sorachi Shimada
- Department of Pediatrics, Asahikawa Medical University, Hokkaido, Japan
| | - Hideharu Oka
- Department of Pediatrics, Asahikawa Medical University, Hokkaido, Japan
| | - Ryo Takeguchi
- Department of Pediatrics, Asahikawa Medical University, Hokkaido, Japan
| | - Ryosuke Tanaka
- Department of Pediatrics, Asahikawa Medical University, Hokkaido, Japan
| | - Tatsutoshi Sugiyama
- Division of Neonatology, Center for Maternity and Infant Care, Asahikawa Medical University Hospital, Hokkaido, Japan
| | - Mitsumaro Nii
- Division of Neonatology, Center for Maternity and Infant Care, Asahikawa Medical University Hospital, Hokkaido, Japan
| | - Toshio Okamoto
- Division of Neonatology, Center for Maternity and Infant Care, Asahikawa Medical University Hospital, Hokkaido, Japan
| | - Ken Nagaya
- Division of Neonatology, Center for Maternity and Infant Care, Asahikawa Medical University Hospital, Hokkaido, Japan
| | - Yoshio Makita
- Department of Genetic Counseling, Asahikawa Medical University Hospital, Hokkaido, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Satoru Takahashi
- Department of Pediatrics, Asahikawa Medical University, Hokkaido, Japan.
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63
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Pennings M, Meijer RPP, Gerrits M, Janssen J, Pfundt R, de Leeuw N, Gilissen C, Gardeitchik T, Schouten M, Voermans N, van de Warrenburg B, Kamsteeg EJ. Copy number variants from 4800 exomes contribute to ~7% of genetic diagnoses in movement disorders, muscle disorders and neuropathies. Eur J Hum Genet 2023; 31:654-662. [PMID: 36781956 PMCID: PMC10250492 DOI: 10.1038/s41431-023-01312-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/11/2023] [Accepted: 02/01/2023] [Indexed: 02/15/2023] Open
Abstract
Various groups of neurological disorders, including movement disorders and neuromuscular diseases, are clinically and genetically heterogeneous. Diagnostic panel-based exome sequencing is a routine test for these disorders. Despite the success rates of exome sequencing, it results in the detection of causative sequence variants in 'only' 25-30% of cases. Copy number variants (CNVs), i.e. deletion or duplications, explain 10-20% of individuals with multisystemic phenotypes, such as co-existing intellectual disability, but may also have a role in disorders affecting a single system (organ), like neurological disorders with normal intelligence. In this study, CNVs were extracted from clinical exome sequencing reports of 4800 probands primarily with a movement disorder, myopathy or neuropathy. In 88 (~2%) probands, phenotype-matching CNVs were detected, representing ~7% of genetically confirmed cases. CNVs varied from involvement of over 100 genes to single exons and explained X-linked, autosomal dominant, or - recessive disorders, the latter due to either a homozygous CNV or a compound heterozygous CNV with a sequence variant on the other allele. CNVs were detected affecting genes where deletions or duplications are established as a common mechanism, like PRKN (in Parkinson's disease), DMD (in Duchenne muscular dystrophy) and PMP22 (in neuropathies), but also genes in which no intragenic CNVs have been reported to date. Analysis of CNVs as part of panel-based exome sequencing for genetically heterogeneous neurological diseases provides an additional diagnostic yield of ~2% without extra laboratory costs. Therefore it is recommended to perform CNV analysis for movement disorders, muscle disease, neuropathies, or any other single-system disorder.
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Affiliation(s)
- Maartje Pennings
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Rowdy P P Meijer
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Monique Gerrits
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Jannie Janssen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Thatjana Gardeitchik
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Meyke Schouten
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Nicol Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical Center, Nijmegen, the Netherlands
| | - Bart van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical Center, Nijmegen, the Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.
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64
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Amenta S, Marangi G, Orteschi D, Frangella S, Gurrieri F, Paccagnella E, Scala M, Romano F, Capra V, Nigro V, Zollino M. CHAMP1-related disorders: pathomechanisms triggered by different genomic alterations define distinct nosological categories. Eur J Hum Genet 2023; 31:648-653. [PMID: 36797464 PMCID: PMC10250409 DOI: 10.1038/s41431-023-01305-z] [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: 09/20/2022] [Revised: 01/17/2023] [Accepted: 01/25/2023] [Indexed: 02/18/2023] Open
Abstract
Loss-of-function variants in CHAMP1 were recently described as cause of a neurodevelopmental disorder characterized by intellectual disability (ID), autism, and distinctive facial characteristics. By exome sequencing (ES), we identified a truncating variant in CHAMP1, c.1858A > T (p.Lys620*), in a patient who exhibited a similar phenotype of severe ID and dysmorphisms. Whether haploinsufficiency or a dominant negative effect is the underlying pathomechanism in these cases is a question that still needs to be addressed. By array-CGH, we detected a 194 kb deletion in 13q34 encompassing CHAMP1, CDC16 and UPF3, in another patient who presented with borderline neurodevelopmental impairment and with no dysmorphisms. In a further patient suffering from early onset refractory seizures, we detected by ES a missense variant in CHAMP1, c.67 G > A (p.Gly23Ser). Genomic abnormalities were all de novo in our patients. We reviewed the clinical and the genetic data of patients reported in the literature with: loss-of-function variants in CHAMP1 (total 40); chromosome 13q34 deletions ranging from 1.1 to 4 Mb (total 7) and of the unique patient with a missense variant. We could infer that loss-of-function variants in CHAMP1 cause a homogeneous phenotype with severe ID, autism spectrum disorders (ASD) and highly distinctive facial characteristics through a dominant negative effect. CHAMP1 haploinsufficiency results in borderline ID with negligible consequences on the quality of life. Missense variants give rise to a severe epileptic encephalopathy through gain-of-function mechanism, most likely. We tentatively define for the first time distinct categories among the CHAMP1-related disorder on the basis of pathomechanisms.
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Affiliation(s)
- Simona Amenta
- Department of Biomedical Sciences, Clinical Genetics Service, Azienda Ospedaliero-Universitaria di Sassari, Sassari, Italy
| | - Giuseppe Marangi
- Genomic Medicine, Policlinico Universitario "A. Gemelli" Foundation IRCCS, Rome, Italy
- Department of Life Sciences and Public Health, Catholic University, Rome, Italy
| | - Daniela Orteschi
- Genomic Medicine, Policlinico Universitario "A. Gemelli" Foundation IRCCS, Rome, Italy
| | - Silvia Frangella
- Genomic Medicine, Policlinico Universitario "A. Gemelli" Foundation IRCCS, Rome, Italy
- Department of Life Sciences and Public Health, Catholic University, Rome, Italy
| | - Fiorella Gurrieri
- Unit of Medical and Functional Genetics, University Campus Bio-Medico, Rome, Italy
| | - Elisa Paccagnella
- Department of Medical-Surgical Sciences and Biotechnologies, La Sapienza University, Rome, Italy
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Ferruccio Romano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Valeria Capra
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Marcella Zollino
- Genomic Medicine, Policlinico Universitario "A. Gemelli" Foundation IRCCS, Rome, Italy.
- Department of Life Sciences and Public Health, Catholic University, Rome, Italy.
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65
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Asahina Y, Tahara U, Aoki S, Nakabayashi K, Tateishi C, Hayashi D, Amagai M, Tsuruta D, Kubo A. Two sporadic cases of childhood-onset Hailey-Hailey disease with superimposed mosaicism. Eur J Hum Genet 2023; 31:716-720. [PMID: 36922631 PMCID: PMC10250405 DOI: 10.1038/s41431-023-01316-w] [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: 03/29/2022] [Revised: 11/09/2022] [Accepted: 02/03/2023] [Indexed: 03/18/2023] Open
Abstract
A prenatal second-hit genetic change that occurs on the wild-type allele in an embryo with a congenital pathogenic variant allele results in mosaicism of monoallelic and biallelic defect of the gene, which is called superimposed mosaicism. Superimposed mosaicism of Hailey-Hailey disease (HHD) has been demonstrated in one familial case. Here, we report two unrelated HHD cases with superimposed mosaicism: a congenital monoallelic pathogenic variant of ATP2C1, followed by a postzygotic copy-neutral loss of heterozygosity. Uniquely, neither patient had a family history of HHD at the time of presentation. In the first case, the congenital pathogenic variant had occurred de novo. In the second case, the father had the pathogenic variant but had not yet developed skin symptoms. Our cases showed that superimposed mosaicism in HHD can lack a family history and that genetic analysis is crucial to classify the type of mosaicism and evaluate the risk of familial occurrence.
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Affiliation(s)
- Yasuhiko Asahina
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Umi Tahara
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Satomi Aoki
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Center for Child Health and Development, Tokyo, Japan
| | - Chiharu Tateishi
- Department of Dermatology, Osaka Metropolitan University, Medical School, Osaka, Japan
| | - Daisuke Hayashi
- Department of Dermatology, Osaka Metropolitan University, Medical School, Osaka, Japan
| | - Masayuki Amagai
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Daisuke Tsuruta
- Department of Dermatology, Osaka Metropolitan University, Medical School, Osaka, Japan
| | - Akiharu Kubo
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan.
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe, Japan.
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66
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Perry DJ, Shapiro MR, Chamberlain SW, Kusmartseva I, Chamala S, Balzano-Nogueira L, Yang M, Brant JO, Brusko M, Williams MD, McGrail KM, McNichols J, Peters LD, Posgai AL, Kaddis JS, Mathews CE, Wasserfall CH, Webb-Robertson BJM, Campbell-Thompson M, Schatz D, Evans-Molina C, Pugliese A, Concannon P, Anderson MS, German MS, Chamberlain CE, Atkinson MA, Brusko TM. A genomic data archive from the Network for Pancreatic Organ donors with Diabetes. Sci Data 2023; 10:323. [PMID: 37237059 PMCID: PMC10219990 DOI: 10.1038/s41597-023-02244-6] [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: 12/24/2022] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The Network for Pancreatic Organ donors with Diabetes (nPOD) is the largest biorepository of human pancreata and associated immune organs from donors with type 1 diabetes (T1D), maturity-onset diabetes of the young (MODY), cystic fibrosis-related diabetes (CFRD), type 2 diabetes (T2D), gestational diabetes, islet autoantibody positivity (AAb+), and without diabetes. nPOD recovers, processes, analyzes, and distributes high-quality biospecimens, collected using optimized standard operating procedures, and associated de-identified data/metadata to researchers around the world. Herein describes the release of high-parameter genotyping data from this collection. 372 donors were genotyped using a custom precision medicine single nucleotide polymorphism (SNP) microarray. Data were technically validated using published algorithms to evaluate donor relatedness, ancestry, imputed HLA, and T1D genetic risk score. Additionally, 207 donors were assessed for rare known and novel coding region variants via whole exome sequencing (WES). These data are publicly-available to enable genotype-specific sample requests and the study of novel genotype:phenotype associations, aiding in the mission of nPOD to enhance understanding of diabetes pathogenesis to promote the development of novel therapies.
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Affiliation(s)
- Daniel J Perry
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Melanie R Shapiro
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Sonya W Chamberlain
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Irina Kusmartseva
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Srikar Chamala
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Leandro Balzano-Nogueira
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Mingder Yang
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Jason O Brant
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL, 32610, USA
| | - Maigan Brusko
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - MacKenzie D Williams
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Kieran M McGrail
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - James McNichols
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Leeana D Peters
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Amanda L Posgai
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - John S Kaddis
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Clayton E Mathews
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Department of Pediatrics, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Clive H Wasserfall
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Bobbie-Jo M Webb-Robertson
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Department of Biomedical Engineering, College of Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Desmond Schatz
- Department of Pediatrics, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Carmella Evans-Molina
- Center for Diabetes and Metabolic Diseases and the Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Alberto Pugliese
- Diabetes Research Institute, Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, 33021, USA
| | - Patrick Concannon
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32601, USA
| | - Mark S Anderson
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Michael S German
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Chester E Chamberlain
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA.
- Department of Pediatrics, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA.
- Department of Pediatrics, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
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Zöllner J, Finer S, Linton KJ, van Heel DA, Williamson C, Dixon PH. Rare variant contribution to cholestatic liver disease in a South Asian population in the United Kingdom. Sci Rep 2023; 13:8120. [PMID: 37208429 PMCID: PMC10199085 DOI: 10.1038/s41598-023-33391-w] [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: 12/14/2022] [Accepted: 04/12/2023] [Indexed: 05/21/2023] Open
Abstract
This study assessed the contribution of five genes previously known to be involved in cholestatic liver disease in British Bangladeshi and Pakistani people. Five genes (ABCB4, ABCB11, ATP8B1, NR1H4, TJP2) were interrogated by exome sequencing data of 5236 volunteers. Included were non-synonymous or loss of function (LoF) variants with a minor allele frequency < 5%. Variants were filtered, and annotated to perform rare variant burden analysis, protein structure, and modelling analysis in-silico. Out of 314 non-synonymous variants, 180 fulfilled the inclusion criteria and were mostly heterozygous unless specified. 90 were novel and of those variants, 22 were considered likely pathogenic and 9 pathogenic. We identified variants in volunteers with gallstone disease (n = 31), intrahepatic cholestasis of pregnancy (ICP, n = 16), cholangiocarcinoma and cirrhosis (n = 2). Fourteen novel LoF variants were identified: 7 frameshift, 5 introduction of premature stop codon and 2 splice acceptor variants. The rare variant burden was significantly increased in ABCB11. Protein modelling demonstrated variants that appeared to likely cause significant structural alterations. This study highlights the significant genetic burden contributing to cholestatic liver disease. Novel likely pathogenic and pathogenic variants were identified addressing the underrepresentation of diverse ancestry groups in genomic research.
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Affiliation(s)
| | - Sarah Finer
- Institute for Population Health Sciences, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Kenneth J Linton
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Catherine Williamson
- Department of Women and Children's Health, School of Life Course Sciences, FOLSM, King's College London, 2.30W Hodgkin Building, Guy's Campus, London, SE1 1UL, UK.
| | - Peter H Dixon
- Department of Women and Children's Health, School of Life Course Sciences, FOLSM, King's College London, 2.30W Hodgkin Building, Guy's Campus, London, SE1 1UL, UK
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Fortugno P, Monetta R, Cinquina V, Rigon C, Boaretto F, De Luca C, Zoppi N, Di Leandro L, De Domenico E, Di Daniele A, Ippoliti R, Angelucci F, Di Cesare E, De Paulis R, Salviati L, Colombi M, Brancati F, Ritelli M. Truncating variants in the penultimate exon of TGFBR1 escaping nonsense-mediated mRNA decay cause Loeys-Dietz syndrome. Eur J Hum Genet 2023; 31:596-601. [PMID: 36599937 PMCID: PMC10172188 DOI: 10.1038/s41431-022-01279-4] [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: 10/21/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023] Open
Abstract
Pathogenic variants in TGFBR1 are a common cause of Loeys-Dietz syndrome (LDS) characterized by life-threatening aortic and arterial disease. Generally, these are missense changes in highly conserved amino acids in the serine-threonine kinase domain. Conversely, nonsense, frameshift, or specific missense changes in the ligand-binding extracellular domain cause multiple self-healing squamous epithelioma (MSSE) lacking the cardiovascular phenotype. Here, we report on two novel variants in the penultimate exon 8 of TGFBR1 were identified in 3 patients from two unrelated LDS families: both were predicted to cause frameshift and premature stop codons (Gln448Profs*15 and Cys446Asnfs*4) resulting in truncated TGFBR1 proteins lacking the last 43 and 56 amino acid residues, respectively. These were classified as variants of uncertain significance based on current criteria. Transcript expression analyses revealed both mutant alleles escaped nonsense-mediated mRNA decay. Functional characterization in patient's dermal fibroblasts showed paradoxically enhanced TGFβ signaling, as observed for pathogenic missense TGFBR1 changes causative of LDS. In summary, we expanded the allelic repertoire of LDS-associated TGFBR1 variants to include truncating variants escaping nonsense-mediated mRNA decay. Our data highlight the importance of functional studies in variants interpretation for correct clinical diagnosis.
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Affiliation(s)
- Paola Fortugno
- Human Functional Genetics Laboratory, IRCCS San Raffaele Roma, Rome, Italy
- Università Telematica San Raffaele, Rome, Italy
| | - Rosanna Monetta
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Valeria Cinquina
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Chiara Rigon
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, Padua, Italy
- IRP Città della Speranza, Padua, Italy
| | - Francesca Boaretto
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, Padua, Italy
- IRP Città della Speranza, Padua, Italy
| | - Chiara De Luca
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Nicoletta Zoppi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Luana Di Leandro
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Emanuela De Domenico
- Laboratory of Molecular and Cell Biology, Istituto Dermopatico dell'Immacolata IDI-IRCCS, Rome, Italy
| | - Arianna Di Daniele
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Rodolfo Ippoliti
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Francesco Angelucci
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Ernesto Di Cesare
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Leonardo Salviati
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, Padua, Italy
- IRP Città della Speranza, Padua, Italy
| | - Marina Colombi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Francesco Brancati
- Human Functional Genetics Laboratory, IRCCS San Raffaele Roma, Rome, Italy.
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Marco Ritelli
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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Aishworiya R, Hwang YH, Santos E, Hayward B, Usdin K, Durbin-Johnson B, Hagerman R, Tassone F. Clinical implications of somatic allele expansion in female FMR1 premutation carriers. Sci Rep 2023; 13:7050. [PMID: 37120588 PMCID: PMC10148869 DOI: 10.1038/s41598-023-33528-x] [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: 11/10/2022] [Accepted: 04/14/2023] [Indexed: 05/01/2023] Open
Abstract
Carriers of a premutation allele (PM) in the FMR1 gene are at risk of developing a number of Fragile X premutation asssociated disorders (FXPAC), including Fragile X-associated Tremor/Ataxia Syndrome (FXTAS), Fragile X-associated Primary Ovarian Insufficiency (FXPOI), and Fragile X-associated neuropsychiatric disorders (FXAND). We have recently reported somatic CGG allele expansion in female PM; however, its clinical significance remains unclear. The aim of this study was to examine the potential clinical association between somatic FMR1 allele instability and PM associated disorders. Participants comprised of 424 female PM carriers age 0.3- 90 years. FMR1 molecular measures and clinical information on the presence of medical conditions, were determined for all subjects for primary analysis. Two sub-groups of participants (age ≥ 25, N = 377 and age ≥ 50, N = 134) were used in the analysis related to presence of FXPOI and FXTAS, respectively. Among all participants (N = 424), the degree of instability (expansion) was significantly higher (median 2.5 vs 2.0, P = 0.026) in participants with a diagnosis of attention deficit hyperactivity disorder (ADHD) compared to those without. FMR1 mRNA expression was significantly higher in subjects with any psychiatric disorder diagnosis (P = 0.0017); specifically, in those with ADHD (P = 0.009), and with depression (P = 0.025). Somatic FMR1 expansion was associated with the presence of ADHD in female PM and FMR1 mRNA levels were associated with the presence of mental health disorders. The findings of our research are innovative as they suggest a potential role of the CGG expansion in the clinical phenotype of PM and may potentially guide clinical prognosis and management.
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Affiliation(s)
- Ramkumar Aishworiya
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50Th Street, Sacramento, CA, 95817, USA
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Singapore
| | - Ye Hyun Hwang
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA
| | - Ellery Santos
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50Th Street, Sacramento, CA, 95817, USA
- Department of Pediatrics, University of California Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA
| | - Bruce Hayward
- Laboratory of Cell and Molecular Biology, Digestive and Kidney Diseases, National Institute of Diabetes, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Karen Usdin
- Laboratory of Cell and Molecular Biology, Digestive and Kidney Diseases, National Institute of Diabetes, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Blythe Durbin-Johnson
- Department of Public Health Sciences, University of California, Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA
| | - Randi Hagerman
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50Th Street, Sacramento, CA, 95817, USA
- Department of Pediatrics, University of California Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA
| | - Flora Tassone
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50Th Street, Sacramento, CA, 95817, USA.
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA.
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70
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Wu Y, Gettler K, Kars ME, Giri M, Li D, Bayrak CS, Zhang P, Jain A, Maffucci P, Sabic K, Van Vleck T, Nadkarni G, Denson LA, Ostrer H, Levine AP, Schiff ER, Segal AW, Kugathasan S, Stenson PD, Cooper DN, Philip Schumm L, Snapper S, Daly MJ, Haritunians T, Duerr RH, Silverberg MS, Rioux JD, Brant SR, McGovern DPB, Cho JH, Itan Y. Identifying high-impact variants and genes in exomes of Ashkenazi Jewish inflammatory bowel disease patients. Nat Commun 2023; 14:2256. [PMID: 37080976 PMCID: PMC10119186 DOI: 10.1038/s41467-023-37849-3] [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: 09/06/2021] [Accepted: 04/03/2023] [Indexed: 04/22/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a group of chronic digestive tract inflammatory conditions whose genetic etiology is still poorly understood. The incidence of IBD is particularly high among Ashkenazi Jews. Here, we identify 8 novel and plausible IBD-causing genes from the exomes of 4453 genetically identified Ashkenazi Jewish IBD cases (1734) and controls (2719). Various biological pathway analyses are performed, along with bulk and single-cell RNA sequencing, to demonstrate the likely physiological relatedness of the novel genes to IBD. Importantly, we demonstrate that the rare and high impact genetic architecture of Ashkenazi Jewish adult IBD displays significant overlap with very early onset-IBD genetics. Moreover, by performing biobank phenome-wide analyses, we find that IBD genes have pleiotropic effects that involve other immune responses. Finally, we show that polygenic risk score analyses based on genome-wide high impact variants have high power to predict IBD susceptibility.
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Affiliation(s)
- Yiming Wu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kyle Gettler
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Meltem Ece Kars
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dalin Li
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Cigdem Sevim Bayrak
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Aayushee Jain
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick Maffucci
- Immunology Institute, Graduate School, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Ksenija Sabic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tielman Van Vleck
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lee A Denson
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Harry Ostrer
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Adam P Levine
- Division of Medicine, University College London (UCL), London, UK
- Research Department of Pathology, University College London (UCL), London, UK
| | - Elena R Schiff
- Division of Medicine, University College London (UCL), London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Anthony W Segal
- Division of Medicine, University College London (UCL), London, UK
| | | | - Peter D Stenson
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - L Philip Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Scott Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Oncology Boston Children's Hospital, Boston, MA, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Talin Haritunians
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Mark S Silverberg
- Inflammatory Bowel Disease Centre, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Steven R Brant
- Division of Gastroenterology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dermot P B McGovern
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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71
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Melo US, Jatzlau J, Prada-Medina CA, Flex E, Hartmann S, Ali S, Schöpflin R, Bernardini L, Ciolfi A, Moeinzadeh MH, Klever MK, Altay A, Vallecillo-García P, Carpentieri G, Delledonne M, Ort MJ, Schwestka M, Ferrero GB, Tartaglia M, Brusco A, Gossen M, Strunk D, Geißler S, Mundlos S, Stricker S, Knaus P, Giorgio E, Spielmann M. Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation. Nat Commun 2023; 14:2034. [PMID: 37041138 PMCID: PMC10090176 DOI: 10.1038/s41467-023-37585-8] [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: 06/08/2022] [Accepted: 03/21/2023] [Indexed: 04/13/2023] Open
Abstract
Heterotopic ossification is a disorder caused by abnormal mineralization of soft tissues in which signaling pathways such as BMP, TGFβ and WNT are known key players in driving ectopic bone formation. Identifying novel genes and pathways related to the mineralization process are important steps for future gene therapy in bone disorders. In this study, we detect an inter-chromosomal insertional duplication in a female proband disrupting a topologically associating domain and causing an ultra-rare progressive form of heterotopic ossification. This structural variant lead to enhancer hijacking and misexpression of ARHGAP36 in fibroblasts, validated here by orthogonal in vitro studies. In addition, ARHGAP36 overexpression inhibits TGFβ, and activates hedgehog signaling and genes/proteins related to extracellular matrix production. Our work on the genetic cause of this heterotopic ossification case has revealed that ARHGAP36 plays a role in bone formation and metabolism, outlining first details of this gene contributing to bone-formation and -disease.
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Affiliation(s)
- Uirá Souto Melo
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany.
- Institute for Medical Genetics and Human Genetics, Charité University Medicine Berlin, 13353, Berlin, Germany.
| | - Jerome Jatzlau
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, 14195, Berlin, Germany
| | - Cesar A Prada-Medina
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
| | - Elisabetta Flex
- Istituto Superiore di Sanità, Department of Oncology and Molecular Medicine, 00161, Rome, Italy
| | - Sunhild Hartmann
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
| | - Salaheddine Ali
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
| | - Laura Bernardini
- Cytogenetics Unit, Casa Sollievo della Sofferenza Foundation, IRCCS, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - M-Hossein Moeinzadeh
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, 14195, Berlin, Germany
| | - Marius-Konstantin Klever
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité University Medicine Berlin, 13353, Berlin, Germany
| | - Aybuge Altay
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, 14195, Berlin, Germany
| | | | - Giovanna Carpentieri
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Melanie-Jasmin Ort
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, 14195, Berlin, Germany
- Julius Wolff Institute (JWI), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Marko Schwestka
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513, Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353, Berlin, Germany
| | | | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10126, Torino, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, 10126, Italy
| | - Manfred Gossen
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513, Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353, Berlin, Germany
| | - Dirk Strunk
- Cell Therapy Institute, Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University (PMU), 5020, Salzburg, Austria
| | - Sven Geißler
- Julius Wolff Institute (JWI), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353, Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité University Medicine Berlin, 13353, Berlin, Germany
| | - Sigmar Stricker
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, 14195, Berlin, Germany
| | - Petra Knaus
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, 14195, Berlin, Germany
| | - Elisa Giorgio
- Department of Molecular Medicine, University of Pavia, 27100, Pavia, Italy.
- Medical Genetics Unit, IRCCS Mondino Foundation, 27100, Pavia, Italy.
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany.
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and University of Kiel, Lübeck, 23562, Germany.
- DZHK (German Centre for Cardiovascular Research) Germany, partner site Hamburg, Lübeck, Kiel, Lübeck, 23562, Germany.
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72
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Soltysova A, Sekelska M, Zatkova A. Breakpoints characterisation of the genomic deletions identified by MLPA in alkaptonuria patients. Eur J Hum Genet 2023; 31:485-489. [PMID: 35110678 PMCID: PMC10133314 DOI: 10.1038/s41431-022-01042-9] [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: 08/24/2021] [Revised: 12/22/2021] [Accepted: 01/10/2022] [Indexed: 11/09/2022] Open
Abstract
Until recently, mainly DNA sequencing has been used to identify variants within the gene coding for homogentisate dioxygenase (HGD, 3q13.33) that cause alkaptonuria (AKU), an autosomal recessive inborn error of metabolism of tyrosine. In order to identify possible larger genomic deletions we have developed a novel Multiplex Ligation-dependent Probe Amplification (MLPA) assay specific for this gene (HGD-MLPA) and tested it successfully in healthy controls and in patients carrying two known previously identified HGD deletions. Subsequently, we analysed 22 AKU patients in whom only one or none classical HGD variant was found by sequencing. Using HGD-MLPA and sequencing, we identified four larger deletions encompassing from 1 to 4 exons of this gene and we defined their exact breakpoints: deletion of exons 1-4 (c.1-8460_282 + 6727del), deletion of exons 5 and 6 (c.283-9199_434 + 1688del), deletion of exon 11 (c.775-1915_879 + 1293del), and deletion of exon 13 (c.1007-1709_1188 + 1121del). We suggest including MLPA in the DNA diagnostic protocols for AKU in cases where DNA sequencing does not lead to identification of both HGD variants.
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Affiliation(s)
- Andrea Soltysova
- Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 841 04, Bratislava, Slovakia
| | - Martina Sekelska
- Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - Andrea Zatkova
- Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia.
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73
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Piceci-Sparascio F, Micale L, Torres B, Guida V, Consoli F, Torrente I, Onori A, Frustaci E, D'Asdia MC, Petrizzelli F, Bernardini L, Mancini C, Soli F, Cocciadiferro D, Guadagnolo D, Mastromoro G, Putotto C, Fontana F, Brunetti-Pierri N, Novelli A, Pizzuti A, Marino B, Digilio MC, Mazza T, Dallapiccola B, Ruiz-Perez VL, Tartaglia M, Castori M, De Luca A. Clinical variability in DYNC2H1-related skeletal ciliopathies includes Ellis-van Creveld syndrome. Eur J Hum Genet 2023; 31:479-484. [PMID: 36599940 PMCID: PMC10133340 DOI: 10.1038/s41431-022-01276-7] [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: 08/19/2022] [Revised: 11/17/2022] [Accepted: 12/15/2022] [Indexed: 01/06/2023] Open
Abstract
Deleterious variants of DYNC2H1 gene are associated with a wide spectrum of skeletal ciliopathies (SC). We used targeted parallel sequencing to analyze 25 molecularly unsolved families with different SCs. Deleterious DYNC2H1 variants were found in six sporadic patients and two monozygotic (MZ) twins. Clinical diagnoses included short rib-polydactyly type 3 in two cases, and asphyxiating thoracic dystrophy (ATD) in one case. Remarkably, clinical diagnosis fitted with EvC, mixed ATD/EvC and short rib-polydactyly/EvC phenotypes in three sporadic patients and the MZ twins. EvC/EvC-like features always occurred in compound heterozygotes sharing a previously unreported splice site change (c.6140-5A>G) or compound heterozygotes for two missense variants. These results expand the DYNC2H1 mutational repertoire and its clinical spectrum, suggesting that EvC may be occasionally caused by DYNC2H1 variants presumably acting as hypomorphic alleles.
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Affiliation(s)
- Francesca Piceci-Sparascio
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Lucia Micale
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Barbara Torres
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Valentina Guida
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Federica Consoli
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Isabella Torrente
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Annamaria Onori
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Emanuela Frustaci
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Maria Cecilia D'Asdia
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Francesco Petrizzelli
- Laboratory of Bioinformatics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Laura Bernardini
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Cecilia Mancini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Fiorenza Soli
- Medical Genetic Unit, Santa Chiara Hospital APSS, Trento, Italy
| | - Dario Cocciadiferro
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital and Research Institute, IRCCS, Rome, Italy
| | - Daniele Guadagnolo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Gioia Mastromoro
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Carolina Putotto
- Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Rome, Italy
| | | | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Section of Pediatrics, Federico II University, Naples, Italy
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital and Research Institute, IRCCS, Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Bruno Marino
- Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Rome, Italy
| | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Tommaso Mazza
- Laboratory of Bioinformatics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Victor Luis Ruiz-Perez
- Instituto de Investigaciones Biomédicas 'Alberto Sols', CSIC-UAM, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IdiPaz-UAM, Madrid, Spain
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Alessandro De Luca
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.
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74
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Nakano Y, Bánfi B. The cause of Jones syndrome put to REST: a mutation in the REST gene causes gingival fibromatosis and hearing loss. Eur J Hum Genet 2023; 31:377-379. [PMID: 36710272 PMCID: PMC10133212 DOI: 10.1038/s41431-023-01292-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Affiliation(s)
- Yoko Nakano
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Inflammation Program, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Botond Bánfi
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA.
- Inflammation Program, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Otolaryngology-Head and Neck Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA.
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75
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Ma Q, Shams H, Didonna A, Baranzini SE, Cree BAC, Hauser SL, Henry RG, Oksenberg JR. Integration of epigenetic and genetic profiles identifies multiple sclerosis disease-critical cell types and genes. Commun Biol 2023; 6:342. [PMID: 36997638 PMCID: PMC10063586 DOI: 10.1038/s42003-023-04713-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 11/02/2022] [Accepted: 03/14/2023] [Indexed: 04/01/2023] Open
Abstract
Genome-wide association studies (GWAS) successfully identified multiple sclerosis (MS) susceptibility variants. Despite this notable progress, understanding the biological context of these associations remains challenging, due in part to the complexity of linking GWAS results to causative genes and cell types. Here, we aimed to address this gap by integrating GWAS data with single-cell and bulk chromatin accessibility data and histone modification profiles from immune and nervous systems. MS-GWAS associations are significantly enriched in regulatory regions of microglia and peripheral immune cell subtypes, especially B cells and monocytes. Cell-specific polygenic risk scores were developed to examine the cumulative impact of the susceptibility genes on MS risk and clinical phenotypes, showing significant associations with risk and brain white matter volume. The findings reveal enrichment of GWAS signals in B cell and monocyte/microglial cell-types, consistent with the known pathology and presumed targets of effective MS therapeutics.
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Affiliation(s)
- Qin Ma
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Hengameh Shams
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Alessandro Didonna
- Department of Anatomy and Cell Biology, Brody School of Medicine, East Carolina University, Greenville, NC, 27834, USA
| | - Sergio E Baranzini
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Bruce A C Cree
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Stephen L Hauser
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Roland G Henry
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jorge R Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA.
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76
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Taniguchi Y, Akune T, Nishida N, Omori G, Ha K, Ueno K, Saito T, Oichi T, Koike A, Mabuchi A, Oka H, Muraki S, Oshima Y, Kawaguchi H, Nakamura K, Tokunaga K, Tanaka S, Yoshimura N. A common variant rs2054564 in ADAMST17 is associated with susceptibility to lumbar spondylosis. Sci Rep 2023; 13:4900. [PMID: 36966180 PMCID: PMC10039864 DOI: 10.1038/s41598-023-32155-w] [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: 12/31/2022] [Accepted: 03/23/2023] [Indexed: 03/27/2023] Open
Abstract
The molecular pathophysiology underlying lumbar spondylosis development remains unclear. To identify genetic factors associated with lumbar spondylosis, we conducted a genome-wide association study using 83 severe lumbar spondylosis cases and 182 healthy controls and identified 65 candidate disease-associated single nucleotide polymorphisms (SNPs). Replication analysis in 510 case and 911 control subjects from five independent Japanese cohorts identified rs2054564, located in intron 7 of ADAMTS17, as a disease-associated SNP with a genome-wide significance threshold (P = 1.17 × 10-11, odds ratio = 1.92). This association was significant even after adjustment of age, sex, and body mass index (P = 7.52 × 10-11). A replication study in a Korean cohort, including 123 case and 319 control subjects, also verified the significant association of this SNP with severe lumbar spondylosis. Immunohistochemistry revealed that fibrillin-1 (FBN1) and ADAMTS17 were co-expressed in the annulus fibrosus of intervertebral discs (IVDs). ADAMTS17 overexpression in MG63 cells promoted extracellular microfibrils biogenesis, suggesting the potential role of ADAMTS17 in IVD function through interaction with fibrillin fibers. Finally, we provided evidence of FBN1 involvement in IVD function by showing that lumbar IVDs in patients with Marfan syndrome, caused by heterozygous FBN1 gene mutation, were significantly more degenerated. We identified a common SNP variant, located in ADAMTS17, associated with susceptibility to lumbar spondylosis and demonstrated the potential role of the ADAMTS17-fibrillin network in IVDs in lumbar spondylosis development.
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Affiliation(s)
- Yuki Taniguchi
- Department of Orthopedics, The University of Tokyo Hospital, Hongo 7-3-1, Bunkyo-Ku, Tokyo, 113-8655, Japan.
- Surgical Center, The University of Tokyo Hospital, Tokyo, 113-8655, Japan.
| | - Toru Akune
- Hospital, National Rehabilitation Center for Persons with Disabilities, Tokorozawa, Saitama, 359-0042, Japan
| | - Nao Nishida
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Go Omori
- Department of Health and Sports, Faculty of Health and Science, Niigata University of Health and Welfare, Niigata, 950-3198, Japan
| | - Kim Ha
- Division of Rheumatology, Department of Internal Medicine, Hallym University Sacred Heart Hospital, Anyang, 18450, Korea
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Taku Saito
- Department of Orthopedics, The University of Tokyo Hospital, Hongo 7-3-1, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Takeshi Oichi
- Department of Orthopedics, The University of Tokyo Hospital, Hongo 7-3-1, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Asako Koike
- Healthcare Business Division, Hitachi, Ltd., Tokyo, 105-6412, Japan
| | - Akihiko Mabuchi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8654, Japan
| | - Hiroyuki Oka
- Department of Medical Research and Management for Musculoskeletal Pain, 22nd Century Medical & Research Center, Faculty of Medicine, The University of Tokyo, Tokyo, 113-8654, Japan
| | - Shigeyuki Muraki
- Department of Preventive Medicine for Locomotive Organ Disorders, 22nd Century Medical and Research Center, The University of Tokyo, Tokyo, 113-8654, Japan
| | - Yasushi Oshima
- Department of Orthopedics, The University of Tokyo Hospital, Hongo 7-3-1, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Hiroshi Kawaguchi
- Orthopaedics and Spine Department, Tokyo Neurological Center, Tokyo, 105-0001, Japan
| | - Kozo Nakamura
- Department of Orthopedics, Towa Hospital, Tokyo, 120-0003, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Sakae Tanaka
- Department of Orthopedics, The University of Tokyo Hospital, Hongo 7-3-1, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Noriko Yoshimura
- Department of Preventive Medicine for Locomotive Organ Disorders, 22nd Century Medical and Research Center, The University of Tokyo, Tokyo, 113-8654, Japan
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77
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Uffelmann E, Posthuma D, Peyrot WJ. Genome-wide association studies of polygenic risk score-derived phenotypes may lead to inflated false positive rates. Sci Rep 2023; 13:4219. [PMID: 36918594 DOI: 10.1038/s41598-023-29428-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/03/2023] [Indexed: 03/16/2023] Open
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78
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Thorlacius GE, Björk A, Wahren-Herlenius M. Genetics and epigenetics of primary Sjögren syndrome: implications for future therapies. Nat Rev Rheumatol 2023;:1-19. [PMID: 36914790 DOI: 10.1038/s41584-023-00932-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2023] [Indexed: 03/14/2023]
Abstract
In primary Sjögren syndrome (pSS), chronic inflammation of exocrine glands results in tissue destruction and sicca symptoms, primarily of the mouth and eyes. Fatigue, arthralgia and myalgia are also common symptoms, whereas extraglandular manifestations that involve the respiratory, nervous and vascular systems occur in a subset of patients. The disease predominantly affects women, with an estimated female to male ratio of 14 to 1. The aetiology of pSS, however, remains incompletely understood, and effective treatment is lacking. Large-scale genetic and epigenetic investigations have revealed associations between pSS and genes in both innate and adaptive immune pathways. The genetic variants mediate context-dependent effects, and both sex and environmental factors can influence the outcome. As such, genetic and epigenetic studies can provide insight into the dysregulated molecular mechanisms, which in turn might reveal new therapeutic possibilities. This Review discusses the genetic and epigenetic features that have been robustly connected with pSS, putting them into the context of cellular function, carrier sex and environmental challenges. In all, the observations point to several novel opportunities for early detection, treatment development and the pathway towards personalized medicine.
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79
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Flanagan FO, Holtz AM, Vargas SO, Genetti CA, Schmitz-Abe K, Casey A, Kennedy JC, Raby BA, Mullen MP, Fishman MP, Agrawal PB. An intronic variant in TBX4 in a single family with variable and severe pulmonary manifestations. NPJ Genom Med 2023; 8:7. [PMID: 36878902 PMCID: PMC9988848 DOI: 10.1038/s41525-023-00350-3] [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: 09/27/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
A male infant presented at term with neonatal respiratory failure and pulmonary hypertension. His respiratory symptoms improved initially, but he exhibited a biphasic clinical course, re-presenting at 15 months of age with tachypnea, interstitial lung disease, and progressive pulmonary hypertension. We identified an intronic TBX4 gene variant in close proximity to the canonical donor splice site of exon 3 (hg 19; chr17:59543302; c.401 + 3 A > T), also carried by his father who had a typical TBX4-associated skeletal phenotype and mild pulmonary hypertension, and by his deceased sister who died shortly after birth of acinar dysplasia. Analysis of patient-derived cells demonstrated a significant reduction in TBX4 expression resulting from this intronic variant. Our study illustrates the variable expressivity in cardiopulmonary phenotype conferred by TBX4 mutation and the utility of genetic diagnostics in enabling accurate identification and classification of more subtly affected family members.
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Affiliation(s)
- Frances O Flanagan
- Division of Pulmonary Medicine, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Alexander M Holtz
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Sara O Vargas
- Department of Pathology, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Casie A Genetti
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, USA
| | - Klaus Schmitz-Abe
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, USA
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Alicia Casey
- Division of Pulmonary Medicine, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA
| | - John C Kennedy
- Division of Pulmonary Medicine, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Benjamin A Raby
- Division of Pulmonary Medicine, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Mary P Mullen
- Department of Cardiology, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA.
| | - Martha P Fishman
- Division of Pulmonary Medicine, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Pankaj B Agrawal
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA.
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, USA.
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, USA.
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80
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Nakahara E, Yamamoto KS, Ogura H, Aoki T, Utsugisawa T, Azuma K, Akagawa H, Watanabe K, Muraoka M, Nakamura F, Kamei M, Tatebayashi K, Shinozuka J, Yamane T, Hibino M, Katsura Y, Nakano-Akamatsu S, Kadowaki N, Maru Y, Ito E, Ohga S, Yagasaki H, Morioka I, Yamamoto T, Kanno H. Variant spectrum of PIEZO1 and KCNN4 in Japanese patients with dehydrated hereditary stomatocytosis. Hum Genome Var 2023; 10:8. [PMID: 36864026 PMCID: PMC9981561 DOI: 10.1038/s41439-023-00235-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 01/26/2023] [Accepted: 02/01/2023] [Indexed: 03/04/2023] Open
Abstract
Hereditary stomatocytosis (HSt) is a type of congenital hemolytic anemia caused by abnormally increased cation permeability of erythrocyte membranes. Dehydrated HSt (DHSt) is the most common subtype of HSt and is diagnosed based on clinical and laboratory findings related to erythrocytes. PIEZO1 and KCNN4 have been recognized as causative genes, and many related variants have been reported. We analyzed the genomic background of 23 patients from 20 Japanese families suspected of having DHSt using a target capture sequence and identified pathogenic/likely pathogenic variants of PIEZO1 or KCNN4 in 12 families.
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Affiliation(s)
- Erina Nakahara
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Keiko Shimojima Yamamoto
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan.
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.
| | - Hiromi Ogura
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Takako Aoki
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Taiju Utsugisawa
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Kenko Azuma
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiroyuki Akagawa
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| | - Kenichiro Watanabe
- Department of Hematology and Oncology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Michiko Muraoka
- Department of Pediatrics, Fukuyama Medical Center, Okayama, Japan
| | - Fumihiko Nakamura
- Department of Laboratory Medicine, Nara Prefecture General Medical Center, Nara, Japan
| | - Michi Kamei
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
| | - Koji Tatebayashi
- Department of Neonatology, Gifu Prefectural General Medical Center, Gifu, Japan
| | - Jun Shinozuka
- Department of Pediatrics, Uji-Tokushukai Medical Center, Kyoto, Japan
| | - Takahisa Yamane
- Department of Hematology, Osaka City General Hospital, Osaka, Japan
| | - Makoto Hibino
- Department of Respiratory Medicine, Shonan Fujisawa Tokushukai Hospital, Fujisawa, Kanagawa, Japan
| | - Yoshiya Katsura
- Department of Metabolism and Endocrinology, Tokyo Medical University Ibaraki Medical Center, Ibaraki, Japan
| | | | - Norimitsu Kadowaki
- Department of Internal Medicine, Division of Hematology, Rheumatology and Respiratory Medicine, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Yoshiro Maru
- Department of Pharmacology, Tokyo Women's Medical University, Tokyo, Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Hiroshi Yagasaki
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
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81
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Greene D, Pirri D, Frudd K, Sackey E, Al-Owain M, Giese APJ, Ramzan K, Riaz S, Yamanaka I, Boeckx N, Thys C, Gelb BD, Brennan P, Hartill V, Harvengt J, Kosho T, Mansour S, Masuno M, Ohata T, Stewart H, Taibah K, Turner CLS, Imtiaz F, Riazuddin S, Morisaki T, Ostergaard P, Loeys BL, Morisaki H, Ahmed ZM, Birdsey GM, Freson K, Mumford A, Turro E. Genetic association analysis of 77,539 genomes reveals rare disease etiologies. Nat Med 2023; 29:679-688. [PMID: 36928819 PMCID: PMC10033407 DOI: 10.1038/s41591-023-02211-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/06/2023] [Indexed: 03/18/2023]
Abstract
The genetic etiologies of more than half of rare diseases remain unknown. Standardized genome sequencing and phenotyping of large patient cohorts provide an opportunity for discovering the unknown etiologies, but this depends on efficient and powerful analytical methods. We built a compact database, the 'Rareservoir', containing the rare variant genotypes and phenotypes of 77,539 participants sequenced by the 100,000 Genomes Project. We then used the Bayesian genetic association method BeviMed to infer associations between genes and each of 269 rare disease classes assigned by clinicians to the participants. We identified 241 known and 19 previously unidentified associations. We validated associations with ERG, PMEPA1 and GPR156 by searching for pedigrees in other cohorts and using bioinformatic and experimental approaches. We provide evidence that (1) loss-of-function variants in the Erythroblast Transformation Specific (ETS)-family transcription factor encoding gene ERG lead to primary lymphoedema, (2) truncating variants in the last exon of transforming growth factor-β regulator PMEPA1 result in Loeys-Dietz syndrome and (3) loss-of-function variants in GPR156 give rise to recessive congenital hearing impairment. The Rareservoir provides a lightweight, flexible and portable system for synthesizing the genetic and phenotypic data required to study rare disease cohorts with tens of thousands of participants.
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Affiliation(s)
- Daniel Greene
- Department of Medicine, University of Cambridge, Cambridge, UK
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniela Pirri
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Karen Frudd
- National Heart and Lung Institute, Imperial College London, London, UK
- University College London Institute of Ophthalmology, University College London, London, UK
| | - Ege Sackey
- Molecular and Clinical Sciences Institute, St. George's University of London, London, UK
| | - Mohammed Al-Owain
- Department of Medical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Arnaud P J Giese
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Khushnooda Ramzan
- Department of Clinical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Sehar Riaz
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Itaru Yamanaka
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Nele Boeckx
- Center for Medical Genetics, Antwerp University Hospital/University of Antwerp, Antwerp, Belgium
| | - Chantal Thys
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, 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
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul Brennan
- Northern Genetics Service, Newcastle upon Tyne Hospitals National Health Service Trust International Centre for Life, Newcastle upon Tyne, UK
| | - Verity Hartill
- Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals National Health Service Trust, Leeds, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Julie Harvengt
- Centre for Medical Genetics, Centre Hospitalier Universitaire de Liège, Liège, Belgium
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Nagano, Japan
- Center for Medical Genetics, Shinshu University Hospital, Nagano, Japan
| | - Sahar Mansour
- Molecular and Clinical Sciences Institute, St. George's University of London, London, UK
- South West Thames Regional Genetics Service, St. George's University Hospitals National Health Service Foundation Trust, London, UK
| | - Mitsuo Masuno
- Department of Medical Genetics, Kawasaki Medical School Hospital, Okayama, Japan
| | | | - Helen Stewart
- Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - Khalid Taibah
- Ear Nose and Throat Medical Centre, Riyadh, Saudi Arabia
| | - Claire L S Turner
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Exeter, UK
| | - Faiqa Imtiaz
- Department of Clinical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Takayuki Morisaki
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
- Division of Molecular Pathology and Department of Internal Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Pia Ostergaard
- Molecular and Clinical Sciences Institute, St. George's University of London, London, UK
| | - Bart L Loeys
- Center for Medical Genetics, Antwerp University Hospital/University of Antwerp, Antwerp, Belgium
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hiroko Morisaki
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
- Department of Medical Genetics, Sakakibara Heart Institute, Tokyo, Japan
| | - Zubair M Ahmed
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Graeme M Birdsey
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Andrew Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- South West National Health Service Genomic Medicine Service Alliance, Bristol, UK
| | - Ernest Turro
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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82
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Ceroni F, Osborne D, Clokie S, Bax DA, Cassidy EJ, Dunn MJ, Harris CM, Self JE, Ragge NK. Analysis of Fibroblast Growth Factor 14 (FGF14) structural variants reveals the genetic basis of the early onset nystagmus locus NYS4 and variable ataxia. Eur J Hum Genet 2023; 31:353-359. [PMID: 36207621 PMCID: PMC9995494 DOI: 10.1038/s41431-022-01197-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/02/2022] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
Nystagmus (involuntary, rhythmical eye movements) can arise due to sensory eye defects, in association with neurological disorders or as an isolated condition. We identified a family with early onset nystagmus and additional neurological features carrying a partial duplication of FGF14, a gene associated with spinocerebellar ataxia type 27 (SCA27) and episodic ataxia. Detailed eye movement analysis revealed oculomotor anomalies strikingly similar to those reported in a previously described four-generation family with early onset nystagmus and linkage to a region on chromosome 13q31.3-q33.1 (NYS4). Since FGF14 lies within NYS4, we revisited the original pedigree using whole genome sequencing, identifying a 161 kb heterozygous deletion disrupting FGF14 and ITGBL1 in the affected individuals, suggesting an FGF14-related condition. Therefore, our study reveals the genetic variant underlying NYS4, expands the spectrum of pathogenic FGF14 variants, and highlights the importance of screening FGF14 in apparently isolated early onset nystagmus.
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Affiliation(s)
- Fabiola Ceroni
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Daniel Osborne
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Samuel Clokie
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Foundation Trust, Birmingham, UK
| | - Dorine A Bax
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Emma J Cassidy
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, UK
| | - Matt J Dunn
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK
| | | | - Jay E Self
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Nicola K Ragge
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK.
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Foundation Trust, Birmingham, UK.
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83
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Reutter H. High molecular diagnostic yields and novel phenotypic expansions involving syndromic anorectal malformations. Eur J Hum Genet 2023; 31:273-274. [PMID: 36599943 PMCID: PMC9995338 DOI: 10.1038/s41431-022-01272-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Affiliation(s)
- Heiko Reutter
- Division of Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
- Institute of Human Genetics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
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84
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Ishiura H, Tsuji S, Toda T. Recent advances in CGG repeat diseases and a proposal of fragile X-associated tremor/ataxia syndrome, neuronal intranuclear inclusion disease, and oculophryngodistal myopathy (FNOP) spectrum disorder. J Hum Genet 2023; 68:169-174. [PMID: 36670296 PMCID: PMC9968658 DOI: 10.1038/s10038-022-01116-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 01/22/2023]
Abstract
While whole genome sequencing and long-read sequencing have become widely available, more and more focuses are on noncoding expanded repeats. Indeed, more than half of noncoding repeat expansions related to diseases have been identified in the five years. An exciting aspect of the progress in this field is an identification of a phenomenon called repeat motif-phenotype correlation. Repeat motif-phenotype correlation in noncoding repeat expansion diseases is first found in benign adult familial myoclonus epilepsy. The concept is extended in the research of CGG repeat expansion diseases. In this review, we focus on newly identified CGG repeat expansion diseases, update the concept of repeat motif-phenotype correlation in CGG repeat expansion diseases, and propose a clinical concept of FNOP (fragile X-associated tremor/ataxia syndrome, neuronal intranuclear inclusion disease, and oculopharyngodistal myopathy)-spectrum disorder, which shares clinical features and thus probably share some common disease pathophysiology, to further facilitate discussion and progress in this field.
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Affiliation(s)
- Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- Department of Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan.
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Institute of Medical Genomics, International University of Health and Welfare, Narita, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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85
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Van Haute L, O'Connor E, Díaz-Maldonado H, Munro B, Polavarapu K, Hock DH, Arunachal G, Athanasiou-Fragkouli A, Bardhan M, Barth M, Bonneau D, Brunetti-Pierri N, Cappuccio G, Caruana NJ, Dominik N, Goel H, Helman G, Houlden H, Lenaers G, Mention K, Murphy D, Nandeesh B, Olimpio C, Powell CA, Preethish-Kumar V, Procaccio V, Rius R, Rebelo-Guiomar P, Simons C, Vengalil S, Zaki MS, Ziegler A, Thorburn DR, Stroud DA, Maroofian R, Christodoulou J, Gustafsson C, Nalini A, Lochmüller H, Minczuk M, Horvath R. TEFM variants impair mitochondrial transcription causing childhood-onset neurological disease. Nat Commun 2023; 14:1009. [PMID: 36823193 PMCID: PMC9950373 DOI: 10.1038/s41467-023-36277-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 09/30/2021] [Accepted: 01/20/2023] [Indexed: 02/25/2023] Open
Abstract
Mutations in the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA biology. The TEFM gene encodes the mitochondrial transcription elongation factor responsible for enhancing the processivity of mitochondrial RNA polymerase, POLRMT. We report for the first time that TEFM variants are associated with mitochondrial respiratory chain deficiency and a wide range of clinical presentations including mitochondrial myopathy with a treatable neuromuscular transmission defect. Mechanistically, we show muscle and primary fibroblasts from the affected individuals have reduced levels of promoter distal mitochondrial RNA transcripts. Finally, tefm knockdown in zebrafish embryos resulted in neuromuscular junction abnormalities and abnormal mitochondrial function, strengthening the genotype-phenotype correlation. Our study highlights that TEFM regulates mitochondrial transcription elongation and its defect results in variable, tissue-specific neurological and neuromuscular symptoms.
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Affiliation(s)
- Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Emily O'Connor
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
| | - Héctor Díaz-Maldonado
- Department of Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Benjamin Munro
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Kiran Polavarapu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
| | - Gautham Arunachal
- Department of Human genetics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Alkyoni Athanasiou-Fragkouli
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Mainak Bardhan
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Magalie Barth
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Dominique Bonneau
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, University of Naples Federico II, Via s. Pansini, 5, 80131, Naples, Italy
| | - Gerarda Cappuccio
- Department of Translational Medicine, University of Naples Federico II, Via s. Pansini, 5, 80131, Naples, Italy
| | - Nikeisha J Caruana
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
- Institute for Health and Sport (IHES), Victoria University, Melbourne, VIC, 3011, Australia
| | - Natalia Dominik
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Himanshu Goel
- Hunter Genetics, Waratah, University of Newcastle, Callaghan, NSW, 2298, Australia
| | - Guy Helman
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Henry Houlden
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Guy Lenaers
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Karine Mention
- Pediatric Inherited Metabolic Disorders, Hôpital Jeanne de Flandre, Lille, France
| | - David Murphy
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Bevinahalli Nandeesh
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Catarina Olimpio
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Vincent Procaccio
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Rocio Rius
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Cas Simons
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Alban Ziegler
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - David R Thorburn
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia
| | - David A Stroud
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Reza Maroofian
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - John Christodoulou
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Claes Gustafsson
- Department of Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK.
| | - Rita Horvath
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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86
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Wu H, Liu Y, Li Y, Li K, Xu C, Gao Y, Lv M, Guo R, Xu Y, Zhou P, Wei Z, Hua R, He X, Cao Y. DNALI1 deficiency causes male infertility with severe asthenozoospermia in humans and mice by disrupting the assembly of the flagellar inner dynein arms and fibrous sheath. Cell Death Dis 2023; 14:127. [PMID: 36792588 DOI: 10.1038/s41419-023-05653-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/17/2023]
Abstract
The axonemal dynein arms (outer (ODA) and inner dynein arms (IDAs)) are multiprotein structures organized by light, intermediate, light intermediate (LIC), and heavy chain proteins. They hydrolyze ATP to promote ciliary and flagellar movement. Till now, a variety of dynein protein deficiencies have been linked with asthenospermia (ASZ), highlighting the significance of these structures in human sperm motility. Herein, we detected bi-allelic DNALI1 mutations [c.663_666del (p.Glu221fs)], in an ASZ patient, which resulted in the complete loss of the DNALI1 in the patient's sperm. We identified loss of sperm DNAH1 and DNAH7 rather than DNAH10 in both DNALI1663_666del patient and Dnali1-/- mice, demonstrating that mammalian DNALI1 is a LIC protein of a partial IDA subspecies. More importantly, we revealed that DNALI1 loss contributed to asymmetries in the most fibrous sheath (FS) of the sperm flagellum in both species. Immunoprecipitation revealed that DNALI1 might interact with the cytoplasmic dynein complex proteins in the testes. Furthermore, DNALI1 loss severely disrupted the transport and assembly of the FS proteins, especially AKAP3 and AKAP4, during flagellogenesis. Hence, DNALI1 may possess a non-classical molecular function, whereby it regulates the cytoplasmic dynein complex that assembles the flagella. We conclude that a DNALI deficiency-induced IDAs injury and an asymmetric FS-driven tail rigid structure alteration may simultaneously cause flagellum immotility. Finally, intracytoplasmic sperm injection (ICSI) can effectively resolve patient infertility. Collectively, we demonstrate that DNALI1 is a newly causative gene for AZS in both humans and mice, which possesses multiple crucial roles in modulating flagellar assembly and motility.
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87
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Morimoto M, Bhambhani V, Gazzaz N, Davids M, Sathiyaseelan P, Macnamara EF, Lange J, Lehman A, Zerfas PM, Murphy JL, Acosta MT, Wang C, Alderman E, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Cassini T, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fieg EL, Fisher PG, Fogel BL, Forghani I, Glass I, Gochuico B, Goddard PC, Godfrey RA, Golden-Grant K, Grajewski A, Gutierrez I, Hadley D, Hahn S, Halley MC, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Hutchison S, Introne WJ, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jean-Marie O, Jobanputra V, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, LeBlanc K, Lee BH, Levitt R, Lewis RA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacRae CA, Maduro VV, Mahoney R, Mak BC, Mamounas LA, Manolio TA, Mao R, Maravilla K, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti P, Nakano-Okuno M, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Pusey Swerdzewski BN, Quinlan A, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Toro C, Tran AA, Ungar RA, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Weisz Hubshman M, Wener M, Wenger T, Wesseling Perry K, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Worley K, Xiao C, Yamamoto S, Yang J, Zhang Z, Zuchner S, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV. Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment. NPJ Genom Med 2023; 8:4. [PMID: 36765070 PMCID: PMC9918471 DOI: 10.1038/s41525-022-00343-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/06/2022] [Indexed: 02/12/2023] Open
Abstract
Autophagy regulates the degradation of damaged organelles and protein aggregates, and is critical for neuronal development, homeostasis, and maintenance, yet few neurodevelopmental disorders have been associated with pathogenic variants in genes encoding autophagy-related proteins. We report three individuals from two unrelated families with a neurodevelopmental disorder characterized by speech and motor impairment, and similar facial characteristics. Rare, conserved, bi-allelic variants were identified in ATG4D, encoding one of four ATG4 cysteine proteases important for autophagosome biogenesis, a hallmark of autophagy. Autophagosome biogenesis and induction of autophagy were intact in cells from affected individuals. However, studies evaluating the predominant substrate of ATG4D, GABARAPL1, demonstrated that three of the four ATG4D patient variants functionally impair ATG4D activity. GABARAPL1 is cleaved or "primed" by ATG4D and an in vitro GABARAPL1 priming assay revealed decreased priming activity for three of the four ATG4D variants. Furthermore, a rescue experiment performed in an ATG4 tetra knockout cell line, in which all four ATG4 isoforms were knocked out by gene editing, showed decreased GABARAPL1 priming activity for the two ATG4D missense variants located in the cysteine protease domain required for priming, suggesting that these variants impair the function of ATG4D. The clinical, bioinformatic, and functional data suggest that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of this syndromic neurodevelopmental disorder.
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Affiliation(s)
- Marie Morimoto
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Vikas Bhambhani
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Nour Gazzaz
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada ,grid.412125.10000 0001 0619 1117Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mariska Davids
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Paalini Sathiyaseelan
- grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Ellen F. Macnamara
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | | | - Anna Lehman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Patricia M. Zerfas
- grid.94365.3d0000 0001 2297 5165Diagnostic and Research Services Branch, Office of Research Services, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jennifer L. Murphy
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Maria T. Acosta
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Camille Wang
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Emily Alderman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | | | - Sara Reichert
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Audrey Thurm
- grid.94365.3d0000 0001 2297 5165Neurodevelopmental and Behavioral Phenotyping Service, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892 USA
| | - David R. Adams
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Wendy J. Introne
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sharon M. Gorski
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Cornelius F. Boerkoel
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | - William A. Gahl
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Cynthia J. Tifft
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - May Christine V. Malicdan
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
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88
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Okano S, Makita Y, Miyamoto A, Taketazu G, Kimura K, Fukuda I, Tanaka H, Yanagi K, Kaname T. GRIA3 p.Met661Thr variant in a female with developmental epileptic encephalopathy. Hum Genome Var 2023; 10:4. [PMID: 36726007 PMCID: PMC9892509 DOI: 10.1038/s41439-023-00232-1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 02/03/2023] Open
Abstract
The X-linked human glutamate receptor subunit 3 (GRIA3) gene (MIM *305915, Xq25) encodes ionotropic α amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA)-type glutamate receptor subunit 3, which mediates postsynaptic neurotransmission. Variants in this gene can cause a variety of neurological disorders, primarily reported in male patients. Here, we report a female patient with developmental and epileptic encephalopathy who carries the novel de novo GRIA3 variant NM_007325.5: c.1982T > C: p.Met661Thr.
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Affiliation(s)
- Satomi Okano
- Department of Pediatrics, Asahikawa Habilitation Center for Children, Hokkaido, Japan
| | - Yoshio Makita
- Department of Genetic Counseling, Asahikawa Medical University Hospital, Hokkaido, Japan.
| | - Akie Miyamoto
- Department of Pediatrics, Asahikawa Habilitation Center for Children, Hokkaido, Japan
| | - Genya Taketazu
- Department of Pediatrics, Asahikawa Kosei Hospital, Hokkaido, Japan
| | - Kayano Kimura
- Department of Pediatrics, Asahikawa Habilitation Center for Children, Hokkaido, Japan
| | - Ikue Fukuda
- Department of Pediatrics, Asahikawa Habilitation Center for Children, Hokkaido, Japan
| | - Hajime Tanaka
- Department of Pediatrics, Asahikawa Habilitation Center for Children, Hokkaido, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Institute for Child Health and Development, Tokyo, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Institute for Child Health and Development, Tokyo, Japan
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89
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Watanabe H, Goto S, Hosojima M, Kabasawa H, Imai N, Ito Y, Narita I. Pathogenic variants of Alport syndrome and monogenic diabetes identified by exome sequencing in a family. Hum Genome Var 2023; 10:5. [PMID: 36732323 PMCID: PMC9894847 DOI: 10.1038/s41439-023-00233-0] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023] Open
Abstract
We present a family of two female Alport syndrome patients with a family history of impaired glucose tolerance. Whole exome sequencing identified a novel heterozygous variant of COL4A5 NM_033380.3: c.2636 C > A (p.S879*) and a rare variant of GCK NM_001354800.1: c.1135 G > A (p.A379T) as the causes of Alport syndrome and monogenic diabetes, respectively. Two independent pathogenic variants affected the clinical phenotypes. Clinical next-generation sequencing is helpful for identifying the causes of patients' manifestations.
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Affiliation(s)
- Hirofumi Watanabe
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
| | - Shin Goto
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Michihiro Hosojima
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hideyuki Kabasawa
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Naofumi Imai
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yumi Ito
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Health Promotion Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ichiei Narita
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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90
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Leonardi E, Aspromonte MC, Drongitis D, Bettella E, Verrillo L, Polli R, McEntagart M, Licchetta L, Dilena R, D'Arrigo S, Ciaccio C, Esposito S, Leuzzi V, Torella A, Baldo D, Lonardo F, Bonato G, Pellegrin S, Stanzial F, Posmyk R, Kaczorowska E, Carecchio M, Gos M, Rzońca-Niewczas S, Miano MG, Murgia A. Expanding the genetics and phenotypic spectrum of Lysine-specific demethylase 5C (KDM5C): a report of 13 novel variants. Eur J Hum Genet 2023; 31:202-215. [PMID: 36434256 PMCID: PMC9905063 DOI: 10.1038/s41431-022-01233-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 10/14/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022] Open
Abstract
Lysine-specific demethylase 5C (KDM5C) has been identified as an important chromatin remodeling gene, contributing to X-linked neurodevelopmental disorders (NDDs). The KDM5C gene, located in the Xp22 chromosomal region, encodes the H3K4me3-me2 eraser involved in neuronal plasticity and dendritic growth. Here we report 30 individuals carrying 13 novel and one previously identified KDM5C variants. Our cohort includes the first reported case of somatic mosaicism in a male carrying a KDM5C nucleotide substitution, and a dual molecular finding in a female carrying a homozygous truncating FUCA1 alteration together with a de novo KDM5C variant. With the use of next generation sequencing strategies, we detected 1 frameshift, 1 stop codon, 2 splice-site and 10 missense variants, which pathogenic role was carefully investigated by a thorough bioinformatic analysis. The pattern of X-chromosome inactivation was found to have an impact on KDM5C phenotypic expression in females of our cohort. The affected individuals of our case series manifested a neurodevelopmental condition characterized by psychomotor delay, intellectual disability with speech disorders, and behavioral features with particular disturbed sleep pattern; other observed clinical manifestations were short stature, obesity and hypertrichosis. Collectively, these findings expand the current knowledge about the pathogenic mechanisms leading to dysfunction of this important chromatin remodeling gene and contribute to a refinement of the KDM5C phenotypic spectrum.
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Affiliation(s)
- Emanuela Leonardi
- Department of Women's and Children's Health, University of Padova, Padova, Italy
- Pediatric Research Institute, Città della Speranza, Padova, Italy
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Maria Cristina Aspromonte
- Department of Women's and Children's Health, University of Padova, Padova, Italy
- Pediatric Research Institute, Città della Speranza, Padova, Italy
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Denise Drongitis
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", CNR, Naples, Italy
| | - Elisa Bettella
- Department of Women's and Children's Health, University of Padova, Padova, Italy
- Pediatric Research Institute, Città della Speranza, Padova, Italy
| | - Lucia Verrillo
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", CNR, Naples, Italy
| | - Roberta Polli
- Department of Women's and Children's Health, University of Padova, Padova, Italy
- Pediatric Research Institute, Città della Speranza, Padova, Italy
| | - Meriel McEntagart
- Medical Genetics Unit, St. George's University Hospitals, London, UK
| | - Laura Licchetta
- IRCCS, Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Robertino Dilena
- Neurophysiopathology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano D'Arrigo
- Department of Pediatric Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Claudia Ciaccio
- Department of Pediatric Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Silvia Esposito
- Department of Pediatric Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Vincenzo Leuzzi
- Unit of Child Neurology and Psychiatry, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Annalaura Torella
- University of Campania "Luigi Vanvitelli", Caserta, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Demetrio Baldo
- Unit of medical genetics, ULSS 2 Treviso Hospital, Treviso, Italy
| | | | - Giulia Bonato
- Movement Disorders Unit, Department of Neuroscience, University of Padova, Padova, Italy
| | - Serena Pellegrin
- Child Neurology and Neurorehabilitation Unit, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Franco Stanzial
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Renata Posmyk
- Department of Clinical Genetics, Medical University in Bialystok, Bialystok, Poland
| | - Ewa Kaczorowska
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Miryam Carecchio
- Movement Disorders Unit, Department of Neuroscience, University of Padova, Padova, Italy
| | - Monika Gos
- Development Genetics Laboratory, Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Sylwia Rzońca-Niewczas
- Development Genetics Laboratory, Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | - Alessandra Murgia
- Department of Women's and Children's Health, University of Padova, Padova, Italy.
- Pediatric Research Institute, Città della Speranza, Padova, Italy.
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91
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Zhang G, Jiang C, Yang Y, Wang Y, Zhou H, Dai S, Liu M, Yang Y, Yang L, Shen Q, Zhang T, Zhang X, Yang Y, Shen Y. Deficiency of cancer/testis antigen gene CT55 causes male infertility in humans and mice. Cell Death Differ 2023; 30:500-514. [PMID: 36481789 PMCID: PMC9950085 DOI: 10.1038/s41418-022-01098-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022] Open
Abstract
The Cancer/Testis Antigen (CTA) genes comprise a group of genes whose expression under physiological conditions is restricted to the testis but is activated in many human cancers. Depending on the particular expression pattern, the CTA genes are speculated to play a role in spermatogenesis, but evidence is limited thus far. Here, we reported patients with a hemizygous nonsense mutation in cancer-testis antigen 55 (CT55) suffering from male infertility with extreme disruption in sperm production, morphology, and locomotion. Specifically, the insufficiency of sperm individualization, excessive residue of unnecessary cytoplasm, and defects in acrosome development were evident in the spermatozoa of the patients. Furthermore, mouse models with depletion of Ct55 showed accelerated infertility with age, mimicking the defects in sperm individualization, unnecessary cytoplasm removal, and meanwhile exhibiting the disrupted cumulus-oocyte complex penetration. Mechanistically, our functional experiments uncovered CT55 as a new autophagic manipulator to regulate spermatogenesis via selectively interacting with LAMP2 and GABARAP (which are key regulators in the autophagy process) and further fine-tuning their expression. Therefore, our findings revealed CT55 as a novel CTA gene involved in spermatogenesis due to its unprecedented autophagy activity.
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Affiliation(s)
- Guohui Zhang
- Department of Obstetrics/Gynecology, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Key Laboratory of reproductive medicine, Sichuan Provincial maternity and Child Health Care Hospital, Chengdu, 610000, China
| | - Chuan Jiang
- Department of Obstetrics/Gynecology, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Yushang Yang
- Department of Thoracic Surgery and Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yan Wang
- Reproduction Medical Center of West China Second University Hospital, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Haimeng Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Siyu Dai
- Department of Obstetrics/Gynecology, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Mohan Liu
- Department of Obstetrics/Gynecology, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Yanting Yang
- Department of Obstetrics/Gynecology, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Li Yang
- Reproduction Medical Center of West China Second University Hospital, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Qiongyan Shen
- Reproduction Medical Center of West China Second University Hospital, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Tao Zhang
- Reproduction Medical Center of West China Second University Hospital, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Xiaodong Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
- Hengyang Medical School, University of South China, Hengyang, 421000, China.
| | - Yihong Yang
- Reproduction Medical Center of West China Second University Hospital, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, 610041, China.
| | - Ying Shen
- Department of Obstetrics/Gynecology, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
- NHC Key Laboratory of Chronobiology, Sichuan University, Chengdu, 610041, China.
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92
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Carstens N, Goolam S, Hulley M, Brandenburg JT, Ramsay M, Williams SEI. Exome-based mutation screening in South African children with primary congenital glaucoma. Eye (Lond) 2023; 37:362-368. [PMID: 35094026 PMCID: PMC9873788 DOI: 10.1038/s41433-022-01941-7] [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: 03/24/2021] [Revised: 01/03/2022] [Accepted: 01/14/2022] [Indexed: 01/29/2023] Open
Abstract
OBJECTIVES To identify pathogenic variants in a cohort of 23 black South African children with sporadic primary congenital glaucoma (PCG) using an exome-based approach. METHODS Children with PCG were recruited from two Paediatric Ophthalmology Clinics in Johannesburg, South Africa. Whole exome sequencing was performed on genomic DNA. Of the 23 children, 19 were male and 19 had bilateral PCG. A variant prioritization strategy was employed whereby variants in known PCG genes (CYP1B1, LTBP2 and TEK) were evaluated first, followed by the identification of putative disease-causing variants in other genes related to eye diseases and phenotypes. RESULTS Validated pathogenic variants in the CYP1B1 gene (c.1169 G>A; p.Arg390His) and TEK gene (c.922 G>A; p.Gly308Arg) were identified in one child each. No LTBP2 mutations were identified in this cohort. In silico predictions identified potentially damaging rare variants in genes previously associated with eye development phenotypes or glaucoma in a further 12 children. CONCLUSIONS This study demonstrates the value of whole exome sequencing in identifying disease-causing variants in African children with PCG. It is the first report of a TEK disease-causing variant in an African PCG patient. Potential causative variants detected in PCG candidate genes warrant further investigation.
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Affiliation(s)
- Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Saadiah Goolam
- Division of Ophthalmology, Department of Neurosciences, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michaella Hulley
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michele Ramsay
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan Eileen Isabella Williams
- Division of Ophthalmology, Department of Neurosciences, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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93
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Ke H, Tang S, Guo T, Hou D, Jiao X, Li S, Luo W, Xu B, Zhao S, Li G, Zhang X, Xu S, Wang L, Wu Y, Wang J, Zhang F, Qin Y, Jin L, Chen ZJ. Landscape of pathogenic mutations in premature ovarian insufficiency. Nat Med 2023; 29:483-492. [PMID: 36732629 PMCID: PMC9941050 DOI: 10.1038/s41591-022-02194-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/20/2022] [Indexed: 02/04/2023]
Abstract
Premature ovarian insufficiency (POI) is a major cause of female infertility due to early loss of ovarian function. POI is a heterogeneous condition, and its molecular etiology is unclear. To identify genetic variants associated with POI, here we performed whole-exome sequencing in a cohort of 1,030 patients with POI. We detected 195 pathogenic/likely pathogenic variants in 59 known POI-causative genes, accounting for 193 (18.7%) cases. Association analyses comparing the POI cohort with a control cohort of 5,000 individuals without POI identified 20 further POI-associated genes with a significantly higher burden of loss-of-function variants. Functional annotations of these novel 20 genes indicated their involvement in ovarian development and function, including gonadogenesis (LGR4 and PRDM1), meiosis (CPEB1, KASH5, MCMDC2, MEIOSIN, NUP43, RFWD3, SHOC1, SLX4 and STRA8) and folliculogenesis and ovulation (ALOX12, BMP6, H1-8, HMMR, HSD17B1, MST1R, PPM1B, ZAR1 and ZP3). Cumulatively, pathogenic and likely pathogenic variants in known POI-causative and novel POI-associated genes contributed to 242 (23.5%) cases. Further genotype-phenotype correlation analyses indicated that genetic contribution was higher in cases with primary amenorrhea compared to that in cases with secondary amenorrhea. This study expands understanding of the genetic landscape underlying POI and presents insights that have the potential to improve the utility of diagnostic genetic screenings.
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Affiliation(s)
- Hanni Ke
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China
| | - Shuyan Tang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Ting Guo
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China
| | - Dong Hou
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China
| | - Xue Jiao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China
| | - Shan Li
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China
| | - Wei Luo
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China
| | - Bingying Xu
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China
| | - Shidou Zhao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China
| | - Guangyu Li
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China
| | - Xiaoxi Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shuhua Xu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Lingbo Wang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Yanhua Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.,Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China. .,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China.
| | - Yingying Qin
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China. .,Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China.
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China. .,Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China.
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China. .,Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China. .,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China. .,Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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94
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Song Y, Chen C, Xie Y, Sun T, Xu K, Li Y. Clinical and genetic findings in a Chinese cohort with choroideremia. Eye (Lond) 2023; 37:459-466. [PMID: 35132212 PMCID: PMC9905080 DOI: 10.1038/s41433-022-01950-6] [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: 06/01/2021] [Revised: 01/06/2022] [Accepted: 01/18/2022] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVE Choroideremia (CHM) is an X-linked chorioretinal dystrophy caused by variants in the CHM gene. The aim of this study was to report the clinical and genetic features of a cohort of affected males with CHM and establish the relationship between best correct visual acuity (BCVA) and age. METHOD Twenty-seven patients from 24 unrelated families underwent detailed ophthalmic examinations and comprehensive molecular genetic analysis. We combined the 27 patients in our own cohort with 68 Chinese patients from six previously reported studies to determine a transition age for BCVA rapid decline in 95 patients. RESULTS Twenty-three causal (9 novel) CHM variants were identified in the 27 patients, who had a mean age of 30.5 ± 17.4 years and a mean BCVA (LogMAR) of 0.61 ± 0.79. Patients at different disease stages showed different extents of retinal pigment epithelium (RPE) and choroid abnormalities. Central retinal optical coherence tomography (OCT) scanning revealed defects in the ellipsoid zone and RPE in all patients and outer retinal tubulations in 75%. The 95 patients had a mean age of 33.27 ± 16.27 years and an average (LogMAR) of 0.72 ± 0.82. The BCVA did not decline rapidly before age 25, but decreased at a mean rate of 0.037logMAR/year after that age. CONCLUSIONS Our results indicated Chinese patients with CHM variants have a younger transition age for rapid BCVA decline than previously reported for other ethnic groups. Central retinal OCT scanning can identify different abnormalities in the retinal structures, and these might be used as other parameters for monitoring disease progression in patients with CHM.
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Affiliation(s)
- Yuning Song
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Ophthalmology & Visual Sciences Key Lab, Capital Medical University, Beijing, China
| | - Chunjie Chen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Ophthalmology & Visual Sciences Key Lab, Capital Medical University, Beijing, China
| | - Yue Xie
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Ophthalmology & Visual Sciences Key Lab, Capital Medical University, Beijing, China
| | - Tengyang Sun
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Ophthalmology & Visual Sciences Key Lab, Capital Medical University, Beijing, China
| | - Ke Xu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Ophthalmology & Visual Sciences Key Lab, Capital Medical University, Beijing, China
| | - Yang Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Ophthalmology & Visual Sciences Key Lab, Capital Medical University, Beijing, China.
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95
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Margolis DJ, Mitra N, Hoffstad OJ, Berna R, Kim BS, Chopra A, Phillips EJ. Association of KIR2DL5, KIR2DS5, and KIR2DS1 allelic variation and atopic dermatitis. Sci Rep 2023; 13:1730. [PMID: 36720995 PMCID: PMC9889380 DOI: 10.1038/s41598-023-28847-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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/25/2023] [Indexed: 02/01/2023] Open
Abstract
Natural killer cells (NK) have been associated with the pathophysiology of atopic dermatitis (AD). NK function is regulated by killer cell Ig-like receptor family (KIR) receptors that interact with HLA ligands. The study goal was to focus on allelic variation in genes KIR2DL5, KIR2DS5, and KIR2DS1 with respect to AD. This was a case-control study of individuals with (n = 313) and without (n = 176) AD. Associations were estimated using logistic regression. The prevalence of KIR2DL5 was 52.5% (95% CI 48.0,57.0), KIR2DS5 was 33.0% (28.8,37.3), and KIR2DS1 was 33.6% (29.4,38.0). The presence of the KIR2DL5*001:01 increased the odds of having AD by about 86% (odds ratio (OR): 1.86(1.23,2.82) p = 0.003). The risk for individuals homozygous for KIR2DL5*001:01 was even greater (OR: 2.16 (95% CI 1.31,3.53) p = 0.0023). The odds of having AD with KIR2DL5*001:01 was similar in Whites and Blacks. Allelic variation in KIR2DS5 and KIR2DS1 was not associated with AD. There is no known HLA binding ligand for KIR2DL5. The effect of KIR2DL5*001:01 increased in the presence of HLA-B*-21TT leader sequence (2.46(1.37,4.41) p = 0.0025) and the HLA-C2 ligand (2.07 (1.37,4.41, p = 0.000002). Our study shows an independent association of the KIR2DL5*001:01 with AD and is the first study to associate AD with KIR allelic variation.
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Affiliation(s)
- David J Margolis
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, Philadelphia, PA, USA. .,Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, 901 Blockley Hall, 423 Guardian Drive, Philadelphia, PA, 19104, USA.
| | - Nandita Mitra
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ole J Hoffstad
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, 901 Blockley Hall, 423 Guardian Drive, Philadelphia, PA, 19104, USA
| | - Ronald Berna
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, 901 Blockley Hall, 423 Guardian Drive, Philadelphia, PA, 19104, USA
| | - Brian S Kim
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Elizabeth J Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia.,Center for Drug Safety and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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96
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Rämö JT, Kiiskinen T, Seist R, Krebs K, Kanai M, Karjalainen J, Kurki M, Hämäläinen E, Häppölä P, Havulinna AS, Hautakangas H, Mägi R, Palta P, Esko T, Metspalu A, Pirinen M, Karczewski KJ, Ripatti S, Milani L, Stankovic KM, Mäkitie A, Daly MJ, Palotie A; FinnGen. Genome-wide screen of otosclerosis in population biobanks: 27 loci and shared associations with skeletal structure. Nat Commun 2023; 14:157. [PMID: 36653343 DOI: 10.1038/s41467-022-32936-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 08/24/2022] [Indexed: 01/19/2023] Open
Abstract
Otosclerosis is one of the most common causes of conductive hearing loss, affecting 0.3% of the population. It typically presents in adulthood and half of the patients have a positive family history. The pathophysiology of otosclerosis is poorly understood. A previous genome-wide association study (GWAS) identified a single association locus in an intronic region of RELN. Here, we report a meta-analysis of GWAS studies of otosclerosis in three population-based biobanks comprising 3504 cases and 861,198 controls. We identify 23 novel risk loci (p < 5 × 10-8) and report an association in RELN and three previously reported candidate gene or linkage regions (TGFB1, MEPE, and OTSC7). We demonstrate developmental stage-dependent immunostaining patterns of MEPE and RUNX2 in mouse otic capsules. In most association loci, the nearest protein-coding genes are implicated in bone remodelling, mineralization or severe skeletal disorders. We highlight multiple genes involved in transforming growth factor beta signalling for follow-up studies.
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97
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Wang Q, Wang Z, Wang Y, Qi Z, Bai D, Wang C, Chen Y, Xu W, Zhu X, Jeon J, Xiong J, Hao C, Zhu MX, Wei A, Li W. A gain-of-function TPC2 variant R210C increases affinity to PI(3,5)P(2) and causes lysosome acidification and hypopigmentation. Nat Commun 2023; 14:226. [PMID: 36641477 DOI: 10.1038/s41467-023-35786-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Albinism is a group of inherited disorders mainly affecting skin, hair and eyes. Here we identify a de novo point mutation, p.R210C, in the TPCN2 gene which encodes Two Pore Channel 2 (TPC2) from a patient with albinism. TPC2 is an endolysosome and melanosome localized non-selective cation channel involved in regulating pigment production. Through inside-out recording of plasma membrane targeted TPC2 and direct recording of enlarged endolysosomal vacuoles, we reveal that the R210C mutant displays constitutive channel activation and markedly increased affinity to PI(3,5)P2. Mice harboring the homologous mutation, R194C, also exhibit hypopigmentation in the fur and skin, as well as less pigment and melanosomes in the retina in a dominant inheritance manner. Moreover, mouse embryonic fibroblasts carrying the R194C mutation show enlarged endolysosomes, enhanced lysosomal Ca2+ release and hyper-acidification. Our data suggest that R210C is a pathogenic gain-of-function TPC2 variant that underlies an unusual dominant type of albinism.
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98
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Abstract
Macroautophagy and microautophagy are highly conserved eukaryotic cellular processes that degrade cytoplasmic material in lysosomes. Both pathways involve characteristic membrane dynamics regulated by autophagy-related proteins and other molecules, some of which are shared between the two pathways. Over the past few years, the application of new technologies, such as cryo-electron microscopy, coevolution-based structural prediction and in vitro reconstitution, has revealed the functions of individual autophagy gene products, especially in autophagy induction, membrane reorganization and cargo recognition. Concomitantly, mutations in autophagy genes have been linked to human disorders, particularly neurodegenerative diseases, emphasizing the potential pathogenic implications of autophagy defects. Accumulating genome data have also illuminated the evolution of autophagy genes within eukaryotes as well as their transition from possible ancestral elements in prokaryotes.
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Affiliation(s)
- Hayashi Yamamoto
- grid.26999.3d0000 0001 2151 536XDepartment of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan ,grid.410821.e0000 0001 2173 8328Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Sidi Zhang
- grid.26999.3d0000 0001 2151 536XDepartment of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- grid.26999.3d0000 0001 2151 536XDepartment of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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99
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Kikas T, Punab AM, Kasak L, Poolamets O, Vihljajev V, Pomm K, Reiman M, Tjagur S, Korrovits P, Punab M, Laan M. Microdeletions and microduplications linked to severe congenital disorders in infertile men. Sci Rep 2023; 13:574. [PMID: 36631630 DOI: 10.1038/s41598-023-27750-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Data on the clinical validity of DNA copy number variants (CNVs) in spermatogenic failure (SPGF) is limited. This study analyzed the genome-wide CNV profile in 215 men with idiopathic SPGF and 62 normozoospermic fertile men, recruited at the Andrology Clinic, Tartu University Hospital, Estonia. A two-fold higher representation of > 1 Mb CNVs was observed in men with SPGF (13%, n = 28) compared to controls (6.5%, n = 4). Seven patients with SPGF were identified as carriers of microdeletions (1q21.1; 2.4 Mb) or microduplications (3p26.3, 1.1 Mb; 7p22.3-p22.2, 1.56 Mb; 10q11.22, 1.42 Mb, three cases; Xp22.33; 2.3 Mb) linked to severe congenital conditions. Large autosomal CNV carriers had oligozoospermia, reduced or low-normal bitesticular volume (22-28 ml). The 7p22.3-p22.2 microduplication carrier presented mild intellectual disability, neuropsychiatric problems, and short stature. The Xp22.33 duplication at the PAR1/non-PAR boundary, previously linked to uterine agenesis, was detected in a patient with non-obstructive azoospermia. A novel recurrent intragenic deletion in testis-specific LRRC69 was significantly overrepresented in patients with SPGF compared to the general population (3.3% vs. 0.85%; χ2 test, OR = 3.9 [95% CI 1.8-8.4], P = 0.0001). Assessment of clinically valid CNVs in patients with SPGF will improve their management and counselling for general and reproductive health, including risk of miscarriage and congenital disorders in future offspring.
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100
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Zhang H, Gong X, Xu X, Wang X, Sun Y. Tooth number abnormality: from bench to bedside. Int J Oral Sci 2023; 15:5. [PMID: 36604408 PMCID: PMC9816303 DOI: 10.1038/s41368-022-00208-x] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/24/2022] [Accepted: 11/01/2022] [Indexed: 01/07/2023] Open
Abstract
Tooth number abnormality is one of the most common dental developmental diseases, which includes both tooth agenesis and supernumerary teeth. Tooth development is regulated by numerous developmental signals, such as the well-known Wnt, BMP, FGF, Shh and Eda pathways, which mediate the ongoing complex interactions between epithelium and mesenchyme. Abnormal expression of these crutial signalling during this process may eventually lead to the development of anomalies in tooth number; however, the underlying mechanisms remain elusive. In this review, we summarized the major process of tooth development, the latest progress of mechanism studies and newly reported clinical investigations of tooth number abnormality. In addition, potential treatment approaches for tooth number abnormality based on developmental biology are also discussed. This review not only provides a reference for the diagnosis and treatment of tooth number abnormality in clinical practice but also facilitates the translation of basic research to the clinical application.
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Affiliation(s)
- Han Zhang
- grid.24516.340000000123704535Department of Implantology, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Xuyan Gong
- grid.24516.340000000123704535Department of Implantology, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Xiaoqiao Xu
- grid.24516.340000000123704535Department of Implantology, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Xiaogang Wang
- grid.64939.310000 0000 9999 1211Key Laboratory of Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China
| | - Yao Sun
- Department of Implantology, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China.
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