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Hong J, Li T, Chao Y, Xu Y, Zhu Z, Zhou Z, Gu W, Qu Q, Li D. Molecular basis of the inositol deacylase PGAP1 involved in quality control of GPI-AP biogenesis. Nat Commun 2024; 15:8. [PMID: 38167496 PMCID: PMC10761859 DOI: 10.1038/s41467-023-44568-2] [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: 08/17/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
The secretion and quality control of glycosylphosphatidylinositol-anchored proteins (GPI-APs) necessitates post-attachment remodeling initiated by the evolutionarily conserved PGAP1, which deacylates the inositol in nascent GPI-APs. Impairment of PGAP1 activity leads to developmental diseases in humans and fatality and infertility in animals. Here, we present three PGAP1 structures (2.66-2.84 Å), revealing its 10-transmembrane architecture and product-enzyme interaction details. PGAP1 holds GPI-AP acyl chains in an optimally organized, guitar-shaped cavity with apparent energetic penalties from hydrophobic-hydrophilic mismatches. However, abundant glycan-mediated interactions in the lumen counterbalance these repulsions, likely conferring substrate fidelity and preventing off-target hydrolysis of bulk membrane lipids. Structural and biochemical analyses uncover a serine hydrolase-type catalysis with atypical features and imply mechanisms for substrate entrance and product release involving a drawing compass movement of GPI-APs. Our findings advance the mechanistic understanding of GPI-AP remodeling.
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Affiliation(s)
- Jingjing Hong
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Tingting Li
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Yulin Chao
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, Shanghai, 200032, China
| | - Yidan Xu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Zhini Zhu
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, Shanghai, 200032, China
| | - Zixuan Zhou
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, Shanghai, 200032, China
| | - Weijie Gu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Qianhui Qu
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, Shanghai, 200032, China.
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
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2
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Gippert S, Wagner M, Brunet T, Berruti R, Brugger M, Schwaibold EMC, Haack TB, Hoffmann GF, Bettendorf M, Choukair D. Exome sequencing (ES) of a pediatric cohort with chronic endocrine diseases: a single-center study (within the framework of the TRANSLATE-NAMSE project). Endocrine 2023:10.1007/s12020-023-03581-7. [PMID: 37940764 DOI: 10.1007/s12020-023-03581-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023]
Abstract
BACKGROUND Endocrine disorders are heterogeneous and include a significant number of rare monogenic diseases. METHODS We performed exome sequencing (ES) in 106 children recruited from a single center within the TRANSLATE‑NAMSE project. They were categorized into subgroups: proportionate short stature (PSS), disproportionate short stature (DSS), hypopituitarism (H), differences in sexual development (DSD), syndromic diseases (SD) and others. RESULTS The overall diagnostic yield was 34.9% (n = 37/106), including 5 patients with variants in candidate genes, which have contributed to collaborations to identify gene-disease associations. The diagnostic yield varied significantly between subgroups: PSS: 16.6% (1/6); DSS: 18.8% (3/16); H: 17.1% (6/35); DSD: 37.5% (3/8); SD: 66.6% (22/33); others: 25% (2/8). Confirmed diagnoses included 75% ultrarare diseases. Three patients harbored more than one disease-causing variant, resulting in dual diagnoses. CONCLUSIONS ES is an effective tool for genetic diagnosis in pediatric patients with complex endocrine diseases. An accurate phenotypic description, including comprehensive endocrine diagnostics, as well as the evaluation of variants in multidisciplinary case conferences involving geneticists, are necessary for personalized diagnostic care. Here, we illustrate the broad spectrum of genetic endocrinopathies that have led to the initiation of specific treatment, surveillance, and family counseling.
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Affiliation(s)
- Sebastian Gippert
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Pediatric Neurology and Developmental Medicine, Hauner Children's Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Riccardo Berruti
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | | | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany and Centre for Rare Diseases, University of Tuebingen, Tübingen, Germany
| | - Georg F Hoffmann
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Markus Bettendorf
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany.
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Paprocka J, Hutny M, Hofman J, Tokarska A, Kłaniewska M, Szczałuba K, Stembalska A, Jezela-Stanek A, Śmigiel R. Spectrum of Neurological Symptoms in Glycosylphosphatidylinositol Biosynthesis Defects: Systematic Review. Front Neurol 2022; 12:758899. [PMID: 35058872 PMCID: PMC8763846 DOI: 10.3389/fneur.2021.758899] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Mutations of genes involved in the synthesis of glycosylphosphatidylinositol and glycosylphosphatidylinositol-anchored proteins lead to rare syndromes called glycosylphosphatidylinositol-anchored proteins biosynthesis defects. Alterations of their structure and function in these disorders impair often fundamental processes in cells, resulting in severe clinical image. This study aimed to provide a systematic review of GPIBD cases reports published in English-language literature. Methods: The browsing of open-access databases (PubMed, PubMed Central. and Medline) was conducted, followed by statistical analysis of gathered information concerning neurological symptomatology. The inclusion criteria were: studies on humans, age at onset (<18 y.o.), and report of GPIBD cases with adequate data on the genetic background and symptomatology. Exclusion criteria were: publication type (manuscripts, personal communication, review articles); reports of cases of GPI biosynthesis genes mutations in terms of other disorders; reports of GPIBD cases concentrating on non-neurological symptoms; or articles concentrating solely on the genetic issues of GPI biosynthesis. Risk of bias was assessed using Joanna Brigs Institute Critical Appraisal Checklists. Data synthesis was conducted using STATISTICA 13.3.721.1 (StatSoft Polska Sp. z.o.o.). Used tests were chi-square, Fisher's exact test (for differences in phenotype), and Mann-Whitney U test (for differences in onset of developmental delay). Results: Browsing returned a total of 973 articles which, after ruling out the repetitions and assessing the inclusion and exclusion criteria, led to final inclusion of 77 articles (337 GPIBD cases) in the analysis. The main outcomes were prevalence of neurological symptoms, onset and semiology of seizures and their response to treatment, and onset of developmental delay. Based on this data a synthesis of phenotypical differences between the groups of GPIBD cases and the general GPIBD cases population was made. Discussion: A synthetical analysis of neurological components in clinical image of GPIBD patients was presented. It highlights the main features of these disorders, which might be useful in clinical practice for consideration in differential diagnosis with children presenting with early-onset seizures and developmental delay. The limitation of this review is the scarcity of the specific data in some reports, concerning the semiology and onset of two main features of GPIBD.
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Affiliation(s)
- Justyna Paprocka
- Department of Pediatric Neurology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Michał Hutny
- Students' Scientific Society, Department of Pediatric Neurology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Jagoda Hofman
- Students' Scientific Society, Department of Pediatric Neurology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Agnieszka Tokarska
- Department of Pediatrics and Developmental Age Neurology, Upper Silesian Child Health Centre, Katowice, Poland
| | | | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Aleksandra Jezela-Stanek
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | - Robert Śmigiel
- Department of Pediatrics, Medical University of Wroclaw, Wroclaw, Poland
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Sundercombe SL, Berbic M, Evans CA, Cliffe C, Elakis G, Temple SEL, Selvanathan A, Ewans L, Quayum N, Nixon CY, Dias KR, Lang S, Richards A, Goh S, Wilson M, Mowat D, Sachdev R, Sandaradura S, Walsh M, Farrar MA, Walsh R, Fletcher J, Kirk EP, Teunisse GM, Schofield D, Buckley MF, Zhu Y, Roscioli T. Clinically Responsive Genomic Analysis Pipelines: Elements to Improve Detection Rate and Efficiency. J Mol Diagn 2021; 23:894-905. [PMID: 33962052 DOI: 10.1016/j.jmoldx.2021.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/27/2021] [Accepted: 04/21/2021] [Indexed: 11/25/2022] Open
Abstract
Massively parallel sequencing has markedly improved mendelian diagnostic rates. This study assessed the effects of custom alterations to a diagnostic genomic bioinformatic pipeline in response to clinical need and derived practice recommendations relative to diagnostic rates and efficiency. The Genomic Annotation and Interpretation Application (GAIA) bioinformatics pipeline was designed to detect panel, exome, and genome sample integrity and prioritize gene variants in mendelian disorders. Reanalysis of selected negative cases was performed after improvements to the pipeline. GAIA improvements and their effect on sensitivity are described, including addition of a PubMed search for gene-disease associations not in the Online Mendelian Inheritance of Man database, inclusion of a process for calling low-quality variants (known as QPatch), and gene symbol nomenclature consistency checking. The new pipeline increased the diagnostic rate and reduced staff costs, resulting in a saving of US$844.34 per additional diagnosis. Recommendations for genomic analysis pipeline requirements are summarized. Clinically responsive bioinformatics pipeline improvements increase diagnostic sensitivity and increase cost-effectiveness.
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Affiliation(s)
| | - Marina Berbic
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, University of New South Wales Sydney, Kensington, New South Wales, Australia
| | - Carey-Anne Evans
- Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia
| | - Corrina Cliffe
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - George Elakis
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Suzanna E L Temple
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Arthavan Selvanathan
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Discipline of Child and Adolescent Health, The University of Sydney, New South Wales, Australia
| | - Lisa Ewans
- Department of Medical Genomics, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia; Central Clinical School, Sydney Medical School, The University of Sydney, New South Wales, Australia
| | - Nila Quayum
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Cheng-Yee Nixon
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia
| | - Kerith-Rae Dias
- Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales Sydney, Kensington, New South Wales, Australia
| | - Sarah Lang
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Anna Richards
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Shuxiang Goh
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney, Westmead, New South Wales, Australia
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Rani Sachdev
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Sarah Sandaradura
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney, Westmead, New South Wales, Australia
| | - Maie Walsh
- Genetic Medicine Department, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michelle A Farrar
- School of Women's and Children's Health, University of New South Wales Sydney, Kensington, New South Wales, Australia; Neurology Department, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Rebecca Walsh
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Janice Fletcher
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Edwin P Kirk
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, University of New South Wales Sydney, Kensington, New South Wales, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Guus M Teunisse
- Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia
| | - Deborah Schofield
- Centre for Economic Impacts of Genomic Medicine, Macquarie Business School, Macquarie University, Macquarie Park, New South Wales, Australia
| | - Michael Francis Buckley
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Ying Zhu
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Genetics of Learning Disability Service, Hunter Genetics, Waratah Newcastle, New South Wales, Australia
| | - Tony Roscioli
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia.
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5
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Guo XY, Liu YS, Gao XD, Kinoshita T, Fujita M. Calnexin mediates the maturation of GPI-anchors through ER retention. J Biol Chem 2020; 295:16393-16410. [PMID: 32967966 DOI: 10.1074/jbc.ra120.015577] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/05/2020] [Indexed: 01/05/2023] Open
Abstract
The protein folding and lipid moiety status of glycosylphosphatidylinositol-anchored proteins (GPI-APs) are monitored in the endoplasmic reticulum (ER), with calnexin playing dual roles in the maturation of GPI-APs. In the present study, we investigated the functions of calnexin in the quality control and lipid remodeling of GPI-APs in the ER. By directly binding the N-glycan on proteins, calnexin was observed to efficiently retain GPI-APs in the ER until they were correctly folded. In addition, sufficient ER retention time was crucial for GPI-inositol deacylation, which is mediated by post-GPI attachment protein 1 (PGAP1). Once the calnexin/calreticulin cycle was disrupted, misfolded and inositol-acylated GPI-APs could not be retained in the ER and were exposed on the plasma membrane. In calnexin/calreticulin-deficient cells, endogenous GPI-anchored alkaline phosphatase was expressed on the cell surface, but its activity was significantly decreased. ER stress induced surface expression of misfolded GPI-APs, but proper GPI-inositol deacylation occurred due to the extended time that they were retained in the ER. Our results indicate that calnexin-mediated ER quality control systems for GPI-APs are necessary for both protein folding and GPI-inositol deacylation.
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Affiliation(s)
- Xin-Yu Guo
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yi-Shi Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Taroh Kinoshita
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.
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6
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Sasorith S, Baux D, Bergougnoux A, Paulet D, Lahure A, Bareil C, Taulan-Cadars M, Roux AF, Koenig M, Claustres M, Raynal C. The CYSMA web server: An example of integrative tool for in silico analysis of missense variants identified in Mendelian disorders. Hum Mutat 2019; 41:375-386. [PMID: 31674704 DOI: 10.1002/humu.23941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 10/02/2019] [Accepted: 10/30/2019] [Indexed: 12/17/2022]
Abstract
Exome sequencing used for molecular diagnosis of Mendelian disorders considerably increases the number of missense variants of unclear significance, whose pathogenicity can be assessed by a variety of prediction tools. As the performance of algorithms may vary according to the datasets, complementary specific resources are needed to improve variant interpretation. As a model, we were interested in the cystic fibrosis transmembrane conductance regulator gene (CFTR) causing cystic fibrosis, in which at least 40% of missense variants are reported. Cystic fibrosis missense analysis (CYSMA) is a new web server designed for online estimation of the pathological relevance of CFTR missense variants. CYSMA generates a set of computationally derived data, ranging from evolutionary conservation to functional observations from three-dimensional structures, provides all available allelic frequencies, clinical observations, and references for functional studies. Compared to software classically used in analysis pipelines on a dataset of 141 well-characterized missense variants, CYSMA was the most efficient tool to discriminate benign missense variants, with a specificity of 85%, and very good sensitivity of 89%. These results suggest that such integrative tools could be adapted to numbers of genes involved in Mendelian disorders to improve the interpretation of missense variants identified in the context of diagnosis.
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Affiliation(s)
- Souphatta Sasorith
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | - David Baux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | - Anne Bergougnoux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | - Damien Paulet
- EA 7402, Université de Montpellier, Montpellier, France
| | - Alan Lahure
- EA 7402, Université de Montpellier, Montpellier, France
| | - Corinne Bareil
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | | | - Anne-Françoise Roux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | - Michel Koenig
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
| | | | - Caroline Raynal
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France.,EA 7402, Université de Montpellier, Montpellier, France
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7
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Kim P, Scott MR, Meador-Woodruff JH. Abnormal ER quality control of neural GPI-anchored proteins via dysfunction in ER export processing in the frontal cortex of elderly subjects with schizophrenia. Transl Psychiatry 2019; 9:6. [PMID: 30664618 PMCID: PMC6341114 DOI: 10.1038/s41398-018-0359-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/09/2018] [Accepted: 12/09/2018] [Indexed: 01/22/2023] Open
Abstract
Abnormalities of posttranslational protein modifications (PTMs) have recently been implicated in the pathophysiology of schizophrenia. Glycosylphosphatidylinositols (GPIs) are a class of complex glycolipids, which anchor surface proteins and glycoproteins to the cell membrane. GPI attachment to proteins represents one of the most common PTMs and GPI-associated proteins (GPI-APs) facilitate many cell surface processes, including synapse development and maintenance. Mutations in the GPI processing pathway are associated with intellectual disability, emphasizing the potential role of GPI-APs in cognition and schizophrenia-associated cognitive dysfunction. As initial endoplasmic reticulum (ER)-associated protein processing is essential for GPI-AP function, we measured protein expression of molecules involved in attachment (GPAA1), modification (PGAP1), and ER export (Tmp21) of GPI-APs, in homogenates and in an ER enriched fraction derived from dorsolateral prefrontal cortex (DLPFC) of 15 matched pairs of schizophrenia and comparison subjects. In total homogenate we found a significant decrease in transmembrane protein 21 (Tmp21) and in the ER-enriched fraction we found reduced expression of post-GPI attachment protein (PGAP1). PGAP1 modifies GPI-anchors through inositol deacylation, allowing it to be recognized by Tmp21. Tmp21 is a component of the p24 complex that recognizes GPI-anchored proteins, senses the status of the GPI-anchor, and regulates incorporation into COPII vesicles for export to the Golgi apparatus. Together, these proteins are the molecular mechanisms underlying GPI-AP quality control and ER export. To investigate the potential consequences of a deficit in export and/or quality control, we measured cell membrane-associated expression of known GPI-APs that have been previously implicated in schizophrenia, including GPC1, NCAM, MDGA2, and EPHA1, using Triton X-114 phase separation. Additionally, we tested the sensitivity of those candidate proteins to phosphatidylinositol-specific phospholipase C (PI-PLC), an enzyme that cleaves GPI from GPI-APs. While we did not observe a difference in the amount of these GPI-APs in Triton X-114 phase separated membrane fractions, we found decreased NCAM and GPC1 within the PI-PLC sensitive fraction. These findings suggest dysregulation of ER-associated GPI-AP protein processing, with impacts on post-translational modifications of proteins previously implicated in schizophrenia such as NCAM and GPC1. These findings provide evidence for a deficit in ER protein processing pathways in this illness.
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Affiliation(s)
- Pitna Kim
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Madeline R Scott
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - James H Meador-Woodruff
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
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8
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Nguyen TTM, Murakami Y, Wigby KM, Baratang NV, Rousseau J, St-Denis A, Rosenfeld JA, Laniewski SC, Jones J, Iglesias AD, Jones MC, Masser-Frye D, Scheuerle AE, Perry DL, Taft RJ, Le Deist F, Thompson M, Kinoshita T, Campeau PM. Mutations in PIGS, Encoding a GPI Transamidase, Cause a Neurological Syndrome Ranging from Fetal Akinesia to Epileptic Encephalopathy. Am J Hum Genet 2018; 103:602-611. [PMID: 30269814 DOI: 10.1016/j.ajhg.2018.08.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/23/2018] [Indexed: 11/17/2022] Open
Abstract
Inherited GPI deficiencies (IGDs) are a subset of congenital disorders of glycosylation that are increasingly recognized as a result of advances in whole-exome sequencing (WES) and whole-genome sequencing (WGS). IGDs cause a series of overlapping phenotypes consisting of seizures, dysmorphic features, multiple congenital malformations, and severe intellectual disability. We present a study of six individuals from three unrelated families in which WES or WGS identified bi-allelic phosphatidylinositol glycan class S (PIGS) biosynthesis mutations. Phenotypes included severe global developmental delay, seizures (partly responding to pyridoxine), hypotonia, weakness, ataxia, and dysmorphic facial features. Two of them had compound-heterozygous variants c.108G>A (p.Trp36∗) and c.101T>C (p.Leu34Pro), and two siblings of another family were homozygous for a deletion and insertion leading to p.Thr439_Lys451delinsArgLeuLeu. The third family had two fetuses with multiple joint contractures consistent with fetal akinesia. They were compound heterozygous for c.923A>G (p.Glu308Gly) and c.468+1G>C, a splicing mutation. Flow-cytometry analyses demonstrated that the individuals with PIGS mutations show a GPI-AP deficiency profile. Expression of the p.Trp36∗ variant in PIGS-deficient HEK293 cells revealed only partial restoration of cell-surface GPI-APs. In terms of both biochemistry and phenotype, loss of function of PIGS shares features with PIGT deficiency and other IGDs. This study contributes to the understanding of the GPI-AP biosynthesis pathway by describing the consequences of PIGS disruption in humans and extending the family of IGDs.
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Affiliation(s)
- Thi Tuyet Mai Nguyen
- Centre Hospitalier Universitaire Sainte Justine Research Center, University of Montreal, Montreal, QC H3T1C5, Canada
| | - Yoshiko Murakami
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Kristen M Wigby
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | - Nissan V Baratang
- Centre Hospitalier Universitaire Sainte Justine Research Center, University of Montreal, Montreal, QC H3T1C5, Canada
| | - Justine Rousseau
- Centre Hospitalier Universitaire Sainte Justine Research Center, University of Montreal, Montreal, QC H3T1C5, Canada
| | - Anik St-Denis
- Centre Hospitalier Universitaire Sainte Justine Research Center, University of Montreal, Montreal, QC H3T1C5, Canada
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Julie Jones
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Alejandro D Iglesias
- NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, NY 10032, USA
| | - Marilyn C Jones
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | | | | | | | | | - Françoise Le Deist
- Centre Hospitalier Universitaire Sainte Justine Research Center, University of Montreal, Montreal, QC H3T1C5, Canada
| | - Miles Thompson
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | - Taroh Kinoshita
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Philippe M Campeau
- Centre Hospitalier Universitaire Sainte Justine Research Center, University of Montreal, Montreal, QC H3T1C5, Canada.
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9
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Bellai‐Dussault K, Nguyen TTM, Baratang NV, Jimenez‐Cruz DA, Campeau PM. Clinical variability in inherited glycosylphosphatidylinositol deficiency disorders. Clin Genet 2018; 95:112-121. [DOI: 10.1111/cge.13425] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Kara Bellai‐Dussault
- Medical Genetics DivisionChildren's Hospital of Eastern Ontario Ottawa ON Canada
| | | | - Nissan V. Baratang
- CHU Sainte‐Justine Research CenterUniversity of Montreal Montreal QC Canada
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10
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Yang J, Wang Q, Zhuo Q, Tian H, Li W, Luo F, Zhang J, Bi D, Peng J, Zhou D, Xin H. A likely pathogenic variant putatively affecting splicing of PIGA identified in a multiple congenital anomalies hypotonia-seizures syndrome 2 (MCAHS2) family pedigree via whole-exome sequencing. Mol Genet Genomic Med 2018; 6:739-748. [PMID: 29974678 PMCID: PMC6160699 DOI: 10.1002/mgg3.428] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/25/2018] [Accepted: 06/11/2018] [Indexed: 12/18/2022] Open
Abstract
Background Glycosylphosphatidylinositol (GPI) anchoring is a special type of protein posttranslational modification, by which proteins with diverse function are attached to cell membrane through a covalent linkage between the protein and the glycolipid. Phosphatidylinositol glycan anchor biosynthesis class A (PIGA) is a key enzyme in GPI anchor biosynthesis, somatic mutations or genetic variants of which have been associated with paroxysmal nocturnal hemoglobinuria (PNH), or PIGA deficiency, respectively. More than 10 PIGA pathogenic or likely pathogenic variants have been reported in a wide spectrum of clinical syndromes of PIGA deficiency, including multiple congenital anomalies hypotonia‐seizures syndrome 2 (MCAHS2). Methods Whole‐exome sequencing (WES) was performed on two trios, that is., the proband's family and his affected maternal cousin's family, from a nonconsanguineous Chinese family pedigree with hypotonia‐encephalopathy‐seizures disease history and putative X‐linked recessive inheritance. Sanger sequencing for PIGA variant was performed on affected members as well as unaffected members in the family pedigree to verify its familial segregation. Results A novel likely pathogenic variant in PIGA was identified through comparative WES analysis of the two affected families. The single‐nucleotide substitution (NC_000023.9:g.15343279T>C) is located in intron 3 of the PIGA gene and within the splice acceptor consensus sequence (NM_002641.3:c.849‐5A>G). Even though we have not performed RNA studies, in silico tools predict that this intronic variant may alter normal splicing, causing a four base pair insertion which creates a frameshift and a premature stop codon at position 297 (NP_002632.1:p.(Arg283Serfs*15)). Sanger sequencing analysis of the extended family members confirmed the presence of the variant and its X‐linked inheritance. Conclusion WES data analysis along with familial segregation of a rare intronic variant are suggestive of a diagnosis of X‐liked PIGA deficiency with clinical features of MCAHS2.
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Affiliation(s)
- Junli Yang
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Qiong Wang
- Institute for Biology and Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Qingcui Zhuo
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Huiling Tian
- Children Rehabilitation Center of Linyi Women and Children's Hospital, Linyi, China
| | - Wen Li
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Fang Luo
- MyGenostics Inc., Beijing, China
| | - Jinghui Zhang
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Dan Bi
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Jing Peng
- Institute for Biology and Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Dong Zhou
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Huawei Xin
- Institute for Biology and Medicine, Wuhan University of Science and Technology, Wuhan, China.,School of Pharmacy, Linyi University, Linyi, China
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11
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Liu YS, Guo XY, Hirata T, Rong Y, Motooka D, Kitajima T, Murakami Y, Gao XD, Nakamura S, Kinoshita T, Fujita M. N-Glycan-dependent protein folding and endoplasmic reticulum retention regulate GPI-anchor processing. J Cell Biol 2017; 217:585-599. [PMID: 29255114 PMCID: PMC5800811 DOI: 10.1083/jcb.201706135] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/23/2017] [Accepted: 11/16/2017] [Indexed: 12/14/2022] Open
Abstract
N-Glycosylation and GPI anchoring of proteins occur in the endoplasmic reticulum (ER). Liu et al. revealed N-glycans participate in quality control and temporal ER retention of GPI-anchored proteins (GPI-APs), ensuring their correct folding and GPI processing before exiting from the ER. Chronic ER stress induced exposure of unprocessed GPI-APs on the cell surface. Glycosylphosphatidylinositol (GPI) anchoring of proteins is a conserved posttranslational modification in the endoplasmic reticulum (ER). Soon after GPI is attached, an acyl chain on the GPI inositol is removed by post-GPI attachment to proteins 1 (PGAP1), a GPI-inositol deacylase. This is crucial for switching GPI-anchored proteins (GPI-APs) from protein folding to transport states. We performed haploid genetic screens to identify factors regulating GPI-inositol deacylation, identifying seven genes. In particular, calnexin cycle impairment caused inefficient GPI-inositol deacylation. Calnexin was specifically associated with GPI-APs, dependent on N-glycan and GPI moieties, and assisted efficient GPI-inositol deacylation by PGAP1. Under chronic ER stress caused by misfolded GPI-APs, inositol-acylated GPI-APs were exposed on the cell surface. These results indicated that N-glycans participate in quality control and temporal ER retention of GPI-APs, ensuring their correct folding and GPI processing before exiting from the ER. Once the system is disrupted by ER stress, unprocessed GPI-APs become exposed on the cell surface.
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Affiliation(s)
- Yi-Shi Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Xin-Yu Guo
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Tetsuya Hirata
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Yao Rong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Toshihiko Kitajima
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Yoshiko Murakami
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Shota Nakamura
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Taroh Kinoshita
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan .,World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Jiangsu, China
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12
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Evers C, Staufner C, Granzow M, Paramasivam N, Hinderhofer K, Kaufmann L, Fischer C, Thiel C, Opladen T, Kotzaeridou U, Wiemann S, Schlesner M, Eils R, Kölker S, Bartram CR, Hoffmann GF, Moog U. Impact of clinical exomes in neurodevelopmental and neurometabolic disorders. Mol Genet Metab 2017; 121:297-307. [PMID: 28688840 DOI: 10.1016/j.ymgme.2017.06.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/29/2017] [Accepted: 06/29/2017] [Indexed: 01/06/2023]
Abstract
Whole exome sequencing (WES) is well established in research and is now being introduced into clinically indicated diagnostics (so-called clinical exomes). We evaluated the diagnostic yield and clinical implications of WES in 72 patients from 60 families with undiagnosed neurodevelopmental disorders (NDD), neurometabolic disorders, and dystonias. Pathogenic or likely pathogenic variants leading to a molecular diagnosis could be identified in 21 of the 60 families (overall 35%, in 36% of patients with NDD, in 43% of patients with neurometabolic disorders, in 25% of patients with dystonias). In one family two coexisting autosomal recessive diseases caused by homozygous pathogenic variants in two different genes were diagnosed. In another family, a homozygous frameshift variant in STRADA was found to cause a severe NDD with early onset epilepsy, brain anomalies, hypotonia, heart defect, nephrocalcinosis, macrocephaly and distinctive facies so far designated as PMSE (polyhydramnios, megalencephaly, symptomatic epilepsy) syndrome. In 7 of the 21 families with a molecular diagnosis the pathogenic variants were only identified by clinical follow-up, manual reevaluation of the literature, a change of filter setting, and/or reconsideration of inheritance pattern. Most importantly, clinical implications included management changes in 8 cases and impact on family planning in 20 families with a molecular diagnosis. This study shows that reevaluation and follow-up can improve the diagnostic rate and that WES results have important implications on medical management and family planning. Furthermore, we could confirm STRADA as a gene associated with syndromic ID but find it questionable if the current designation as PMSE depicts the most important clinical features.
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Affiliation(s)
- Christina Evers
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany.
| | - Christian Staufner
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Martin Granzow
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Nagarajan Paramasivam
- Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Katrin Hinderhofer
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Lilian Kaufmann
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Christine Fischer
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Christian Thiel
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Thomas Opladen
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Urania Kotzaeridou
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Stefan Wiemann
- Genomics & Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, 69120 Heidelberg, Germany
| | - Stefan Kölker
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Claus R Bartram
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Georg F Hoffmann
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Ute Moog
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
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13
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Evers C, Seitz A, Assmann B, Opladen T, Karch S, Hinderhofer K, Granzow M, Paramasivam N, Eils R, Diessl N, Bartram CR, Moog U. Diagnosis of CoPAN by whole exome sequencing: Waking up a sleeping tiger's eye. Am J Med Genet A 2017; 173:1878-1886. [PMID: 28489334 DOI: 10.1002/ajmg.a.38252] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 03/13/2017] [Indexed: 12/17/2022]
Abstract
Neurodegeneration with brain iron accumulation (NBIA) is a group of neurodegenerative disorders characterized by iron accumulation in the basal ganglia. Recently, mutations in CoA synthase (COASY) have been identified as a cause of a novel NBIA subtype (COASY Protein-Associated Neurodegeneration, CoPAN) in two patients with dystonic paraparesis, parkinsonian features, cognitive impairment, behavior abnormalities, and axonal neuropathy. COASY encodes an enzyme required for Coenzyme A (CoA) biosynthesis. Using whole exome sequencing (WES) we identified compound heterozygous COASY mutations in two siblings with intellectual disability, ataxic gait, progressive spasticity, and obsessive-compulsive behavior. The "eye-of-the tiger-sign," a characteristic hypointense spot within the hyperintense globi pallidi on MRI found in the most common subtype of NBIA (Pantothenate Kinase-Associated Neurodegeneration, PKAN), was not present. Instead, bilateral hyperintensity and swelling of caudate nucleus, putamen, and thalamus were found. In addition, our patients showed a small corpus callosum and frontotemporal and parietal white matter changes, expanding the brain phenotype of patients with CoPAN. Metabolic investigations showed increased free carnitine and decreased acylcarnitines in the patientś dried blood samples. Carnitine palmitoyl transferase 1 (CPT1) deficiency was excluded by further enzymatic and metabolic investigations. As CoA and its derivate Acetyl-CoA play an essential role in fatty acid metabolism, we assume that abnormal acylcarnitine profiles are a result of the COASY mutations. This report not only illustrates that WES is a powerful tool to elucidate the etiology of rare genetic diseases, but also identifies unique neuroimaging and metabolic findings that may be key features for an early diagnosis of CoPAN.
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Affiliation(s)
- Christina Evers
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Angelika Seitz
- Department of Neuroradiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Birgit Assmann
- Center for Child and Adolescent Medicine, Pediatric Neurology, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Opladen
- Center for Child and Adolescent Medicine, Pediatric Neurology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stephanie Karch
- Center for Child and Adolescent Medicine, Pediatric Neurology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Martin Granzow
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Nagarajan Paramasivam
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Medical Faculty Heidelberg, Heidelberg University, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Nicolle Diessl
- Genomics and Proteomics Core Facility (GPCF), High Throughput Sequencing, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claus R Bartram
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
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14
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Dikow N, Granzow M, Graul-Neumann LM, Karch S, Hinderhofer K, Paramasivam N, Behl LJ, Kaufmann L, Fischer C, Evers C, Schlesner M, Eils R, Borck G, Zweier C, Bartram CR, Carey JC, Moog U. DDX3X
mutations in two girls with a phenotype overlapping Toriello-Carey syndrome. Am J Med Genet A 2017; 173:1369-1373. [DOI: 10.1002/ajmg.a.38164] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 12/20/2016] [Accepted: 01/05/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Nicola Dikow
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Martin Granzow
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | | | - Stephanie Karch
- Center for Child and Adolescent Medicine Pediatric Neurology; Heidelberg University Hospital; Heidelberg Germany
| | | | - Nagarajan Paramasivam
- Medical Faculty Heidelberg; Heidelberg University; Heidelberg Germany
- Division of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Laura-Jane Behl
- Genomics and Proteomics Core Facility; High Throughput Sequencing; German Cancer Research Center; Heidelberg Germany
| | - Lilian Kaufmann
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Christine Fischer
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Christina Evers
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
- Department for Bioinformatics and Functional Genomics; Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant; Heidelberg University; Heidelberg Germany
| | - Guntram Borck
- Institute of Human Genetics; University of Ulm; Ulm Germany
| | - Christiane Zweier
- Institute of Human Genetics; Friedrich-Alexander-Universität Erlangen-Nürnberg; Erlangen Germany
| | - Claus R. Bartram
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - John C. Carey
- Division of Medical Genetics; Department of Pediatrics; University of Utah School of Medicine; Salt Lake City Utah
| | - Ute Moog
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
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15
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Johnstone DL, Nguyen TTM, Murakami Y, Kernohan KD, Tétreault M, Goldsmith C, Doja A, Wagner JD, Huang L, Hartley T, St-Denis A, le Deist F, Majewski J, Bulman DE, Kinoshita T, Dyment DA, Boycott KM, Campeau PM. Compound heterozygous mutations in the gene PIGP are associated with early infantile epileptic encephalopathy. Hum Mol Genet 2017; 26:1706-1715. [DOI: 10.1093/hmg/ddx077] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 02/27/2017] [Indexed: 12/27/2022] Open
Affiliation(s)
- Devon L. Johnstone
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario K1H8L1, Canada
| | - Thi-Tuyet-Mai Nguyen
- Research Center, CHU Sainte-Justine, University of Montreal, Montreal, Quebec H3T1C5, Canada
| | - Yoshiko Murakami
- WPI Immunology Frontier Research Center and Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Kristin D. Kernohan
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario K1H8L1, Canada
| | - Martine Tétreault
- Department of Human Genetics, McGill University, Montreal, Quebec H3A1B1, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec H3A0G1, Canada
| | - Claire Goldsmith
- Department of Genetics, Children’s Hospital of Eastern Ontario, Ottawa, Ontario K1H8L1, Canada
| | - Asif Doja
- Division of Neurology, Department of Pediatrics, Children’s Hospital of Eastern Ontario, Ottawa, Ontario K1H8L1, Canada
| | - Justin D. Wagner
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario K1H8L1, Canada
| | - Lijia Huang
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario K1H8L1, Canada
| | - Taila Hartley
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario K1H8L1, Canada
| | - Anik St-Denis
- Research Center, CHU Sainte-Justine, University of Montreal, Montreal, Quebec H3T1C5, Canada
| | - Françoise le Deist
- Research Center, CHU Sainte-Justine, University of Montreal, Montreal, Quebec H3T1C5, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Quebec H3A1B1, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec H3A0G1, Canada
| | - Dennis E. Bulman
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario K1H8L1, Canada
| | - Taroh Kinoshita
- WPI Immunology Frontier Research Center and Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - David A. Dyment
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario K1H8L1, Canada
- Department of Genetics, Children’s Hospital of Eastern Ontario, Ottawa, Ontario K1H8L1, Canada
| | - Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario K1H8L1, Canada
- Department of Genetics, Children’s Hospital of Eastern Ontario, Ottawa, Ontario K1H8L1, Canada
| | - Philippe M. Campeau
- Research Center, CHU Sainte-Justine, University of Montreal, Montreal, Quebec H3T1C5, Canada
- Department of Pediatrics, Sainte-Justine Hospital, University of Montreal, Montreal, Quebec H3T1C5, Canada
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16
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Identification of genetic defects in pulmonary arterial hypertension by a new gene panel diagnostic tool. Clin Sci (Lond) 2016; 130:2043-2052. [DOI: 10.1042/cs20160531] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/09/2016] [Indexed: 11/17/2022]
Abstract
We developed a new candidate gene approach for pulmonary arterial hypertension based on a customized kit and new sequencing technologies. In this manner we identified mutations in routinely assessed genes and one additional gene in PAH patients.
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17
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Kettwig M, Elpeleg O, Wegener E, Dreha-Kulaczewski S, Henneke M, Gärtner J, Huppke P. Compound heterozygous variants in PGAP1 causing severe psychomotor retardation, brain atrophy, recurrent apneas and delayed myelination: a case report and literature review. BMC Neurol 2016; 16:74. [PMID: 27206732 PMCID: PMC4875637 DOI: 10.1186/s12883-016-0602-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 05/12/2016] [Indexed: 11/25/2022] Open
Abstract
Background Mutations in proteins involved in the glycosylphosphatidylinositol anchor biosynthesis and remodeling pathway are associated with autosomal recessive forms of intellectual disability. Recently mutations in the PGAP1 gene that codes for PGAP1, a protein localized in the endoplasmic reticulum responsible for the first step of the remodeling of glycosylphosphatidylinositol was linked to a disorder characterized by psychomotor retardation and facial dysmorphism. Whole exome sequencing (WES) was performed in siblings with severely delayed myelination and psychomotor retardation. Mutations in PGAP1 were confirmed by Sanger sequencing and RNA analysis. A literature search was performed to describe the emerging phenotype of PGAP1 related disease. Case presentation WES resulted in the detection of two novel compound heterozygous mutations in PGAP1, one base pair insertion leading to a frame shift c.334_335InsA (p.A112fs) and a splice site mutation leading to exon skipping c.G1173C (p.L391L). A symptom not described in PGAP1 related disorder before but prominent in the siblings were recurrent apnea especially during sleep that persisted at least until age 2 years. Sequential cerebral MRI at age one and two year(s) respectively revealed frontal accentuated brain atrophy and significantly delayed myelination. Conclusion We report siblings with two novel mutations in PGAP1. Other that the common symptoms related to PGAP1 mutations including non-progressive psychomotor retardation, neonatal feeding problems, microcephaly and brain atrophy these patients displayed severely delayed myelination and recurrent apneas thereby widing the clinical spectrum associated with such mutations. Electronic supplementary material The online version of this article (doi:10.1186/s12883-016-0602-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthias Kettwig
- Department of Pediatrics and Pediatric Neurology, University Medical Center, Georg August University, 37075, Göttingen, Germany.
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eike Wegener
- Department of Pediatrics and Pediatric Neurology, University Medical Center, Georg August University, 37075, Göttingen, Germany
| | - Steffi Dreha-Kulaczewski
- Department of Pediatrics and Pediatric Neurology, University Medical Center, Georg August University, 37075, Göttingen, Germany
| | - Marco Henneke
- Department of Pediatrics and Pediatric Neurology, University Medical Center, Georg August University, 37075, Göttingen, Germany
| | - Jutta Gärtner
- Department of Pediatrics and Pediatric Neurology, University Medical Center, Georg August University, 37075, Göttingen, Germany
| | - Peter Huppke
- Department of Pediatrics and Pediatric Neurology, University Medical Center, Georg August University, 37075, Göttingen, Germany
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Evers C, Kaufmann L, Seitz A, Paramasivam N, Granzow M, Karch S, Fischer C, Hinderhofer K, Gdynia G, Elsässer M, Pinkert S, Schlesner M, Bartram CR, Moog U. Exome sequencing reveals a novelCWF19L1mutation associated with intellectual disability and cerebellar atrophy. Am J Med Genet A 2016; 170:1502-9. [DOI: 10.1002/ajmg.a.37632] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/07/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Christina Evers
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Lilian Kaufmann
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Angelika Seitz
- Department of Neuroradiology; University Hospital Heidelberg; Heidelberg Germany
| | - Nagarajan Paramasivam
- Division of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
- Medical Faculty Heidelberg; Heidelberg University; Germany
| | - Martin Granzow
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Stephanie Karch
- Center for Child and Adolescent Medicine, Pediatric Neurology; Heidelberg University Hospital; Heidelberg Germany
| | - Christine Fischer
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | | | - Georg Gdynia
- Institute of Pathology; University of Heidelberg; Heidelberg Germany
- German Cancer Research Center; Clinical Cooperation Unit Molecular Tumor Pathology; Heidelberg Germany
| | - Michael Elsässer
- Department of Obstetrics and Gynecology, Prenatal Medicine; University Hospital Heidelberg; Heidelberg Germany
| | - Stefan Pinkert
- Genomics and Proteomics Core Facility (GPCF); High Throughput Sequencing, German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Claus R. Bartram
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Ute Moog
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
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Kinoshita T, Fujita M. Biosynthesis of GPI-anchored proteins: special emphasis on GPI lipid remodeling. J Lipid Res 2015; 57:6-24. [PMID: 26563290 DOI: 10.1194/jlr.r063313] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Indexed: 02/06/2023] Open
Abstract
Glycosylphosphatidylinositols (GPIs) act as membrane anchors of many eukaryotic cell surface proteins. GPIs in various organisms have a common backbone consisting of ethanolamine phosphate (EtNP), three mannoses (Mans), one non-N-acetylated glucosamine, and inositol phospholipid, whose structure is EtNP-6Manα-2Manα-6Manα-4GlNα-6myoinositol-P-lipid. The lipid part is either phosphatidylinositol of diacyl or 1-alkyl-2-acyl form, or inositol phosphoceramide. GPIs are attached to proteins via an amide bond between the C-terminal carboxyl group and an amino group of EtNP. Fatty chains of inositol phospholipids are inserted into the outer leaflet of the plasma membrane. More than 150 different human proteins are GPI anchored, whose functions include enzymes, adhesion molecules, receptors, protease inhibitors, transcytotic transporters, and complement regulators. GPI modification imparts proteins with unique characteristics, such as association with membrane microdomains or rafts, transient homodimerization, release from the membrane by cleavage in the GPI moiety, and apical sorting in polarized cells. GPI anchoring is essential for mammalian embryogenesis, development, neurogenesis, fertilization, and immune system. Mutations in genes involved in remodeling of the GPI lipid moiety cause human diseases characterized by neurological abnormalities. Yeast Saccharomyces cerevisiae has >60 GPI-anchored proteins (GPI-APs). GPI is essential for growth of yeast. In this review, we discuss biosynthesis of GPI-APs in mammalian cells and yeast with emphasis on the lipid moiety.
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Affiliation(s)
- Taroh Kinoshita
- WPI Immunology Frontier Research Center and Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
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