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Van Lent J, Prior R, Pérez Siles G, Cutrupi AN, Kennerson ML, Vangansewinkel T, Wolfs E, Mukherjee-Clavin B, Nevin Z, Judge L, Conklin B, Tyynismaa H, Clark AJ, Bennett DL, Van Den Bosch L, Saporta M, Timmerman V. Advances and challenges in modeling inherited peripheral neuropathies using iPSCs. Exp Mol Med 2024:10.1038/s12276-024-01250-x. [PMID: 38825644 DOI: 10.1038/s12276-024-01250-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/21/2024] [Accepted: 03/18/2024] [Indexed: 06/04/2024] Open
Abstract
Inherited peripheral neuropathies (IPNs) are a group of diseases associated with mutations in various genes with fundamental roles in the development and function of peripheral nerves. Over the past 10 years, significant advances in identifying molecular disease mechanisms underlying axonal and myelin degeneration, acquired from cellular biology studies and transgenic fly and rodent models, have facilitated the development of promising treatment strategies. However, no clinical treatment has emerged to date. This lack of treatment highlights the urgent need for more biologically and clinically relevant models recapitulating IPNs. For both neurodevelopmental and neurodegenerative diseases, patient-specific induced pluripotent stem cells (iPSCs) are a particularly powerful platform for disease modeling and preclinical studies. In this review, we provide an update on different in vitro human cellular IPN models, including traditional two-dimensional monoculture iPSC derivatives, and recent advances in more complex human iPSC-based systems using microfluidic chips, organoids, and assembloids.
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Affiliation(s)
- Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, 2610, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born Bunge, 2610, Antwerp, Belgium
- Institute of Oncology Research (IOR), BIOS+, 6500, Bellinzona, Switzerland
- Università della Svizzera Italiana, 6900, Lugano, Switzerland
| | - Robert Prior
- Universitätsklinikum Bonn (UKB), University of Bonn, Bonn, Germany
| | - Gonzalo Pérez Siles
- Northcott Neuroscience Laboratory, ANZAC Research Institute Sydney Local Health District and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Anthony N Cutrupi
- Northcott Neuroscience Laboratory, ANZAC Research Institute Sydney Local Health District and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute Sydney Local Health District and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Molecular Medicine Laboratory, Concord Hospital, Sydney, NSW, Australia
| | - Tim Vangansewinkel
- UHasselt - Hasselt University, BIOMED, Laboratory for Functional Imaging and Research on Stem Cells (FIERCE Lab), Agoralaan, 3590, Diepenbeek, Belgium
- VIB-Center for Brain and Disease Research, Laboratory of Neurobiology, 3000, Leuven, Belgium
| | - Esther Wolfs
- UHasselt - Hasselt University, BIOMED, Laboratory for Functional Imaging and Research on Stem Cells (FIERCE Lab), Agoralaan, 3590, Diepenbeek, Belgium
| | | | | | - Luke Judge
- Gladstone Institutes, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Bruce Conklin
- Gladstone Institutes, San Francisco, CA, USA
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Alex J Clark
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - David L Bennett
- Nuffield Department of Clinical Neuroscience, Oxford University, Oxford, UK
| | - Ludo Van Den Bosch
- VIB-Center for Brain and Disease Research, Laboratory of Neurobiology, 3000, Leuven, Belgium
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute, KU Leuven-University of Leuven, 3000, Leuven, Belgium
| | - Mario Saporta
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, 2610, Antwerp, Belgium.
- Laboratory of Neuromuscular Pathology, Institute Born Bunge, 2610, Antwerp, Belgium.
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Parmar JM, Laing NG, Kennerson ML, Ravenscroft G. Genetics of inherited peripheral neuropathies and the next frontier: looking backwards to progress forwards. J Neurol Neurosurg Psychiatry 2024:jnnp-2024-333436. [PMID: 38744462 DOI: 10.1136/jnnp-2024-333436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Inherited peripheral neuropathies (IPNs) encompass a clinically and genetically heterogeneous group of disorders causing length-dependent degeneration of peripheral autonomic, motor and/or sensory nerves. Despite gold-standard diagnostic testing for pathogenic variants in over 100 known associated genes, many patients with IPN remain genetically unsolved. Providing patients with a diagnosis is critical for reducing their 'diagnostic odyssey', improving clinical care, and for informed genetic counselling. The last decade of massively parallel sequencing technologies has seen a rapid increase in the number of newly described IPN-associated gene variants contributing to IPN pathogenesis. However, the scarcity of additional families and functional data supporting variants in potential novel genes is prolonging patient diagnostic uncertainty and contributing to the missing heritability of IPNs. We review the last decade of IPN disease gene discovery to highlight novel genes, structural variation and short tandem repeat expansions contributing to IPN pathogenesis. From the lessons learnt, we provide our vision for IPN research as we anticipate the future, providing examples of emerging technologies, resources and tools that we propose that will expedite the genetic diagnosis of unsolved IPN families.
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Affiliation(s)
- Jevin M Parmar
- Rare Disease Genetics and Functional Genomics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Nigel G Laing
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Preventive Genetics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, New South Wales, Australia
| | - Gianina Ravenscroft
- Rare Disease Genetics and Functional Genomics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
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Li D, Yu H, Zhou M, Fan W, Guan Q, Li L. Case report: Chronic inflammatory demyelinating polyneuropathy superimposed on Charcot-Marie-tooth type 1A disease after SARS-CoV-2 vaccination and COVID-19 infection. Front Neurol 2024; 15:1358881. [PMID: 38651106 PMCID: PMC11033519 DOI: 10.3389/fneur.2024.1358881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/28/2024] [Indexed: 04/25/2024] Open
Abstract
Background There is growing evidence that severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) or COVID-19 infection is associated with the development of immune mediated neuropathies like chronic inflammatory demyelinating polyneuropathy (CIDP), but the impact of SARS-CoV-2 vaccination and COVID-19 infection on genetic disorders such as Charcot-MarieTooth (CMT) remains unclear. Case presentation A 42-year-old male with occulted CMT neuropathy type lA (CMT1A) who developed limb numbness and weakness after the second SARS-CoV-2-vaccination was confirmed by identifying characteristic repeats in the p11.2 region of chromosome 17. Due to the progressive deterioration of muscle strength over 8 weeks, limb atrophy, moderately elevated protein counts in the cerebrospinal fluid, and significant improvement with intravenous human immunoglobulin, which were characteristic of acquired inflammatory neuropathies, he was eventually diagnosed with CIDP superimposed on CMT1A. However, after a three-month plateau, the patient contracted COVID-19, which led to repeated and worsening symptoms of limb weakness and atrophy, thus was diagnosed with a recurrence of CIDP and treated with Intravenous immunoglobulin and methylprednisolone 500 mg/d for 5 consecutive days, followed by oral prednisone and mycophenolate mofetil tablets. On 2 month follow-up, he exhibited remarkable clinical improvement and could walk independently with rocking gait. After 1 year of follow-up, the patient's condition was stable without further change. Conclusion Our case indicates that CMT1A can deteriorate after SARS-CoV-2 vaccination. Thus, SARS-CoV-2 vaccination should be considered a potential predisposing factor for CMT1A worsening. The possible superposition of CMTIA and CIDP in the context of SARS-CoV-2 infection or immunity suggests that any clinical exacerbation in patients with CMT1A should be carefully evaluated to rule out treatable superposition inflammation. In addition, electrophysiological and imaging examination of the proximal nerves, such as the axillary nerve, is helpful for the diagnosis of CIDP.
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Affiliation(s)
| | | | | | | | | | - Li Li
- Department of Neurology, Ningbo, Zhejiang, China
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4
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Allou L, Mundlos S. Disruption of regulatory domains and novel transcripts as disease-causing mechanisms. Bioessays 2023; 45:e2300010. [PMID: 37381881 DOI: 10.1002/bies.202300010] [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: 01/16/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023]
Abstract
Deletions, duplications, insertions, inversions, and translocations, collectively called structural variations (SVs), affect more base pairs of the genome than any other sequence variant. The recent technological advancements in genome sequencing have enabled the discovery of tens of thousands of SVs per human genome. These SVs primarily affect non-coding DNA sequences, but the difficulties in interpreting their impact limit our understanding of human disease etiology. The functional annotation of non-coding DNA sequences and methodologies to characterize their three-dimensional (3D) organization in the nucleus have greatly expanded our understanding of the basic mechanisms underlying gene regulation, thereby improving the interpretation of SVs for their pathogenic impact. Here, we discuss the various mechanisms by which SVs can result in altered gene regulation and how these mechanisms can result in rare genetic disorders. Beyond changing gene expression, SVs can produce novel gene-intergenic fusion transcripts at the SV breakpoints.
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Affiliation(s)
- Lila Allou
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Mundlos
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Cutrupi AN, Narayanan RK, Perez-Siles G, Grosz BR, Lai K, Boyling A, Ellis M, Lin RCY, Neumann B, Mao D, Uesugi M, Nicholson GA, Vucic S, Saporta MA, Kennerson ML. Novel gene-intergenic fusion involving ubiquitin E3 ligase UBE3C causes distal hereditary motor neuropathy. Brain 2023; 146:880-897. [PMID: 36380488 PMCID: PMC9976978 DOI: 10.1093/brain/awac424] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 10/30/2022] [Indexed: 11/17/2022] Open
Abstract
Distal hereditary motor neuropathies (dHMNs) are a group of inherited diseases involving the progressive, length-dependent axonal degeneration of the lower motor neurons. There are currently 29 reported causative genes and four disease loci implicated in dHMN. Despite the high genetic heterogeneity, mutations in the known genes account for less than 20% of dHMN cases, with the mutations identified predominantly being point mutations or indels. We have expanded the spectrum of dHMN mutations with the identification of a 1.35 Mb complex structural variation (SV) causing a form of autosomal dominant dHMN (DHMN1 OMIM %182906). Given the complex nature of SV mutations and the importance of studying pathogenic mechanisms in a neuronal setting, we generated a patient-derived DHMN1 motor neuron model harbouring the 1.35 Mb complex insertion. The DHMN1 complex insertion creates a duplicated copy of the first 10 exons of the ubiquitin-protein E3 ligase gene (UBE3C) and forms a novel gene-intergenic fusion sense transcript by incorporating a terminal pseudo-exon from intergenic sequence within the DHMN1 locus. The UBE3C intergenic fusion (UBE3C-IF) transcript does not undergo nonsense-mediated decay and results in a significant reduction of wild-type full-length UBE3C (UBE3C-WT) protein levels in DHMN1 iPSC-derived motor neurons. An engineered transgenic Caenorhabditis elegans model expressing the UBE3C-IF transcript in GABA-ergic motor neurons shows neuronal synaptic transmission deficits. Furthermore, the transgenic animals are susceptible to heat stress, which may implicate defective protein homeostasis underlying DHMN1 pathogenesis. Identification of the novel UBE3C-IF gene-intergenic fusion transcript in motor neurons highlights a potential new disease mechanism underlying axonal and motor neuron degeneration. These complementary models serve as a powerful paradigm for studying the DHMN1 complex SV and an invaluable tool for defining therapeutic targets for DHMN1.
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Affiliation(s)
- Anthony N Cutrupi
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Ramesh K Narayanan
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Gonzalo Perez-Siles
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Bianca R Grosz
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Kaitao Lai
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Alexandra Boyling
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Melina Ellis
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Ruby C Y Lin
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
| | - Brent Neumann
- Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Di Mao
- Institute for Integrated Cell-Material Sciences and Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Motonari Uesugi
- Institute for Integrated Cell-Material Sciences and Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Garth A Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Molecular Medicine Laboratory, Concord Repatriation General Hospital, Sydney, NSW 2139, Australia
| | - Steve Vucic
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
- Brain and Nerve Research Centre, Concord Repatriation General Hospital, Sydney, NSW 2139, Australia
| | - Mario A Saporta
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
- Molecular Medicine Laboratory, Concord Repatriation General Hospital, Sydney, NSW 2139, Australia
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Karakaya T, Turkyilmaz A, Sager G, Inan R, Yarali O, Cebi AH, Akin Y. Molecular characterization of Turkish patients with demyelinating Charcot-Marie-Tooth disease. Neurogenetics 2022; 23:213-221. [DOI: 10.1007/s10048-022-00693-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
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Concomitant MPZ and MFN2 Gene Variants and Charcot Marie Tooth Disease in a Boy: Clinical and Genetic Analysis—Literature Review. Case Rep Pediatr 2022; 2022:3793226. [PMID: 35449525 PMCID: PMC9017559 DOI: 10.1155/2022/3793226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/04/2022] Open
Abstract
Charcot- Marie- Tooth (CMT) disease includes a group of clinically and genetically heterogeneous neuropathic disorders with an estimated frequency of 1 on 2.500 individuals. CMTs are differently classified according to the age of onset, type of inheritance, and type of inheritance plus clinical features. For these disorders, more than 100 genes have been implicated as causal factors, with mutations in the PMP22 being one of the most common. The demyelinating type (CMT1) affects more than 30% of the CMTs patients and manifests with motor and sensory dysfunctions of the peripheral nervous system mainly starting with slow progressive weakness of the lower extremities. We report here a 12 year- old boy presenting with typical features of CMT1 type, hearing impairment, and inguinal hernia who at the next-generation sequence analysis displayed a concomitant presence of two variants: the c.233 C>T p.Ser 78Leu of the MPZ gene (NM_000530.6) characterized as pathogenetic and the c.1403 G>A p.Arg 468His of the MFN2 gene (NM_014874.3) characterized as VUS. Concomitant variant mutations in CMTs have been uncommonly reported. The role of these gene mutations on the clinical expression and a literature review on this topic is discussed.
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Boyling A, Perez-Siles G, Kennerson ML. Structural Variation at a Disease Mutation Hotspot: Strategies to Investigate Gene Regulation and the 3D Genome. Front Genet 2022; 13:842860. [PMID: 35401663 PMCID: PMC8990796 DOI: 10.3389/fgene.2022.842860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/21/2022] [Indexed: 12/18/2022] Open
Abstract
A rare form of X-linked Charcot-Marie-Tooth neuropathy, CMTX3, is caused by an interchromosomal insertion occurring at chromosome Xq27.1. Interestingly, eight other disease phenotypes have been associated with insertions (or insertion-deletions) occurring at the same genetic locus. To date, the pathogenic mechanism underlying most of these diseases remains unsolved, although local gene dysregulation has clearly been implicated in at least two phenotypes. The challenges of accessing disease-relevant tissue and modelling these complex genomic rearrangements has led to this research impasse. We argue that recent technological advancements can overcome many of these challenges, particularly induced pluripotent stem cells (iPSC) and their capacity to provide access to patient-derived disease-relevant tissue. However, to date these valuable tools have not been utilized to investigate the disease-associated insertions at chromosome Xq27.1. Therefore, using CMTX3 as a reference disease, we propose an experimental approach that can be used to explore these complex mutations, as well as similar structural variants located elsewhere in the genome. The mutational hotspot at Xq27.1 is a valuable disease paradigm with the potential to improve our understanding of the pathogenic consequences of complex structural variation, and more broadly, refine our knowledge of the multifaceted process of long-range gene regulation. Intergenic structural variation is a critically understudied class of mutation, although it is likely to contribute significantly to unsolved genetic disease.
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Affiliation(s)
- Alexandra Boyling
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- *Correspondence: Alexandra Boyling, ; Marina L. Kennerson,
| | - Gonzalo Perez-Siles
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Marina L. Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Molecular Medicine Laboratory, Concord Repatriation General Hospital, Sydney, NSW, Australia
- *Correspondence: Alexandra Boyling, ; Marina L. Kennerson,
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Matsuda N, Ootsuki K, Kobayashi S, Nemoto A, Kubo H, Usami SI, Kanani K. A novel case of concurrent occurrence of demyelinating-polyneuropathy-causing PMP22 duplication and SOX10 gene mutation producing severe hypertrophic neuropathy. BMC Neurol 2021; 21:243. [PMID: 34171997 PMCID: PMC8228911 DOI: 10.1186/s12883-021-02256-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/26/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Hereditary motor and sensory neuropathy, also referred to as Charcot-Marie-Tooth disease (CMT), is most often caused by a duplication of the peripheral myelin protein 22 (PMP22) gene. This duplication causes CMT type 1A (CMT1A). CMT1A rarely occurs in combination with other hereditary neuromuscular disorders. However, such rare genetic coincidences produce a severe phenotype and have been reported in terms of "double trouble" overlapping syndrome. Waardenburg syndrome (WS) is the most common form of a hereditary syndromic deafness. It is primarily characterized by pigmentation anomalies and classified into four major phenotypes. A mutation in the SRY sex determining region Y-box 10 (SOX10) gene causes WS type 2 or 4 and peripheral demyelinating neuropathy, central dysmyelinating leukodystrophy, WS, and Hirschsprung disease. We describe a 11-year-old boy with extreme hypertrophic neuropathy because of a combination of CMT1A and WS type 2. This is the first published case on the co-occurrence of CMT1A and WS type 2. CASE PRESENTATION The 11-year-old boy presented with motor developmental delay and a deterioration in unstable walking at 6 years of age. In addition, he had congenital hearing loss and heterochromia iridis. The neurological examination revealed weakness in the distal limbs with pes cavus. He was diagnosed with CMT1A by the fluorescence in situ hybridization method. His paternal pedigree had a history of CMT1A. However, no family member had congenital hearing loss. His clinical manifestation was apparently severe than those of his relatives with CMT1A. In addition, a whole-body magnetic resonance neurography revealed an extreme enlargement of his systemic cranial and spinal nerves. Subsequently, a genetic analysis revealed a heterozygous frameshift mutation c.876delT (p.F292Lfs*19) in the SOX10 gene. He was eventually diagnosed with WS type 2. CONCLUSIONS We described a patient with a genetically confirmed overlapping diagnoses of CMT1A and WS type 2. The double trouble with the genes created a significant impact on the peripheral nerves system. Severe phenotype in the proband can be attributed to the cumulative effect of mutations in both PMP22 and SOX10 genes, responsible for demyelinating neuropathy.
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Affiliation(s)
- Nozomu Matsuda
- Department of Neurology, Fukushima Medical University, 1 Hikarigaoka, Fukushima, Fukushima, 960-1295, Japan.
| | - Koushi Ootsuki
- Department of Otorhinolaryngology, Fukushima Medical University, 1 Hikarigaoka, Fukushima, Fukushima, 960-1295, Japan
| | - Shunsuke Kobayashi
- Department of Neurology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo, 173-8606, Japan
| | - Ayaka Nemoto
- Advanced Clinical Research Center, Fukushima Medical University, 1 Hikarigaoka, Fukushima, Fukushima, 960-1295, Japan
| | - Hitoshi Kubo
- Advanced Clinical Research Center, Fukushima Medical University, 1 Hikarigaoka, Fukushima, Fukushima, 960-1295, Japan.,Preparing Section for New Faculty of Medical Science, Fukushima Medical University, 1 Hikarigaoka, Fukushima, Fukushima, 960-1295, Japan
| | - Shin-Ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Kazuaki Kanani
- Department of Neurology, Fukushima Medical University, 1 Hikarigaoka, Fukushima, Fukushima, 960-1295, Japan
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10
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Boutary S, Caillaud M, El Madani M, Vallat JM, Loisel-Duwattez J, Rouyer A, Richard L, Gracia C, Urbinati G, Desmaële D, Echaniz-Laguna A, Adams D, Couvreur P, Schumacher M, Massaad C, Massaad-Massade L. Squalenoyl siRNA PMP22 nanoparticles are effective in treating mouse models of Charcot-Marie-Tooth disease type 1 A. Commun Biol 2021; 4:317. [PMID: 33750896 PMCID: PMC7943818 DOI: 10.1038/s42003-021-01839-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/11/2021] [Indexed: 02/08/2023] Open
Abstract
Charcot-Marie-Tooth disease type 1 A (CMT1A) lacks an effective treatment. We provide a therapy for CMT1A, based on siRNA conjugated to squalene nanoparticles (siRNA PMP22-SQ NPs). Their administration resulted in normalization of Pmp22 protein levels, restored locomotor activity and electrophysiological parameters in two transgenic CMT1A mouse models with different severity of the disease. Pathological studies demonstrated the regeneration of myelinated axons and myelin compaction, one major step in restoring function of myelin sheaths. The normalization of sciatic nerve Krox20, Sox10 and neurofilament levels reflected the regeneration of both myelin and axons. Importantly, the positive effects of siRNA PMP22-SQ NPs lasted for three weeks, and their renewed administration resulted in full functional recovery. Beyond CMT1A, our findings can be considered as a potent therapeutic strategy for inherited peripheral neuropathies. They provide the proof of concept for a new precision medicine based on the normalization of disease gene expression by siRNA.
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Affiliation(s)
- Suzan Boutary
- U1195 Diseases and Hormones of the Nervous System, Inserm and University Paris-Saclay, 94276, Le Kremlin-Bicêtre, France
| | - Marie Caillaud
- U1195 Diseases and Hormones of the Nervous System, Inserm and University Paris-Saclay, 94276, Le Kremlin-Bicêtre, France
| | - Mévidette El Madani
- U1195 Diseases and Hormones of the Nervous System, Inserm and University Paris-Saclay, 94276, Le Kremlin-Bicêtre, France
- National Research Centre, Cairo, Egypt
| | - Jean-Michel Vallat
- Service de Neurologie - Centre de Référence Neuropathies Périphérique Rares, CHU de Limoges - Hôpital Dupuytren, 2 Avenue Martin Luther King, 87042, LIMOGES CEDEX, France
| | - Julien Loisel-Duwattez
- U1195 Diseases and Hormones of the Nervous System, Inserm and University Paris-Saclay, 94276, Le Kremlin-Bicêtre, France
- Neurology Department, AP-HP, Université Paris-Saclay and French Reference Center for Familial Amyloid Polyneuropathy and other rare peripheral neuropathies (CRMR-NNERF), Bicêtre University Hospital, Le Kremlin-Bicêtre, France
| | - Alice Rouyer
- U1195 Diseases and Hormones of the Nervous System, Inserm and University Paris-Saclay, 94276, Le Kremlin-Bicêtre, France
| | - Laurence Richard
- Service de Neurologie - Centre de Référence Neuropathies Périphérique Rares, CHU de Limoges - Hôpital Dupuytren, 2 Avenue Martin Luther King, 87042, LIMOGES CEDEX, France
| | - Céline Gracia
- UMR 8203 CNRS, newly UMR 9018 CNRS, Université Paris-Saclay, 94805, Villejuif, France
| | - Giorgia Urbinati
- UMR 8203 CNRS, newly UMR 9018 CNRS, Université Paris-Saclay, 94805, Villejuif, France
| | - Didier Desmaële
- Institut Galien Paris-Sud, CNRS UMR 8612, Université Paris-Sud, Université Paris-Saclay, 92290, Châtenay-Malabry, France
| | - Andoni Echaniz-Laguna
- U1195 Diseases and Hormones of the Nervous System, Inserm and University Paris-Saclay, 94276, Le Kremlin-Bicêtre, France
- Neurology Department, AP-HP, Université Paris-Saclay and French Reference Center for Familial Amyloid Polyneuropathy and other rare peripheral neuropathies (CRMR-NNERF), Bicêtre University Hospital, Le Kremlin-Bicêtre, France
| | - David Adams
- U1195 Diseases and Hormones of the Nervous System, Inserm and University Paris-Saclay, 94276, Le Kremlin-Bicêtre, France
- Neurology Department, AP-HP, Université Paris-Saclay and French Reference Center for Familial Amyloid Polyneuropathy and other rare peripheral neuropathies (CRMR-NNERF), Bicêtre University Hospital, Le Kremlin-Bicêtre, France
| | - Patrick Couvreur
- Institut Galien Paris-Sud, CNRS UMR 8612, Université Paris-Sud, Université Paris-Saclay, 92290, Châtenay-Malabry, France
| | - Michael Schumacher
- U1195 Diseases and Hormones of the Nervous System, Inserm and University Paris-Saclay, 94276, Le Kremlin-Bicêtre, France
| | - Charbel Massaad
- Faculty of Basic and Biomedical Sciences, Paris Descartes University, INSERM UMRS 1124, 75006, Paris, France
| | - Liliane Massaad-Massade
- U1195 Diseases and Hormones of the Nervous System, Inserm and University Paris-Saclay, 94276, Le Kremlin-Bicêtre, France.
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11
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Gray JS, Campbell MJ. Challenges and Opportunities of Genomic Approaches in Therapeutics Development. Methods Mol Biol 2021; 2194:107-126. [PMID: 32926364 DOI: 10.1007/978-1-0716-0849-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The magnitude of all therapeutic responses is significantly determined by genome structure, variation, and functional interactions. This determination occurs at many levels which are discussed in the current review. Well-established examples of structural variation between individuals are known to dictate an individual's response to numerous drugs, as clearly illustrated by warfarin. The exponential rate of genomic-based interrogation is coupled with an expanding repertoire of genomic technologies and applications. This is leading to an ever more sophisticated appreciation of how structural variation, regulation of transcription and genomic structure, both individually and collectively, define cell therapeutic responses.
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Affiliation(s)
- Jaimie S Gray
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Moray J Campbell
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA.
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12
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Pipis M, Houlden H, Reilly MM. Advancing Charcot-Marie-Tooth disease diagnostics, through the UK 100,000 Genomes Project. MED GENET-BERLIN 2020. [DOI: 10.1515/medgen-2020-2037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Whole genome sequencing (WGS) is regarded by many as the pinnacle of contemporary molecular genetic testing, and has only been possible because of the rapid development and roll-out of next-generation sequencing technologies. It provides a phenotype-agnostic analysis of the genome and has important advantages compared to other techniques including a consistent coverage across the coding and non-coding genome, the application of high resolution homozygosity mapping and the ability to detect and highlight structural variation.
Realising this potential and with a bid to sequence 100,000 genomes, the UK rolled out the 100,000 Genomes Project as a proof of concept of integrating genomics in the national health service. Participants with cancer and rare diseases enrolled in the project whose infrastructure comprises of a central national biorepository and 13 regional genomic medicine centres where clinicians, geneticists and other scientists work as part of a multidisciplinary team. Amongst participants are also patients with genetically unclassified Charcot-Marie-Tooth disease who have benefited substantially from improved diagnostic rates and many more stand to benefit as the analysis of genomic data is ongoing.
WGS is an important tool as we head towards more personalised medicine and in our quest to improve public health and treat and where possible prevent disease.
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Affiliation(s)
- Menelaos Pipis
- MRC Centre for Neuromuscular Diseases , UCL Queen Square Institute of Neurology , London , UK
| | - Henry Houlden
- MRC Centre for Neuromuscular Diseases , UCL Queen Square Institute of Neurology , London , UK
| | - Mary M. Reilly
- MRC Centre for Neuromuscular Diseases , UCL Queen Square Institute of Neurology , London , UK
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13
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A novel missense pathogenic variant in NEFH causing rare Charcot-Marie-Tooth neuropathy type 2CC. Neurol Sci 2020; 42:757-763. [PMID: 32780247 DOI: 10.1007/s10072-020-04595-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/11/2020] [Indexed: 10/23/2022]
Abstract
The purpose of this research is to explore the underlying genes of Charcot-Marie-Tooth (CMT). Technologies such as electrophysiological testing and gene sequencing have been applied. We identified a novel variant NEFH c.2215C>T(p.P739S)(HGNC:7737) in a heterozygous state, which was considered to be pathogenic for CMT2CC(OMIM:616924).The proband and his brothers presented with muscle atrophy of hand and calf and moderately decreased conduction velocities. By whole exome sequencing analysis, we found the novel missense pathogenic variant in the proband, his brother and mother. This report broadened current knowledge about intermediate CMT and the phenotypic spectrum of defects associated with NEFH. In addition, the proband carried other five variants {HSPD1c.695C>A (p.S232X), FLNCc.1073A>G (p.N358S), GUSBc.323C>A (p.P108Q), ACY1 c.1063-1G>A and APTX c.484-2A>T}, which have not been reported until now. The NEFH c.2215C>T (p.P739S) give us a new understanding of CMT, which might provide new therapeutic targets in the future.
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14
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Rzepnikowska W, Kaminska J, Kabzińska D, Binięda K, Kochański A. A Yeast-Based Model for Hereditary Motor and Sensory Neuropathies: A Simple System for Complex, Heterogeneous Diseases. Int J Mol Sci 2020; 21:ijms21124277. [PMID: 32560077 PMCID: PMC7352270 DOI: 10.3390/ijms21124277] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022] Open
Abstract
Charcot–Marie–Tooth (CMT) disease encompasses a group of rare disorders that are characterized by similar clinical manifestations and a high genetic heterogeneity. Such excessive diversity presents many problems. Firstly, it makes a proper genetic diagnosis much more difficult and, even when using the most advanced tools, does not guarantee that the cause of the disease will be revealed. Secondly, the molecular mechanisms underlying the observed symptoms are extremely diverse and are probably different for most of the disease subtypes. Finally, there is no possibility of finding one efficient cure for all, or even the majority of CMT diseases. Every subtype of CMT needs an individual approach backed up by its own research field. Thus, it is little surprise that our knowledge of CMT disease as a whole is selective and therapeutic approaches are limited. There is an urgent need to develop new CMT models to fill the gaps. In this review, we discuss the advantages and disadvantages of yeast as a model system in which to study CMT diseases. We show how this single-cell organism may be used to discriminate between pathogenic variants, to uncover the mechanism of pathogenesis, and to discover new therapies for CMT disease.
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Affiliation(s)
- Weronika Rzepnikowska
- Neuromuscular Unit, Mossakowski Medical Research Centre Polish Academy of Sciences, 02-106 Warsaw, Poland; (W.R.); (D.K.); (K.B.)
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Dagmara Kabzińska
- Neuromuscular Unit, Mossakowski Medical Research Centre Polish Academy of Sciences, 02-106 Warsaw, Poland; (W.R.); (D.K.); (K.B.)
| | - Katarzyna Binięda
- Neuromuscular Unit, Mossakowski Medical Research Centre Polish Academy of Sciences, 02-106 Warsaw, Poland; (W.R.); (D.K.); (K.B.)
| | - Andrzej Kochański
- Neuromuscular Unit, Mossakowski Medical Research Centre Polish Academy of Sciences, 02-106 Warsaw, Poland; (W.R.); (D.K.); (K.B.)
- Correspondence:
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15
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Mortreux J, Bacquet J, Boyer A, Alazard E, Bellance R, Giguet-Valard AG, Cerino M, Krahn M, Audic F, Chabrol B, Laugel V, Desvignes JP, Béroud C, Nguyen K, Verschueren A, Lévy N, Attarian S, Delague V, Missirian C, Bonello-Palot N. Identification of novel pathogenic copy number variations in Charcot-Marie-Tooth disease. J Hum Genet 2019; 65:313-323. [PMID: 31852984 DOI: 10.1038/s10038-019-0710-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/03/2019] [Accepted: 12/08/2019] [Indexed: 12/13/2022]
Abstract
Charcot-Marie-Tooth disease (CMT) is a hereditary sensory-motor neuropathy characterized by a strong clinical and genetic heterogeneity. Over the past few years, with the occurrence of whole-exome sequencing (WES) or whole-genome sequencing (WGS), the molecular diagnosis rate has been improved by allowing the screening of more than 80 genes at one time. In CMT, except the recurrent PMP22 duplication accounting for about 60% of pathogenic variations, pathogenic copy number variations (CNVs) are rarely reported and only a few studies screening specifically CNVs have been performed. The aim of the present study was to screen for CNVs in the most prevalent genes associated with CMT in a cohort of 200 patients negative for the PMP22 duplication. CNVs were screened using the Exome Depth software on next generation sequencing (NGS) data obtained by targeted capture and sequencing of a panel of 81 CMT associated genes. Deleterious CNVs were identified in four patients (2%), in four genes: GDAP1, LRSAM1, GAN, and FGD4. All CNVs were confirmed by high-resolution oligonucleotide array Comparative Genomic Hybridization (aCGH) and/or quantitative PCR. By identifying four new CNVs in four different genes, we demonstrate that, although they are rare mutational events in CMT, CNVs might contribute significantly to mutational spectrum of Charcot-Marie-Tooth disease and should be searched in routine NGS diagnosis. This strategy increases the molecular diagnosis rate of patients with neuropathy.
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Affiliation(s)
- J Mortreux
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - J Bacquet
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - A Boyer
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France
| | - E Alazard
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France
| | - R Bellance
- Centre de référence Caribéen pour les maladies neuromusculaires, CeRCa, Hôpital Pierre-Zobda-Quitman, CHU de Martinique, France
| | - A G Giguet-Valard
- Centre de référence Caribéen pour les maladies neuromusculaires, CeRCa, Hôpital Pierre-Zobda-Quitman, CHU de Martinique, France
| | - M Cerino
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - M Krahn
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - F Audic
- Centre de référence des maladies neuromusculaires, Hôpital de la Timone enfant, Assistance-Publique Hôpitaux de Marseille, Marseille, France
| | - B Chabrol
- Centre de référence des maladies neuromusculaires, Hôpital de la Timone enfant, Assistance-Publique Hôpitaux de Marseille, Marseille, France
| | - V Laugel
- Centre de référence des maladies neuromusculaires, Service de pédiatrie, CHU Strasbourg, France
| | - J P Desvignes
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - C Béroud
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - K Nguyen
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - A Verschueren
- Centre de référence des maladies neuromusculaires, Hôpital de la Timone Adulte, Assistance-Publique Hôpitaux de Marseille, Marseille, France
| | - N Lévy
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - S Attarian
- Centre de référence des maladies neuromusculaires, Hôpital de la Timone Adulte, Assistance-Publique Hôpitaux de Marseille, Marseille, France
| | - V Delague
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - C Missirian
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - N Bonello-Palot
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France. .,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France.
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16
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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: 67] [Impact Index Per Article: 13.4] [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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17
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Campbell MJ. Tales from topographic oceans: topologically associated domains and cancer. Endocr Relat Cancer 2019; 26:R611-R626. [PMID: 31505466 PMCID: PMC7664306 DOI: 10.1530/erc-19-0348] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/09/2019] [Indexed: 01/03/2023]
Abstract
The 3D organization of the genome within the cell nucleus has come into sharp focus over the last decade. This has largely arisen because of the application of genomic approaches that have revealed numerous levels of genomic and chromatin interactions, including topologically associated domains (TADs). The current review examines how these domains were identified, are organized, how their boundaries arise and are regulated, and how genes within TADs are coordinately regulated. There are many examples of the disruption to TAD structure in cancer and the altered regulation, structure and function of TADs are discussed in the context of hormone responsive cancers, including breast, prostate and ovarian cancer. Finally, some aspects of the statistical insight and computational skills required to interrogate TAD organization are considered and future directions discussed.
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Affiliation(s)
- Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
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18
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Abstract
Complexity in genome architecture determines how gene expression programs are established, maintained, and modified from early developmental stages to normal adult phenotypes. Large scale and hierarchical organization of the genome impacts various aspects of cell functions, ranging from X-chromosome inactivation, stem-cell fate determination to transcription, DNA replication, and cellular repair. While chromatin loops and topologically-associated domains represent a basic structural or fundamental unit of chromatin organization, spatio-temporal organization of the genome further creates a complex network of interacting genome patterns, forming chromosomal compartments and chromosome territories. The understanding of human diseases, including cancers, auto-immune disorders, Alzheimer's, and cardiovascular diseases, relies on the associated molecular and epigenetic mechanisms. There is a growing interest in the impact of three-dimensional chromatin folding upon the genome structure and function, which gives rise to the question "What's in the fold?" and is the main focus of this review. Here we discuss the principles determining the spatial and regulatory relationships between gene regulation and three-dimensional chromatin landscapes, and how changes in chromatin-folding could influence the outcome of genome function in healthy and disease states.
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19
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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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