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Rebelo AP, Tomaselli PJ, Medina J, Wang Y, Dohrn MF, Nyvltova E, Danzi MC, Garrett M, Smith SE, Pestronk A, Li C, Ruiz A, Jacobs E, Feely SME, França MC, Gomes MV, Santos DF, Kumar S, Lombard DB, Saporta M, Hekimi S, Barrientos A, Weihl C, Shy ME, Marques W, Zuchner S. Biallelic variants in COQ7 cause distal hereditary motor neuropathy with upper motor neuron signs. Brain 2023; 146:4191-4199. [PMID: 37170631 PMCID: PMC10545612 DOI: 10.1093/brain/awad158] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 04/12/2023] [Accepted: 04/23/2023] [Indexed: 05/13/2023] Open
Abstract
COQ7 encodes a hydroxylase responsible for the penultimate step of coenzyme Q10 (CoQ10) biosynthesis in mitochondria. CoQ10 is essential for multiple cellular functions, including mitochondrial oxidative phosphorylation, lipid metabolism, and reactive oxygen species homeostasis. Mutations in COQ7 have been previously associated with primary CoQ10 deficiency, a clinically heterogeneous multisystemic mitochondrial disorder. We identified COQ7 biallelic variants in nine families diagnosed with distal hereditary motor neuropathy with upper neuron involvement, expending the clinical phenotype associated with defects in this gene. A recurrent p.Met1? change was identified in five families from Brazil with evidence of a founder effect. Fibroblasts isolated from patients revealed a substantial depletion of COQ7 protein levels, indicating protein instability leading to loss of enzyme function. High-performance liquid chromatography assay showed that fibroblasts from patients had reduced levels of CoQ10, and abnormal accumulation of the biosynthetic precursor DMQ10. Accordingly, fibroblasts from patients displayed significantly decreased oxygen consumption rates in patients, suggesting mitochondrial respiration deficiency. Induced pluripotent stem cell-derived motor neurons from patient fibroblasts showed significantly increased levels of extracellular neurofilament light protein, indicating axonal degeneration. Our findings indicate a molecular pathway involving CoQ10 biosynthesis deficiency and mitochondrial dysfunction in patients with distal hereditary motor neuropathy. Further studies will be important to evaluate the potential benefits of CoQ10 supplementation in the clinical outcome of the disease.
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Affiliation(s)
- Adriana P Rebelo
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Pedro J Tomaselli
- Department of Neurology, University of São Paulo, Ribeirão Preto, 14048-900, Brazil
| | - Jessica Medina
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Ying Wang
- Department of Biology, McGill University, Montreal, QC, H3A 1A1, Canada
| | - Maike F Dohrn
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Department of Neurology, Medical Faculty, RWTH Aachen University, Aachen 52074, Germany
| | - Eva Nyvltova
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Matt C Danzi
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Mark Garrett
- Department of Neurology, Washington University, St. Louis, MO 63112, USA
| | - Sean E Smith
- Department of Neurology, Washington University, St. Louis, MO 63112, USA
| | - Alan Pestronk
- Department of Neurology, Washington University, St. Louis, MO 63112, USA
| | - Chengcheng Li
- Department of Neurology, Washington University, St. Louis, MO 63112, USA
| | - Ariel Ruiz
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Elizabeth Jacobs
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Shawna M E Feely
- Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Marcondes C França
- Department of Neurology, University of São Paulo, Ribeirão Preto, 14048-900, Brazil
| | - Marcus V Gomes
- Department of Neurology, University of São Paulo, Ribeirão Preto, 14048-900, Brazil
| | - Diogo F Santos
- Department of Neurology, Federal University of Uberlândia, Uberlândia, MG 38405-320, Brazil
| | - Surinder Kumar
- Department of Pathology & Laboratory Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - David B Lombard
- Department of Pathology & Laboratory Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mario Saporta
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Siegfried Hekimi
- Department of Biology, McGill University, Montreal, QC, H3A 1A1, Canada
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Conrad Weihl
- Department of Neurology, Washington University, St. Louis, MO 63112, USA
| | - Michael E Shy
- Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Wilson Marques
- Department of Neurology, University of São Paulo, Ribeirão Preto, 14048-900, Brazil
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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Gonzalez-Calderon G, Liu R, Carvajal R, Teer JK. A negative storage model for precise but compact storage of genetic variation data. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5820061. [PMID: 32293013 PMCID: PMC7157186 DOI: 10.1093/database/baz158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/21/2019] [Accepted: 12/09/2020] [Indexed: 12/30/2022]
Abstract
Falling sequencing costs and large initiatives are resulting in increasing amounts of data available for investigator use. However, there are informatics challenges in being able to access genomic data. Performance and storage are well-appreciated issues, but precision is critical for meaningful analysis and interpretation of genomic data. There is an inherent accuracy vs. performance trade-off with existing solutions. The most common approach (Variant-only Storage Model, VOSM) stores only variant data. Systems must therefore assume that everything not variant is reference, sacrificing precision and potentially accuracy. A more complete model (Full Storage Model, FSM) would store the state of every base (variant, reference and missing) in the genome thereby sacrificing performance. A compressed variation of the FSM can store the state of contiguous regions of the genome as blocks (Block Storage Model, BLSM), much like the file-based gVCF model. We propose a novel approach by which this state is encoded such that both performance and accuracy are maintained. The Negative Storage Model (NSM) can store and retrieve precise genomic state from different sequencing sources, including clinical and whole exome sequencing panels. Reduced storage requirements are achieved by storing only the variant and missing states and inferring the reference state. We evaluate the performance characteristics of FSM, BLSM and NSM and demonstrate dramatic improvements in storage and performance using the NSM approach.
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Affiliation(s)
- Guillermo Gonzalez-Calderon
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL, 33912, USA
| | - Ruizheng Liu
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL, 33912, USA
| | - Rodrigo Carvajal
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL, 33912, USA
| | - Jamie K Teer
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL, 33912, USA.,Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL, 33912, USA
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3
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Lup SD, Wilson-Sánchez D, Andreu-Sánchez S, Micol JL. Easymap: A User-Friendly Software Package for Rapid Mapping-by-Sequencing of Point Mutations and Large Insertions. FRONTIERS IN PLANT SCIENCE 2021; 12:655286. [PMID: 34040621 PMCID: PMC8143052 DOI: 10.3389/fpls.2021.655286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/18/2021] [Indexed: 05/15/2023]
Abstract
Mapping-by-sequencing strategies combine next-generation sequencing (NGS) with classical linkage analysis, allowing rapid identification of the causal mutations of the phenotypes exhibited by mutants isolated in a genetic screen. Computer programs that analyze NGS data obtained from a mapping population of individuals derived from a mutant of interest to identify a causal mutation are available; however, the installation and usage of such programs requires bioinformatic skills, modifying or combining pieces of existing software, or purchasing licenses. To ease this process, we developed Easymap, an open-source program that simplifies the data analysis workflows from raw NGS reads to candidate mutations. Easymap can perform bulked segregant mapping of point mutations induced by ethyl methanesulfonate (EMS) with DNA-seq or RNA-seq datasets, as well as tagged-sequence mapping for large insertions, such as transposons or T-DNAs. The mapping analyses implemented in Easymap have been validated with experimental and simulated datasets from different plant and animal model species. Easymap was designed to be accessible to all users regardless of their bioinformatics skills by implementing a user-friendly graphical interface, a simple universal installation script, and detailed mapping reports, including informative images and complementary data for assessment of the mapping results. Easymap is available at http://genetics.edu.umh.es/resources/easymap; its Quickstart Installation Guide details the recommended procedure for installation.
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Rebelo AP, Saade D, Pereira CV, Farooq A, Huff TC, Abreu L, Moraes CT, Mnatsakanova D, Mathews K, Yang H, Schon EA, Zuchner S, Shy ME. SCO2 mutations cause early-onset axonal Charcot-Marie-Tooth disease associated with cellular copper deficiency. Brain 2019; 141:662-672. [PMID: 29351582 DOI: 10.1093/brain/awx369] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/14/2017] [Indexed: 01/06/2023] Open
Abstract
Recessive mutations in the mitochondrial copper-binding protein SCO2, cytochrome c oxidase (COX) assembly protein, have been reported in several cases with fatal infantile cardioencephalomyopathy with COX deficiency. Significantly expanding the known phenotypic spectrum, we identified compound heterozygous variants in SCO2 in two unrelated patients with axonal polyneuropathy, also known as Charcot-Marie-Tooth disease type 4. Different from previously described cases, our patients developed predominantly motor neuropathy, they survived infancy, and they have not yet developed the cardiomyopathy that causes death in early infancy in reported patients. Both of our patients harbour missense mutations near the conserved copper-binding motif (CXXXC), including the common pathogenic variant E140K and a novel change D135G. In addition, each patient carries a second mutation located at the same loop region, resulting in compound heterozygote changes E140K/P169T and D135G/R171Q. Patient fibroblasts showed reduced levels of SCO2, decreased copper levels and COX deficiency. Given that another Charcot-Marie-Tooth disease gene, ATP7A, is a known copper transporter, our findings further underline the relevance of copper metabolism in Charcot-Marie-Tooth disease.
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Affiliation(s)
- Adriana P Rebelo
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, USA
| | - Dimah Saade
- Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, USA
| | | | - Amjad Farooq
- Biochemistry Department, University of Miami Miller School of Medicine, Miami, USA
| | - Tyler C Huff
- Department of Neurology, University of Miami, Miami, USA
| | - Lisa Abreu
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, USA
| | | | - Diana Mnatsakanova
- Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Kathy Mathews
- Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Hua Yang
- Department of Neurology, Columbia University Medical Center, New York, USA
| | - Eric A Schon
- Department of Neurology, Columbia University Medical Center, New York, USA.,Department of Genetics and Development, Columbia University Medical Center, New York, USA
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, USA
| | - Michael E Shy
- Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, USA
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Myopathy associated BAG3 mutations lead to protein aggregation by stalling Hsp70 networks. Nat Commun 2018; 9:5342. [PMID: 30559338 PMCID: PMC6297355 DOI: 10.1038/s41467-018-07718-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/16/2018] [Indexed: 02/03/2023] Open
Abstract
BAG3 is a multi-domain hub that connects two classes of chaperones, small heat shock proteins (sHSPs) via two isoleucine-proline-valine (IPV) motifs and Hsp70 via a BAG domain. Mutations in either the IPV or BAG domain of BAG3 cause a dominant form of myopathy, characterized by protein aggregation in both skeletal and cardiac muscle tissues. Surprisingly, for both disease mutants, impaired chaperone binding is not sufficient to explain disease phenotypes. Recombinant mutants are correctly folded, show unaffected Hsp70 binding but are impaired in stimulating Hsp70-dependent client processing. As a consequence, the mutant BAG3 proteins become the node for a dominant gain of function causing aggregation of itself, Hsp70, Hsp70 clients and tiered interactors within the BAG3 interactome. Importantly, genetic and pharmaceutical interference with Hsp70 binding completely reverses stress-induced protein aggregation for both BAG3 mutations. Thus, the gain of function effects of BAG3 mutants act as Achilles heel of the HSP70 machinery.
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Eidhof I, Baets J, Kamsteeg EJ, Deconinck T, van Ninhuijs L, Martin JJ, Schüle R, Züchner S, De Jonghe P, Schenck A, van de Warrenburg BP. GDAP2 mutations implicate susceptibility to cellular stress in a new form of cerebellar ataxia. Brain 2018; 141:2592-2604. [PMID: 30084953 PMCID: PMC7534050 DOI: 10.1093/brain/awy198] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/09/2018] [Accepted: 06/11/2018] [Indexed: 12/18/2022] Open
Abstract
Autosomal recessive cerebellar ataxias are a group of rare disorders that share progressive degeneration of the cerebellum and associated tracts as the main hallmark. Here, we report two unrelated patients with a new subtype of autosomal recessive cerebellar ataxia caused by biallelic, gene-disruptive mutations in GDAP2, a gene previously not implicated in disease. Both patients had onset of ataxia in the fourth decade. Other features included progressive spasticity and dementia. Neuropathological examination showed degenerative changes in the cerebellum, olive inferior, thalamus, substantia nigra, and pyramidal tracts, as well as tau pathology in the hippocampus and amygdala. To provide further evidence for a causative role of GDAP2 mutations in autosomal recessive cerebellar ataxia pathophysiology, its orthologous gene was investigated in the fruit fly Drosophila melanogaster. Ubiquitous knockdown of Drosophila Gdap2 resulted in shortened lifespan and motor behaviour anomalies such as righting defects, reduced and uncoordinated walking behaviour, and compromised flight. Gdap2 expression levels responded to stress treatments in control flies, and Gdap2 knockdown flies showed increased sensitivity to deleterious effects of stressors such as reactive oxygen species and nutrient deprivation. Thus, Gdap2 knockdown in Drosophila and GDAP2 loss-of-function mutations in humans lead to locomotor phenotypes, which may be mediated by altered responses to cellular stress.
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Affiliation(s)
- Ilse Eidhof
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Centre, GA Nijmegen, The Netherlands
| | - Jonathan Baets
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Centre, GA Nijmegen, The Netherlands
| | - Tine Deconinck
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Lisa van Ninhuijs
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Centre, GA Nijmegen, The Netherlands
| | | | - Rebecca Schüle
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Stephan Züchner
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miami, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, USA
| | - Peter De Jonghe
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Centre, GA Nijmegen, The Netherlands
| | - Bart P van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Centre, GC Nijmegen, The Netherlands
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A MECOM variant in an African American child with radioulnar synostosis and thrombocytopenia. Clin Dysmorphol 2018; 27:9-11. [PMID: 29200407 DOI: 10.1097/mcd.0000000000000200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Wilke C, Baets J, De Bleecker JL, Deconinck T, Biskup S, Hayer SN, Züchner S, Schüle R, De Jonghe P, Synofzik M. Beyond ALS and FTD: the phenotypic spectrum of TBK1 mutations includes PSP-like and cerebellar phenotypes. Neurobiol Aging 2017; 62:244.e9-244.e13. [PMID: 29137817 DOI: 10.1016/j.neurobiolaging.2017.10.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 10/07/2017] [Accepted: 10/12/2017] [Indexed: 12/12/2022]
Abstract
Mutations in the TANK-binding kinase 1 gene (TBK1) are a rare, but recurrent cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). However, the complete phenotypic spectrum of syndromes associated with TBK1 mutations remains to be elucidated. Using next-generation panel-sequencing of neurodegenerative disease genes, we identified a TBK1 index patient presenting with a progressive supranuclear palsy-like syndrome. Consecutively, we screened the whole-exome sequencing data of 439 index subjects presenting with various neurodegenerative syndromes outside the ALS-FTD spectrum for TBK1 mutations. Based on this genetic screen, we identified another TBK1 index patient presenting with progressive cerebellar ataxia. Both index patients carried the established p.Glu643del TBK1 mutation (c.1928_1930delAAG). In the index patients' families, we identified mesencephalic and cerebellar atrophy as recurrent imaging findings of TBK1-associated neurodegeneration, with cerebellar atrophy occurring even in presymptomatic mutation carriers. Our findings demonstrate that the phenotypic spectrum of TBK1 mutations extends beyond ALS and FTD to include also progressive supranuclear palsy-like and cerebellar syndromes, with mesencephalon and cerebellum representing recurrent sites of TBK1-associated neurodegeneration.
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Affiliation(s)
- Carlo Wilke
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - Jonathan Baets
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratories of Neurogenetics and Ultrastructural Neuropathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | | | - Tine Deconinck
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratories of Neurogenetics and Ultrastructural Neuropathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Saskia Biskup
- CeGaT GmbH, Center for Genomics and Transcriptomics, Tübingen, Germany
| | - Stefanie N Hayer
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - Stephan Züchner
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miami, USA; John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, USA
| | - Rebecca Schüle
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - Peter De Jonghe
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratories of Neurogenetics and Ultrastructural Neuropathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany.
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Sobreira NLM, Arachchi H, Buske OJ, Chong JX, Hutton B, Foreman J, Schiettecatte F, Groza T, Jacobsen JOB, Haendel MA, Boycott KM, Hamosh A, Rehm HL. Matchmaker Exchange. ACTA ACUST UNITED AC 2017; 95:9.31.1-9.31.15. [PMID: 29044468 DOI: 10.1002/cphg.50] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In well over half of the individuals with rare disease who undergo clinical or research next-generation sequencing, the responsible gene cannot be determined. Some reasons for this relatively low yield include unappreciated phenotypic heterogeneity; locus heterogeneity; somatic and germline mosaicism; variants of uncertain functional significance; technically inaccessible areas of the genome; incorrect mode of inheritance investigated; and inadequate communication between clinicians and basic scientists with knowledge of particular genes, proteins, or biological systems. To facilitate such communication and improve the search for patients or model organisms with similar phenotypes and variants in specific candidate genes, we have developed the Matchmaker Exchange (MME). MME was created to establish a federated network connecting databases of genomic and phenotypic data using a common application programming interface (API). To date, seven databases can exchange data using the API (GeneMatcher, PhenomeCentral, DECIPHER, MyGene2, matchbox, Australian Genomics Health Alliance Patient Archive, and Monarch Initiative; the latter included for model organism matching). This article guides usage of the MME for rare disease gene discovery. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nara L M Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | | | - Orion J Buske
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - Ben Hutton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Julia Foreman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | | | - Tudor Groza
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales, Australia
| | - Julius O B Jacobsen
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Melissa A Haendel
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine (IGM), Clinical Director, IGM. Scientific Director, OMIM. Johns Hopkins University. Baltimore, Maryland
| | - Heidi L Rehm
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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Soualmia LF, Lecroq T. Bioinformatics Methods and Tools to Advance Clinical Care. Findings from the Yearbook 2015 Section on Bioinformatics and Translational Informatics. Yearb Med Inform 2017; 10:170-3. [PMID: 26293864 DOI: 10.15265/iy-2015-026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. METHOD We provide a synopsis of the articles selected for the IMIA Yearbook 2015, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor has evaluated separately the set of 1,594 articles and the evaluation results were merged for retaining 15 articles for peer-review. RESULTS The selection and evaluation process of this Yearbook's section on Bioinformatics and Translational Informatics yielded four excellent articles regarding data management and genome medicine that are mainly tool-based papers. In the first article, the authors present PPISURV a tool for uncovering the role of specific genes in cancer survival outcome. The second article describes the classifier PredictSNP which combines six performing tools for predicting disease-related mutations. In the third article, by presenting a high-coverage map of the human proteome using high resolution mass spectrometry, the authors highlight the need for using mass spectrometry to complement genome annotation. The fourth article is also related to patient survival and decision support. The authors present datamining methods of large-scale datasets of past transplants. The objective is to identify chances of survival. CONCLUSIONS The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care. Indeed, there is a need for powerful tools for managing and interpreting complex, large-scale genomic and biological datasets, but also a need for user-friendly tools developed for the clinicians in their daily practice. All the recent research and development efforts contribute to the challenge of impacting clinically the obtained results towards a personalized medicine.
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Affiliation(s)
- L F Soualmia
- Dr Lina F. Soualmia, Normandie Univ., Rouen University and Hospital, SIBM & LITIS EA 4108, Information Processing in Biology & Health, 1, rue de Germont, Cour Leschevin porte 21, 76031 Rouen Cedex, France, Tel : +33 232 885 869, E-mail:
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11
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Zou Y, Donkervoort S, Salo AM, Foley AR, Barnes AM, Hu Y, Makareeva E, Leach ME, Mohassel P, Dastgir J, Deardorff MA, Cohn RD, DiNonno WO, Malfait F, Lek M, Leikin S, Marini JC, Myllyharju J, Bönnemann CG. P4HA1 mutations cause a unique congenital disorder of connective tissue involving tendon, bone, muscle and the eye. Hum Mol Genet 2017; 26:2207-2217. [PMID: 28419360 PMCID: PMC6075373 DOI: 10.1093/hmg/ddx110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 11/14/2022] Open
Abstract
Collagen prolyl 4-hydroxylases (C-P4Hs) play a central role in the formation and stabilization of the triple helical domain of collagens. P4HA1 encodes the catalytic α(I) subunit of the main C-P4H isoenzyme (C-P4H-I). We now report human bi-allelic P4HA1 mutations in a family with a congenital-onset disorder of connective tissue, manifesting as early-onset joint hypermobility, joint contractures, muscle weakness and bone dysplasia as well as high myopia, with evidence of clinical improvement of motor function over time in the surviving patient. Similar to P4ha1 null mice, which die prenatally, the muscle tissue from P1 and P2 was found to have reduced collagen IV immunoreactivity at the muscle basement membrane. Patients were compound heterozygous for frameshift and splice site mutations leading to reduced, but not absent, P4HA1 protein level and C-P4H activity in dermal fibroblasts compared to age-matched control samples. Differential scanning calorimetry revealed reduced thermal stability of collagen in patient-derived dermal fibroblasts versus age-matched control samples. Mutations affecting the family of C-P4Hs, and in particular C-P4H-I, should be considered in patients presenting with congenital connective tissue/myopathy overlap disorders with joint hypermobility, contractures, mild skeletal dysplasia and high myopia.
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Affiliation(s)
- Yaqun Zou
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Antti M. Salo
- Oulu Center for Cell-Matrix Research, Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu, Finland
| | - A. Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Aileen M. Barnes
- Section on Heritable Disorders of Bone and Extracellular Matrix, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Elena Makareeva
- Section on Physical Biochemistry, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Meganne E. Leach
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Children’s National Health System, Washington, DC, USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jahannaz Dastgir
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Matthew A. Deardorff
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Ronald D. Cohn
- Division of Clinical and Metabolic Genetics, Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Wendy O. DiNonno
- Department of Maternal-Fetal Medicine, Eastern Virginia Medical School, VA, USA
| | - Fransiska Malfait
- Center for Medical Genetics, Ghent University Hospital and Ghent University, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sergey Leikin
- Section on Physical Biochemistry, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Joan C. Marini
- Section on Heritable Disorders of Bone and Extracellular Matrix, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Johanna Myllyharju
- Oulu Center for Cell-Matrix Research, Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu, Finland
| | - Carsten G. Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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12
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Ozes B, Karagoz N, Schüle R, Rebelo A, Sobrido MJ, Harmuth F, Synofzik M, Pascual SIP, Colak M, Ciftci-Kavaklioglu B, Kara B, Ordóñez-Ugalde A, Quintáns B, Gonzalez MA, Soysal A, Zuchner S, Battaloglu E. PLA2G6 mutations associated with a continuous clinical spectrum from neuroaxonal dystrophy to hereditary spastic paraplegia. Clin Genet 2017; 92:534-539. [PMID: 28295203 DOI: 10.1111/cge.13008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/07/2017] [Accepted: 03/09/2017] [Indexed: 11/28/2022]
Abstract
PLA2G6-associated neurodegeneration (PLAN) and hereditary spastic paraplegia (HSP) are 2 groups of heterogeneous neurodegenerative diseases. In this study, we report PLA2G6 gene mutations in 3 families from Turkey, Morocco, and Romania. Two affected Turkish siblings presenting HSP adds the disease to PLAN phenotypes. They were homozygous for the PLA2G6 missense c.2239C>T, p.Arg747Trp variant and the ages of onset were 9 and 21. Parkinsonism, dystonia or cognitive decline were not the clinical elements in these patients contrary to the cases that has been previously reported with the same variant, however, iron accumulation was evident in their cranial magnetic resonance imaging. The Moroccan patient was homozygous for a novel missense c.1786C>T, p.Leu596Phe variant and the Romanian patient had 2 novel mutations; c.1898C>T, p.Ala633Val and c.1765_1768del, p.Ser589ThrfsTer76. Both of these patients conformed better to childhood onset PLAN with the age of onset at 4 and 7 years, respectively. Interestingly, all identified mutations were affecting the highly conserved patatin-like phospholipase domain of the PLA2G6 protein.
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Affiliation(s)
- B Ozes
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
| | - N Karagoz
- Department of Neurology, Bakirkoy Training and Research Hospital for Psychiatry and Neurological Diseases, Istanbul, Turkey
| | - R Schüle
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research and Centre of Neurology, Tuebingen, Germany.,University of Tuebingen, German Research Center for Neurodegenerative Diseases (DZNE), Tuebingen, Germany
| | - A Rebelo
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - M-J Sobrido
- Neurogenetics Group, FPGMX-IDIS, Santiago de Compostela, Spain
| | - F Harmuth
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - M Synofzik
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research and Centre of Neurology, Tuebingen, Germany.,University of Tuebingen, German Research Center for Neurodegenerative Diseases (DZNE), Tuebingen, Germany
| | - S I P Pascual
- Servicio de Neurologia Pediátrica, Hospital Universitario La Paz, Prof. Asociado Departamento de Pediatria, Universidad Autónoma de Madrid, Madrid, Spain
| | - M Colak
- Department of Neurology, Bakirkoy Training and Research Hospital for Psychiatry and Neurological Diseases, Istanbul, Turkey
| | - B Ciftci-Kavaklioglu
- Department of Neurology, Bakirkoy Training and Research Hospital for Psychiatry and Neurological Diseases, Istanbul, Turkey
| | - B Kara
- Department of Radiology, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, Istanbul, Turkey
| | | | - B Quintáns
- Neurogenetics Group, FPGMX-IDIS, Santiago de Compostela, Spain
| | - M A Gonzalez
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - A Soysal
- Department of Neurology, Bakirkoy Training and Research Hospital for Psychiatry and Neurological Diseases, Istanbul, Turkey
| | - S Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - E Battaloglu
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
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13
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Hayer SN, Deconinck T, Bender B, Smets K, Züchner S, Reich S, Schöls L, Schüle R, De Jonghe P, Baets J, Synofzik M. STUB1/CHIP mutations cause Gordon Holmes syndrome as part of a widespread multisystemic neurodegeneration: evidence from four novel mutations. Orphanet J Rare Dis 2017; 12:31. [PMID: 28193273 PMCID: PMC5307643 DOI: 10.1186/s13023-017-0580-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 01/26/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND CHIP, the protein encoded by STUB1, is a central component of cellular protein homeostasis and interacts with several key proteins involved in the pathogenesis of manifold neurodegenerative diseases. This gives rise to the hypothesis that mutations in STUB1 might cause a far more multisystemic neurodegenerative phenotype than the previously reported cerebellar ataxia syndrome. METHODS Whole exome sequencing data-sets from n = 87 index subjects of two ataxia cohorts were screened for individuals with STUB1 mutations. In-depth phenotyping by clinical evaluation and neuroimaging was performed in mutation carriers. RESULTS We identified four novel STUB1 mutations in three affected subjects from two index families (frequency 2/87 = 2.3%). All three subjects presented with a severe multisystemic phenotype including severe dementia, spastic tetraparesis, epilepsy, and autonomic dysfunction in addition to cerebellar ataxia, plus hypogonadism in one index patient. Diffusion tensor imaging revealed degeneration of manifold supra- and infratentorial tracts. CONCLUSIONS Our findings provide clinical and imaging support for the notion that CHIP is a crucial converging point of manifold neurodegenerative processes, corresponding with its universal biological function in neurodegeneration. Further, our data reveal the second STUB1 family with ataxia plus hypogonadism reported so far, demonstrating that Gordon Holmes syndrome is indeed a recurrent manifestation of STUB1. However, it does not present in isolation, but as part of a broad multisystemic neurodegenerative process. This supports the notion that STUB1 disease should be conceptualized not by historical or clinical syndromic names, but as a variable multisystemic disease defined by disturbed function of the underlying STUB1 gene, which translates into a multidimensional gradual spectrum of variably associated clinical signs and symptoms.
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Affiliation(s)
- Stefanie Nicole Hayer
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research & Center of Neurology, University of Tuebingen, Hoppe-Seyler-Str. 3, 72076 Tuebingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tuebingen, Tuebingen, Germany
| | - Tine Deconinck
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
- Laboratories of Neurogenetics and Ultrastructural Neuropathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Benjamin Bender
- Department of Diagnostic and Interventional Neuroradiology, University Hospital Tuebingen, Tuebingen, Germany
| | - Katrien Smets
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
- Laboratories of Neurogenetics and Ultrastructural Neuropathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Stephan Züchner
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miami, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, USA
| | - Selina Reich
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research & Center of Neurology, University of Tuebingen, Hoppe-Seyler-Str. 3, 72076 Tuebingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tuebingen, Tuebingen, Germany
| | - Ludger Schöls
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research & Center of Neurology, University of Tuebingen, Hoppe-Seyler-Str. 3, 72076 Tuebingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tuebingen, Tuebingen, Germany
| | - Rebecca Schüle
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research & Center of Neurology, University of Tuebingen, Hoppe-Seyler-Str. 3, 72076 Tuebingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tuebingen, Tuebingen, Germany
| | - Peter De Jonghe
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
- Laboratories of Neurogenetics and Ultrastructural Neuropathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Jonathan Baets
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
- Laboratories of Neurogenetics and Ultrastructural Neuropathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research & Center of Neurology, University of Tuebingen, Hoppe-Seyler-Str. 3, 72076 Tuebingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tuebingen, Tuebingen, Germany
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14
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Qu C, Liang F, Long Q, Zhao M, Shang H, Fan L, Wang L, Foster J, Yan D, Liu X. Genetic screening revealed usher syndrome in a paediatric Chinese patient. HEARING BALANCE AND COMMUNICATION 2017; 15:98-106. [PMID: 30800556 DOI: 10.1080/21695717.2017.1321217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Introduction Usher syndrome is the most common cause of hereditary deaf-blindness. Three clinical subtypes have been classified. Usher syndrome type I is the most severe subtype characterized by congenital severe-to-profound hearing loss, retinitis pigmentosa and vestibular dysfunction. Methods One family was analyzed and the analysis included the combination of a custom capture/next-generation sequencing panel of 180 known deafness gene, Sanger sequencing and bioinformatics approaches. Results Compound heterozygous mutations in the MYO7A gene: a known missense mutation c.494C>T (p.Thr165Met) and a novel missense mutation c.6113G>A (p.Gly2038Glu) were identified in a proband. This Chinese hearing-impaired child was misdiagnosed as non-syndromic hearing loss which was later changed to the diagnosis of Usher syndrome type I after comprehensive audiometric, vestibular and ophthalmological examinations at 9 years old. Conclusions Due to the features of genetic heterogeneity and variation in clinical manifestation, molecular diagnosis and ophthalmological examinations by skilled ophthalmologists with knowledge of Usher syndrome should be suggested as a routine assessment which may improve the accuracy and reliability of etiological diagnosis for hearing loss.
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Affiliation(s)
- Chunyan Qu
- China Rehabilitation and Research Center for Deaf Children, Beijing 100029, China
| | - Fenghe Liang
- Department of Otolaryngology-Head and Neck Surgery, Capital Medical University, Beijing Tongren Hospital, Beijing 100730, China
| | - Qin Long
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Min Zhao
- China Rehabilitation and Research Center for Deaf Children, Beijing 100029, China
| | - Haiqiong Shang
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, China
| | - Lynn Fan
- BSc, University of Miami, Miami, FL 33136, USA
| | - Li Wang
- Institute of Medical Genetics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Joseph Foster
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, FL 33136, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xuezhong Liu
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, FL 33136, USA.,Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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15
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Magariello A, Russo C, Citrigno L, Züchner S, Patitucci A, Mazzei R, Conforti FL, Ferlazzo E, Aguglia U, Muglia M. Exome sequencing reveals two FA2H mutations in a family with a complicated form of Hereditary Spastic Paraplegia and psychiatric impairments. J Neurol Sci 2016; 372:347-349. [PMID: 28017243 DOI: 10.1016/j.jns.2016.11.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 11/09/2016] [Accepted: 11/28/2016] [Indexed: 01/15/2023]
Affiliation(s)
- A Magariello
- Institute of Neurological Sciences, National Research Council, Mangone, CS, Italy
| | - C Russo
- Regional Epilepsy Centre, Bianchi-Melacrino-Morelli Hospital, Reggio Calabria, Italy
| | - L Citrigno
- Institute of Neurological Sciences, National Research Council, Mangone, CS, Italy
| | - S Züchner
- Department of Human Genetics and Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - A Patitucci
- Institute of Neurological Sciences, National Research Council, Mangone, CS, Italy
| | - R Mazzei
- Institute of Neurological Sciences, National Research Council, Mangone, CS, Italy
| | - F L Conforti
- Institute of Neurological Sciences, National Research Council, Mangone, CS, Italy
| | - E Ferlazzo
- Regional Epilepsy Centre, Bianchi-Melacrino-Morelli Hospital, Reggio Calabria, Italy
| | - U Aguglia
- Regional Epilepsy Centre, Bianchi-Melacrino-Morelli Hospital, Reggio Calabria, Italy; Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - M Muglia
- Institute of Neurological Sciences, National Research Council, Mangone, CS, Italy.
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16
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Hu B, Arpag S, Zuchner S, Li J. A novel missense mutation of CMT2P alters transcription machinery. Ann Neurol 2016; 80:834-845. [PMID: 27615052 DOI: 10.1002/ana.24776] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/29/2016] [Accepted: 09/01/2016] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Charcot-Marie-Tooth type 2P (CMT2P) has been associated with frameshift mutations in the RING domain of LRSAM1 (an E3 ligase). This study describes families with a novel missense mutation of LRSAM1 gene and explores pathogenic mechanisms of CMT2P. METHODS Patients with CMT2P were characterized clinically, electrophysiologically, and genetically. A neuronal model with the LRSAM1 mutation was created using CRISPR/Cas9 technology. The neuronal cell line along with fibroblasts isolated from the patients was used to study RNA-binding proteins. RESULTS This American family with dominantly inherited axonal polyneuropathy reveals a phenotype similar to those in previously reported non-US families. The affected members in our family cosegregated with a novel missense mutation Cys694Arg that alters a highly conserved cysteine in the RING domain. This mutation leads to axonal degeneration in the in vitro neuronal cell line. Moreover, using protein mass spectrometry, we identified a group of RNA-binding proteins (including FUS, a protein critically involved in motor neuron degeneration) that interacted with LRSAM1. The interactions were disrupted by the Cys694Arg mutation, which resulted in reduction of intranuclear RNA-binding proteins. INTERPRETATION Our findings suggest that the mutant LRSAM1 may aberrantly affect the formation of transcription machinery. Given that a similar mechanism has been reported in motor neuron degeneration of amyotrophic lateral sclerosis, abnormalities of RNA/RNA-binding protein complex may play a role in the neuronal degeneration of CMT2P. Ann Neurol 2016;80:834-845.
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Affiliation(s)
- Bo Hu
- Department of Neurology, Center for Human Genetic Research, and Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN
| | - Sezgi Arpag
- Department of Neurology, Center for Human Genetic Research, and Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN
| | - Stephan Zuchner
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL
| | - Jun Li
- Department of Neurology, Center for Human Genetic Research, and Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN
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17
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Helbig KL, Hedrich UBS, Shinde DN, Krey I, Teichmann AC, Hentschel J, Schubert J, Chamberlin AC, Huether R, Lu HM, Alcaraz WA, Tang S, Jungbluth C, Dugan SL, Vainionpää L, Karle KN, Synofzik M, Schöls L, Schüle R, Lehesjoki AE, Helbig I, Lerche H, Lemke JR. A recurrent mutation in KCNA2 as a novel cause of hereditary spastic paraplegia and ataxia. Ann Neurol 2016; 80. [PMID: 27543892 PMCID: PMC5129488 DOI: 10.1002/ana.24762] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 08/02/2016] [Accepted: 08/14/2016] [Indexed: 01/30/2023]
Abstract
The hereditary spastic paraplegias (HSPs) are heterogeneous neurodegenerative disorders with over 50 known causative genes. We identified a recurrent mutation in KCNA2 (c.881G>A, p.R294H), encoding the voltage-gated K(+) -channel, KV 1.2, in two unrelated families with HSP, intellectual disability (ID), and ataxia. Follow-up analysis of > 2,000 patients with various neurological phenotypes identified a de novo p.R294H mutation in a proband with ataxia and ID. Two-electrode voltage-clamp recordings of Xenopus laevis oocytes expressing mutant KV 1.2 channels showed loss of function with a dominant-negative effect. Our findings highlight the phenotypic spectrum of a recurrent KCNA2 mutation, implicating ion channel dysfunction as a novel HSP disease mechanism. Ann Neurol 2016.
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Affiliation(s)
| | - Ulrike B S Hedrich
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | | | - Ilona Krey
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | | | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Julian Schubert
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | | | - Robert Huether
- Department of Bioinformatics, Ambry Genetics, Aliso Viejo, CA
| | - Hsiao-Mei Lu
- Department of Bioinformatics, Ambry Genetics, Aliso Viejo, CA
| | - Wendy A Alcaraz
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA
| | - Sha Tang
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA
| | - Chelsy Jungbluth
- Department of Medical Genetics, Children's Hospitals and Clinics of Minnesota, Minneapolis, MN
| | - Sarah L Dugan
- Department of Medical Genetics, Children's Hospitals and Clinics of Minnesota, Minneapolis, MN.,Division of Medical Genetics, University of Utah, Salt Lake City, UT
| | - Leena Vainionpää
- Department of Pediatrics and Adolescence, Oulu University Hospital, PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - Kathrin N Karle
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.,Department of Psychiatry and Psychotherapy, University of Tübingen, Tübingen, Germany
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ludger Schöls
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Rebecca Schüle
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Anna-Elina Lehesjoki
- Folkhälsan Institute of Genetics, Helsinki, Finland; Research Programs Unit, Molecular Neurology and Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Ingo Helbig
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian-Albrechts-University, Kiel, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany.
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18
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Pottier C, Ravenscroft TA, Brown PH, Finch NA, Baker M, Parsons M, Asmann YW, Ren Y, Christopher E, Levitch D, van Blitterswijk M, Cruchaga C, Campion D, Nicolas G, Richard AC, Guerreiro R, Bras JT, Zuchner S, Gonzalez MA, Bu G, Younkin S, Knopman DS, Josephs KA, Parisi JE, Petersen RC, Ertekin-Taner N, Graff-Radford NR, Boeve BF, Dickson DW, Rademakers R. TYROBP genetic variants in early-onset Alzheimer's disease. Neurobiol Aging 2016; 48:222.e9-222.e15. [PMID: 27658901 DOI: 10.1016/j.neurobiolaging.2016.07.028] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/01/2016] [Accepted: 07/30/2016] [Indexed: 12/30/2022]
Abstract
We aimed to identify new candidate genes potentially involved in early-onset Alzheimer's disease (EOAD). Exome sequencing was conducted on 45 EOAD patients with either a family history of Alzheimer's disease (AD, <65 years) or an extremely early age at the onset (≤55 years) followed by multiple variant filtering according to different modes of inheritance. We identified 29 candidate genes potentially involved in EOAD, of which the gene TYROBP, previously implicated in AD, was selected for genetic and functional follow-up. Using 3 patient cohorts, we observed rare coding TYROBP variants in 9 out of 1110 EOAD patients, whereas no such variants were detected in 1826 controls (p = 0.0001), suggesting that at least some rare TYROBP variants might contribute to EOAD risk. Overexpression of the p.D50_L51ins14 TYROBP mutant led to a profound reduction of TREM2 expression, a well-established risk factor for AD. This is the first study supporting a role for genetic variation in TYROBP in EOAD, with in vitro support for a functional effect of the p.D50_L51ins14 TYROBP mutation on TREM2 expression.
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Affiliation(s)
- Cyril Pottier
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - NiCole A Finch
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Matt Baker
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Meeia Parsons
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yan W Asmann
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL, USA
| | - Yingxue Ren
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Denise Levitch
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Dominique Campion
- Inserm U1079, Rouen University, Normandy Center for Genomic Medicine and Personalized Medicine, Normandy University, Rouen, France; CNR-MAJ, Rouen University Hospital, Rouen, France; Department of Research, Rouvray Psychiatric Hospital, Rouen, France
| | - Gaël Nicolas
- Inserm U1079, Rouen University, Normandy Center for Genomic Medicine and Personalized Medicine, Normandy University, Rouen, France; CNR-MAJ, Rouen University Hospital, Rouen, France; Department of Genetics, Rouen University Hospital, Rouen, France
| | - Anne-Claire Richard
- Inserm U1079, Rouen University, Normandy Center for Genomic Medicine and Personalized Medicine, Normandy University, Rouen, France; CNR-MAJ, Rouen University Hospital, Rouen, France
| | - Rita Guerreiro
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Jose T Bras
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Stephan Zuchner
- Dr John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | | | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Steven Younkin
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | | | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
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19
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Kahle KT, Flores B, Bharucha-Goebel D, Zhang J, Donkervoort S, Hegde M, Hussain G, Duran D, Liang B, Sun D, Bönnemann CG, Delpire E. Peripheral motor neuropathy is associated with defective kinase regulation of the KCC3 cotransporter. Sci Signal 2016; 9:ra77. [PMID: 27485015 PMCID: PMC5506493 DOI: 10.1126/scisignal.aae0546] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Using exome sequencing, we identified a de novo mutation (c.2971A>G; T991A) in SLC12A6, the gene encoding the K(+)-Cl(-) cotransporter KCC3, in a patient with an early-onset, progressive, and severe peripheral neuropathy primarily affecting motor neurons. Normally, the WNK kinase-dependent phosphorylation of T(991) tonically inhibits KCC3; however, cell swelling triggers Thr(991) dephosphorylation to activate the transporter and restore cell volume. KCC3 T991A mutation in patient cells abolished Thr(991) phosphorylation, resulted in constitutive KCC3 activity, and compromised cell volume homeostasis. KCC3(T991A/T991A) mutant mice exhibited constitutive KCC3 activity and recapitulated aspects of the clinical, electrophysiological, and histopathological findings of the patient. These results suggest that the function of the peripheral nervous system depends on finely tuned, kinase-regulated KCC3 activity and implicate abnormal cell volume homeostasis as a previously unreported mechanism of axonal degeneration.
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Affiliation(s)
- Kristopher T Kahle
- Departments of Neurosurgery and Pediatrics and Cellular and Molecular Physiology, Centers for Mendelian Genomics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Bianca Flores
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Diana Bharucha-Goebel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20814, USA. Department of Neurology, Children's National Health System, Washington, DC 20010, USA
| | - Jinwei Zhang
- Departments of Neurosurgery and Pediatrics and Cellular and Molecular Physiology, Centers for Mendelian Genomics, Yale School of Medicine, New Haven, CT 06510, USA. MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20814, USA
| | - Madhuri Hegde
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Gulnaz Hussain
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA. Veterans Affairs Pittsburgh Health Care System, Geriatric Research, Educational and Clinical Center Pittsburgh, PA 15240, USA
| | - Daniel Duran
- Departments of Neurosurgery and Pediatrics and Cellular and Molecular Physiology, Centers for Mendelian Genomics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Bo Liang
- Departments of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02114, USA
| | - Dandan Sun
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA. Veterans Affairs Pittsburgh Health Care System, Geriatric Research, Educational and Clinical Center Pittsburgh, PA 15240, USA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20814, USA.
| | - Eric Delpire
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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20
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Tuschl K, Meyer E, Valdivia LE, Zhao N, Dadswell C, Abdul-Sada A, Hung CY, Simpson MA, Chong WK, Jacques TS, Woltjer RL, Eaton S, Gregory A, Sanford L, Kara E, Houlden H, Cuno SM, Prokisch H, Valletta L, Tiranti V, Younis R, Maher ER, Spencer J, Straatman-Iwanowska A, Gissen P, Selim LAM, Pintos-Morell G, Coroleu-Lletget W, Mohammad SS, Yoganathan S, Dale RC, Thomas M, Rihel J, Bodamer OA, Enns CA, Hayflick SJ, Clayton PT, Mills PB, Kurian MA, Wilson SW. Mutations in SLC39A14 disrupt manganese homeostasis and cause childhood-onset parkinsonism-dystonia. Nat Commun 2016; 7:11601. [PMID: 27231142 PMCID: PMC4894980 DOI: 10.1038/ncomms11601] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 04/12/2016] [Indexed: 02/07/2023] Open
Abstract
Although manganese is an essential trace metal, little is known about its transport and homeostatic regulation. Here we have identified a cohort of patients with a novel autosomal recessive manganese transporter defect caused by mutations in SLC39A14. Excessive accumulation of manganese in these patients results in rapidly progressive childhood-onset parkinsonism-dystonia with distinctive brain magnetic resonance imaging appearances and neurodegenerative features on post-mortem examination. We show that mutations in SLC39A14 impair manganese transport in vitro and lead to manganese dyshomeostasis and altered locomotor activity in zebrafish with CRISPR-induced slc39a14 null mutations. Chelation with disodium calcium edetate lowers blood manganese levels in patients and can lead to striking clinical improvement. Our results demonstrate that SLC39A14 functions as a pivotal manganese transporter in vertebrates.
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Affiliation(s)
- Karin Tuschl
- Genetics and Genomic Medicine, UCL Institute of Child Health, University College London, London WC1N 1EH, UK.,Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Esther Meyer
- Developmental Neurosciences, UCL Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Leonardo E Valdivia
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Ningning Zhao
- Department of Cell, Development and Cancer Biology, Oregon Health &Sciences University, Portland, Oregon 97239, USA
| | - Chris Dadswell
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | - Alaa Abdul-Sada
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | - Christina Y Hung
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Michael A Simpson
- Division of Genetics and Molecular Medicine, King's College London School of Medicine, London SE1 9RT, UK
| | - W K Chong
- Department of Radiology, Great Ormond Street Hospital for Children NHS Trust, London WC1N 3JH, UK
| | - Thomas S Jacques
- Developmental Biology and Cancer, UCL Institute of Child Health and Department of Histopathology, Great Ormond Street Hospital for Children NHS Trust, London WC1N 3JH, UK
| | - Randy L Woltjer
- Department of Pathology, Oregon Health &Science University, Portland, Oregon 97239, USA
| | - Simon Eaton
- Developmental Biology and Cancer Programme, UCL Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Allison Gregory
- Department of Molecular &Medical Genetics, Oregon Health &Science University, Portland, Oregon 97239, USA
| | - Lynn Sanford
- Department of Molecular &Medical Genetics, Oregon Health &Science University, Portland, Oregon 97239, USA
| | - Eleanna Kara
- Institute of Neurology, University College London, London WC1N 3BG, UK.,Alzheimer's Disease Research Centre, Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | - Henry Houlden
- Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Stephan M Cuno
- Institute of Human Genetics, Technische Universität München, Munich 81675, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, Munich 81675, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Lorella Valletta
- Unit of Molecular Neurogenetics, IRCCS, Foundation Neurological Institute 'C. Besta', Milan 20133, Italy
| | - Valeria Tiranti
- Unit of Molecular Neurogenetics, IRCCS, Foundation Neurological Institute 'C. Besta', Milan 20133, Italy
| | - Rasha Younis
- Department of Medical and Molecular Genetics, University of Birmingham, Birmingham B15 2TT, UK
| | - Eamonn R Maher
- Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.,Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - John Spencer
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | - Ania Straatman-Iwanowska
- MRC Laboratory for Molecular Cell Biology and Cell Biology Unit, University College London, London WC1E 6BT, UK
| | - Paul Gissen
- Genetics and Genomic Medicine, UCL Institute of Child Health, University College London, London WC1N 1EH, UK.,MRC Laboratory for Molecular Cell Biology and Cell Biology Unit, University College London, London WC1E 6BT, UK.,Department of Metabolic Medicine, Great Ormond Street Hospital for Children NHS Trust, London WC1N 3JH, UK
| | - Laila A M Selim
- Department of Paediatric Neurology, Faculty of Medicine, Cairo University Children's Hospital, Cairo 11432, Egypt
| | - Guillem Pintos-Morell
- Department of Paediatrics, Section of Paediatric Nephrology, Genetics and Metabolism, Unit of Rare Diseases, University Hospital 'Germans Trias I Pujol', Universitat Autònoma de Barcelona, Badalona 08916, Spain
| | - Wifredo Coroleu-Lletget
- Department of Paediatrics, Paediatric Neurology and Neonatology Unit, University Hospital 'Germans Trias I Pujol', Badalona 08916, Spain
| | - Shekeeb S Mohammad
- Neuroimmunology Group, Institute for Neuroscience and Muscle Research, Kids Research Institute at the Children's Hospital at Westmead, University of Sydney, Westmead NSW 2145, Australia
| | - Sangeetha Yoganathan
- Department of Neurological Sciences, Christian Medical College Hospital, Vellore 632 004, India
| | - Russell C Dale
- Neuroimmunology Group, Institute for Neuroscience and Muscle Research, Kids Research Institute at the Children's Hospital at Westmead, University of Sydney, Westmead NSW 2145, Australia
| | - Maya Thomas
- Department of Neurological Sciences, Christian Medical College Hospital, Vellore 632 004, India
| | - Jason Rihel
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Olaf A Bodamer
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Caroline A Enns
- Department of Cell, Development and Cancer Biology, Oregon Health &Sciences University, Portland, Oregon 97239, USA
| | - Susan J Hayflick
- Department of Molecular &Medical Genetics, Oregon Health &Science University, Portland, Oregon 97239, USA.,Department of Neurology, Oregon Health &Science University, Portland, Oregon 97239, USA.,Department of Pediatrics, Oregon Health &Science University, Portland, Oregon 97239, USA
| | - Peter T Clayton
- Genetics and Genomic Medicine, UCL Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Philippa B Mills
- Genetics and Genomic Medicine, UCL Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Manju A Kurian
- Developmental Neurosciences, UCL Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
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21
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Warman Chardon J, Beaulieu C, Hartley T, Boycott KM, Dyment DA. Axons to Exons: the Molecular Diagnosis of Rare Neurological Diseases by Next-Generation Sequencing. Curr Neurol Neurosci Rep 2016; 15:64. [PMID: 26289954 DOI: 10.1007/s11910-015-0584-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Neurological disorders secondary to single gene mutations are an extremely heterogeneous group of diseases, individually rare, and often associated with progressive and severe disability. Given the degree of both clinical and genetic heterogeneity, next-generation sequencing (NGS) has become an important diagnostic tool. Multi-gene panel testing based on NGS is now prominently used, while whole-exome sequencing and whole-genome sequencing are emerging to facilitate the molecular diagnosis for many genetic neurological diseases. Although single-gene testing remains an important first tier test for disorders with clear phenotype-genotype correlation, NGS provides an expanding unbiased approach to identify rare mutations in genes known to be associated with genetically heterogeneous diseases, and those not initially considered by the clinician due to rarity or atypical clinical presentation. Given the decreasing costs and relatively rapid time to results, NGS-based assessment is quickly becoming a standard-of-care test for patients with genetic neurological diseases.
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Affiliation(s)
- Jodi Warman Chardon
- Division of Neurology, The Ottawa Hospital, 1053 Carling Avenue, Ottawa, ON, K1Y 4E9, Canada
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22
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Falk MJ, Shen L, Gai X. From case studies to community knowledge base: MSeqDR provides a platform for the curation and genomic analysis of mitochondrial diseases. Cold Spring Harb Mol Case Stud 2016; 2:a001065. [PMID: 27148591 PMCID: PMC4853518 DOI: 10.1101/mcs.a001065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Marni J Falk
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Lishuang Shen
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, California 90027, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, California 90027, USA
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23
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Synofzik M, Smets K, Mallaret M, Di Bella D, Gallenmüller C, Baets J, Schulze M, Magri S, Sarto E, Mustafa M, Deconinck T, Haack T, Züchner S, Gonzalez M, Timmann D, Stendel C, Klopstock T, Durr A, Tranchant C, Sturm M, Hamza W, Nanetti L, Mariotti C, Koenig M, Schöls L, Schüle R, de Jonghe P, Anheim M, Taroni F, Bauer P. SYNE1 ataxia is a common recessive ataxia with major non-cerebellar features: a large multi-centre study. ACTA ACUST UNITED AC 2016; 139:1378-93. [PMID: 27086870 DOI: 10.1093/brain/aww079] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 01/11/2016] [Indexed: 12/21/2022]
Abstract
Mutations in the synaptic nuclear envelope protein 1 (SYNE1) gene have been reported to cause a relatively pure, slowly progressive cerebellar recessive ataxia mostly identified in Quebec, Canada. Combining next-generation sequencing techniques and deep-phenotyping (clinics, magnetic resonance imaging, positron emission tomography, muscle histology), we here established the frequency, phenotypic spectrum and genetic spectrum of SYNE1 in a screening of 434 non-Canadian index patients from seven centres across Europe. Patients were screened by whole-exome sequencing or targeted panel sequencing, yielding 23 unrelated families with recessive truncating SYNE1 mutations (23/434 = 5.3%). In these families, 35 different mutations were identified, 34 of them not previously linked to human disease. While only 5/26 patients (19%) showed the classical SYNE1 phenotype of mildly progressive pure cerebellar ataxia, 21/26 (81%) exhibited additional complicating features, including motor neuron features in 15/26 (58%). In three patients, respiratory dysfunction was part of an early-onset multisystemic neuromuscular phenotype with mental retardation, leading to premature death at age 36 years in one of them. Positron emission tomography imaging confirmed hypometabolism in extra-cerebellar regions such as the brainstem. Muscle biopsy reliably showed severely reduced or absent SYNE1 staining, indicating its potential use as a non-genetic indicator for underlying SYNE1 mutations. Our findings, which present the largest systematic series of SYNE1 patients and mutations outside Canada, revise the view that SYNE1 ataxia causes mainly a relatively pure cerebellar recessive ataxia and that it is largely limited to Quebec. Instead, complex phenotypes with a wide range of extra-cerebellar neurological and non-neurological dysfunctions are frequent, including in particular motor neuron and brainstem dysfunction. The disease course in this multisystemic neurodegenerative disease can be fatal, including premature death due to respiratory dysfunction. With a relative frequency of ∼5%, SYNE1 is one of the more common recessive ataxias worldwide.
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Affiliation(s)
- Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Germany German Research Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Germany
| | - Katrien Smets
- Neurogenetics Group, Department of Molecular Genetics, University of Antwerp, VIB Belgium Department of Neurology, Antwerp University Hospital, Belgium Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Belgium
| | - Martial Mallaret
- Department of Neurology, Hôpital de Hautepierre, Strasbourg, France Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM-U964/CNRS-UMR7104/Université de Strasbourg, Collège de France, 67404 Illkirch, France
| | - Daniela Di Bella
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Constanze Gallenmüller
- Department of Neurology with Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich, Germany German Research Center for Neurodegenerative Diseases (DZNE), Munich, Germany Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Jonathan Baets
- Neurogenetics Group, Department of Molecular Genetics, University of Antwerp, VIB Belgium Department of Neurology, Antwerp University Hospital, Belgium Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Belgium
| | - Martin Schulze
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Germany
| | - Stefania Magri
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Elisa Sarto
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Mona Mustafa
- Department of Nuclear Medicine, Ludwig-Maximilians-University, Munich, Germany
| | - Tine Deconinck
- Neurogenetics Group, Department of Molecular Genetics, University of Antwerp, VIB Belgium Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Belgium
| | - Tobias Haack
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Stephan Züchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, USA
| | - Michael Gonzalez
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, USA
| | - Dagmar Timmann
- Department of Neurology, University of Duisburg-Essen, Essen, Germany
| | - Claudia Stendel
- Department of Neurology with Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich, Germany German Research Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Thomas Klopstock
- Department of Neurology with Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich, Germany German Research Center for Neurodegenerative Diseases (DZNE), Munich, Germany Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Alexandra Durr
- APHP Genetic department and Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière (ICM), UPMC University Paris VI, UMR975; CNRS UMR 7225; INSERM U975; University Hospital Pitié-Salpêtrière, 75013 Paris, France
| | - Christine Tranchant
- Department of Neurology, Hôpital de Hautepierre, Strasbourg, France Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM-U964/CNRS-UMR7104/Université de Strasbourg, Collège de France, 67404 Illkirch, France
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Germany
| | - Wahiba Hamza
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, USTHB, Algiers, Algeria
| | - Lorenzo Nanetti
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Caterina Mariotti
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Michel Koenig
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM-U964/CNRS-UMR7104/Université de Strasbourg, Collège de France, 67404 Illkirch, France Laboratoire de Genetique de Maladies Rares, EA 7402, Institut Universitaire de Recherche Clinique, Université et CHU de Montpellier, 34093 Montpellier cedex 5, France
| | - Ludger Schöls
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Germany German Research Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Germany
| | - Rebecca Schüle
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Germany German Research Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Germany Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, USA
| | - Peter de Jonghe
- Neurogenetics Group, Department of Molecular Genetics, University of Antwerp, VIB Belgium Department of Neurology, Antwerp University Hospital, Belgium Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Belgium
| | - Mathieu Anheim
- Department of Neurology, Hôpital de Hautepierre, Strasbourg, France Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM-U964/CNRS-UMR7104/Université de Strasbourg, Collège de France, 67404 Illkirch, France Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Franco Taroni
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Germany
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24
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Rebelo AP, Abrams AJ, Cottenie E, Horga A, Gonzalez M, Bis DM, Sanchez-Mejias A, Pinto M, Buglo E, Markel K, Prince J, Laura M, Houlden H, Blake J, Woodward C, Sweeney MG, Holton JL, Hanna M, Dallman JE, Auer-Grumbach M, Reilly MM, Zuchner S. Cryptic Amyloidogenic Elements in the 3' UTRs of Neurofilament Genes Trigger Axonal Neuropathy. Am J Hum Genet 2016; 98:597-614. [PMID: 27040688 PMCID: PMC4833435 DOI: 10.1016/j.ajhg.2016.02.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/16/2016] [Indexed: 12/14/2022] Open
Abstract
Abnormal protein aggregation is observed in an expanding number of neurodegenerative diseases. Here, we describe a mechanism for intracellular toxic protein aggregation induced by an unusual mutation event in families affected by axonal neuropathy. These families carry distinct frameshift variants in NEFH (neurofilament heavy), leading to a loss of the terminating codon and translation of the 3' UTR into an extra 40 amino acids. In silico aggregation prediction suggested the terminal 20 residues of the altered NEFH to be amyloidogenic, which we confirmed experimentally by serial deletion analysis. The presence of this amyloidogenic motif fused to NEFH caused prominent and toxic protein aggregates in transfected cells and disrupted motor neurons in zebrafish. We identified a similar aggregation-inducing mechanism in NEFL (neurofilament light) and FUS (fused in sarcoma), in which mutations are known to cause aggregation in Charcot-Marie-Tooth disease and amyotrophic lateral sclerosis, respectively. In summary, we present a protein-aggregation-triggering mechanism that should be taken into consideration during the evaluation of stop-loss variants.
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Affiliation(s)
- Adriana P Rebelo
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Alexander J Abrams
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ellen Cottenie
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Alejandro Horga
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Michael Gonzalez
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Dana M Bis
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Avencia Sanchez-Mejias
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Milena Pinto
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Elena Buglo
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Kasey Markel
- Department of Biology, University of Miami, Miami, FL 33146, USA
| | - Jeffrey Prince
- Department of Biology, University of Miami, Miami, FL 33146, USA
| | - Matilde Laura
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Henry Houlden
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Neurogenetics Laboratory, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Julian Blake
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Clinical Neurophysiology, Norfolk and Norwich University Hospital, Norwich NR4 7UY, UK
| | - Cathy Woodward
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Mary G Sweeney
- Neurogenetics Laboratory, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Janice L Holton
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Michael Hanna
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Julia E Dallman
- Department of Biology, University of Miami, Miami, FL 33146, USA
| | | | - Mary M Reilly
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Molecular Neurosciences, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Stephan Zuchner
- Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.
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25
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Motley WW, Palaima P, Yum SW, Gonzalez MA, Tao F, Wanschitz JV, Strickland AV, Löscher WN, De Vriendt E, Koppi S, Medne L, Janecke AR, Jordanova A, Zuchner S, Scherer SS. De novo PMP2 mutations in families with type 1 Charcot-Marie-Tooth disease. Brain 2016; 139:1649-56. [PMID: 27009151 DOI: 10.1093/brain/aww055] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 01/25/2016] [Indexed: 11/12/2022] Open
Abstract
We performed whole exome sequencing on a patient with Charcot-Marie-Tooth disease type 1 and identified a de novo mutation in PMP2, the gene that encodes the myelin P2 protein. This mutation (p.Ile52Thr) was passed from the proband to his one affected son, and segregates with clinical and electrophysiological evidence of demyelinating neuropathy. We then screened a cohort of 136 European probands with uncharacterized genetic cause of Charcot-Marie-Tooth disease and identified another family with Charcot-Marie-Tooth disease type 1 that has a mutation affecting an adjacent amino acid (p.Thr51Pro), which segregates with disease. Our genetic and clinical findings in these kindred demonstrate that dominant PMP2 mutations cause Charcot-Marie-Tooth disease type 1.
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Affiliation(s)
- William W Motley
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA Department of Medicine, Pennsylvania Hospital, University of Pennsylvania, Philadelphia, Pennsylvania 19107, USA
| | - Paulius Palaima
- Molecular Neurogenomics Group, VIB Department of Molecular Genetics, University of Antwerp, Universiteitsplein 1, 2650-Antwerpen, Belgium Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Universiteitsplein 1, 2650-Antwerpen, Belgium
| | - Sabrina W Yum
- Department of Pediatrics, Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Michael A Gonzalez
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, Florida 33136, USA
| | - Feifei Tao
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, Florida 33136, USA
| | | | - Alleene V Strickland
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, Florida 33136, USA
| | | | - Els De Vriendt
- Molecular Neurogenomics Group, VIB Department of Molecular Genetics, University of Antwerp, Universiteitsplein 1, 2650-Antwerpen, Belgium Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Universiteitsplein 1, 2650-Antwerpen, Belgium
| | - Stefan Koppi
- Department of Neurology, State Hospital of Rankweil, Rankweil, Austria
| | - Livija Medne
- Individualized Medical Genetics Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Andreas R Janecke
- Division of Human Genetics, Department of Pediatrics, Medical University of Innsbruck, Innsbruck, Austria
| | - Albena Jordanova
- Molecular Neurogenomics Group, VIB Department of Molecular Genetics, University of Antwerp, Universiteitsplein 1, 2650-Antwerpen, Belgium Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Universiteitsplein 1, 2650-Antwerpen, Belgium
| | - Stephan Zuchner
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, Florida 33136, USA
| | - Steven S Scherer
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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26
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Genetic background of the hereditary spastic paraplegia phenotypes in Hungary - An analysis of 58 probands. J Neurol Sci 2016; 364:116-21. [PMID: 27084228 DOI: 10.1016/j.jns.2016.03.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND Hereditary spastic paraplegias (HSPs) are a clinically and genetically heterogeneous group of neurodegenerative diseases with progressive lower limb spasticity and weakness. The aim of this study is to determine the frequency of different SPG mutations in Hungarian patients, and to provide further genotype-phenotype correlations for the known HSP causing genes. METHODS We carried out genetic testing for 58 probands with clinical characteristics of HSP. For historical reasons, three different approaches were followed in different patients: 1) Sanger sequencing of ATL1 and SPAST genes, 2) whole exome, and 3) targeted panel sequencing by next generation sequencing. RESULTS Genetic diagnosis was established for 20 probands (34.5%). We detected nine previously unreported mutations with high confidence for pathogenicity. The most frequently affected gene was SPAST with pathogenic or likely pathogenic mutations in 10 probands. The most frequently detected variant in our cohort was the SPG7 p.Leu78*, observed in four probands. Altogether five probands were diagnosed with SPG7. Additional mutations were detected in SPG11, ATL1, NIPA1, and ABCD1. CONCLUSION This is the first comprehensive genetic epidemiological study of patients with HSP in Hungary. Next generation sequencing improved the yield of genetic diagnostics in this disease group even when the phenotype was atypical. However, considering the frequency of the HSP-causing gene defects, SPG4, the most common form of the disease, should be tested first to be cost effective in this economic region.
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27
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Schüle R, Wiethoff S, Martus P, Karle KN, Otto S, Klebe S, Klimpe S, Gallenmüller C, Kurzwelly D, Henkel D, Rimmele F, Stolze H, Kohl Z, Kassubek J, Klockgether T, Vielhaber S, Kamm C, Klopstock T, Bauer P, Züchner S, Liepelt-Scarfone I, Schöls L. Hereditary spastic paraplegia: Clinicogenetic lessons from 608 patients. Ann Neurol 2016; 79:646-58. [DOI: 10.1002/ana.24611] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 12/14/2022]
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28
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Tekin D, Yan D, Bademci G, Feng Y, Guo S, Foster J, Blanton S, Tekin M, Liu X. A next-generation sequencing gene panel (MiamiOtoGenes) for comprehensive analysis of deafness genes. Hear Res 2016; 333:179-184. [PMID: 26850479 DOI: 10.1016/j.heares.2016.01.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/06/2015] [Accepted: 01/31/2016] [Indexed: 12/30/2022]
Abstract
Extreme genetic heterogeneity along with remarkable variation in the distribution of causative variants across in different ethnicities makes single gene testing inefficient for hearing loss. We developed a custom capture/next-generation sequencing gene panel of 146 known deafness genes with a total target size of approximately 1 MB. The genes were identified by searching databases including Hereditary Hearing Loss Homepage, the Human Genome Mutation Database (HGMD), Online Mendelian Inheritance in Man (OMIM) and most recent peer-reviewed publications related to the genetics of deafness. The design covered all coding exons, UTRs and 25 bases of intronic flanking sequences for each exon. To validate our panel, we used 6 positive controls with variants in known deafness genes and 8 unsolved samples from individuals with hearing loss. Mean coverage of the targeted exons was 697X. On average, each sample had 99.8%, 96.2% and 92.7% of the targeted region coverage of 1X, 50X and 100X reads, respectively. Analysis detected all known variants in nuclear genes. These results prove the accuracy and reliability of the custom capture experiment.
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Affiliation(s)
- Demet Tekin
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Guney Bademci
- Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Yong Feng
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shengru Guo
- Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Joseph Foster
- Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Susan Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Mustafa Tekin
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Xuezhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA.,Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
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29
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Albulym OM, Kennerson ML, Harms MB, Drew AP, Siddell AH, Auer-Grumbach M, Pestronk A, Connolly A, Baloh RH, Zuchner S, Reddel SW, Nicholson GA. MORC2 mutations cause axonal Charcot-Marie-Tooth disease with pyramidal signs. Ann Neurol 2016; 79:419-27. [PMID: 26659848 DOI: 10.1002/ana.24575] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 12/02/2015] [Accepted: 12/04/2015] [Indexed: 01/14/2023]
Abstract
OBJECTIVE To use linkage analysis and whole exome sequencing to identify the genetic mutation in a multigenerational Australian family with Charcot-Marie-Tooth disease type 2 (CMT2) and pyramidal signs. METHODS Genome-wide linkage analysis was performed to map the locus. Whole exome sequencing was undertaken on selected individuals (3 affected, 1 normal), and segregation analysis and mutation screening were carried out using high-resolution melt analysis. The GEM.app database was queried to identify additional families with mutations. RESULTS Significant linkage (2-point LOD score ≥ +3) and haplotype analysis mapped a new locus for CMT2 and pyramidal signs to a 6.6Mb interval on chromosome 22q12.1-q12.3. Whole exome sequencing identified a novel mutation (p.R252W) in the microrchidia CW-type zinc finger 2 (MORC2) gene mapping within the linkage region. The mutation fully segregated with the disease phenotype in the family. Screening additional families and querying unsolved CMT2 exomes, we identified the p.R252W mutation in 2 unrelated early onset CMT2 families and a second mutation p.E236G in 2 unrelated CMT2 families. Both the mutations occurred at highly conserved amino acid residues and were absent in the normal population. INTERPRETATION We have identified a new locus in which MORC2 mutations are the likely pathogenic cause of CMT2 and pyramidal signs in these families. MORC2 encodes the human CW-type zinc finger 2 protein, which is a chromatin modifier involved in the regulation of DNA repair as well as gene transcription.
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Affiliation(s)
- Obaid M Albulym
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
| | - Matthew B Harms
- Department of Neurology, Washington University School of Medicine, St Louis, MO
| | - Alexander P Drew
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Anna H Siddell
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | | | - Alan Pestronk
- Department of Neurology, Washington University School of Medicine, St Louis, MO
| | - Anne Connolly
- Department of Neurology, Washington University School of Medicine, St Louis, MO
| | - Robert H Baloh
- Department of Neurology, Cedars Sinai Medical Center, Los Angeles, CA
| | - Stephan Zuchner
- Dr John T. MacDonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL
| | - Stephen W Reddel
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
| | - Garth A Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
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30
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Donkervoort S, Papadaki M, de Winter JM, Neu MB, Kirschner J, Bolduc V, Yang ML, Gibbons MA, Hu Y, Dastgir J, Leach ME, Rutkowski A, Foley AR, Krüger M, Wartchow EP, McNamara E, Ong R, Nowak KJ, Laing NG, Clarke NF, Ottenheijm C, Marston SB, Bönnemann CG. TPM3 deletions cause a hypercontractile congenital muscle stiffness phenotype. Ann Neurol 2015; 78:982-994. [PMID: 26418456 DOI: 10.1002/ana.24535] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 09/02/2015] [Accepted: 09/05/2015] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Mutations in TPM3, encoding Tpm3.12, cause a clinically and histopathologically diverse group of myopathies characterized by muscle weakness. We report two patients with novel de novo Tpm3.12 single glutamic acid deletions at positions ΔE218 and ΔE224, resulting in a significant hypercontractile phenotype with congenital muscle stiffness, rather than weakness, and respiratory failure in one patient. METHODS The effect of the Tpm3.12 deletions on the contractile properties in dissected patient myofibers was measured. We used quantitative in vitro motility assay to measure Ca(2+) sensitivity of thin filaments reconstituted with recombinant Tpm3.12 ΔE218 and ΔE224. RESULTS Contractility studies on permeabilized myofibers demonstrated reduced maximal active tension from both patients with increased Ca(2+) sensitivity and altered cross-bridge cycling kinetics in ΔE224 fibers. In vitro motility studies showed a two-fold increase in Ca(2+) sensitivity of the fraction of filaments motile and the filament sliding velocity concentrations for both mutations. INTERPRETATION These data indicate that Tpm3.12 deletions ΔE218 and ΔE224 result in increased Ca(2+) sensitivity of the troponin-tropomyosin complex, resulting in abnormally active interaction of the actin and myosin complex. Both mutations are located in the charged motifs of the actin-binding residues of tropomyosin 3, thus disrupting the electrostatic interactions that facilitate accurate tropomyosin binding with actin necessary to prevent the on-state. The mutations destabilize the off-state and result in excessively sensitized excitation-contraction coupling of the contractile apparatus. This work expands the phenotypic spectrum of TPM3-related disease and provides insights into the pathophysiological mechanisms of the actin-tropomyosin complex.
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Affiliation(s)
- S Donkervoort
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA
| | - M Papadaki
- National Heart and Lung Institute, Imperial College London, London, UK
| | - J M de Winter
- Department of Physiology, VU University Medical Center, Amsterdam, The Netherlands
| | - M B Neu
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA
| | - J Kirschner
- Department of Neuropediatrics and Muscle Disorders, University Medical Center Freiburg, Freiburg, Germany
| | - V Bolduc
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA
| | - M L Yang
- University of Colorado School of Medicine, Department of Pediatrics and Neurology, Section of Child Neurology, Aurora, CO, USA
| | - M A Gibbons
- University of Colorado Denver School of Medicine, Aurora, CO, USA
| | - Y Hu
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA
| | - J Dastgir
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA
| | - M E Leach
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA.,Children's National Health System, Washington DC, USA
| | - A Rutkowski
- Kaiser SCPMG, Cure CMD, P.O. Box 701, Olathe, KS 66051, USA
| | - A R Foley
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA
| | - M Krüger
- Department of General Pediatrics, Adolescent Medicine and Neonatology, University Medical Center Freiburg, Freiburg, Germany
| | - E P Wartchow
- Department of Pathology, Children's Hospital Colorado, Aurora, Colorado, USA
| | - E McNamara
- Neuromuscular Diseases Laboratory, Centre for Medical Research, Faculty of Medicine, Dentistry and Health Sciences, The University of Western Australia Crawley, WA, Australia
| | - R Ong
- Neuromuscular Diseases Laboratory, Centre for Medical Research, Faculty of Medicine, Dentistry and Health Sciences, The University of Western Australia Crawley, WA, Australia
| | - K J Nowak
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA
| | - N G Laing
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Perth, Western Australia, Australia
| | - N F Clarke
- Institute for Neuroscience and Muscle Research, The Children's Hospital at Westmead, University of Sydney, Sydney, Australia
| | - Cac Ottenheijm
- Department of Physiology, VU University Medical Center, Amsterdam, The Netherlands
| | - S B Marston
- National Heart and Lung Institute, Imperial College London, London, UK
| | - C G Bönnemann
- National Institutes of Health, Neuromuscular and Neurogenetic Disorders of Childhood Section, Bethesda, MD, USA
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31
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Human genotype–phenotype databases: aims, challenges and opportunities. Nat Rev Genet 2015; 16:702-15. [DOI: 10.1038/nrg3932] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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32
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Brennan KM, Bai Y, Pisciotta C, Wang S, Feely SME, Hoegger M, Gutmann L, Moore SA, Gonzalez M, Sherman DL, Brophy PJ, Züchner S, Shy ME. Absence of Dystrophin Related Protein-2 disrupts Cajal bands in a patient with Charcot-Marie-Tooth disease. Neuromuscul Disord 2015; 25:786-93. [PMID: 26227883 PMCID: PMC4920059 DOI: 10.1016/j.nmd.2015.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/28/2015] [Accepted: 07/01/2015] [Indexed: 12/12/2022]
Abstract
Using exome sequencing in an individual with Charcot-Marie-Tooth disease (CMT) we have identified a mutation in the X-linked dystrophin-related protein 2 (DRP2) gene. A 60-year-old gentleman presented to our clinic and underwent clinical, electrophysiological and skin biopsy studies. The patient had clinical features of a length dependent sensorimotor neuropathy with an age of onset of 50 years. Neurophysiology revealed prolonged latencies with intermediate conduction velocities but no conduction block or temporal dispersion. A panel of 23 disease causing genes was sequenced and ultimately was uninformative. Whole exome sequencing revealed a stop mutation in DRP2, c.805C>T (Q269*). DRP2 interacts with periaxin and dystroglycan to form the periaxin-DRP2-dystroglycan complex which plays a role in the maintenance of the well-characterized Cajal bands of myelinating Schwann cells. Skin biopsies from our patient revealed a lack of DRP2 in myelinated dermal nerves by immunofluorescence. Furthermore electron microscopy failed to identify Cajal bands in the patient's dermal myelinated axons in keeping with ultrastructural pathology seen in the Drp2 knockout mouse. Both the electrophysiologic and dermal nerve twig pathology support the interpretation that this patient's DRP2 mutation causes characteristic morphological abnormalities recapitulating the Drp2 knockout model and potentially represents a novel genetic cause of CMT.
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Affiliation(s)
- Kathryn M Brennan
- Department of Neurology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA.
| | - Yunhong Bai
- Department of Neurology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Chiara Pisciotta
- Department of Neurology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Suola Wang
- Department of Neurology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Shawna M E Feely
- Department of Neurology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Mark Hoegger
- Department of Neurology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Laurie Gutmann
- Department of Neurology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Steven A Moore
- Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Michael Gonzalez
- Department of Human Genetics and Hussmann Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Diane L Sherman
- Centre for Neuroregeneration, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Peter J Brophy
- Centre for Neuroregeneration, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Stephan Züchner
- Department of Human Genetics and Hussmann Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Michael E Shy
- Department of Neurology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
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33
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Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat 2015; 36:915-21. [PMID: 26295439 PMCID: PMC4610002 DOI: 10.1002/humu.22858] [Citation(s) in RCA: 351] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/21/2015] [Indexed: 12/21/2022]
Abstract
There are few better examples of the need for data sharing than in the rare disease community, where patients, physicians, and researchers must search for "the needle in a haystack" to uncover rare, novel causes of disease within the genome. Impeding the pace of discovery has been the existence of many small siloed datasets within individual research or clinical laboratory databases and/or disease-specific organizations, hoping for serendipitous occasions when two distant investigators happen to learn they have a rare phenotype in common and can "match" these cases to build evidence for causality. However, serendipity has never proven to be a reliable or scalable approach in science. As such, the Matchmaker Exchange (MME) was launched to provide a robust and systematic approach to rare disease gene discovery through the creation of a federated network connecting databases of genotypes and rare phenotypes using a common application programming interface (API). The core building blocks of the MME have been defined and assembled. Three MME services have now been connected through the API and are available for community use. Additional databases that support internal matching are anticipated to join the MME network as it continues to grow.
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Affiliation(s)
- Anthony A. Philippakis
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cardiology, Brigham & Women's Hospital,
Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Danielle R. Azzariti
- Laboratory for Molecular Medicine, Partners Personalized
Medicine, Boston, MA USA
| | - Sergi Beltran
- Centro Nacional de Análisis Genómico, Barcelona,
Spain
| | | | - Catherine A. Brownstein
- Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics and the Manton Center for
Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Genetics and Genome Biology Program, The Hospital for Sick
Children, Toronto, Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | - Han G. Brunner
- Radboud University Medical Center,Department of Human
Genetics, PO Box 9101, 6500HB Nijmegen, The Netherlands
- Maastricht University Medical Center, Department of Clinical
Genetics,PO Box 5800, 6202AZ Maastricht, The Netherlands
| | - Orion J. Buske
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Genetics and Genome Biology Program, The Hospital for Sick
Children, Toronto, Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | | | - Sergiu Dumitriu
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | - Stephanie O.M. Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill
University, Canada
| | - Johan T. den Dunnen
- Human and Clinical Genetics, Leiden University Medical Center,
Leiden, Nederland
| | - Helen V. Firth
- East Anglian Medical Genetics Service, Box 134, Cambridge
University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0QQ,
UK
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Tx 77030, U.S.A
| | - Marta Girdea
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | - Melissa A. Haendel
- Department of Medical Informatics and Clinical Epidemiology,
Oregon Health & Science University, Portland, OR, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins
University, Baltimore, MD, USA
| | - Ingrid A. Holm
- Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics and the Manton Center for
Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Lijia Huang
- The Children's Hospital of Eastern Ontario Research Institute,
Ottawa, ON, Canada
| | - Matthew E. Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Ben Hutton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Joel B. Krier
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital, 41 Avenue Louis Pasteur, Suite 301, Boston, MA 02115, USA
| | - Andriy Misyura
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | - Justin Paschall
- European Molecular Biology Laboratory - European
Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD,
UK
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, 1156 High Street, Santa
Cruz, CA, USA
| | - Peter N. Robinson
- Institute for Medical Genetics and Human Genetics,
Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195 Berlin,
Germany
- Institute for Bioinformatics, Department of Mathematics and
Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
- Berlin Brandenburg Center for Regenerative Therapies, 13353
Berlin, Germany
| | | | - Nara L. Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins
University, Baltimore, MD, USA
| | - Ganesh J. Swaminathan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Peter E. Taschner
- Department of Medical Informatics and Clinical Epidemiology,
Oregon Health & Science University, Portland, OR, USA
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital, 41 Avenue Louis Pasteur, Suite 301, Boston, MA 02115, USA
| | | | | | - Stephan Züchner
- Dr. John T. Macdonald Foundation Department of Human Genetics
and John P. Hussman Institute for Human Genomics, University of Miami Miller School of
Medicine, Miami, FL, USA
| | - Kym M. Boycott
- Department of Genetics, Children's Hospital of Eastern
Ontario, Ottawa, Ontario, Canada
| | - Heidi L. Rehm
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Laboratory for Molecular Medicine, Partners Personalized
Medicine, Boston, MA USA
- Department of Pathology, Brigham & Women's Hospital, Boston,
MA, USA
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34
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Lambertson KF, Damiani SA, Might M, Shelton R, Terry SF. Participant-driven matchmaking in the genomic era. Hum Mutat 2015; 36:965-73. [PMID: 26252162 DOI: 10.1002/humu.22852] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/15/2015] [Indexed: 01/16/2023]
Abstract
Whole-genome and whole-exome sequencing are increasingly useful diagnostic tools for novel monogenic conditions. In order to confirm diagnoses made using these technologies, genomic matchmaking-the matching of cases with similar phenotypic and/or genotypic profiles, to narrow the number of candidate genes or ascertain a condition's etiology with greater certainty-is essential. Yet, due to current limitations on the size of matchmaking networks and data sets available to support them, identifying a match can be difficult. We argue that matchmaking efforts led by affected individuals and their families-participant-led efforts-offer a twofold solution to this need, in that participants both have the capacity to access larger networks and to provide more detailed sets of phenotypic and genotypic data. These features of participant-led efforts have the potential to increase the value of matchmaking networks, both in terms of number of matches and in terms of the overall energy of the network. We provide two examples of participant-led matchmaking, and propose a model for scaling these efforts.
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Affiliation(s)
| | - Stephen A Damiani
- Mission Massimo Foundation, Inc., Elsternwick, Victoria, Australia.,Mission Massimo Foundation, Inc., Westlake Village, California
| | - Matthew Might
- NGLY1.org, Salt Lake City, Utah.,University of Utah, Salt Lake City, Utah, United States
| | | | - Sharon F Terry
- Genetic Alliance, Washington, District of Columbia.,PXE International, Inc, Washington, District of Columbia
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35
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Gonzalez M, Falk MJ, Gai X, Postrel R, Schüle R, Zuchner S. Innovative genomic collaboration using the GENESIS (GEM.app) platform. Hum Mutat 2015; 36:950-6. [PMID: 26173844 DOI: 10.1002/humu.22836] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/29/2015] [Indexed: 11/10/2022]
Abstract
Next-generation sequencing has led to an unparalleled pace of Mendelian disease gene discovery in recent years. To address the challenges of analysis and sharing of large datasets, we had previously introduced the collaborative web-based GEM.app software [Gonzalez et al., ]. Here, we are presenting the results of using GEM.app over nearly 3 years and introducing the next generation of this platform. First, GEM.app has been renamed to GENESIS since it is now part of "The Genesis Project" (501c3), a not-for-profit foundation that is committed to providing the best technology to enable research scientists and to connecting patients and clinicians to genomic information. Second, GENESIS (GEM.app) has grown to nearly 600 registered users from 44 countries, who have collectively achieved 62 gene identifications or published studies that have expanded phenotype/genotype correlations. Our concept of user-driven data sharing and matchmaking is now the main cause for gene discoveries within GENESIS. In many of these findings, researchers from across the globe have been connected, which gave rise to the genetic evidence needed to successfully pinpoint-specific gene mutations that explained patients' disease. Here, we present an overview of the various novel insights that have been made possible through the data-sharing capabilities of GENESIS/GEM.app.
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Affiliation(s)
| | - Marni J Falk
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104
| | - Xiaowu Gai
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | | | - Rebecca Schüle
- Center for Neurology and Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, 72076, Germany.,German Center for Neurodegenerative Diseases, Tübingen, 72076, Germany.,Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136
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36
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First de novo KCND3 mutation causes severe Kv4.3 channel dysfunction leading to early onset cerebellar ataxia, intellectual disability, oral apraxia and epilepsy. BMC MEDICAL GENETICS 2015; 16:51. [PMID: 26189493 PMCID: PMC4557545 DOI: 10.1186/s12881-015-0200-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 07/10/2015] [Indexed: 11/10/2022]
Abstract
Background Identification of the first de novo mutation in potassium voltage-gated channel, shal-related subfamily, member 3 (KCND3) in a patient with complex early onset cerebellar ataxia in order to expand the genetic and phenotypic spectrum. Methods Whole exome sequencing in a cerebellar ataxia patient and subsequent immunocytochemistry, immunoblotting and patch clamp assays of the channel were performed. Results A de novo KCND3 mutation (c.877_885dupCGCGTCTTC; p.Arg293_Phe295dup) was found duplicating the RVF motif and thereby adding an extra positive charge to voltage-gated potassium 4.3 (Kv4.3) in the voltage-sensor domain causing a severe shift of the voltage-dependence gating to more depolarized voltages. The patient displayed a severe phenotype with early onset cerebellar ataxia complicated by intellectual disability, epilepsy, attention deficit hyperactivity disorder, strabismus, oral apraxia and joint hyperlaxity. Conclusions We identified a de novo KCND3 mutation causing the most marked change in Kv4.3’s channel properties reported so far, which correlated with a severe and unique spinocerebellar ataxia (SCA) type 19/22 disease phenotype.
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37
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Mutations in SLC25A46, encoding a UGO1-like protein, cause an optic atrophy spectrum disorder. Nat Genet 2015; 47:926-32. [PMID: 26168012 PMCID: PMC4520737 DOI: 10.1038/ng.3354] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 06/18/2015] [Indexed: 01/11/2023]
Abstract
Dominant optic atrophy (DOA)1,2 and axonal peripheral neuropathy (Charcot-Marie-Tooth Type 2 or CMT2)3 are hereditary neurodegenerative disorders most commonly caused by mutations in the canonical mitochondrial fusion genes OPA1 and MFN2, respectively4. In yeast, homologs of OPA1(Mgm1) and MFN2(Fzo1) work in concert with Ugo15,6, which has no human equivalent to date7. By whole exome sequencing patients with optic atrophy and CMT2, we identified four families with recessive mutations in SLC25A46. We demonstrate that SLC25A46, like Ugo1, is a modified carrier protein that has been recruited to the outer mitochondrial membrane and interacts with the inner membrane remodeling protein, mitofilin(Fcj1). Loss-of-function in cultured cells and in zebrafish unexpectedly leads to increased mitochondrial connectivity, while severely affecting the development and maintenance of neurons in the fish. The discovery of SLC25A46 strengthens the genetic overlap between optic atrophy and CMT2, while exemplifying a novel class of modified solute transporters linked to mitochondrial dynamics.
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38
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Mutation screen reveals novel variants and expands the phenotypes associated with DYNC1H1. J Neurol 2015; 262:2124-34. [PMID: 26100331 DOI: 10.1007/s00415-015-7727-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 03/25/2015] [Accepted: 03/26/2015] [Indexed: 12/21/2022]
Abstract
Dynein, cytoplasmic 1, heavy chain 1 (DYNC1H1) encodes a necessary subunit of the cytoplasmic dynein complex, which traffics cargo along microtubules. Dominant DYNC1H1 mutations are implicated in neural diseases, including spinal muscular atrophy with lower extremity dominance (SMA-LED), intellectual disability with neuronal migration defects, malformations of cortical development, and Charcot-Marie-Tooth disease, type 2O. We hypothesized that additional variants could be found in these and novel motoneuron and related diseases. Therefore, we analyzed our database of 1024 whole exome sequencing samples of motoneuron and related diseases for novel single nucleotide variations. We filtered these results for significant variants, which were further screened using segregation analysis in available family members. Analysis revealed six novel, rare, and highly conserved variants. Three of these are likely pathogenic and encompass a broad phenotypic spectrum with distinct disease clusters. Our findings suggest that DYNC1H1 variants can cause not only lower, but also upper motor neuron disease. It thus adds DYNC1H1 to the growing list of spastic paraplegia related genes in microtubule-dependent motor protein pathways.
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39
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Safka Brozkova D, Deconinck T, Griffin LB, Ferbert A, Haberlova J, Mazanec R, Lassuthova P, Roth C, Pilunthanakul T, Rautenstrauss B, Janecke AR, Zavadakova P, Chrast R, Rivolta C, Zuchner S, Antonellis A, Beg AA, De Jonghe P, Senderek J, Seeman P, Baets J. Loss of function mutations in HARS cause a spectrum of inherited peripheral neuropathies. Brain 2015; 138:2161-72. [PMID: 26072516 DOI: 10.1093/brain/awv158] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 04/17/2015] [Indexed: 12/12/2022] Open
Abstract
Inherited peripheral neuropathies are a genetically heterogeneous group of disorders characterized by distal muscle weakness and sensory loss. Mutations in genes encoding aminoacyl-tRNA synthetases have been implicated in peripheral neuropathies, suggesting that these tRNA charging enzymes are uniquely important for the peripheral nerve. Recently, a mutation in histidyl-tRNA synthetase (HARS) was identified in a single patient with a late-onset, sensory-predominant peripheral neuropathy; however, the genetic evidence was lacking, making the significance of the finding unclear. Here, we present clinical, genetic, and functional data that implicate HARS mutations in inherited peripheral neuropathies. The associated phenotypic spectrum is broad and encompasses axonal and demyelinating motor and sensory neuropathies, including four young patients presenting with pure motor axonal neuropathy. Genome-wide linkage studies in combination with whole-exome and conventional sequencing revealed four distinct and previously unreported heterozygous HARS mutations segregating with autosomal dominant peripheral neuropathy in four unrelated families (p.Thr132Ile, p.Pro134His, p.Asp175Glu and p.Asp364Tyr). All mutations cause a loss of function in yeast complementation assays, and p.Asp364Tyr is dominantly neurotoxic in a Caenorhabditis elegans model. This study demonstrates the role of HARS mutations in peripheral neuropathy and expands the genetic and clinical spectrum of aminoacyl-tRNA synthetase-related human disease.
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Affiliation(s)
- Dana Safka Brozkova
- 1 DNA Laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague 150 06, Czech Republic
| | - Tine Deconinck
- 2 Neurogenetics Group, VIB-Department of Molecular Genetics, University of Antwerp, Antwerpen 2610, Belgium 3 Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerpen 2610, Belgium
| | - Laurie Beth Griffin
- 4 Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI-48109, USA 5 Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI-48109, USA
| | - Andreas Ferbert
- 6 Department of Neurology, Klinikum Kassel, Kassel 34125, Germany
| | - Jana Haberlova
- 1 DNA Laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague 150 06, Czech Republic
| | - Radim Mazanec
- 7 Department of Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague 150 06, Czech Republic
| | - Petra Lassuthova
- 1 DNA Laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague 150 06, Czech Republic
| | - Christian Roth
- 6 Department of Neurology, Klinikum Kassel, Kassel 34125, Germany
| | - Thanita Pilunthanakul
- 8 Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI-48109, USA
| | - Bernd Rautenstrauss
- 9 Medizinisch Genetisches Zentrum, Munich 80335, Germany 10 Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians-University, Munich 80336, Germany
| | - Andreas R Janecke
- 11 Division of Human Genetics and Department of Pediatrics I, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Petra Zavadakova
- 12 Department of Medical Genetics, University of Lausanne, Lausanne 1005, Switzerland
| | - Roman Chrast
- 12 Department of Medical Genetics, University of Lausanne, Lausanne 1005, Switzerland
| | - Carlo Rivolta
- 12 Department of Medical Genetics, University of Lausanne, Lausanne 1005, Switzerland
| | - Stephan Zuchner
- 13 Dr John T McDonald Foundation Department of Human Genetics, John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL-33136, USA
| | - Anthony Antonellis
- 4 Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI-48109, USA 14 Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI-48109, USA 15 Department of Neurology, University of Michigan Medical School, Ann Arbor, MI-48109, USA
| | - Asim A Beg
- 8 Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI-48109, USA
| | - Peter De Jonghe
- 2 Neurogenetics Group, VIB-Department of Molecular Genetics, University of Antwerp, Antwerpen 2610, Belgium 3 Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerpen 2610, Belgium 16 Department of Neurology, Antwerp University Hospital, Antwerpen 2610, Belgium
| | - Jan Senderek
- 10 Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians-University, Munich 80336, Germany
| | - Pavel Seeman
- 1 DNA Laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague 150 06, Czech Republic
| | - Jonathan Baets
- 2 Neurogenetics Group, VIB-Department of Molecular Genetics, University of Antwerp, Antwerpen 2610, Belgium 3 Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerpen 2610, Belgium 16 Department of Neurology, Antwerp University Hospital, Antwerpen 2610, Belgium
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40
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Coutelier M, Goizet C, Durr A, Habarou F, Morais S, Dionne-Laporte A, Tao F, Konop J, Stoll M, Charles P, Jacoupy M, Matusiak R, Alonso I, Tallaksen C, Mairey M, Kennerson M, Gaussen M, Schule R, Janin M, Morice-Picard F, Durand CM, Depienne C, Calvas P, Coutinho P, Saudubray JM, Rouleau G, Brice A, Nicholson G, Darios F, Loureiro JL, Zuchner S, Ottolenghi C, Mochel F, Stevanin G. Alteration of ornithine metabolism leads to dominant and recessive hereditary spastic paraplegia. Brain 2015; 138:2191-205. [PMID: 26026163 DOI: 10.1093/brain/awv143] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 04/04/2015] [Indexed: 12/30/2022] Open
Abstract
Hereditary spastic paraplegias are heterogeneous neurological disorders characterized by a pyramidal syndrome with symptoms predominantly affecting the lower limbs. Some limited pyramidal involvement also occurs in patients with an autosomal recessive neurocutaneous syndrome due to ALDH18A1 mutations. ALDH18A1 encodes delta-1-pyrroline-5-carboxylate synthase (P5CS), an enzyme that catalyses the first and common step of proline and ornithine biosynthesis from glutamate. Through exome sequencing and candidate gene screening, we report two families with autosomal recessive transmission of ALDH18A1 mutations, and predominant complex hereditary spastic paraplegia with marked cognitive impairment, without any cutaneous abnormality. More interestingly, we also identified monoallelic ALDH18A1 mutations segregating in three independent families with autosomal dominant pure or complex hereditary spastic paraplegia, as well as in two sporadic patients. Low levels of plasma ornithine, citrulline, arginine and proline in four individuals from two families suggested P5CS deficiency. Glutamine loading tests in two fibroblast cultures from two related affected subjects confirmed a metabolic block at the level of P5CS in vivo. Besides expanding the clinical spectrum of ALDH18A1-related pathology, we describe mutations segregating in an autosomal dominant pattern. The latter are associated with a potential trait biomarker; we therefore suggest including amino acid chromatography in the clinico-genetic work-up of hereditary spastic paraplegia, particularly in dominant cases, as the associated phenotype is not distinct from other causative genes.
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Affiliation(s)
- Marie Coutelier
- 1 INSERM, U 1127, F-75013, Paris, France 2 CNRS, UMR 7225, F-75013, Paris, France 3 Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, F-75013, Paris, France 4 Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France 5 Laboratory of Human Molecular Genetics, de Duve Institute, Université catholique de Louvain, B-1200, Brussels, Belgium 6 Ecole Pratique des Hautes Etudes, F-75014, Paris, France
| | - Cyril Goizet
- 7 Univ. Bordeaux, Laboratoire Maladies Rares: Génétique et Métabolisme, EA4576, F-33000, Bordeaux, France 8 CHU Pellegrin, Service de Génétique Médicale, F-33000, Bordeaux, France
| | - Alexandra Durr
- 1 INSERM, U 1127, F-75013, Paris, France 2 CNRS, UMR 7225, F-75013, Paris, France 3 Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, F-75013, Paris, France 4 Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France 9 APHP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France
| | - Florence Habarou
- 10 Metabolic Biochemistry Lab, Necker-Enfants Malades Hospital, APHP, F-75015; and University Paris Descartes, F-75006, Paris, France
| | - Sara Morais
- 1 INSERM, U 1127, F-75013, Paris, France 2 CNRS, UMR 7225, F-75013, Paris, France 3 Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, F-75013, Paris, France 4 Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France 6 Ecole Pratique des Hautes Etudes, F-75014, Paris, France 11 UnIGENe, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, P-4150, Porto, Portugal 12 Instituto de Investigação e Inovação em Saúde, Universidade do Porto, P-4150, Porto, Portugal 13 Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, P-4150, Porto, Portugal
| | - Alexandre Dionne-Laporte
- 14 Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Feifei Tao
- 15 Dr John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Juliette Konop
- 1 INSERM, U 1127, F-75013, Paris, France 2 CNRS, UMR 7225, F-75013, Paris, France 3 Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, F-75013, Paris, France 4 Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France 6 Ecole Pratique des Hautes Etudes, F-75014, Paris, France
| | - Marion Stoll
- 16 Northcott Neuroscience Laboratory, ANZAC Research Institute; Molecular Medicine Laboratory, Concord Hospital; Sydney Medical School University of Sydney, NSW 2138, Sydney, Australia
| | - Perrine Charles
- 9 APHP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France
| | - Maxime Jacoupy
- 1 INSERM, U 1127, F-75013, Paris, France 2 CNRS, UMR 7225, F-75013, Paris, France 3 Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, F-75013, Paris, France 4 Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - Raphaël Matusiak
- 1 INSERM, U 1127, F-75013, Paris, France 2 CNRS, UMR 7225, F-75013, Paris, France 3 Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, F-75013, Paris, France 4 Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - Isabel Alonso
- 11 UnIGENe, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, P-4150, Porto, Portugal 12 Instituto de Investigação e Inovação em Saúde, Universidade do Porto, P-4150, Porto, Portugal 13 Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, P-4150, Porto, Portugal
| | - Chantal Tallaksen
- 1 INSERM, U 1127, F-75013, Paris, France 2 CNRS, UMR 7225, F-75013, Paris, France 3 Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, F-75013, Paris, France 4 Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - Mathilde Mairey
- 1 INSERM, U 1127, F-75013, Paris, France 2 CNRS, UMR 7225, F-75013, Paris, France 3 Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, F-75013, Paris, France 4 Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France 6 Ecole Pratique des Hautes Etudes, F-75014, Paris, France
| | - Marina Kennerson
- 16 Northcott Neuroscience Laboratory, ANZAC Research Institute; Molecular Medicine Laboratory, Concord Hospital; Sydney Medical School University of Sydney, NSW 2138, Sydney, Australia
| | - Marion Gaussen
- 1 INSERM, U 1127, F-75013, Paris, France 2 CNRS, UMR 7225, F-75013, Paris, France 3 Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, F-75013, Paris, France 4 Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France 6 Ecole Pratique des Hautes Etudes, F-75014, Paris, France
| | - Rebecca Schule
- 15 Dr John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA 17 Centre for Neurology and Hertie Institute for Clinical Brain Research, Eberhard-Karls-University, G-72074, Tübingen, Germany 18 German Centre of Neurodegenerative Diseases (DZNE), Eberhard-Karls-University, G-72074, Tübingen, Germany
| | - Maxime Janin
- 10 Metabolic Biochemistry Lab, Necker-Enfants Malades Hospital, APHP, F-75015; and University Paris Descartes, F-75006, Paris, France
| | - Fanny Morice-Picard
- 7 Univ. Bordeaux, Laboratoire Maladies Rares: Génétique et Métabolisme, EA4576, F-33000, Bordeaux, France 8 CHU Pellegrin, Service de Génétique Médicale, F-33000, Bordeaux, France
| | - Christelle M Durand
- 7 Univ. Bordeaux, Laboratoire Maladies Rares: Génétique et Métabolisme, EA4576, F-33000, Bordeaux, France
| | - Christel Depienne
- 1 INSERM, U 1127, F-75013, Paris, France 2 CNRS, UMR 7225, F-75013, Paris, France 3 Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, F-75013, Paris, France 4 Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France 9 APHP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France
| | - Patrick Calvas
- 19 Fédération de Neurologie et Service de Génétique Médicale, CHU de Toulouse, Hôpital Purpan, F-31059, Toulouse, France
| | - Paula Coutinho
- 11 UnIGENe, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, P-4150, Porto, Portugal 12 Instituto de Investigação e Inovação em Saúde, Universidade do Porto, P-4150, Porto, Portugal 20 Serviço de Neurologia, Centro Hospitalar de Entre o Douro e Vouga, P-4520-211, Santa Maria da Feira, Portugal
| | - Jean-Marie Saudubray
- 9 APHP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France
| | - Guy Rouleau
- 14 Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada 21 Department of Neurology and Neurosurgery, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alexis Brice
- 1 INSERM, U 1127, F-75013, Paris, France 2 CNRS, UMR 7225, F-75013, Paris, France 3 Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, F-75013, Paris, France 4 Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France 9 APHP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France
| | - Garth Nicholson
- 16 Northcott Neuroscience Laboratory, ANZAC Research Institute; Molecular Medicine Laboratory, Concord Hospital; Sydney Medical School University of Sydney, NSW 2138, Sydney, Australia
| | - Frédéric Darios
- 1 INSERM, U 1127, F-75013, Paris, France 2 CNRS, UMR 7225, F-75013, Paris, France 3 Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, F-75013, Paris, France 4 Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - José L Loureiro
- 11 UnIGENe, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, P-4150, Porto, Portugal 20 Serviço de Neurologia, Centro Hospitalar de Entre o Douro e Vouga, P-4520-211, Santa Maria da Feira, Portugal
| | - Stephan Zuchner
- 15 Dr John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Chris Ottolenghi
- 10 Metabolic Biochemistry Lab, Necker-Enfants Malades Hospital, APHP, F-75015; and University Paris Descartes, F-75006, Paris, France
| | - Fanny Mochel
- 1 INSERM, U 1127, F-75013, Paris, France 2 CNRS, UMR 7225, F-75013, Paris, France 3 Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, F-75013, Paris, France 4 Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France 9 APHP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France
| | - Giovanni Stevanin
- 1 INSERM, U 1127, F-75013, Paris, France 2 CNRS, UMR 7225, F-75013, Paris, France 3 Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, F-75013, Paris, France 4 Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France 6 Ecole Pratique des Hautes Etudes, F-75014, Paris, France 9 APHP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France
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41
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Abstract
Next-generation sequencing (NGS) technologies have played a central role in the genetic revolution. These technologies, especially whole-exome sequencing, have become the primary tool of geneticists to identify the causative DNA variants in Mendelian disorders, including hereditary deafness. Current research estimates that 1% of all human genes have a function in hearing. To date, mutations in over 80 genes have been reported to cause nonsyndromic hearing loss (NSHL). Strikingly, more than a quarter of all known genes related to NSHL were discovered in the past 5 years via NGS technologies. In this article, we review recent developments in the usage of NGS for hereditary deafness, with an emphasis on whole-exome sequencing.
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Tétreault M, Gonzalez M, Dicaire MJ, Allard P, Gehring K, Leblanc D, Leclerc N, Schondorf R, Mathieu J, Zuchner S, Brais B. Adult-onset painful axonal polyneuropathy caused by a dominant NAGLU mutation. Brain 2015; 138:1477-83. [PMID: 25818867 DOI: 10.1093/brain/awv074] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/12/2015] [Indexed: 01/31/2023] Open
Abstract
Late-onset painful sensory neuropathies are usually acquired conditions associated with common diseases. Adult presentations of known hereditary forms are often accompanied by other organ involvement. We recruited a large French-Canadian family with a dominantly inherited late-onset painful sensory neuropathy. The main clinical feature is recurrent leg pain that progresses to constant painful paraesthesias in the feet and later the hands. As it evolves, some patients develop a mild sensory ataxia. We selected four affected individuals for whole exome sequencing. Analysis of rare variants shared by all cases led to a list of four candidate variants. Segregation analysis in all 45 recruited individuals has shown that only the p.Ile403Thr variant in the α-N-acetyl-glucosaminidase (NAGLU) gene segregates with the disease. Recessive NAGLU mutations cause the severe childhood lysosomal disease mucopolysacharidosis IIIB. Family members carrying the mutation showed a significant decrease of the enzymatic function (average 45%). The late-onset and variable severity of the symptoms may have precluded the description of such symptoms in parents of mucopolysaccharidosis IIIB cases. The identification of a dominant phenotype associated with a NAGLU mutation supports that some carriers of lysosomal enzyme mutations may develop later in life much milder phenotypes.
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Affiliation(s)
- Martine Tétreault
- 1 Neurogenetics of Motion Laboratory, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Michael Gonzalez
- 2 Dr John T Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Marie-Josée Dicaire
- 1 Neurogenetics of Motion Laboratory, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Pierre Allard
- 3 Laboratoire de génétique médicale, CHU-Ste-Justine, Montreal, Quebec, H3T 1C5, Canada
| | - Kalle Gehring
- 4 Department of Biochemistry, McGill University, Montreal, Quebec, H3G 0B1, Canada
| | - Diane Leblanc
- 3 Laboratoire de génétique médicale, CHU-Ste-Justine, Montreal, Quebec, H3T 1C5, Canada
| | - Nadine Leclerc
- 5 Cliniques des maladies neuromusculaires, CSSS-Jonquière, Quebec, G7H 7K9, Canada
| | - Ronald Schondorf
- 6 Department of Neurology and Neurosurgery, Jewish General Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada
| | - Jean Mathieu
- 5 Cliniques des maladies neuromusculaires, CSSS-Jonquière, Quebec, G7H 7K9, Canada
| | - Stephan Zuchner
- 2 Dr John T Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Bernard Brais
- 1 Neurogenetics of Motion Laboratory, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada 5 Cliniques des maladies neuromusculaires, CSSS-Jonquière, Quebec, G7H 7K9, Canada
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43
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Falk MJ, Shen L, Gonzalez M, Leipzig J, Lott MT, Stassen APM, Diroma MA, Navarro-Gomez D, Yeske P, Bai R, Boles RG, Brilhante V, Ralph D, DaRe JT, Shelton R, Terry SF, Zhang Z, Copeland WC, van Oven M, Prokisch H, Wallace DC, Attimonelli M, Krotoski D, Zuchner S, Gai X. Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities. Mol Genet Metab 2015; 114:388-96. [PMID: 25542617 PMCID: PMC4512182 DOI: 10.1016/j.ymgme.2014.11.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 11/26/2022]
Abstract
Success rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires the establishment of robust data resources to enable data sharing that informs accurate understanding of genes, variants, and phenotypes. The "Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium" is a grass-roots effort facilitated by the United Mitochondrial Disease Foundation to identify and prioritize specific genomic data analysis needs of the global mitochondrial disease clinical and research community. A central Web portal (https://mseqdr.org) facilitates the coherent compilation, organization, annotation, and analysis of sequence data from both nuclear and mitochondrial genomes of individuals and families with suspected mitochondrial disease. This Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through the use of a convenient distributed annotation system (DAS) mechanism. A range of data visualization and analysis tools are provided to facilitate user interrogation and understanding of genomic, and ultimately phenotypic, data of relevance to mitochondrial biology and disease. Currently available tools for nuclear and mitochondrial gene analyses include an MSeqDR GBrowse instance that hosts optimized mitochondrial disease and mitochondrial DNA (mtDNA) specific annotation tracks, as well as an MSeqDR locus-specific database (LSDB) that curates variant data on more than 1300 genes that have been implicated in mitochondrial disease and/or encode mitochondria-localized proteins. MSeqDR is integrated with a diverse array of mtDNA data analysis tools that are both freestanding and incorporated into an online exome-level dataset curation and analysis resource (GEM.app) that is being optimized to support needs of the MSeqDR community. In addition, MSeqDR supports mitochondrial disease phenotyping and ontology tools, and provides variant pathogenicity assessment features that enable community review, feedback, and integration with the public ClinVar variant annotation resource. A centralized Web-based informed consent process is being developed, with implementation of a Global Unique Identifier (GUID) system to integrate data deposited on a given individual from different sources. Community-based data deposition into MSeqDR has already begun. Future efforts will enhance capabilities to incorporate phenotypic data that enhance genomic data analyses. MSeqDR will fill the existing void in bioinformatics tools and centralized knowledge that are necessary to enable efficient nuclear and mtDNA genomic data interpretation by a range of shareholders across both clinical diagnostic and research settings. Ultimately, MSeqDR is focused on empowering the global mitochondrial disease community to better define and explore mitochondrial diseases.
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Affiliation(s)
- Marni J Falk
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, USA.
| | - Lishuang Shen
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Michael Gonzalez
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, FL, USA
| | - Jeremy Leipzig
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alphons P M Stassen
- Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands
| | - Maria Angela Diroma
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | | | - Philip Yeske
- United Mitochondrial Disease Foundation, Pittsburgh, PA, USA
| | | | | | - Virginia Brilhante
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, Finland
| | | | | | | | | | - Zhe Zhang
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - William C Copeland
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Mannis van Oven
- Department of Forensic Molecular Biology, Erasmus MC - University Medical Center Rotterdam, The Netherlands
| | - Holger Prokisch
- Institute of Human Genetics, Technical University Munich and Helmholtz Zentrum Munich, Munich, Germany
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Danuta Krotoski
- National Institute of Child Health and Development, The National Institutes of Health, Bethesda, MD, USA
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, FL, USA
| | - Xiaowu Gai
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA.
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44
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Rossor AM, Oates EC, Salter HK, Liu Y, Murphy SM, Schule R, Gonzalez MA, Scoto M, Phadke R, Sewry CA, Houlden H, Jordanova A, Tournev I, Chamova T, Litvinenko I, Zuchner S, Herrmann DN, Blake J, Sowden JE, Acsadi G, Rodriguez ML, Menezes MP, Clarke NF, Auer Grumbach M, Bullock SL, Muntoni F, Reilly MM, North KN. Phenotypic and molecular insights into spinal muscular atrophy due to mutations in BICD2. ACTA ACUST UNITED AC 2014; 138:293-310. [PMID: 25497877 DOI: 10.1093/brain/awu356] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Spinal muscular atrophy is a disorder of lower motor neurons, most commonly caused by recessive mutations in SMN1 on chromosome 5q. Cases without SMN1 mutations are subclassified according to phenotype. Spinal muscular atrophy, lower extremity-predominant, is characterized by lower limb muscle weakness and wasting, associated with reduced numbers of lumbar motor neurons and is caused by mutations in DYNC1H1, which encodes a microtubule motor protein in the dynein-dynactin complex and one of its cargo adaptors, BICD2. We have now identified 32 patients with BICD2 mutations from nine different families, providing detailed insights into the clinical phenotype and natural history of BICD2 disease. BICD2 spinal muscular atrophy, lower extremity predominant most commonly presents with delayed motor milestones and ankle contractures. Additional features at presentation include arthrogryposis and congenital dislocation of the hips. In all affected individuals, weakness and wasting is lower-limb predominant, and typically involves both proximal and distal muscle groups. There is no evidence of sensory nerve involvement. Upper motor neuron signs are a prominent feature in a subset of individuals, including one family with exclusively adult-onset upper motor neuron features, consistent with a diagnosis of hereditary spastic paraplegia. In all cohort members, lower motor neuron features were static or only slowly progressive, and the majority remained ambulant throughout life. Muscle MRI in six individuals showed a common pattern of muscle involvement with fat deposition in most thigh muscles, but sparing of the adductors and semitendinosus. Muscle pathology findings were highly variable and included pseudomyopathic features, neuropathic features, and minimal change. The six causative mutations, including one not previously reported, result in amino acid changes within all three coiled-coil domains of the BICD2 protein, and include a possible 'hot spot' mutation, p.Ser107Leu present in four families. We used the recently solved crystal structure of a highly conserved region of the Drosophila orthologue of BICD2 to further-explore how the p.Glu774Gly substitution inhibits the binding of BICD2 to Rab6. Overall, the features of BICD2 spinal muscular atrophy, lower extremity predominant are consistent with a pathological process that preferentially affects lumbar lower motor neurons, with or without additional upper motor neuron involvement. Defining the phenotypic features in this, the largest BICD2 disease cohort reported to date, will facilitate focused genetic testing and filtering of next generation sequencing-derived variants in cases with similar features.
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Affiliation(s)
- Alexander M Rossor
- 1 MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, WC1N 3BG, UK
| | - Emily C Oates
- 2 Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, New South Wales, 2145, Australia 3 Discipline of Paediatrics and Child Health, Faculty of Medicine, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Hannah K Salter
- 4 Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Yang Liu
- 4 Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Sinead M Murphy
- 5 Department of Neurology, Adelaide and Meath Hospitals Incorporating the National Children's Hospital, Tallaght, Dublin, Ireland 6 Academic Unit of Neurology, Trinity College Dublin, Ireland
| | - Rebecca Schule
- 7 Hertie Institute for Clinical Brain Research and Centre for Neurology, Department of Neurodegenerative Disease, University of Tübingen and the German Research Centre for Neurodegenerative Diseases (DZNE), Tübingen, Germany 8 Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA
| | - Michael A Gonzalez
- 8 Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA
| | - Mariacristina Scoto
- 9 Dubowitz Neuromuscular Centre, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Rahul Phadke
- 1 MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, WC1N 3BG, UK
| | - Caroline A Sewry
- 9 Dubowitz Neuromuscular Centre, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Henry Houlden
- 1 MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, WC1N 3BG, UK
| | - Albena Jordanova
- 10 Molecular Neurogenomics Group, Department of Molecular Genetics, VIB, Antwerp 2610, Belgium 11 Neurogenetics Laboratory, Institute Born-Bunge, University of Antwerp, Antwerp 2610, Belgium 12 Department of Medical Chemistry and Biochemistry, Molecular Medicine Centre, Medical University-Sofia, Sofia 1431, Bulgaria
| | - Iyailo Tournev
- 13 Department of Neurology, Medical University-Sofia, Sofia 1000, Bulgaria 14 Department of Cognitive Science and Psychology, New Bulgarian University, Sofia
| | - Teodora Chamova
- 13 Department of Neurology, Medical University-Sofia, Sofia 1000, Bulgaria
| | - Ivan Litvinenko
- 15 Clinic of Child Neurology, Department of Paediatrics, Medical University-Sofia, Sofia 1000, Bulgaria
| | - Stephan Zuchner
- 8 Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, 33136, USA
| | - David N Herrmann
- 16 University of Rochester Medical Centre, Departments of Neurology and Pathology, Rochester, NY, 14642, USA
| | - Julian Blake
- 17 Department of Clinical Neurophysiology, The National Hospital for Neurology and Neurosurgery and Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK 18 Department of Clinical Neurophysiology, Norfolk and Norwich University Hospital, UK
| | - Janet E Sowden
- 19 University of Rochester Medical Centre, Department of Neurology, Rochester, NY, 14642, USA
| | - Gyuda Acsadi
- 20 Connecticut Children's Medical Centre, Department of Neurology, Hartford Connecticut, 06106, USA
| | - Michael L Rodriguez
- 21 Department of Forensic Medicine, Sydney Local Health District, New South Wales, 2037, Australia 22 Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Manoj P Menezes
- 2 Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, New South Wales, 2145, Australia 3 Discipline of Paediatrics and Child Health, Faculty of Medicine, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Nigel F Clarke
- 2 Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, New South Wales, 2145, Australia 3 Discipline of Paediatrics and Child Health, Faculty of Medicine, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Michaela Auer Grumbach
- 23 Division of Orthopaedics, Medical University of Vienna, Währinger Gürtel 18-20, A-1090 Vienna, Austria
| | - Simon L Bullock
- 4 Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Francesco Muntoni
- 1 MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, WC1N 3BG, UK 9 Dubowitz Neuromuscular Centre, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Mary M Reilly
- 1 MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, WC1N 3BG, UK
| | - Kathryn N North
- 2 Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, New South Wales, 2145, Australia 3 Discipline of Paediatrics and Child Health, Faculty of Medicine, The University of Sydney, Sydney, New South Wales, 2006, Australia 24 Murdoch Children's Research Institute. The Royal Children's Hospital, Parkville Victoria 3052 Australia 25 Department of Paediatrics, University of Melbourne Parkville Victoria 3010 Australia
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45
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Synofzik M, Haack T, Kopajtich R, Gorza M, Rapaport D, Greiner M, Schönfeld C, Freiberg C, Schorr S, Holl R, Gonzalez M, Fritsche A, Fallier-Becker P, Zimmermann R, Strom T, Meitinger T, Züchner S, Schüle R, Schöls L, Prokisch H. Absence of BiP co-chaperone DNAJC3 causes diabetes mellitus and multisystemic neurodegeneration. Am J Hum Genet 2014; 95:689-97. [PMID: 25466870 DOI: 10.1016/j.ajhg.2014.10.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/28/2014] [Indexed: 10/24/2022] Open
Abstract
Diabetes mellitus and neurodegeneration are common diseases for which shared genetic factors are still only partly known. Here, we show that loss of the BiP (immunoglobulin heavy-chain binding protein) co-chaperone DNAJC3 leads to diabetes mellitus and widespread neurodegeneration. We investigated three siblings with juvenile-onset diabetes and central and peripheral neurodegeneration, including ataxia, upper-motor-neuron damage, peripheral neuropathy, hearing loss, and cerebral atrophy. Exome sequencing identified a homozygous stop mutation in DNAJC3. Screening of a diabetes database with 226,194 individuals yielded eight phenotypically similar individuals and one family carrying a homozygous DNAJC3 deletion. DNAJC3 was absent in fibroblasts from all affected subjects in both families. To delineate the phenotypic and mutational spectrum and the genetic variability of DNAJC3, we analyzed 8,603 exomes, including 506 from families affected by diabetes, ataxia, upper-motor-neuron damage, peripheral neuropathy, or hearing loss. This analysis revealed only one further loss-of-function allele in DNAJC3 and no further associations in subjects with only a subset of the features of the main phenotype. Our findings demonstrate that loss-of-function DNAJC3 mutations lead to a monogenic, recessive form of diabetes mellitus in humans. Moreover, they present a common denominator for diabetes and widespread neurodegeneration. This complements findings from mice in which knockout of Dnajc3 leads to diabetes and modifies disease in a neurodegenerative model of Marinesco-Sjögren syndrome.
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46
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Qing J, Yan D, Zhou Y, Liu Q, Wu W, Xiao Z, Liu Y, Liu J, Du L, Xie D, Liu XZ. Whole-exome sequencing to decipher the genetic heterogeneity of hearing loss in a Chinese family with deaf by deaf mating. PLoS One 2014; 9:e109178. [PMID: 25289672 PMCID: PMC4188603 DOI: 10.1371/journal.pone.0109178] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 08/13/2014] [Indexed: 01/12/2023] Open
Abstract
Inherited deafness has been shown to have high genetic heterogeneity. For many decades, linkage analysis and candidate gene approaches have been the main tools to elucidate the genetics of hearing loss. However, this associated study design is costly, time-consuming, and unsuitable for small families. This is mainly due to the inadequate numbers of available affected individuals, locus heterogeneity, and assortative mating. Exome sequencing has now become technically feasible and a cost-effective method for detection of disease variants underlying Mendelian disorders due to the recent advances in next-generation sequencing (NGS) technologies. In the present study, we have combined both the Deafness Gene Mutation Detection Array and exome sequencing to identify deafness causative variants in a large Chinese composite family with deaf by deaf mating. The simultaneous screening of the 9 common deafness mutations using the allele-specific PCR based universal array, resulted in the identification of the 1555A>G in the mitochondrial DNA (mtDNA) 12S rRNA in affected individuals in one branch of the family. We then subjected the mutation-negative cases to exome sequencing and identified novel causative variants in the MYH14 and WFS1 genes. This report confirms the effective use of a NGS technique to detect pathogenic mutations in affected individuals who were not candidates for classical genetic studies.
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Affiliation(s)
- Jie Qing
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Denise Yan
- Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Yuan Zhou
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiong Liu
- Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Weijing Wu
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zian Xiao
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuyuan Liu
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jia Liu
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lilin Du
- Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Dinghua Xie
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xue Zhong Liu
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, Florida, United States of America
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47
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Herrmann DN, Horvath R, Sowden JE, Gonzalez M, Gonzales M, Sanchez-Mejias A, Guan Z, Whittaker RG, Almodovar JL, Lane M, Bansagi B, Pyle A, Boczonadi V, Lochmüller H, Griffin H, Chinnery PF, Lloyd TE, Littleton JT, Zuchner S. Synaptotagmin 2 mutations cause an autosomal-dominant form of lambert-eaton myasthenic syndrome and nonprogressive motor neuropathy. Am J Hum Genet 2014; 95:332-9. [PMID: 25192047 PMCID: PMC4157148 DOI: 10.1016/j.ajhg.2014.08.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 08/15/2014] [Indexed: 12/28/2022] Open
Abstract
Synaptotagmin 2 is a synaptic vesicle protein that functions as a calcium sensor for neurotransmission but has not been previously associated with human disease. Via whole-exome sequencing, we identified heterozygous missense mutations in the C2B calcium-binding domain of the gene encoding Synaptotagmin 2 in two multigenerational families presenting with peripheral motor neuron syndromes. An essential calcium-binding aspartate residue, Asp307Ala, was disrupted by a c.920A>C change in one family that presented with an autosomal-dominant presynaptic neuromuscular junction disorder resembling Lambert-Eaton myasthenic syndrome. A c.923C>T variant affecting an adjacent residue (p.Pro308Leu) produced a presynaptic neuromuscular junction defect and a dominant hereditary motor neuropathy in a second family. Characterization of the mutation homologous to the human c.920A>C variant in Drosophila Synaptotagmin revealed a dominant disruption of synaptic vesicle exocytosis using this transgenic model. These findings indicate that Synaptotagmin 2 regulates neurotransmitter release at human peripheral motor nerve terminals. In addition, mutations in the Synaptotagmin 2 C2B domain represent an important cause of presynaptic congenital myasthenic syndromes and link them with hereditary motor axonopathies.
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Affiliation(s)
- David N Herrmann
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Rita Horvath
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Janet E Sowden
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | | | - Michael Gonzales
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Avencia Sanchez-Mejias
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Zhuo Guan
- The Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Roger G Whittaker
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Jorge L Almodovar
- Department of Neurology, Dartmouth Hitchcock Clinic, Geisel School of Medicine, Hanover, NH 03755, USA
| | - Maria Lane
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Boglarka Bansagi
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Angela Pyle
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Veronika Boczonadi
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Hanns Lochmüller
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Helen Griffin
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Patrick F Chinnery
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Thomas E Lloyd
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - J Troy Littleton
- The Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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48
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Dolzhanskaya N, Gonzalez MA, Sperziani F, Stefl S, Messing J, Wen GY, Alexov E, Zuchner S, Velinov M. A novel p.Leu(381)Phe mutation in presenilin 1 is associated with very early onset and unusually fast progressing dementia as well as lysosomal inclusions typically seen in Kufs disease. J Alzheimers Dis 2014; 39:23-7. [PMID: 24121961 DOI: 10.3233/jad-131340] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Whole exome sequencing in a family with suspected dominant Kufs disease identified a novel Presenilin 1 mutation p.Leu(381)Phe in three brothers who, along with their father, developed progressive dementia and motor deficits in their early 30 s. All affected relatives had unusually rapid disease progression (on average 3.6 years from disease onset to death). In silico analysis of mutation p.Leu(381)Phe predicted more detrimental effects when compared to the common Presenilin 1 mutation p.Glu(280)Ala. Electron microscopy study of peripheral fibroblast cells of the proband showed lysosomal inclusions typical for Kufs disease. However, brain autopsy demonstrated typical changes of Alzheimer's disease.
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Affiliation(s)
- Natalia Dolzhanskaya
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Michael A Gonzalez
- Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Fiorella Sperziani
- Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Jeffrey Messing
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Guang Y Wen
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | | | - Stephan Zuchner
- Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Milen Velinov
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA Albert Einstein College of Medicine, Bronx, NY, USA
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49
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Lecroq T, Soualmia LF. Managing large-scale genomic datasets and translation into clinical practice. Yearb Med Inform 2014; 9:212-4. [PMID: 25123745 DOI: 10.15265/iy-2014-0039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain. METHOD We provide a synopsis of the articles selected for the IMIA Yearbook 2014, from which we attempt to derive a synthetic overview of current and future activities in the field. A first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor evaluated independently the set of 1,851 articles and 15 articles were retained for peer-review. RESULTS The selection and evaluation process of this Yearbook's section on Bioinformatics and Translational Informatics yielded three excellent articles regarding data management and genome medicine. In the first article, the authors present VEST (Variant Effect Scoring Tool) which is a supervised machine learning tool for prioritizing variants found in exome sequencing projects that are more likely involved in human Mendelian diseases. In the second article, the authors show how to infer surnames of male individuals by crossing anonymous publicly available genomic data from the Y chromosome and public genealogy data banks. The third article presents a statistical framework called iCluster+ that can perform pattern discovery in integrated cancer genomic data. This framework was able to determine different tumor subtypes in colon cancer. CONCLUSIONS The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on large-scale biological, genomic, and Electronic Health Records data. Indeed, there is a need for powerful tools for managing and interpreting complex data, but also a need for user-friendly tools developed for the clinicians in their daily practice. All the recent research and development efforts are contributing to the challenge of impacting clinically the results and even going towards a personalized medicine in the near future.
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50
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Gonzalez MA, Feely SM, Speziani F, Strickland AV, Danzi M, Bacon C, Lee Y, Chou TF, Blanton SH, Weihl CC, Zuchner S, Shy ME. A novel mutation in VCP causes Charcot-Marie-Tooth Type 2 disease. ACTA ACUST UNITED AC 2014; 137:2897-902. [PMID: 25125609 DOI: 10.1093/brain/awu224] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Mutations in VCP have been reported to account for a spectrum of phenotypes that include inclusion body myopathy with Paget's disease of the bone and frontotemporal dementia, hereditary spastic paraplegia, and 1-2% of familial amyotrophic lateral sclerosis. We identified a novel VCP mutation (p.Glu185Lys) segregating in an autosomal dominant Charcot-Marie-Tooth disease type 2 family. Functional studies showed that the Glu185Lys variant impaired autophagic function leading to the accumulation of immature autophagosomes. VCP mutations should thus be considered for genetically undefined Charcot-Marie-Tooth disease type 2.
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Affiliation(s)
- Michael A Gonzalez
- 1 Dr John T Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Shawna M Feely
- 2 Department of Neurology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Fiorella Speziani
- 1 Dr John T Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Alleene V Strickland
- 1 Dr John T Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Matt Danzi
- 1 Dr John T Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Chelsea Bacon
- 2 Department of Neurology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Youjin Lee
- 3 Department of Neurology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Tsui-Fen Chou
- 4 Division of Medical Genetics, Department of Paediatrics, Harbor-UCLA Medical Centre and Los Angeles Biomedical Research Institute, Torrance, CA 90502, USA
| | - Susan H Blanton
- 1 Dr John T Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Conrad C Weihl
- 3 Department of Neurology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Stephan Zuchner
- 1 Dr John T Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Michael E Shy
- 2 Department of Neurology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
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