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Zhang Y, Gao H, Zhang L, Zhao Y, Qiu C, Liu X. Novel Germline KIT Variants in Families With Severe Piebaldism: Case Series and Literature Review. J Clin Lab Anal 2024:e25073. [PMID: 38887855 DOI: 10.1002/jcla.25073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
INTRODUCTION Piebaldism is a rare autosomal dominant disorder characterized by congenital white forelock and depigmented patches, which is most commonly caused by deleterious variants in the KIT gene. METHODS Four KIT variants were identified in a piebaldism case series by whole-exome sequencing. Functional experiments, including in vitro minigene reporter assay and enzyme-linked immunosorbent assay, were carried out to elucidate the pathogenicity of the variants. The genotype-phenotype correlation was summarized through extensive literature reviewing. RESULTS All the four cases had severe piebaldism presented with typical white forelock and diffuse depigmentation on the ventral trunk and limbs. Four germline variants at the tyrosine kinase (TK) domains of the KIT gene were identified: two novel variants c.1990+1G>A (p.Pro627_Gly664delinsArg) and c.2716T>C (p.Cys906Arg), and two known variants c.1879+1G>A (p.Gly592_Pro627delinsAla) and c.1747G>A (p.Glu583Lys). Both splicing variants caused exon skipping and inframe deletions in the TK1 domain. The missense variants resided at the TK1 and TK2 domains respectively impairing PI3K/AKT and MAPK/ERK signaling pathways, the downstream of KIT. All severe cases were associated with variants in the TK domains, eliciting a major dominant-negative mechanism of the disease. CONCLUSION Our data expand the mutation spectrum of KIT, emphasized by a dominant-negative effect of variants in the critical TK domains in severe cases. We also share the experience of prenatal diagnosis and informed reproductive choices for the affected families.
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Affiliation(s)
- Yuanyuan Zhang
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Haiming Gao
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Lu Zhang
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yunjing Zhao
- Department of Developmental Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Chuang Qiu
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaoliang Liu
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
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Riva N, Domi T, Pozzi L, Lunetta C, Schito P, Spinelli EG, Cabras S, Matteoni E, Consonni M, Bella ED, Agosta F, Filippi M, Calvo A, Quattrini A. Update on recent advances in amyotrophic lateral sclerosis. J Neurol 2024:10.1007/s00415-024-12435-9. [PMID: 38802624 DOI: 10.1007/s00415-024-12435-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
In the last few years, our understanding of disease molecular mechanisms underpinning ALS has advanced greatly, allowing the first steps in translating into clinical practice novel research findings, including gene therapy approaches. Similarly, the recent advent of assistive technologies has greatly improved the possibility of a more personalized approach to supportive and symptomatic care, in the context of an increasingly complex multidisciplinary line of actions, which remains the cornerstone of ALS management. Against this rapidly growing background, here we provide an comprehensive update on the most recent studies that have contributed towards our understanding of ALS pathogenesis, the latest results from clinical trials as well as the future directions for improving the clinical management of ALS patients.
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Affiliation(s)
- Nilo Riva
- 3Rd Neurology Unit and Motor Neuron Disease Centre, Fondazione IRCCS "Carlo Besta" Neurological Insitute, Milan, Italy.
| | - Teuta Domi
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Pozzi
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Christian Lunetta
- Istituti Clinici Scientifici Maugeri IRCCS, Neurorehabilitation Unit of Milan Institute, 20138, Milan, Italy
| | - Paride Schito
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Edoardo Gioele Spinelli
- Department of Neurology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Neuroimaging Research Unit, Department of Neurology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sara Cabras
- ALS Centre, 'Rita Levi Montalcini' Department of Neuroscience, University of Turin; SC Neurologia 1U, AOU città della Salute e della Scienza di Torino, Turin, Italy
| | - Enrico Matteoni
- ALS Centre, 'Rita Levi Montalcini' Department of Neuroscience, University of Turin; SC Neurologia 1U, AOU città della Salute e della Scienza di Torino, Turin, Italy
| | - Monica Consonni
- 3Rd Neurology Unit and Motor Neuron Disease Centre, Fondazione IRCCS "Carlo Besta" Neurological Insitute, Milan, Italy
| | - Eleonora Dalla Bella
- 3Rd Neurology Unit and Motor Neuron Disease Centre, Fondazione IRCCS "Carlo Besta" Neurological Insitute, Milan, Italy
| | - Federica Agosta
- Department of Neurology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Neuroimaging Research Unit, Department of Neurology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute Huniversity, Milan, Italy
| | - Massimo Filippi
- Department of Neurology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Neuroimaging Research Unit, Department of Neurology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute Huniversity, Milan, Italy
| | - Andrea Calvo
- ALS Centre, 'Rita Levi Montalcini' Department of Neuroscience, University of Turin; SC Neurologia 1U, AOU città della Salute e della Scienza di Torino, Turin, Italy
| | - Angelo Quattrini
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Wu L, Chen J. Type 3 IP3 receptor: Its structure, functions, and related disease implications. Channels (Austin) 2023; 17:2267416. [PMID: 37818548 PMCID: PMC10569359 DOI: 10.1080/19336950.2023.2267416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 10/02/2023] [Indexed: 10/12/2023] Open
Abstract
Cell-fate decisions depend on the precise and strict regulation of multiple signaling molecules and transcription factors, especially intracellular Ca2+ homeostasis and dynamics. Type 3 inositol 1,4,5-triphosphate receptor (IP3R3) is an a tetrameric channel that can mediate the release of Ca2+ from the endoplasmic reticulum (ER) in response to extracellular stimuli. The gating of IP3R3 is regulated not only by ligands but also by other interacting proteins. To date, extensive research conducted on the basic structure of IP3R3, as well as its regulation by ligands and interacting proteins, has provided novel perspectives on its biological functions and pathogenic mechanisms. This review aims to discuss recent advancements in the study of IP3R3 and provides a comprehensive overview of the relevant literature pertaining to its structure, biological functions, and pathogenic mechanisms.
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Affiliation(s)
- Lvying Wu
- Institute of Clinical Medicine, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Jin Chen
- Institute of Clinical Medicine, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
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Sarparanta J, Jonson PH, Reimann J, Vihola A, Luque H, Penttilä S, Johari M, Savarese M, Hackman P, Kornblum C, Udd B. Extension of the DNAJB2a isoform in a dominant neuromyopathy family. Hum Mol Genet 2023; 32:3029-3039. [PMID: 37070754 PMCID: PMC10586202 DOI: 10.1093/hmg/ddad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/19/2023] Open
Abstract
Recessive mutations in the DNAJB2 gene, encoding the J-domain co-chaperones DNAJB2a and DNAJB2b, have previously been reported as the genetic cause of progressive peripheral neuropathies, rarely involving pyramidal signs, parkinsonism and myopathy. We describe here a family with the first dominantly acting DNAJB2 mutation resulting in a late-onset neuromyopathy phenotype. The c.832 T > G p.(*278Glyext*83) mutation abolishes the stop codon of the DNAJB2a isoform resulting in a C-terminal extension of the protein, with no direct effect predicted on the DNAJB2b isoform of the protein. Analysis of the muscle biopsy showed reduction of both protein isoforms. In functional studies, the mutant protein mislocalized to the endoplasmic reticulum due to a transmembrane helix in the C-terminal extension. The mutant protein underwent rapid proteasomal degradation and also increased the turnover of co-expressed wild-type DNAJB2a, potentially explaining the reduced protein amount in the patient muscle tissue. In line with this dominant negative effect, both wild-type and mutant DNAJB2a were shown to form polydisperse oligomers.
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Affiliation(s)
- Jaakko Sarparanta
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
| | - Per Harald Jonson
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
| | - Jens Reimann
- Klinik und Poliklinik für Neurologie, Sektion Neuromuskuläre Erkrankungen, Universitätsklinikum Bonn, D-53127 Bonn, Germany
| | - Anna Vihola
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
- Neuromuscular Research Center, Tampere University Hospital and Fimlab Laboratories, FI-33520 Tampere, Finland
| | - Helena Luque
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
| | - Sini Penttilä
- Neuromuscular Research Center, Tampere University Hospital and Fimlab Laboratories, FI-33520 Tampere, Finland
| | - Mridul Johari
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands WA, Australia
| | - Marco Savarese
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
| | - Peter Hackman
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
| | - Cornelia Kornblum
- Klinik und Poliklinik für Neurologie, Sektion Neuromuskuläre Erkrankungen, Universitätsklinikum Bonn, D-53127 Bonn, Germany
| | - Bjarne Udd
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
- Neuromuscular Research Center, Tampere University Hospital and Fimlab Laboratories, FI-33520 Tampere, Finland
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Rönkkö J, Rodriguez Y, Rasila T, Torregrosa-Muñumer R, Pennonen J, Kvist J, Kuuluvainen E, Bosch LVD, Hietakangas V, Bultynck G, Tyynismaa H, Ylikallio E. Human IP 3 receptor triple knockout stem cells remain pluripotent despite altered mitochondrial metabolism. Cell Calcium 2023; 114:102782. [PMID: 37481871 DOI: 10.1016/j.ceca.2023.102782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/14/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
Inositol 1,4,5-trisphosphate receptors (IP3Rs) are ER Ca2+-release channels that control a broad set of cellular processes. Animal models lacking IP3Rs in different combinations display severe developmental phenotypes. Given the importance of IP3Rs in human diseases, we investigated their role in human induced pluripotent stem cells (hiPSC) by developing single IP3R and triple IP3R knockouts (TKO). Genome edited TKO-hiPSC lacking all three IP3R isoforms, IP3R1, IP3R2, IP3R3, failed to generate Ca2+ signals in response to agonists activating GPCRs, but retained stemness and pluripotency. Steady state metabolite profiling and flux analysis of TKO-hiPSC indicated distinct alterations in tricarboxylic acid cycle metabolites consistent with a deficiency in their pyruvate utilization via pyruvate dehydrogenase, shifting towards pyruvate carboxylase pathway. These results demonstrate that IP3Rs are not essential for hiPSC identity and pluripotency but regulate mitochondrial metabolism. This set of knockout hiPSC is a valuable resource for investigating IP3Rs in human cell types of interest.
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Affiliation(s)
- Julius Rönkkö
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Yago Rodriguez
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Tiina Rasila
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Rubén Torregrosa-Muñumer
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Jana Pennonen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Jouni Kvist
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Emilia Kuuluvainen
- Molecular and Integrative Bioscience Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00790, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, 00790, Finland
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute, KU Leuven - University of Leuven, 3000, Leuven, Belgium; VIB Center for Brain & Disease Research, Laboratory of Neurobiology, 3000, Leuven, Belgium
| | - Ville Hietakangas
- Molecular and Integrative Bioscience Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00790, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, 00790, Finland
| | - Geert Bultynck
- KU Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, Leuven, 3000, Belgium
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Emil Ylikallio
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland; Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, 00290, Finland.
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Ma X, Liu X, Duan X, Fan D. Screening for PRX mutations in a large Chinese Charcot-Marie-Tooth disease cohort and literature review. Front Neurol 2023; 14:1148044. [PMID: 37470010 PMCID: PMC10352492 DOI: 10.3389/fneur.2023.1148044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/06/2023] [Indexed: 07/21/2023] Open
Abstract
Background Periaxins (encoded by PRX) play an important role in the stabilization of peripheral nerve myelin. Mutations in PRX can lead to Charcot-Marie-Tooth disease type 4F (CMT4F). Methods In this study, we screened for PRX mutations using next-generation sequencing and whole-exome sequencing in a large Chinese CMT cohort consisting of 465 unrelated index patients and 650 healthy controls. Sanger sequencing was used for the validation of all identified variants. We also reviewed all previously reported PRX-related CMT cases and summarized the clinical manifestations and genetic features of PRX-related CMTs. Results The hit rate for biallelic PRX variants in our cohort of Chinese CMT patients was 0.43% (2/465). One patient carried a previously unreported splice-site mutation (c.25_27 + 9del) compound heterozygous with a known nonsense variant. Compiling data on CMT4F cases and PRX variants from the medical literature confirmed that early-onset (95.2%), distal amyotrophy or weakness (94.0%), feet deformity (75.0%), sensory impairment or sensory ataxia (65.5%), delayed motor milestones (60.7%), and spinal deformity (59.5%) are typical features for CMT4F. Less frequent features were auditory impairments, respiratory symptoms, late onset, dysarthria or hoarseness, ophthalmic problems, and central nervous system involvement. The two cases with biallelic missense mutations have later onset age than those with nonsense or frameshift mutations. We did not note clear correlations between the type and site of mutations and clinical severity or distinct constellations of symptoms. Conclusion Consistent with observations in other countries and ethnic groups, PRX-related CMT is rare in China. The clinical spectrum is wider than previously anticipated.
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Affiliation(s)
- Xinran Ma
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
| | - Xiaoxuan Liu
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
| | - Xiaohui Duan
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
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Kim YG, Kwon H, Park JH, Nam SH, Ha C, Shin S, Heo WY, Kim HJ, Chung KW, Jang JH, Kim JW, Choi BO. Whole-genome sequencing in clinically diagnosed Charcot-Marie-Tooth disease undiagnosed by whole-exome sequencing. Brain Commun 2023; 5:fcad139. [PMID: 37180992 PMCID: PMC10174204 DOI: 10.1093/braincomms/fcad139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/16/2023] [Accepted: 04/27/2023] [Indexed: 05/16/2023] Open
Abstract
Whole-genome sequencing is the most comprehensive form of next-generation sequencing method. We aimed to assess the additional diagnostic yield of whole-genome sequencing in patients with clinically diagnosed Charcot-Marie-Tooth disease when compared with whole-exome sequencing, which has not been reported in the literature. Whole-genome sequencing was performed on 72 families whose genetic cause of clinically diagnosed Charcot-Marie-Tooth disease was not revealed after the whole-exome sequencing and 17p12 duplication screening. Among the included families, 14 (19.4%) acquired genetic diagnoses that were compatible with their phenotypes. The most common factor that led to the additional diagnosis in the whole-genome sequencing was genotype-driven analysis (four families, 4/14), in which a wider range of genes, not limited to peripheral neuropathy-related genes, were analysed. Another four families acquired diagnosis due to the inherent advantage of whole-genome sequencing such as better coverage than the whole-exome sequencing (two families, 2/14), structural variants (one family, 1/14) and non-coding variants (one family, 1/14). In conclusion, an evident gain in diagnostic yield was obtained from whole-genome sequencing of the whole-exome sequencing-negative cases. A wide range of genes, not limited to inherited peripheral neuropathy-related genes, should be targeted during whole-genome sequencing.
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Affiliation(s)
- Young-gon Kim
- Correspondence to: Jong-Won Kim, MD, PhD Department of Laboratory Medicine and Genetics, Samsung Medical Center 81 Irwon-ro, Gangnam-gu, Seoul 06351, South Korea E-mail:
| | | | - Jong-ho Park
- Clinical Genomics Center, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Soo Hyun Nam
- Cell and Gene Therapy Institute (CGTI), Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Changhee Ha
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Sunghwan Shin
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Won Young Heo
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Hye Jin Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Ki Wha Chung
- Department of Biological Sciences, Kongju National University, Gongju 32588, South Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Clinical Genomics Center, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Byung-Ok Choi
- Correspondence may also be sent to: Byung-Ok Choi, MD, PhD Department of Neurology, Samsung Medical Center 81 Irwon-ro, Gangnam-gu, Seoul 06351, South Korea E-mail:
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Terry LE, Arige V, Neumann J, Wahl AM, Knebel TR, Chaffer JW, Malik S, Liston A, Humblet-Baron S, Bultynck G, Yule DI. Missense mutations in inositol 1,4,5-trisphosphate receptor type 3 result in leaky Ca 2+ channels and activation of store-operated Ca 2+ entry. iScience 2022; 25:105523. [PMID: 36444295 PMCID: PMC9700043 DOI: 10.1016/j.isci.2022.105523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/10/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Mutations in all subtypes of the inositol 1,4,5-trisphosphate receptor Ca2+ release channel are associated with human diseases. In this report, we investigated the functionality of three neuropathy-associated missense mutations in IP3R3 (V615M, T1424M, and R2524C). The mutants only exhibited function when highly over-expressed compared to endogenous hIP3R3. All variants resulted in elevated basal cytosolic Ca2+ levels, decreased endoplasmic reticulum Ca2+ store content, and constitutive store-operated Ca2+ entry in the absence of any stimuli, consistent with a leaky IP3R channel pore. These variants differed in channel function; when stably over-expressed the R2524C mutant was essentially dead, V615M was poorly functional, and T1424M exhibited activity greater than that of the corresponding wild-type following threshold stimulation. These results demonstrate that a common feature of these mutations is decreased IP3R3 function. In addition, these mutations exhibit a novel phenotype manifested as a constitutively open channel, which inappropriately gates SOCE in the absence of stimulation.
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Affiliation(s)
- Lara E. Terry
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
| | - Vikas Arige
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
| | - Julika Neumann
- KU Leuven, Department of Microbiology and Immunology, Leuven, Belgium
| | - Amanda M. Wahl
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
| | - Taylor R. Knebel
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
| | - James W. Chaffer
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
| | - Sundeep Malik
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
| | - Adrian Liston
- KU Leuven, Department of Microbiology and Immunology, Leuven, Belgium
| | | | - Geert Bultynck
- KU Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - David I. Yule
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
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Setlere S, Jurcenko M, Gailite L, Rots D, Kenina V. Alanyl-tRNA Synthetase 1 Gene Variants in Hereditary Neuropathy. Neurol Genet 2022; 8:e200019. [PMID: 36092982 PMCID: PMC9450682 DOI: 10.1212/nxg.0000000000200019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022]
Abstract
Background and ObjectivesOur objective was to report 2 novel variants and to reclassify previously reported alanyl-tRNA synthetase 1 (AARS1) variants associated with hereditary neuropathy and to summarize the clinical features of a previously published cohort of patients.MethodsWe performed detailed neurologic and electrophysiologic assessments and segregation analysis of 2 unrelated families with Charcot-Marie-Tooth (CMT) disease with novel variants in the AARS1 gene. Via literature search, we found studies that included neuropathy cases with AARS1 variants; we then reviewed and reclassified these variants.ResultsWe identified 2 CMT families harboring previously unreported likely pathogenic AARS1 variants: c.1823C>A p.(Thr608Lys) and c.1815C>G p.(His605Gln). In addition, we reinterpreted a total of 35 different AARS1 variants reported in cases with neuropathy from the literature: 9 variants fulfilled the current criteria for being (likely) pathogenic. We compiled and summarized standardized clinical and genotypic information for 90 affected individuals from 32 families with (likely) pathogenic AARS1 variants. Most experienced motor weakness and sensory loss in the lower limbs.DiscussionIn total, 11 AARS1 variants can currently be classified as pathogenic or likely pathogenic and are associated with sensorimotor axonal or intermediate, slowly progressive polyneuropathy with common asymmetry and variable age of symptom onset with no apparent involvement of other organ systems.
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Narayanaswami P, Živković S. Molecular and Genetic Therapies. Neuromuscul Disord 2022. [DOI: 10.1016/b978-0-323-71317-7.00011-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Yubero D, Natera-de Benito D, Pijuan J, Armstrong J, Martorell L, Fernàndez G, Maynou J, Jou C, Roldan M, Ortez C, Nascimento A, Hoenicka J, Palau F. The Increasing Impact of Translational Research in the Molecular Diagnostics of Neuromuscular Diseases. Int J Mol Sci 2021; 22:4274. [PMID: 33924139 PMCID: PMC8074304 DOI: 10.3390/ijms22084274] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
The diagnosis of neuromuscular diseases (NMDs) has been progressively evolving from the grouping of clinical symptoms and signs towards the molecular definition. Optimal clinical, biochemical, electrophysiological, electrophysiological, and histopathological characterization is very helpful to achieve molecular diagnosis, which is essential for establishing prognosis, treatment and genetic counselling. Currently, the genetic approach includes both the gene-targeted analysis in specific clinically recognizable diseases, as well as genomic analysis based on next-generation sequencing, analyzing either the clinical exome/genome or the whole exome or genome. However, as of today, there are still many patients in whom the causative genetic variant cannot be definitely established and variants of uncertain significance are often found. In this review, we address these drawbacks by incorporating two additional biological omics approaches into the molecular diagnostic process of NMDs. First, functional genomics by introducing experimental cell and molecular biology to analyze and validate the variant for its biological effect in an in-house translational diagnostic program, and second, incorporating a multi-omics approach including RNA-seq, metabolomics, and proteomics in the molecular diagnosis of neuromuscular disease. Both translational diagnostics programs and omics are being implemented as part of the diagnostic process in academic centers and referral hospitals and, therefore, an increase in the proportion of neuromuscular patients with a molecular diagnosis is expected. This improvement in the process and diagnostic performance of patients will allow solving aspects of their health problems in a precise way and will allow them and their families to take a step forward in their lives.
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Affiliation(s)
- Dèlia Yubero
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Daniel Natera-de Benito
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.N.-d.B.); (C.O.)
| | - Jordi Pijuan
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Judith Armstrong
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Loreto Martorell
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Guerau Fernàndez
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Joan Maynou
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Cristina Jou
- Department of Pathology, Hospital Sant Joan de Déu, Pediatric Biobank for Research, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Mònica Roldan
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Confocal Microscopy and Cellular Imaging Unit, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain
| | - Carlos Ortez
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.N.-d.B.); (C.O.)
- Division of Pediatrics, Clinic Institute of Medicine & Dermatology, Hospital Clínic, University of Barcelona School of Medicine and Health Sciences, 08950 Barcelona, Spain
| | - Andrés Nascimento
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.N.-d.B.); (C.O.)
| | - Janet Hoenicka
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Francesc Palau
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
- Department of Pathology, Hospital Sant Joan de Déu, Pediatric Biobank for Research, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
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12
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Zhang J, Wang H, Liu W, Wang J, Zhang J, Chang X, Huang S, Pang X, Guo J, Wang Q, Zhang W. A novel Q93H missense mutation in DCTN1 caused distal hereditary motor neuropathy type 7B and Perry syndrome from a Chinese family. Neurol Sci 2021; 42:3695-3705. [DOI: 10.1007/s10072-020-04962-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/03/2020] [Indexed: 01/20/2023]
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13
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Terry LE, Alzayady KJ, Wahl AM, Malik S, Yule DI. Disease-associated mutations in inositol 1,4,5-trisphosphate receptor subunits impair channel function. J Biol Chem 2020; 295:18160-18178. [PMID: 33093175 PMCID: PMC7939385 DOI: 10.1074/jbc.ra120.015683] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/21/2020] [Indexed: 01/27/2023] Open
Abstract
The inositol 1,4,5-trisphosphate (IP3) receptors (IP3Rs), which form tetrameric channels, play pivotal roles in regulating the spatiotemporal patterns of intracellular calcium signals. Mutations in IP3Rs have been increasingly associated with many debilitating human diseases such as ataxia, Gillespie syndrome, and generalized anhidrosis. However, how these mutations affect IP3R function, and how the perturbation of as-sociated calcium signals contribute to the pathogenesis and severity of these diseases remains largely uncharacterized. Moreover, many of these diseases occur as the result of autosomal dominant inheritance, suggesting that WT and mutant subunits associate in heterotetrameric channels. How the in-corporation of different numbers of mutant subunits within the tetrameric channels affects its activities and results in different disease phenotypes is also unclear. In this report, we investigated representative disease-associated missense mutations to determine their effects on IP3R channel activity. Additionally, we designed concatenated IP3R constructs to create tetrameric channels with a predefined subunit composition to explore the functionality of heteromeric channels. Using calcium imaging techniques to assess IP3R channel function, we observed that all the mutations studied resulted in severely attenuated Ca2+ release when expressed as homotetramers. However, some heterotetramers retained varied degrees of function dependent on the composition of the tetramer. Our findings suggest that the effect of mutations depends on the location of the mutation in the IP3R structure, as well as on the stoichiometry of mutant subunits assembled within the tetrameric channel. These studies provide insight into the pathogenesis and penetrance of these devastating human diseases.
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Affiliation(s)
- Lara E Terry
- Department of Pharmacology and Physiology, University of Rochester, Rochester, New York, USA
| | - Kamil J Alzayady
- Department of Pharmacology and Physiology, University of Rochester, Rochester, New York, USA
| | - Amanda M Wahl
- Department of Pharmacology and Physiology, University of Rochester, Rochester, New York, USA
| | - Sundeep Malik
- Department of Pharmacology and Physiology, University of Rochester, Rochester, New York, USA
| | - David I Yule
- Department of Pharmacology and Physiology, University of Rochester, Rochester, New York, USA.
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14
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Mironovich O, Dadali E, Malmberg S, Markova T, Ryzhkova O, Poliakov A. Identification of a Novel de Novo Variant in the SYT2 Gene Causing a Rare Type of Distal Hereditary Motor Neuropathy. Genes (Basel) 2020; 11:genes11111238. [PMID: 33105646 PMCID: PMC7690400 DOI: 10.3390/genes11111238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 01/31/2023] Open
Abstract
Objective: To report the first de novo missense mutation in the SYT2 gene causing distal hereditary motor neuropathy. Methods: Genetic testing was carried out, including clinical exome sequencing for the proband and Sanger sequencing for the proband and his parents. We described the clinical and electrophysiological features found in the patient. Results: We reported a proband with a new de novo missense mutation, c.917C>T (p.Ser306Leu), in the C2B domain of SYT2. The clinical presentation was similar to that of phenotypes described in previous studies. A notable feature in our study was normal electrophysiological testing results of the patient. Conclusions: In this study we reinforced the association between SYT2 mutations and distal hereditary motor neuropathy. We also described the clinical presentation of the patient carrying this pathogenic variant and provided unusual results of electrophysiological testing. The results showed that a diagnosis of SYT2-associated neuropathy should be based on the similarity of clinical manifestations, rather than the results of electrophysiological testing.
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Affiliation(s)
- Olga Mironovich
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, Moscow 115478, Russia; (E.D.); (T.M.); (O.R.); (A.P.)
- Correspondence: ; Tel.: +7-909-687-3104
| | - Elena Dadali
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, Moscow 115478, Russia; (E.D.); (T.M.); (O.R.); (A.P.)
| | - Sergey Malmberg
- Federal State Budget Healthcare Institution “Central Children Clinical Hospital” at FMBA of Russia, Moscow 115409, Russia;
| | - Tatyana Markova
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, Moscow 115478, Russia; (E.D.); (T.M.); (O.R.); (A.P.)
| | - Oxana Ryzhkova
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, Moscow 115478, Russia; (E.D.); (T.M.); (O.R.); (A.P.)
| | - Aleksander Poliakov
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, Moscow 115478, Russia; (E.D.); (T.M.); (O.R.); (A.P.)
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15
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Rönkkö J, Molchanova S, Revah‐Politi A, Pereira EM, Auranen M, Toppila J, Kvist J, Ludwig A, Neumann J, Bultynck G, Humblet‐Baron S, Liston A, Paetau A, Rivera C, Harms MB, Tyynismaa H, Ylikallio E. Dominant mutations in ITPR3 cause Charcot-Marie-Tooth disease. Ann Clin Transl Neurol 2020; 7:1962-1972. [PMID: 32949214 PMCID: PMC7545616 DOI: 10.1002/acn3.51190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE ITPR3, encoding inositol 1,4,5-trisphosphate receptor type 3, was previously reported as a potential candidate disease gene for Charcot-Marie-Tooth neuropathy. Here, we present genetic and functional evidence that ITPR3 is a Charcot-Marie-Tooth disease gene. METHODS Whole-exome sequencing of four affected individuals in an autosomal dominant family and one individual who was the only affected individual in his family was used to identify disease-causing variants. Skin fibroblasts from two individuals of the autosomal dominant family were analyzed functionally by western blotting, quantitative reverse transcription PCR, and Ca2+ imaging. RESULTS Affected individuals in the autosomal dominant family had onset of symmetrical neuropathy with demyelinating and secondary axonal features at around age 30, showing signs of gradual progression with severe distal leg weakness and hand involvement in the proband at age 64. Exome sequencing identified a heterozygous ITPR3 p.Val615Met variant segregating with the disease. The individual who was the only affected in his family had disease onset at age 4 with demyelinating neuropathy. His condition was progressive, leading to severe muscle atrophy below knees and atrophy of proximal leg and hand muscles by age 16. Trio exome sequencing identified a de novo ITPR3 variant p.Arg2524Cys. Altered Ca2+ -transients in p.Val615Met patient fibroblasts suggested that the variant has a dominant-negative effect on inositol 1,4,5-trisphosphate receptor type 3 function. INTERPRETATION Together with two previously identified variants, our report adds further evidence that ITPR3 is a disease-causing gene for CMT and indicates altered Ca2+ homeostasis in disease pathogenesis.
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Affiliation(s)
- Julius Rönkkö
- Stem Cells and Metabolism Research ProgramFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Svetlana Molchanova
- Stem Cells and Metabolism Research ProgramFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Molecular and Integrative Biosciences Research ProgramFaculty of Bio‐ and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Anya Revah‐Politi
- Institute for Genomic MedicineColumbia University Medical CenterNew YorkNew YorkUSA
- Precision Genomics LaboratoryColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Elaine M. Pereira
- Department of PediatricsColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Mari Auranen
- Clinical NeurosciencesNeurologyUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Jussi Toppila
- Department of Clinical NeurophysiologyMedical Imaging CenterHelsinki University Central HospitalHelsinkiFinland
| | - Jouni Kvist
- Stem Cells and Metabolism Research ProgramFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Anastasia Ludwig
- Neuroscience CenterHelsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Julika Neumann
- Department of Microbiology and ImmunologyLaboratory of Adaptive ImmunityKU LeuvenLeuvenBelgium
- VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
| | - Geert Bultynck
- Laboratory of Molecular and Cellular SignalingDepartment of Cellular and Molecular Medicine & Leuven Kanker InstituutKU LeuvenLeuvenBelgium
| | | | - Adrian Liston
- Department of Microbiology and ImmunologyLaboratory of Adaptive ImmunityKU LeuvenLeuvenBelgium
- VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
- Laboratory of Lymphocyte Signalling and DevelopmentBabraham InstituteCambridgeUnited Kingdom
| | - Anders Paetau
- Department of PathologyHUSLAB and University of HelsinkiHelsinkiFinland
| | - Claudio Rivera
- Neuroscience CenterHelsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
- Institut de Neurobiologie de la Méditerranée INMED UMR901MarseilleFrance
| | | | - Henna Tyynismaa
- Stem Cells and Metabolism Research ProgramFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Neuroscience CenterHelsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
- Department of Medical and Clinical GeneticsUniversity of HelsinkiHelsinkiFinland
| | - Emil Ylikallio
- Stem Cells and Metabolism Research ProgramFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Clinical NeurosciencesNeurologyUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
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16
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Safka Brozkova D, Stojkovic T, Haberlová J, Mazanec R, Windhager R, Fernandes Rosenegger P, Hacker S, Züchner S, Kochański A, Leonard‐Louis S, Francou B, Latour P, Senderek J, Seeman P, Auer‐Grumbach M. Demyelinating Charcot–Marie–Tooth neuropathy associated with
FBLN5
mutations. Eur J Neurol 2020; 27:2568-2574. [DOI: 10.1111/ene.14463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 07/29/2020] [Indexed: 12/14/2022]
Affiliation(s)
- D. Safka Brozkova
- DNA Laboratory Department of Paediatric Neurology 2nd Faculty of Medicine Charles University in Prague and Motol University Hospital Prague Czech Republic
| | - T. Stojkovic
- Centre de Référence des Maladies Neuromusculaires Nord/Est/Ile de France Institut de Myologie APHPG‐H Pitié‐Salpêtrière Paris France
| | - J. Haberlová
- DNA Laboratory Department of Paediatric Neurology 2nd Faculty of Medicine Charles University in Prague and Motol University Hospital Prague Czech Republic
| | - R. Mazanec
- Department of Neurology 2nd Faculty of Medicine Charles University in Prague and Motol University Hospital Prague Czech Republic
| | - R. Windhager
- Department of Orthopaedics and Trauma Surgery Medical University of Vienna Vienna Austria
| | | | - S. Hacker
- Department of Orthopaedics and Trauma Surgery Medical University of Vienna Vienna Austria
| | - S. Züchner
- Dr John T. Macdonald Foundation Department of Human Genetics John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - A. Kochański
- Neuromuscular Unit Mossakowski Medical Research Centre Polish Academy of Sciences Warsaw Poland
| | - S. Leonard‐Louis
- Unité de Pathologie Neuromusculaire Centre de Référence des Maladies Neuromusculaires Nord/Est/Ile de France APHPG‐H Pitié‐Salpêtrière Paris France
| | - B. Francou
- Service de Génétique Moléculaire Pharmacogénétique et Hormonologie APHPHôpital Kremlin‐Bicêtre Paris France
| | - P. Latour
- Service de Biochimie et Biologie Moléculaire Grand Est CHU de LyonGH Est Bron France
| | - J. Senderek
- Department of Neurology Friedrich‐Baur‐Institute LMU Munich Munich Germany
| | - P. Seeman
- DNA Laboratory Department of Paediatric Neurology 2nd Faculty of Medicine Charles University in Prague and Motol University Hospital Prague Czech Republic
| | - M. Auer‐Grumbach
- Department of Orthopaedics and Trauma Surgery Medical University of Vienna Vienna Austria
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17
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Rexach J, Lee H, Martinez-Agosto JA, Németh AH, Fogel BL. Clinical application of next-generation sequencing to the practice of neurology. Lancet Neurol 2020; 18:492-503. [PMID: 30981321 DOI: 10.1016/s1474-4422(19)30033-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/21/2018] [Accepted: 01/02/2019] [Indexed: 01/05/2023]
Abstract
Next-generation sequencing technologies allow for rapid and inexpensive large-scale genomic analysis, creating unprecedented opportunities to integrate genomic data into the clinical diagnosis and management of neurological disorders. However, the scale and complexity of these data make them difficult to interpret and require the use of sophisticated bioinformatics applied to extensive datasets, including whole exome and genome sequences. Detailed analysis of genetic data has shown that accurate phenotype information is essential for correct interpretation of genetic variants and might necessitate re-evaluation of the patient in some cases. A multidisciplinary approach that incorporates bioinformatics, clinical evaluation, and human genetics can help to address these challenges. However, despite numerous studies that show the efficacy of next-generation sequencing in establishing molecular diagnoses, pathogenic mutations are generally identified in fewer than half of all patients with genetic neurological disorders, exposing considerable gaps in the understanding of the human genome and providing opportunities to focus research on improving the usefulness of genomics in clinical practice. Looking forward, the emergence of precision health in neurological care will increasingly apply genomic data analysis to pharmacogenetics, preventive medicine, and patient-targeted therapies.
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Affiliation(s)
- Jessica Rexach
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - Brent L Fogel
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Clinical Neurogenomics Research Center, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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18
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Raasakka A, Kursula P. Flexible Players within the Sheaths: The Intrinsically Disordered Proteins of Myelin in Health and Disease. Cells 2020; 9:cells9020470. [PMID: 32085570 PMCID: PMC7072810 DOI: 10.3390/cells9020470] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/16/2020] [Accepted: 02/16/2020] [Indexed: 02/07/2023] Open
Abstract
Myelin ensheathes selected axonal segments within the nervous system, resulting primarily in nerve impulse acceleration, as well as mechanical and trophic support for neurons. In the central and peripheral nervous systems, various proteins that contribute to the formation and stability of myelin are present, which also harbor pathophysiological roles in myelin disease. Many myelin proteins have common attributes, including small size, hydrophobic segments, multifunctionality, longevity, and regions of intrinsic disorder. With recent advances in protein biophysical characterization and bioinformatics, it has become evident that intrinsically disordered proteins (IDPs) are abundant in myelin, and their flexible nature enables multifunctionality. Here, we review known myelin IDPs, their conservation, molecular characteristics and functions, and their disease relevance, along with open questions and speculations. We place emphasis on classifying the molecular details of IDPs in myelin, and we correlate these with their various functions, including susceptibility to post-translational modifications, function in protein–protein and protein–membrane interactions, as well as their role as extended entropic chains. We discuss how myelin pathology can relate to IDPs and which molecular factors are potentially involved.
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Affiliation(s)
- Arne Raasakka
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, NO-5009 Bergen, Norway;
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, NO-5009 Bergen, Norway;
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Aapistie 7A, FI-90220 Oulu, Finland
- Correspondence:
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19
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YARS as an oncogenic protein that promotes gastric cancer progression through activating PI3K-Akt signaling. J Cancer Res Clin Oncol 2020; 146:329-342. [PMID: 31912229 PMCID: PMC6985085 DOI: 10.1007/s00432-019-03115-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Members of the aaRS (aminoacyl-tRNA synthetase) family are proteins controlling the aminoacylation process, in which YARS (tyrosyl-tRNA synthetase) catalyzes the binding of tyrosine to its cognate tRNA and plays an important role in basic biosynthesis. Several studies have demonstrated the association between YARS mutation and certain developmental abnormalities/diseases, yet YARS's linkage with cancer remains uncategorized. In this study, by combining in silico, in vitro, and in vivo studies, we explored the expressions and functions of YARS in gastric cancer (GC). METHODS We evaluated YARS's distribution in tumor and paired normal tissues/specimens of GC by referring to large cohort online datasets and patient-derived tissue specimens. YARS-related changes were assessed by phenotypical/molecular experiments and RNA-sequencing analysis in GC cell lines harboring YARS knockdown or overexpression. RESULTS Both the transcript and protein levels of YARS were evidently higher in gastric cancer tissues than in paired normal tissues. YARS knockdown induced repressed proliferation and invasiveness, as well as enhanced apoptosis in GC cell lines, while abnormally upregulating YARS expression promoted gastric cancer growth in vivo. We inferred based on RNA-sequencing that YARS modulates multiple cancerous signaling pathways and proved through cellular experiments that YARS promoted GC progression, as well as homologous recombination by activating PI3K-Akt signaling. CONCLUSIONS By revealing the existence of a YARS-PI3K-Akt signaling axis in gastric cancer, we discovered that tRNA synthetase YARS is a novel tumorigenic factor, characterized by its upregulation in tumor-derived specimens, as well as its functions in promoting gastric cancer progression.
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20
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Honsho M, Okumoto K, Tamura S, Fujiki Y. Peroxisome Biogenesis Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1299:45-54. [PMID: 33417206 DOI: 10.1007/978-3-030-60204-8_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Peroxisomes are presented in all eukaryotic cells and play essential roles in many of lipid metabolic pathways, including β-oxidation of fatty acids and synthesis of ether-linked glycerophospholipids, such as plasmalogens. Impaired peroxisome biogenesis, including defects of membrane assembly, import of peroxisomal matrix proteins, and division of peroxisome, causes peroxisome biogenesis disorders (PBDs). Fourteen complementation groups of PBDs are found, and their complementing genes termed PEXs are isolated. Several new mutations in peroxins from patients with mild PBD phenotype or patients with phenotypes unrelated to the commonly observed impairments of PBD patients are found by next-generation sequencing. Exploring a dysfunctional step(s) caused by the mutation is important for unveiling the pathogenesis of novel mutation by means of cellular and biochemical analyses.
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Affiliation(s)
| | - Kanji Okumoto
- Department of Biology, Faculty of Sciences, Kyushu University Graduate School, Fukuoka, Japan
| | | | - Yukio Fujiki
- Institute of Rheological Functions of Food, Fukuoka, Japan. .,Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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21
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Cortese A, Wilcox JE, Polke JM, Poh R, Skorupinska M, Rossor AM, Laura M, Tomaselli PJ, Houlden H, Shy ME, Reilly MM. Targeted next-generation sequencing panels in the diagnosis of Charcot-Marie-Tooth disease. Neurology 2019; 94:e51-e61. [PMID: 31827005 PMCID: PMC7011687 DOI: 10.1212/wnl.0000000000008672] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/24/2019] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE To investigate the effectiveness of targeted next-generation sequencing (NGS) panels in achieving a molecular diagnosis in Charcot-Marie-Tooth disease (CMT) and related disorders in a clinical setting. METHODS We prospectively enrolled 220 patients from 2 tertiary referral centers, one in London, United Kingdom (n = 120), and one in Iowa (n = 100), in whom a targeted CMT NGS panel had been requested as a diagnostic test. PMP22 duplication/deletion was previously excluded in demyelinating cases. We reviewed the genetic and clinical data upon completion of the diagnostic process. RESULTS After targeted NGS sequencing, a definite molecular diagnosis, defined as a pathogenic or likely pathogenic variant, was reached in 30% of cases (n = 67). The diagnostic rate was similar in London (32%) and Iowa (29%). Variants of unknown significance were found in an additional 33% of cases. Mutations in GJB1, MFN2, and MPZ accounted for 39% of cases that received genetic confirmation, while the remainder of positive cases had mutations in diverse genes, including SH3TC2, GDAP1, IGHMBP2, LRSAM1, FDG4, and GARS, and another 12 less common genes. Copy number changes in PMP22, MPZ, MFN2, SH3TC2, and FDG4 were also accurately detected. A definite genetic diagnosis was more likely in cases with an early onset, a positive family history of neuropathy or consanguinity, and a demyelinating neuropathy. CONCLUSIONS NGS panels are effective tools in the diagnosis of CMT, leading to genetic confirmation in one-third of cases negative for PMP22 duplication/deletion, thus highlighting how rarer and previously undiagnosed subtypes represent a relevant part of the genetic landscape of CMT.
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Affiliation(s)
- Andrea Cortese
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Janel E Wilcox
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - James M Polke
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Roy Poh
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Mariola Skorupinska
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Alexander M Rossor
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Matilde Laura
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Pedro J Tomaselli
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Henry Houlden
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Michael E Shy
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Mary M Reilly
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City.
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Takashima S, Saitsu H, Shimozawa N. Expanding the concept of peroxisomal diseases and efficient diagnostic system in Japan. J Hum Genet 2018; 64:145-152. [PMID: 30237433 DOI: 10.1038/s10038-018-0512-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 01/02/2023]
Abstract
The concept of peroxisomal diseases is expanding because of improvements in diagnostic technology based on advanced biochemical analysis and development of next-generation sequencing. For quicker and more accurate diagnosis of as many patients as possible, we developed a new diagnostic system combining the conventional diagnostic system and comprehensive mutational analysis by whole-exome sequencing in Japan. Adrenoleukodystrophy (ALD) is the most common peroxisomal disease. In the cerebral type of ALD, hematopoietic stem cell transplantation is the only treatment in the early stage, and thus prompt diagnosis will improve the prognosis of affected patients. Furthermore, it is also important to identify pre-symptomatic patients by family analysis of probands by providing appropriate disease information and genetic counseling, which will also lead to early intervention. Here, we summarize current information related to peroxisomal diseases and ALD and introduce our efficient diagnostic system for use in Japan, which resulted in the diagnosis of 73 Japanese patients with peroxisome biogenesis disorders, 16 with impaired β-oxidation of fatty acids, three with impaired etherphospholipid biosynthesis, and 191 Japanese families with ALD so far.
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Affiliation(s)
- Shigeo Takashima
- Division of Genomics Research, Life Science Research Center, Gifu University, Gifu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Nobuyuki Shimozawa
- Division of Genomics Research, Life Science Research Center, Gifu University, Gifu, Japan.
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23
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Fogel BL. Genetic and genomic testing for neurologic disease in clinical practice. HANDBOOK OF CLINICAL NEUROLOGY 2018; 147:11-22. [PMID: 29325607 DOI: 10.1016/b978-0-444-63233-3.00002-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The influence of genetics on neurologic disease is broad and it is becoming more common that clinicians are presented with a patient whose disease is likely of genetic origin. In the search for mutations causing Mendelian disorders, advances in genetic testing methodology have propelled modern neurologic practice beyond single-gene testing into the realm of genomic medicine, where routine evaluations encompass hundreds or thousands of genes, or even the entire exome, representing all protein-coding genes in the genome. The role of various single-gene, multigene, and genomic testing methods, including chromosomal microarray and next-generation sequencing, in the evaluation of neurologic disease is discussed here to provide a framework for their use in a modern neurologic practice. Understanding the inherent issues that arise during the interpretation of sequence variants as pathogenic or benign and the potential discovery of incidental medically relevant findings are important considerations for neurologists utilizing these tests clinically. Strategies for the evaluation of clinically heterogeneous disorders are presented to guide neurologists in the transition from single-gene to genomic considerations and toward the prospect of the widespread routine use of exome sequencing in the continuing goal to achieve more rapid and more precise diagnoses that will improve management and outcome in patients challenged by neurologic disease.
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Affiliation(s)
- Brent L Fogel
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, United States.
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24
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Karakaya M, Storbeck M, Strathmann EA, Delle Vedove A, Hölker I, Altmueller J, Naghiyeva L, Schmitz-Steinkrüger L, Vezyroglou K, Motameny S, Alawbathani S, Thiele H, Polat AI, Okur D, Boostani R, Karimiani EG, Wunderlich G, Ardicli D, Topaloglu H, Kirschner J, Schrank B, Maroofian R, Magnusson O, Yis U, Nürnberg P, Heller R, Wirth B. Targeted sequencing with expanded gene profile enables high diagnostic yield in non-5q-spinal muscular atrophies. Hum Mutat 2018; 39:1284-1298. [PMID: 29858556 DOI: 10.1002/humu.23560] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/14/2018] [Accepted: 05/30/2018] [Indexed: 11/08/2022]
Abstract
Spinal muscular atrophies (SMAs) are a heterogeneous group of disorders characterized by muscular atrophy, weakness, and hypotonia due to suspected lower motor neuron degeneration (LMND). In a large cohort of 3,465 individuals suspected with SMA submitted for SMN1 testing to our routine diagnostic laboratory, 48.8% carried a homozygous SMN1 deletion, 2.8% a subtle mutation, and an SMN1 deletion, whereas 48.4% remained undiagnosed. Recently, several other genes implicated in SMA/LMND have been reported. Despite several efforts to establish a diagnostic algorithm for non-5q-SMA (SMA without deletion or point mutations in SMN1 [5q13.2]), data from large-scale studies are not available. We tested the clinical utility of targeted sequencing in non-5q-SMA by developing two different gene panels. We first analyzed 30 individuals with a small panel including 62 genes associated with LMND using IonTorrent-AmpliSeq target enrichment. Then, additional 65 individuals were tested with a broader panel encompassing up to 479 genes implicated in neuromuscular diseases (NMDs) with Agilent-SureSelect target enrichment. The NMD panel provided a higher diagnostic yield (33%) than the restricted LMND panel (13%). Nondiagnosed cases were further subjected to exome or genome sequencing. Our experience supports the use of gene panels covering a broad disease spectrum for diseases that are highly heterogeneous and clinically difficult to differentiate.
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Affiliation(s)
- Mert Karakaya
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Markus Storbeck
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Eike A Strathmann
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Andrea Delle Vedove
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Irmgard Hölker
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Janine Altmueller
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Leyla Naghiyeva
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Lea Schmitz-Steinkrüger
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Katharina Vezyroglou
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Susanne Motameny
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Salem Alawbathani
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Ayse Ipek Polat
- Dokuz Eylül University, Department of Pediatric Neurology, Izmir, Turkey
| | - Derya Okur
- Dokuz Eylül University, Department of Pediatric Neurology, Izmir, Turkey
| | - Reza Boostani
- Mashhad University of Medical Sciences, Department of Neurology, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Next Generation Genetic Polyclinic, Mashhad, Iran.,Razavi Cancer Research Center, Razavi Hospital, Imam Reza International University, Mashhad, Iran
| | | | - Didem Ardicli
- Hacettepe University, Department of Pediatric Neurology, Ankara, Turkey
| | - Haluk Topaloglu
- Hacettepe University, Department of Pediatric Neurology, Ankara, Turkey
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Bertold Schrank
- DKD HELIOS Kliniken, Department of Neurology, Wiesbaden, Germany
| | - Reza Maroofian
- Genetics and Molecular Cell Sciences Research Centre, St George's University of London, London, UK
| | | | - Uluc Yis
- Dokuz Eylül University, Department of Pediatric Neurology, Izmir, Turkey
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Raoul Heller
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
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25
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Cutrupi AN, Brewer MH, Nicholson GA, Kennerson M. Structural variations causing inherited peripheral neuropathies: A paradigm for understanding genomic organization, chromatin interactions, and gene dysregulation. Mol Genet Genomic Med 2018; 6:422-433. [PMID: 29573232 PMCID: PMC6014456 DOI: 10.1002/mgg3.390] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/09/2018] [Accepted: 03/01/2018] [Indexed: 11/16/2022] Open
Abstract
Inherited peripheral neuropathies (IPNs) are a clinically and genetically heterogeneous group of diseases affecting the motor and sensory peripheral nerves. IPNs have benefited from gene discovery and genetic diagnosis using next-generation sequencing with over 80 causative genes available for testing. Despite this success, up to 50% of cases remain genetically unsolved. In the absence of protein coding mutations, noncoding DNA or structural variation (SV) mutations are a possible explanation. The most common IPN, Charcot-Marie-Tooth neuropathy type 1A (CMT1A), is caused by a 1.5 Mb duplication causing trisomy of the dosage sensitive gene PMP22. Using genome sequencing, we recently identified two large genomic rearrangements causing IPN subtypes X-linked CMT (CMTX3) and distal hereditary motor neuropathy (DHMN1), thereby expanding the spectrum of SV mutations causing IPN. Understanding how newly discovered SVs can cause IPN may serve as a useful paradigm to examine the role of topologically associated domains (TADs), chromatin interactions, and gene dysregulation in disease. This review will describe the growing role of SV in the pathogenesis of IPN and the importance of considering this type of mutation in Mendelian diseases where protein coding mutations cannot be identified.
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Affiliation(s)
- Anthony N. Cutrupi
- Northcott Neuroscience LaboratoryANZAC Research InstituteSydneyNSWAustralia
- Sydney Medical SchoolUniversity of SydneySydneyNSWAustralia
| | - Megan H. Brewer
- Northcott Neuroscience LaboratoryANZAC Research InstituteSydneyNSWAustralia
- Sydney Medical SchoolUniversity of SydneySydneyNSWAustralia
| | - Garth A. Nicholson
- Northcott Neuroscience LaboratoryANZAC Research InstituteSydneyNSWAustralia
- Sydney Medical SchoolUniversity of SydneySydneyNSWAustralia
- Molecular Medicine LaboratoryConcord HospitalSydneyNSWAustralia
| | - Marina L. Kennerson
- Northcott Neuroscience LaboratoryANZAC Research InstituteSydneyNSWAustralia
- Sydney Medical SchoolUniversity of SydneySydneyNSWAustralia
- Molecular Medicine LaboratoryConcord HospitalSydneyNSWAustralia
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26
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Abstract
PURPOSE OF REVIEW The development of massively parallel sequencing (MPS) has revolutionized molecular genetic diagnostics in monogenic disorders. The present review gives a brief overview of different MPS-based approaches used in clinical diagnostics of neuromuscular disorders (NMDs) and highlights their advantages and limitations. RECENT FINDINGS MPS-based approaches like gene panel sequencing, (whole) exome sequencing, (whole) genome sequencing, and RNA sequencing have been used to identify the genetic cause in NMDs. Although gene panel sequencing has evolved as a standard test for heterogeneous diseases, it is still debated, mainly because of financial issues and unsolved problems of variant interpretation, whether genome sequencing (and to a lesser extent also exome sequencing) of single patients can already be regarded as routine diagnostics. However, it has been shown that the inclusion of parents and additional family members often leads to a substantial increase in the diagnostic yield in exome-wide/genome-wide MPS approaches. In addition, MPS-based RNA sequencing just enters the research and diagnostic scene. SUMMARY Next-generation sequencing increasingly enables the detection of the genetic cause in highly heterogeneous diseases like NMDs in an efficient and affordable way. Gene panel sequencing and family-based exome sequencing have been proven as potent and cost-efficient diagnostic tools. Although clinical validation and interpretation of genome sequencing is still challenging, diagnostic RNA sequencing represents a promising tool to bypass some hurdles of diagnostics using genomic DNA.
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27
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Pakhrin PS, Xie Y, Hu Z, Li X, Liu L, Huang S, Wang B, Yang Z, Zhang J, Liu X, Xia K, Tang B, Zhang R. Genotype–phenotype correlation and frequency of distribution in a cohort of Chinese Charcot–Marie–Tooth patients associated with GDAP1 mutations. J Neurol 2018; 265:637-646. [DOI: 10.1007/s00415-018-8743-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/13/2017] [Accepted: 01/07/2018] [Indexed: 01/08/2023]
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28
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Zarouchlioti C, Parfitt DA, Li W, Gittings LM, Cheetham ME. DNAJ Proteins in neurodegeneration: essential and protective factors. Philos Trans R Soc Lond B Biol Sci 2018; 373:20160534. [PMID: 29203718 PMCID: PMC5717533 DOI: 10.1098/rstb.2016.0534] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2017] [Indexed: 12/16/2022] Open
Abstract
Maintenance of protein homeostasis is vitally important in post-mitotic cells, particularly neurons. Neurodegenerative diseases such as polyglutamine expansion disorders-like Huntington's disease or spinocerebellar ataxia (SCA), Alzheimer's disease, fronto-temporal dementia (FTD), amyotrophic lateral sclerosis (ALS) and Parkinson's disease-are often characterized by the presence of inclusions of aggregated protein. Neurons contain complex protein networks dedicated to protein quality control and maintaining protein homeostasis, or proteostasis. Molecular chaperones are a class of proteins with prominent roles in maintaining proteostasis, which act to bind and shield hydrophobic regions of nascent or misfolded proteins while allowing correct folding, conformational changes and enabling quality control. There are many different families of molecular chaperones with multiple functions in proteostasis. The DNAJ family of molecular chaperones is the largest chaperone family and is defined by the J-domain, which regulates the function of HSP70 chaperones. DNAJ proteins can also have multiple other protein domains such as ubiquitin-interacting motifs or clathrin-binding domains leading to diverse and specific roles in the cell, including targeting client proteins for degradation via the proteasome, chaperone-mediated autophagy and uncoating clathrin-coated vesicles. DNAJ proteins can also contain ER-signal peptides or mitochondrial leader sequences, targeting them to specific organelles in the cell. In this review, we discuss the multiple roles of DNAJ proteins and in particular focus on the role of DNAJ proteins in protecting against neurodegenerative diseases caused by misfolded proteins. We also discuss the role of DNAJ proteins as direct causes of inherited neurodegeneration via mutations in DNAJ family genes.This article is part of the theme issue 'Heat shock proteins as modulators and therapeutic targets of chronic disease: an integrated perspective'.
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Affiliation(s)
| | - David A Parfitt
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1 V 9EL, UK
| | - Wenwen Li
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1 V 9EL, UK
| | - Lauren M Gittings
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1 V 9EL, UK
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29
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Hartley T, Wagner JD, Warman-Chardon J, Tétreault M, Brady L, Baker S, Tarnopolsky M, Bourque PR, Parboosingh JS, Smith C, McInnes B, Innes AM, Bernier F, Curry CJ, Yoon G, Horvath GA, Bareke E, Gillespie M, Majewski J, Bulman DE, Dyment DA, Boycott KM. Whole-exome sequencing is a valuable diagnostic tool for inherited peripheral neuropathies: Outcomes from a cohort of 50 families. Clin Genet 2017; 93:301-309. [PMID: 28708278 DOI: 10.1111/cge.13101] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/04/2017] [Accepted: 07/09/2017] [Indexed: 01/02/2023]
Abstract
The inherited peripheral neuropathies (IPNs) are characterized by marked clinical and genetic heterogeneity and include relatively frequent presentations such as Charcot-Marie-Tooth disease and hereditary motor neuropathy, as well as more rare conditions where peripheral neuropathy is associated with additional features. There are over 250 genes known to cause IPN-related disorders but it is estimated that in approximately 50% of affected individuals a molecular diagnosis is not achieved. In this study, we examine the diagnostic utility of whole-exome sequencing (WES) in a cohort of 50 families with 1 or more affected individuals with a molecularly undiagnosed IPN with or without additional features. Pathogenic or likely pathogenic variants in genes known to cause IPN were identified in 24% (12/50) of the families. A further 22% (11/50) of families carried sequence variants in IPN genes in which the significance remains unclear. An additional 12% (6/50) of families had variants in novel IPN candidate genes, 3 of which have been published thus far as novel discoveries (KIF1A, TBCK, and MCM3AP). This study highlights the use of WES in the molecular diagnostic approach of highly heterogeneous disorders, such as IPNs, places it in context of other published neuropathy cohorts, while further highlighting associated benefits for discovery.
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Affiliation(s)
- T Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - J D Wagner
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - J Warman-Chardon
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - M Tétreault
- Department of Human Genetics, McGill University, Montréal, Canada
| | - L Brady
- Department of Pediatrics, McMaster University Medical Centre, Hamilton, Canada
| | - S Baker
- Department of Medicine, McMaster University Medical Centre, Hamilton, Canada
| | - M Tarnopolsky
- Department of Pediatrics, McMaster University Medical Centre, Hamilton, Canada
| | - P R Bourque
- Department of Medicine, University of Ottawa, Ottawa, Canada
| | - J S Parboosingh
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - C Smith
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - B McInnes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - A M Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - F Bernier
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - C J Curry
- Department of Pediatrics, University of California, San Francisco, California
| | - G Yoon
- Divisions of Neurology and Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - G A Horvath
- Division of Biochemical Diseases, Department of Pediatrics, B.C. Children's Hospital, University of British Columbia, Vancouver, Canada
| | - E Bareke
- Department of Human Genetics, McGill University, Montréal, Canada
| | - M Gillespie
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | | | | | - J Majewski
- Department of Human Genetics, McGill University, Montréal, Canada
| | - D E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - K M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
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30
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Mori M, Haskell G, Kazi Z, Zhu X, DeArmey SM, Goldstein JL, Bali D, Rehder C, Cirulli ET, Kishnani PS. Sensitivity of whole exome sequencing in detecting infantile- and late-onset Pompe disease. Mol Genet Metab 2017; 122:189-197. [PMID: 29122469 PMCID: PMC5907499 DOI: 10.1016/j.ymgme.2017.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 10/13/2017] [Indexed: 12/30/2022]
Abstract
Pompe disease is a metabolic myopathy with a wide spectrum of clinical presentation. The gold-standard diagnostic test is acid alpha-glucosidase assay on skin fibroblasts, muscle or blood. Identification of two GAA pathogenic variants in-trans is confirmatory. Optimal effectiveness of enzyme replacement therapy hinges on early diagnosis, which is challenging in late-onset form of the disease due to non-specific presentation. Next-generation sequencing-based panels effectively facilitate diagnosis, but the sensitivity of whole-exome sequencing (WES) in detecting pathogenic GAA variants remains unknown. We analyzed WES data from 93 patients with confirmed Pompe disease and GAA genotypes based on PCR/Sanger sequencing. After ensuring that the common intronic variant c.-32-13T>G is not filtered out, whole-exome sequencing identified both GAA pathogenic variants in 77/93 (83%) patients. However, one variant was missed in 14/93 (15%), and both variants were missed in 2/93 (2%). One complex indel leading to a severe phenotype was incorrectly called a nonsynonymous substitution c.-32-13T>C due to misalignment. These results demonstrate that WES may fail to diagnose Pompe disease. Clinicians need to be aware of limitations of WES, and consider tests specific to Pompe disease when WES does not provide a diagnosis in patients with proximal myopathy, progressive respiratory failure or other subtle symptoms.
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Affiliation(s)
- Mari Mori
- Department of Pediatrics, Warren Alpert Medical School, Brown University, Providence, RI, USA; Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Gloria Haskell
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Zoheb Kazi
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Xiaolin Zhu
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | | | - Jennifer L Goldstein
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Deeksha Bali
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Catherine Rehder
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | | | - Priya S Kishnani
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA.
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31
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Konno T, Ross OA, Teive HAG, Sławek J, Dickson DW, Wszolek ZK. DCTN1-related neurodegeneration: Perry syndrome and beyond. Parkinsonism Relat Disord 2017. [PMID: 28625595 DOI: 10.1016/j.parkreldis.2017.06.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Perry syndrome (PS) is a rare hereditary neurodegenerative disease characterized by autosomal dominant parkinsonism, psychiatric symptoms, weight loss, central hypoventilation, and distinct TDP-43 pathology. The mutated causative gene for PS is DCTN1, which encodes the dynactin subunit p150Glued. Dynactin is a motor protein involved in axonal transport; the p150Glued subunit has a critical role in the overall function. Since the discovery of DCTN1 in PS, it has been increasingly recognized that DCTN1 mutations can exhibit more diverse phenotypes than previously thought. Progressive supranuclear palsy- and/or frontotemporal dementia-like phenotypes have been associated with the PS phenotypes. In addition, DCTN1 mutations were identified in a family with motor-neuron disease before the discovery in PS. In this review, we analyze the clinical and genetic aspects of DCTN1-related neurodegeneration and discuss its pathogenesis. We also describe three families with PS, Canadian, Polish, and Brazilian. DCTN1 mutation was newly identified in two of them, the Canadian and Polish families. The Canadian family was first described in late 1970's but was never genetically tested. We recently had the opportunity to evaluate this family and to test the gene status of an affected family member. The Polish family is newly identified and is the first PS family in Poland. Although still rare, DCTN1-related neurodegeneration needs to be considered in a differential diagnosis of parkinsonian disorders, frontotemporal dementia, and motor-neuron diseases, especially if there is family history.
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Affiliation(s)
- Takuya Konno
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Hélio A G Teive
- Movement Disorders Unit, Neurology Service, Hospital de Clínicas, Federal University of Paraná, Rua General Carneiro 1103/102, Centro, Curitiba, PR, 80060-150, Brazil
| | - Jarosław Sławek
- Department of Neurological-Psychiatric Nursing, Medical University of Gdansk, Poland; Department of Neurology, St. Adalbert Hospital, Copernicus Ltd., Gdansk, Poland
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Zbigniew K Wszolek
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.
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32
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Walsh M, Bell KM, Chong B, Creed E, Brett GR, Pope K, Thorne NP, Sadedin S, Georgeson P, Phelan DG, Day T, Taylor JA, Sexton A, Lockhart PJ, Kiers L, Fahey M, Macciocca I, Gaff CL, Oshlack A, Yiu EM, James PA, Stark Z, Ryan MM. Diagnostic and cost utility of whole exome sequencing in peripheral neuropathy. Ann Clin Transl Neurol 2017; 4:318-325. [PMID: 28491899 PMCID: PMC5420808 DOI: 10.1002/acn3.409] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/07/2017] [Accepted: 03/15/2017] [Indexed: 12/15/2022] Open
Abstract
Objective To explore the diagnostic utility and cost effectiveness of whole exome sequencing (WES) in a cohort of individuals with peripheral neuropathy. Methods Singleton WES was performed in individuals recruited though one pediatric and one adult tertiary center between February 2014 and December 2015. Initial analysis was restricted to a virtual panel of 55 genes associated with peripheral neuropathies. Patients with uninformative results underwent expanded analysis of the WES data. Data on the cost of prior investigations and assessments performed for diagnostic purposes in each patient was collected. Results Fifty patients with a peripheral neuropathy were recruited (median age 18 years; range 2–68 years). The median time from initial presentation to study enrollment was 6 years 9 months (range 2 months–62 years), and the average cost of prior investigations and assessments for diagnostic purposes AU$4013 per patient. Eleven individuals received a diagnosis from the virtual panel. Eight individuals received a diagnosis following expanded analysis of the WES data, increasing the overall diagnostic yield to 38%. Two additional individuals were diagnosed with pathogenic copy number variants through SNP microarray. Conclusions This study provides evidence that WES has a high diagnostic utility and is cost effective in patients with a peripheral neuropathy. Expanded analysis of WES data significantly improves the diagnostic yield in patients in whom a diagnosis is not found on the initial targeted analysis. This is primarily due to diagnosis of conditions caused by newly discovered genes and the resolution of complex and atypical phenotypes.
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Affiliation(s)
- Maie Walsh
- Murdoch Childrens Research Institute Melbourne Australia.,Royal Melbourne Hospital Melbourne Australia
| | - Katrina M Bell
- Murdoch Childrens Research Institute Melbourne Australia
| | - Belinda Chong
- Murdoch Childrens Research Institute Melbourne Australia
| | - Emma Creed
- Royal Melbourne Hospital Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia
| | - Gemma R Brett
- Murdoch Childrens Research Institute Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia
| | - Kate Pope
- Murdoch Childrens Research Institute Melbourne Australia
| | - Natalie P Thorne
- Melbourne Genomics Health Alliance Melbourne Australia.,Murdoch Childrens Research Institute Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Simon Sadedin
- Murdoch Childrens Research Institute Melbourne Australia
| | | | - Dean G Phelan
- Murdoch Childrens Research Institute Melbourne Australia
| | - Timothy Day
- Royal Melbourne Hospital Melbourne Australia
| | | | | | - Paul J Lockhart
- Murdoch Childrens Research Institute Melbourne Australia.,Bruce Lefroy Centre Murdoch Childrens Research Institute Parkville Australia.,Department of Paediatrics The University of Melbourne Melbourne Australia
| | | | | | - Ivan Macciocca
- Murdoch Childrens Research Institute Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia
| | - Clara L Gaff
- Melbourne Genomics Health Alliance Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Alicia Oshlack
- Murdoch Childrens Research Institute Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Eppie M Yiu
- Bruce Lefroy Centre Murdoch Childrens Research Institute Parkville Australia.,Department of Paediatrics The University of Melbourne Melbourne Australia.,Royal Children's Hospital Melbourne Australia
| | - Paul A James
- Royal Melbourne Hospital Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Zornitza Stark
- Murdoch Childrens Research Institute Melbourne Australia
| | - Monique M Ryan
- Murdoch Childrens Research Institute Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia.,Department of Paediatrics The University of Melbourne Melbourne Australia.,Royal Children's Hospital Melbourne Australia
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33
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Affiliation(s)
| | - Maria Daniela D'Agostino
- McGill University Department of Human Genetics and McGill University Health Center, Department of Medical Genetics, Montreal, QC, Canada
| | - Nancy Braverman
- McGill University Department of Human Genetics and Pediatrics, and The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
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34
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Nowaczyk MJM, Huang L, Tarnopolsky M, Schwartzentruber J, Majewski J, Bulman DE, Hartley T, Boycott KM. A novel multisystem disease associated with recessive mutations in the tyrosyl-tRNA synthetase (YARS) gene. Am J Med Genet A 2016; 173:126-134. [PMID: 27633801 DOI: 10.1002/ajmg.a.37973] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/15/2016] [Indexed: 01/14/2023]
Abstract
Aminoacyl-tRNA synthetases (ARSs) are a group of ubiquitously expressed enzymes that are best known for their function in the first step of protein translation but have been increasingly associated with secondary functions including transcription and translation control and extracellular signaling. Mutations in numerous ARSs have been linked to a growing number of both autosomal dominant and autosomal recessive human diseases. The tyrosyl-tRNA synthetase (YARS) links the amino acid tyrosine to its cognate tRNA. We report two siblings who presented with failure to thrive (FTT), hypertriglyceridemia, developmental delay, liver dysfunction, lung cysts, and abnormal subcortical white matter. Using exome sequencing the siblings were found to harbor bi-allelic pathogenic-appearing variants within the YARS gene (NM_003680.3):c.638C>T p.(Pro213Leu) and c.1573G>A p.(Gly525Arg). These YARS variants occur in the catalytic domain and the C-terminal domain, respectively. Mutations in YARS have been previously associated with an autosomal dominant form of Charcot-Marie-Tooth (CMT); our findings suggest the disease spectrum associated with YARS dysregulation is broader than peripheral neuropathy. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Małgorzata J M Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Lijia Huang
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Mark Tarnopolsky
- Department of Paediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | - Jacek Majewski
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Dennis E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
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35
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Elsayed LEO, Mohammed IN, Hamed AAA, Elseed MA, Johnson A, Mairey M, Mohamed HESA, Idris MN, Salih MAM, El-Sadig SM, Koko ME, Mohamed AYO, Raymond L, Coutelier M, Darios F, Siddig RA, Ahmed AKMA, Babai AMA, Malik HMO, Omer ZMBM, Mohamed EOE, Eltahir HB, Magboul NAA, Bushara EE, Elnour A, Rahim SMA, Alattaya A, Elbashir MI, Ibrahim ME, Durr A, Audhya A, Brice A, Ahmed AE, Stevanin G. Hereditary spastic paraplegias: identification of a novel SPG57 variant affecting TFG oligomerization and description of HSP subtypes in Sudan. Eur J Hum Genet 2016; 25:100-110. [PMID: 27601211 DOI: 10.1038/ejhg.2016.108] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/31/2016] [Accepted: 06/14/2016] [Indexed: 12/11/2022] Open
Abstract
Hereditary spastic paraplegias (HSP) are the second most common type of motor neuron disease recognized worldwide. We investigated a total of 25 consanguineous families from Sudan. We used next-generation sequencing to screen 74 HSP-related genes in 23 families. Linkage analysis and candidate gene sequencing was performed in two other families. We established a genetic diagnosis in six families with autosomal recessive HSP (SPG11 in three families and TFG/SPG57, SACS and ALS2 in one family each). A heterozygous mutation in a gene involved in an autosomal dominant HSP (ATL1/SPG3A) was also identified in one additional family. Six out of seven identified variants were novel. The c.64C>T (p.(Arg22Trp)) TFG/SPG57 variant (PB1 domain) is the second identified that underlies HSP, and we demonstrated its impact on TFG oligomerization in vitro. Patients did not present with visual impairment as observed in a previously reported SPG57 family (c.316C>T (p.(Arg106Cys)) in coiled-coil domain), suggesting unique contributions of the PB1 and coiled-coil domains in TFG complex formation/function and a possible phenotype correlation to variant location. Some families manifested marked phenotypic variations implying the possibility of modifier factors complicated by high inbreeding. Finally, additional genetic heterogeneity is expected in HSP Sudanese families. The remaining families might unravel new genes or uncommon modes of inheritance.
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Affiliation(s)
- Liena E O Elsayed
- Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR7225, Sorbonne Universités, UPMC Université Paris VI UMR_S1127, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL université, Paris, France.,University of Khartoum, Khartoum, Sudan
| | | | | | | | - Adam Johnson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Mathilde Mairey
- Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR7225, Sorbonne Universités, UPMC Université Paris VI UMR_S1127, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL université, Paris, France
| | | | - Mohamed N Idris
- University of Khartoum, Khartoum, Sudan.,Sudan Medical Council, Neurology, Sudan
| | - Mustafa A M Salih
- Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Sarah M El-Sadig
- University of Khartoum, Khartoum, Sudan.,Department of Neurology, Soba University Hospital, Khartoum, Sudan
| | - Mahmoud E Koko
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Ashraf Y O Mohamed
- Department of Biochemistry, Faculty of Medicine, National University, Khartoum, Sudan
| | - Laure Raymond
- Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR7225, Sorbonne Universités, UPMC Université Paris VI UMR_S1127, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL université, Paris, France.,Department of genetics, APHP Pitié-Salpêtrière Hospital, Paris, France
| | - Marie Coutelier
- Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR7225, Sorbonne Universités, UPMC Université Paris VI UMR_S1127, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL université, Paris, France
| | - Frédéric Darios
- Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR7225, Sorbonne Universités, UPMC Université Paris VI UMR_S1127, Paris, France
| | | | | | | | | | | | | | - Hanan B Eltahir
- Department of Biochemistry, El Imam EL Mahdi University, Kosti, Sudan
| | | | | | | | | | | | | | - Muntaser E Ibrahim
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Alexandra Durr
- Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR7225, Sorbonne Universités, UPMC Université Paris VI UMR_S1127, Paris, France.,Department of genetics, APHP Pitié-Salpêtrière Hospital, Paris, France
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Alexis Brice
- Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR7225, Sorbonne Universités, UPMC Université Paris VI UMR_S1127, Paris, France. .,Department of genetics, APHP Pitié-Salpêtrière Hospital, Paris, France.
| | - Ammar E Ahmed
- University of Khartoum, Khartoum, Sudan.,Sudan Medical Council, Neurology, Sudan
| | - Giovanni Stevanin
- Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR7225, Sorbonne Universités, UPMC Université Paris VI UMR_S1127, Paris, France. .,Ecole Pratique des Hautes Etudes, EPHE, PSL université, Paris, France. .,Department of genetics, APHP Pitié-Salpêtrière Hospital, Paris, France.
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36
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Laššuthová P, Šafka Brožková D, Krůtová M, Neupauerová J, Haberlová J, Mazanec R, Dřímal P, Seeman P. Improving diagnosis of inherited peripheral neuropathies through gene panel analysis. Orphanet J Rare Dis 2016; 11:118. [PMID: 27549087 PMCID: PMC4994270 DOI: 10.1186/s13023-016-0500-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/09/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Inherited peripheral neuropathies (IPN) are the most common inherited neurological condition. It represents a highly heterogeneous group, both clinically and genetically. Targeted disease specific gene panel massively parallel sequencing (MPS) seems to be a useful tool in diagnosis of disorders with high genetic heterogeneity. METHODS In our study, we have designed, validated and updated our own custom gene panel of all known genes associated with IPN. One hundred and ninety-eight patients have been tested so far. Only patients in whom mutations in more common causes or relevant genes have already been excluded were enrolled. Five consecutive panel designs were prepared according to recent literature search, the last one covering ninety-three genes. Each patient was tested only once. All data were evaluated with at least two different pipelines. RESULTS In summary, causative mutation has been found in fifty-one patients (26 %). The results were inconclusive in thirty-one (16 %) patients. No variants of likely significance to IPN were found in one hundred and sixteen (58 %) patients. CONCLUSION MPS gene panel enables testing of all known IPN causes at once with high coverage and at an affordable cost making it truly a method of choice also in IPN. Gene panel testing results in several interesting results and findings.
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Affiliation(s)
- Petra Laššuthová
- Department of Paediatric Neurology, DNA Laboratory, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Dana Šafka Brožková
- Department of Paediatric Neurology, DNA Laboratory, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Marcela Krůtová
- Department of Paediatric Neurology, DNA Laboratory, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Jana Neupauerová
- Department of Paediatric Neurology, DNA Laboratory, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Jana Haberlová
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Radim Mazanec
- Department of Neurology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Pavel Dřímal
- Department of Paediatric Neurology, DNA Laboratory, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Pavel Seeman
- Department of Paediatric Neurology, DNA Laboratory, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
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37
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Sanchez E, Darvish H, Mesias R, Taghavi S, Firouzabadi SG, Walker RH, Tafakhori A, Paisán-Ruiz C. Identification of a Large DNAJB2 Deletion in a Family with Spinal Muscular Atrophy and Parkinsonism. Hum Mutat 2016; 37:1180-1189. [PMID: 27449489 DOI: 10.1002/humu.23055] [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: 04/29/2016] [Accepted: 07/20/2016] [Indexed: 01/10/2023]
Abstract
In this study, we described the identification of a large DNAJB2 (HSJ1) deletion in a family with recessive spinal muscular atrophy and Parkinsonism. After performing homozygosity mapping and whole genome sequencing, we identified a 3.8 kb deletion, spanning the entire DnaJ domain of the HSJ1 protein, as the disease-segregating mutation. By performing functional assays, we showed that HSJ1b-related DnaJ domain deletion leads to loss of HSJ1b mRNA and protein levels, increased HSJ1a mRNA and protein expressions, increased cell death, protein aggregation, and enhanced autophagy. Given the role of HSJ1 proteins in the degradation of misfolded proteins, we speculated that enhanced autophagy might be promoted by the elevated HSJ1a expression seen in HSJ1b-deficient cells. We also observed a significant reduction in both tau and brain-derived neurotrophic factor levels, which may explain the dopaminergic deficits seen in one of the affected siblings. We concluded that HSJ1b deficiency leads to a complex neurological phenotype, possibly due to the accumulation of misfolded proteins, caused by the lack of the DnaJ domain activity. We thus expand the phenotypic and genotypic spectrums associated with DNAJB2 disease and suggest relevant disease-associated mechanisms.
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Affiliation(s)
- Elena Sanchez
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York City, New York
| | - Hossein Darvish
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Roxana Mesias
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York City, New York.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York City, New York
| | - Shaghyegh Taghavi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Ruth H Walker
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York City, New York.,Department of Neurology, James J. Peters Veterans Affairs Medical Center, Bronx, New York City, New York
| | - Abbas Tafakhori
- Department of Neurology, School of Medicine, Imam Khomeini Hospital and Iranian Center of Neurological Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Coro Paisán-Ruiz
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York City, New York. .,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York City, New York. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York City, New York. .,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York City, New York. .,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York City, New York.
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38
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Fattahi Z, Kalhor Z, Fadaee M, Vazehan R, Parsimehr E, Abolhassani A, Beheshtian M, Zamani G, Nafissi S, Nilipour Y, Akbari M, Kahrizi K, Kariminejad A, Najmabadi H. Improved diagnostic yield of neuromuscular disorders applying clinical exome sequencing in patients arising from a consanguineous population. Clin Genet 2016; 91:386-402. [DOI: 10.1111/cge.12810] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 04/28/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Z. Fattahi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - Z. Kalhor
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
| | - M. Fadaee
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - R. Vazehan
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - E. Parsimehr
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - A. Abolhassani
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - M. Beheshtian
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - G. Zamani
- Department of NeurologyTehran University of Medical Sciences Tehran Iran
| | - S. Nafissi
- Department of Pediatric Neurology, Pediatrics Center of Excellence, Children's Medical CenterTehran University of Medical Sciences Tehran Iran
| | - Y. Nilipour
- Pediatric Pathology Research Center, Mofid Children HospitalShahid Beheshti University of Medical Sciences Tehran Iran
| | - M.R. Akbari
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Women's College Research InstituteWomen's College Hospital Toronto Canada
- Dalla Lana School of Public HealthUniversity of Toronto Toronto Canada
| | - K. Kahrizi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
| | - A. Kariminejad
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - H. Najmabadi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
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39
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Brewer MH, Chaudhry R, Qi J, Kidambi A, Drew AP, Menezes MP, Ryan MM, Farrar MA, Mowat D, Subramanian GM, Young HK, Zuchner S, Reddel SW, Nicholson GA, Kennerson ML. Whole Genome Sequencing Identifies a 78 kb Insertion from Chromosome 8 as the Cause of Charcot-Marie-Tooth Neuropathy CMTX3. PLoS Genet 2016; 12:e1006177. [PMID: 27438001 PMCID: PMC4954712 DOI: 10.1371/journal.pgen.1006177] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/15/2016] [Indexed: 11/18/2022] Open
Abstract
With the advent of whole exome sequencing, cases where no pathogenic coding mutations can be found are increasingly being observed in many diseases. In two large, distantly-related families that mapped to the Charcot-Marie-Tooth neuropathy CMTX3 locus at chromosome Xq26.3-q27.3, all coding mutations were excluded. Using whole genome sequencing we found a large DNA interchromosomal insertion within the CMTX3 locus. The 78 kb insertion originates from chromosome 8q24.3, segregates fully with the disease in the two families, and is absent from the general population as well as 627 neurologically normal chromosomes from in-house controls. Large insertions into chromosome Xq27.1 are known to cause a range of diseases and this is the first neuropathy phenotype caused by an interchromosomal insertion at this locus. The CMTX3 insertion represents an understudied pathogenic structural variation mechanism for inherited peripheral neuropathies. Our finding highlights the importance of considering all structural variation types when studying unsolved inherited peripheral neuropathy cases with no pathogenic coding mutations.
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Affiliation(s)
- Megan H. Brewer
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- * E-mail:
| | - Rabia Chaudhry
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
| | - Jessica Qi
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Discipline of Pathology, University of Sydney, Camperdown, New South Wales, Australia
| | - Aditi Kidambi
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
| | - Alexander P. Drew
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
| | - Manoj P. Menezes
- The Institute for Neuroscience and Muscle Research, The Children’s Hospital at Westmead, Westmead, New South Wales, Australia
- T.Y. Nelson Department of Neurology and Neurosurgery, The Children’s Hospital at Westmead, Westmead, New South Wales, Australia
- Paediatrics and Child Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Monique M. Ryan
- Department of Neurology, Royal Children’s Hospital, Parkville, Victoria, Australia
- Murdoch Childrens Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Michelle A. Farrar
- Department of Neurology, Sydney Children’s Hospital, Randwick, New South Wales, Australia
- School of Women’s and Children’s Health, UNSW Medicine, University of New South Wales, Kensington, New South Wales, Australia
| | - David Mowat
- School of Women’s and Children’s Health, UNSW Medicine, University of New South Wales, Kensington, New South Wales, Australia
- Department of Medical Genetics, Sydney Children’s Hospital, Randwick, New South Wales, Australia
| | - Gopinath M. Subramanian
- Department of Paediatrics, John Hunter Children’s Hospital, Newcastle, New South Wales, Australia
| | - Helen K. Young
- Department of Paediatrics, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Northern Clinical School, Sydney Medical School, University of Sydney, St Leonards, New South Wales, Australia
- Department of Neurogenetics, The Children’s Hospital at Westmead, Westmead, New South Wales, Australia
| | - Stephan Zuchner
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Stephen W. Reddel
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales, Australia
| | - Garth A. Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine, Concord Repatriation General Hospital, Concord, New South Wales, Australia
| | - Marina L. Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine, Concord Repatriation General Hospital, Concord, New South Wales, Australia
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Riva N, Agosta F, Lunetta C, Filippi M, Quattrini A. Recent advances in amyotrophic lateral sclerosis. J Neurol 2016; 263:1241-54. [PMID: 27025851 PMCID: PMC4893385 DOI: 10.1007/s00415-016-8091-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 02/12/2016] [Indexed: 10/28/2022]
Abstract
ALS is a relentlessly progressive and fatal disease, with no curative therapies available to date. Symptomatic and palliative care, provided in a multidisciplinary context, still remains the cornerstone of ALS management. However, our understanding of the molecular mechanisms underlying the disease has advanced greatly over the past years, giving new hope for the development of novel diagnostic and therapeutic approaches. Here, we have reviewed the most recent studies that have contributed to improving both clinical management and our understanding of ALS pathogenesis.
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Affiliation(s)
- Nilo Riva
- Neuropathology Unit, INSPE and Division of Neuroscience, Department of Neurology, Institute of Experimental Neurology, San Raffaele Scientific Institute, Via Olgettina 48, 20132, Milan, Italy.
| | - Federica Agosta
- Neuroimaging Research Unit, Division of Neuroscience, Department of Neurology, Institute of Experimental Neurology, San Raffaele Scientific Institute, Milan, Italy
| | - Christian Lunetta
- NEuroMuscular Omnicentre (NEMO), Niguarda Ca Granda Hospital, Milan, Italy
| | - Massimo Filippi
- Neuroimaging Research Unit, Division of Neuroscience, Department of Neurology, Institute of Experimental Neurology, San Raffaele Scientific Institute, Milan, Italy
| | - Angelo Quattrini
- Neuropathology Unit, INSPE and Division of Neuroscience, Department of Neurology, Institute of Experimental Neurology, San Raffaele Scientific Institute, Via Olgettina 48, 20132, Milan, Italy
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41
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Braverman NE, Raymond GV, Rizzo WB, Moser AB, Wilkinson ME, Stone EM, Steinberg SJ, Wangler MF, Rush ET, Hacia JG, Bose M. Peroxisome biogenesis disorders in the Zellweger spectrum: An overview of current diagnosis, clinical manifestations, and treatment guidelines. Mol Genet Metab 2016; 117:313-21. [PMID: 26750748 PMCID: PMC5214431 DOI: 10.1016/j.ymgme.2015.12.009] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/21/2015] [Accepted: 12/21/2015] [Indexed: 10/22/2022]
Abstract
Peroxisome biogenesis disorders in the Zellweger spectrum (PBD-ZSD) are a heterogeneous group of genetic disorders caused by mutations in PEX genes responsible for normal peroxisome assembly and functions. As a result of impaired peroxisomal activities, individuals with PBD-ZSD can manifest a complex spectrum of clinical phenotypes that typically result in shortened life spans. The extreme variability in disease manifestation ranging from onset of profound neurologic symptoms in newborns to progressive degenerative disease in adults presents practical challenges in disease diagnosis and medical management. Recent advances in biochemical methods for newborn screening and genetic testing have provided unprecedented opportunities for identifying patients at the earliest possible time and defining the molecular bases for their diseases. Here, we provide an overview of current clinical approaches for the diagnosis of PBD-ZSD and provide broad guidelines for the treatment of disease in its wide variety of forms. Although we anticipate future progress in the development of more effective targeted interventions, the current guidelines are meant to provide a starting point for the management of these complex conditions in the context of personalized health care.
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Affiliation(s)
- Nancy E Braverman
- McGill University Health Centre, 1001 Décarie Blvd Block E, EM02230, Montreal, QC H4A3J1, Canada.
| | - Gerald V Raymond
- Department of Neurology, University of Minnesota, 516 Delaware Street SE, Minneapolis, MN 55455, USA,.
| | - William B Rizzo
- Department of Pediatrics, University of Nebraska Medical Center, 985456 Nebraska Medical Center - MMI 3062, Omaha, NE 68198-5456, USA.
| | - Ann B Moser
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD 21205, USA.
| | - Mark E Wilkinson
- Carver College of Medicine, Department of Ophthalmology and Visual Sciences, University of Iowa, Stephen A. Wynn Institute for Vision Research, 200 Hawkins Drive, Iowa City, IA 52242, USA.
| | - Edwin M Stone
- Carver College of Medicine, Department of Ophthalmology and Visual Sciences, University of Iowa, Stephen A. Wynn Institute for Vision Research, 200 Hawkins Drive, Iowa City, IA 52242, USA.
| | - Steven J Steinberg
- Institute of Genetic Medicine and Department of Neurology, Johns Hopkins University School of Medicine, CMSC1004B, 600 N Wolfe Street, Baltimore, MD 21287, USA.
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Duncan Neurological Research Institute, DNRI-1050, Houston, TX 77030, USA.
| | - Eric T Rush
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, 985440 Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Joseph G Hacia
- Department of Biochemistry and Molecular Biology, University of Southern California, 1975 Zonal Ave, Los Angeles, CA 90033, USA.
| | - Mousumi Bose
- Global Foundation for Peroxisomal Disorders, 5147 S. Harvard Avenue, Suite 181, Tulsa, OK 74135, USA.
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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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Abstract
PURPOSE OF REVIEW This article focuses on recent advances in Charcot-Marie-Tooth disease, in particular additions to the genetic spectrum, novel paradigms in molecular techniques and an update on therapeutic strategies. RECENT FINDINGS Several new Charcot-Marie-Tooth disease-causing genes have been recently identified, further enlarging the genetic diversity and phenotypic variability, including: SBF1, DHTKD1, TFG, MARS, HARS, HINT1, TRIM1, AIFM1, PDK3 and GNB4. The increasing availability and affordability of next-generation sequencing technologies has ramped up gene discovery and drastically changed genetic screening strategies. All large-scale trials studying the effect of ascorbic acid in Charcot-Marie-Tooth 1A have now been completed and were negative. Efforts have been made to design more robust outcome-measures for clinical trials. Promising results with lonaprisan, curcumin and histone deacetylase 6 inhibitors have been obtained in animal models. SUMMARY Charcot-Marie-Tooth is the most common form of inherited peripheral neuropathy and represents the most prevalent hereditary neuromuscular disorder. The genetic spectrum spans more than 70 genes. Gene discovery has been revolutionized recently by new high-throughput molecular technologies. In addition, the phenotypic diversity has grown tremendously. This is a major challenge for geneticists and neurologists. No effective therapy is available for Charcot-Marie-Tooth. Several large trials with ascorbic acid were negative but research into novel compounds continues.
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Affiliation(s)
- Jonathan Baets
- aNeurogenetics Group bPeripheral Neuropathy Group, VIB-Department of Molecular Genetics cLaboratory of Neurogenetics, Institute Born-Bunge dDepartment of Neurology, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium
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Dohrn N, Le VQ, Petersen A, Skovbo P, Pedersen IS, Ernst A, Krarup H, Petersen MB. ECEL1 mutation causes fetal arthrogryposis multiplex congenita. Am J Med Genet A 2015; 167A:731-43. [PMID: 25708584 DOI: 10.1002/ajmg.a.37018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 01/28/2015] [Indexed: 12/14/2022]
Abstract
Arthrogryposis multiplex congenita (AMC) is a descriptor for the clinical finding of congenital fixation of multiple joints. We present a consanguineous healthy couple with two pregnancies described with AMC due to characteristic findings on ultrasonography of fixated knee extension and reduced fetal movement at the gestational age of 13 weeks + 2 days and 12 weeks + 4 days. Both pregnancies were terminated and postmortem examinations were performed. The postmortem examinations confirmed AMC and suggested a diagnosis of centronuclear myopathy (CNM) due to characteristic histological findings in muscle biopsies. Whole exome sequencing (WES) was performed on all four individuals and the outcome was filtered by application of multiple filtration parameters satisfying a recessive inheritance pattern. Only one gene, ECEL1, was predicted damaging and had previously been associated with neuromuscular disease or AMC. The variant found ECEL1 is a missense mutation in a highly conserved residue and was predicted pathogenic by prediction software. The finding expands the molecular basis of congenital contractures and the phenotypic spectrum of ECEL1 mutations. The histological pattern suggestive of CNM in the fetuses can expand the spectrum of genes causing CNM, as we propose that mutations in ECEL1 can cause CNM or a condition similar to this. Further investigation of this is needed and we advocate that future patients with similar clinical presentation or proven ECEL1 mutations are examined with muscle biopsy. Secondly, this study illustrates the great potential of the clinical application of WES in couples with recurrent abortions or stillborn neonates.
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Affiliation(s)
- N Dohrn
- Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
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Copy number variations in a population-based study of Charcot-Marie-Tooth disease. BIOMED RESEARCH INTERNATIONAL 2015; 2015:960404. [PMID: 25648254 PMCID: PMC4306395 DOI: 10.1155/2015/960404] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/13/2014] [Indexed: 12/14/2022]
Abstract
Copy number variations (CNVs) are important in relation to diversity and evolution but can sometimes cause disease. The most common genetic cause of the inherited peripheral neuropathy Charcot-Marie-Tooth disease is the PMP22 duplication; otherwise, CNVs have been considered rare. We investigated CNVs in a population-based sample of Charcot-Marie-Tooth (CMT) families. The 81 CMT families had previously been screened for the PMP22 duplication and point mutations in 51 peripheral neuropathy genes, and a genetic cause was identified in 37 CMT families (46%). Index patients from the 44 CMT families with an unknown genetic diagnosis were analysed by whole-genome array comparative genomic hybridization to investigate the entire genome for larger CNVs and multiplex ligation-dependent probe amplification to detect smaller intragenomic CNVs in MFN2 and MPZ. One patient had the pathogenic PMP22 duplication not detected by previous methods. Three patients had potentially pathogenic CNVs in the CNTNAP2, LAMA2, or SEMA5A, that is, genes related to neuromuscular or neurodevelopmental disease. Genotype and phenotype correlation indicated likely pathogenicity for the LAMA2 CNV, whereas the CNTNAP2 and SEMA5A CNVs remained potentially pathogenic. Except the PMP22 duplication, disease causing CNVs are rare but may cause CMT in about 1% (95% CI 0–7%) of the Norwegian CMT families.
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46
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The Rapidly Emerging Role for Whole Exome Sequencing in Clinical Genetics. CURRENT GENETIC MEDICINE REPORTS 2014. [DOI: 10.1007/s40142-014-0044-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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