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Ma Z, Sharma R, Rogers AN. Physiological Consequences of Nonsense-Mediated Decay and Its Role in Adaptive Responses. Biomedicines 2024; 12:1110. [PMID: 38791071 PMCID: PMC11117581 DOI: 10.3390/biomedicines12051110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
The evolutionarily conserved nonsense-mediated mRNA decay (NMD) pathway is a quality control mechanism that degrades aberrant mRNA containing one or more premature termination codons (PTCs). Recent discoveries indicate that NMD also differentially regulates mRNA from wild-type protein-coding genes despite lacking PTCs. Together with studies showing that NMD is involved in development and adaptive responses that influence health and longevity, these findings point to an expanded role of NMD that adds a new layer of complexity in the post-transcriptional regulation of gene expression. However, the extent of its control, whether different types of NMD play different roles, and the resulting physiological outcomes remain unclear and need further elucidation. Here, we review different branches of NMD and what is known of the physiological outcomes associated with this type of regulation. We identify significant gaps in the understanding of this process and the utility of genetic tools in accelerating progress in this area.
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Affiliation(s)
- Zhengxin Ma
- MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Ratna Sharma
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA;
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Kassabian B, Levy AM, Gardella E, Aledo-Serrano A, Ananth AL, Brea-Fernández AJ, Caumes R, Chatron N, Dainelli A, De Wachter M, Denommé-Pichon AS, Dye TJ, Fazzi E, Felt R, Fernández-Jaén A, Fernández-Prieto M, Gantz E, Gasperowicz P, Gil-Nagel A, Gómez-Andrés D, Greiner HM, Guerrini R, Haanpää MK, Helin M, Hoyer J, Hurst ACE, Kallish S, Karkare SN, Khan A, Kleinendorst L, Koch J, Kothare SV, Koudijs SM, Lagae L, Lakeman P, Leppig KA, Lesca G, Lopergolo D, Lusk L, Mackenzie A, Mei D, Møller RS, Pereira EM, Platzer K, Quelin C, Revah-Politi A, Rheims S, Rodríguez-Palmero A, Rossi A, Santorelli F, Seinfeld S, Sell E, Stephenson D, Szczaluba K, Trinka E, Umair M, Van Esch H, van Haelst MM, Veenma DCM, Weber S, Weckhuysen S, Zacher P, Tümer Z, Rubboli G. Developmental epileptic encephalopathy in DLG4-related synaptopathy. Epilepsia 2024; 65:1029-1045. [PMID: 38135915 DOI: 10.1111/epi.17876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/05/2023] [Accepted: 12/20/2023] [Indexed: 12/24/2023]
Abstract
OBJECTIVE The postsynaptic density protein of excitatory neurons PSD-95 is encoded by discs large MAGUK scaffold protein 4 (DLG4), de novo pathogenic variants of which lead to DLG4-related synaptopathy. The major clinical features are developmental delay, intellectual disability (ID), hypotonia, sleep disturbances, movement disorders, and epilepsy. Even though epilepsy is present in 50% of the individuals, it has not been investigated in detail. We describe here the phenotypic spectrum of epilepsy and associated comorbidities in patients with DLG4-related synaptopathy. METHODS We included 35 individuals with a DLG4 variant and epilepsy as part of a multicenter study. The DLG4 variants were detected by the referring laboratories. The degree of ID, hypotonia, developmental delay, and motor disturbances were evaluated by the referring clinician. Data on awake and sleep electroencephalography (EEG) and/or video-polygraphy and brain magnetic resonance imaging were collected. Antiseizure medication response was retrospectively assessed by the referring clinician. RESULTS A large variety of seizure types was reported, although focal seizures were the most common. Encephalopathy related to status epilepticus during slow-wave sleep (ESES)/developmental epileptic encephalopathy with spike-wave activation during sleep (DEE-SWAS) was diagnosed in >25% of the individuals. All but one individual presented with neurodevelopmental delay. Regression in verbal and/or motor domains was observed in all individuals who suffered from ESES/DEE-SWAS, as well as some who did not. We could not identify a clear genotype-phenotype relationship even between individuals with the same DLG4 variants. SIGNIFICANCE Our study shows that a subgroup of individuals with DLG4-related synaptopathy have DEE, and approximately one fourth of them have ESES/DEE-SWAS. Our study confirms DEE as part of the DLG4-related phenotypic spectrum. Occurrence of ESES/DEE-SWAS in DLG4-related synaptopathy requires proper investigation with sleep EEG.
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Affiliation(s)
- Benedetta Kassabian
- Department of Epilepsy Genetics and Precision Medicine, Danish Epilepsy Center Filadelfia, member of the European Reference Network EpiCARE, Dianalund, Denmark
- Neurology Unit, Department of Neurosciences, University of Padua, Padua, Italy
| | - Amanda M Levy
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Elena Gardella
- Department of Epilepsy Genetics and Precision Medicine, Danish Epilepsy Center Filadelfia, member of the European Reference Network EpiCARE, Dianalund, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Angel Aledo-Serrano
- Epilepsy and Neurogenetics Unit, Vithas la Milagrosa University Hospital, Vithas Hospital Group, Madrid, Spain
| | - Amitha L Ananth
- Division of Pediatric Neurology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alejandro J Brea-Fernández
- Grupo de Genómica y Bioinformática, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CiMUS), Centro de Investigación Biomédica en Red de Enfermedades Raras del Instituto de Salud Carlos III (CIBERER-ISCIII), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Grupo de Genética, Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Biomédica de Santiago (IDIS), Santiago de Compostela, Spain
| | | | - Nicolas Chatron
- Service de Genetique, Hospices Civils de Lyon, Bron, France
- Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Centre National de la recherche scientifique (CNRS) Unité mixte de recherche (UMR) 5261- L'Institut national de la santé et de la recherche médicale (INSERM) U1315, Université de Lyon-Université Claude Bernard Lyon 1, Lyon, France
| | - Alice Dainelli
- Neuroscience Department, Meyer Children's Hospital IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico), member of the European Reference Network EpiCARE, Florence, Italy
| | - Matthias De Wachter
- Department of Pediatric Neurology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Anne-Sophie Denommé-Pichon
- Functional Unit for Diagnostic Innovation in Rare Diseases, Fédération Hospitalo-Universitaire Médecine TRANSLationnelle et Anomalies du Développement (FHU-TRANSLAD), Dijon Bourgogne University Hospital, Dijon, France
- L'Institut national de la santé et de la recherche médicale (INSERM) Unité mixte de recherche (UMR) 1231, Génétique des Anomalies du Développement (GAD), Fédération Hospitalo-Universitaire Médecine TRANSLationnelle et Anomalies du Développement (FHU-TRANSLAD), University of Burgundy, Dijon, France
| | - Thomas J Dye
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Elisa Fazzi
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- Unit of Child Neurology and Psychiatry, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili of Brescia, Brescia, Italy
| | - Roxanne Felt
- Department of Neurology, Kaiser Permanente Bellevue Medical Center, Bellevue, Washington, USA
| | - Alberto Fernández-Jaén
- Department of Pediatric Neurology, Neurogenetics Section, Hospital Universitario Quirónsalud, Madrid, Spain
- Facultad de Medicina, Universidad Europea, Madrid, Spain
| | - Montse Fernández-Prieto
- Grupo de Genómica y Bioinformática, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CiMUS), Centro de Investigación Biomédica en Red de Enfermedades Raras del Instituto de Salud Carlos III (CIBERER-ISCIII), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Grupo de Genética, Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Biomédica de Santiago (IDIS), Santiago de Compostela, Spain
| | - Emily Gantz
- Division of Pediatric Neurology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Piotr Gasperowicz
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Antonio Gil-Nagel
- Neurology Department, Epilepsy Program, Ruber Internacional Hospital, Madrid, Spain
| | - David Gómez-Andrés
- Child Neurology Unit, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Hansel M Greiner
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Renzo Guerrini
- Neuroscience Department, Meyer Children's Hospital IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico), member of the European Reference Network EpiCARE, Florence, Italy
| | - Maria K Haanpää
- Department of Genomics, Turku University Hospital, Turku, Finland
| | - Minttu Helin
- Department of Pediatric Neurology, Turku University Hospital, Turku, Finland
| | - Juliane Hoyer
- Friedrich-Alexander-Universität Erlangen Nürnberg, Institute of Human Genetics, Erlangen, Germany
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Staci Kallish
- Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shefali N Karkare
- Division of Pediatric Neurology, Department of Pediatrics, Cohen Children's Medical Center, New Hyde Park, New York, USA
| | - Amjad Khan
- Department of Zoology, Faculty of Biological Sciences, University of Lakki Marwat, Lakki Marwat, Pakistan
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Lotte Kleinendorst
- Department of Human Genetics, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, the Netherlands
- Emma Center for Personalized Medicine, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Johannes Koch
- University Children's Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Sanjeev V Kothare
- Division of Pediatric Neurology, Department of Pediatrics, Cohen Children's Medical Center, New Hyde Park, New York, USA
| | - Suzanna M Koudijs
- Department of Neurology, Erasmus Medical Center (MC) Sophia Children's Hospital, Rotterdam, the Netherlands
- Erfelijke Neuro-Cognitieve Ontwikkelingsstoornissen, Rotterdam, Erasmus Medical Center (ENCORE)-GRIN Expertise Center, Rotterdam, the Netherlands
| | - Lieven Lagae
- Department of Development and Regeneration, Section Paediatric Neurology, member of the European Reference Network EpiCARE, University Hospitals Leuven, Leuven, Belgium
| | - Phillis Lakeman
- Department of Human Genetics, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Kathleen A Leppig
- Genetic Services, Kaiser Permanente of Washington, Seattle, Washington, USA
| | - Gaetan Lesca
- Service de Genetique, Hospices Civils de Lyon, Bron, France
- Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Centre National de la recherche scientifique (CNRS) Unité mixte de recherche (UMR) 5261- L'Institut national de la santé et de la recherche médicale (INSERM) U1315, Université de Lyon-Université Claude Bernard Lyon 1, Lyon, France
| | - Diego Lopergolo
- Department of Medicine, Surgery, and Neurosciences, University of Siena, Siena, Italy
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Stella Maris Foundation, Pisa, Italy
| | - Laina Lusk
- Division of Neurology, Epilepsy Neurogenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Alex Mackenzie
- Research Institute, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Davide Mei
- Neuroscience Department, Meyer Children's Hospital IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico), member of the European Reference Network EpiCARE, Florence, Italy
| | - Rikke S Møller
- Department of Epilepsy Genetics and Precision Medicine, Danish Epilepsy Center Filadelfia, member of the European Reference Network EpiCARE, Dianalund, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Elaine M Pereira
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children's Hospital, New York, New York, USA
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Chloe Quelin
- Department of Medical Genetics, CHU de Rennes, Rennes, France
| | - Anya Revah-Politi
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Sylvain Rheims
- Department of Functional Neurology and Epileptology, member of the European Reference Network EpiCARE, Hospices Civils de Lyon and Lyon 1 University, Lyon, France
| | - Agustí Rodríguez-Palmero
- Paediatric Neurology Unit, Department of Pediatrics, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Barcelona, Spain
- Grupo de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Andrea Rossi
- Unit of Child Neurology and Psychiatry, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili of Brescia, Brescia, Italy
| | - Filippo Santorelli
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Stella Maris Foundation, Pisa, Italy
| | - Syndi Seinfeld
- Department of Pediatric Neurology, Neuroscience Center, Joe DiMaggio Children's Hospital, Hollywood, Florida, USA
| | - Erick Sell
- Division of Neurology, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Donna Stephenson
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Krzysztof Szczaluba
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
- Center of Excellence for Rare and Undiagnosed Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Eugen Trinka
- Department of Neurology, Neurointensive Care and Neurorehabilitation, Christian Doppler University Hospital, member of the European Reference Network EpiCARE, Paracelsus Medical University, Center for Cognitive Neuroscience, Salzburg, Austria
- Neuroscience Institute, Christian Doppler University Hospital, member of the European Reference Network EpiCARE, Paracelsus Medical University, Center for Cognitive Neuroscience, Salzburg, Austria
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Mieke M van Haelst
- Department of Human Genetics, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, the Netherlands
- Emma Center for Personalized Medicine, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Danielle C M Veenma
- Erfelijke Neuro-Cognitieve Ontwikkelingsstoornissen, Rotterdam, Erasmus Medical Center (ENCORE)-GRIN Expertise Center, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus Medical Center (MC)-Sophia Hospital, Rotterdam, the Netherlands
| | - Sacha Weber
- Service de Génétique, Centre Hospitalier Universitaire (CHU) de Caen-Normandie, Caen, France
- Service de Neurologie, Centre Hospitalier Universitaire (CHU) de Caen-Normandie, Caen, France
| | - Sarah Weckhuysen
- Applied and Translational Neurogenomics Group, Vlaams Instituut voor Biotechnologie (VIB) Center for Molecular Neurology, Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Pia Zacher
- Center for Adults with Disability (MZEB), Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Zeynep Tümer
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Guido Rubboli
- Department of Epilepsy Genetics and Precision Medicine, Danish Epilepsy Center Filadelfia, member of the European Reference Network EpiCARE, Dianalund, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Dulski J, Muthusamy K, Lund TC, Wszolek ZK. CSF1R-related disorder: State of the art, challenges, and proposition of a new terminology. Parkinsonism Relat Disord 2024; 121:105894. [PMID: 37839910 DOI: 10.1016/j.parkreldis.2023.105894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
Recent developments in adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) and other disorders due to CSF1R variants led to the emergence of symptomatic and prophylactic treatment options. The growing body of knowledge on genetics, pathomechanisms, clinical, and radiological features in patients harboring CSF1R variants challenges the current concepts and terminology to define the disorders, in addition to bringing up new questions on genotype-phenotype relationships. Therefore, this paper discusses the present complexities and challenges in the research on ALSP due to CSF1R variants. We illustrate our new concepts with two cases that are compound heterozygotes for CSF1R variants. Although their clinical phenotype resembles ALSP, the diagnosis of brain abnormalities, neurodegeneration, and dysosteosclerosis (BANDDOS) seems more appropriate based on their genotype. As the diagnostic classification dilemma cannot be resolved with currently used concepts and terminology on these disorders, we propose a new nomenclature of "CSF1R-related disorder" with subcategories of "early-onset (<18 years old) and late-onset (≥18 years old) forms". We highlight the heterogeneity of CSF1R variant carriers in age at onset, spectrum and severity of clinical presentation, and progression rate, even within the same family. We argue that multiple factors, including genetic architecture and environment, converge to result in an individual's disease phenotype.
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Affiliation(s)
- Jarosław Dulski
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA; Division of Neurological and Psychiatric Nursing, Faculty of Health Sciences, Medical University of Gdansk, Gdansk, Poland; Neurology Department, St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland
| | | | - Troy C Lund
- Department of Pediatrics, Division of Blood and Marrow Transplant, University of Minnesota, Minneapolis, MN, USA
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Alayoubi AM, Iqbal M, Aman H, Hashmi JA, Alayadhi L, Al-Regaiey K, Basit S. Loss-of-function variant in spermidine/spermine N1-acetyl transferase like 1 (SATL1) gene as an underlying cause of autism spectrum disorder. Sci Rep 2024; 14:5765. [PMID: 38459140 PMCID: PMC10923806 DOI: 10.1038/s41598-024-56253-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/04/2024] [Indexed: 03/10/2024] Open
Abstract
Autism spectrum disorder (ASD) is a complicated, lifelong neurodevelopmental disorder affecting verbal and non-verbal communication and social interactions. ASD signs and symptoms appear early in development before the age of 3 years. It is unlikely for a person to acquire autism after a period of normal development. However, we encountered an 8-year-old child who developed ASD later in life although his developmental milestones were normal at the beginning of life. Sequencing the complete coding part of the genome identified a hemizygous nonsense mutation (NM_001367857.2):c.1803C>G; (p.Tyr601Ter) in the gene (SATL1) encoding spermidine/spermine N1-acetyl transferase like 1. Screening an ASD cohort of 28 isolated patients for the SATL1 gene identified another patient with the same variant. Although SATL1 mutations have not been associated with any human diseases, our data suggests that a mutation in SATL1 is the underlying cause of ASD in our cases. In mammals, mutations in spermine synthase (SMS), an enzyme needed for the synthesis of spermidine polyamine, have been reported in a syndromic form of the X-linked mental retardation. Moreover, SATL1 gene expression studies showed a relatively higher expression of SATL1 transcripts in ASD related parts of the brain including the cerebellum, amygdala and frontal cortex. Additionally, spermidine has been characterized in the context of learning and memory and supplementations with spermidine increase neuroprotective effects and decrease age-induced memory impairment. Furthermore, spermidine biosynthesis is required for spontaneous axonal regeneration and prevents α-synuclein neurotoxicity in invertebrate models. Thus, we report, for the first time, that a mutation in the SATL1 gene could be a contributing factor in the development of autistic symptoms in our patients.
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Affiliation(s)
- Abdulfatah M Alayoubi
- Department of Basic Medical Sciences, Taibah University Medina, Almadinah Almunawwarah, Saudi Arabia
| | - Muhammad Iqbal
- Department of Physiology, Faculty of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Hassan Aman
- Al-Amal Psychiatry Hospital Medina, Almadinah Almunawwarrah, Saudi Arabia
| | - Jamil A Hashmi
- Center for Genetics and Inherited Diseases, Taibah University Medina, Almadinah Almunawwarrah, Saudi Arabia
| | - Laila Alayadhi
- Department of Physiology, Faculty of Medicine, King Saud University, Riyadh, Saudi Arabia
- Autism Research and Treatment Center, Riyadh, Saudi Arabia
| | - Khalid Al-Regaiey
- Department of Physiology, Faculty of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Sulman Basit
- Department of Basic Medical Sciences, Taibah University Medina, Almadinah Almunawwarah, Saudi Arabia.
- Center for Genetics and Inherited Diseases, Taibah University Medina, Almadinah Almunawwarrah, Saudi Arabia.
- Department of Basic Medical Sciences, Taibah University Medina, Almadinah Almunawwarrah, Saudi Arabia.
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Machida R, Ogawa T, Min Soe K, Moriyama K. Nonsense-mediated mRNA decay affects hyperactive root formation in oculo-facio-cardio-dental syndrome via up-frameshift protein 1. J Oral Biosci 2024; 66:225-231. [PMID: 38244688 DOI: 10.1016/j.job.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/22/2024]
Abstract
OBJECTIVES Oculo-facio-cardio-dental (OFCD) syndrome is a rare X-linked genetic disorder caused by mutations in the BCL6 co-repressor (BCOR) and is mainly characterized by radiculomegaly (elongated dental roots). All BCOR mutations reported to date have been associated with premature termination codons, indicating that nonsense-mediated mRNA decay (NMD) might play a vital role in the pathogenesis of OFCD syndrome. However, the molecular mechanisms underlying NMD remain unclear. In this study, we investigated the involvement of up-frameshift protein 1 (UPF1), which plays a central role in NMD, in the hyperactive root formation caused by BCOR mutations. METHODS Periodontal ligament cells, isolated from a Japanese woman with a c.3668delC frameshift mutation in BCOR, and primary human periodontal ligament fibroblasts (HPdLFs) were used for an RNA immunoprecipitation assay to confirm the binding of UPF1 to mutated BCOR. Additionally, the effects of UPF1 on the BCOR transcription levels and corresponding gene expression were determined by performing relative quantitative real-time polymerase chain reactions. RESULTS RNA immunoprecipitation revealed that UPF1 binds to exon 9 of mutated BCOR. Additionally, UPF1 knockdown via siRNA upregulated the transcription of BCOR, whereas overexpression of wild-type and mutated BCOR with the same frameshift mutation in HPdLFs altered bone morphogenetic protein 2 (BMP2) expression. CONCLUSIONS Our findings indicate that BCOR mutations regulate the transcription of BCOR via UPF1, which may in turn regulate the expression of BMP2. NMD, caused by a c.3668delC mutation, potentially leads to an OFCD syndrome phenotype, including elongated dental roots.
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Affiliation(s)
- Ryoto Machida
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
| | - Takuya Ogawa
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
| | - Kyaw Min Soe
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
| | - Keiji Moriyama
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
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Osawa Y, Ichiwata N, Kenmotsu J, Okada T, Masunaga Y, Ogata T, Morioka I, Urakami T. Diabetes mellitus with severe insulin resistance in a young male patient with a heterozygous pathogenic IRS1 frameshift variant. Clin Pediatr Endocrinol 2024; 33:87-93. [PMID: 38572380 PMCID: PMC10985017 DOI: 10.1297/cpe.2023-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/01/2024] [Indexed: 04/05/2024] Open
Abstract
We present the case of a young male patient (height, 158.1 cm [+3.3 standard deviation (SD)]; weight, 63.7 kg [body mass index, 25.5]) with diabetes mellitus and severe insulin resistance associated with a heterozygous pathogenic insulin receptor substrate 1 (IRS1) frameshift mutation. The patient also had severe acanthosis nigricans. Notably, the patient's father was undergoing treatment with high doses of insulin for diabetes mellitus, and had been experiencing angina pectoris. Laboratory data showed a fasting plasma glucose level of 88 mg/dL, hemoglobin A1C (HbA1c) of 7.4%, fasting insulin level of 43.1 µg/mL, and a homeostasis model assessment-insulin resistance (HOMA-IR) score of 9.36, indicating hyperinsulinism. Oral glucose tolerance test revealed a diabetic pattern and insulin hypersecretion. In addition, the patient had hyperlipidemia. Genetic studies revealed a heterozygous frameshift variant of IRS1 [NM_005544.3:c.1791dupG:p.(His598Alafs*13)] in the patient and his father, which can impair the binding and activation of phosphoinositide 3 (PI-3) kinase and defectively mediate the translocation of glucose transporter type 4 (GLUT4) in adipose tissues, possibly leading to glucose intolerance. Therefore, this variant may be disease causing. After confirming IRS1 mutation, metformin was administered, and physical exercise and dietary management were initiated; metformin was well tolerated, and optimal glycemic control was maintained.
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Affiliation(s)
- Yamato Osawa
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
- Department of Pediatrics, Kobari General Hospital, Chiba, Japan
| | - Nobutaka Ichiwata
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
- Department of Pediatrics, Kobari General Hospital, Chiba, Japan
| | - Junko Kenmotsu
- Department of Pediatrics, Kobari General Hospital, Chiba, Japan
| | | | - Yohei Masunaga
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
- Department of Regional Medical Care Support, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
- Department of Pediatrics, Hamamatsu Medical Center, Hamamatsu, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Tatsuhiko Urakami
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
- Department of Pediatrics, Kobari General Hospital, Chiba, Japan
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7
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Sano S, Iwamoto S, Matsushita R, Masunaga Y, Fujisawa Y, Ogata T. A novel GNAS-Gsα splice donor site variant in a girl with pseudohypoparathyroidism type 1A and her mother with pseudopseudohypoparathyroidism. Clin Pediatr Endocrinol 2024; 33:66-70. [PMID: 38572379 PMCID: PMC10985010 DOI: 10.1297/cpe.2023-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/19/2023] [Indexed: 04/05/2024] Open
Abstract
We encountered a Chinese girl with pseudohypoparathyroidism type 1A (PHP1A) and her mother with pseudopseudohypoparathyroidism (PPHP). Sequencing analysis of GNAS-Gsα revealed a heterozygous c.212+2T>C variant (NM_000516.4) affecting the canonical splice donor site of intron 2 in the girl and her mother. RT-PCR performed on mRNA samples obtained from cycloheximide-treated and cycloheximide-untreated lymphoblastoid cell lines of this girl revealed the utilization of an alternative splice donor site at 33-34 bp from the boundary between exon 2 and intron 2 and the production of an aberrant mRNA with a retention of a 32 bp intronic sequence between exon 2 and exon 3 (p.(Gly72Lysfs*39)), which satisfied the condition for the occurrence of nonsense-mediated mRNA decay, as predicted by SpliceAI. This study revealed the molecular consequences of disruption of the canonical splice donor site and confirmed the clinical utility of SpliceAI.
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Affiliation(s)
- Shinichiro Sano
- Department of Pediatric Endocrinology and Metabolism, Shizuoka Children's Hospital, Shizuoka, Japan
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Shotaro Iwamoto
- Total Care Center for AYA with Cancer and Children, Mie University, Mie, Japan
| | - Rie Matsushita
- Department of Pharmacoepidemiology, Kyoto University Graduate School of Medicine and Public Health, Kyoto, Japan
| | - Yohei Masunaga
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yasuko Fujisawa
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
- Department of Pediatrics, Hamamatsu Medical Center, Hamamatsu, Japan
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8
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Bogaert E, Garde A, Gautier T, Rooney K, Duffourd Y, LeBlanc P, van Reempts E, Tran Mau-Them F, Wentzensen IM, Au KS, Richardson K, Northrup H, Gatinois V, Geneviève D, Louie RJ, Lyons MJ, Laulund LW, Brasch-Andersen C, Maxel Juul T, El It F, Marle N, Callier P, Relator R, Haghshenas S, McConkey H, Kerkhof J, Cesario C, Novelli A, Brunetti-Pierri N, Pinelli M, Pennamen P, Naudion S, Legendre M, Courdier C, Trimouille A, Fenzy MD, Pais L, Yeung A, Nugent K, Roeder ER, Mitani T, Posey JE, Calame D, Yonath H, Rosenfeld JA, Musante L, Faletra F, Montanari F, Sartor G, Vancini A, Seri M, Besmond C, Poirier K, Hubert L, Hemelsoet D, Munnich A, Lupski JR, Philippe C, Thauvin-Robinet C, Faivre L, Sadikovic B, Govin J, Dermaut B, Vitobello A. SRSF1 haploinsufficiency is responsible for a syndromic developmental disorder associated with intellectual disability. Am J Hum Genet 2023; 110:790-808. [PMID: 37071997 PMCID: PMC10183470 DOI: 10.1016/j.ajhg.2023.03.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/23/2023] [Indexed: 04/20/2023] Open
Abstract
SRSF1 (also known as ASF/SF2) is a non-small nuclear ribonucleoprotein (non-snRNP) that belongs to the arginine/serine (R/S) domain family. It recognizes and binds to mRNA, regulating both constitutive and alternative splicing. The complete loss of this proto-oncogene in mice is embryonically lethal. Through international data sharing, we identified 17 individuals (10 females and 7 males) with a neurodevelopmental disorder (NDD) with heterozygous germline SRSF1 variants, mostly de novo, including three frameshift variants, three nonsense variants, seven missense variants, and two microdeletions within region 17q22 encompassing SRSF1. Only in one family, the de novo origin could not be established. All individuals featured a recurrent phenotype including developmental delay and intellectual disability (DD/ID), hypotonia, neurobehavioral problems, with variable skeletal (66.7%) and cardiac (46%) anomalies. To investigate the functional consequences of SRSF1 variants, we performed in silico structural modeling, developed an in vivo splicing assay in Drosophila, and carried out episignature analysis in blood-derived DNA from affected individuals. We found that all loss-of-function and 5 out of 7 missense variants were pathogenic, leading to a loss of SRSF1 splicing activity in Drosophila, correlating with a detectable and specific DNA methylation episignature. In addition, our orthogonal in silico, in vivo, and epigenetics analyses enabled the separation of clearly pathogenic missense variants from those with uncertain significance. Overall, these results indicated that haploinsufficiency of SRSF1 is responsible for a syndromic NDD with ID due to a partial loss of SRSF1-mediated splicing activity.
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Affiliation(s)
- Elke Bogaert
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Aurore Garde
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs", Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Thierry Gautier
- University Grenoble Alpes, Inserm U1209, CNRS UMR 5309, Institute for Advanced Biosciences (IAB), 38000 Grenoble, France
| | - Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Yannis Duffourd
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Pontus LeBlanc
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Emma van Reempts
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Frederic Tran Mau-Them
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | | | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Kate Richardson
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Vincent Gatinois
- Unité de Génétique Chromosomique, CHU Montpellier, Montpellier, France
| | - David Geneviève
- Montpellier University, Inserm U1183, Montpellier, France; Reference center for rare disease developmental anomaly malformative syndrome, Department of Medical Genetics, Montpellier Hospital, Montpellier, France
| | | | | | | | - Charlotte Brasch-Andersen
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark; Human Genetics, Department of Clinical Research, Health Faculty, University of Southern Denmark, 5000 Odense, Denmark
| | - Trine Maxel Juul
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Fatima El It
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France
| | - Nathalie Marle
- Laboratoire de Génétique Chromosomique et Moléculaire, Pôle de Biologie, CHU de Dijon, Dijon, France
| | - Patrick Callier
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Laboratoire de Génétique Chromosomique et Moléculaire, Pôle de Biologie, CHU de Dijon, Dijon, France
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Claudia Cesario
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | | | - Sophie Naudion
- Medical Genetics Department, CHU Bordeaux, Bordeaux, France
| | | | | | - Aurelien Trimouille
- INSERM U1211, Laboratoire MRGM, Bordeaux University, Bordeaux, France; Pathology Department, CHU Bordeaux, Bordeaux, France
| | - Martine Doco Fenzy
- Service de génétique, CHU de Reims, Reims, France; Service de génétique médicale, CHU de Nantes, Nantes, France; L'institut du thorax, INSERM, CNRS, UNIV Nantes, CHU de Nantes, Nantes, France
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Kimberly Nugent
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Daniel Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Hagith Yonath
- Internal Medicine A, Danek Gertner Institute of Human Genetics, Sheba Medical Center, Ramat Gan, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics Laboratories, Houston, TX, USA
| | - Luciana Musante
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Francesca Montanari
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanna Sartor
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Marco Seri
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Claude Besmond
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Karine Poirier
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Laurence Hubert
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Dimitri Hemelsoet
- Department of Neurology, Ghent University Hospital, 9000 Ghent, Belgium
| | - Arnold Munnich
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Christophe Philippe
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Christel Thauvin-Robinet
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France; Centre de Référence Maladies Rares « Déficiences intellectuelles de causes rares », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Laurence Faivre
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs", Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Jérôme Govin
- University Grenoble Alpes, Inserm U1209, CNRS UMR 5309, Institute for Advanced Biosciences (IAB), 38000 Grenoble, France
| | - Bart Dermaut
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium.
| | - Antonio Vitobello
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France.
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9
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Jamshed F, Dashti F, Ouyang X, Mehal WZ, Banini BA. New uses for an old remedy: Digoxin as a potential treatment for steatohepatitis and other disorders. World J Gastroenterol 2023; 29:1824-1837. [PMID: 37032732 PMCID: PMC10080697 DOI: 10.3748/wjg.v29.i12.1824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/12/2023] [Accepted: 03/14/2023] [Indexed: 03/28/2023] Open
Abstract
Repurposing of the widely available and relatively cheap generic cardiac gly-coside digoxin for non-cardiac indications could have a wide-ranging impact on the global burden of several diseases. Over the past several years, there have been significant advances in the study of digoxin pharmacology and its potential non-cardiac clinical applications, including anti-inflammatory, antineoplastic, metabolic, and antimicrobial use. Digoxin holds promise in the treatment of gastrointestinal disease, including nonalcoholic steatohepatitis and alcohol-associated steatohepatitis as well as in obesity, cancer, and treatment of viral infections, among other conditions. In this review, we provide a summary of the clinical uses of digoxin to date and discuss recent research on its emerging applications.
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Affiliation(s)
- Fatima Jamshed
- Section of Digestive Diseases, Yale School of Medicine, New Haven, CT 06510, United States
- Griffin Hospital-Yale University, Derby, CT 06418, United States
| | - Farzaneh Dashti
- Section of Digestive Diseases, Yale School of Medicine, New Haven, CT 06510, United States
| | - Xinshou Ouyang
- Section of Digestive Diseases, Yale School of Medicine, New Haven, CT 06510, United States
| | - Wajahat Z Mehal
- Section of Digestive Diseases, Yale School of Medicine, New Haven, CT 06510, United States
- West Haven Veterans Medical Center, West Haven, CT 06516, United States
| | - Bubu A Banini
- Section of Digestive Diseases, Yale School of Medicine, New Haven, CT 06510, United States
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10
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Recoding of Nonsense Mutation as a Pharmacological Strategy. Biomedicines 2023; 11:biomedicines11030659. [PMID: 36979640 PMCID: PMC10044939 DOI: 10.3390/biomedicines11030659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Approximately 11% of genetic human diseases are caused by nonsense mutations that introduce a premature termination codon (PTC) into the coding sequence. The PTC results in the production of a potentially harmful shortened polypeptide and activation of a nonsense-mediated decay (NMD) pathway. The NMD pathway reduces the burden of unproductive protein synthesis by lowering the level of PTC mRNA. There is an endogenous rescue mechanism that produces a full-length protein from a PTC mRNA. Nonsense suppression therapies aim to increase readthrough, suppress NMD, or are a combination of both strategies. Therefore, treatment with translational readthrough-inducing drugs (TRIDs) and NMD inhibitors may increase the effectiveness of PTC suppression. Here we discuss the mechanism of PTC readthrough and the development of novel approaches to PTC suppression. We also discuss the toxicity and bioavailability of therapeutics used to stimulate PTC readthrough.
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11
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Masunaga Y, Nishimura G, Takahashi K, Hishiyama T, Imamura M, Kashimada K, Kadoya M, Wada Y, Okamoto N, Oba D, Ohashi H, Ikeno M, Sakamoto Y, Fukami M, Saitsu H, Ogata T. Clinical and molecular findings in three Japanese patients with N-acetylneuraminic acid synthetase-congenital disorder of glycosylation (NANS-CDG). Sci Rep 2022; 12:17079. [PMID: 36224347 PMCID: PMC9556533 DOI: 10.1038/s41598-022-21751-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/30/2022] [Indexed: 01/04/2023] Open
Abstract
We report clinical and molecular findings in three Japanese patients with N-acetylneuraminic acid synthetase-congenital disorder of glycosylation (NANS-CDG). Patient 1 exhibited a unique constellation of clinical features including marked hydrocephalus, spondyloepimetaphyseal dysplasia (SEMD), and thrombocytopenia which is comparable to that of an infant reported by Faye-Peterson et al., whereas patients 2 and 3 showed Camera-Genevieve type SMED with intellectual/developmental disability which is currently known as the sole disease name for NANS-CDG. Molecular studies revealed a maternally inherited likely pathogenic c.207del:p.(Arg69Serfs*57) variant and a paternally derived likely pathogenic c.979_981dup:p.(Ile327dup) variant in patient 1, a homozygous likely pathogenic c.979_981dup:p.(Ile327dup) variant caused by maternal segmental isodisomy involving NANS in patient 2, and a paternally inherited pathogenic c.133-12T>A variant leading to aberrant splicing and a maternally inherited likely pathogenic c.607T>C:p.(Tyr203His) variant in patient 3 (reference mRNA: NM_018946.4). The results, together with previously reported data, imply that (1) NANS plays an important role in postnatal growth and fetal brain development; (2) SMED is recognizable at birth and shows remarkable postnatal evolution; (3) NANS-CDG is associated with low-normal serum sialic acid, obviously elevated urine N-acetylmannosamine, and normal N- and O-glycosylation of serum proteins; and (4) NANS-CDG is divided into Camera-Genevieve type and more severe Faye-Peterson type.
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Affiliation(s)
- Yohei Masunaga
- grid.505613.40000 0000 8937 6696Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Gen Nishimura
- grid.430047.40000 0004 0640 5017Center for Intractable Diseases, Saitama Medical University Hospital, Saitama, Japan
| | - Koji Takahashi
- grid.410824.b0000 0004 1764 0813Department of Pediatrics, Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - Tomiyuki Hishiyama
- grid.410824.b0000 0004 1764 0813Department of Neonatology, Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - Masatoshi Imamura
- grid.410824.b0000 0004 1764 0813Department of Neonatology, Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - Kenichi Kashimada
- grid.410824.b0000 0004 1764 0813Department of Pediatrics, Tsuchiura Kyodo General Hospital, Tsuchiura, Japan ,grid.265073.50000 0001 1014 9130Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Machiko Kadoya
- grid.416629.e0000 0004 0377 2137Department of Molecular Medicine, Osaka Women’s and Children’s Hospital, Osaka, Japan
| | - Yoshinao Wada
- grid.416629.e0000 0004 0377 2137Department of Molecular Medicine, Osaka Women’s and Children’s Hospital, Osaka, Japan
| | - Nobuhiko Okamoto
- grid.416629.e0000 0004 0377 2137Department of Molecular Medicine, Osaka Women’s and Children’s Hospital, Osaka, Japan
| | - Daiju Oba
- grid.416697.b0000 0004 0569 8102Division of Medical Genetics, Saitama Children’s Medical Center, Saitama, Japan
| | - Hirofumi Ohashi
- grid.416697.b0000 0004 0569 8102Division of Medical Genetics, Saitama Children’s Medical Center, Saitama, Japan
| | - Mitsuru Ikeno
- grid.258269.20000 0004 1762 2738Department of Pediatrics, Juntendo University School of Medicine, Tokyo, Japan
| | - Yuko Sakamoto
- grid.482668.60000 0004 1769 1784Department of Orthopedics, Juntendo University Nerima Hospital, Tokyo, Japan
| | - Maki Fukami
- grid.63906.3a0000 0004 0377 2305Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hirotomo Saitsu
- grid.505613.40000 0000 8937 6696Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tsutomu Ogata
- grid.505613.40000 0000 8937 6696Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan ,grid.63906.3a0000 0004 0377 2305Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan ,grid.505613.40000 0000 8937 6696Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan ,grid.413553.50000 0004 1772 534XDepartment of Pediatrics, Hamamatsu Medical Center, Hamamatsu, Japan
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12
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Bowling A, Eastman A, Merlo C, Lin G, West N, Patel S, Cutting G, Sharma N. Downstream Alternate Start Site Allows N-Terminal Nonsense Variants to Escape NMD and Results in Functional Recovery by Readthrough and Modulator Combination. J Pers Med 2022; 12:jpm12091448. [PMID: 36143233 PMCID: PMC9504986 DOI: 10.3390/jpm12091448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
Genetic variants that introduce premature termination codons (PTCs) have remained difficult to therapeutically target due to lack of protein product. Nonsense mediated mRNA decay (NMD) targets PTC-bearing transcripts to reduce the potentially damaging effects of truncated proteins. Readthrough compounds have been tested on PTC-generating variants in attempt to permit translation through a premature stop. However, readthrough compounds have not proved efficacious in a clinical setting due to lack of stable mRNA. Here, we investigate N-terminal variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which have been shown to escape NMD, potentially through a mechanism of alternative translation initiation at downstream AUG codons. We hypothesized that N-terminal variants in CFTR that evade NMD will produce stable transcript, allowing CFTR function to be restored by a combination of readthrough and protein modulator therapy. We investigate this using two cell line models expressing CFTR-expression minigenes (EMG; HEK293s and CFBEs) and primary human nasal epithelial (NE) cells, and we test readthrough compounds G418 and ELX-02 in combination with CFTR protein modulators. HEK293 cells expressing the variants E60X and L88X generate CFTR-specific core glycosylated products that are consistent with downstream translation initiation. Mutation of downstream methionines at codons 150 and 152 does not result in changes in CFTR protein processing in cells expressing L88X-CFTR-EMG. However, mutation of methionine at 265 results in loss of detectable CFTR protein in cells expressing E60X, L88X, and Y122X CFTR-EMGs, indicating that downstream translation initiation is occurring at the AUG codon at position M265. In HEK293 stable cells harboring L88X, treatment with readthrough compounds alone allows for formation of full-length, but misfolded CFTR protein. Upon addition of protein modulators in combination with readthrough, we observe formation of mature, complex-glycosylated CFTR. In CFBE and NE cells, addition of readthrough ELX-02 and modulator therapy results in substantial recovery of CFTR function. Our work indicates that N-terminal variants generate stable CFTR transcript due to translation initiation at a downstream AUG codon. Thus, individuals with CF bearing 5′ nonsense variants that evade NMD are ideal candidates for treatment with clinically safe readthrough compounds and modulator therapy.
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Affiliation(s)
- Alyssa Bowling
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alice Eastman
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christian Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21205, USA
| | - Gabrielle Lin
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Natalie West
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21205, USA
| | - Shivani Patel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21205, USA
| | - Garry Cutting
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Neeraj Sharma
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Correspondence:
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13
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Lombardi S, Testa MF, Pinotti M, Branchini A. Translation termination codons in protein synthesis and disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:1-48. [PMID: 36088072 DOI: 10.1016/bs.apcsb.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Fidelity of protein synthesis, a process shaped by several mechanisms involving specialized ribosome regions and external factors, ensures the precise reading of sense as well as stop codons (UGA, UAG, UAA), which are usually localized at the 3' of mRNA and drive the release of the polypeptide chain. However, either natural (NTCs) or premature (PTCs) termination codons, the latter arising from nucleotide changes, can undergo a recoding process named ribosome or translational readthrough, which insert specific amino acids (NTCs) or subset(s) depending on the stop codon type (PTCs). This process is particularly relevant for nonsense mutations, a relatively frequent cause of genetic disorders, which impair gene expression at different levels by potentially leading to mRNA degradation and/or synthesis of truncated proteins. As a matter of fact, many efforts have been made to develop efficient and safe readthrough-inducing compounds, which have been challenged in several models of human disease to provide with a therapy. In this view, the dissection of the molecular determinants shaping the outcome of readthrough, namely nucleotide and protein contexts as well as their interplay and impact on protein structure/function, is crucial to identify responsive nonsense mutations resulting in functional full-length proteins. The interpretation of experimental and mechanistic findings is also important to define a possibly clear picture of potential readthrough-favorable features useful to achieve rescue profiles compatible with therapeutic thresholds typical of each targeted disorder, which is of primary importance for the potential translatability of readthrough into a personalized and mutation-specific, and thus patient-oriented, therapeutic strategy.
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Affiliation(s)
- Silvia Lombardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Maria Francesca Testa
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
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14
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Christensen MB, Levy AM, Mohammadi NA, Niceta M, Kaiyrzhanov R, Dentici ML, Alam CA, Alesi V, Benoit V, Bhatia KP, Bierhals T, Boßelmann CM, Buratti J, Callewaert B, Ceulemans B, Charles P, De Wachter M, Dehghani M, D'haenens E, Doco-Fenzy M, Geßner M, Gobert C, Guliyeva U, Haack TB, Hammer TB, Heinrich T, Hempel M, Herget T, Hoffmann U, Horvath J, Houlden H, Keren B, Kresge C, Kumps C, Lederer D, Lermine A, Magrinelli F, Maroofian R, Mehrjardi MYV, Moudi M, Müller AJ, Oostra AJ, Pletcher BA, Ros-Pardo D, Samarasekera S, Tartaglia M, Van Schil K, Vogt J, Wassmer E, Winkelmann J, Zaki MS, Zech M, Lerche H, Radio FC, Gomez-Puertas P, Møller RS, Tümer Z. Biallelic variants in ZNF142 lead to a syndromic neurodevelopmental disorder. Clin Genet 2022; 102:98-109. [PMID: 35616059 PMCID: PMC9546172 DOI: 10.1111/cge.14165] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 11/28/2022]
Abstract
Biallelic variants of the gene encoding for the zinc-finger protein 142 (ZNF142) have recently been associated with intellectual disability (ID), speech impairment, seizures, and movement disorders in nine individuals from five families. In this study, we obtained phenotype and genotype information of 26 further individuals from 16 families. Among the 27 different ZNF142 variants identified in the total of 35 individuals only four were missense. Missense variants may give a milder phenotype by changing the local structure of ZF motifs as suggested by protein modelling; but this correlation should be validated in larger cohorts and pathogenicity of the missense variants should be investigated with functional studies. Clinical features of the 35 individuals suggest that biallelic ZNF142 variants lead to a syndromic neurodevelopmental disorder with mild to moderate ID, varying degrees of delay in language and gross motor development, early onset seizures, hypotonia, behavioral features, movement disorders, and facial dysmorphism. The differences in symptom frequencies observed in the unpublished individuals compared to those of published, and recognition of previously underemphasized facial features are likely to be due to the small sizes of the previous cohorts, which underlines the importance of larger cohorts for the phenotype descriptions of rare genetic disorders. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Maria B Christensen
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Amanda M Levy
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Nazanin A Mohammadi
- Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark.,Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London, United Kingdom
| | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy.,Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chadi Al Alam
- Pediatric Neurology department, American center for Psychiatry and Neurology, Abu Dhabi and Al Ain, United Arab Emirates.,Pediatric Neurology department, Haykel Hospital, El Koura, Lebanon
| | - Viola Alesi
- Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | - Kailash P Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian M Boßelmann
- Department of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Julien Buratti
- Department of Medical Genetics, Pitié-Salpêtrière Hospital, AP- HP, Sorbonne Université, Paris, France
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Berten Ceulemans
- Department of Pediatric Neurology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Perrine Charles
- Department of Medical Genetics, Pitié-Salpêtrière Hospital, AP- HP, Sorbonne Université, Paris, France
| | - Matthias De Wachter
- Department of Pediatric Neurology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Mohammadreza Dehghani
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Erika D'haenens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Martine Doco-Fenzy
- SFR CAP SANTE, HMB2 CHU, Reims, France.,CHU de Nantes, service de génétique médicale, Nantes, France
| | - Michaela Geßner
- KfH-Board of Trustees for Dialysis and Kidney Transplantation (KfH-Kuratorium für Dialyse und Nierentransplantation e.V.), Neu Isenburg, Germany
| | - Cyrielle Gobert
- Neuropediatric department, Centre Hospitalier Neurologique William Lennox, Ottignies, Belgium
| | | | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Trine B Hammer
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark
| | - Tilman Heinrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,MVZ Humangenetik und Molekularpathologie GmbH, Rostock, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Judit Horvath
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Henry Houlden
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London, United Kingdom
| | - Boris Keren
- Department of Medical Genetics, Pitié-Salpêtrière Hospital, AP- HP, Sorbonne Université, Paris, France
| | | | - Candy Kumps
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | | | - Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London, United Kingdom
| | | | - Mahdiyeh Moudi
- Department of Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Amelie J Müller
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Anna J Oostra
- Neuropediatric department, Ghent University Hospital, Ghent, Belgium.,Centre for Developmental disorders, Ghent, Belgium
| | | | - David Ros-Pardo
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), Madrid, Spain
| | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Kristof Van Schil
- Department of Medical Genetics, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham, United Kingdom
| | - Evangeline Wassmer
- Birmingham Women and Children's Hospital, Birmingham, United Kingdom.,Institute of Health and Neurodevelopment, Aston University, Birmingham, United Kingdom
| | - Juliane Winkelmann
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt.,Genetics Department, Armed Forces College of Medicine (AFCM), Cairo, Egypt
| | - Michael Zech
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | | | - Paulino Gomez-Puertas
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), Madrid, Spain
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark.,Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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15
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ACAN biallelic variants in a girl with severe idiopathic short stature. J Hum Genet 2022; 67:481-486. [PMID: 35314765 DOI: 10.1038/s10038-022-01030-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 11/08/2022]
Abstract
Although ACAN heterozygous loss-of-function variants often cause idiopathic short stature (ISS) phenotype, there is no report describing ISS phenotype caused by ACAN biallelic loss-of-function variants. We encountered a 4 1/12-year-old Japanese girl with a height of 80.4 cm (-5.2 SD), a weight of 11.4 kg (-1.9 SD), a head circumference of 48.7 cm (-0.6 SD), and an arm span/height ratio of 1.0 (+1.1 SD). Endocrine studies and bone survey showed no abnormal findings. Whole exome sequencing revealed biallelic rare variants in ACAN, i.e., NM_013227.4:c.4214delC:p.(Pro1405Leufs*3) derived from her father and paternal grandfather with short stature (-2.9 and -2.0 SD, respectively) and NM_013227.4:c.7124 A>G:p.(Gln2375Arg) inherited from her mother and maternal grandmother with short stature (-2.1 and -3.0 SD, respectively). The frameshift variant underwent nonsense mediated mRNA decay, and the missense variant was assessed to have high pathogenicity. The results imply for the first time that ACAN biallelic loss-of-function variants can cause severe ISS phenotype.
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16
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Molecular Determinants and Specificity of mRNA with Alternatively-Spliced UPF1 Isoforms, Influenced by an Insertion in the 'Regulatory Loop'. Int J Mol Sci 2021; 22:ijms222312744. [PMID: 34884553 PMCID: PMC8657986 DOI: 10.3390/ijms222312744] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 01/25/2023] Open
Abstract
The nonsense-mediated mRNA decay (NMD) pathway rapidly detects and degrades mRNA containing premature termination codons (PTCs). UP-frameshift 1 (UPF1), the master regulator of the NMD process, has two alternatively-spliced isoforms; one carries 353-GNEDLVIIWLR-363 insertion in the ‘regulatory loop (involved in mRNA binding)’. Such insertion can induce catalytic and/or ATPase activity, as determined experimentally; however, the kinetics and molecular level information are not fully understood. Herein, applying all-atom molecular dynamics, we probe the binding specificity of UPF1 with different GC- and AU-rich mRNA motifs and the influence of insertion to the viable control over UPF1 catalytic activity. Our results indicate two distinct conformations between 1B and RecA2 domains of UPF1: ‘open (isoform_2; without insertion)’ and ‘closed (isoform_1; with insertion)’. These structural movements correspond to an important stacking pattern in mRNA motifs, i.e., absence of stack formation in mRNA, with UPF1 isoform_2 results in the ‘open conformation’. Particularly, for UPF1 isoform_1, the increased distance between 1B and RecA2 domains has resulted in reducing the mRNA–UPF1 interactions. Lower fluctuating GC-rich mRNA motifs have better binding with UPF1, compared with AU-rich sequences. Except CCUGGGG, all other GC-rich motifs formed a 4-stack pattern with UPF1. High occupancy R363, D364, T627, and G862 residues were common binding GC-rich motifs, as were R363, N535, and T627 for the AU-rich motifs. The GC-rich motifs behave distinctly when bound to either of the isoforms; lower stability was observed with UPF1 isoform_2. The cancer-associated UPF1 variants (P533L/T and A839T) resulted in decreased protein–mRNA binding efficiency. Lack of mRNA stacking poses in the UPF1P533T system significantly decreased UPF1-mRNA binding efficiency and increased distance between 1B-RecA2. These novel findings can serve to further inform NMD-associated mechanistic and kinetic studies.
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17
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Wang H, Huo L, Wang Y, Sun W, Gu W. Usher syndrome type 2A complicated with glycogen storage disease type 3 due to paternal uniparental isodisomy of chromosome 1 in a sporadic patient. Mol Genet Genomic Med 2021; 9:e1779. [PMID: 34405590 PMCID: PMC8580083 DOI: 10.1002/mgg3.1779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 05/01/2021] [Accepted: 07/08/2021] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The condition of uniparental disomy (UPD) occurs when an individual inherits two copies of a chromosome, or part of a chromosome, from one parent. Most cases of uniparental heterodisomy (UPhD) do not cause diseases, whereas cases of uniparental isodisomy (UPiD), while rare, may be pathogenic. Theoretically, UPiD may cause rare genetic diseases in a homozygous recessive manner. METHODS A 4-year-old girl presented with congenital hearing loss, developmental delay, hepatomegaly, and other clinical features. She and her parents were genetically tested using trio whole exome sequencing (Trio-WES) and copy number variation sequencing (CNV-seq). In addition, we built a structural model to further examine the pathogenicity of the UPiD variants. RESULTS Trio-WES identified a paternal UPiD in chromosome 1, and two homozygous pathogenic variants AGL c.4284T>G/p.Tyr1428* and USH2A c.6528T>A/p.Tyr2176* in the UPiD region. We further analyzed the pathogenicity of these two variations. The patient was diagnosed with Usher syndrome type 2A (USH2A) and glycogen storage disease type III (GSD3). CONCLUSIONS Our study reports a rare case of a patient carrying two pathogenic variants of different genes caused by paternal UPiD, supporting the potential application of Trio-WES in detecting and facilitating the diagnosis of UPD.
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Affiliation(s)
- Hua Wang
- Department of Pediatric Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Liang Huo
- Department of Pediatric Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Yajian Wang
- Chigene (Beijing) Translational Medical Research Center Co., Ltd., Beijing, P.R. China
| | - Weiwei Sun
- Chigene (Beijing) Translational Medical Research Center Co., Ltd., Beijing, P.R. China
| | - Weiyue Gu
- Chigene (Beijing) Translational Medical Research Center Co., Ltd., Beijing, P.R. China
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18
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Kagami M, Hara-Isono K, Matsubara K, Nakabayashi K, Narumi S, Fukami M, Ohkubo Y, Saitsu H, Takada S, Ogata T. ZNF445: a homozygous truncating variant in a patient with Temple syndrome and multilocus imprinting disturbance. Clin Epigenetics 2021; 13:119. [PMID: 34039421 PMCID: PMC8157728 DOI: 10.1186/s13148-021-01106-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/18/2021] [Indexed: 11/12/2022] Open
Abstract
Background ZNF445, as well as ZFP57, is involved in the postfertilization methylation maintenance of multiple imprinting-associated differentially methylated regions (iDMRs). Thus, ZNF445 pathogenic variants are predicted to cause multilocus imprinting disturbances (MLIDs), as do ZFP57 pathogenic variants. In particular, the MEG3/DLK1:IG-DMR would be affected, because the postzygotic methylation imprint of the MEG3/DLK1:IG-DMR is maintained primarily by ZNF445, whereas that of most iDMRs is preserved by both ZFP57 and ZNF445 or primarily by ZFP57. Results We searched for a ZNF445 variant(s) in six patients with various imprinting disorders (IDs) caused by epimutations and MLIDs revealed by pyrosequencing for nine iDMRs, without a selection for the original IDs. Re-analysis of the previously obtained whole exome sequencing data identified a homozygous ZNF445 variant (NM_181489.6:c.2803C>T:p.(Gln935*)) producing a truncated protein missing two of 14 zinc finger domains in a patient with Temple syndrome and MLID. In this patient, array-based genomewide methylation analysis revealed severe hypomethylation of most CpGs at the MEG3:TSS-DMR, moderate hypomethylation of roughly two-thirds of CpGs at the H19/IGF2:IG-DMR, and mild-to-moderate hypomethylation of a few CpGs at the DIRAS3:TSS-DMR, MEST:alt-TSS-DMR, IGF2:Ex9-DMR, IGF2:alt-TSS, and GNAS-AS1:TSS-DMR. Furthermore, bisulfite sequencing analysis for the MEG3/DLK1:IG-DMR delineated a markedly hypomethylated segment (CG-A). The heterozygous parents were clinically normal and had virtually no aberrant methylation pattern. Conclusions We identified a ZNF445 pathogenic variant for the first time. Since ZNF445 binds to the MEG3/DLK1:IG-DMR and other iDMRs affected in this patient, the development of Temple syndrome and MLID would primarily be explained by the ZNF445 variant. Furthermore, CG-A may be the target site for ZNF445 within the MEG3/DLK1:IG-DMR. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01106-5.
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Affiliation(s)
- Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
| | - Kaori Hara-Isono
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Yumiko Ohkubo
- Department of Pediatrics, Shizuoka Saiseikai Hospital, Oshika 1-1-1, Suruga-ku, Shizuoka, 422-8527, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan. .,Department of Pediatrics, Shizuoka Saiseikai Hospital, Oshika 1-1-1, Suruga-ku, Shizuoka, 422-8527, Japan. .,Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan. .,Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan. .,Department of Pediatrics, Hamamatsu Medical Center, Tomitsuka 328, Naka-ku, Hamamatsu, 432-8580, Japan.
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19
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Seike N, Yokoseki A, Takeuchi R, Saito K, Miyahara H, Miyashita A, Ikeda T, Aida I, Nakajima T, Kanazawa M, Wakabayashi M, Toyoshima Y, Takahashi H, Matsumoto R, Toda T, Onodera O, Ishikawa A, Ikeuchi T, Kakita A. Genetic Variations and Neuropathologic Features of Patients with PRKN Mutations. Mov Disord 2021; 36:1634-1643. [PMID: 33570211 DOI: 10.1002/mds.28521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/07/2021] [Accepted: 01/15/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Mutations in PRKN are the most common cause of autosomal recessive juvenile parkinsonism. The objective of this study was to investigate the association between genotype and pathology in patients with PRKN mutations. METHODS We performed a sequence and copy number variation analysis of PRKN, mRNA transcripts, Parkin protein expression, and neuropathology in 8 autopsied patients. RESULTS All the patients harbored biallelic PRKN mutations. Two patients were homozygous and heterozygous, respectively, for the missense mutation p.C431F. Seven patients had exon rearrangements, including 2 patients from a single family who harbored a homozygous deletion of exon 4, and 3 patients who carried a homozygous duplication of exons 6-7, a homozygous duplication of exons 10-11, and a heterozygous duplication of exons 2-4. In the other 2 patients, we found a compound heterozygous duplication of exon 2, deletion of exon 3, and a heterozygous duplication of exon 2. However, sequencing of cDNA prepared from mRNA revealed 2 different transcripts derived from triplication of exon 2 and deletion of exons 2-3 and from duplication of exons 2-4 and deletion of exons 3-4. Western blotting and immunohistochemistry revealed faint or no expression of Parkin in their brains. In the substantia nigra pars compacta, a subfield-specific pattern of neuronal loss and mild gliosis were evident. Lewy bodies were found in 3 patients. Peripheral sensory neuronopathy was a feature. CONCLUSIONS Genomic and mRNA analysis is needed to identify the PRKN mutations. Variable mutations may result in no or little production of mature Parkin and the histopathologic features may be similar. © 2021 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Naohiko Seike
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan.,Division of Neurology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Akio Yokoseki
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Ryoko Takeuchi
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kento Saito
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hiroaki Miyahara
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akinori Miyashita
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Tetsuhiko Ikeda
- Department of Neurology, NHO Niigata National Hospital, Kashiwazaki, Japan
| | - Izumi Aida
- Department of Neurology, NHO Niigata National Hospital, Kashiwazaki, Japan
| | - Takashi Nakajima
- Department of Neurology, NHO Niigata National Hospital, Kashiwazaki, Japan
| | - Masato Kanazawa
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | | | - Yasuko Toyoshima
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hitoshi Takahashi
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Riki Matsumoto
- Division of Neurology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Osamu Onodera
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Atsushi Ishikawa
- Department of Neurology, Brain Disease Center Agano Hospital, Agano, Japan
| | - Takeshi Ikeuchi
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
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20
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Signatures of Dermal Fibroblasts from RDEB Pediatric Patients. Int J Mol Sci 2021; 22:ijms22041792. [PMID: 33670258 PMCID: PMC7918539 DOI: 10.3390/ijms22041792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
The recessive form of dystrophic epidermolysis bullosa (RDEB) is a debilitating disease caused by impairments in the junctions of the dermis and the basement membrane of the epidermis. Mutations in the COL7A1 gene induce multiple abnormalities, including chronic inflammation and profibrotic changes in the skin. However, the correlations between the specific mutations in COL7A1 and their phenotypic output remain largely unexplored. The mutations in the COL7A1 gene, described here, were found in the DEB register. Among them, two homozygous mutations and two cases of compound heterozygous mutations were identified. We created the panel of primary patient-specific RDEB fibroblast lines (FEB) and compared it with control fibroblasts from healthy donors (FHC). The set of morphological features and the contraction capacity of the cells distinguished FEB from FHC. We also report the relationships between the mutations and several phenotypic traits of the FEB. Based on the analysis of the available RNA-seq data of RDEB fibroblasts, we performed an RT-qPCR gene expression analysis of our cell lines, confirming the differential status of multiple genes while uncovering the new ones. We anticipate that our panels of cell lines will be useful not only for studying RDEB signatures but also for investigating the overall mechanisms involved in disease progression.
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Alharbi A, Hashmi JA, Alharby E, Albalawi AM, Ramzan K, Basit S. A novel frameshift mutation in the ITGB3 gene leading to Glanzmann's thrombasthenia in a Saudi Arabian family. Hematol Oncol Stem Cell Ther 2021; 15:21-26. [PMID: 33600779 DOI: 10.1016/j.hemonc.2021.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/19/2021] [Indexed: 11/25/2022] Open
Abstract
Glanzmann's thrombasthenia (GT) is an autosomal recessive congenital bleeding disorder of platelet aggregation. Mutations in ITGA2B and ITGB3 genes result in quantitative and/or qualitative abnormalities of the glycoprotein receptor complex IIb/IIIa (integrin αIIbβ3), which in turn impairs platelet aggregation and lead to GT. In this study, whole genome single nucleotide polymorphism (SNP) genotyping as well as whole exome sequencing was performed in a large family segregating GT. Analysis of the genotypes localized the disease region to chromosome 17q21.2-q21.3. Filtration of whole exome data and candidate variants prioritization identified a pathogenic variant in the ITGB3 gene. The single nucleotide deletion variant (c.2113delC) in exon 13 of the ITGB3 gene is predicted to cause a frameshift and absence of vital C-terminal domains including the transmembrane helix and the cytoplasmic domain. Clinical variability of the bleeding phenotype in affected individuals with the same mutation suggests that other genetic and nongenetic factors are responsible for determining GT features.
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Affiliation(s)
- Asma Alharbi
- Center for Genetics and Inherited Diseases, Taibah University Almadinah Almunawwarah, Medina, Saudi Arabia
| | - Jamil A Hashmi
- Center for Genetics and Inherited Diseases, Taibah University Almadinah Almunawwarah, Medina, Saudi Arabia
| | - Essa Alharby
- Center for Genetics and Inherited Diseases, Taibah University Almadinah Almunawwarah, Medina, Saudi Arabia
| | - Alia M Albalawi
- Center for Genetics and Inherited Diseases, Taibah University Almadinah Almunawwarah, Medina, Saudi Arabia
| | - Khushnooda Ramzan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University Almadinah Almunawwarah, Medina, Saudi Arabia.
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22
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Reeskamp LF, Balvers M, Peter J, van de Kerkhof L, Klaaijsen LN, Motazacker MM, Grefhorst A, van Riel NAW, Hovingh GK, Defesche JC, Zuurbier L. Intronic variant screening with targeted next-generation sequencing reveals first pseudoexon in LDLR in familial hypercholesterolemia. Atherosclerosis 2021; 321:14-20. [PMID: 33601267 DOI: 10.1016/j.atherosclerosis.2021.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 01/23/2023]
Abstract
BACKGROUND AND AIMS Familial hypercholesterolemia (FH) is caused by pathogenic variants in LDLR, APOB, or PCSK9 genes (designated FH+). However, a significant number of clinical FH patients do not carry these variants (designated FH-). Here, we investigated whether variants in intronic regions of LDLR attribute to FH by affecting pre-mRNA splicing. METHODS LDLR introns are partly covered in routine sequencing of clinical FH patients using next-generation sequencing. Deep intronic variants, >20 bp from intron-exon boundary, were considered of interest once (a) present in FH- patients (n = 909) with LDL-C >7 mmol/L (severe FH-) or after in silico analysis in patients with LDL-C >5 mmol/L (moderate FH-) and b) absent in FH + patients (control group). cDNA analysis and co-segregation analysis were performed to assess pathogenicity of the identified variants. RESULTS Three unique variants were present in the severe FH- group. One of these was the previously described likely pathogenic variant c.2140+103G>T. Three additional variants were selected based on in silico analyses in the moderate FH- group. One of these variants, c.2141-218G>A, was found to result in a pseudo-exon inclusion, producing a premature stop codon. This variant co-segregated with the hypercholesterolemic phenotype. CONCLUSIONS Through a screening approach, we identified a deep intronic variant causal for FH. This finding indicates that filtering intronic variants in FH- patients for the absence in FH + patients might enrich for true FH-causing variants and suggests that intronic regions of LDLR need to be considered for sequencing in FH- patients.
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Affiliation(s)
- Laurens F Reeskamp
- Department of Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Manon Balvers
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands; HORAIZON Technology BV, Delft, the Netherlands
| | - Jorge Peter
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Laura van de Kerkhof
- Department of Clinical Genetics, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Lisette N Klaaijsen
- Department of Clinical Genetics, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Mahdi M Motazacker
- Department of Clinical Genetics, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Aldo Grefhorst
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Natal A W van Riel
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - G Kees Hovingh
- Department of Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Joep C Defesche
- Department of Clinical Genetics, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Linda Zuurbier
- Department of Clinical Genetics, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands.
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23
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Kaur R, Attri SV, Saini AG, Sankhyan N. A high frequency and geographical distribution of MMACHC R132* mutation in children with cobalamin C defect. Amino Acids 2021; 53:253-264. [PMID: 33515116 DOI: 10.1007/s00726-021-02942-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 12/19/2020] [Indexed: 12/16/2022]
Abstract
Cobalamin C defect is caused by pathogenic variants in the MMACHC gene leading to impaired conversion of dietary vitamin B12 into methylcobalamin and adenosylcobalamin. Variants in the MMACHC gene cause accumulation of methylmalonic acid and homocysteine along with decreased methionine synthesis. The spectrum of MMACHC gene variants differs in various populations. A total of 19 North Indian children (age 0-18 years) with elevated methylmalonic acid and homocysteine were included in the study, and their DNA samples were subjected to Sanger sequencing of coding exons with flanking intronic regions of MMACHC gene. The genetic analysis resulted in the identification of a common pathogenic nonsense mutation, c.394C > T (R132*) in 85.7% of the unrelated cases with suspected cobalamin C defect. Two other known mutations c.347T > C (7%) and c.316G > A were also detected. Plasma homocysteine was significantly elevated (> 100 µmol/L) in 75% of the cases and methionine was decreased in 81% of the cases. Propionyl (C3)-carnitine, the primary marker for cobalamin C defect, was found to be elevated in only 43.75% of cases. However, the secondary markers such as C3/C2 and C3/C16 ratios were elevated in 87.5% and 100% of the cases, respectively. Neurological manifestations were the most common in our cohort. Our findings of the high frequency of a single MMACHC R132* mutation in cases with combined homocystinuria and methylmalonic aciduria may be proven helpful in designing a cost-effective and time-saving diagnostic strategy for resource-constraint settings. Since the R132* mutation is located near the last exon-exon junction, this is a potential target for the read-through therapeutics.
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Affiliation(s)
- Rajdeep Kaur
- Pediatric Biochemistry Unit, Department of Pediatrics, PGIMER, Chandigarh, 160012, India
| | - Savita Verma Attri
- Pediatric Biochemistry Unit, Department of Pediatrics, PGIMER, Chandigarh, 160012, India.
| | - Arushi Gahlot Saini
- Pediatric Neurology Unit, Department of Pediatrics, PGIMER, Chandigarh, India
| | - Naveen Sankhyan
- Pediatric Neurology Unit, Department of Pediatrics, PGIMER, Chandigarh, India
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24
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Molecular Insights into Determinants of Translational Readthrough and Implications for Nonsense Suppression Approaches. Int J Mol Sci 2020; 21:ijms21249449. [PMID: 33322589 PMCID: PMC7764779 DOI: 10.3390/ijms21249449] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/27/2020] [Accepted: 12/05/2020] [Indexed: 02/07/2023] Open
Abstract
The fidelity of protein synthesis, a process shaped by several mechanisms involving specialized ribosome regions and external factors, ensures the precise reading of sense and stop codons. However, premature termination codons (PTCs) arising from mutations may, at low frequency, be misrecognized and result in PTC suppression, named ribosome readthrough, with production of full-length proteins through the insertion of a subset of amino acids. Since some drugs have been identified as readthrough inducers, this fidelity drawback has been explored as a therapeutic approach in several models of human diseases caused by nonsense mutations. Here, we focus on the mechanisms driving translation in normal and aberrant conditions, the potential fates of mRNA in the presence of a PTC, as well as on the results obtained in the research of efficient readthrough-inducing compounds. In particular, we describe the molecular determinants shaping the outcome of readthrough, namely the nucleotide and protein context, with the latter being pivotal to produce functional full-length proteins. Through the interpretation of experimental and mechanistic findings, mainly obtained in lysosomal and coagulation disorders, we also propose a scenario of potential readthrough-favorable features to achieve relevant rescue profiles, representing the main issue for the potential translatability of readthrough as a therapeutic strategy.
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25
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Palma M, Lejeune F. Deciphering the molecular mechanism of stop codon readthrough. Biol Rev Camb Philos Soc 2020; 96:310-329. [PMID: 33089614 DOI: 10.1111/brv.12657] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 12/11/2022]
Abstract
Recognition of the stop codon by the translation machinery is essential to terminating translation at the right position and to synthesizing a protein of the correct size. Under certain conditions, the stop codon can be recognized as a coding codon promoting translation, which then terminates at a later stop codon. This event, called stop codon readthrough, occurs either by error, due to a dedicated regulatory environment leading to generation of different protein isoforms, or through the action of a readthrough compound. This review focuses on the mechanisms of stop codon readthrough, the nucleotide and protein environments that facilitate or inhibit it, and the therapeutic interest of stop codon readthrough in the treatment of genetic diseases caused by nonsense mutations.
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Affiliation(s)
- Martine Palma
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
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26
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van der Bijl N, Röpke A, Biswas U, Wöste M, Jessberger R, Kliesch S, Friedrich C, Tüttelmann F. Mutations in the stromal antigen 3 (STAG3) gene cause male infertility due to meiotic arrest. Hum Reprod 2020; 34:2112-2119. [PMID: 31682730 DOI: 10.1093/humrep/dez204] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/18/2019] [Indexed: 01/18/2023] Open
Abstract
STUDY QUESTION Are sequence variants in the stromal antigen 3 (STAG3) gene a cause for non-obstructive azoospermia (NOA) in infertile human males? SUMMARY ANSWER Sequence variants affecting protein function of STAG3 cause male infertility due to meiotic arrest. WHAT IS KNOWN ALREADY In both women and men, STAG3 encodes for a meiosis-specific protein that is crucial for the functionality of meiotic cohesin complexes. Sequence variants in STAG3 have been reported to cause meiotic arrest in male and female mice and premature ovarian failure in human females, but not in infertile human males so far. STUDY DESIGN, SIZE, DURATION The full coding region of STAG3 was sequenced directly in a cohort of 28 men with NOA due to meiotic arrest. In addition, a larger group of 275 infertile men that underwent whole-exome sequencing (WES) was screened for potential STAG3 sequence variants. Furthermore, meiotic spreads, immunohistochemistry, WES and population sampling probability (PSAP) have been conducted in the index case. PARTICIPANTS/MATERIALS, SETTING, METHODS This study included 28 infertile but otherwise healthy human males who underwent Sanger sequencing of the full coding region of STAG3. Additionally, WES data of 275 infertile human males with different infertility phenotypes have been screened for relevant STAG3 variants. All participants underwent karyotype analysis and azoospermia factor (AZF) screening in advance. In the index patient, segregation analysis, WES data, PSAP, lab parameters, testis histology and nuclear spreads have been added to suplort the findings. MAIN RESULTS AND THE ROLE OF CHANCE Two compound-heterozygous variants in STAG3 (c.[1262T>G];[1312C>T], p.[(Leu421Arg)];[(Arg438Ter)]) have been found to cause male infertility due to complete bilateral meiotic arrest in an otherwise healthy human male. Compound heterozygosity was confirmed by Sanger sequencing of the parents and the patient's brother. Other variants which may affect spermatogenesis have been ruled out through analysis of the patient's WES data and application of the PSAP pipeline. As expected from Stag3 knockout-mice meiotic spreads, germ cells did not develop further than zygotene and showed drastic chromosome aberrations. No rare variants in STAG3 were found in the 275 infertile males with other phenotypes. Our results indicate that STAG3 variants that negatively affect its protein function are a rare cause of NOA (<1% of cases). LIMITATIONS, REASONS FOR CAUTION We identified only one patient with compound-heterozygous variants in STAG3 causing NOA due to meiotic arrest. Future studies should evaluate STAG3 variants in larger cohorts to support this finding. WIDER IMPLICATIONS OF THE FINDINGS Identification of STAG3 sequence variants in infertile human males should improve genetic counselling as well as diagnostics and treatment. Especially before testicular sperm extraction (TESE) for ICSI, STAG3 variants should be ruled out to prevent unnecessary interventions with frustrating outcomes for both patients and clinicians. STUDY FUNDING/COMPETING INTEREST(S) This work was carried out within the frame of the German Research Foundation (DFG) Clinical Research Unit 'Male Germ Cells: from Genes to Function' (CRU326). Work in the laboratory of R.J. is supported by a grant of the European Union H2020 program GermAge. The authors declare no conflicts of interest. TRIAL REGISTRATION NUMBER Not applicable.
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Affiliation(s)
- N van der Bijl
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
| | - A Röpke
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
| | - U Biswas
- Institute of Physiological Chemistry, TU Dresden, 01307 Dresden, Germany
| | - M Wöste
- Institute of Medical Informatics, University of Münster, 48149 Münster, Germany
| | - R Jessberger
- Institute of Physiological Chemistry, TU Dresden, 01307 Dresden, Germany
| | - S Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, 48149 Münster, Germany
| | - C Friedrich
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
| | - F Tüttelmann
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany
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27
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Uchiyama H, Masunaga Y, Ishikawa T, Fukuoka T, Fukami M, Saitsu H, Ogata T. TSC1 intragenic deletion transmitted from a mosaic father to two siblings with cardiac rhabdomyomas: Identification of two aberrant transcripts. Eur J Med Genet 2020; 63:104060. [PMID: 32889144 DOI: 10.1016/j.ejmg.2020.104060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/10/2020] [Accepted: 08/31/2020] [Indexed: 10/23/2022]
Abstract
Tuberous sclerosis complex (TSC) is a rare autosomal dominant disorder characterized by non-cancerous tumors in multiple organs including the brain, kidney, lung, heart, and skin. We encountered a Japanese family consisting of two siblings (a four-year-old boy and a one-year-old girl) with multiple cardiac rhabdomyomas conveying a high risk of TSC and apparently unaffected sibling (a two-year-old girl) and parents. Whole exome sequencing and application of Integrative Genomic Viewer revealed an identical intragenic TSC1 deletion with the breakpoints on intron 15 and exon 19 in the affected siblings, but not in the apparently unaffected sibling and parents. Subsequently, PCR-based analyses were performed using primers flanking the deletion, showing that the deletion was also present in the father and that the deletion occurred between chr9:135,777,038 (bp) and chr9:135,780,540 (bp) in association with a one bp overlap. Furthermore, RT-PCR analyses were carried out using lymphoblastoid cell lines, revealing a major in-frame insertion/deletion transcript produced by aberrant splicing using a cryptic ″ag″ splice acceptor motif at intron 15 (r.1998_2438delinsTTCATTAGGTGG) and a minor frameshift transcript generated by aberrant splicing between exon 15 and exon 20 (r.1998_2502del, p.Lys666Asnfs*15) in the affected siblings. These findings imply that the intragenic deletion producing two aberrant transcripts was generated as a somatic pathogenic variant involving the germline in the father and was transmitted to the affected siblings.
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Affiliation(s)
- Hiroki Uchiyama
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yohei Masunaga
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takamichi Ishikawa
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tetsuya Fukuoka
- Department of Pediatrics, Shizuoka Saiseikai General Hospital, Shizuoka, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan.
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28
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Collin GB, Won J, Krebs MP, Hicks WJ, Charette JR, Naggert JK, Nishina PM. Disruption in murine Eml1 perturbs retinal lamination during early development. Sci Rep 2020; 10:5647. [PMID: 32221352 PMCID: PMC7101416 DOI: 10.1038/s41598-020-62373-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/09/2020] [Indexed: 11/23/2022] Open
Abstract
During mammalian development, establishing functional neural networks in stratified tissues of the mammalian central nervous system depends upon the proper migration and positioning of neurons, a process known as lamination. In particular, the pseudostratified neuroepithelia of the retina and cerebrocortical ventricular zones provide a platform for progenitor cell proliferation and migration. Lamination defects in these tissues lead to mispositioned neurons, disrupted neuronal connections, and abnormal function. The molecular mechanisms necessary for proper lamination in these tissues are incompletely understood. Here, we identified a nonsense mutation in the Eml1 gene in a novel murine model, tvrm360, displaying subcortical heterotopia, hydrocephalus and disorganization of retinal architecture. In the retina, Eml1 disruption caused abnormal positioning of photoreceptor cell nuclei early in development. Upon maturation, these ectopic photoreceptors possessed cilia and formed synapses but failed to produce robust outer segments, implying a late defect in photoreceptor differentiation secondary to mislocalization. In addition, abnormal positioning of Müller cell bodies and bipolar cells was evident throughout the inner neuroblastic layer. Basal displacement of mitotic nuclei in the retinal neuroepithelium was observed in tvrm360 mice at postnatal day 0. The abnormal positioning of retinal progenitor cells at birth and ectopic presence of photoreceptors and secondary neurons upon maturation suggest that EML1 functions early in eye development and is crucial for proper retinal lamination during cellular proliferation and development.
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Affiliation(s)
- G B Collin
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
| | - J Won
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
| | - M P Krebs
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
| | - W J Hicks
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
| | - J R Charette
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
| | - J K Naggert
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
| | - P M Nishina
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA.
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29
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2,6-Diaminopurine as a highly potent corrector of UGA nonsense mutations. Nat Commun 2020; 11:1509. [PMID: 32198346 PMCID: PMC7083880 DOI: 10.1038/s41467-020-15140-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/21/2020] [Indexed: 12/21/2022] Open
Abstract
Nonsense mutations cause about 10% of genetic disease cases, and no treatments are available. Nonsense mutations can be corrected by molecules with nonsense mutation readthrough activity. An extract of the mushroom Lepista inversa has recently shown high-efficiency correction of UGA and UAA nonsense mutations. One active constituent of this extract is 2,6-diaminopurine (DAP). In Calu-6 cancer cells, in which TP53 gene has a UGA nonsense mutation, DAP treatment increases p53 level. It also decreases the growth of tumors arising from Calu-6 cells injected into immunodeficient nude mice. DAP acts by interfering with the activity of a tRNA-specific 2′-O-methyltransferase (FTSJ1) responsible for cytosine 34 modification in tRNATrp. Low-toxicity and high-efficiency UGA nonsense mutation correction make DAP a good candidate for the development of treatments for genetic diseases caused by nonsense mutations. Nonsense mutations can be corrected by several molecules that activate readthrough of premature termination codon. Here, the authors report that 2,6-diaminopurine efficiently corrects UGA nonsense mutations with no significant toxicity.
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30
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Meyer C, Garzia A, Morozov P, Molina H, Tuschl T. The G3BP1-Family-USP10 Deubiquitinase Complex Rescues Ubiquitinated 40S Subunits of Ribosomes Stalled in Translation from Lysosomal Degradation. Mol Cell 2020; 77:1193-1205.e5. [PMID: 31981475 DOI: 10.1016/j.molcel.2019.12.024] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/11/2019] [Accepted: 12/20/2019] [Indexed: 02/05/2023]
Abstract
Ribosome-associated quality control (RQC) purges aberrant mRNAs and nascent polypeptides in a multi-step molecular process initiated by the E3 ligase ZNF598 through sensing of ribosomes collided at aberrant mRNAs and monoubiquitination of distinct small ribosomal subunit proteins. We show that G3BP1-family-USP10 complexes are required for deubiquitination of RPS2, RPS3, and RPS10 to rescue modified 40S subunits from programmed degradation. Knockout of USP10 or G3BP1 family proteins increased lysosomal ribosomal degradation and perturbed ribosomal subunit stoichiometry, both of which were rescued by a single K214R substitution of RPS3. While the majority of RPS2 and RPS3 monoubiquitination resulted from ZNF598-dependent sensing of ribosome collisions initiating RQC, another minor pathway contributed to their monoubiquitination. G3BP1 family proteins have long been considered RNA-binding proteins, however, our results identified 40S subunits and associated mRNAs as their predominant targets, a feature shared by stress granules to which G3BP1 family proteins localize under stress.
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Affiliation(s)
- Cindy Meyer
- Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY 10065, USA
| | - Aitor Garzia
- Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY 10065, USA
| | - Pavel Morozov
- Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, 1230 York Ave, Box 105, New York, NY 10065, USA
| | - Thomas Tuschl
- Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY 10065, USA.
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31
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Masunaga Y, Inoue T, Yamoto K, Fujisawa Y, Sato Y, Kawashima-Sonoyama Y, Morisada N, Iijima K, Ohata Y, Namba N, Suzumura H, Kuribayashi R, Yamaguchi Y, Yoshihashi H, Fukami M, Saitsu H, Kagami M, Ogata T. IGF2 Mutations. J Clin Endocrinol Metab 2020; 105:5572642. [PMID: 31544945 DOI: 10.1210/clinem/dgz034] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/20/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE IGF2 is a paternally expressed growth-promoting gene. Here, we report five cases with IGF2 mutations and review IGF2 mutation-positive patients described in the literature. We also compare clinical features between patients with IGF2 mutations and those with H19/IGF2:IG-DMR epimutations. RESULTS We recruited five cases with IGF2 mutations: case 1 with a splice site mutation (c.-6-1G>C) leading to skipping of exon 2 and cases 2-5 with different missense mutations (p.(Cys70Tyr), p.(Cys71Arg), p.(Cys33Ser), and p.(Cys45Ser)) affecting cysteine residues involved in the S-S bindings. All the mutations resided on the paternally inherited allele, and the mutation of case 5 was present in a mosaic condition. Clinical assessment revealed Silver-Russell syndrome (SRS) phenotype with Netchine-Harbison scores of ≥5/6 in all the apparently nonmosaic 14 patients with IGF2 mutations (cases 1-4 described in this study and 10 patients reported in the literature). Furthermore, compared with H19/IGF2:IG-DMR epimutations, IGF2 mutations were associated with low frequency of hemihypoplasia, high frequency of feeding difficulty and/or reduced body mass index, and mild degree of relative macrocephaly, together with occasional development of severe limb malformations, high frequency of cardiovascular anomalies and developmental delay, and low serum IGF-II values. CONCLUSIONS This study indicates that IGF2 mutations constitute a rare but important cause of SRS. Furthermore, while both IGF2 mutations and H19/IGF2:IG-DMR epimutations lead to SRS, a certain degree of phenotypic difference is observed between the two groups, probably due to the different IGF2 expression pattern in target tissues.
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Affiliation(s)
- Yohei Masunaga
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takanobu Inoue
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kaori Yamoto
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yasuko Fujisawa
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yasuhiro Sato
- Department of Pediatrics, Teikyo University School of Medicine, Tokyo, Japan
| | - Yuki Kawashima-Sonoyama
- Division of Pediatrics and Perinatology, Faculty of Medicine Tottori University, Yonago, Japan
| | - Naoya Morisada
- Department of Clinical Genetics, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yasuhisa Ohata
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Noriyuki Namba
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Pediatrics, Osaka Hospital, Japan Community Healthcare Organization, Osaka, Japan
| | - Hiroshi Suzumura
- Department of Pediatrics, Dokkyo Medical University, Mibu, Japan
| | | | - Yu Yamaguchi
- Department of Genetics, Gunma Children's Medical Center, Shibukawa, Japan
| | - Hiroshi Yoshihashi
- Department of Clinical Genetics, Tokyo Metropolitan Children's Medical Center, Fuchu, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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Peled A, Samuelov L, Sarig O, Bochner R, Malki L, Pavlovsky M, Pichinuk E, Weil M, Sprecher E. Treatment of hereditary hypotrichosis simplex of the scalp with topical gentamicin. Br J Dermatol 2019; 183:114-120. [DOI: 10.1111/bjd.18718] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2019] [Indexed: 12/11/2022]
Affiliation(s)
- A. Peled
- Division of Dermatology Tel Aviv Sourasky Medical Center Tel Aviv Israel
- Department of Human Molecular Genetics and Biochemistry Tel Aviv University Tel Aviv Israel
| | - L. Samuelov
- Division of Dermatology Tel Aviv Sourasky Medical Center Tel Aviv Israel
| | - O. Sarig
- Division of Dermatology Tel Aviv Sourasky Medical Center Tel Aviv Israel
| | - R. Bochner
- Division of Dermatology Tel Aviv Sourasky Medical Center Tel Aviv Israel
| | - L. Malki
- Division of Dermatology Tel Aviv Sourasky Medical Center Tel Aviv Israel
- Department of Human Molecular Genetics and Biochemistry Tel Aviv University Tel Aviv Israel
| | - M. Pavlovsky
- Division of Dermatology Tel Aviv Sourasky Medical Center Tel Aviv Israel
| | - E. Pichinuk
- Blavatnik Center for Drug Discovery Tel Aviv University Tel Aviv Israel
| | - M. Weil
- Blavatnik Center for Drug Discovery Tel Aviv University Tel Aviv Israel
| | - E. Sprecher
- Division of Dermatology Tel Aviv Sourasky Medical Center Tel Aviv Israel
- Department of Human Molecular Genetics and Biochemistry Tel Aviv University Tel Aviv Israel
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33
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Reeskamp LF, Hartgers ML, Peter J, Dallinga-Thie GM, Zuurbier L, Defesche JC, Grefhorst A, Hovingh GK. A Deep Intronic Variant in LDLR in Familial Hypercholesterolemia. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 11:e002385. [PMID: 30562117 DOI: 10.1161/circgen.118.002385] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Familial hypercholesterolemia (FH) is an inherited disorder characterized by high plasma LDL-C (low-density lipoprotein-cholesterol) levels. The vast majority of FH patients carry a mutation in the coding region of LDLR, APOB, or PCSK9. We set out to identify the culprit genetic defect in a large family with clinical FH, in whom no mutations were identified in the coding regions of these FH genes. METHODS Whole genome sequencing was performed in 5 affected and 4 unaffected individuals from a family with an unexplained autosomal dominant FH trait. The effect on splicing of the identified novel intronic LDLR mutation was ascertained by cDNA sequencing. The prevalence of the novel variant was assessed in 1 245 FH patients without an FH causing mutation identified by Sanger sequencing and in 2 154 patients referred for FH analysis by next-generation sequencing (covering the intronic region). RESULTS A novel deep intronic variant in LDLR (c.2140+103G>T) was found to cosegregate with high LDL-C in 5 patients, but was not present in 4 unaffected family members. The variant was shown to result in a 97 nucleotides insertion leading to a frameshift and premature stop codon in exon 15 of LDLR. The prevalence of the intronic variant was 0.24% (3/1245) in a cohort of FH patients without a known FH causing mutation and 0.23% (5/2154) in a population of FH patients referred for analysis by next-generation sequencing. Cosegregation analysis of a second family showed full penetrance of the novel variant with the FH phenotype over 3 generations. CONCLUSIONS The c.2140+103G>T mutation in LDLR is a novel intronic variant identified in FH that cosegregates with the FH phenotype. Our findings underline the need to analyze the intronic regions of LDLR in patients with FH, especially those in whom no mutation is found in the coding regions of LDLR, APOB, or PCSK9.
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Affiliation(s)
- Laurens F Reeskamp
- Department of Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands (L.F.R., M.L.H., G.M.D.-T., G.K.H.)
| | - Merel L Hartgers
- Department of Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands (L.F.R., M.L.H., G.M.D.-T., G.K.H.)
| | - Jorge Peter
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands (J.P., G.M.D.-T., A.G.)
| | - Geesje M Dallinga-Thie
- Department of Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands (L.F.R., M.L.H., G.M.D.-T., G.K.H.).,Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands (J.P., G.M.D.-T., A.G.)
| | - Linda Zuurbier
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands (L.Z., J.C.D.)
| | - Joep C Defesche
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands (L.Z., J.C.D.)
| | - Aldo Grefhorst
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands (J.P., G.M.D.-T., A.G.)
| | - G Kees Hovingh
- Department of Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands (L.F.R., M.L.H., G.M.D.-T., G.K.H.)
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Yamoto K, Saitsu H, Nishimura G, Kosaki R, Takayama S, Haga N, Tonoki H, Okumura A, Horii E, Okamoto N, Suzumura H, Ikegawa S, Kato F, Fujisawa Y, Nagata E, Takada S, Fukami M, Ogata T. Comprehensive clinical and molecular studies in split-hand/foot malformation: identification of two plausible candidate genes (LRP6 and UBA2). Eur J Hum Genet 2019; 27:1845-1857. [PMID: 31332306 DOI: 10.1038/s41431-019-0473-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/27/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022] Open
Abstract
Split-hand/foot malformation (SHFM) is a clinically and genetically heterogeneous condition. We sequentially performed screening of the previously identified Japanese founder 17p13.3 duplication/triplication involving BHLHA9, array comparative genomic hybridization, and whole exome sequencing (WES) in newly recruited 41 Japanese families with non-syndromic and syndromic SHFM. We also carried out WES in seven families with nonsyndromic and syndromic SHFM in which underlying genetic causes including pathogenic copy-number variants (CNVs) remained undetected in our previous studies of 56 families. Consequently, we identified not only known pathogenic CNVs (17p13.3 duplications/triplications [n = 21], 2q31 deletion [n = 1], and 10q24 duplications [n = 3]) and rare variants in known causative genes (TP63 [n = 3], DLX5 [n = 1], IGF2 [n = 1], WNT10B [n = 3], WNT10B/PORCN [n = 1], and PORCN [n = 1]), but also a de novo 19q13.11 deletion disrupting UBA2 (n = 1) and variants that probably affect function in LRP6 (n = 1) and UBA2 (n = 1). Thus, together with our previous data based on testing of 56 families, molecular studies for a total of 97 families with SHFM revealed underlying genetic causes in 75 families, and clinical studies for the 75 families indicated a certain degree of correlation between genetic causes and phenotypes. The results imply that SHFM primarily occurs as a genetic disorder with genotype-phenotype correlations. Furthermore, the results together with previous data such as the development of SHFM in Lrp6 knockout mice, the presence of SHFM in two subjects with 19q13 deletions involving UBA2, and strong mouse Uba2 expression in the developing limb buds, imply that LRP6 and UBA2 represent plausible candidate genes for SHFM.
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Affiliation(s)
- Kaori Yamoto
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Gen Nishimura
- Center for Intractable Diseases, Saitama Medical University Hospital, Iruma, Japan
| | - Rika Kosaki
- Division of Medical Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Shinichiro Takayama
- Division of Orthopedic Surgery, National Center for Child Health and Development, Tokyo, Japan
| | - Nobuhiko Haga
- Department of Rehabilitation Medicine, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Hidefumi Tonoki
- Department of Pediatrics, Sapporo Tenshi Hospital, Sapporo, Japan
| | - Akihisa Okumura
- Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Emiko Horii
- Department of Orthopedic Surgery, Nagoya First Red Cross Hospital, Nagoya, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Hiroshi Suzumura
- Department of Pediatrics, Dokkyo Medical University School of Medicine, Mibu, Japan
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - Fumiko Kato
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yasuko Fujisawa
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Eiko Nagata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan. .,Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.
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35
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Mendez AS, Vogt C, Bohne J, Glaunsinger BA. Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX. Nucleic Acids Res 2019; 46:11968-11979. [PMID: 30321376 PMCID: PMC6294519 DOI: 10.1093/nar/gky932] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/04/2018] [Indexed: 12/24/2022] Open
Abstract
A number of viruses remodel the cellular gene expression landscape by globally accelerating messenger RNA (mRNA) degradation. Unlike the mammalian basal mRNA decay enzymes, which largely target mRNA from the 5′ and 3′ end, viruses instead use endonucleases that cleave their targets internally. This is hypothesized to more rapidly inactivate mRNA while maintaining selective power, potentially though the use of a targeting motif(s). Yet, how mRNA endonuclease specificity is achieved in mammalian cells remains largely unresolved. Here, we reveal key features underlying the biochemical mechanism of target recognition and cleavage by the SOX endonuclease encoded by Kaposi's sarcoma-associated herpesvirus (KSHV). Using purified KSHV SOX protein, we reconstituted the cleavage reaction in vitro and reveal that SOX displays robust, sequence-specific RNA binding to residues proximal to the cleavage site, which must be presented in a particular structural context. The strength of SOX binding dictates cleavage efficiency, providing an explanation for the breadth of mRNA susceptibility observed in cells. Importantly, we establish that cleavage site specificity does not require additional cellular cofactors, as had been previously proposed. Thus, viral endonucleases may use a combination of RNA sequence and structure to capture a broad set of mRNA targets while still preserving selectivity.
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Affiliation(s)
- Aaron S Mendez
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Carolin Vogt
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, USA
- Hannover Medical School Institute of Virology, Hannover, Germany
| | - Jens Bohne
- Hannover Medical School Institute of Virology, Hannover, Germany
| | - Britt A Glaunsinger
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- To whom correspondence should be addressed. Tel: +1 510 642 5427;
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36
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Yabe SG, Nishida J, Fukuda S, Takeda F, Nasiro K, Yasuda K, Iwasaki N, Okochi H. Expression of mutant mRNA and protein in pancreatic cells derived from MODY3- iPS cells. PLoS One 2019; 14:e0217110. [PMID: 31145732 PMCID: PMC6542550 DOI: 10.1371/journal.pone.0217110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/03/2019] [Indexed: 12/12/2022] Open
Abstract
Maturity-onset diabetes of the young (MODY) is a heterozygous monogenic diabetes; more than 14 disease genes have been identified. However, the pathogenesis of MODY is not fully understood because the patients' pancreatic beta cells are inaccessible. To elucidate the pathology of MODY, we established MODY3 patient-derived iPS (MODY3-iPS) cells using non-integrating Sendai virus (SeV) vector and examined the mutant mRNA and protein of HNF1A (Hepatocyte Nuclear factor 1A) after pancreatic lineage differentiation. Our patient had a cytosine insertion in the HNF1A gene (P291fsinsC) causing frameshift and making a premature termination codon (PTC). We confirmed these MODY3-iPS cells possessed the characteristics of pluripotent stem cells. After we differentiated them into pancreatic beta cells, transcripts of HNF1A gene were cloned and sequenced. We found that P291fsinsC mutant transcripts were much less frequent than wild ones, but they increased after adding cycloheximide (CHX) to the medium. These results suggested that mutant mRNA was destroyed by nonsense-mediated mRNA decay (NMD). Moreover, we were not able to detect any band of mutant proteins in pancreatic lineage cells which were differentiated from MODY3-iPSCs by western blot (WB) analysis. A scarcity of the truncated form of mutant protein may indicate that MODY3 might be caused by a haplo-insufficiency effect rather than a dominant negative manner.
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Affiliation(s)
- Shigeharu G. Yabe
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Junko Nishida
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Satsuki Fukuda
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Fujie Takeda
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kiyoko Nasiro
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuki Yasuda
- Department of Metabolic Disorders, Diabetes Research Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Naoko Iwasaki
- Institute of Geriatrics, Diabetes Center, Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
| | - Hitoshi Okochi
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
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37
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Treating Rett syndrome: from mouse models to human therapies. Mamm Genome 2019; 30:90-110. [PMID: 30820643 PMCID: PMC6606665 DOI: 10.1007/s00335-019-09793-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/09/2019] [Indexed: 02/06/2023]
Abstract
Rare diseases are very difficult to study mechanistically and to develop therapies for because of the scarcity of patients. Here, the rare neuro-metabolic disorder Rett syndrome (RTT) is discussed as a prototype for precision medicine, demonstrating how mouse models have led to an understanding of the development of symptoms. RTT is caused by mutations in the X-linked gene methyl-CpG-binding protein 2 (MECP2). Mecp2-mutant mice are being used in preclinical studies that target the MECP2 gene directly, or its downstream pathways. Importantly, this work may improve the health of RTT patients. Clinical presentation may vary widely among individuals based on their mutation, but also because of the degree of X chromosome inactivation and the presence of modifier genes. Because it is a complex disorder involving many organ systems, it is likely that recovery of RTT patients will involve a combination of treatments. Precision medicine is warranted to provide the best efficacy to individually treat RTT patients.
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38
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Clarke LA, Awatade NT, Felício VM, Silva IA, Calucho M, Pereira L, Azevedo P, Cavaco J, Barreto C, Bertuzzo C, Gartner S, Beekman J, Amaral MD. The effect of premature termination codon mutations on CFTR mRNA abundance in human nasal epithelium and intestinal organoids: a basis for read-through therapies in cystic fibrosis. Hum Mutat 2018; 40:326-334. [PMID: 30488522 DOI: 10.1002/humu.23692] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/08/2018] [Accepted: 11/27/2018] [Indexed: 02/06/2023]
Abstract
A major challenge in cystic fibrosis (CF) research is applying mutation-specific therapy to individual patients with diverse and rare CF transmembrane conductance regulator (CFTR) genotypes. Read-through agents are currently the most promising approach for Class I mutations that introduce premature termination codons (PTCs) into CFTR mRNA. However, variations in degradation of PTC containing transcripts by nonsense mediated decay (NMD) might lower read-through efficacy. Allele specific quantitative real time (qRT)-PCR was used to measure variations in CFTR mRNA abundance for several PTC mutations in respiratory cells and intestinal organoids. The majority of PTC mutations were associated with reduced levels of relative mRNA transcript abundance (∼33% and 26% of total CFTR mRNA in respiratory cells and intestinal organoids, respectively, compared to >50% for non-PTC causing mutations). These levels were generally not affected by PTC mutation type or position, but there could be twofold variations between individuals bearing the same genotype. Most PTC mutations in CFTR are subject to similar levels of NMD, which reduce but do not abolish PTC bearing mRNAs. Measurement of individual NMD levels in intestinal organoids and HNE cells might, therefore, be useful in predicting efficacy of PTC read-through in the context of personalized CFTR modulator therapy.
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Affiliation(s)
- Luka A Clarke
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
| | - Nikhil T Awatade
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
| | - Veronica M Felício
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
| | - Iris A Silva
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
| | - Maite Calucho
- Pediatric Pulmonology & CF Unit. Hospital Universitari, Vall d'Hebron, Spain
| | - Luisa Pereira
- Department of Pediatrics, Hospital de Santa Maria, Lisboa, Portugal
| | - Pilar Azevedo
- Department of Pediatrics, Hospital de Santa Maria, Lisboa, Portugal
| | - José Cavaco
- Centro de Referência de Fibrose Quística, Hospital de Dona Estefânia, Centro Hospitalar de Lisboa Central, Lisboa, Portugal
| | - Celeste Barreto
- Department of Pediatrics, Hospital de Santa Maria, Lisboa, Portugal
| | - Carmen Bertuzzo
- Human Genetics Department, Faculty of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Silvia Gartner
- Pediatric Pulmonology & CF Unit. Hospital Universitari, Vall d'Hebron, Spain
| | - Jeffrey Beekman
- Department of Pediatric Pulmonology, UMCU, Utrecht, Netherlands
| | - Margarida D Amaral
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
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Sharma N, Evans TA, Pellicore MJ, Davis E, Aksit MA, McCague AF, Joynt AT, Lu Z, Han ST, Anzmann AF, Lam ATN, Thaxton A, West N, Merlo C, Gottschalk LB, Raraigh KS, Sosnay PR, Cotton CU, Cutting GR. Capitalizing on the heterogeneous effects of CFTR nonsense and frameshift variants to inform therapeutic strategy for cystic fibrosis. PLoS Genet 2018; 14:e1007723. [PMID: 30444886 PMCID: PMC6267994 DOI: 10.1371/journal.pgen.1007723] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 11/30/2018] [Accepted: 09/28/2018] [Indexed: 12/18/2022] Open
Abstract
CFTR modulators have revolutionized the treatment of individuals with cystic fibrosis (CF) by improving the function of existing protein. Unfortunately, almost half of the disease-causing variants in CFTR are predicted to introduce premature termination codons (PTC) thereby causing absence of full-length CFTR protein. We hypothesized that a subset of nonsense and frameshift variants in CFTR allow expression of truncated protein that might respond to FDA-approved CFTR modulators. To address this concept, we selected 26 PTC-generating variants from four regions of CFTR and determined their consequences on CFTR mRNA, protein and function using intron-containing minigenes expressed in 3 cell lines (HEK293, MDCK and CFBE41o-) and patient-derived conditionally reprogrammed primary nasal epithelial cells. The PTC-generating variants fell into five groups based on RNA and protein effects. Group A (reduced mRNA, immature (core glycosylated) protein, function <1% (n = 5)) and Group B (normal mRNA, immature protein, function <1% (n = 10)) variants were unresponsive to modulator treatment. However, Group C (normal mRNA, mature (fully glycosylated) protein, function >1% (n = 5)), Group D (reduced mRNA, mature protein, function >1% (n = 5)) and Group E (aberrant RNA splicing, mature protein, function > 1% (n = 1)) variants responded to modulators. Increasing mRNA level by inhibition of NMD led to a significant amplification of modulator effect upon a Group D variant while response of a Group A variant was unaltered. Our work shows that PTC-generating variants should not be generalized as genetic 'nulls' as some may allow generation of protein that can be targeted to achieve clinical benefit.
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Affiliation(s)
- Neeraj Sharma
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Taylor A. Evans
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Matthew J. Pellicore
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Emily Davis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Melis A. Aksit
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Allison F. McCague
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Anya T. Joynt
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Zhongzhu Lu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sangwoo T. Han
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Arianna F. Anzmann
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Anh-Thu N. Lam
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Abigail Thaxton
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Natalie West
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Christian Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Laura B. Gottschalk
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Karen S. Raraigh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Patrick R. Sosnay
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Calvin U. Cotton
- Departments of Pediatrics, Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Garry R. Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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40
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Miura T, Mezaki N, Konno T, Iwasaki A, Hara N, Miura M, Funayama M, Unai Y, Tashiro Y, Okita K, Kihara T, Ito N, Kanatsuka Y, Jones DT, Hara N, Ishiguro T, Tokutake T, Kasuga K, Nozaki H, Dickson DW, Onodera O, Wszolek ZK, Ikeuchi T. Identification and functional characterization of novel mutations including frameshift mutation in exon 4 of CSF1R in patients with adult-onset leukoencephalopathy with axonal spheroids and pigmented glia. J Neurol 2018; 265:2415-2424. [PMID: 30136118 PMCID: PMC6182692 DOI: 10.1007/s00415-018-9017-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/01/2018] [Accepted: 08/06/2018] [Indexed: 11/30/2022]
Abstract
Objective Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) is caused by mutations in CSF1R. Pathogenic mutations in exons 12–22 including coding sequence of the tyrosine kinase domain (TKD) of CSF1R were previously identified. We aimed to identify CSF1R mutations in patients who were clinically suspected of having ALSP and to determine the pathogenicity of novel CSF1R variants. Methods Sixty-one patients who fulfilled the diagnostic criteria of ALSP were included in this study. Genetic analysis of CSF1R was performed for all the coding exons. The haploinsufficiency of CSF1R was examined for frameshift mutations by RT-PCR. Ligand-dependent autophosphorylation of CSF1R was examined in cells expressing CSF1R mutants. Results We identified ten variants in CSF1R including two novel frameshift, five novel missense, and two known missense mutations as well as one known missense variant. Eight mutations were located in TKD. One frameshift mutation (p.Pro104LeufsTer8) and one missense variant (p.His362Arg) were located in the extracellular domain. RT-PCR analysis revealed that the frameshift mutation of p.Pro104LeufsTer8 caused nonsense-mediated mRNA decay. Functional assay revealed that none of the mutations within TKD showed autophosphorylation of CSF1R. The p.His362Arg variant located in the extracellular domain showed comparable autophosphorylation of CSF1R to the wild type, suggesting that this variant is not likely pathogenic. Conclusions The detection of the CSF1R mutation outside of the region-encoding TKD may extend the genetic spectrum of ALSP with CSF1R mutations. Mutational analysis of all the coding exons of CSF1R should be considered for patients clinically suspected of having ALSP. Electronic supplementary material The online version of this article (10.1007/s00415-018-9017-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Takeshi Miura
- Department of Molecular Genetics, Brain Research Institute, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata, 951-8585, Japan.,Department of Neurology, Brain Research Institute, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata, 951-8585, Japan
| | - Naomi Mezaki
- Department of Molecular Genetics, Brain Research Institute, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata, 951-8585, Japan.,Department of Neurology, Brain Research Institute, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata, 951-8585, Japan
| | - Takuya Konno
- Department of Neurology, Brain Research Institute, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata, 951-8585, Japan.,Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Akio Iwasaki
- Department of Neurology, Dokkyo Medical University, 880 Kitakobayashi, Mibu-machi, Shimotsuga, 321-0293, Japan
| | - Naoyuki Hara
- Department of Clinical Neuroscience and Therapeutics, Hiroshima University Graduate School of Biomedical and Health Science, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Masatomo Miura
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo,Chuo-ku, Kumamoto, 860-8555, Japan
| | - Michitaka Funayama
- Department of Neuropsychiatry, Ashikaga Red Cross Hospital, 284-1 Yobe, Ashikaga, 326-0843, Japan
| | - Yuki Unai
- Department of Neurology, Sumitomo Hospital, 5-3-20 Nakanoshima, Kita-ku, Osaka, 530-0005, Japan
| | - Yuichi Tashiro
- Department of Neurology, National Hospital Organization Mito Medical Center, 280 Sakuranosato, Ibarakimachi, Higashiibaraki, 311-3193, Japan
| | - Kenji Okita
- Department of Neurology, Nagoya City University Graduate School of Medical Sciences, Kawasumi 1-40, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Takeshi Kihara
- Department of Neurology, Rakuwakai Otowa Rehabilitation Hospital, 32-1 Koyamakitamizocho, Yamashina-ku, Kyoto, 607-8113, Japan
| | - Nobuo Ito
- Department of Neurology, Suzuka General Hospital, 1275-53 Yamanohana, Yasuzukacho, Suzuka, 513-8630, Japan
| | - Yoichi Kanatsuka
- Department of Neurology, Yokohama Municipal Citizen's Hospital, 56 Okazawacho, Hodogaya-ku, Yokohama, 240-8555, Japan
| | - David T Jones
- Department of Neurology, Mayo Clinic, 200 First Street S.W., Rochester, MN, 55905, USA
| | - Norikazu Hara
- Department of Molecular Genetics, Brain Research Institute, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata, 951-8585, Japan
| | - Takanobu Ishiguro
- Department of Molecular Genetics, Brain Research Institute, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata, 951-8585, Japan.,Department of Neurology, Brain Research Institute, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata, 951-8585, Japan
| | - Takayoshi Tokutake
- Department of Neurology, Brain Research Institute, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata, 951-8585, Japan
| | - Kensaku Kasuga
- Department of Molecular Genetics, Brain Research Institute, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata, 951-8585, Japan
| | - Hiroaki Nozaki
- Graduate School of Health Sciences, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata, 951-8585, Japan
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Osamu Onodera
- Department of Neurology, Brain Research Institute, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata, 951-8585, Japan
| | - Zbigniew K Wszolek
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Takeshi Ikeuchi
- Department of Molecular Genetics, Brain Research Institute, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata, 951-8585, Japan.
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41
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Balak C, Belnap N, Ramsey K, Joss S, Devriendt K, Naymik M, Jepsen W, Siniard AL, Szelinger S, Parker ME, Richholt R, Izatt T, LaFleur M, Terraf P, Llaci L, De Both M, Piras IS, Rangasamy S, Schrauwen I, Craig DW, Huentelman M, Narayanan V. A novel
FBXO28
frameshift mutation in a child with developmental delay, dysmorphic features, and intractable epilepsy: A second gene that may contribute to the 1q41‐q42 deletion phenotype. Am J Med Genet A 2018; 176:1549-1558. [DOI: 10.1002/ajmg.a.38712] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Chris Balak
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Newell Belnap
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Keri Ramsey
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Shelagh Joss
- West of Scotland Genetics ServiceQueen Elizabeth University HospitalGlasgow United Kingdom
| | - Koen Devriendt
- Center for Human Genetics (Centrum Menselijke Erfelijkheid)University of LeuvenLeuven Belgium
| | - Marcus Naymik
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Wayne Jepsen
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Ashley L. Siniard
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Szabolcs Szelinger
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
- UCLA Pathology & Laboratory MedicineUCLA Center for the Health SciencesLos Angeles California
| | - Mary E. Parker
- Department of Physical TherapyTexas State UniversitySan Marcos Texas
- U.R. Our Hope, Undiagnosed and Rare Disorder OrganizationAustin Texas
| | - Ryan Richholt
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Tyler Izatt
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Madison LaFleur
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Panieh Terraf
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Lorida Llaci
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Matt De Both
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Ignazio S. Piras
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Sampathkumar Rangasamy
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Isabelle Schrauwen
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
- Department of Molecular and Human Genetics, Center for Statistical GeneticsBaylor College of MedicineHouston Texas
| | - David W. Craig
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
- Department of Translational GenomicsKeck School of Medicine of USCLos Angeles California
| | - Matt Huentelman
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Vinodh Narayanan
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
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42
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Dabrowski M, Bukowy-Bieryllo Z, Zietkiewicz E. Advances in therapeutic use of a drug-stimulated translational readthrough of premature termination codons. Mol Med 2018; 24:25. [PMID: 30134808 PMCID: PMC6016875 DOI: 10.1186/s10020-018-0024-7] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/01/2018] [Indexed: 12/31/2022] Open
Abstract
Premature termination codons (PTCs) in the coding regions of mRNA lead to the incorrect termination of translation and generation of non-functional, truncated proteins. Translational readthrough of PTCs induced by pharmaceutical compounds is a promising way of restoring functional protein expression and reducing disease symptoms, without affecting the genome or transcriptome of the patient. While in some cases proven effective, the clinical use of readthrough-inducing compounds is still associated with many risks and difficulties. This review focuses on problems directly associated with compounds used to stimulate PTC readthrough, such as their interactions with the cell and organism, their toxicity and bioavailability (cell permeability; tissue deposition etc.). Various strategies designed to overcome these problems are presented.
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Affiliation(s)
- Maciej Dabrowski
- Institute of Human Genetics; Polish Academy of Sciences, Poznan, Poland
| | | | - Ewa Zietkiewicz
- Institute of Human Genetics; Polish Academy of Sciences, Poznan, Poland.
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43
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Al-Ashwal AA, Al-Sagheir A, Ramzan K, Al-Owain M, Allam R, Qari A, Al-Numair NS, Imtiaz F. Clinical, Endocrine, and Molecular Genetic Analysis of a Large Cohort of Saudi Arabian Patients with Laron Syndrome. Horm Res Paediatr 2018; 88:119-126. [PMID: 28743110 DOI: 10.1159/000475991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/24/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND/AIMS Laron syndrome (LS) is an autosomal recessive disease characterized by marked short stature and very low serum IGF-1 and IGFBP-3 levels. This study assessed the clinical and endocrine features alongside determining the growth hormone receptor gene (GHR) mutation in Saudi Arabian patients with LS in order to establish whether or not a genotype/phenotype correlation is evident in this large cohort. SUBJECTS AND METHODS A total of 40 Saudi Arabian patients with a suspected diagnosis of LS were recruited and subjected to a full clinical and endocrine investigation together with direct sequencing of the coding regions of the GHR gene. RESULTS GHR mutations were identified in 34 patients from 22 separate nuclear families. All 34 molecularly confirmed patients had the typical clinical and endocrinological manifestations of LS. Eleven different mutations (9 previously unreported) were detected in this cohort of patients, all inherited in an autosomal recessive homozygous form. No genotype/phenotype correlation was apparent. CONCLUSION The identification of pathogenic mutations causing LS will be of tremendous use for the molecular diagnosis of patients in Saudi Arabia and the region in general, with respect to prevention of this disease in the forms of future carrier testing, prenatal testing, premarital screening and preimplantation genetic diagnosis.
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Affiliation(s)
- Abdullah A Al-Ashwal
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Afaf Al-Sagheir
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Khushnooda Ramzan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rabab Allam
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Alya Qari
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nouf S Al-Numair
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Faiqa Imtiaz
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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44
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Nakamura S, Kobori Y, Ueda Y, Tanaka Y, Ishikawa H, Yoshida A, Katsumi M, Saito K, Nakamura A, Ogata T, Okada H, Nakai H, Miyado M, Fukami M. STX2 is a causative gene for nonobstructive azoospermia. Hum Mutat 2018; 39:830-833. [PMID: 29570232 DOI: 10.1002/humu.23423] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/08/2018] [Accepted: 03/08/2018] [Indexed: 12/29/2022]
Abstract
STX2 encodes a sulfoglycolipid transporter. Although Stx2 nullizygosity is known to cause spermatogenic failure in mice, STX2 mutations have not been identified in humans. Here, we performed STX2 mutation analysis for 131 Japanese men clinically diagnosed with nonobstructive azoospermia. As a result, we identified a homozygous frameshift mutation [c.8_12delACCGG, p.(Asp3Alafs*8)] in one patient. The mutation-positive patient exhibited loss-of-heterozygosity for 58.4 Mb genomic regions involving STX2, suggesting possible parental consanguinity. The patient showed azoospermia, relatively small testes, and a mildly elevated follicle stimulating hormone level, but no additional clinical features. Testicular histology of the patient showed universal maturation arrest and multinucleated spermatocytes, which have also been observed in mice lacking Stx2. PCR-based cDNA screening revealed wildtype STX2 expression in various tissues including the testis. Our results indicate that STX2 nullizygosity results in nonsyndromic maturation arrest with multinucleated spermatocytes, and accounts for a small fraction of cases with nonobstructive azoospermia.
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Affiliation(s)
- Shigeru Nakamura
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatric Urology, Jichi Medical University, Children's Medical Center Tochigi, Tochigi, Japan
| | - Yoshitomo Kobori
- Department of Urology, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Yoshihiko Ueda
- Department of Pathology, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Yoko Tanaka
- Department of Pediatrics, Tokyo Dental College Ichikawa General Hospital, Ichikawa, Japan
| | - Hiromichi Ishikawa
- Reproduction Center, Tokyo Dental College Ichikawa General Hospital, Ichikawa, Japan
| | | | - Momori Katsumi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuki Saito
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akie Nakamura
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hiroshi Okada
- Department of Urology, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Hideo Nakai
- Department of Pediatric Urology, Jichi Medical University, Children's Medical Center Tochigi, Tochigi, Japan
| | - Mami Miyado
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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45
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van der Schoot V, de Munnik S, Venselaar H, Elting M, Mancini GMS, Ravenswaaij-Arts CMA, Anderlid BM, Brunner HG, Stevens SJC. Toward clinical and molecular understanding of pathogenic variants in the ZBTB18 gene. Mol Genet Genomic Med 2018; 6:393-400. [PMID: 29573576 PMCID: PMC6014478 DOI: 10.1002/mgg3.387] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 12/25/2022] Open
Abstract
Background Patients with pathogenic variants in ZBTB18 present with Intellectual Disability (ID) with frequent co‐occurrence of corpus callosum (CC) anomalies, hypotonia, microcephaly, growth problems and variable facial dysmorphologies. These features illustrate a key role for ZBTB18 in brain development. Methods Patients with a pathogenic variant in ZBTB18 were detected by diagnostic whole exome sequencing (WES) performed in our center. We reviewed the literature and used GeneMatcher to include other cases. YASARA and WHAT IF were used to provide insight into the structural effect of missense variants located in the C2H2 zinc finger domains of the ZBTB18 protein. Results We give a complete overview of pathogenic variants in ZBTB18 detected to date, showing inconsistent presence of clinical features, including CC anomalies. We present four new cases with a de novo pathogenic variant in the ZBTB18 gene, including the fourth case in which a de novo p.Arg464His variant was found. Conclusion Homology modeling of protein structure points to a variable degree of impaired DNA binding caused by missense variants in these domains probably leading to Loss of Function (LoF). Putative partial LoF may present with a less distinctive phenotype than complete LoF, as seen in truncating variants, which presents with an extensive variability in the phenotypic spectrum. Our data do not support a clear genotype to phenotype correlation.
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Affiliation(s)
- Vyne van der Schoot
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Sonja de Munnik
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, the Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre Nijmegen, Nijmegen, the Netherlands
| | - Mariet Elting
- Department of Clinical Genetics, Vrije Universiteit, Amsterdam, the Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Centre, Rotterdam, the Netherlands
| | - Conny M A Ravenswaaij-Arts
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, the Netherlands
| | - Britt-Marie Anderlid
- Department of Clinical Genetics, Karolinska Universitetssjukhuset, Solna, Sweden
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands.,Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, the Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
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46
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Ono H, Saitsu H, Horikawa R, Nakashima S, Ohkubo Y, Yanagi K, Nakabayashi K, Fukami M, Fujisawa Y, Ogata T. Partial androgen insensitivity syndrome caused by a deep intronic mutation creating an alternative splice acceptor site of the AR gene. Sci Rep 2018; 8:2287. [PMID: 29396419 PMCID: PMC5797100 DOI: 10.1038/s41598-018-20691-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/23/2018] [Indexed: 11/16/2022] Open
Abstract
Although partial androgen insensitivity syndrome (PAIS) is caused by attenuated responsiveness to androgens, androgen receptor gene (AR) mutations on the coding regions and their splice sites have been identified only in <25% of patients with a diagnosis of PAIS. We performed extensive molecular studies including whole exome sequencing in a Japanese family with PAIS, identifying a deep intronic variant beyond the branch site at intron 6 of AR (NM_000044.4:c.2450−42 G > A). This variant created the splice acceptor motif that was accompanied by pyrimidine-rich sequence and two candidate branch sites. Consistent with this, reverse transcriptase (RT)-PCR experiments for cycloheximide-treated lymphoblastoid cell lines revealed a relatively large amount of aberrant mRNA produced by the newly created splice acceptor site and a relatively small amount of wildtype mRNA produced by the normal splice acceptor site. Furthermore, most of the aberrant mRNA was shown to undergo nonsense mediated decay (NMD) and, if a small amount of aberrant mRNA may have escaped NMD, such mRNA was predicted to generate a truncated AR protein missing some functional domains. These findings imply that the deep intronic mutation creating an alternative splice acceptor site resulted in the production of a relatively small amount of wildtype AR mRNA, leading to PAIS.
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Affiliation(s)
- Hiroyuki Ono
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Reiko Horikawa
- Division of Endocrinology and Metabolism, National Medical Center for Children and Mother, Tokyo, Japan
| | - Shinichi Nakashima
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yumiko Ohkubo
- Department of Pediatrics, Shizuoka Saiseikai Hospital, Shizuoka, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yasuko Fujisawa
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan. .,Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.
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47
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Lejeune F. Nonsense-mediated mRNA decay at the crossroads of many cellular pathways. BMB Rep 2018; 50:175-185. [PMID: 28115040 PMCID: PMC5437961 DOI: 10.5483/bmbrep.2017.50.4.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Indexed: 12/22/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism ensuring the fast decay of mRNAs harboring a premature termination codon (PTC). As a quality control mechanism, NMD distinguishes PTCs from normal termination codons in order to degrade PTC-carrying mRNAs only. For this, NMD is connected to various other cell processes which regulate or activate it under specific cell conditions or in response to mutations, mis-regulations, stresses, or particular cell programs. These cell processes and their connections with NMD are the focus of this review, which aims both to illustrate the complexity of the NMD mechanism and its regulation and to highlight the cellular consequences of NMD inhibition.
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Affiliation(s)
- Fabrice Lejeune
- University Lille, UMR8161 - M3T - Mechanisms of Tumorigenesis and Target Therapies; CNRS, UMR 8161, 3Institut Pasteur de Lille, F-59000 Lille, France
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48
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Abstract
Long QT syndrome type 2 (LQT2) is caused by mutations in the human ether-à-go-go related gene (hERG), which encodes the Kv11.1 potassium channel in the heart. Over 30% of identified LQT2 mutations are nonsense or frameshift mutations that introduce premature termination codons (PTCs). Contrary to intuition, the predominant consequence of LQT2 nonsense and frameshift mutations is not the production of truncated proteins, but rather the degradation of mutant mRNA by nonsense-mediated mRNA decay (NMD), an RNA surveillance mechanism that selectively eliminates the mRNA transcripts that contain PTCs. In this chapter, we describe methods to study NMD of hERG nonsense and frameshift mutations in long QT syndrome.
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Affiliation(s)
- Qiuming Gong
- Knight Cardiovascular Institute, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Rd., Mail Code CHH14Z, Portland, OR, 97239, USA
| | - Zhengfeng Zhou
- Knight Cardiovascular Institute, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Rd., Mail Code CHH14Z, Portland, OR, 97239, USA.
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49
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Optimized approach for the identification of highly efficient correctors of nonsense mutations in human diseases. PLoS One 2017; 12:e0187930. [PMID: 29131862 PMCID: PMC5683606 DOI: 10.1371/journal.pone.0187930] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 10/27/2017] [Indexed: 11/23/2022] Open
Abstract
About 10% of patients with a genetic disease carry a nonsense mutation causing their pathology. A strategy for correcting nonsense mutations is premature termination codon (PTC) readthrough, i.e. incorporation of an amino acid at the PTC position during translation. PTC-readthrough-activating molecules appear as promising therapeutic tools for these patients. Unfortunately, the molecules shown to induce PTC readthrough show low efficacy, probably because the mRNAs carrying a nonsense mutation are scarce, as they are also substrates of the quality control mechanism called nonsense-mediated mRNA decay (NMD). The screening systems previously developed to identify readthrough-promoting molecules used cDNA constructs encoding mRNAs immune to NMD. As the molecules identified were not selected for the ability to correct nonsense mutations on NMD-prone PTC-mRNAs, they could be unsuitable for the context of nonsense-mutation-linked human pathologies. Here, a screening system based on an NMD-prone mRNA is described. It should be suitable for identifying molecules capable of efficiently rescuing the expression of human genes harboring a nonsense mutation. This system should favor the discovery of candidate drugs for treating genetic diseases caused by nonsense mutations. One hit selected with this screening system is presented and validated on cells from three cystic fibrosis patients.
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Ohguchi Y, Nomura T, Suzuki S, Takeda M, Miyauchi T, Mizuno O, Shinkuma S, Fujita Y, Nemoto O, Ono K, McLean WHI, Shimizu H. Gentamicin-Induced Readthrough and Nonsense-Mediated mRNA Decay of SERPINB7 Nonsense Mutant Transcripts. J Invest Dermatol 2017; 138:836-843. [PMID: 29106929 DOI: 10.1016/j.jid.2017.10.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/19/2017] [Accepted: 10/10/2017] [Indexed: 10/18/2022]
Abstract
Nagashima-type palmoplantar keratosis (NPPK) is an autosomal recessive skin disorder with a high, unmet medical need that is caused by mutations in SERPINB7. Almost all NPPK patients carry the founder nonsense mutation c.796C>T (p.Arg266Ter) in the last exon of SERPINB7. Here we sought to determine whether topical nonsense-suppression (readthrough) therapy using gentamicin is applicable to NPPK. First, we demonstrated that gentamicin enhanced readthrough activity in cells transfected with SERPINB7 cDNA carrying the mutation and promoted full-length SERPINB7 protein synthesis in NPPK keratinocytes. We next conducted an investigator-blinded, randomized, bilaterally controlled compassionate use study of topical gentamicin in which five NPPK patients with c.796C>T were enrolled. Patients' self-reported improvement of hyperkeratosis was significantly greater on the gentamicin side than the control side (P = 0.0349). In two patients, hyperkeratosis was improved on the gentamicin side, as determined by a blinded-investigator assessment. These results indicate the therapeutic potential of topical gentamicin for NPPK. Unexpectedly, we also found that mutant SERPINB7 mRNAs harboring r.796c>u were degraded by nonsense-mediated mRNA decay. Furthermore, the truncated SERPINB7 protein was degraded via a proteasome-mediated pathway. These findings provide important insights into the mRNA/protein quality-control system in humans, which could be a potential therapeutic target for genetic diseases.
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Affiliation(s)
- Yuka Ohguchi
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Toshifumi Nomura
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan.
| | - Shotaro Suzuki
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Masae Takeda
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Toshinari Miyauchi
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Osamu Mizuno
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Satoru Shinkuma
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Yasuyuki Fujita
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | | | - Kota Ono
- Clinical Research and Medical Innovation Center, Hokkaido University Hospital, Sapporo, Japan
| | - W H Irwin McLean
- Dermatology and Genetic Medicine, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Hiroshi Shimizu
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan.
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