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McCluskey G, Morrison KE, Donaghy C, McConville J, McCarron MO, McVerry F, Duddy W, Duguez S. Serum Neurofilaments in Motor Neuron Disease and Their Utility in Differentiating ALS, PMA and PLS. Life (Basel) 2023; 13:1301. [PMID: 37374084 DOI: 10.3390/life13061301] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Neurofilament levels are elevated in many neurodegenerative diseases and have shown promise as diagnostic and prognostic biomarkers in Amyotrophic Lateral Sclerosis (ALS), the most common form of Motor Neuron Disease (MND). This study assesses serum neurofilament light (NFL) and neurofilament heavy (NFH) chain concentrations in patients with ALS, other variants of motor neuron disease such as Progressive Muscular Atrophy (PMA) and Primary Lateral Sclerosis (PLS), and a range of other neurological diseases. It aims to evaluate the use of NFL and NFH to differentiate these conditions and for the prognosis of MND disease progression. NFL and NFH levels were quantified using electrochemiluminescence immunoassays (ECLIA). Both were elevated in 47 patients with MND compared to 34 patients with other neurological diseases and 33 healthy controls. NFL was able to differentiate patients with MND from the other groups with a Receiver Operating Characteristic (ROC) curve area under the curve (AUC) of 0.90 (p < 0.001). NFL correlated with the rate of disease progression in MND (rho 0.758, p < 0.001) and with the ALS Functional Rating Scale (rho -0.335, p = 0.021). NFL levels were higher in patients with ALS compared to both PMA (p = 0.032) and PLS (p = 0.012) and were able to distinguish ALS from both PMA and PLS with a ROC curve AUC of 0.767 (p = 0.005). These findings support the use of serum NFL to help diagnose and differentiate types of MND, in addition to providing prognostic information to patients and their families.
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Affiliation(s)
- Gavin McCluskey
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry BT47 6SB, UK
- Department of Neurology, Royal Victoria Hospital, Belfast BT12 6BA, UK
- Department of Neurology, Altnagelvin Hospital, Derry BT47 6SB, UK
| | - Karen E Morrison
- Department of Neurology, Royal Victoria Hospital, Belfast BT12 6BA, UK
- Faculty of Medicine, Health & Life Sciences, Queen's University, Belfast BT9 6AG, UK
| | - Colette Donaghy
- Department of Neurology, Altnagelvin Hospital, Derry BT47 6SB, UK
| | - John McConville
- Department of Neurology, Royal Victoria Hospital, Belfast BT12 6BA, UK
- Department of Neurology, Ulster Hospital, Belfast BT16 1RH, UK
| | - Mark O McCarron
- Department of Neurology, Altnagelvin Hospital, Derry BT47 6SB, UK
| | - Ferghal McVerry
- Department of Neurology, Altnagelvin Hospital, Derry BT47 6SB, UK
| | - William Duddy
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry BT47 6SB, UK
| | - Stephanie Duguez
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry BT47 6SB, UK
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Vasilopoulou C, McDaid-McCloskey SL, McCluskey G, Duguez S, Morris AP, Duddy W. Genome-Wide Gene-Set Analysis Identifies Molecular Mechanisms Associated with ALS. Int J Mol Sci 2023; 24:4021. [PMID: 36835433 PMCID: PMC9966913 DOI: 10.3390/ijms24044021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal late-onset motor neuron disease characterized by the loss of the upper and lower motor neurons. Our understanding of the molecular basis of ALS pathology remains elusive, complicating the development of efficient treatment. Gene-set analyses of genome-wide data have offered insight into the biological processes and pathways of complex diseases and can suggest new hypotheses regarding causal mechanisms. Our aim in this study was to identify and explore biological pathways and other gene sets having genomic association to ALS. Two cohorts of genomic data from the dbGaP repository were combined: (a) the largest available ALS individual-level genotype dataset (N = 12,319), and (b) a similarly sized control cohort (N = 13,210). Following comprehensive quality control pipelines, imputation and meta-analysis, we assembled a large European descent ALS-control cohort of 9244 ALS cases and 12,795 healthy controls represented by genetic variants of 19,242 genes. Multi-marker analysis of genomic annotation (MAGMA) gene-set analysis was applied to an extensive collection of 31,454 gene sets from the molecular signatures database (MSigDB). Statistically significant associations were observed for gene sets related to immune response, apoptosis, lipid metabolism, neuron differentiation, muscle cell function, synaptic plasticity and development. We also report novel interactions between gene sets, suggestive of mechanistic overlaps. A manual meta-categorization and enrichment mapping approach is used to explore the overlap of gene membership between significant gene sets, revealing a number of shared mechanisms.
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Affiliation(s)
- Christina Vasilopoulou
- Personalised Medicine Centre, School of Medicine, Ulster University, Londonderry BT47 6SB, UK
| | | | - Gavin McCluskey
- Personalised Medicine Centre, School of Medicine, Ulster University, Londonderry BT47 6SB, UK
| | - Stephanie Duguez
- Personalised Medicine Centre, School of Medicine, Ulster University, Londonderry BT47 6SB, UK
| | - Andrew P. Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, University of Manchester, Manchester M13 9PT, UK
| | - William Duddy
- Personalised Medicine Centre, School of Medicine, Ulster University, Londonderry BT47 6SB, UK
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McCluskey G, Morrison KE, Donaghy C, Rene F, Duddy W, Duguez S. Extracellular Vesicles in Amyotrophic Lateral Sclerosis. Life (Basel) 2022; 13:life13010121. [PMID: 36676070 PMCID: PMC9867379 DOI: 10.3390/life13010121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023]
Abstract
Amyotrophic Lateral Sclerosis is a progressive neurodegenerative disease and is the most common adult motor neuron disease. The disease pathogenesis is complex with the perturbation of multiple pathways proposed, including mitochondrial dysfunction, RNA processing, glutamate excitotoxicity, endoplasmic reticulum stress, protein homeostasis and endosomal transport/extracellular vesicle (EV) secretion. EVs are nanoscopic membrane-bound particles that are released from cells, involved in the intercellular communication of proteins, lipids and genetic material, and there is increasing evidence of their role in ALS. After discussing the biogenesis of EVs, we review their roles in the propagation of pathological proteins in ALS, such as TDP-43, SOD1 and FUS, and their contribution to disease pathology. We also discuss the ALS related genes which are involved in EV formation and vesicular trafficking, before considering the EV protein and RNA dysregulation found in ALS and how these have been investigated as potential biomarkers. Finally, we highlight the potential use of EVs as therapeutic agents in ALS, in particular EVs derived from mesenchymal stem cells and EVs as drug delivery vectors for potential treatment strategies.
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Affiliation(s)
- Gavin McCluskey
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry BT47 6SB, UK
- Department of Neurology, Altnagelvin Hospital, Derry BT47 6SB, UK
- Department of Neurology, Royal Victoria Hospital, Belfast BT12 6BA, UK
- Correspondence: (G.M.); (S.D.)
| | - Karen E. Morrison
- Department of Neurology, Royal Victoria Hospital, Belfast BT12 6BA, UK
- Faculty of Medicine, Health & Life Sciences, Queen’s University, Belfast BT9 6AG, UK
| | - Colette Donaghy
- Department of Neurology, Altnagelvin Hospital, Derry BT47 6SB, UK
| | - Frederique Rene
- INSERM U1118, Centre de Recherche en Biomédecine de Strasbourg, Université de Strasbourg, 67000 Strasbourg, France
| | - William Duddy
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry BT47 6SB, UK
| | - Stephanie Duguez
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry BT47 6SB, UK
- Correspondence: (G.M.); (S.D.)
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McCluskey G, Donaghy C, Morrison KE, McConville J, Duddy W, Duguez S. The Role of Sphingomyelin and Ceramide in Motor Neuron Diseases. J Pers Med 2022; 12:jpm12091418. [PMID: 36143200 PMCID: PMC9501626 DOI: 10.3390/jpm12091418] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS), Spinal Bulbar Muscular Atrophy (SBMA), and Spinal Muscular Atrophy (SMA) are motor neuron diseases (MNDs) characterised by progressive motor neuron degeneration, weakness and muscular atrophy. Lipid dysregulation is well recognised in each of these conditions and occurs prior to neurodegeneration. Several lipid markers have been shown to predict prognosis in ALS. Sphingolipids are complex lipids enriched in the central nervous system and are integral to key cellular functions including membrane stability and signalling pathways, as well as being mediators of neuroinflammation and neurodegeneration. This review highlights the metabolism of sphingomyelin (SM), the most abundant sphingolipid, and of its metabolite ceramide, and its role in the pathophysiology of neurodegeneration, focusing on MNDs. We also review published lipidomic studies in MNDs. In the 13 studies of patients with ALS, 12 demonstrated upregulation of multiple SM species and 6 demonstrated upregulation of ceramides. SM species also correlated with markers of clinical progression in five of six studies. These data highlight the potential use of SM and ceramide as biomarkers in ALS. Finally, we review potential therapeutic strategies for targeting sphingolipid metabolism in neurodegeneration.
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Affiliation(s)
- Gavin McCluskey
- Personalised Medicine Center, School of Medicine, Ulster University, Derry BT47 6SB, UK
- Department of Neurology, Altnagelvin Hospital, Derry, BT47 6SB, UK
- Department of Neurology, Royal Victoria Hospital, Belfast BT12 6BA, UK
| | - Colette Donaghy
- Department of Neurology, Altnagelvin Hospital, Derry, BT47 6SB, UK
| | - Karen E. Morrison
- Department of Neurology, Royal Victoria Hospital, Belfast BT12 6BA, UK
- Faculty of Medicine, Health & Life Sciences, Queen’s University, Belfast BT9 6AG, UK
| | - John McConville
- Department of Neurology, Royal Victoria Hospital, Belfast BT12 6BA, UK
- Department of Neurology, Ulster Hospital, Dundonald, Belfast BT16 1RH, UK
| | - William Duddy
- Personalised Medicine Center, School of Medicine, Ulster University, Derry BT47 6SB, UK
| | - Stephanie Duguez
- Personalised Medicine Center, School of Medicine, Ulster University, Derry BT47 6SB, UK
- Correspondence:
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Mariot V, Joubert R, Le Gall L, Sidlauskaite E, Hourde C, Duddy W, Voit T, Bencze M, Dumonceaux J. RIPK3-mediated cell death is involved in DUX4-mediated toxicity in facioscapulohumeral dystrophy. J Cachexia Sarcopenia Muscle 2021; 12:2079-2090. [PMID: 34687171 PMCID: PMC8718031 DOI: 10.1002/jcsm.12813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 06/14/2021] [Accepted: 09/07/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Facioscapulohumeral dystrophy (FSHD) is caused by mutations leading to the aberrant expression of the DUX4 transcription factor in muscles. DUX4 was proposed to induce cell death, but the involvement of different death pathways is still discussed. A possible pro-apoptotic role of DUX4 was proposed, but as FSHD muscles are characterized by necrosis and inflammatory infiltrates, non-apoptotic pathways may be also involved. METHODS We explored DUX4-mediated cell death by focusing on the role of one regulated necrosis pathway called necroptosis, which is regulated by RIPK3. We investigated the effect of necroptosis on cell death in vitro and in vivo experiments using RIPK3 inhibitors and a RIPK3-deficient transgenic mouse model. RESULTS We showed in vitro that DUX4 expression causes a caspase-independent and RIPK3-mediated cell death in both myoblasts and myotubes. In vivo, RIPK3-deficient animals present improved body and muscle weights, a reduction of the aberrant activation of the DUX4 network genes, and an improvement of muscle histology. CONCLUSIONS These results provide evidence for a role of RIPK3 in DUX4-mediated cell death and open new avenues of research.
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Affiliation(s)
- Virginie Mariot
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, London, UK
| | - Romain Joubert
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, London, UK.,United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Laura Le Gall
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, London, UK
| | - Eva Sidlauskaite
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, London, UK
| | - Christophe Hourde
- Laboratoire Interuniversitaire de Biologie de la Motricité, Université Savoie Mont Blanc, Chambéry, France
| | - William Duddy
- Northern Ireland Center for Stratified/Personalised Medicine, Biomedical Sciences Research Institute, Ulster University, Derry~Londonderry, Northern Ireland, UK
| | - Thomas Voit
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, London, UK
| | - Maximilien Bencze
- University Paris Est Créteil, INSERM, IMRB, Créteil, France.,The Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neurosciences Programme, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Julie Dumonceaux
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, London, UK.,Northern Ireland Center for Stratified/Personalised Medicine, Biomedical Sciences Research Institute, Ulster University, Derry~Londonderry, Northern Ireland, UK
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McCluskey G, Duddy W, Haffey S, Morrison K, Donaghy C, Duguez S. Epidemiology and survival trends of motor neurone disease in Northern Ireland from 2015 to 2019. Eur J Neurol 2021; 29:707-714. [PMID: 34748676 DOI: 10.1111/ene.15172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/02/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND AND PURPOSE This study evaluates the incidence, prevalence and survival trends of motor neurone disease (MND) in Northern Ireland from 2015 to 2019. METHODS A capture-recapture analysis was performed using five independent data sources. Incidence and prevalence rates were standardized to the European Standard Population. Survival outcomes were analysed using Kaplan-Meier curves and Cox regression analysis. RESULTS Amongst 254 total cases of MND, capture-recapture analysis estimated three missing cases (case ascertainment 98.8%). Age standardized incidence of captured cases was 3.12 per 100,000 (2.73, 3.50) and standardized prevalence ranged from 9.45 to 6.49 per 100,000 from 2015 to 2019. Standardized incidence and prevalence rates in 2006 were 1.4 and 3.3 per 100,000 respectively. Of identified cases, 133 (52.4%) were male; 94.5% had amyotrophic lateral sclerosis; median age of onset was 67 years; median time to diagnosis was 12 months (95% confidence interval 11.2, 12.8); survival from diagnosis was 12 months (95% confidence interval 10.6, 15.4); 25 (9.8%) reported a family history of MND or frontotemporal dementia; and a known MND-associated genetic mutation was identified in 7.9% of total cases, of which the most common was C9orf72 (5.7% of all patients). Factors associated with improved survival were younger age at onset, longer time to diagnosis, attendance at regional MND clinic, and initial neurology presentation as outpatient (all p < 0.001). CONCLUSION The incidence and prevalence of MND in Northern Ireland has increased over the last 10 years, in line with increasing rates reported from other European countries. Improved survival was associated with younger age at onset, longer time to diagnosis, attendance at a regional MND clinic and outpatient presentation to a Neurology Department.
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Affiliation(s)
- Gavin McCluskey
- Department of Neurology, Royal Victoria Hospital, Belfast, UK.,Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Derry, UK
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Derry, UK
| | - Stephen Haffey
- Department of Neurophysiology, Royal Victoria Hospital, Belfast, UK
| | - Karen Morrison
- Department of Neurology, Royal Victoria Hospital, Belfast, UK.,Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, UK
| | | | - Stephanie Duguez
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Derry, UK
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Morgan S, Malatras A, Duguez S, Duddy W. Optimized Molecular Interaction Networks for the Study of Skeletal Muscle. J Neuromuscul Dis 2021; 8:S223-S239. [PMID: 34308911 DOI: 10.3233/jnd-210680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Molecular interaction networks (MINs) aim to capture the complex relationships between interacting molecules within a biological system. MINs can be constructed from existing knowledge of molecular functional associations, such as protein-protein binding interactions (PPI) or gene co-expression, and these different sources may be combined into a single MIN. A given MIN may be more or less optimal in its representation of the important functional relationships of molecules in a tissue. OBJECTIVE The aim of this study was to establish whether a combined MIN derived from different types of functional association could better capture muscle-relevant biology compared to its constituent single-source MINs. METHODS MINs were constructed from functional association databases for both protein-binding and gene co-expression. The networks were then compared based on the capture of muscle-relevant genes and gene ontology (GO) terms, tested in two different ways using established biological network clustering algorithms. The top performing MINs were combined to test whether an optimal MIN for skeletal muscle could be constructed. RESULTS The STRING PPI network was the best performing single-source MIN among those tested. Combining STRING with interactions from either the MyoMiner or CoXPRESSdb gene co-expression sources resulted in a combined network with improved performance relative to its constituent networks. CONCLUSION MINs constructed from multiple types of functional association can better represent the functional relationships of molecules in a given tissue. Such networks may be used to improve the analysis and interpretation of functional genomics data in the study of skeletal muscle and neuromuscular diseases. Networks and clusters described by this study, including the combinations of STRING with MyoMiner or with CoXPRESSdb, are available for download from https://www.sys-myo.com/myominer/download.php.
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Affiliation(s)
- Stephen Morgan
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, Northern Ireland, UK
| | - Apostolos Malatras
- Department of Biological Sciences, Molecular Medicine Research Center, University of Cyprus, University Avenue, Nicosia, Cyprus
| | - Stephanie Duguez
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, Northern Ireland, UK
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, Northern Ireland, UK
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Chiba S, Lim KRQ, Sheri N, Anwar S, Erkut E, Shah MNA, Aslesh T, Woo S, Sheikh O, Maruyama R, Takano H, Kunitake K, Duddy W, Okuno Y, Aoki Y, Yokota T. eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping. Nucleic Acids Res 2021; 49:W193-W198. [PMID: 34104972 PMCID: PMC8265194 DOI: 10.1093/nar/gkab442] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/18/2021] [Accepted: 05/12/2021] [Indexed: 01/13/2023] Open
Abstract
Exon skipping using antisense oligonucleotides (ASOs) has recently proven to be a powerful tool for mRNA splicing modulation. Several exon-skipping ASOs have been approved to treat genetic diseases worldwide. However, a significant challenge is the difficulty in selecting an optimal sequence for exon skipping. The efficacy of ASOs is often unpredictable, because of the numerous factors involved in exon skipping. To address this gap, we have developed a computational method using machine-learning algorithms that factors in many parameters as well as experimental data to design highly effective ASOs for exon skipping. eSkip-Finder (https://eskip-finder.org) is the first web-based resource for helping researchers identify effective exon skipping ASOs. eSkip-Finder features two sections: (i) a predictor of the exon skipping efficacy of novel ASOs and (ii) a database of exon skipping ASOs. The predictor facilitates rapid analysis of a given set of exon/intron sequences and ASO lengths to identify effective ASOs for exon skipping based on a machine learning model trained by experimental data. We confirmed that predictions correlated well with in vitro skipping efficacy of sequences that were not included in the training data. The database enables users to search for ASOs using queries such as gene name, species, and exon number.
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Affiliation(s)
- Shuntaro Chiba
- HPC- and AI-driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan
| | - Kenji Rowel Q Lim
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Narin Sheri
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Saeed Anwar
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Esra Erkut
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Md Nur Ahad Shah
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Tejal Aslesh
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Stanley Woo
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Omar Sheikh
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Rika Maruyama
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
| | - Hiroaki Takano
- HPC- and AI-driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan
| | - Katsuhiko Kunitake
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan
| | - William Duddy
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, C-TRIC, Altnagelvin Hospital Campus, Ulster University, Londonderry BT47 6SB, UK
| | - Yasushi Okuno
- HPC- and AI-driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan.,Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan
| | - Toshifumi Yokota
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, 8613-114 St, Edmonton, AB, Canada
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Vasilopoulou C, Wingfield B, Morris AP, Duddy W. snpQT: flexible, reproducible, and comprehensive quality control and imputation of genomic data. F1000Res 2021; 10:567. [PMID: 34900230 PMCID: PMC8637247 DOI: 10.12688/f1000research.53821.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 11/20/2022] Open
Abstract
Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of different bioinformatics tools. Software incompatibilities, and inconsistencies across computing environments, are recurrent challenges, leading to poor reproducibility. Existing semi-automated or automated solutions lack comprehensive quality checks, flexible workflow architecture, and user control. To address these challenges, we have developed snpQT: a scalable, stand-alone software pipeline using nextflow and BioContainers, for comprehensive, reproducible and interactive quality control of human genomic data. snpQT offers some 36 discrete quality filters or correction steps in a complete standardised pipeline, producing graphical reports to demonstrate the state of data before and after each quality control procedure. This includes human genome build conversion, population stratification against data from the 1,000 Genomes Project, automated population outlier removal, and built-in imputation with its own pre- and post- quality controls. Common input formats are used, and a synthetic dataset and comprehensive online tutorial are provided for testing, educational purposes, and demonstration. The snpQT pipeline is designed to run with minimal user input and coding experience; quality control steps are implemented with numerous user-modifiable thresholds, and workflows can be flexibly combined in custom combinations. snpQT is open source and freely available at https://github.com/nebfield/snpQT. A comprehensive online tutorial and installation guide is provided through to GWAS (https://snpqt.readthedocs.io/en/latest/), introducing snpQT using a synthetic demonstration dataset and a real-world Amyotrophic Lateral Sclerosis SNP-array dataset.
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Affiliation(s)
- Christina Vasilopoulou
- Northern Ireland Centre for Stratified Medicine, University of Ulster, Derry/Londonderry, BT47 6SB, UK
| | - Benjamin Wingfield
- Centre for Personalised Medicine, University of Ulster, Derry/Londonderry, BT47 6SB, UK
| | - Andrew P. Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, University of Manchester, Manchester, UK
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, University of Ulster, Derry/Londonderry, BT47 6SB, UK
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10
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Vasilopoulou C, Wingfield B, Morris AP, Duddy W. snpQT: flexible, reproducible, and comprehensive quality control and imputation of genomic data. F1000Res 2021; 10:567. [PMID: 34900230 PMCID: PMC8637247 DOI: 10.12688/f1000research.53821.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/17/2021] [Indexed: 11/09/2023] Open
Abstract
Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of different bioinformatics tools. Dependency hell and reproducibility are recurrent challenges. Existing semi-automated or automated solutions lack comprehensive quality checks, flexible workflow architecture, and user control. To address these challenges, we have developed snpQT: a scalable, stand-alone software pipeline using nextflow and BioContainers, for comprehensive, reproducible and interactive quality control of human genomic data. snpQT offers some 36 discrete quality filters or correction steps in a complete standardised pipeline, producing graphical reports to demonstrate the state of data before and after each quality control procedure. This includes human genome build conversion, population stratification against data from the 1,000 Genomes Project, automated population outlier removal, and built-in imputation with its own pre- and post- quality controls. Common input formats are used, and a synthetic dataset and comprehensive online tutorial are provided for testing, educational purposes, and demonstration. The snpQT pipeline is designed to run with minimal user input and coding experience; quality control steps are implemented with default thresholds which can be modified by the user, and workflows can be flexibly combined in custom combinations. snpQT is open source and freely available at https://github.com/nebfield/snpQT. A comprehensive online tutorial and installation guide is provided through to GWAS (https://snpqt.readthedocs.io/en/latest/), introducing snpQT using a synthetic demonstration dataset and a real-world Amyotrophic Lateral Sclerosis SNP-array dataset.
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Affiliation(s)
- Christina Vasilopoulou
- Northern Ireland Centre for Stratified Medicine, University of Ulster, Derry/Londonderry, BT47 6SB, UK
| | - Benjamin Wingfield
- Centre for Personalised Medicine, University of Ulster, Derry/Londonderry, BT47 6SB, UK
| | - Andrew P. Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, University of Manchester, Manchester, UK
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, University of Ulster, Derry/Londonderry, BT47 6SB, UK
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11
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Le Gall L, Ouandaogo ZG, Anakor E, Connolly O, Butler Browne G, Laine J, Duddy W, Duguez S. Optimized method for extraction of exosomes from human primary muscle cells. Skelet Muscle 2020; 10:20. [PMID: 32641118 PMCID: PMC7341622 DOI: 10.1186/s13395-020-00238-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/22/2020] [Indexed: 01/19/2023] Open
Abstract
Skeletal muscle is increasingly considered an endocrine organ secreting myokines and extracellular vesicles (exosomes and microvesicles), which can affect physiological changes with an impact on different pathological conditions, including regenerative processes, aging, and myopathies. Primary human myoblasts are an essential tool to study the muscle vesicle secretome. Since their differentiation in conditioned media does not induce any signs of cell death or cell stress, artefactual effects from those processes are unlikely. However, adult human primary myoblasts senesce in long-term tissue culture, so a major technical challenge is posed by the need to avoid artefactual effects resulting from pre-senescent changes. Since these cells should be studied within a strictly controlled pre-senescent division count (<21 divisions), and yields of myoblasts per muscle biopsy are low, it is difficult or impossible to amplify sufficiently large cell numbers (some 250 × 106 myoblasts) to obtain sufficient conditioned medium for the standard ultracentrifugation approach to exosome isolation. Thus, an optimized strategy to extract and study secretory muscle vesicles is needed. In this study, conditions are optimized for the in vitro cultivation of human myoblasts, and the quality and yield of exosomes extracted using an ultracentrifugation protocol are compared with a modified polymer-based precipitation strategy combined with extra washing steps. Both vesicle extraction methods successfully enriched exosomes, as vesicles were positive for CD63, CD82, CD81, floated at identical density (1.15-1.27 g.ml−1), and exhibited similar size and cup-shape using electron microscopy and NanoSight tracking. However, the modified polymer-based precipitation was a more efficient strategy to extract exosomes, allowing their extraction in sufficient quantities to explore their content or to isolate a specific subpopulation, while requiring >30 times fewer differentiated myoblasts than what is required for the ultracentrifugation method. In addition, exosomes could still be integrated into recipient cells such as human myotubes or iPSC-derived motor neurons. Modified polymer-based precipitation combined with extra washing steps optimizes exosome yield from a lower number of differentiated myoblasts and less conditioned medium, avoiding senescence and allowing the execution of multiple experiments without exhausting the proliferative capacity of the myoblasts.
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Affiliation(s)
- Laura Le Gall
- Northern Ireland Center for Stratified/Personalised Medicine, Biomedical Sciences Research Institute, Ulster University, Derry~Londonderry, UK
| | | | - Ekene Anakor
- Northern Ireland Center for Stratified/Personalised Medicine, Biomedical Sciences Research Institute, Ulster University, Derry~Londonderry, UK
| | - Owen Connolly
- Northern Ireland Center for Stratified/Personalised Medicine, Biomedical Sciences Research Institute, Ulster University, Derry~Londonderry, UK
| | | | - Jeanne Laine
- Centre for Research in Myology, INSERM UMRS_974, Sorbonne Université, Paris, France
| | - William Duddy
- Northern Ireland Center for Stratified/Personalised Medicine, Biomedical Sciences Research Institute, Ulster University, Derry~Londonderry, UK
| | - Stephanie Duguez
- Northern Ireland Center for Stratified/Personalised Medicine, Biomedical Sciences Research Institute, Ulster University, Derry~Londonderry, UK.
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12
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Echigoya Y, Lim KRQ, Melo D, Bao B, Trieu N, Mizobe Y, Maruyama R, Mamchaoui K, Tanihata J, Aoki Y, Takeda S, Mouly V, Duddy W, Yokota T. Exons 45-55 Skipping Using Mutation-Tailored Cocktails of Antisense Morpholinos in the DMD Gene. Mol Ther 2019; 27:2005-2017. [PMID: 31416775 DOI: 10.1016/j.ymthe.2019.07.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 12/16/2022] Open
Abstract
Mutations in the dystrophin (DMD) gene and consequent loss of dystrophin cause Duchenne muscular dystrophy (DMD). A promising therapy for DMD, single-exon skipping using antisense phosphorodiamidate morpholino oligomers (PMOs), currently confronts major issues in that an antisense drug induces the production of functionally undefined dystrophin and may not be similarly efficacious among patients with different mutations. Accordingly, the applicability of this approach is limited to out-of-frame mutations. Here, using an exon-skipping efficiency predictive tool, we designed three different PMO cocktail sets for exons 45-55 skipping aiming to produce a dystrophin variant with preserved functionality as seen in milder or asymptomatic individuals with an in-frame exons 45-55 deletion. Of them, the most effective set was composed of select PMOs that each efficiently skips an assigned exon in cell-based screening. These combinational PMOs fitted to different deletions of immortalized DMD patient muscle cells significantly induced exons 45-55 skipping with removing 3, 8, or 10 exons and dystrophin restoration as represented by western blotting. In vivo skipping of the maximum 11 human DMD exons was confirmed in humanized mice. The finding indicates that our PMO set can be used to create mutation-tailored cocktails for exons 45-55 skipping and treat over 65% of DMD patients carrying out-of-frame or in-frame deletions.
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Affiliation(s)
- Yusuke Echigoya
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; Laboratory of Biomedical Science, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Kenji Rowel Q Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Dyanna Melo
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Bo Bao
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Nhu Trieu
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Yoshitaka Mizobe
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Rika Maruyama
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Kamel Mamchaoui
- UPMC-Sorbonne Universités-University Paris 6, UPMC/INSERM UMRS974, CNRS FRE 3617, Myology Centre for Research, Paris Cedex 13 75651, France
| | - Jun Tanihata
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan; Department of Cell Physiology, The Jikei University School of Medicine, Minato, Tokyo 105-8461, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Vincent Mouly
- UPMC-Sorbonne Universités-University Paris 6, UPMC/INSERM UMRS974, CNRS FRE 3617, Myology Centre for Research, Paris Cedex 13 75651, France
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry BT47 6SB, UK
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; Muscular Dystrophy Canada Research Chair, Edmonton, AB T6G 2H7, Canada.
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Vijayakumar UG, Milla V, Cynthia Stafford MY, Bjourson AJ, Duddy W, Duguez SMR. A Systematic Review of Suggested Molecular Strata, Biomarkers and Their Tissue Sources in ALS. Front Neurol 2019; 10:400. [PMID: 31139131 PMCID: PMC6527847 DOI: 10.3389/fneur.2019.00400] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/02/2019] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS), also known as motor neuron disease, is an incurable neurodegenerative condition, characterized by the loss of upper and lower motor neurons. It affects 1–1.8/100,000 individuals worldwide, and the number of cases is projected to increase as the population ages. Thus, there is an urgent need to identify both therapeutic targets and disease-specific biomarkers–biomarkers that would be useful to diagnose and stratify patients into different sub-groups for therapeutic strategies, as well as biomarkers to follow the efficacy of any treatment tested during clinical trials. There is a lack of knowledge about pathogenesis and many hypotheses. Numerous “omics” studies have been conducted on ALS in the past decade to identify a disease-signature in tissues and circulating biomarkers. The first goal of the present review was to group the molecular pathways that have been implicated in monogenic forms of ALS, to enable the description of patient strata corresponding to each pathway grouping. This strategy allowed us to suggest 14 strata, each potentially targetable by different pharmacological strategies. The second goal of this review was to identify diagnostic/prognostic biomarker candidates consistently observed across the literature. For this purpose, we explore previous biomarker-relevant “omics” studies of ALS and summarize their findings, focusing on potential circulating biomarker candidates. We systematically review 118 papers on biomarkers published during the last decade. Several candidate markers were consistently shared across the results of different studies in either cerebrospinal fluid (CSF) or blood (leukocyte or serum/plasma). Although these candidates still need to be validated in a systematic manner, we suggest the use of combinations of biomarkers that would likely reflect the “health status” of different tissues, including motor neuron health (e.g., pNFH and NF-L, cystatin C, Transthyretin), inflammation status (e.g., MCP-1, miR451), muscle health (miR-338-3p, miR-206) and metabolism (homocysteine, glutamate, cholesterol). In light of these studies and because ALS is increasingly perceived as a multi-system disease, the identification of a panel of biomarkers that accurately reflect features of pathology is a priority, not only for diagnostic purposes but also for prognostic or predictive applications.
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Affiliation(s)
- Udaya Geetha Vijayakumar
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, Londonderry, United Kingdom
| | - Vanessa Milla
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, Londonderry, United Kingdom
| | - Mei Yu Cynthia Stafford
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, Londonderry, United Kingdom
| | - Anthony J Bjourson
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, Londonderry, United Kingdom
| | - William Duddy
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, Londonderry, United Kingdom
| | - Stephanie Marie-Rose Duguez
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, Londonderry, United Kingdom
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14
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Malatras A, Duguez S, Duddy W. Muscle Gene Sets: a versatile methodological aid to functional genomics in the neuromuscular field. Skelet Muscle 2019; 9:10. [PMID: 31053169 PMCID: PMC6498474 DOI: 10.1186/s13395-019-0196-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 04/09/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The approach of building large collections of gene sets and then systematically testing hypotheses across these collections is a powerful tool in functional genomics, both in the pathway analysis of omics data and to uncover the polygenic effects associated with complex diseases in genome-wide association study. The Molecular Signatures Database includes collections of oncogenic and immunologic signatures enabling researchers to compare transcriptional datasets across hundreds of previous studies and leading to important insights in these fields, but such a resource does not currently exist for neuromuscular research. In previous work, we have shown the utility of gene set approaches to understand muscle cell physiology and pathology. METHODS Following a systematic survey of public muscle data, we passed gene expression profiles from 4305 samples through a robust pre-processing and standardized data analysis pipeline. Two hundred eighty-two samples were discarded based on a battery of rigorous global quality controls. From among the remaining studies, 578 comparisons of interest were identified by a combination of text mining and manual curation of the study meta-data. For each comparison, significantly dysregulated genes (FDR adjusted p < 0.05) were identified. RESULTS Lists of dysregulated genes were divided between upregulated and downregulated to give 1156 Muscle Gene Sets (MGS). This resource is available for download ( www.sys-myo.com/muscle_gene_sets ) and is accessible through three commonly used functional genomics platforms (GSEA, EnrichR, and WebGestalt). Basic guidance and recommendations are provided for the use of MGS through these platforms. In addition, consensus muscle gene sets were created to capture the overlap between the results of similar studies, and analysis of these highlighted the potential for novel disease-relevant findings. CONCLUSIONS The MGS resource can be used to investigate the behaviour of any list of genes across previous comparisons of muscle conditions, to compare previous studies to one another, and to explore the functional relationship of muscle dysregulation to the Gene Ontology. Its major intended use is in enrichment testing for functional genomics analysis.
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Affiliation(s)
- Apostolos Malatras
- Myologie Centre de Recherche, Université Sorbonne, UMRS 974 UPMC, INSERM, FRE 3617 CNRS, AIM, Paris, France
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, C-TRIC, Ulster University, Altnagelvin Hospital Campus, Glenshane Road, Derry/Londonderry, BT47 6SB UK
- Department of Biological Sciences, Molecular Medicine Research Center, University of Cyprus, 1 University Avenue, 2109 Nicosia, Cyprus
| | - Stephanie Duguez
- Myologie Centre de Recherche, Université Sorbonne, UMRS 974 UPMC, INSERM, FRE 3617 CNRS, AIM, Paris, France
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, C-TRIC, Ulster University, Altnagelvin Hospital Campus, Glenshane Road, Derry/Londonderry, BT47 6SB UK
| | - William Duddy
- Myologie Centre de Recherche, Université Sorbonne, UMRS 974 UPMC, INSERM, FRE 3617 CNRS, AIM, Paris, France
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, C-TRIC, Ulster University, Altnagelvin Hospital Campus, Glenshane Road, Derry/Londonderry, BT47 6SB UK
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15
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Morgan S, Duguez S, Duddy W. Personalized Medicine and Molecular Interaction Networks in Amyotrophic Lateral Sclerosis (ALS): Current Knowledge. J Pers Med 2018; 8:E44. [PMID: 30551677 PMCID: PMC6313785 DOI: 10.3390/jpm8040044] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/27/2018] [Accepted: 12/05/2018] [Indexed: 12/12/2022] Open
Abstract
Multiple genes and mechanisms of pathophysiology have been implicated in amyotrophic lateral sclerosis (ALS), suggesting it is a complex systemic disease. With this in mind, applying personalized medicine (PM) approaches to tailor treatment pipelines for ALS patients may be necessary. The modelling and analysis of molecular interaction networks could represent valuable resources in defining ALS-associated pathways and discovering novel therapeutic targets. Here we review existing omics datasets and analytical approaches, in order to consider how molecular interaction networks could improve our understanding of the molecular pathophysiology of this fatal neuromuscular disorder.
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Affiliation(s)
- Stephen Morgan
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, BT47 6SB, Northern Ireland, UK.
| | - Stephanie Duguez
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, BT47 6SB, Northern Ireland, UK.
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, BT47 6SB, Northern Ireland, UK.
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16
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Lee JJA, Maruyama R, Duddy W, Sakurai H, Yokota T. Identification of Novel Antisense-Mediated Exon Skipping Targets in DYSF for Therapeutic Treatment of Dysferlinopathy. Mol Ther Nucleic Acids 2018; 13:596-604. [PMID: 30439648 PMCID: PMC6234522 DOI: 10.1016/j.omtn.2018.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/05/2018] [Accepted: 10/05/2018] [Indexed: 12/20/2022]
Abstract
Dysferlinopathy is a progressive myopathy caused by mutations in the dysferlin (DYSF) gene. Dysferlin protein plays a major role in plasma-membrane resealing. Some patients with DYSF deletion mutations exhibit mild symptoms, suggesting some regions of DYSF can be removed without significantly impacting protein function. Antisense-mediated exon-skipping therapy uses synthetic molecules called antisense oligonucleotides to modulate splicing, allowing exons harboring or near genetic mutations to be removed and the open reading frame corrected. Previous studies have focused on DYSF exon 32 skipping as a potential therapeutic approach, based on the association of a mild phenotype with the in-frame deletion of exon 32. To date, no other DYSF exon-skipping targets have been identified, and the relationship between DYSF exon deletion pattern and protein function remains largely uncharacterized. In this study, we utilized a membrane-wounding assay to evaluate the ability of plasmid constructs carrying mutant DYSF, as well as antisense oligonucleotides, to rescue membrane resealing in patient cells. We report that multi-exon skipping of DYSF exons 26–27 and 28–29 rescues plasma-membrane resealing. Successful translation of these findings into the development of clinical antisense drugs would establish new therapeutic approaches that would be applicable to ∼5%–7% (exons 26–27 skipping) and ∼8% (exons 28–29 skipping) of dysferlinopathy patients worldwide.
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Affiliation(s)
- Joshua J A Lee
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Rika Maruyama
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, United Kingdom
| | - Hidetoshi Sakurai
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Toshifumi Yokota
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada; The Friends of Garrett Cumming Research & Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB T6G 2H7, Canada.
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17
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Gall IL, Lucas O, Roquevière S, Mariot V, Dumonceaux J, Ouandaogo G, TRANE study G, Ratti F, Mejat A, Durieux A, Gonzales De Aguilar J, Martinat C, Knoblach S, Raoul C, Duddy W, Pradat P, Duguez S. NEW INSIGHTS INTO CELLULAR FUNCTIONS. Neuromuscul Disord 2018. [DOI: 10.1016/j.nmd.2018.06.232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Lee J, Echigoya Y, Duddy W, Saito T, Aoki Y, Takeda S, Yokota T. Antisense PMO cocktails effectively skip dystrophin exons 45-55 in myotubes transdifferentiated from DMD patient fibroblasts. PLoS One 2018; 13:e0197084. [PMID: 29771942 PMCID: PMC5957359 DOI: 10.1371/journal.pone.0197084] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/25/2018] [Indexed: 01/01/2023] Open
Abstract
Antisense-mediated exon skipping has made significant progress as a therapeutic platform in recent years, especially in the case of Duchenne muscular dystrophy (DMD). Despite FDA approval of eteplirsen-the first-ever antisense drug clinically marketed for DMD-exon skipping therapy still faces the significant hurdles of limited applicability and unknown truncated protein function. In-frame exon skipping of dystrophin exons 45-55 represents a significant approach to treating DMD, as a large proportion of patients harbor mutations within this "hotspot" region. Additionally, patients harboring dystrophin exons 45-55 deletion mutations are reported to have exceptionally mild to asymptomatic phenotypes. Here, we demonstrate that a cocktail of phosphorodiamidate morpholino oligomers can effectively skip dystrophin exons 45-55 in vitro in myotubes transdifferentiated from DMD patient fibroblast cells. This is the first report of substantive exons 45-55 skipping in DMD patient cells. These findings help validate the use of transdifferentiated patient fibroblast cells as a suitable cell model for dystrophin exon skipping assays and further emphasize the feasibility of dystrophin exons 45-55 skipping in patients.
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Affiliation(s)
- Joshua Lee
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Yusuke Echigoya
- Department of Veterinary Medicine, Nihon University, Fujisawa, Kanagawa, Japan
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, United Kingdom
| | - Takashi Saito
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Shin’ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
- The Friends of Garrett Cumming Research & Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada
- * E-mail:
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Defour A, Medikayala S, Van der Meulen JH, Hogarth MW, Holdreith N, Malatras A, Duddy W, Boehler J, Nagaraju K, Jaiswal JK. Annexin A2 links poor myofiber repair with inflammation and adipogenic replacement of the injured muscle. Hum Mol Genet 2017; 26:1979-1991. [PMID: 28334824 DOI: 10.1093/hmg/ddx065] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/17/2017] [Indexed: 01/12/2023] Open
Abstract
Repair of skeletal muscle after sarcolemmal damage involves dysferlin and dysferlin-interacting proteins such as annexins. Mice and patient lacking dysferlin exhibit chronic muscle inflammation and adipogenic replacement of the myofibers. Here, we show that similar to dysferlin, lack of annexin A2 (AnxA2) also results in poor myofiber repair and progressive muscle weakening with age. By longitudinal analysis of AnxA2-deficient muscle we find that poor myofiber repair due to the lack of AnxA2 does not result in chronic inflammation or adipogenic replacement of the myofibers. Further, deletion of AnxA2 in dysferlin deficient mice reduced muscle inflammation, adipogenic replacement of myofibers, and improved muscle function. These results identify multiple roles of AnxA2 in muscle repair, which includes facilitating myofiber repair, chronic muscle inflammation and adipogenic replacement of dysferlinopathic muscle. It also identifies inhibition of AnxA2-mediated inflammation as a novel therapeutic avenue for treating muscle loss in dysferlinopathy.
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Affiliation(s)
- Aurelia Defour
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC 20010, USA
| | - Sushma Medikayala
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC 20010, USA
| | - Jack H Van der Meulen
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC 20010, USA
| | - Marshall W Hogarth
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC 20010, USA
| | - Nicholas Holdreith
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC 20010, USA
| | - Apostolos Malatras
- Center for Research in Myology 75013, Sorbonne Universités, UPMC University Paris 06, INSERM UMRS975, CNRS FRE3617, GH Pitié Salpêtrière, Paris 13, Paris, France
| | - William Duddy
- Center for Research in Myology 75013, Sorbonne Universités, UPMC University Paris 06, INSERM UMRS975, CNRS FRE3617, GH Pitié Salpêtrière, Paris 13, Paris, France
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, Northern Ireland, BT52 1SJ UK
| | - Jessica Boehler
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC 20010, USA
| | - Kanneboyina Nagaraju
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC 20010, USA
- Department of Integrative Systems Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, 20052 USA
| | - Jyoti K Jaiswal
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC 20010, USA
- Department of Integrative Systems Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, 20052 USA
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20
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Echigoya Y, Lim KRQ, Trieu N, Bao B, Miskew Nichols B, Vila MC, Novak JS, Hara Y, Lee J, Touznik A, Mamchaoui K, Aoki Y, Takeda S, Nagaraju K, Mouly V, Maruyama R, Duddy W, Yokota T. Quantitative Antisense Screening and Optimization for Exon 51 Skipping in Duchenne Muscular Dystrophy. Mol Ther 2017; 25:2561-2572. [PMID: 28865998 DOI: 10.1016/j.ymthe.2017.07.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 12/28/2022] Open
Abstract
Duchenne muscular dystrophy (DMD), the most common lethal genetic disorder, is caused by mutations in the dystrophin (DMD) gene. Exon skipping is a therapeutic approach that uses antisense oligonucleotides (AOs) to modulate splicing and restore the reading frame, leading to truncated, yet functional protein expression. In 2016, the US Food and Drug Administration (FDA) conditionally approved the first phosphorodiamidate morpholino oligomer (morpholino)-based AO drug, eteplirsen, developed for DMD exon 51 skipping. Eteplirsen remains controversial with insufficient evidence of its therapeutic effect in patients. We recently developed an in silico tool to design antisense morpholino sequences for exon skipping. Here, we designed morpholino AOs targeting DMD exon 51 using the in silico tool and quantitatively evaluated the effects in immortalized DMD muscle cells in vitro. To our surprise, most of the newly designed morpholinos induced exon 51 skipping more efficiently compared with the eteplirsen sequence. The efficacy of exon 51 skipping and rescue of dystrophin protein expression were increased by up to more than 12-fold and 7-fold, respectively, compared with the eteplirsen sequence. Significant in vivo efficacy of the most effective morpholino, determined in vitro, was confirmed in mice carrying the human DMD gene. These findings underscore the importance of AO sequence optimization for exon skipping.
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Affiliation(s)
- Yusuke Echigoya
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Kenji Rowel Q Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Nhu Trieu
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Bo Bao
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Bailey Miskew Nichols
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Maria Candida Vila
- Center for Genetic Medicine Research, Children's National Medical Center, 111 Michigan Avenue Northwest, Washington, DC 20010, USA
| | - James S Novak
- Center for Genetic Medicine Research, Children's National Medical Center, 111 Michigan Avenue Northwest, Washington, DC 20010, USA
| | - Yuko Hara
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Joshua Lee
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Aleksander Touznik
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Kamel Mamchaoui
- UPMC-Sorbonne Universités-University Paris 6, UPMC/INSERM UMRS974, CNRS FRE 3617, Myology Centre for Research, Paris Cedex 13 75651, France
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Kanneboyina Nagaraju
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, SUNY-Binghamton University, Binghamton, NY 13902-6000, USA
| | - Vincent Mouly
- UPMC-Sorbonne Universités-University Paris 6, UPMC/INSERM UMRS974, CNRS FRE 3617, Myology Centre for Research, Paris Cedex 13 75651, France
| | - Rika Maruyama
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry BT47 6SB, UK
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; Muscular Dystrophy Canada Research Chair, Edmonton, AB T6G 2H7, Canada.
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21
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Thorley M, Duguez S, Mazza EMC, Valsoni S, Bigot A, Mamchaoui K, Harmon B, Voit T, Mouly V, Duddy W. Skeletal muscle characteristics are preserved in hTERT/cdk4 human myogenic cell lines. Skelet Muscle 2016; 6:43. [PMID: 27931240 PMCID: PMC5146814 DOI: 10.1186/s13395-016-0115-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 11/18/2016] [Indexed: 12/31/2022] Open
Abstract
Background hTERT/cdk4 immortalized myogenic human cell lines represent an important tool for skeletal muscle research, being used as therapeutically pertinent models of various neuromuscular disorders and in numerous fundamental studies of muscle cell function. However, the cell cycle is linked to other cellular processes such as integrin regulation, the PI3K/Akt pathway, and microtubule stability, raising the question as to whether genetic modification related to the cell cycle results in secondary effects that could undermine the validity of these cell models. Results Here we subjected five healthy and disease muscle cell isolates to transcriptomic analysis, comparing immortalized lines with their parent primary populations in both differentiated and undifferentiated states, and testing their myogenic character by comparison with non-myogenic (CD56-negative) cells. Principal component analysis of global gene expression showed tight clustering of immortalized myoblasts to their parent primary populations, with clean separation from the non-myogenic reference. Comparison was made to publicly available transcriptomic data from studies of muscle human pathology, cell, and animal models, including to derive a consensus set of genes previously shown to have altered regulation during myoblast differentiation. Hierarchical clustering of samples based on gene expression of this consensus set showed that immortalized lines retained the myogenic expression patterns of their parent primary populations. Of 2784 canonical pathways and gene ontology terms tested by gene set enrichment analysis, none were significantly enriched in immortalized compared to primary cell populations. We observed, at the whole transcriptome level, a strong signature of cell cycle shutdown associated with senescence in one primary myoblast population, whereas its immortalized clone was protected. Conclusions Immortalization had no observed effect on the myogenic cascade or on any other cellular processes, and it was protective against the systems level effects of senescence that are observed at higher division counts of primary cells. Electronic supplementary material The online version of this article (doi:10.1186/s13395-016-0115-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew Thorley
- INSERM, CNRS, Institute of Myology, Center of Research in Myology, Sorbonne Universities, UPMC Univ Paris 6, Paris, France
| | - Stéphanie Duguez
- INSERM, CNRS, Institute of Myology, Center of Research in Myology, Sorbonne Universities, UPMC Univ Paris 6, Paris, France.,Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, Northern Ireland UK
| | - Emilia Maria Cristina Mazza
- Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy
| | - Sara Valsoni
- Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy
| | - Anne Bigot
- INSERM, CNRS, Institute of Myology, Center of Research in Myology, Sorbonne Universities, UPMC Univ Paris 6, Paris, France
| | - Kamel Mamchaoui
- INSERM, CNRS, Institute of Myology, Center of Research in Myology, Sorbonne Universities, UPMC Univ Paris 6, Paris, France
| | - Brennan Harmon
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010 USA
| | - Thomas Voit
- NIHR Biomedical Research Centre, Institute of Child Health, University College London, 30 Guilford Street, London, UK
| | - Vincent Mouly
- INSERM, CNRS, Institute of Myology, Center of Research in Myology, Sorbonne Universities, UPMC Univ Paris 6, Paris, France
| | - William Duddy
- INSERM, CNRS, Institute of Myology, Center of Research in Myology, Sorbonne Universities, UPMC Univ Paris 6, Paris, France.,Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, Northern Ireland UK
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22
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Thorley M, Malatras A, Duddy W, Le Gall L, Mouly V, Butler Browne G, Duguez S. Changes in Communication between Muscle Stem Cells and their Environment with Aging. J Neuromuscul Dis 2015; 2:205-217. [PMID: 27858742 PMCID: PMC5240546 DOI: 10.3233/jnd-150097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aging is associated with both muscle weakness and a loss of muscle mass, contributing towards overall frailty in the elderly. Aging skeletal muscle is also characterised by a decreasing efficiency in repair and regeneration, together with a decline in the number of adult stem cells. Commensurate with this are general changes in whole body endocrine signalling, in local muscle secretory environment, as well as in intrinsic properties of the stem cells themselves. The present review discusses the various mechanisms that may be implicated in these age-associated changes, focusing on aspects of cell-cell communication and long-distance signalling factors, such as levels of circulating growth hormone, IL-6, IGF1, sex hormones, and inflammatory cytokines. Changes in the local environment are also discussed, implicating IL-6, IL-4, FGF-2, as well as other myokines, and processes that lead to thickening of the extra-cellular matrix. These factors, involved primarily in communication, can also modulate the intrinsic properties of muscle stem cells, including reduced DNA accessibility and repression of specific genes by methylation. Finally we discuss the decrease in the stem cell pool, particularly the failure of elderly myoblasts to re-quiesce after activation, and the consequences of all these changes on general muscle homeostasis.
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Affiliation(s)
- Matthew Thorley
- Sorbonne Universités, UPMC Univ Paris 06, Center of Research in Myology UMRS 974, F-75013, Paris, France.,INSERM UMRS 974, F-75013, Paris, France.,CNRS FRE 3617, F-75013, Paris, France.,Institut de Myologie, F-75013, Paris, France
| | - Apostolos Malatras
- Sorbonne Universités, UPMC Univ Paris 06, Center of Research in Myology UMRS 974, F-75013, Paris, France.,INSERM UMRS 974, F-75013, Paris, France.,CNRS FRE 3617, F-75013, Paris, France.,Institut de Myologie, F-75013, Paris, France
| | - William Duddy
- Sorbonne Universités, UPMC Univ Paris 06, Center of Research in Myology UMRS 974, F-75013, Paris, France.,INSERM UMRS 974, F-75013, Paris, France.,CNRS FRE 3617, F-75013, Paris, France.,Institut de Myologie, F-75013, Paris, France
| | - Laura Le Gall
- Sorbonne Universités, UPMC Univ Paris 06, Center of Research in Myology UMRS 974, F-75013, Paris, France.,INSERM UMRS 974, F-75013, Paris, France.,CNRS FRE 3617, F-75013, Paris, France.,Institut de Myologie, F-75013, Paris, France
| | - Vincent Mouly
- Sorbonne Universités, UPMC Univ Paris 06, Center of Research in Myology UMRS 974, F-75013, Paris, France.,INSERM UMRS 974, F-75013, Paris, France.,CNRS FRE 3617, F-75013, Paris, France.,Institut de Myologie, F-75013, Paris, France
| | - Gillian Butler Browne
- Sorbonne Universités, UPMC Univ Paris 06, Center of Research in Myology UMRS 974, F-75013, Paris, France.,CNRS FRE 3617, F-75013, Paris, France.,INSERM UMRS 974, F-75013, Paris, France.,CNRS FRE 3617, F-75013, Paris, France.,Institut de Myologie, F-75013, Paris, France
| | - Stéphanie Duguez
- Sorbonne Universités, UPMC Univ Paris 06, Center of Research in Myology UMRS 974, F-75013, Paris, France.,INSERM UMRS 974, F-75013, Paris, France.,CNRS FRE 3617, F-75013, Paris, France.,Institut de Myologie, F-75013, Paris, France
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23
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Duddy W, Duguez S, Johnston H, Cohen TV, Phadke A, Gordish-Dressman H, Nagaraju K, Gnocchi V, Low S, Partridge T. Muscular dystrophy in the mdx mouse is a severe myopathy compounded by hypotrophy, hypertrophy and hyperplasia. Skelet Muscle 2015; 5:16. [PMID: 25987977 PMCID: PMC4434871 DOI: 10.1186/s13395-015-0041-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 04/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Preclinical testing of potential therapies for Duchenne muscular dystrophy (DMD) is conducted predominantly of the mdx mouse. But lack of a detailed quantitative description of the pathology of this animal limits our ability to evaluate the effectiveness of putative therapies or their relevance to DMD. METHODS Accordingly, we have measured the main cellular components of muscle growth and regeneration over the period of postnatal growth and early pathology in mdx and wild-type (WT) mice; phalloidin binding is used as a measure of fibre size, myonuclear counts and BrdU labelling as records of myogenic activity. RESULTS We confirm a two-phase postnatal growth pattern in WT muscle: first, increase in myonuclear number over weeks 1 to 3, then expansion of myonuclear domain. Mdx muscle growth lags behind that of WT prior to overt signs of pathology. Fibres are smaller, with fewer myonuclei and smaller myonuclear domains. Moreover, satellite cells are more readily detached from mdx than WT muscle fibres. At 3 weeks, mdx muscles enter a phase of florid myonecrosis, accompanied by concurrent regeneration of an intensity that results in complete replacement of pre-existing muscle over the succeeding 3 to 4 weeks. Both WT and mdx muscles attain maximum size by 12 to 14 weeks, mdx muscle fibres being up to 50% larger than those of WT as they become increasingly branched. Mdx muscle fibres also become hypernucleated, containing twice as many myonuclei per sarcoplasmic volume, as those of WT, the excess corresponding to the number of centrally placed myonuclei. CONCLUSIONS The best-known consequence of lack of dystrophin that is common to DMD and the mdx mouse is the conspicuous necrosis and regeneration of muscle fibres. We present protocols for measuring this in terms both of loss of muscle nuclei previously labelled with BrdU and of the intensity of myonuclear labelling with BrdU administered during the regeneration period. Both measurements can be used to assess the efficacy of putative antinecrotic agents. We also show that lack of dystrophin is associated with a number of previously unsuspected abnormalities of muscle fibre structure and function that do not appear to be directly associated with myonecrosis.
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Affiliation(s)
- William Duddy
- Center for Genetic Medicine Research, Children's National Medical Center, 111 Michigan Avenue NW, Washington DC, 20010 USA ; Myology Center of Research, Institut de Myologie Pitié-Salpétrière - Bâtiment Babinski, 75651 Paris Cedex 13, France
| | - Stephanie Duguez
- Center for Genetic Medicine Research, Children's National Medical Center, 111 Michigan Avenue NW, Washington DC, 20010 USA ; Myology Center of Research, Institut de Myologie Pitié-Salpétrière - Bâtiment Babinski, 75651 Paris Cedex 13, France
| | - Helen Johnston
- Center for Genetic Medicine Research, Children's National Medical Center, 111 Michigan Avenue NW, Washington DC, 20010 USA
| | - Tatiana V Cohen
- Center for Genetic Medicine Research, Children's National Medical Center, 111 Michigan Avenue NW, Washington DC, 20010 USA ; Center for Genetic Muscle Disorders, Kennedy Krieger Institute, 801 N. Broadway, Baltimore, MD 21205 USA
| | - Aditi Phadke
- Center for Genetic Medicine Research, Children's National Medical Center, 111 Michigan Avenue NW, Washington DC, 20010 USA
| | - Heather Gordish-Dressman
- Center for Genetic Medicine Research, Children's National Medical Center, 111 Michigan Avenue NW, Washington DC, 20010 USA
| | - Kanneboyina Nagaraju
- Center for Genetic Medicine Research, Children's National Medical Center, 111 Michigan Avenue NW, Washington DC, 20010 USA
| | - Viola Gnocchi
- Center for Genetic Medicine Research, Children's National Medical Center, 111 Michigan Avenue NW, Washington DC, 20010 USA
| | - SiewHui Low
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218 USA
| | - Terence Partridge
- Center for Genetic Medicine Research, Children's National Medical Center, 111 Michigan Avenue NW, Washington DC, 20010 USA
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Zhu L, Malatras A, Thorley M, Aghoghogbe I, Mer A, Duguez S, Butler-Browne G, Voit T, Duddy W. CellWhere: graphical display of interaction networks organized on subcellular localizations. Nucleic Acids Res 2015; 43:W571-5. [PMID: 25883154 PMCID: PMC4489307 DOI: 10.1093/nar/gkv354] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/02/2015] [Indexed: 01/18/2023] Open
Abstract
Given a query list of genes or proteins, CellWhere produces an interactive graphical display that mimics the structure of a cell, showing the local interaction network organized into subcellular locations. This user-friendly tool helps in the formulation of mechanistic hypotheses by enabling the experimental biologist to explore simultaneously two elements of functional context: (i) protein subcellular localization and (ii) protein–protein interactions or gene functional associations. Subcellular localization terms are obtained from public sources (the Gene Ontology and UniProt—together containing several thousand such terms) then mapped onto a smaller number of CellWhere localizations. These localizations include all major cell compartments, but the user may modify the mapping as desired. Protein–protein interaction listings, and their associated evidence strength scores, are obtained from the Mentha interactome server, or power-users may upload a pre-made network produced using some other interactomics tool. The Cytoscape.js JavaScript library is used in producing the graphical display. Importantly, for a protein that has been observed at multiple subcellular locations, users may prioritize the visual display of locations that are of special relevance to their research domain. CellWhere is at http://cellwhere-myology.rhcloud.com.
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Affiliation(s)
- Lu Zhu
- Bioinformatics Department, Bielefeld University, Bielefeld, D-33501, Germany Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France
| | - Apostolos Malatras
- Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France
| | - Matthew Thorley
- Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France
| | - Idonnya Aghoghogbe
- Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France Orthopaedics and Musculoskeletal Science, University College London, London, WC1E 6BT, UK
| | - Arvind Mer
- Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, SE-17177, Sweden
| | - Stéphanie Duguez
- Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France
| | - Gillian Butler-Browne
- Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France
| | - Thomas Voit
- Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France
| | - William Duddy
- Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France
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Echigoya Y, Mouly V, Garcia L, Yokota T, Duddy W. In silico screening based on predictive algorithms as a design tool for exon skipping oligonucleotides in Duchenne muscular dystrophy. PLoS One 2015; 10:e0120058. [PMID: 25816009 PMCID: PMC4376395 DOI: 10.1371/journal.pone.0120058] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/03/2015] [Indexed: 12/27/2022] Open
Abstract
The use of antisense 'splice-switching' oligonucleotides to induce exon skipping represents a potential therapeutic approach to various human genetic diseases. It has achieved greatest maturity in exon skipping of the dystrophin transcript in Duchenne muscular dystrophy (DMD), for which several clinical trials are completed or ongoing, and a large body of data exists describing tested oligonucleotides and their efficacy. The rational design of an exon skipping oligonucleotide involves the choice of an antisense sequence, usually between 15 and 32 nucleotides, targeting the exon that is to be skipped. Although parameters describing the target site can be computationally estimated and several have been identified to correlate with efficacy, methods to predict efficacy are limited. Here, an in silico pre-screening approach is proposed, based on predictive statistical modelling. Previous DMD data were compiled together and, for each oligonucleotide, some 60 descriptors were considered. Statistical modelling approaches were applied to derive algorithms that predict exon skipping for a given target site. We confirmed (1) the binding energetics of the oligonucleotide to the RNA, and (2) the distance in bases of the target site from the splice acceptor site, as the two most predictive parameters, and we included these and several other parameters (while discounting many) into an in silico screening process, based on their capacity to predict high or low efficacy in either phosphorodiamidate morpholino oligomers (89% correctly predicted) and/or 2'O Methyl RNA oligonucleotides (76% correctly predicted). Predictions correlated strongly with in vitro testing for sixteen de novo PMO sequences targeting various positions on DMD exons 44 (R² 0.89) and 53 (R² 0.89), one of which represents a potential novel candidate for clinical trials. We provide these algorithms together with a computational tool that facilitates screening to predict exon skipping efficacy at each position of a target exon.
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Affiliation(s)
- Yusuke Echigoya
- University of Alberta, Faculty of Medicine and Dentistry, Department of Medical Genetics, Edmonton, Alberta, Canada
| | - Vincent Mouly
- UPMC-Sorbonne Universités-Univ. Paris 6, UPMC/INSERM UMRS974, CNRS FRE 3617, Center of Research in Myology, Paris, 75651 cedex 13, France
| | - Luis Garcia
- UFR des Sciences de la Santé, Université de Versailles Saint-Quentin-en-Yvelines, 78180 Montigny-le-Bretonneux, France
| | - Toshifumi Yokota
- University of Alberta, Faculty of Medicine and Dentistry, Department of Medical Genetics, Edmonton, Alberta, Canada; Muscular Dystrophy Canada Research Chair, University of Alberta, Edmonton, Alberta, Canada
| | - William Duddy
- UPMC-Sorbonne Universités-Univ. Paris 6, UPMC/INSERM UMRS974, CNRS FRE 3617, Center of Research in Myology, Paris, 75651 cedex 13, France
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26
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Duguez S, Duddy W, Johnston H, Lainé J, Le Bihan MC, Brown KJ, Bigot A, Hathout Y, Butler-Browne G, Partridge T. Dystrophin deficiency leads to disturbance of LAMP1-vesicle-associated protein secretion. Cell Mol Life Sci 2013; 70:2159-74. [PMID: 23344255 PMCID: PMC11113779 DOI: 10.1007/s00018-012-1248-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 12/13/2012] [Accepted: 12/17/2012] [Indexed: 01/06/2023]
Abstract
Duchenne muscular dystrophy results from loss of the protein dystrophin, which links the intracellular cytoskeletal network with the extracellular matrix, but deficiency in this function does not fully explain the onset or progression of the disease. While some intracellular events involved in the degeneration of dystrophin-deficient muscle fibers have been well characterized, changes in their secretory profile are undescribed. To analyze the secretome profile of mdx myotubes independently of myonecrosis, we labeled the proteins of mdx and wild-type myotubes with stable isotope-labeled amino acids (SILAC), finding marked enrichment of vesicular markers in the mdx secretome. These included the lysosomal-associated membrane protein, LAMP1, that co-localized in vesicles with an over-secreted cytoskeletal protein, myosin light chain 1. These LAMP1/MLC1-3-positive vesicles accumulated in the cytosol of mdx myotubes and were secreted into the culture medium in a range of abnormal densities. Restitution of dystrophin expression, by exon skipping, to some 30 % of the control value, partially normalized the secretome profile and the excess LAMP1 accumulation. Together, our results suggest that a lack of dystrophin leads to a general dysregulation of vesicle trafficking. We hypothesize that disturbance of the export of proteins through vesicles occurs before, and then concurrently with, the myonecrotic cascade and contributes chronically to the pathophysiology of DMD, thereby presenting us with a range of new potential therapeutic targets.
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Affiliation(s)
- Stephanie Duguez
- Center for Genetic Medicine, Children’s Research Institute, Children’s National Medical Center, 111 Michigan Avenue, Washington, DC USA
- Institut de Myologie, UM76, Inserm U974, CNRS, UMR7215, Université Pierre et Marie Curie-Paris 6, Paris, 75013 France
| | - William Duddy
- Center for Genetic Medicine, Children’s Research Institute, Children’s National Medical Center, 111 Michigan Avenue, Washington, DC USA
- Institut de Myologie, UM76, Inserm U974, CNRS, UMR7215, Université Pierre et Marie Curie-Paris 6, Paris, 75013 France
| | - Helen Johnston
- Center for Genetic Medicine, Children’s Research Institute, Children’s National Medical Center, 111 Michigan Avenue, Washington, DC USA
| | - Jeanne Lainé
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Département de Physiologie, Université Pierre Et Marie Curie-Paris 06, Site Pitié-Salpêtrière, Paris, 75013 France
| | - Marie Catherine Le Bihan
- Institut de Myologie, UM76, Inserm U974, CNRS, UMR7215, Université Pierre et Marie Curie-Paris 6, Paris, 75013 France
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Kristy J. Brown
- Center for Genetic Medicine, Children’s Research Institute, Children’s National Medical Center, 111 Michigan Avenue, Washington, DC USA
| | - Anne Bigot
- Institut de Myologie, UM76, Inserm U974, CNRS, UMR7215, Université Pierre et Marie Curie-Paris 6, Paris, 75013 France
| | - Yetrib Hathout
- Center for Genetic Medicine, Children’s Research Institute, Children’s National Medical Center, 111 Michigan Avenue, Washington, DC USA
| | - Gillian Butler-Browne
- Institut de Myologie, UM76, Inserm U974, CNRS, UMR7215, Université Pierre et Marie Curie-Paris 6, Paris, 75013 France
| | - Terence Partridge
- Center for Genetic Medicine, Children’s Research Institute, Children’s National Medical Center, 111 Michigan Avenue, Washington, DC USA
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Yokota T, Duddy W, Echigoya Y, Kolski H. Exon skipping for nonsense mutations in Duchenne muscular dystrophy: too many mutations, too few patients? Expert Opin Biol Ther 2012; 12:1141-52. [PMID: 22650324 DOI: 10.1517/14712598.2012.693469] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Duchenne muscular dystrophy (DMD), one of the most common and lethal genetic disorders, is caused by mutations of the dystrophin gene. Removal of an exon or of multiple exons using antisense molecules has been demonstrated to allow synthesis of truncated 'Becker muscular dystrophy-like' dystrophin. AREAS COVERED Approximately 15% of DMD cases are caused by a nonsense mutation. Although patient databases have previously been surveyed for applicability to each deletion mutation pattern, this is not so for nonsense mutations. Here, we examine the world-wide database containing notations for more than 1200 patients with nonsense mutations. Approximately 47% of nonsense mutations can be potentially treated with single exon skipping, rising to 90% with double exon skipping, but to reach this proportion requires the development of exon skipping molecules targeting some 68 of dystrophin's 79 exons, with patient numbers spread thinly across those exons. In this review, we discuss progress and remaining hurdles in exon skipping and an alternative strategy, stop-codon readthrough. EXPERT OPINION Antisense-mediated exon skipping therapy is targeted highly at the individual patient and is a clear example of personalized medicine. An efficient regulatory path for drug approval will be a key to success.
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Affiliation(s)
- Toshifumi Yokota
- University of Alberta, Department of Medical Genetics, School of Human Development, Faculty of Medicine and Dentistry, 829 Medical Sciences Building, Edmonton, AB T6G 2H7, Canada.
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Yokota T, Duddy W, Partridge T. Optimizing exon skipping therapies for DMD. Acta Myol 2007; 26:179-184. [PMID: 18646569 PMCID: PMC2949311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Exon skipping is one of the more promising therapeutic options for Duchenne Muscular Dystrophy (DMD). The idea is to use antisense oligonucleotides to splice out selected exons from the pre-mRNA, at or next to the mutation site, so as to generate a translatable transcript from the mutant dystrophin gene. In principle, the majority of DMD mutations can be rescued by targeting selected exons. Recent developments of antisense oligonucleotides (AOs) such as 2O-methylated antisense oligonucleotides (2OMeAOs) or phosphorodiamidate morpholino oligomers (morpholinos, PMOs) have made it possible to restore dystrophin expression body-wide in dystrophic mice and dystrophic dogs by single or multi-exon skipping with no obvious side-effect. Since such treatment would, in many cases, require bespoke design of AOs, it is important to demonstrate treatment of a variety of mutations in dystrophic animals. In-frame deletion patterns usually result in a mix of Duchenne and milder Becker Muscular Dystrophy (BMD), but the ratio of Duchenne to Becker varies between patterns, and this provides useful information for selection of the exons that might most profitably be targeted. This review summarizes recent progress in exon skipping therapy and discusses future strategies.
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Affiliation(s)
- T Yokota
- Children's National Medical Center, Center for Genetic Medicine, Washington, DC 20010, USA.
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Abstract
Many of the mutations associated with Duchenne muscular dystrophy can potentially be rescued by exon-skipping therapy, targeting selected exons of prespliced mRNA for the dystrophin gene with antisense oligonucleotides, thereby restoring reading frames. The recent development of antisense oligonucleotides with higher stability and lower toxicity, such as morpholinos, has made it possible to restore dystrophin efficiently in dystrophic mice in vivo with no obvious side effects. There seems little doubt that such exon-skipping therapy is destined to proceed to the clinical application stage in patients with Duchenne muscular dystrophy. One of the remaining issues to be addressed is the skipping of multiple exons because such multi-exon skipping therapy could expand the potential patient target population to include 80% of those with duplication mutations and 90% of those with deletion mutations. At present, this multi-exon skipping strategy is being investigated in dystrophic dogs as well as dystrophic mice. There are several challenges that still need to be overcome, including the low uptake of antisense oligonucleotides into the heart and the need to design efficient, nontoxic, cost-effective oligonucleotides. This review summarizes recent progress in exon-skipping therapy and discusses future perspectives with regard to human clinical trials.
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Affiliation(s)
- Toshifumi Yokota
- Children's National Medical Center, Research Center for Genetic Medicine, Washington, DC 20010, USA.
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