1
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Zhao P, Wang C, Sun S, Wang X, Balch WE. Tracing genetic diversity captures the molecular basis of misfolding disease. Nat Commun 2024; 15:3333. [PMID: 38637533 PMCID: PMC11026414 DOI: 10.1038/s41467-024-47520-0] [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: 04/04/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Genetic variation in human populations can result in the misfolding and aggregation of proteins, giving rise to systemic and neurodegenerative diseases that require management by proteostasis. Here, we define the role of GRP94, the endoplasmic reticulum Hsp90 chaperone paralog, in managing alpha-1-antitrypsin deficiency on a residue-by-residue basis using Gaussian process regression-based machine learning to profile the spatial covariance relationships that dictate protein folding arising from sequence variants in the population. Covariance analysis suggests a role for the ATPase activity of GRP94 in controlling the N- to C-terminal cooperative folding of alpha-1-antitrypsin responsible for the correction of liver aggregation and lung-disease phenotypes of alpha-1-antitrypsin deficiency. Gaussian process-based spatial covariance profiling provides a standard model built on covariant principles to evaluate the role of proteostasis components in guiding information flow from genome to proteome in response to genetic variation, potentially allowing us to intervene in the onset and progression of complex multi-system human diseases.
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Affiliation(s)
- Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
- Department of Nutrition and Food Hygiene, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Collaborative Innovation Center for Cancer Personalized Medicine, and Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Xi Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
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2
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Watanabe K, Nishio SY, Usami SI. The prevalence and clinical features of MYO7A-related hearing loss including DFNA11, DFNB2 and USH1B. Sci Rep 2024; 14:8326. [PMID: 38594301 PMCID: PMC11003999 DOI: 10.1038/s41598-024-57415-1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/18/2024] [Indexed: 04/11/2024] Open
Abstract
The MYO7A gene is known to be responsible for both syndromic hearing loss (Usher syndrome type1B:USH1B) and non-syndromic hearing loss including autosomal dominant and autosomal recessive inheritance (DFNA11, DFNB2). However, the prevalence and detailed clinical features of MYO7A-associated hearing loss across a large population remain unclear. In this study, we conducted next-generation sequencing analysis for a large cohort of 10,042 Japanese hearing loss patients. As a result, 137 patients were identified with MYO7A-associated hearing loss so that the prevalence among Japanese hearing loss patients was 1.36%. We identified 70 disease-causing candidate variants in this study, with 36 of them being novel variants. All variants identified in autosomal dominant cases were missense or in-frame deletion variants. Among the autosomal recessive cases, all patients had at least one missense variant. On the other hand, in patients with Usher syndrome, almost half of the patients carried biallelic null variants (nonsense, splicing, and frameshift variants). Most of the autosomal dominant cases showed late-onset progressive hearing loss. On the other hand, cases with autosomal recessive inheritance or Usher syndrome showed congenital or early-onset hearing loss. The visual symptoms in the Usher syndrome cases developed between age 5-15, and the condition was diagnosed at about 6-15 years of age.
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Affiliation(s)
- Kizuki Watanabe
- Department of Otorhinolaryngology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Shin-Ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
| | - Shin-Ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan.
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3
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Masalkhi M, Ong J, Waisberg E, Lee AG. Ocular oxidative changes and antioxidant therapy during spaceflight. Eye (Lond) 2024; 38:1034-1035. [PMID: 38001279 PMCID: PMC11009295 DOI: 10.1038/s41433-023-02841-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 11/03/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Affiliation(s)
- Mouayad Masalkhi
- University College Dublin School of Medicine, Belfield, Dublin, Ireland.
| | - Joshua Ong
- Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Ethan Waisberg
- Department of Ophthalmology, University of Cambridge, Cambridge, UK
| | - Andrew G Lee
- Center for Space Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Ophthalmology, Blanton Eye Institute, Houston Methodist Hospital, Houston, TX, USA
- The Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
- Departments of Ophthalmology, Neurology, and Neurosurgery, Weill Cornell Medicine, New York, NY, USA
- Department of Ophthalmology, University of Texas Medical Branch, Galveston, TX, USA
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Texas A&M College of Medicine, Houston, TX, USA
- Department of Ophthalmology, The University of Iowa Hospitals and Clinics, Iowa City, IA, USA
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4
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Meester JAN, Hebert A, Bastiaansen M, Rabaut L, Bastianen J, Boeckx N, Ashcroft K, Atwal PS, Benichou A, Billon C, Blankensteijn JD, Brennan P, Bucks SA, Campbell IM, Conrad S, Curtis SL, Dasouki M, Dent CL, Eden J, Goel H, Hartill V, Houweling AC, Isidor B, Jackson N, Koopman P, Korpioja A, Kraatari-Tiri M, Kuulavainen L, Lee K, Low KJ, Lu AC, McManus ML, Oakley SP, Oliver J, Organ NM, Overwater E, Revencu N, Trainer AH, Trivedi B, Turner CLS, Whittington R, Zankl A, Zentner D, Van Laer L, Verstraeten A, Loeys BL. Expanding the clinical spectrum of biglycan-related Meester-Loeys syndrome. NPJ Genom Med 2024; 9:22. [PMID: 38531898 PMCID: PMC10966070 DOI: 10.1038/s41525-024-00413-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
Pathogenic loss-of-function variants in BGN, an X-linked gene encoding biglycan, are associated with Meester-Loeys syndrome (MRLS), a thoracic aortic aneurysm/dissection syndrome. Since the initial publication of five probands in 2017, we have considerably expanded our MRLS cohort to a total of 18 probands (16 males and 2 females). Segregation analyses identified 36 additional BGN variant-harboring family members (9 males and 27 females). The identified BGN variants were shown to lead to loss-of-function by cDNA and Western Blot analyses of skin fibroblasts or were strongly predicted to lead to loss-of-function based on the nature of the variant. No (likely) pathogenic missense variants without additional (predicted) splice effects were identified. Interestingly, a male proband with a deletion spanning the coding sequence of BGN and the 5' untranslated region of the downstream gene (ATP2B3) presented with a more severe skeletal phenotype. This may possibly be explained by expressional activation of the downstream ATPase ATP2B3 (normally repressed in skin fibroblasts) driven by the remnant BGN promotor. This study highlights that aneurysms and dissections in MRLS extend beyond the thoracic aorta, affecting the entire arterial tree, and cardiovascular symptoms may coincide with non-specific connective tissue features. Furthermore, the clinical presentation is more severe and penetrant in males compared to females. Extensive analysis at RNA, cDNA, and/or protein level is recommended to prove a loss-of-function effect before determining the pathogenicity of identified BGN missense and non-canonical splice variants. In conclusion, distinct mechanisms may underlie the wide phenotypic spectrum of MRLS patients carrying loss-of-function variants in BGN.
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Affiliation(s)
- Josephina A N Meester
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Anne Hebert
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Maaike Bastiaansen
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Laura Rabaut
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Jarl Bastianen
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Nele Boeckx
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Kathryn Ashcroft
- Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals, NHS Foundation Trust, Leeds, UK
| | - Paldeep S Atwal
- Genomic and Personalized Medicine, Atwal Clinic, Palm Beach, FL, USA
| | - Antoine Benichou
- Department of Internal and Vascular Medicine, CHU Nantes, Nantes Université, Nantes, France
| | - Clarisse Billon
- Service de Médecine Génomique des Maladies Rares, Groupe Hospitalier Universitaire Centre, Paris, Assistance Publique Hôpitaux de Paris, Paris, France
- Université de Paris Cité, Inserm, PARCC, Paris, France
| | - Jan D Blankensteijn
- Department of Vascular Surgery, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Paul Brennan
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Ian M Campbell
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Solène Conrad
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Stephanie L Curtis
- Bristol Heart Institute, University Hospitals Bristol & Weston NHS Foundation Trust, Bristol, UK
| | - Majed Dasouki
- Department of Medical Genetics & Genomics, AdventHealth Medical Group, Orlando, FL, USA
| | - Carolyn L Dent
- South West Genomic Laboratory Hub, Bristol Genetics Laboratory, Bristol, UK
| | - James Eden
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester, UK
| | | | - Verity Hartill
- Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals, NHS Foundation Trust, Leeds, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Arjan C Houweling
- Department of Human Genetics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Nicola Jackson
- Clinical Genetics Service, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Pieter Koopman
- Department of Cardiology, Heart Centre Hasselt, Jessa Hospital, Hasselt, Belgium
| | - Anita Korpioja
- Department of Clinical Genetics, Research Unit of Clinical Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Minna Kraatari-Tiri
- Department of Clinical Genetics, Research Unit of Clinical Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Liina Kuulavainen
- Department of Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kelvin Lee
- Department of Medical Genetics & Genomics, AdventHealth Medical Group, Orlando, FL, USA
| | - Karen J Low
- Clinical Genetics Department, University Hospitals Bristol and Weston NHS Foundation Trust St Michael's Hospital, Bristol, UK
- University of Bristol, Canynge Hall, Bristol, UK
| | - Alan C Lu
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Morgan L McManus
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stephen P Oakley
- John Hunter Hospital, New Lambton Heights, NSW, Australia
- College of Health, Medicine and Wellbeing, School of Medicine, University of Newcastle, Newcastle, NSW, Australia
| | - James Oliver
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Manchester, UK
| | - Nicole M Organ
- John Hunter Hospital, New Lambton Heights, NSW, Australia
| | - Eline Overwater
- Department of Human Genetics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Nicole Revencu
- Center for Human Genetics, Cliniques Universitaires Saint-Luc and Université Catholique de Louvain, Brussels, Belgium
| | - Alison H Trainer
- Department of Genomic Medicine, The Royal Melbourne Hospital and University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Bhavya Trivedi
- Department of Medical Genetics & Genomics, AdventHealth Medical Group, Orlando, FL, USA
| | - Claire L S Turner
- Department of Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | | | - Andreas Zankl
- Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney, NSW, Australia
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Dominica Zentner
- Department of Genomic Medicine, The Royal Melbourne Hospital and University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Lut Van Laer
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Aline Verstraeten
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Bart L Loeys
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.
- Department of Clinical Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
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5
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Wang X, Wang J, Chen Y, Qian X, Luo S, Wang X, Ma C, Ge W. The aldehyde dehydrogenase 2 rs671 variant enhances amyloid β pathology. Nat Commun 2024; 15:2594. [PMID: 38519490 PMCID: PMC10959958 DOI: 10.1038/s41467-024-46899-0] [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: 08/11/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
In the ALDH2 rs671 variant, a guanine changes to an adenine, resulting in a dramatic decrease in the catalytic activity of the enzyme. Population-based data are contradictory about whether this variant increases the risk of Alzheimer's disease. In East Asian populations, the prevalence of the ALDH2 rs671 variant is 30-50%, making the National Human Brain Bank for Development and Function (the largest brain bank in East Asia) an important resource to explore the link between the ALDH2 rs671 polymorphism and Alzheimer's disease pathology. Here, using 469 postmortem brains, we find that while the ALDH2 rs671 variant is associated with increased plaque deposits and a higher Aβ40/42 ratio, it is not an independent risk factor for Alzheimer's disease. Mechanistically, we show that lower ALDH2 activity leads to 4-HNE accumulation in the brain. The (R)-4-HNE enantiomer adducts to residue Lys53 of C99, favoring Aβ40 generation in the Golgi apparatus. Decreased ALDH2 activity also lowers inflammatory factor secretion, as well as amyloid β phagocytosis and spread in brains of patients with Alzheimer's disease. We thus define the relationship between the ALDH2 rs671 polymorphism and amyloid β pathology, and find that ALDH2 rs671 is a key regulator of Aβ40 or Aβ42 generation.
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Affiliation(s)
- Xia Wang
- Department of Immunology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Jiayu Wang
- Department of Immunology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yashuang Chen
- Department of Immunology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xiaojing Qian
- Department of Human Anatomy, Histology and Embryology, Neuroscience Center, National Human Brain Bank for Development and Function, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Shiqi Luo
- Department of Immunology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xue Wang
- Department of Human Anatomy, Histology and Embryology, Neuroscience Center, National Human Brain Bank for Development and Function, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Chao Ma
- Department of Human Anatomy, Histology and Embryology, Neuroscience Center, National Human Brain Bank for Development and Function, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.
| | - Wei Ge
- Department of Immunology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.
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6
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Chelban V, Aksnes H, Maroofian R, LaMonica LC, Seabra L, Siggervåg A, Devic P, Shamseldin HE, Vandrovcova J, Murphy D, Richard AC, Quenez O, Bonnevalle A, Zanetti MN, Kaiyrzhanov R, Salpietro V, Efthymiou S, Schottlaender LV, Morsy H, Scardamaglia A, Tariq A, Pagnamenta AT, Pennavaria A, Krogstad LS, Bekkelund ÅK, Caiella A, Glomnes N, Brønstad KM, Tury S, Moreno De Luca A, Boland-Auge A, Olaso R, Deleuze JF, Anheim M, Cretin B, Vona B, Alajlan F, Abdulwahab F, Battini JL, İpek R, Bauer P, Zifarelli G, Gungor S, Kurul SH, Lochmuller H, Da'as SI, Fakhro KA, Gómez-Pascual A, Botía JA, Wood NW, Horvath R, Ernst AM, Rothman JE, McEntagart M, Crow YJ, Alkuraya FS, Nicolas G, Arnesen T, Houlden H. Biallelic NAA60 variants with impaired n-terminal acetylation capacity cause autosomal recessive primary familial brain calcifications. Nat Commun 2024; 15:2269. [PMID: 38480682 PMCID: PMC10937998 DOI: 10.1038/s41467-024-46354-0] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Primary familial brain calcification (PFBC) is characterized by calcium deposition in the brain, causing progressive movement disorders, psychiatric symptoms, and cognitive decline. PFBC is a heterogeneous disorder currently linked to variants in six different genes, but most patients remain genetically undiagnosed. Here, we identify biallelic NAA60 variants in ten individuals from seven families with autosomal recessive PFBC. The NAA60 variants lead to loss-of-function with lack of protein N-terminal (Nt)-acetylation activity. We show that the phosphate importer SLC20A2 is a substrate of NAA60 in vitro. In cells, loss of NAA60 caused reduced surface levels of SLC20A2 and a reduction in extracellular phosphate uptake. This study establishes NAA60 as a causal gene for PFBC, provides a possible biochemical explanation of its disease-causing mechanisms and underscores NAA60-mediated Nt-acetylation of transmembrane proteins as a fundamental process for healthy neurobiological functioning.
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Affiliation(s)
- Viorica Chelban
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK.
- Neurobiology and Medical Genetics Laboratory, "Nicolae Testemitanu" State University of Medicine and Pharmacy, 165, Stefan cel Mare si Sfant Boulevard, MD, 2004, Chisinau, Republic of Moldova.
| | - Henriette Aksnes
- Department of Biomedicine, University of Bergen, Bergen, Norway.
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Lauren C LaMonica
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Luis Seabra
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR 1163, Paris, France
| | | | - Perrine Devic
- Hospices Civils de Lyon, Groupement Hospitalier Sud, Service d'Explorations Fonctionnelles Neurologiques, Lyon, France
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Anne-Claire Richard
- Univ Rouen Normandie, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, F-76000, Rouen, France
| | - Olivier Quenez
- Univ Rouen Normandie, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, F-76000, Rouen, France
| | - Antoine Bonnevalle
- Univ Rouen Normandie, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, F-76000, Rouen, France
| | - M Natalia Zanetti
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- South Kazakhstan Medical Academy Shymkent, Shymkent, 160019, Kazakhstan
| | - Vincenzo Salpietro
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Lucia V Schottlaender
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Instituto de Investigaciones en Medicina Traslacional (IIMT), CONICET-Universidad Austral, Av. Juan Domingo Perón 1500, B1629AHJ, Pilar, Argentina
- Instituto de medicina genómica (IMeG), Hospital Universitario Austral, Universidad Austral, Av. Juan Domingo Perón 1500, B1629AHJ, Pilar, Argentina
| | - Heba Morsy
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Annarita Scardamaglia
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Ambreen Tariq
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Alistair T Pagnamenta
- Oxford NIHR Biomedical Research Centre, Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Ajia Pennavaria
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Liv S Krogstad
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Åse K Bekkelund
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Alessia Caiella
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Nina Glomnes
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Clinical Science, University of Bergen, 5020, Bergen, Norway
| | | | - Sandrine Tury
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS, Montpellier, France
| | - Andrés Moreno De Luca
- Department of Radiology, Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
- Department of Radiology, Neuroradiology Section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Anne Boland-Auge
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Mathieu Anheim
- Neurology Department, Strasbourg University Hospital, Strasbourg, France
- Strasbourg Federation of Translational Medicine (FMTS), Strasbourg University, Strasbourg, France
- INSERM-U964; CNRS-UMR7104, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Benjamin Cretin
- Neurology Department, Strasbourg University Hospital, Strasbourg, France
- Strasbourg Federation of Translational Medicine (FMTS), Strasbourg University, Strasbourg, France
- INSERM-U964; CNRS-UMR7104, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, 37073, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Fahad Alajlan
- Department of Neuroscience Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jean-Luc Battini
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS, Montpellier, France
| | - Rojan İpek
- Paediatric Neurology, Faculty of Medicine, Dicle University, Diyarbakır, Turkey
| | - Peter Bauer
- Centogene GmbH, Am Strande 7, 18055, Rostock, Germany
| | | | - Serdal Gungor
- Inonu University, Faculty of Medicine, Turgut Ozal Research Center, Department of Pediatrics, Division of Pediatric Neurology, Malatya, Turkey
| | - Semra Hiz Kurul
- Dokuz Eylul University, School of Medicine, Department of Paediatric Neurology, Izmir, Turkey
| | - Hanns Lochmuller
- Children's Hospital of Eastern Ontario Research Institute and Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
- Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
- Department of Neuropediatrics and Muscle Disorders, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Sahar I Da'as
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Weill Cornell Medical College, Doha, Qatar
| | - Alicia Gómez-Pascual
- Department of Information and Communications Engineering, University of Murcia, Campus Espinardo, 30100, Murcia, Spain
| | - Juan A Botía
- Department of Information and Communications Engineering, University of Murcia, Campus Espinardo, 30100, Murcia, Spain
| | - Nicholas W Wood
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Neurogenetics Laboratory, The National Hospital for Neurology and Neurosurgery, London, WC1N 3BG, UK
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Andreas M Ernst
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - James E Rothman
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Meriel McEntagart
- Medical Genetics Department, St George's University Hospitals, London, SWI7 0RE, UK
| | - Yanick J Crow
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR 1163, Paris, France
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, F-76000, Rouen, France
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, Bergen, Norway.
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK.
- Neurogenetics Laboratory, The National Hospital for Neurology and Neurosurgery, London, WC1N 3BG, UK.
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7
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Gillentine MA. Comment on Gustavson syndrome is caused by an in-frame deletion in RBMX associated with potentially disturbed SH3 domain interactions. Eur J Hum Genet 2024; 32:253-256. [PMID: 38017187 PMCID: PMC10923807 DOI: 10.1038/s41431-023-01498-3] [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: 10/26/2023] [Accepted: 11/08/2023] [Indexed: 11/30/2023] Open
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8
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Traverso M, Baratto S, Iacomino M, Di Duca M, Panicucci C, Casalini S, Grandis M, Falace A, Torella A, Picillo E, Onore ME, Politano L, Nigro V, Innes AM, Barresi R, Bruno C, Zara F, Fiorillo C, Scala M. DAG1 haploinsufficiency is associated with sporadic and familial isolated or pauci-symptomatic hyperCKemia. Eur J Hum Genet 2024; 32:342-349. [PMID: 38177406 PMCID: PMC10923780 DOI: 10.1038/s41431-023-01516-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/31/2023] [Accepted: 11/27/2023] [Indexed: 01/06/2024] Open
Abstract
DAG1 encodes for dystroglycan, a key component of the dystrophin-glycoprotein complex (DGC) with a pivotal role in skeletal muscle function and maintenance. Biallelic loss-of-function DAG1 variants cause severe muscular dystrophy and muscle-eye-brain disease. A possible contribution of DAG1 deficiency to milder muscular phenotypes has been suggested. We investigated the genetic background of twelve subjects with persistent mild-to-severe hyperCKemia to dissect the role of DAG1 in this condition. Genetic testing was performed through exome sequencing (ES) or custom NGS panels including various genes involved in a spectrum of muscular disorders. Histopathological and Western blot analyses were performed on muscle biopsy samples obtained from three patients. We identified seven novel heterozygous truncating variants in DAG1 segregating with isolated or pauci-symptomatic hyperCKemia in all families. The variants were rare and predicted to lead to nonsense-mediated mRNA decay or the formation of a truncated transcript. In four cases, DAG1 variants were inherited from similarly affected parents. Histopathological analysis revealed a decreased expression of dystroglycan subunits and Western blot confirmed a significantly reduced expression of beta-dystroglycan in muscle samples. This study supports the pathogenic role of DAG1 haploinsufficiency in isolated or pauci-symptomatic hyperCKemia, with implications for clinical management and genetic counseling.
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Affiliation(s)
- Monica Traverso
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Serena Baratto
- Centre of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Michele Iacomino
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marco Di Duca
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Chiara Panicucci
- Centre of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Sara Casalini
- Centre of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Antonio Falace
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Annalaura Torella
- Department of Precision Medicine, University "Luigi Vanvitelli", Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Esther Picillo
- Department of Precision Medicine, University "Luigi Vanvitelli", Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Maria Elena Onore
- Department of Precision Medicine, University "Luigi Vanvitelli", Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Luisa Politano
- Department of Precision Medicine, University "Luigi Vanvitelli", Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Vincenzo Nigro
- Department of Precision Medicine, University "Luigi Vanvitelli", Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - A Micheil Innes
- Department of Medical Genetics and Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Claudio Bruno
- Centre of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Federico Zara
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.
| | - Chiara Fiorillo
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.
- Child Neuropsychiatry Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | - Marcello Scala
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.
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9
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Huyghebaert J, Mateiu L, Elinck E, Van Rossem KE, Christiaenssen B, D'Incal CP, McCormack MK, Lazzarini A, Vandeweyer G, Kooy RF. Identification of a DLG3 stop mutation in the MRX20 family. Eur J Hum Genet 2024; 32:317-323. [PMID: 38273165 PMCID: PMC10923781 DOI: 10.1038/s41431-024-01537-7] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
Here, we identified the causal mutation in the MRX20 family, one of the larger X-linked pedigrees that have been described in which no gene had been identified up till now. In 1995, the putative disease gene had been mapped to the pericentromeric region on the X chromosome, but no follow-up studies were performed. Here, whole exome sequencing (WES) on two affected and one unaffected family member revealed the c.195del/p.(Thr66ProfsTer55) mutation in the DLG3 gene (NM_021120.4) that segregated with the affected individuals in the family. DLG3 mutations have been consequently associated with intellectual disability and are a plausible explanation for the clinical abnormalities observed in this family. In addition, we identified two other variants co-segregating with the phenotype: a stop gain mutation in SSX1 (c.358G>T/p.(Glu120Ter)) (NM_001278691.2) and a nonsynonymous SNV in USP27X (c.56 A>G/p.(Gln19Arg)) (NM_001145073.3). RNA sequencing revealed 14 differentially expressed genes (p value < 0.1) in 7 affected males compared to 4 unaffected males of the family, including four genes known to be associated with neurological disorders. Thus, in this paper we identified the c.195del/p.(Thr66ProfsTer55) mutation in the DLG3 gene (NM_021120.4) as likely responsible for the phenotype observed in the MRX20 family.
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Affiliation(s)
| | - Ligia Mateiu
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Ellen Elinck
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | | | | | | | - Michael K McCormack
- Department of Psychiatry, Rutgers University-Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
- Department of Cell Biology and Neurosciences, Virtua Health College of Medicine and Life Sciences of Rowan University, Stratford, NJ, 08084, USA
| | - Alice Lazzarini
- Department of Neurology, Rutgers University-Robert Wood Johnson Medical School, New Brunswick, NJ, 08903, USA
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.
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10
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Kishio N, Iwama K, Nakanishi S, Shindo R, Yasui M, Nicho N, Takahashi A, Kohara M, Hirata M, Kemmotsu T, Tanoshima M, Ito S. A deletion variant in LMX1B causing nail-patella syndrome in Japanese twins. Hum Genome Var 2024; 11:10. [PMID: 38424113 PMCID: PMC10904864 DOI: 10.1038/s41439-024-00266-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 03/02/2024] Open
Abstract
Nail-patella syndrome (NPS) is a hereditary disease caused by pathogenic variants in LMX1B and characterized by nail, limb, and renal symptoms. This study revealed a likely pathogenic LMX1B variant, NM_002316.4: c.723_726delinsC (p.Ser242del), in Japanese twins with clubfoot. The patients' mother, who shared this variant, developed proteinuria after delivery. p.Ser242del is located in the homeodomain of the protein, in which variants that cause renal disease tend to cluster. Our findings highlight p.Ser242del as a likely pathogenic variant, expanding our knowledge of NPS.
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Affiliation(s)
- Nozomu Kishio
- Department of Maternal and Perinatal Center, Yokohama City University Medical Center, Yokohama, Japan.
- Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.
| | - Kazuhiro Iwama
- Department of Maternal and Perinatal Center, Yokohama City University Medical Center, Yokohama, Japan.
- Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.
- Department of Clinical Genetics, Yokohama City University Medical Center, Yokohama, Japan.
| | - Sayuri Nakanishi
- Department of Maternal and Perinatal Center, Yokohama City University Medical Center, Yokohama, Japan
- Department of Clinical Genetics, Yokohama City University Medical Center, Yokohama, Japan
| | - Ryosuke Shindo
- Department of Maternal and Perinatal Center, Yokohama City University Medical Center, Yokohama, Japan
- Department of Clinical Genetics, Yokohama City University Medical Center, Yokohama, Japan
| | - Masaki Yasui
- Department of Maternal and Perinatal Center, Yokohama City University Medical Center, Yokohama, Japan
- Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naoki Nicho
- Department of Maternal and Perinatal Center, Yokohama City University Medical Center, Yokohama, Japan
- Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Atsushi Takahashi
- Department of Maternal and Perinatal Center, Yokohama City University Medical Center, Yokohama, Japan
- Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Mana Kohara
- Department of Maternal and Perinatal Center, Yokohama City University Medical Center, Yokohama, Japan
- Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Michisato Hirata
- Department of Maternal and Perinatal Center, Yokohama City University Medical Center, Yokohama, Japan
- Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Takahiro Kemmotsu
- Department of Maternal and Perinatal Center, Yokohama City University Medical Center, Yokohama, Japan
- Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Miki Tanoshima
- Department of Maternal and Perinatal Center, Yokohama City University Medical Center, Yokohama, Japan
- Department of Clinical Genetics, Yokohama City University Medical Center, Yokohama, Japan
| | - Shuichi Ito
- Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
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11
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Venner E, Patterson K, Kalra D, Wheeler MM, Chen YJ, Kalla SE, Yuan B, Karnes JH, Walker K, Smith JD, McGee S, Radhakrishnan A, Haddad A, Empey PE, Wang Q, Lichtenstein L, Toledo D, Jarvik G, Musick A, Gibbs RA. The frequency of pathogenic variation in the All of Us cohort reveals ancestry-driven disparities. Commun Biol 2024; 7:174. [PMID: 38374434 PMCID: PMC10876563 DOI: 10.1038/s42003-023-05708-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/13/2023] [Indexed: 02/21/2024] Open
Abstract
Disparities in data underlying clinical genomic interpretation is an acknowledged problem, but there is a paucity of data demonstrating it. The All of Us Research Program is collecting data including whole-genome sequences, health records, and surveys for at least a million participants with diverse ancestry and access to healthcare, representing one of the largest biomedical research repositories of its kind. Here, we examine pathogenic and likely pathogenic variants that were identified in the All of Us cohort. The European ancestry subgroup showed the highest overall rate of pathogenic variation, with 2.26% of participants having a pathogenic variant. Other ancestry groups had lower rates of pathogenic variation, including 1.62% for the African ancestry group and 1.32% in the Latino/Admixed American ancestry group. Pathogenic variants were most frequently observed in genes related to Breast/Ovarian Cancer or Hypercholesterolemia. Variant frequencies in many genes were consistent with the data from the public gnomAD database, with some notable exceptions resolved using gnomAD subsets. Differences in pathogenic variant frequency observed between ancestral groups generally indicate biases of ascertainment of knowledge about those variants, but some deviations may be indicative of differences in disease prevalence. This work will allow targeted precision medicine efforts at revealed disparities.
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Affiliation(s)
- Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | - Karynne Patterson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Divya Kalra
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Marsha M Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Yi-Ju Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Sara E Kalla
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Bo Yuan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jason H Karnes
- University of Arizona, R Ken Coit College of Pharmacy, Department of Pharmacy Practice and Science, Tucson, AZ, USA
- Vanderbilt University Medical Center, Department of Biomedical Informatics, Boston, MA, USA
| | - Kimberly Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sean McGee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Andrew Haddad
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Philip E Empey
- Department of Pharmacy and Therapeutics, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Qiaoyan Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Diana Toledo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gail Jarvik
- Department of Medicine (Medical Genetics), University of Washington School of Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Anjene Musick
- NIH All of Us Research Program, National Institutes of Health Office of the Director, Bethesda, MD, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
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12
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Zhao S, Zhao H, Zhao L, Cheng X, Zheng Z, Wu M, Wen W, Wang S, Zhou Z, Xie H, Ruan D, Li Q, Liu X, Ou C, Li G, Zhao Z, Chen G, Niu Y, Yin X, Hu Y, Zhang X, Liu P, Qiu G, Liu W, Zhao C, Wu Z, Zhang J, Wu N. Unraveling the genetic architecture of congenital vertebral malformation with reference to the developing spine. Nat Commun 2024; 15:1125. [PMID: 38321032 PMCID: PMC10847475 DOI: 10.1038/s41467-024-45442-5] [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: 09/02/2023] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Congenital vertebral malformation, affecting 0.13-0.50 per 1000 live births, has an immense locus heterogeneity and complex genetic architecture. In this study, we analyze exome/genome sequencing data from 873 probands with congenital vertebral malformation and 3794 control individuals. Clinical interpretation identifies Mendelian etiologies in 12.0% of the probands and reveals a muscle-related disease mechanism. Gene-based burden test of ultra-rare variants identifies risk genes with large effect sizes (ITPR2, TBX6, TPO, H6PD, and SEC24B). To further investigate the biological relevance of the genetic association signals, we perform single-nucleus RNAseq on human embryonic spines. The burden test signals are enriched in the notochord at early developmental stages and myoblast/myocytes at late stages, highlighting their critical roles in the developing spine. Our work provides insights into the developmental biology of the human spine and the pathogenesis of spine malformation.
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Affiliation(s)
- Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lina Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xi Cheng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhifa Zheng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Mengfan Wu
- Institute of Evolution & Marine Biodiversity, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Wen Wen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shengru Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zixiang Zhou
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Haibo Xie
- Institute of Evolution & Marine Biodiversity, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Dengfeng Ruan
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400, China
| | - Qing Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xinquan Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Chengzhu Ou
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Guozhuang Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhengye Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Guilin Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yuchen Niu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiangjie Yin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yuhong Hu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiaochen Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Wanlu Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400, China
| | - Chengtian Zhao
- Institute of Evolution & Marine Biodiversity, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Zhihong Wu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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13
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Svetina M, Šelb J, Lyons JJ, Korošec P, Rijavec M. Clinically accessible amplitude-based multiplex ddPCR assay for tryptase genotyping. Sci Rep 2024; 14:2416. [PMID: 38287122 PMCID: PMC10825142 DOI: 10.1038/s41598-024-52983-8] [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: 10/13/2023] [Accepted: 01/25/2024] [Indexed: 01/31/2024] Open
Abstract
Hereditary α tryptasemia (HαT) is an autosomal dominant trait characterized by increased TPSAB1 copy number (CN) encoding α-tryptase. The determination of HαT is being discussed as an important biomarker to be included in risk assessment models and future diagnostic algorithms for patients with mastocytosis and anaphylaxis. Due to the complex genetic structure at the human tryptase locus, genetic testing for tryptase gene composition is presently notably limited and infrequently pursued. This study aimed to develop, optimise and validate a multiplex droplet digital PCR (ddPCR) assay that can reliably quantify α- and β-tryptase encoding sequences in a single reaction. To optimise the ddPCR conditions and establish an amplitude-based multiplex ddPCR assay, additional primers and probes, a thermal gradient with varying annealing temperatures, different primers/probe concentrations, and various initial DNA quantities were tested. Results obtained from all 114 samples analysed using multiplex ddPCR were identical to those obtained through the use of original duplex assays. Utilizing this multiplex ddPCR assay, in contrast to conducting distinct duplex ddPCRs, presents noteworthy benefits for tryptase genotyping. These advantages encompass a substantial threefold decrease in material costs and considerable time savings. Consequently, this approach exhibits high suitability and particularly captures interest for routine clinical implementation.
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Affiliation(s)
- Manca Svetina
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Julij Šelb
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jonathan J Lyons
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | - Peter Korošec
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Matija Rijavec
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia.
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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14
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Miura S, Watanabe E, Senzaki K, Hiruki S, Matsumoto S, Morikawa T, Uchiyama Y, Kurata S, Ochi M, Ohyagi Y, Shibata H. Episodic ataxia type 2 with a novel missense variant (Leu602Arg) in CACNA1A. Hum Genome Var 2024; 11:3. [PMID: 38221525 PMCID: PMC10788331 DOI: 10.1038/s41439-023-00261-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 01/16/2024] Open
Abstract
Autosomal dominant episodic ataxia type 2 (EA2) is caused by variants in CACNA1A. We examined a 20-year-old male with EA symptoms from a Japanese family with hereditary EA. Cerebellar atrophy was not evident, but single photon emission computed tomography showed cerebellar hypoperfusion. We identified a novel nonsynonymous variant in CACNA1A, NM_001127222.2:c.1805T>G (p.Leu602Arg), which is predicted to be functionally deleterious; therefore, this variant is likely responsible for EA2 in this pedigree.
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Affiliation(s)
- Shiroh Miura
- Department of Neurology and Geriatric Medicine, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan.
| | - Emina Watanabe
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Kensuke Senzaki
- Department of Neurology and Geriatric Medicine, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Shigeyoshi Hiruki
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Sayaka Matsumoto
- Department of Neurology and Geriatric Medicine, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Takuya Morikawa
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Yusuke Uchiyama
- Department of Radiology, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka, Japan
| | - Seiji Kurata
- Department of Radiology, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka, Japan
| | - Masayuki Ochi
- Department of Neurology and Geriatric Medicine, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Yasumasa Ohyagi
- Department of Neurology and Geriatric Medicine, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, Japan
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15
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Shah AM, Myhre PL, Arthur V, Dorbala P, Rasheed H, Buckley LF, Claggett B, Liu G, Ma J, Nguyen NQ, Matsushita K, Ndumele C, Tin A, Hveem K, Jonasson C, Dalen H, Boerwinkle E, Hoogeveen RC, Ballantyne C, Coresh J, Omland T, Yu B. Large scale plasma proteomics identifies novel proteins and protein networks associated with heart failure development. Nat Commun 2024; 15:528. [PMID: 38225249 PMCID: PMC10789789 DOI: 10.1038/s41467-023-44680-3] [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: 03/02/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024] Open
Abstract
Heart failure (HF) causes substantial morbidity and mortality but its pathobiology is incompletely understood. The proteome is a promising intermediate phenotype for discovery of novel mechanisms. We measured 4877 plasma proteins in 13,900 HF-free individuals across three analysis sets with diverse age, geography, and HF ascertainment to identify circulating proteins and protein networks associated with HF development. Parallel analyses in Atherosclerosis Risk in Communities study participants in mid-life and late-life and in Trøndelag Health Study participants identified 37 proteins consistently associated with incident HF independent of traditional risk factors. Mendelian randomization supported causal effects of 10 on HF, HF risk factors, or left ventricular size and function, including matricellular (e.g. SPON1, MFAP4), senescence-associated (FSTL3, IGFBP7), and inflammatory (SVEP1, CCL15, ITIH3) proteins. Protein co-regulation network analyses identified 5 modules associated with HF risk, two of which were influenced by genetic variants that implicated trans hotspots within the VTN and CFH genes.
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Affiliation(s)
- Amil M Shah
- Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Peder L Myhre
- Akershus University Hospital and K.G. Jebsen Center for Cardiac Biomarkers, University of Oslo, Oslo, Norway
| | - Victoria Arthur
- Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Pranav Dorbala
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Humaira Rasheed
- Akershus University Hospital and K.G. Jebsen Center for Cardiac Biomarkers, University of Oslo, Oslo, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Public Health and Nursing, HUNT Research Center, Norwegian University of Science and Technology, Trondheim, Norway
| | - Leo F Buckley
- Department of Pharmacy, Brigham and Women's Hospital, Boston, MA, USA
| | - Brian Claggett
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Guning Liu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Jianzhong Ma
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Ngoc Quynh Nguyen
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Kunihiro Matsushita
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Chiadi Ndumele
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Adrienne Tin
- University of Mississippi Medical Center, Jackson, MS, USA
| | - Kristian Hveem
- Department of Public Health and Nursing, HUNT Research Center, Norwegian University of Science and Technology, Trondheim, Norway
| | - Christian Jonasson
- Department of Public Health and Nursing, HUNT Research Center, Norwegian University of Science and Technology, Trondheim, Norway
| | - Håvard Dalen
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway
- Clinic of Cardiology, St Olavs University Hospital, Trondheim, Norway
- Department of Internal Medicine, Levanger Hospital, Levanger, Norway
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Ron C Hoogeveen
- Division of Cardiology, Baylor College of Medicine, Houston, TX, USA
| | | | - Josef Coresh
- Departments of Medicine and Population Health, NYU Langone Health, New York, NY, USA
| | - Torbjørn Omland
- Akershus University Hospital and K.G. Jebsen Center for Cardiac Biomarkers, University of Oslo, Oslo, Norway
| | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Sciences Center at Houston, Houston, TX, USA
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16
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Lauffer MC, van Roon-Mom W, Aartsma-Rus A. Possibilities and limitations of antisense oligonucleotide therapies for the treatment of monogenic disorders. Commun Med (Lond) 2024; 4:6. [PMID: 38182878 PMCID: PMC10770028 DOI: 10.1038/s43856-023-00419-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/27/2023] [Indexed: 01/07/2024] Open
Abstract
Antisense oligonucleotides (ASOs) are incredibly versatile molecules that can be designed to specifically target and modify RNA transcripts to slow down or halt rare genetic disease progression. They offer the potential to target groups of patients or can be tailored for individual cases. Nonetheless, not all genetic variants and disorders are amenable to ASO-based treatments, and hence, it is important to consider several factors before embarking on the drug development journey. Here, we discuss which genetic disorders have the potential to benefit from a specific type of ASO approach, based on the pathophysiology of the disease and pathogenic variant type, as well as those disorders that might not be suitable for ASO therapies. We further explore additional aspects, such as the target tissues, intervention time points, and potential clinical benefits, which need to be considered before developing a compound. Overall, we provide an overview of the current potentials and limitations of ASO-based therapeutics for the treatment of monogenic disorders.
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Affiliation(s)
- Marlen C Lauffer
- Dutch Center for RNA Therapeutics, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Willeke van Roon-Mom
- Dutch Center for RNA Therapeutics, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Annemieke Aartsma-Rus
- Dutch Center for RNA Therapeutics, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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17
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Worthmann A, Ridder J, Piel SYL, Evangelakos I, Musfeldt M, Voß H, O'Farrell M, Fischer AW, Adak S, Sundd M, Siffeti H, Haumann F, Kloth K, Bierhals T, Heine M, Pertzborn P, Pauly M, Scholz JJ, Kundu S, Fuh MM, Neu A, Tödter K, Hempel M, Knippschild U, Semenkovich CF, Schlüter H, Heeren J, Scheja L, Kubisch C, Schlein C. Fatty acid synthesis suppresses dietary polyunsaturated fatty acid use. Nat Commun 2024; 15:45. [PMID: 38167725 PMCID: PMC10762034 DOI: 10.1038/s41467-023-44364-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: 06/19/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Dietary polyunsaturated fatty acids (PUFA) are increasingly recognized for their health benefits, whereas a high production of endogenous fatty acids - a process called de novo lipogenesis (DNL) - is closely linked to metabolic diseases. Determinants of PUFA incorporation into complex lipids are insufficiently understood and may influence the onset and progression of metabolic diseases. Here we show that fatty acid synthase (FASN), the key enzyme of DNL, critically determines the use of dietary PUFA in mice and humans. Moreover, the combination of FASN inhibition and PUFA-supplementation decreases liver triacylglycerols (TAG) in mice fed with high-fat diet. Mechanistically, FASN inhibition causes higher PUFA uptake via the lysophosphatidylcholine transporter MFSD2A, and a diacylglycerol O-acyltransferase 2 (DGAT2)-dependent incorporation of PUFA into TAG. Overall, the outcome of PUFA supplementation may depend on the degree of endogenous DNL and combining PUFA supplementation and FASN inhibition might be a promising approach to target metabolic disease.
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Affiliation(s)
- Anna Worthmann
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julius Ridder
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sharlaine Y L Piel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ioannis Evangelakos
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Melina Musfeldt
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hannah Voß
- Section / Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marie O'Farrell
- Sagimet Biosciences Inc., 155 Bovet Rd., San Mateo, CA, 94402, USA
| | - Alexander W Fischer
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Sangeeta Adak
- Division of Endocrinology, Metabolism & Lipid Research, Department of Medicine, Washington University, St. Louis, MO, USA
| | - Monica Sundd
- National Institute of Immunology, New Delhi, India
| | - Hasibullah Siffeti
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friederike Haumann
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katja Kloth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Heine
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paul Pertzborn
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mira Pauly
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia-Josefine Scholz
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021 and Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K K Birla Goa Campus, Goa, 403726, India
| | - Marceline M Fuh
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Axel Neu
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Tödter
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Human Genetics, University Hospital Heidelberg, Im Neuenheimer Feld 440, 69120, Heidelberg, Germany
| | - Uwe Knippschild
- Department of General and Visceral Surgery, University Hospital Ulm, Ulm, Germany
| | - Clay F Semenkovich
- Division of Endocrinology, Metabolism & Lipid Research, Department of Medicine, Washington University, St. Louis, MO, USA
| | - Hartmut Schlüter
- Section / Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joerg Heeren
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ludger Scheja
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Schlein
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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18
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Uctepe E, Vona B, Esen FN, Sonmez FM, Smol T, Tümer S, Mancılar H, Geylan Durgun DE, Boute O, Moghbeli M, Ghayoor Karimiani E, Hashemi N, Bakhshoodeh B, Kim HG, Maroofian R, Yesilyurt A. Bi-allelic truncating variants in CASP2 underlie a neurodevelopmental disorder with lissencephaly. Eur J Hum Genet 2024; 32:52-60. [PMID: 37880421 PMCID: PMC10772072 DOI: 10.1038/s41431-023-01461-2] [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: 05/04/2023] [Revised: 07/24/2023] [Accepted: 09/11/2023] [Indexed: 10/27/2023] Open
Abstract
Lissencephaly (LIS) is a malformation of cortical development due to deficient neuronal migration and abnormal formation of cerebral convolutions or gyri. Thirty-one LIS-associated genes have been previously described. Recently, biallelic pathogenic variants in CRADD and PIDD1, have associated with LIS impacting the previously established role of the PIDDosome in activating caspase-2. In this report, we describe biallelic truncating variants in CASP2, another subunit of PIDDosome complex. Seven patients from five independent families presenting with a neurodevelopmental phenotype were identified through GeneMatcher-facilitated international collaborations. Exome sequencing analysis was carried out and revealed two distinct novel homozygous (NM_032982.4:c.1156delT (p.Tyr386ThrfsTer25), and c.1174 C > T (p.Gln392Ter)) and compound heterozygous variants (c.[130 C > T];[876 + 1 G > T] p.[Arg44Ter];[?]) in CASP2 segregating within the families in a manner compatible with an autosomal recessive pattern. RNA studies of the c.876 + 1 G > T variant indicated usage of two cryptic splice donor sites, each introducing a premature stop codon. All patients from whom brain MRIs were available had a typical fronto-temporal LIS and pachygyria, remarkably resembling the CRADD and PIDD1-related neuroimaging findings. Other findings included developmental delay, attention deficit hyperactivity disorder, hypotonia, seizure, poor social skills, and autistic traits. In summary, we present patients with CASP2-related ID, anterior-predominant LIS, and pachygyria similar to previously reported patients with CRADD and PIDD1-related disorders, expanding the genetic spectrum of LIS and lending support that each component of the PIDDosome complex is critical for normal development of the human cerebral cortex and brain function.
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Affiliation(s)
- Eyyup Uctepe
- Acibadem Ankara Tissue Typing Laboratory, Ankara, Türkiye
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | | | - F Mujgan Sonmez
- Department of Child Neurology, Faculty of Medicine, Retired lecturer, Karadeniz Technical University, Trabzon, Türkiye
- Private Office, Ankara, Türkiye
| | - Thomas Smol
- Institut de Génétique Médicale, Université de Lille, ULR7364 RADEME, CHU Lille, F-59000, Lille, France
| | - Sait Tümer
- Acibadem Labgen Genetic Diagnosis Center, Istanbul, Türkiye
| | | | | | - Odile Boute
- Clinique de Génétique, Université de Lille, ULR7364 RADEME, CHU Lille, F-59000, Lille, France
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Narges Hashemi
- Department of Pediatrics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Hyung Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Ahmet Yesilyurt
- Acibadem Labgen Genetic Diagnosis Center, Istanbul, Türkiye.
- Acibadem Maslak Hospital, Istanbul, Türkiye.
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19
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Rosén A, Krajc M, Ehrencrona H, Bajalica-Lagercrantz S. Public attitudes challenge clinical practice on genetic risk disclosure in favour of healthcare-provided direct dissemination to relatives. Eur J Hum Genet 2024; 32:6-7. [PMID: 37474788 PMCID: PMC10772116 DOI: 10.1038/s41431-023-01428-3] [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: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/22/2023] Open
Affiliation(s)
- Anna Rosén
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden.
| | - Mateja Krajc
- Department of Clinical Cancer Genetics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Hans Ehrencrona
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Svetlana Bajalica-Lagercrantz
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Hereditary Cancer Unit, Karolinska University Hospital, Stockholm, Sweden
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20
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Klemenzdottir EO, Arnadottir GA, Jensson BO, Jonasdottir A, Katrinardottir H, Fridriksdottir R, Jonasdottir A, Sigurdsson A, Gudjonsson SA, Jonsson JJ, Stefansdottir V, Danielsen R, Palsdottir A, Jonsson H, Helgason A, Magnusson OT, Thorsteinsdottir U, Bjornsson HT, Stefansson K, Sulem P. A population-based survey of FBN1 variants in Iceland reveals underdiagnosis of Marfan syndrome. Eur J Hum Genet 2024; 32:44-51. [PMID: 37684520 PMCID: PMC10772070 DOI: 10.1038/s41431-023-01455-0] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 08/18/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
Marfan syndrome (MFS) is an autosomal dominant condition characterized by aortic aneurysm, skeletal abnormalities, and lens dislocation, and is caused by variants in the FBN1 gene. To explore causes of MFS and the prevalence of the disease in Iceland we collected information from all living individuals with a clinical diagnosis of MFS in Iceland (n = 32) and performed whole-genome sequencing of those who did not have a confirmed genetic diagnosis (27/32). Moreover, to assess a potential underdiagnosis of MFS in Iceland we attempted a genotype-based approach to identify individuals with MFS. We interrogated deCODE genetics' database of 35,712 whole-genome sequenced individuals to search for rare sequence variants in FBN1. Overall, we identified 15 pathogenic or likely pathogenic variants in FBN1 in 44 individuals, only 22 of whom were previously diagnosed with MFS. The most common of these variants, NM_000138.4:c.8038 C > T p.(Arg2680Cys), is present in a multi-generational pedigree, and was found to stem from a single forefather born around 1840. The p.(Arg2680Cys) variant associates with a form of MFS that seems to have an enrichment of abdominal aortic aneurysm, suggesting that this may be a particularly common feature of p.(Arg2680Cys)-associated MFS. Based on these combined genetic and clinical data, we show that MFS prevalence in Iceland could be as high as 1/6,600 in Iceland, compared to 1/10,000 based on clinical diagnosis alone, which indicates underdiagnosis of this actionable genetic disorder.
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Affiliation(s)
| | - Gudny Anna Arnadottir
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | - Jon Johannes Jonsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Department of Genetics, Landspitali Universtity Hospital, Reykjavik, Iceland
| | | | - Ragnar Danielsen
- Department of Cardiology, Landspitali University Hospital, Reykjavik, Iceland
| | - Astridur Palsdottir
- Institute for Experimental Pathology at Keldur, University of Iceland, 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, University of Iceland, Reykjavik, Iceland
| | - Hans Tomas Bjornsson
- Department of Pediatrics, Landspitali University Hospital, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Department of Genetics, Landspitali Universtity Hospital, Reykjavik, Iceland
- McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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21
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Yap P, Riley LG, Kakadia PM, Bohlander SK, Curran B, Rahimi MJ, Alburaiky S, Hayes I, Oppermann H, Print C, Cooper ST, Le Quesne Stabej P. Biallelic ATP2B1 variants as a likely cause of a novel neurodevelopmental malformation syndrome with primary hypoparathyroidism. Eur J Hum Genet 2024; 32:125-129. [PMID: 37926713 PMCID: PMC10772071 DOI: 10.1038/s41431-023-01484-9] [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: 02/02/2023] [Revised: 08/22/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
ATP2B1 encodes plasma membrane calcium-transporting-ATPase1 and plays an essential role in maintaining intracellular calcium homeostasis that regulates diverse signaling pathways. Heterozygous de novo missense and truncating ATP2B1 variants are associated with a neurodevelopmental phenotype of variable expressivity. We describe a proband with distinctive craniofacial gestalt, Pierre-Robin sequence, neurodevelopmental and growth deficit, periventricular heterotopia, brachymesophalangy, cutaneous syndactyly, and persistent hypocalcemia from primary hypoparathyroidism. Proband-parent trio exome sequencing identified compound heterozygous ATP2B1 variants: a maternally inherited splice-site (c.3060+2 T > G) and paternally inherited missense c.2938 G > T; p.(Val980Leu). Reverse-transcription-PCR on the proband's fibroblast-derived mRNA showed aberrantly spliced ATP2B1 transcripts targeted for nonsense-mediated decay. All correctly-spliced ATP2B1 mRNA encoding p.(Val980Leu) functionally causes decreased cellular Ca2+ extrusion. Immunoblotting showed reduced fibroblast ATP2B1. We conclude that biallelic ATP2B1 variants are the likely cause of the proband's phenotype, strengthening the association of ATP2B1 as a neurodevelopmental gene and expanding the phenotypic characterization of a biallelic loss-of-function genotype.
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Affiliation(s)
- Patrick Yap
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand.
- Genetic Health Service New Zealand - Northern hub, Auckland, New Zealand.
| | - Lisa G Riley
- Rare Diseases Functional Genomics, Kids Research, The Children's Hospital at Westmead and The Children's Medical Research Institute, Sydney, NSW, 2145, Australia
- Specialty of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Purvi M Kakadia
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Stefan K Bohlander
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Ben Curran
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Meer Jacob Rahimi
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, 04103, Germany
| | - Salam Alburaiky
- Genetic Health Service New Zealand - Northern hub, Auckland, New Zealand
| | - Ian Hayes
- Genetic Health Service New Zealand - Northern hub, Auckland, New Zealand
| | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, 04103, Germany
| | - Cristin Print
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Sandra T Cooper
- Specialty of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, NSW, 2145, Australia
- The Children's Medical Research Institute, 214 Hawkesbury Road, Westmead, NSW, 2145, Australia
| | - Polona Le Quesne Stabej
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
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22
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Abstract
Accurately benchmarking small variant calling accuracy is critical for the continued improvement of human whole genome sequencing. In this work, we show that current variant calling evaluations are biased towards certain variant representations and may misrepresent the relative performance of different variant calling pipelines. We propose solutions, first exploring the affine gap parameter design space for complex variant representation and suggesting a standard. Next, we present our tool vcfdist and demonstrate the importance of enforcing local phasing for evaluation accuracy. We then introduce the notion of partial credit for mostly-correct calls and present an algorithm for clustering dependent variants. Lastly, we motivate using alignment distance metrics to supplement precision-recall curves for understanding variant calling performance. We evaluate the performance of 64 phased Truth Challenge V2 submissions and show that vcfdist improves measured insertion and deletion performance consistency across variant representations from R2 = 0.97243 for baseline vcfeval to 0.99996 for vcfdist.
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Affiliation(s)
- Tim Dunn
- Computer Science and Engineering, University of Michigan, 2260 Hayward Street, Ann Arbor, MI, 48109, USA.
| | - Satish Narayanasamy
- Computer Science and Engineering, University of Michigan, 2260 Hayward Street, Ann Arbor, MI, 48109, USA
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23
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Ballios BG, Mandola A, Tayyib A, Tumber A, Garkaby J, Vong L, Heon E, Roifman CM, Vincent A. Deep phenotypic characterization of the retinal dystrophy in patients with RNU4ATAC-associated Roifman syndrome. Eye (Lond) 2023; 37:3734-3742. [PMID: 37225827 PMCID: PMC10697969 DOI: 10.1038/s41433-023-02581-1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/01/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023] Open
Abstract
PURPOSE To characterize the retinal phenotype in RNU4ATAC-associated Roifman syndrome. METHODS Ten patients (including 8 males) with molecularly confirmed Roifman syndrome underwent detailed ophthalmologic evaluation including fundus imaging, fundus autofluorescence (FAF) imaging, spectral-domain optical coherence tomography (SD-OCT), and electroretinography (ERG). Six patients had follow-up eye exams. All patients also underwent comprehensive examination for features of extra-retinal Roifman syndrome. RESULTS All patients had biallelic RNU4ATAC variants. Nyctalopia was common (7/10). Visual acuity at presentation ranged from 20/20 to 20/200 (Age Range: 5-41 years). Retinal exam revealed features of generalized retinopathy with mid-peripheral pigment epithelial changes. A para or peri-foveal ring of hyper-autofluorescence was the commonest FAF abnormality noted (6/8). The SD-OCT demonstrated relative preservation of the foveal ellipsoid zone in six cases; associated features included cystoid changes (5/10) and posterior staphyloma (3/10). The ERG was abnormal in all patients; nine showed generalized rod-cone dystrophy, whilst one patient with sectoral retinal involvement only had isolated rod dystrophy (20 years old). On follow-up examination (Mean duration: 8.16 years), progressive loss of visual acuity (2/6), mid-peripheral retinal atrophy (3/6) or shortening of ellipsoid zone width (1/6) were observed. CONCLUSION This study has characterized the retinal phenotype in RNU4ATAC-associated Roifman syndrome. Retinal involvement is universal, early-onset, and overall, the retinal and FAF features are consistent with rod-cone degeneration that is slowly progressive over time. The sub-foveal retinal ultrastructure is relatively preserved in majority of patients. Phenotypic variability independent of age exists, and more study of allelic- and sex-based determinants of disease severity are necessary.
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Affiliation(s)
- Brian G Ballios
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
| | - Amarilla Mandola
- Division of Immunology and Allergy, The Hospital for Sick Children and the University of Toronto, Toronto, ON, Canada
| | - Alaa Tayyib
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anupreet Tumber
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jenny Garkaby
- Division of Immunology and Allergy, The Hospital for Sick Children and the University of Toronto, Toronto, ON, Canada
| | - Linda Vong
- The Canadian Centre for Primary Immunodeficiency and The Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, The Hospital for Sick Children, Toronto, ON, Canada
| | - Elise Heon
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada
| | - Chaim M Roifman
- Division of Immunology and Allergy, The Hospital for Sick Children and the University of Toronto, Toronto, ON, Canada
- The Canadian Centre for Primary Immunodeficiency and The Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ajoy Vincent
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada.
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada.
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24
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Jain V, Foo SH, Chooi S, Moss C, Goodwin R, Berland S, Clarke AJ, Davies SJ, Corrin S, Murch O, Doyle S, Graham GE, Greenhalgh L, Holder SE, Johnson D, Kumar A, Ladda RL, Sell S, Begtrup A, Lynch SA, McCann E, Østern R, Pottinger C, Splitt M, Fry AE. Börjeson-Forssman-Lehmann syndrome: delineating the clinical and allelic spectrum in 14 new families. Eur J Hum Genet 2023; 31:1421-1429. [PMID: 37704779 PMCID: PMC10689765 DOI: 10.1038/s41431-023-01447-0] [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: 02/06/2023] [Revised: 05/15/2023] [Accepted: 08/03/2023] [Indexed: 09/15/2023] Open
Abstract
Börjeson-Forssman-Lehmann syndrome (BFLS) is an X-linked intellectual disability syndrome caused by variants in the PHF6 gene. We ascertained 19 individuals from 15 families with likely pathogenic or pathogenic PHF6 variants (11 males and 8 females). One family had previously been reported. Six variants were novel. We analysed the clinical and genetic findings in our series and compared them with reported BFLS patients. Affected males had classic features of BFLS including intellectual disability, distinctive facies, large ears, gynaecomastia, hypogonadism and truncal obesity. Carrier female relatives of affected males were unaffected or had only mild symptoms. The phenotype of affected females with de novo variants overlapped with the males but included linear skin hyperpigmentation and a higher frequency of dental, retinal and cortical brain anomalies. Complications observed in our series included keloid scarring, digital fibromas, absent vaginal orifice, neuropathy, umbilical hernias, and talipes. Our analysis highlighted sex-specific differences in PHF6 variant types and locations. Affected males often have missense variants or small in-frame deletions while affected females tend to have truncating variants or large deletions/duplications. Missense variants were found in a minority of affected females and clustered in the highly constrained PHD2 domain of PHF6. We propose recommendations for the evaluation and management of BFLS patients. These results further delineate and extend the genetic and phenotypic spectrum of BFLS.
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Affiliation(s)
- Vani Jain
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK.
| | - Seow Hoong Foo
- Department of Dermatology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, B4 6NH, UK
- Department of Dermatology, Gleneagles Hospital Medini, Nusajaya, 79250, Johor, Malaysia
| | - Stephen Chooi
- School of Medicine, Cardiff University, Heath Park Campus, Cardiff, CF14 4YS, UK
| | - Celia Moss
- Department of Dermatology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, B4 6NH, UK
- University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Richard Goodwin
- Department of Dermatology, Royal Gwent Hospital, Newport, NP20 2UB, UK
| | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Angus J Clarke
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
- Division of Cancer and Genetics, Cardiff University, Cardiff, CF14 4XN, UK
| | - Sally J Davies
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - Sian Corrin
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - Oliver Murch
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - Samantha Doyle
- Department of Medical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin, D12 N512, Ireland
- Department of Clinical Genetics, The National Maternity Hospital, Holles Street, Dublin, D02 YH21, Ireland
| | - Gail E Graham
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, K1H 8L1, Canada
| | - Lynn Greenhalgh
- Liverpool Centre for Genomic Medicine, Liverpool Women's Hospital, Liverpool, L8 7SS, UK
| | - Susan E Holder
- North West Thames Regional Genetic Service, Kennedy Galton Centre, Northwick Park Hospital, Harrow, HA1 3UJ, UK
| | - Diana Johnson
- Department of Clinical Genetics, Northern General Hospital, Sheffield, S5 7AU, UK
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London, WC1N 3JH, UK
| | - Roger L Ladda
- Department of Pediatrics, Division of Human Genetics, Penn State Health Children's Hospital, Hershey, Pennsylvania, 17033, USA
| | - Susan Sell
- Department of Pediatrics, Division of Human Genetics, Penn State Health Children's Hospital, Hershey, Pennsylvania, 17033, USA
| | | | - Sally A Lynch
- Department of Medical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin, D12 N512, Ireland
| | - Emma McCann
- Liverpool Centre for Genomic Medicine, Liverpool Women's Hospital, Liverpool, L8 7SS, UK
| | - Rune Østern
- Department of Medical Genetics, St. Olavs Hospital, Trondheim University Hospital, 7030, Trondheim, Norway
| | - Caroline Pottinger
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - Miranda Splitt
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 3BZ, UK
| | - Andrew E Fry
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK.
- Division of Cancer and Genetics, Cardiff University, Cardiff, CF14 4XN, UK.
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25
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Ronchi D, Garbellini M, Magri F, Menni F, Meneri M, Bedeschi MF, Dilena R, Cecchetti V, Picciolli I, Furlan F, Polimeni V, Salani S, Pezzoli L, Fortunato F, Bellini M, Piga D, Ripolone M, Zanotti S, Napoli L, Ciscato P, Sciacco M, Mangili G, Mosca F, Corti S, Iascone M, Comi GP. A biallelic variant in COX18 cause isolated Complex IV deficiency associated with neonatal encephalo-cardio-myopathy and axonal sensory neuropathy. Eur J Hum Genet 2023; 31:1414-1420. [PMID: 37468577 PMCID: PMC10689781 DOI: 10.1038/s41431-023-01433-6] [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: 02/22/2023] [Revised: 07/03/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
Pathogenic variants impacting upon assembly of mitochondrial respiratory chain Complex IV (Cytochrome c Oxidase or COX) predominantly result in early onset mitochondrial disorders often leading to CNS, skeletal and cardiac muscle manifestations. The aim of this study is to describe a molecular defect in the COX assembly factor gene COX18 as the likely cause of a neonatal form of mitochondrial encephalo-cardio-myopathy and axonal sensory neuropathy. The proband is a 19-months old female displaying hypertrophic cardiomyopathy at birth and myopathy with axonal sensory neuropathy and failure to thrive developing in the first months of life. Serum lactate was consistently increased. Whole exome sequencing allowed the prioritization of the unreported homozygous substitution NM_001297732.2:c.667 G > C p.(Asp223His) in COX18. Patient's muscle biopsy revealed severe and diffuse COX deficiency and striking mitochondrial abnormalities. Biochemical and enzymatic studies in patient's myoblasts and in HEK293 cells after COX18 silencing showed a severe impairment of both COX activity and assembly. The biochemical defect was partially rescued by delivery of wild-type COX18 cDNA into patient's myoblasts. Our study identifies a novel defect of COX assembly and expands the number of nuclear genes involved in a mitochondrial disorder due to isolated COX deficiency.
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Affiliation(s)
- Dario Ronchi
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Manuela Garbellini
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Francesca Magri
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Francesca Menni
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Regional Clinical Center for expanded newborn screening, Milan, Italy
| | - Megi Meneri
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | | | - Robertino Dilena
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, UO Neurofisiopatologia, Milan, Italy
| | - Valeria Cecchetti
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit, Milan, Italy
| | - Irene Picciolli
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit, Milan, Italy
| | - Francesca Furlan
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Regional Clinical Center for expanded newborn screening, Milan, Italy
| | - Valentina Polimeni
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit, Milan, Italy
| | - Sabrina Salani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Laura Pezzoli
- ASST Papa Giovanni XXIII, Laboratorio di Genetica Medica, Bergamo, Italy
| | - Francesco Fortunato
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Matteo Bellini
- ASST Papa Giovanni XXIII, Laboratorio di Genetica Medica, Bergamo, Italy
| | - Daniela Piga
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Michela Ripolone
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
| | - Simona Zanotti
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
| | - Laura Napoli
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
| | - Patrizia Ciscato
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
| | - Monica Sciacco
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
| | | | - Fabio Mosca
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Stefania Corti
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
| | - Maria Iascone
- ASST Papa Giovanni XXIII, Laboratorio di Genetica Medica, Bergamo, Italy
| | - Giacomo Pietro Comi
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy.
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy.
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26
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Wang H, Yu L, Wang J, Zhang Y, Xu M, Lv C, Cui B, Yuan M, Zhang Y, Yan Y, Hui R, Wang Y. SLC35D3 promotes white adipose tissue browning to ameliorate obesity by NOTCH signaling. Nat Commun 2023; 14:7643. [PMID: 37996411 PMCID: PMC10667520 DOI: 10.1038/s41467-023-43418-5] [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: 02/20/2022] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
White adipose tissue browning can promote lipid burning to increase energy expenditure and improve adiposity. Here, we show that Slc35d3 expression is significantly lower in adipose tissues of obese mice. While adipocyte-specific Slc35d3 knockin is protected against diet-induced obesity, adipocyte-specific Slc35d3 knockout inhibits white adipose tissue browning and causes decreased energy expenditure and impaired insulin sensitivity in mice. Mechanistically, we confirm that SLC35D3 interacts with the NOTCH1 extracellular domain, which leads to the accumulation of NOTCH1 in the endoplasmic reticulum and thus inhibits the NOTCH1 signaling pathway. In addition, knockdown of Notch1 in mouse inguinal white adipose tissue mediated by orthotopic injection of AAV8-adiponectin-shNotch1 shows considerable improvement in obesity and glucolipid metabolism, which is more pronounced in adipocyte-specific Slc35d3 knockout mice than in knockin mice. Overall, in this study, we reveal that SLC35D3 is involved in obesity via NOTCH1 signaling, and low adipose SLC35D3 expression in obesity might be a therapeutic target for obesity and associated metabolic disorders.
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Affiliation(s)
- Hongrui Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liang Yu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jin'e Wang
- College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Yaqing Zhang
- College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Mengchen Xu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cheng Lv
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bing Cui
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengmeng Yuan
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yupeng Yan
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rutai Hui
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yibo Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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27
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Jacob P, Lindelöf H, Rustad CF, Sutton VR, Moosa S, Udupa P, Hammarsjö A, Bhavani GS, Batkovskyte D, Tveten K, Dalal A, Horemuzova E, Nordgren A, Tham E, Shah H, Merckoll E, Orellana L, Nishimura G, Girisha KM, Grigelioniene G. Clinical, genetic and structural delineation of RPL13-related spondyloepimetaphyseal dysplasia suggest extra-ribosomal functions of eL13. NPJ Genom Med 2023; 8:39. [PMID: 37993442 PMCID: PMC10665555 DOI: 10.1038/s41525-023-00380-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/10/2023] [Indexed: 11/24/2023] Open
Abstract
Spondyloepimetaphyseal dysplasia with severe short stature, RPL13-related (SEMD-RPL13), MIM#618728), is a rare autosomal dominant disorder characterized by short stature and skeletal changes such as mild spondylar and epimetaphyseal dysplasia affecting primarily the lower limbs. The genetic cause was first reported in 2019 by Le Caignec et al., and six disease-causing variants in the gene coding for a ribosomal protein, RPL13 (NM_000977.3) have been identified to date. This study presents clinical and radiographic data from 12 affected individuals aged 2-64 years from seven unrelated families, showing highly variable manifestations. The affected individuals showed a range from mild to severe short stature, retaining the same radiographic pattern of spondylar- and epi-metaphyseal dysplasia, but with varying severity of the hip and knee deformities. Two new missense variants, c.548 G>A, p.(Arg183His) and c.569 G>T, p.(Arg190Leu), and a previously known splice variant c.477+1G>A were identified, confirming mutational clustering in a highly specific RNA binding motif. Structural analysis and interpretation of the variants' impact on the protein suggests that disruption of extra-ribosomal functions of the protein through binding of mRNA may play a role in the skeletal phenotype of SEMD-RPL13. In addition, we present gonadal and somatic mosaicism for the condition.
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Affiliation(s)
- Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Hillevi Lindelöf
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilie F Rustad
- Department of Medial Genetics, Oslo University Hospital, Oslo, Norway
| | - Vernon Reid Sutton
- Department of Molecular & Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Shahida Moosa
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University and Medical Genetics, Tygerberg Hospital, Cape Town, South Africa
| | - Prajna Udupa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anna Hammarsjö
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dominyka Batkovskyte
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Eva Horemuzova
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Biomedicine, Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Else Merckoll
- Department of Radiology, Oslo University Hospital, Oslo, Norway
| | - Laura Orellana
- Protein Dynamics and Mutation lab, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Gen Nishimura
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Radiology, Musashino-Yowakai Hospital, Tokyo, Japan
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
| | - Giedre Grigelioniene
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
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28
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Niida Y, Kobayashi A, Togi S, Ura H. Recessive dystrophic epidermolysis bullosa caused by a novel COL7A1 variant with isodisomy. Hum Genome Var 2023; 10:29. [PMID: 37985760 PMCID: PMC10661991 DOI: 10.1038/s41439-023-00257-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023] Open
Abstract
Recessive dystrophic epidermolysis bullosa is a genetic collagen disorder characterized by skin fragility that leads to generalized severe blistering, wounds, and scarring. In this report, we present a patient with a novel COL7A1 homozygous nonsense variant, c.793C>T p.(Gln265*). Although the parents were not consanguineous, both were heterozygous carriers of the variant. Single nucleotide polymorphism (SNP) array analysis revealed an isodisomy area on 3p22.1p21.1, encompassing COL7A1, suggesting that the variant originated from a common ancestor.
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Affiliation(s)
- Yo Niida
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Ishikawa, Uchinada, Japan.
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Ishikawa, Uchinada, Japan.
| | - Azusa Kobayashi
- Department of Pediatrics, Kanazawa Medical University, Ishikawa, Uchinada, Japan
| | - Sumihito Togi
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Ishikawa, Uchinada, Japan
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Ishikawa, Uchinada, Japan
| | - Hiroki Ura
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Ishikawa, Uchinada, Japan
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Ishikawa, Uchinada, Japan
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29
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Nam DW, Song YK, Kim JH, Lee EK, Park KH, Cha J, Choi BY, Lee JH, Oh SH, Jo DH, Lee SY. Allelic hierarchy for USH2A influences auditory and visual phenotypes in South Korean patients. Sci Rep 2023; 13:20239. [PMID: 37981655 PMCID: PMC10658080 DOI: 10.1038/s41598-023-47166-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: 03/14/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023] Open
Abstract
When medical genetic syndromes are influenced by allelic hierarchies, mutant alleles have distinct effects on clinical phenotypes. Genotype-phenotype correlations for Usher syndrome type 2 (USH2) suggest that the USH2A gene exhibits an allelic hierarchy. Here, we analyzed the phenotypes and genotypes of 16 South Korean patients with USH2A biallelic variants to investigate an allelic hierarchy from audiological and ophthalmological perspectives. Using whole exome and genome sequencing, 18 mutant alleles, including 4 novel alleles, were identified and implicated in USH2A-related disorders. Truncated alleles were linked to earlier onset of subjective hearing loss and more severe thresholds; biallelic truncated alleles had more severe effects. Truncated alleles were also associated with retinal structure degeneration and severe functional deterioration. However, younger patients (aged < 16 years) did not exhibit overt retinitis pigmentosa even when they had biallelic truncated alleles, suggesting that USH2A-related USH2 can mimic nonsyndromic hearing loss. For truncated alleles, there was a clear correlation between mean hearing threshold and 30-Hz flicker electroretinography implicit time. This study provides the first evidence of an USH2A-related allelic hierarchy among South Korean patients; our data yield valuable insights concerning the natural courses of clinical phenotypes and how genotype-based therapies may be used.
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Affiliation(s)
- Dong Woo Nam
- Department of Otorhinolaryngology, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Yong Keun Song
- Department of Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeong Hun Kim
- Fight Against Angiogenesis-Related Blindness (FARB) Laboratory, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Ophthalmology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eun Kyoung Lee
- Department of Ophthalmology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - JuHyuen Cha
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Seung Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Dong Hyun Jo
- Department of Anatomy and Cell Biology, Seoul National University College of Medicine, 103, Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Republic of Korea.
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30
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Ba R, Durand A, Mauduit V, Chauveau C, Le Bas-Bernardet S, Salle S, Guérif P, Morin M, Petit C, Douillard V, Rousseau O, Blancho G, Kerleau C, Vince N, Giral M, Gourraud PA, Limou S. KiT-GENIE, the French genetic biobank of kidney transplantation. Eur J Hum Genet 2023; 31:1291-1299. [PMID: 36737541 PMCID: PMC10620190 DOI: 10.1038/s41431-023-01294-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: 10/04/2022] [Revised: 12/16/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
KiT-GENIE is a monocentric DNA biobank set up to consolidate the very rich and homogeneous DIVAT French cohort of kidney donors and recipients (D/R) in order to explore the molecular factors involved in kidney transplantation outcomes. We collected DNA samples for kidney transplantations performed in Nantes, and we leveraged GWAS genotyping data for securing high-quality genetic data with deep SNP and HLA annotations through imputations and for inferring D/R genetic ancestry. Overall, the biobank included 4217 individuals (n = 1945 D + 2,272 R, including 1969 D/R pairs), 7.4 M SNPs and over 200 clinical variables. KiT-GENIE represents an accurate snapshot of kidney transplantation clinical practice in Nantes between 2002 and 2018, with an enrichment in living kidney donors (17%) and recipients with focal segmental glomerulosclerosis (4%). Recipients were predominantly male (63%), of European ancestry (93%), with a mean age of 51yo and 86% experienced their first graft over the study period. D/R pairs were 93% from European ancestry, and 95% pairs exhibited at least one HLA allelic mismatch. The mean follow-up time was 6.7 years with a hindsight up to 25 years. Recipients experienced biopsy-proven rejection and graft loss for 16.6% and 21.3%, respectively. KiT-GENIE constitutes one of the largest kidney transplantation genetic cohorts worldwide to date. It includes homogeneous high-quality clinical and genetic data for donors and recipients, hence offering a unique opportunity to investigate immunogenetic and genetic factors, as well as donor-recipient interactions and mismatches involved in rejection, graft survival, primary disease recurrence and other comorbidities.
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Affiliation(s)
- Rokhaya Ba
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Axelle Durand
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Vincent Mauduit
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Christine Chauveau
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Stéphanie Le Bas-Bernardet
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Sonia Salle
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Pierrick Guérif
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Martin Morin
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Clémence Petit
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Venceslas Douillard
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Olivia Rousseau
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Gilles Blancho
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Clarisse Kerleau
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Nicolas Vince
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Magali Giral
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Pierre-Antoine Gourraud
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Sophie Limou
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France.
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Reynolds G, Cardaropoli S, Carli D, Luca M, Gazzin A, Coppo P, La Selva R, Piglionica M, Bagnulo R, Turchiano A, Ranieri C, Resta N, Mussa A. Epidemiology of the disorders of the Pik3ca-related overgrowth spectrum (Pros). Eur J Hum Genet 2023; 31:1333-1336. [PMID: 37365400 PMCID: PMC10620148 DOI: 10.1038/s41431-023-01414-9] [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: 01/30/2023] [Revised: 05/18/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
PIK3CA pathogenic variants are responsible for a group of overgrowth syndromes, collectively known as PIK3CA-Related Overgrowth Spectrum (PROS). These gain-of-function variants arise postzygotically, and, according to time of onset, kind of embryonal tissue affected and regional body extension, give rise to heterogeneous phenotypes. PROS rarity and heterogeneity hamper the correct estimation of its epidemiology. Our work represents the first attempt to define the prevalence of PROS according to the established diagnostic criteria and molecular analysis and based on solid demographic data. We assessed the prevalence in Piedmont Region (Italy), including in the study all participants diagnosed with PROS born there from 1998 to 2021. The search identified 37 cases of PROS born across the 25-year period, providing a prevalence of 1:22,313 live births. Molecular analysis was positive in 81.0% of participants. Taking into account the cases with a detected variant in PIK3CA (n = 30), prevalence of molecularly positive PROS was 1:27,519.
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Affiliation(s)
- Giuseppe Reynolds
- Department of Public Health and Pediatric Sciences, School of Medicine, University of Torino, Torino, Italy
| | - Simona Cardaropoli
- Department of Public Health and Pediatric Sciences, School of Medicine, University of Torino, Torino, Italy
| | - Diana Carli
- Department of Medical Science, University of Torino, Torino, Italy
| | - Maria Luca
- Department of Medical Science, University of Torino, Torino, Italy
| | - Andrea Gazzin
- Department of Public Health and Pediatric Sciences, School of Medicine, University of Torino, Torino, Italy
| | - Paola Coppo
- Pediatric Dermatology, Regina Margherita Children's Hospital, Città della Salute e della Scienza di Torino, Torino, Italy
| | - Roberta La Selva
- Pediatric Dermatology, Regina Margherita Children's Hospital, Città della Salute e della Scienza di Torino, Torino, Italy
| | - Marilidia Piglionica
- Medical Genetics Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J) University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Rosanna Bagnulo
- Medical Genetics Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J) University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Antonella Turchiano
- Medical Genetics Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J) University of Bari "Aldo Moro", 70124, Bari, Italy
| | | | - Nicoletta Resta
- Medical Genetics Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J) University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Alessandro Mussa
- Department of Public Health and Pediatric Sciences, School of Medicine, University of Torino, Torino, Italy.
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32
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Giovenino C, Trajkova S, Pavinato L, Cardaropoli S, Pullano V, Ferrero E, Sukarova-Angelovska E, Carestiato S, Salmin P, Rinninella A, Battaglia A, Bertoli L, Fadda A, Palermo F, Carli D, Mussa A, Dimartino P, Bruselles A, Froukh T, Mandrile G, Pasini B, De Rubeis S, Buxbaum JD, Pippucci T, Tartaglia M, Rossato M, Delledonne M, Ferrero GB, Brusco A. Skewed X-chromosome inactivation in unsolved neurodevelopmental disease cases can guide re-evaluation For X-linked genes. Eur J Hum Genet 2023; 31:1228-1236. [PMID: 36879111 PMCID: PMC10620389 DOI: 10.1038/s41431-023-01324-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: 10/18/2022] [Revised: 01/24/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
Despite major advances in genome technology and analysis, >50% of patients with a neurodevelopmental disorder (NDD) remain undiagnosed after extensive evaluation. A point in case is our clinically heterogeneous cohort of NDD patients that remained undiagnosed after FRAXA testing, chromosomal microarray analysis and trio exome sequencing (ES). In this study, we explored the frequency of non-random X chromosome inactivation (XCI) in the mothers of male patients and affected females, the rationale being that skewed XCI might be masking previously discarded genetic variants found on the X chromosome. A multiplex fluorescent PCR-based assay was used to analyse the pattern of XCI after digestion with HhaI methylation-sensitive restriction enzyme. In families with skewed XCI, we re-evaluated trio-based ES and identified pathogenic variants and a deletion on the X chromosome. Linkage analysis and RT-PCR were used to further study the inactive X chromosome allele, and Xdrop long-DNA technology was used to define chromosome deletion boundaries. We found skewed XCI (>90%) in 16/186 (8.6%) mothers of NDD males and in 12/90 (13.3%) NDD females, far beyond the expected rate of XCI in the normal population (3.6%, OR = 4.10; OR = 2.51). By re-analyzing ES and clinical data, we solved 7/28 cases (25%) with skewed XCI, identifying variants in KDM5C, PDZD4, PHF6, TAF1, OTUD5 and ZMYM3, and a deletion in ATRX. We conclude that XCI profiling is a simple assay that targets a subgroup of patients that can benefit from re-evaluation of X-linked variants, thus improving the diagnostic yield in NDD patients and identifying new X-linked disorders.
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Affiliation(s)
- Chiara Giovenino
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Slavica Trajkova
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Simona Cardaropoli
- Department of Public Health and Pediatrics, University of Turin, 10126, Turin, Italy
| | - Verdiana Pullano
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Enza Ferrero
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Elena Sukarova-Angelovska
- Department of Endocrinology and Genetics, University Clinic for Pediatric Diseases, Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, 1000, Skopje, Republic of North Macedonia
| | - Silvia Carestiato
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Paola Salmin
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126, Turin, Italy
| | - Antonina Rinninella
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, 94124, Catania, Italy
| | - Anthony Battaglia
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Luca Bertoli
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Antonio Fadda
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Flavia Palermo
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Diana Carli
- Department of Public Health and Pediatrics, University of Turin, 10126, Turin, Italy
| | - Alessandro Mussa
- Department of Public Health and Pediatrics, University of Turin, 10126, Turin, Italy
| | - Paola Dimartino
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Alessandro Bruselles
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Tawfiq Froukh
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Giorgia Mandrile
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, University of Torino, Orbassano, TO, Italy
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126, Turin, Italy
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tommaso Pippucci
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italia
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marzia Rossato
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Massimo Delledonne
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | | | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy.
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126, Turin, Italy.
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33
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Steyaert W, Haer-Wigman L, Pfundt R, Hellebrekers D, Steehouwer M, Hampstead J, de Boer E, Stegmann A, Yntema H, Kamsteeg EJ, Brunner H, Hoischen A, Gilissen C. Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation. Nat Commun 2023; 14:6845. [PMID: 37891200 PMCID: PMC10611741 DOI: 10.1038/s41467-023-42531-9] [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: 11/22/2022] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
The short lengths of short-read sequencing reads challenge the analysis of paralogous genomic regions in exome and genome sequencing data. Most genetic variants within these homologous regions therefore remain unidentified in standard analyses. Here, we present a method (Chameleolyser) that accurately identifies single nucleotide variants and small insertions/deletions (SNVs/Indels), copy number variants and ectopic gene conversion events in duplicated genomic regions using whole-exome sequencing data. Application to a cohort of 41,755 exome samples yields 20,432 rare homozygous deletions and 2,529,791 rare SNVs/Indels, of which we show that 338,084 are due to gene conversion events. None of the SNVs/Indels are detectable using regular analysis techniques. Validation by high-fidelity long-read sequencing in 20 samples confirms >88% of called variants. Focusing on variation in known disease genes leads to a direct molecular diagnosis in 25 previously undiagnosed patients. Our method can readily be applied to existing exome data.
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Affiliation(s)
- Wouter Steyaert
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Debby Hellebrekers
- Maastricht University Medical Center + , Department of Clinical Genetics, Maastricht, Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Juliet Hampstead
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Elke de Boer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
- Radboud University, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, Netherlands
| | - Alexander Stegmann
- Maastricht University Medical Center + , Department of Clinical Genetics, Maastricht, Netherlands
| | - Helger Yntema
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Han Brunner
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
- Maastricht University Medical Center + , Department of Clinical Genetics, Maastricht, Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands
- Radboud University Medical Center, Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Nijmegen, Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands.
- Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands.
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34
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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. Author Correction: Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation. Nat Commun 2023; 14:6301. [PMID: 37813867 PMCID: PMC10562428 DOI: 10.1038/s41467-023-42123-7] [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: 10/11/2023] Open
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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Kesim Y, Ceroni F, Damián A, Blanco-Kelly F, Ayuso C, Williamson K, Paquis-Flucklinger V, Bax DA, Plaisancié J, Rieubland C, Chamlal M, Cortón M, Chassaing N, Calvas P, Ragge NK. Correction: Clinical and genetic analysis further delineates the phenotypic spectrum of ALDH1A3-related anophthalmia and microphthalmia. Eur J Hum Genet 2023; 31:1196-1198. [PMID: 37106145 PMCID: PMC10545745 DOI: 10.1038/s41431-023-01363-3] [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: 04/29/2023] Open
Affiliation(s)
- Yesim Kesim
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Fabiola Ceroni
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Alejandra Damián
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Kathy Williamson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | - Dorine A Bax
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Julie Plaisancié
- INSERM U1214, ToNIC, Université Toulouse III, Toulouse, France
- Centre de Référence des Affections Rares en Génétique Ophtalmologique CARGO, Site Constitutif, CHU Toulouse, Toulouse, France
| | - Claudine Rieubland
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Mostafa Chamlal
- Department of Pediatrics, RAZI-CLINIC Hospital, Tangier, Morocco
| | - Marta Cortón
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Nicolas Chassaing
- Centre de Référence des Affections Rares en Génétique Ophtalmologique CARGO, Site Constitutif, CHU Toulouse, Toulouse, France
| | - Patrick Calvas
- Centre de Référence des Affections Rares en Génétique Ophtalmologique CARGO, Site Constitutif, CHU Toulouse, Toulouse, France
| | - Nicola K Ragge
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK.
- Department of Clinical Genetics, West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Foundation Trust, Birmingham, UK.
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36
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Kesim Y, Ceroni F, Damián A, Blanco-Kelly F, Ayuso C, Williamson K, Paquis-Flucklinger V, Bax DA, Plaisancié J, Rieubland C, Chamlal M, Cortón M, Chassaing N, Calvas P, Ragge NK. Clinical and genetic analysis further delineates the phenotypic spectrum of ALDH1A3-related anophthalmia and microphthalmia. Eur J Hum Genet 2023; 31:1175-1180. [PMID: 36997679 PMCID: PMC10545824 DOI: 10.1038/s41431-023-01342-8] [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: 08/26/2022] [Revised: 01/30/2023] [Accepted: 03/13/2023] [Indexed: 04/29/2023] Open
Abstract
Biallelic pathogenic variants in ALDH1A3 are responsible for approximately 11% of recessively inherited cases of severe developmental eye anomalies. Some individuals can display variable neurodevelopmental features, but the relationship to the ALDH1A3 variants remains unclear. Here, we describe seven unrelated families with biallelic pathogenic ALDH1A3 variants: four compound heterozygous and three homozygous. All affected individuals had bilateral anophthalmia/microphthalmia (A/M), three with additional intellectual or developmental delay, one with autism and seizures and three with facial dysmorphic features. This study confirms that individuals with biallelic pathogenic ALDH1A3 variants consistently manifest A/M, but additionally display neurodevelopmental features with significant intra- and interfamilial variability. Furthermore, we describe the first case with cataract and highlight the importance of screening ALDH1A3 variants in nonconsanguineous families with A/M.
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Affiliation(s)
- Yesim Kesim
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Fabiola Ceroni
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Alejandra Damián
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Kathy Williamson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | - Dorine A Bax
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Julie Plaisancié
- INSERM U1214, ToNIC, Université Toulouse III, Toulouse, France
- Centre de Référence des Affections Rares en Génétique Ophtalmologique CARGO, Site Constitutif, CHU Toulouse, Toulouse, France
| | - Claudine Rieubland
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Mostafa Chamlal
- Department of Pediatrics, RAZI-CLINIC Hospital, Tangier, Morocco
| | - Marta Cortón
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Nicolas Chassaing
- Centre de Référence des Affections Rares en Génétique Ophtalmologique CARGO, Site Constitutif, CHU Toulouse, Toulouse, France
| | - Patrick Calvas
- Centre de Référence des Affections Rares en Génétique Ophtalmologique CARGO, Site Constitutif, CHU Toulouse, Toulouse, France
| | - Nicola K Ragge
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK.
- Department of Clinical Genetics, West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Foundation Trust, Birmingham, UK.
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Chen Y, Jiao D, Liu Y, Xu X, Wang Y, Luo X, Saiyin H, Li Y, Gao K, Chen Y, Zhao SM, Ma L, Wang C. FBXL4 mutations cause excessive mitophagy via BNIP3/BNIP3L accumulation leading to mitochondrial DNA depletion syndrome. Cell Death Differ 2023; 30:2351-2363. [PMID: 37568009 PMCID: PMC10589232 DOI: 10.1038/s41418-023-01205-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/29/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Mitochondria are essential organelles found in eukaryotic cells that play a crucial role in ATP production through oxidative phosphorylation (OXPHOS). Mitochondrial DNA depletion syndrome (MTDPS) is a group of genetic disorders characterized by the reduction of mtDNA copy number, leading to deficiencies in OXPHOS and mitochondrial functions. Mutations in FBXL4, a substrate-binding adaptor of Cullin 1-RING ubiquitin ligase complex (CRL1), are associated with MTDPS, type 13 (MTDPS13). Here, we demonstrate that, FBXL4 directly interacts with the mitophagy cargo receptors BNIP3 and BNIP3L, promoting their degradation through the ubiquitin-proteasome pathway via the assembly of an active CRL1FBXL4 complex. However, MTDPS13-associated FBXL4 mutations impair the assembly of an active CRL1FBXL4 complex. This results in a notable accumulation of BNIP3/3L proteins and robust mitophagy even at basal levels. Excessive mitophagy was observed in Knockin (KI) mice carrying a patient-derived FBXL4 mutation and cortical neurons (CNs)-induced from MTDPS13 patient human induced pluripotent stem cells (hiPSCs). In summary, our findings suggest that abnormal activation of BNIP3/BNIP3L-dependent mitophagy impairs mitochondrial homeostasis and underlies FBXL4-mutated MTDPS13.
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Affiliation(s)
- Yingji Chen
- Obstetrics & Gynecology Hospital of Fudan University, Institutes of Metabolism and Integrative Biology, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Dongyue Jiao
- Obstetrics & Gynecology Hospital of Fudan University, Institutes of Metabolism and Integrative Biology, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Yang Liu
- Department of Anatomy, Histology & Embryology, School of Basic Medical Science, Fudan University, Shanghai, PR China
| | - Xiayun Xu
- Obstetrics & Gynecology Hospital of Fudan University, Institutes of Metabolism and Integrative Biology, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Yilin Wang
- Department of Neurology, Shanghai Children's Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, PR China
| | - Xiaona Luo
- Department of Neurology, Shanghai Children's Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, PR China
| | - Hexige Saiyin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Yao Li
- Obstetrics & Gynecology Hospital of Fudan University, Institutes of Metabolism and Integrative Biology, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Kun Gao
- Department of Clinical Laboratory, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, PR China
| | - Yucai Chen
- Department of Neurology, Shanghai Children's Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, PR China.
| | - Shi-Min Zhao
- Obstetrics & Gynecology Hospital of Fudan University, Institutes of Metabolism and Integrative Biology, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, PR China.
| | - Lixiang Ma
- Department of Anatomy, Histology & Embryology, School of Basic Medical Science, Fudan University, Shanghai, PR China.
| | - Chenji Wang
- Obstetrics & Gynecology Hospital of Fudan University, Institutes of Metabolism and Integrative Biology, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, PR China.
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38
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Chen J, Xu X, Chen S, Lu T, Zheng Y, Gan Z, Shen Z, Ma S, Wang D, Su L, He F, Shang X, Xu H, Chen D, Zhang L, Xiong F. Double heterozygous pathogenic mutations in KIF3C and ZNF513 cause hereditary gingival fibromatosis. Int J Oral Sci 2023; 15:46. [PMID: 37752101 PMCID: PMC10522663 DOI: 10.1038/s41368-023-00244-1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/28/2023] Open
Abstract
Hereditary gingival fibromatosis (HGF) is a rare inherited condition with fibromatoid hyperplasia of the gingival tissue that exhibits great genetic heterogeneity. Five distinct loci related to non-syndromic HGF have been identified; however, only two disease-causing genes, SOS1 and REST, inducing HGF have been identified at two loci, GINGF1 and GINGF5, respectively. Here, based on a family pedigree with 26 members, including nine patients with HGF, we identified double heterozygous pathogenic mutations in the ZNF513 (c.C748T, p.R250W) and KIF3C (c.G1229A, p.R410H) genes within the GINGF3 locus related to HGF. Functional studies demonstrated that the ZNF513 p.R250W and KIF3C p.R410H variants significantly increased the expression of ZNF513 and KIF3C in vitro and in vivo. ZNF513, a transcription factor, binds to KIF3C exon 1 and participates in the positive regulation of KIF3C expression in gingival fibroblasts. Furthermore, a knock-in mouse model confirmed that heterozygous or homozygous mutations within Zfp513 (p.R250W) or Kif3c (p.R412H) alone do not led to clear phenotypes with gingival fibromatosis, whereas the double mutations led to gingival hyperplasia phenotypes. In addition, we found that ZNF513 binds to the SOS1 promoter and plays an important positive role in regulating the expression of SOS1. Moreover, the KIF3C p.R410H mutation could activate the PI3K and KCNQ1 potassium channels. ZNF513 combined with KIF3C regulates gingival fibroblast proliferation, migration, and fibrosis response via the PI3K/AKT/mTOR and Ras/Raf/MEK/ERK pathways. In summary, these results demonstrate ZNF513 + KIF3C as an important genetic combination in HGF manifestation and suggest that ZNF513 mutation may be a major risk factor for HGF.
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Affiliation(s)
- Jianfan Chen
- Department of Medical Genetics, Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Experimental Department of Obstetrics and Gynecology Institute, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xueqing Xu
- Department of Precision Medicine, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Song Chen
- Department of Medical Genetics, Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ting Lu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yingchun Zheng
- Department of Medical Genetics, Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhongzhi Gan
- Department of Medical Genetics, Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zongrui Shen
- Department of Medical Genetics, Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shunfei Ma
- Department of Medical Genetics, Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Duocai Wang
- Department of Medical Genetics, Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Leyi Su
- Department of Medical Genetics, Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Fei He
- Department of Medical Genetics, Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xuan Shang
- Department of Medical Genetics, Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Huiyong Xu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dong Chen
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Leitao Zhang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Fu Xiong
- Department of Medical Genetics, Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China.
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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39
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Liu WW, Kinzy TG, Cooke Bailey JN, Xu Z, Hysi P, Wiggs JL. Mechanosensitive ion channel gene survey suggests potential roles in primary open angle glaucoma. Sci Rep 2023; 13:15871. [PMID: 37741866 PMCID: PMC10517927 DOI: 10.1038/s41598-023-43072-3] [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: 05/22/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023] Open
Abstract
Although glaucoma is a disease modulated by eye pressure, the mechanisms of pressure sensing in the eye are not well understood. Here, we investigated associations between mechanosensitive ion channel gene variants and primary open-angle glaucoma (POAG). Common (minor allele frequency > 5%) single nucleotide polymorphisms located within the genomic regions of 20 mechanosensitive ion channel genes in the K2P, TMEM63, PIEZO and TRP channel families were assessed using genotype data from the NEIGHBORHOOD consortium of 3853 cases and 33,480 controls. Rare (minor allele frequency < 1%) coding variants were assessed using exome array genotyping data for 2606 cases and 2606 controls. Association with POAG was analyzed using logistic regression adjusting for age and sex. Two rare PIEZO1 coding variants with protective effects were identified in the NEIGHBOR dataset: R1527H, (OR 0.17, P = 0.0018) and a variant that alters a canonical splice donor site, g.16-88737727-C-G Hg38 (OR 0.38, P = 0.02). Both variants showed similar effects in the UK Biobank and the R1527H also in the FinnGen database. Several common variants also reached study-specific thresholds for association in the NEIGHBORHOOD dataset. These results identify novel variants in several mechanosensitive channel genes that show associations with POAG, suggesting that these channels may be potential therapeutic targets.
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Affiliation(s)
- Wendy W Liu
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, 2370 Watson Court, Palo Alto, CA, 94303, USA.
| | - Tyler G Kinzy
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Zihe Xu
- Department of Ophthalmology, King's College London, St. Thomas' Hospital, London, UK
| | - Pirro Hysi
- Department of Ophthalmology, King's College London, St. Thomas' Hospital, London, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, St. Thomas' Hospital, London, UK
| | - Janey L Wiggs
- Massachusetts Eye and Ear, Harvard Medical School Boston, Boston, MA, USA
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40
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Tsai MJM, Hung MZ, Lin YL, Lee NC, Chien YH, Hwu WL. Curated incidence of lysosomal storage diseases from the Taiwan Biobank. NPJ Genom Med 2023; 8:27. [PMID: 37741878 PMCID: PMC10517920 DOI: 10.1038/s41525-023-00372-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 09/04/2023] [Indexed: 09/25/2023] Open
Abstract
Lysosomal storage diseases (LSDs) are a group of metabolic disorders resulting from a deficiency in one of the lysosomal hydrolases. Most LSDs are inherited in an autosomal or X-linked recessive manner. As LSDs are rare, their true incidence in Taiwan remains unknown. In this study, we used high-coverage whole-genome sequencing data from 1,495 Taiwanese individuals obtained from the Taiwan Biobank. We found 3826 variants in 71 genes responsible for autosomal recessive LSDs. We first excluded benign variants by allele frequency and other criteria. As a result, 270 variants were considered disease-causing. We curated these variants using published guidelines from the American College of Medical Genetics and Genomics (ACMG). Our results revealed a combined incidence rate of 13 per 100,000 (conservative estimation by pathologic and likely pathogenic variants; 95% CI 6.92-22.23) to 94 per 100,000 (extended estimation by the inclusion of variants of unknown significance; 95% CI 75.96-115.03) among 71 autosomal recessive disease-associated genes. The conservative estimations were similar to those in published clinical data. No disease-causing mutations were found for 18 other diseases; thus, these diseases are likely extremely rare in Taiwan. The study results are important for designing screening and treatment methods for LSDs in Taiwan and demonstrate the importance of mutation curation to avoid overestimating disease incidences from genomic data.
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Affiliation(s)
- Meng-Ju Melody Tsai
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan
| | - Miao-Zi Hung
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Lin Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yin-Hsiu Chien
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Wuh-Liang Hwu
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan.
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan.
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Pálla S, Tőke J, Bozsik A, Butz H, Papp J, Likó I, Kuroli E, Bánvölgyi A, Hamar M, Bertherat J, Medvecz M, Patócs A. Whole genome sequencing resolves 10 years diagnostic odyssey in familiar myxoma. Sci Rep 2023; 13:14658. [PMID: 37670105 PMCID: PMC10480295 DOI: 10.1038/s41598-023-41878-9] [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: 01/07/2023] [Accepted: 09/01/2023] [Indexed: 09/07/2023] Open
Abstract
Carney complex (CNC) is an ultrarare disorder causing cutaneous and cardiac myxomas, primary pigmented nodular adrenocortical disease, hypophyseal adenoma, and gonadal tumours. Genetic alterations are often missed under routine genetic testing. Pathogenic variants in PRKAR1A are identified in most cases, while large exonic or chromosomal deletions have only been reported in a few cases. Our aim was to identify the causal genetic alteration in our kindred with a clinical diagnosis of CNC and prove its pathogenic role by functional investigation. Targeted testing of PRKAR1A gene, whole exome and whole genome sequencing (WGS) were performed in the proband, one clinically affected and one unaffected relative. WGS identified a novel, large, 10,662 bp (10.6 kbp; LRG_514t1:c.-10403_-7 + 265del; hg19, chr17:g.66498293_66508954del) deletion in the promoter of PRKAR1A in heterozygous form in the affected family members. The exact breakpoints and the increased enzyme activity in deletion carriers compared to wild type carrier were proved. Segregation analysis and functional evaluation of PKA activity confirmed the pathogenic role of this alteration. A novel deletion upstream of the PRKAR1A gene was proved to be the cause of CNC. Our study underlines the need for WGS in molecular genetic testing of patients with monogenic disorders where conventional genetic analysis fails.
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Affiliation(s)
- Sára Pálla
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Judit Tőke
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
- ENDO-ERN HCP Semmelweis University, Budapest, Hungary
| | - Anikó Bozsik
- Department of Molecular Genetics, National Institute of Oncology, Ráth György U. 7-9, 1122, Budapest, Hungary
- Hereditary Cancers Research Group, Eötvös Loránd Research Network, Semmelweis University, Budapest, Hungary
- National Tumorbiology Laboratory, Budapest, Hungary
| | - Henriett Butz
- Department of Molecular Genetics, National Institute of Oncology, Ráth György U. 7-9, 1122, Budapest, Hungary
- Hereditary Cancers Research Group, Eötvös Loránd Research Network, Semmelweis University, Budapest, Hungary
- National Tumorbiology Laboratory, Budapest, Hungary
| | - János Papp
- Department of Molecular Genetics, National Institute of Oncology, Ráth György U. 7-9, 1122, Budapest, Hungary
- Hereditary Cancers Research Group, Eötvös Loránd Research Network, Semmelweis University, Budapest, Hungary
| | - István Likó
- Hereditary Cancers Research Group, Eötvös Loránd Research Network, Semmelweis University, Budapest, Hungary
| | - Enikő Kuroli
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, Hungary
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - András Bánvölgyi
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Mátyás Hamar
- Department of Surgery, Transplantation and Gastroenterology, Semmelweis University, Budapest, Hungary
| | - Jerome Bertherat
- Université Paris Cité, Institut Cochin, Inserm U1016, Paris, France
- Department of Endocrinology and National Reference Center for Rare Adrenal Disorders, Hôpital Cochin, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Márta Medvecz
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, Hungary
- ERN-Skin Semmelweis University, Budapest, Hungary
| | - Attila Patócs
- ENDO-ERN HCP Semmelweis University, Budapest, Hungary.
- Department of Molecular Genetics, National Institute of Oncology, Ráth György U. 7-9, 1122, Budapest, Hungary.
- Hereditary Cancers Research Group, Eötvös Loránd Research Network, Semmelweis University, Budapest, Hungary.
- National Tumorbiology Laboratory, Budapest, Hungary.
- National Institute of Oncology, Oncology Biobank Center, Budapest, Hungary.
- Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary.
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Wang G, Hou Y, Lv X, Yan C, Lin P. Somatic and germinal mosaicism in a Han Chinese family with laminopathies. Eur J Hum Genet 2023; 31:1073-1077. [PMID: 36526864 PMCID: PMC10474091 DOI: 10.1038/s41431-022-01266-9] [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: 06/08/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
"Laminopathies" refers to a wide spectrum of myopathies caused by mutations in the LMNA gene. These myopathies include limb girdle muscular dystrophy type 1B (LGMD1B) and dilated cardiomyopathy 1 A (DCM1A), which are both autosomal dominant neurogenetic diseases. There have been few studies on mosaicism in laminopathies. Herein, a Han Chinese family with laminopathies was enrolled in our study. Genetic analysis revealed that the proband carried a novel splice site mutation, c. 1158-3 C > T, in the LMNA gene due to her mother having de novo somatic and gonadal mosaicism. Reverse-transcription polymerase chain reaction (RT-PCR) analysis revealed reduced levels of LMNA mRNA in the proband, which were probably due to nonsense-mediated mRNA decay (NMD). Western blotting revealed reduced lamin A/C protein levels in the skeletal muscle tissue of the proband. In this family, the clinical phenotypes of the proband's mother were normal, and the c. 1158-3 C > T splicing mutation was identified in the blood sample of the proband's mother. Thus, the mutation could be easily considered to be nonpathogenic. Our study emphasizes the importance of mosaicism in the identification of pathogenic variants and genetic counseling.
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Affiliation(s)
- Guangyu Wang
- Department of Neurology and Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Ying Hou
- Department of Neurology and Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Xiaoqing Lv
- Department of Neurology and Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Chuanzhu Yan
- Department of Neurology and Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Pengfei Lin
- Department of Neurology and Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China.
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Rebelo Neves E, Carvalho AL, Mesquita T, Paiva C, Alfaiate M, Figueira J, Murta J, Marques JP. Bilateral functional worsening following voretigene neparvovec therapy. Eye (Lond) 2023; 37:2828-2829. [PMID: 36801965 PMCID: PMC10482937 DOI: 10.1038/s41433-023-02411-4] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/14/2022] [Accepted: 01/18/2023] [Indexed: 02/19/2023] Open
Affiliation(s)
- Emmanuel Rebelo Neves
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Ana Luísa Carvalho
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- Medical Genetics Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
- University Clinic of Medical Genetics, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Teresa Mesquita
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Catarina Paiva
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Mário Alfaiate
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - João Figueira
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Joaquim Murta
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - João Pedro Marques
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal.
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.
- University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal.
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Engel C, Valence S, Delplancq G, Maroofian R, Accogli A, Agolini E, Alkuraya FS, Baglioni V, Bagnasco I, Becmeur-Lefebvre M, Bertini E, Borggraefe I, Brischoux-Boucher E, Bruel AL, Brusco A, Bubshait DK, Cabrol C, Cilio MR, Cornet MC, Coubes C, Danhaive O, Delague V, Denommé-Pichon AS, Di Giacomo MC, Doco-Fenzy M, Engels H, Cremer K, Gérard M, Gleeson JG, Heron D, Goffeney J, Guimier A, Harms FL, Houlden H, Iacomino M, Kaiyrzhanov R, Kamien B, Karimiani EG, Kraus D, Kuentz P, Kutsche K, Lederer D, Massingham L, Mignot C, Morris-Rosendahl D, Nagarajan L, Odent S, Ormières C, Partlow JN, Pasquier L, Penney L, Philippe C, Piccolo G, Poulton C, Putoux A, Rio M, Rougeot C, Salpietro V, Scheffer I, Schneider A, Srivastava S, Straussberg R, Striano P, Valente EM, Venot P, Villard L, Vitobello A, Wagner J, Wagner M, Zaki MS, Zara F, Lesca G, Yassaee VR, Miryounesi M, Hashemi-Gorji F, Beiraghi M, Ashrafzadeh F, Galehdari H, Walsh C, Novelli A, Tacke M, Sadykova D, Maidyrov Y, Koneev K, Shashkin C, Capra V, Zamani M, Van Maldergem L, Burglen L, Piard J. BRAT1-related disorders: phenotypic spectrum and phenotype-genotype correlations from 97 patients. Eur J Hum Genet 2023; 31:1023-1031. [PMID: 37344571 PMCID: PMC10474045 DOI: 10.1038/s41431-023-01410-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: 12/22/2022] [Revised: 04/26/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
BRAT1 biallelic variants are associated with rigidity and multifocal seizure syndrome, lethal neonatal (RMFSL), and neurodevelopmental disorder associating cerebellar atrophy with or without seizures syndrome (NEDCAS). To date, forty individuals have been reported in the literature. We collected clinical and molecular data from 57 additional cases allowing us to study a large cohort of 97 individuals and draw phenotype-genotype correlations. Fifty-nine individuals presented with BRAT1-related RMFSL phenotype. Most of them had no psychomotor acquisition (100%), epilepsy (100%), microcephaly (91%), limb rigidity (93%), and died prematurely (93%). Thirty-eight individuals presented a non-lethal phenotype of BRAT1-related NEDCAS phenotype. Seventy-six percent of the patients in this group were able to walk and 68% were able to say at least a few words. Most of them had cerebellar ataxia (82%), axial hypotonia (79%) and cerebellar atrophy (100%). Genotype-phenotype correlations in our cohort revealed that biallelic nonsense, frameshift or inframe deletion/insertion variants result in the severe BRAT1-related RMFSL phenotype (46/46; 100%). In contrast, genotypes with at least one missense were more likely associated with NEDCAS (28/34; 82%). The phenotype of patients carrying splice variants was variable: 41% presented with RMFSL (7/17) and 59% with NEDCAS (10/17).
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Affiliation(s)
- Camille Engel
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France.
| | - Stéphanie Valence
- Service de Neurologie Pédiatrique, Hôpital Armand Trousseau, APHP Sorbonne Université, Paris, France
| | - Geoffroy Delplancq
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Reza Maroofian
- Department of Neuromuscular Diseases UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Andrea Accogli
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montreal, QC, Canada
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Valentina Baglioni
- Department of Human Neurosciences, Institute of Child and Adolescent Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Irene Bagnasco
- Division of Neuropsychiatry, Epilepsy Center for Children, Martini Hospital, 10141, Turin, Italy
| | | | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Ingo Borggraefe
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics, University of Munich, 80337, Munich, Germany
| | - Elise Brischoux-Boucher
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Ange-Line Bruel
- UMR 1231 GAD, Inserm, Université de Bourgogne Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10126, Turin, Italy
| | - Dalal K Bubshait
- Department of Pediatrics, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Christelle Cabrol
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Maria Roberta Cilio
- Department of Pediatrics, Division of Pediatric Neurology Saint-Luc University Hospital, and Institute of Neuroscience (IoNS), Catholic University of Louvain, Brussels, Belgium
| | - Marie-Coralie Cornet
- Department of Pediatrics, Division of Neonatology, University of California San Francisco, San Francisco, CA, USA
| | - Christine Coubes
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Olivier Danhaive
- Division of Neonatology, Saint-Luc university Hospital, and Institut of Clinical and Experimental Research (IREC), Bruxelles, Belgium
| | - Valérie Delague
- Aix Marseille Univ, INSERM, Marseille Medical Genetics Center, MMG, Marseille, France
| | - Anne-Sophie Denommé-Pichon
- UMR 1231 GAD, Inserm, Université de Bourgogne Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Marilena Carmela Di Giacomo
- Medical Genetics Service and Laboratory of Cytogenetics, SIC Anatomia Patologica, "San Carlo" Hospital, 85100, Potenza, Italy
| | - Martine Doco-Fenzy
- CHU Reims, Service de Génétique, Reims, France
- CHU de Nantes, service de génétique médicale, Nantes, France
- L'institut du thorax, INSERM, UNIV Nantes, Nantes, France
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Marion Gérard
- Clinical Genetics, Côte de Nacre University Hospital Center, Caen, France
| | - Joseph G Gleeson
- University of California San Diego, Department of Neurosciences, Rady Children's Institute for Genomic Medicine, San Diego, CA, 92037, USA
| | - Delphine Heron
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne University, Paris, France
| | - Joanna Goffeney
- Service de neuropédiatrie, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Anne Guimier
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker Enfants Malades, Institut Imagine et Université Paris-Cité, Paris, France
| | - Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Henry Houlden
- Department of Neuromuscular Diseases UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Michele Iacomino
- Unit of Medical Genetics, IRCCS Instituto Giannina Gaslini, Genova, Italy
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Diseases UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Benjamin Kamien
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, 6008, Australia
| | - Ehsan Ghayoor Karimiani
- Department of Molecular Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Dror Kraus
- Department of Neurology, Schneider Children's Medical Center of Israel, Petah Tiqva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Paul Kuentz
- UMR 1231 GAD, Inserm, Université de Bourgogne Franche Comté, Dijon, France
- Oncobiologie Génétique Bioinformatique, PCBio, CHU Besançon, Besançon, France
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Damien Lederer
- Institute for Pathology and Genetics, 6040, Gosselies, Belgium
| | - Lauren Massingham
- Division of Medical Genetics, Department of Pediatrics, Hasbro Children's Hospital, Providence, RI, USA
| | - Cyril Mignot
- APHP, Sorbonne Université, Département de Génétique, Paris, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, GH Pitié-Salpêtrière/Hôpital Armand Trousseau, Paris, France
| | - Déborah Morris-Rosendahl
- Clinical Genetics and Genomics, Royal Brompton and Harefield NHS Foundation Trust, London, UK
- NHLI, Imperial College London, London, UK
| | - Lakshmi Nagarajan
- Department of Neurology, Perth Children's Hospital, Nedlands, WA, Australia
- University of Western Australia, Nedlands, WA, Australia
| | - Sylvie Odent
- Service de Génétique Clinique, Centre Référence "Déficiences Intellectuelles de causes rares" (CRDI), Centre Référence Anomalies du développement (CLAD-Ouest), CHU Rennes, Univ Rennes, Rennes, France
| | - Clothilde Ormières
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker Enfants Malades, Institut Imagine et Université Paris-Cité, Paris, France
| | - Jennifer Neil Partlow
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Laurent Pasquier
- Service de Génétique Clinique, Centre Référence "Déficiences Intellectuelles de causes rares" (CRDI), Centre Référence Anomalies du développement (CLAD-Ouest), CHU Rennes, Univ Rennes, Rennes, France
| | - Lynette Penney
- Department of Pediatrics, IWK Health Centre, Dalhousie University, Halifax, NS, Canada
| | - Christophe Philippe
- UMR 1231 GAD, Inserm, Université de Bourgogne Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | | | - Cathryn Poulton
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, 6008, Australia
| | - Audrey Putoux
- Hospices Civils de Lyon, Service de Génétique, Bron, France
- Équipe GENDEV, Centre de Recherche en Neurosciences de Lyon, INSERM U1028 CNRS UMR5292, Université Claude Bernard Lyon 1, Lyon, France
| | - Marlène Rio
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker Enfants Malades, Institut Imagine et Université Paris-Cité, Paris, France
| | | | - Vincenzo Salpietro
- Department of Neuromuscular Diseases UCL Queen Square Institute of Neurology, University College London, London, UK
- IRCCS Giannina Gaslini Institute, Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, Genova, Italy
| | - Ingrid Scheffer
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC, Australia
- Royal Children's Hospital, Florey Institute and Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Amy Schneider
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC, Australia
| | | | - Rachel Straussberg
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Pasquale Striano
- IRCCS Giannina Gaslini Institute, Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, Genova, Italy
| | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Perrine Venot
- Neonatal Intensive Care Unit, Institut Alix de Champagne, Reims, France
| | - Laurent Villard
- Aix Marseille Univ, INSERM, Marseille Medical Genetics Center, MMG, Marseille, France
- Département de Génétique Médicale, AP-HM, Hôpital d'Enfants de La Timone, Marseille, France
| | - Antonio Vitobello
- UMR 1231 GAD, Inserm, Université de Bourgogne Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Johanna Wagner
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics, University of Munich, 80337, Munich, Germany
| | - Matias Wagner
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics, University of Munich, 80337, Munich, Germany
- Institute for Neurogenomics, Helmholtz Center Munich, Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University Munich, Munich, Germany
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Federizo Zara
- IRCCS Giannina Gaslini Institute, Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, Genova, Italy
| | - Gaetan Lesca
- Hospices Civils de Lyon, Service de Génétique, Bron, France
- Pathophysiology and Genetics of Neuron and Muscle (PGNM, UCBL - CNRS UMR5261 - INSERM U1315), Université Claude Bernard Lyon 1, Lyon, France
| | - Vahid Reza Yassaee
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Miryounesi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzad Hashemi-Gorji
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehran Beiraghi
- Department of Pediatrics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farah Ashrafzadeh
- Department of Pediatrics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Christopher Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Moritz Tacke
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics, University of Munich, 80337, Munich, Germany
| | | | - Yerdan Maidyrov
- S. D. Asfendiyarov Kazakh National Medical University Almaty, Almaty, Kazakhstan
| | - Kairgali Koneev
- Department of Neurology and Neurosurgery, Asfendiyarov Kazakh National Medical University, Almaty, 050000, Kazakhstan
| | - Chingiz Shashkin
- Department of Neurology, The International Institute of Postraduate Education, Almaty, Kazakhstan
| | - Valeria Capra
- Unit of Medical Genetics, IRCCS Instituto Giannina Gaslini, Genova, Italy
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Lionel Van Maldergem
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Lydie Burglen
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Département de Génétique, AP-HP, Sorbonne Université, Hôpital Trousseau, Paris, France
| | - Juliette Piard
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
- UMR 1231 GAD, Inserm, Université de Bourgogne Franche Comté, Dijon, France
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Metzgeroth G, Steiner L, Naumann N, Lübke J, Kreil S, Fabarius A, Haferlach C, Haferlach T, Hofmann WK, Cross NCP, Schwaab J, Reiter A. Myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase gene fusions: reevaluation of the defining characteristics in a registry-based cohort. Leukemia 2023; 37:1860-1867. [PMID: 37454239 PMCID: PMC10457188 DOI: 10.1038/s41375-023-01958-1] [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: 10/12/2022] [Revised: 05/18/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
In a registry-based analysis of 135 patients with "myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase gene fusions" (MLN-TK; FIP1L1::PDGFRA, n = 78; PDGFRB, diverse fusions, n = 26; FGFR1, diverse, n = 9; JAK2, diverse, n = 11; ETV6::ABL1, n = 11), we sought to evaluate the disease-defining characteristics. In 81/135 (60%) evaluable patients, hypereosinophilia (>1.5 × 109/l) was observed in 40/44 (91%) FIP1L1::PDGFRA and 7/7 (100%) ETV6::ABL1 positive patients but only in 13/30 (43%) patients with PDGFRB, FGFR1, and JAK2 fusion genes while 9/30 (30%) patients had no eosinophilia. Monocytosis >1 × 109/l was identified in 27/81 (33%) patients, most frequently in association with hypereosinophilia (23/27, 85%). Overall, a blast phase (BP) was diagnosed in 38/135 (28%) patients (myeloid, 61%; lymphoid, 39%), which was at extramedullary sites in 18 (47%) patients. The comparison between patients with PDGFRA/PDGFRB vs. FGFR1, JAK2, and ETV6::ABL1 fusion genes revealed a similar occurrence of primary BP (17/104, 16% vs. 8/31 26%, p = 0.32), a lower frequency (5/87, 6% vs. 8/23, 35%, p = 0.003) of and a later progression (median 87 vs. 19 months, p = 0.053) into secondary BP, and a better overall survival from diagnosis of BP (17.1 vs. 1.7 years, p < 0.0008). We conclude that hypereosinophilia with or without monocytosis and various phenotypes of BP occur at variable frequencies in MLN-TK.
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Affiliation(s)
- Georgia Metzgeroth
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Laurenz Steiner
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Nicole Naumann
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Johannes Lübke
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Sebastian Kreil
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Alice Fabarius
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | | | | | - Wolf-Karsten Hofmann
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Nicholas C P Cross
- Wessex Regional Genetics Laboratory, Salisbury, UK
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Juliana Schwaab
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Andreas Reiter
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany.
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Augusto DG, Murdolo LD, Chatzileontiadou DSM, Sabatino JJ, Yusufali T, Peyser ND, Butcher X, Kizer K, Guthrie K, Murray VW, Pae V, Sarvadhavabhatla S, Beltran F, Gill GS, Lynch KL, Yun C, Maguire CT, Peluso MJ, Hoh R, Henrich TJ, Deeks SG, Davidson M, Lu S, Goldberg SA, Kelly JD, Martin JN, Vierra-Green CA, Spellman SR, Langton DJ, Dewar-Oldis MJ, Smith C, Barnard PJ, Lee S, Marcus GM, Olgin JE, Pletcher MJ, Maiers M, Gras S, Hollenbach JA. A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection. Nature 2023; 620:128-136. [PMID: 37468623 PMCID: PMC10396966 DOI: 10.1038/s41586-023-06331-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [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: 10/10/2022] [Accepted: 06/15/2023] [Indexed: 07/21/2023]
Abstract
Studies have demonstrated that at least 20% of individuals infected with SARS-CoV-2 remain asymptomatic1-4. Although most global efforts have focused on severe illness in COVID-19, examining asymptomatic infection provides a unique opportunity to consider early immunological features that promote rapid viral clearance. Here, postulating that variation in the human leukocyte antigen (HLA) loci may underly processes mediating asymptomatic infection, we enrolled 29,947 individuals, for whom high-resolution HLA genotyping data were available, in a smartphone-based study designed to track COVID-19 symptoms and outcomes. Our discovery cohort (n = 1,428) comprised unvaccinated individuals who reported a positive test result for SARS-CoV-2. We tested for association of five HLA loci with disease course and identified a strong association between HLA-B*15:01 and asymptomatic infection, observed in two independent cohorts. Suggesting that this genetic association is due to pre-existing T cell immunity, we show that T cells from pre-pandemic samples from individuals carrying HLA-B*15:01 were reactive to the immunodominant SARS-CoV-2 S-derived peptide NQKLIANQF. The majority of the reactive T cells displayed a memory phenotype, were highly polyfunctional and were cross-reactive to a peptide derived from seasonal coronaviruses. The crystal structure of HLA-B*15:01-peptide complexes demonstrates that the peptides NQKLIANQF and NQKLIANAF (from OC43-CoV and HKU1-CoV) share a similar ability to be stabilized and presented by HLA-B*15:01. Finally, we show that the structural similarity of the peptides underpins T cell cross-reactivity of high-affinity public T cell receptors, providing the molecular basis for HLA-B*15:01-mediated pre-existing immunity.
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Affiliation(s)
- Danillo G Augusto
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, USA
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Lawton D Murdolo
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Demetra S M Chatzileontiadou
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Joseph J Sabatino
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Tasneem Yusufali
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Noah D Peyser
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Xochitl Butcher
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Kerry Kizer
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Karoline Guthrie
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Victoria W Murray
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Vivian Pae
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Sannidhi Sarvadhavabhatla
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Fiona Beltran
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Gurjot S Gill
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Kara L Lynch
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Cassandra Yun
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Colin T Maguire
- Clinical and Translational Science Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Michelle Davidson
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- F.I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Cynthia A Vierra-Green
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Stephen R Spellman
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | | | - Michael J Dewar-Oldis
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Corey Smith
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development Brisbane, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Peter J Barnard
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Sulggi Lee
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Gregory M Marcus
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Jeffrey E Olgin
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Mark J Pletcher
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Division of General Internal Medicine, University of California, San Francisco, CA, USA
| | - Martin Maiers
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jill A Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
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Osborne A, Phelan JE, Vanheer LN, Manjurano A, Gitaka J, Drakeley CJ, Kaneko A, Kita K, Campino S, Clark TG. High throughput human genotyping for variants associated with malarial disease outcomes using custom targeted amplicon sequencing. Sci Rep 2023; 13:12062. [PMID: 37495620 PMCID: PMC10371994 DOI: 10.1038/s41598-023-39233-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: 01/04/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023] Open
Abstract
Malaria has exhibited the strongest known selective pressure on the human genome in recent history and is the evolutionary driving force behind genetic conditions, such as sickle-cell disease, glucose-6-phosphatase deficiency, and some other erythrocyte defects. Genomic studies (e.g., The 1000 Genomes project) have provided an invaluable baseline for human genetics, but with an estimated two thousand ethno-linguistic groups thought to exist across the African continent, our understanding of the genetic differences between indigenous populations and their implications on disease is still limited. Low-cost sequencing-based approaches make it possible to target specific molecular markers and genes of interest, leading to potential insights into genetic diversity. Here we demonstrate the versatility of custom dual-indexing technology and Illumina next generation sequencing to generate a genetic profile of human polymorphisms associated with malaria pathology. For 100 individuals diagnosed with severe malaria in Northeast Tanzania, variants were successfully characterised on the haemoglobin subunit beta (HBB), glucose-6-phosphate dehydrogenase (G6PD), atypical chemokine receptor 1 (ACKR1) genes, and the intergenic Dantu genetic blood variant, then validated using pre-existing genotyping data. High sequencing coverage was observed across all amplicon targets in HBB, G6PD, ACKR1, and the Dantu blood group, with variants identified at frequencies previously observed within this region of Tanzania. Sequencing data exhibited high concordance rates to pre-existing genotyping data (> 99.5%). Our work demonstrates the potential utility of amplicon sequencing for applications in human genetics, including to personalise medicine and understand the genetic diversity of loci linked to important host phenotypes, such as malaria susceptibility.
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Affiliation(s)
- Ashley Osborne
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Leen N Vanheer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Alphaxard Manjurano
- Mwanza Medical Research Centre, National Institute for Medical Research, Mwanza, Tanzania
- Joint Malaria Program, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
- Centre for Malaria Elimination, Mount Kenya University, Thika, Kenya
| | - Christopher J Drakeley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Akira Kaneko
- Department of Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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48
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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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49
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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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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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