1
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Kandasamy P, McClorey G, Shimizu M, Kothari N, Alam R, Iwamoto N, Kumarasamy J, Bommineni GR, Bezigian A, Chivatakarn O, Butler DC, Byrne M, Chwalenia K, Davies KE, Desai J, Shelke JD, Durbin AF, Ellerington R, Edwards B, Godfrey J, Hoss A, Liu F, Longo K, Lu G, Marappan S, Oieni J, Paik IH, Estabrook EP, Shivalila C, Tischbein M, Kawamoto T, Rinaldi C, Rajão-Saraiva J, Tripathi S, Yang H, Yin Y, Zhao X, Zhou C, Zhang J, Apponi L, Wood MJ, Vargeese C. Control of backbone chemistry and chirality boost oligonucleotide splice switching activity. Nucleic Acids Res 2022; 50:5443-5466. [PMID: 35061895 PMCID: PMC9178015 DOI: 10.1093/nar/gkac018] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/18/2021] [Accepted: 01/07/2022] [Indexed: 01/04/2023] Open
Abstract
Although recent regulatory approval of splice-switching oligonucleotides (SSOs) for the treatment of neuromuscular disease such as Duchenne muscular dystrophy has been an advance for the splice-switching field, current SSO chemistries have shown limited clinical benefit due to poor pharmacology. To overcome limitations of existing technologies, we engineered chimeric stereopure oligonucleotides with phosphorothioate (PS) and phosphoryl guanidine-containing (PN) backbones. We demonstrate that these chimeric stereopure oligonucleotides have markedly improved pharmacology and efficacy compared with PS-modified oligonucleotides, preventing premature death and improving median survival from 49 days to at least 280 days in a dystrophic mouse model with an aggressive phenotype. These data demonstrate that chemical optimization alone can profoundly impact oligonucleotide pharmacology and highlight the potential for continued innovation around the oligonucleotide backbone. More specifically, we conclude that chimeric stereopure oligonucleotides are a promising splice-switching modality with potential for the treatment of neuromuscular and other genetic diseases impacting difficult to reach tissues such as the skeletal muscle and heart.
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Affiliation(s)
| | - Graham McClorey
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | | | | | | | | | | | | | | | | | | | | | - Katarzyna Chwalenia
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Kay E Davies
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | | | | | | | - Ruth Ellerington
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Ben Edwards
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | | | | | | | - Kenneth Longo
- Wave Life Sciences, Cambridge, MA, USA
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford OX2 9DU, UK
| | | | | | - Jacopo Oieni
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | | | | | | | | | | | - Carlo Rinaldi
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford OX2 9DU, UK
| | - Joana Rajão-Saraiva
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | | | | | - Yuan Yin
- Wave Life Sciences, Cambridge, MA, USA
| | | | - Cong Zhou
- Wave Life Sciences, Cambridge, MA, USA
| | | | | | - Matthew J A Wood
- Department of Paediatrics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford OX2 9DU, UK
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2
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Flynn LL, Li R, Pitout IL, Aung-Htut MT, Larcher LM, Cooper JAL, Greer KL, Hubbard A, Griffiths L, Bond CS, Wilton SD, Fox AH, Fletcher S. Single Stranded Fully Modified-Phosphorothioate Oligonucleotides can Induce Structured Nuclear Inclusions, Alter Nuclear Protein Localization and Disturb the Transcriptome In Vitro. Front Genet 2022; 13:791416. [PMID: 35464859 PMCID: PMC9019733 DOI: 10.3389/fgene.2022.791416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/02/2022] [Indexed: 01/12/2023] Open
Abstract
Oligonucleotides and nucleic acid analogues that alter gene expression are now showing therapeutic promise in human disease. Whilst the modification of synthetic nucleic acids to protect against nuclease degradation and to influence drug function is common practice, such modifications may also confer unexpected physicochemical and biological properties. Gapmer mixed-modified and DNA oligonucleotides on a phosphorothioate backbone can bind non-specifically to intracellular proteins to form a variety of toxic inclusions, driven by the phosphorothioate linkages, but also influenced by the oligonucleotide sequence. Recently, the non-antisense or other off-target effects of 2′ O- fully modified phosphorothioate linkage oligonucleotides are becoming better understood. Here, we report chemistry-specific effects of oligonucleotides composed of modified or unmodified bases, with phosphorothioate linkages, on subnuclear organelles and show altered distribution of nuclear proteins, the appearance of highly stable and strikingly structured nuclear inclusions, and disturbed RNA processing in primary human fibroblasts and other cultured cells. Phosphodiester, phosphorodiamidate morpholino oligomers, and annealed complimentary phosphorothioate oligomer duplexes elicited no such consequences. Disruption of subnuclear structures and proteins elicit severe phenotypic disturbances, revealed by transcriptomic analysis of transfected fibroblasts exhibiting such disruption. Our data add to the growing body of evidence of off-target effects of some phosphorothioate nucleic acid drugs in primary cells and suggest alternative approaches to mitigate these effects.
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Affiliation(s)
- Loren L Flynn
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia.,Black Swan Pharmaceuticals, Wake Forest, NC, United States
| | - Ruohan Li
- Cell and Tissue Therapies WA, Royal Perth Hospital, Perth, WA, Australia.,School of Human Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Ianthe L Pitout
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,PYC Therapeutics, Nedlands, WA, Australia
| | - May T Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia
| | - Leon M Larcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Jack A L Cooper
- School of Human Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Kane L Greer
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia
| | - Alysia Hubbard
- Centre for Microscopy, Characterization and Analysis, The University of Western Australia, Nedlands, WA, Australia
| | - Lisa Griffiths
- Anatomical Pathology, Department of Health, Nedlands, WA, Australia
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia
| | - Archa H Fox
- School of Human Sciences, The University of Western Australia, Nedlands, WA, Australia.,School of Molecular Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia.,PYC Therapeutics, Nedlands, WA, Australia
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3
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Gimenez Molina A, Raguraman P, Delcomyn L, Veedu RN, Nielsen P. Oligonucleotides containing 2'-O-methyl-5-(1-phenyl-1,2,3-triazol-4-yl)uridines demonstrate increased affinity for RNA and induce exon-skipping in vitro. Bioorg Med Chem 2022; 55:116559. [PMID: 34999527 DOI: 10.1016/j.bmc.2021.116559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 11/21/2022]
Abstract
The nucleotide monomer containing the 1-phenyl-1,2,3-triazole group attached to the 5-position of 2'-O-methyluridine is hereby presented together with a derivative further substituted with a p-sulfonamide group on the phenyl ring. Both were conveniently synthesised, and synergistic effect of the modifications were demonstrated when introduced into oligonucleotides and hybridised to complementary RNA. The combination of stacking of the phenyltriazoles and the conformational steering from the 2'-OMe group gave thermally very stable duplexes. Exon skipping in the distrophin transcript using 20-mer 2'-OMePS sequences with two phenyltriazoles introduced in different positions with and without the sulfonamide demonstrated efficient exon skipping but at the same level as the 2'-OMePS reference ASO.
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Affiliation(s)
- Alejandro Gimenez Molina
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Prithi Raguraman
- Centre for Molecular Medicine and Innovative therapeutics, Murdoch University, Perth 6150, Australia; Perron Institute for Neurological and Translational Science, Perth 6009, Australia
| | - Line Delcomyn
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative therapeutics, Murdoch University, Perth 6150, Australia; Perron Institute for Neurological and Translational Science, Perth 6009, Australia.
| | - Poul Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark.
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4
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Carmen L, Maria V, Morales-Medina JC, Vallelunga A, Palmieri B, Iannitti T. Role of proteoglycans and glycosaminoglycans in Duchenne muscular dystrophy. Glycobiology 2019; 29:110-123. [PMID: 29924302 DOI: 10.1093/glycob/cwy058] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 06/18/2018] [Indexed: 12/25/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is an inherited fatal X-linked myogenic disorder with a prevalence of 1 in 3500 male live births. It affects voluntary muscles, and heart and breathing muscles. DMD is characterized by continuous degeneration and regeneration cycles resulting in extensive fibrosis and a progressive reduction in muscle mass. Since the identification of a reduction in dystrophin protein as the cause of this disorder, numerous innovative and experimental therapies, focusing on increasing the levels of dystrophin, have been proposed, but the clinical improvement has been unsatisfactory. Dystrophin forms the dystrophin-associated glycoprotein complex and its proteins have been studied as a promising novel therapeutic target to treat DMD. Among these proteins, cell surface glycosaminoglycans (GAGs) are found almost ubiquitously on the surface and in the extracellular matrix (ECM) of mammalian cells. These macromolecules interact with numerous ligands, including ECM constituents, adhesion molecules and growth factors that play a crucial role in muscle development and maintenance. In this article, we have reviewed in vitro, in vivo and clinical studies focused on the functional role of GAGs in the pathophysiology of DMD with the final aim of summarizing the state of the art of GAG dysregulation within the ECM in DMD and discussing future therapeutic perspectives.
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Affiliation(s)
- Laurino Carmen
- Department of General Surgery and Surgical Specialties, University of Modena and Reggio Emilia Medical School, Surgical Clinic, Modena, Italy
| | - Vadala' Maria
- Department of General Surgery and Surgical Specialties, University of Modena and Reggio Emilia Medical School, Surgical Clinic, Modena, Italy
| | - Julio Cesar Morales-Medina
- Centro de Investigación en Reproducción Animal, CINVESTAV-Universidad Autónoma de Tlaxcala, CP, AP 62, Mexico
| | - Annamaria Vallelunga
- Department of Medicine and Surgery, Centre for Neurodegenerative Diseases (CEMAND), University of Salerno, Salerno, Italy
| | - Beniamino Palmieri
- Department of General Surgery and Surgical Specialties, University of Modena and Reggio Emilia Medical School, Surgical Clinic, Modena, Italy
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5
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Pitout I, Flynn LL, Wilton SD, Fletcher S. Antisense-mediated splice intervention to treat human disease: the odyssey continues. F1000Res 2019; 8. [PMID: 31164976 PMCID: PMC6534073 DOI: 10.12688/f1000research.18466.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 12/24/2022] Open
Abstract
Recent approvals of oligonucleotide analogue drugs to alter gene expression have been welcomed by patient communities but not universally supported. These compounds represent a class of drugs that are designed to target a specific gene transcript, and they include a number of chemical entities to evoke different antisense mechanisms, depending upon the disease aetiology. To date, oligonucleotide therapeutics that are in the clinic or at advanced stages of translation target rare diseases, posing challenges to clinical trial design, recruitment and evaluation and requiring new evaluation paradigms. This review discusses the currently available and emerging therapeutics that alter exon selection through an effect on pre-mRNA splicing and explores emerging concerns over safety and efficacy. Although modification of synthetic nucleic acids destined for therapeutic application is common practice to protect against nuclease degradation and to influence drug function, such modifications may also confer unexpected physicochemical and biological properties. Negatively charged oligonucleotides have a strong propensity to bind extra- and intra-cellular proteins, whereas those analogues with a neutral backbone show inefficient cellular uptake but excellent safety profiles. In addition, the potential for incorporation of chemically modified nucleic acid monomers, yielded by nuclease degradation of exogenous oligonucleotides, into biomolecules has been raised and the possibility not entirely discounted. We conclude with a commentary on the ongoing efforts to develop novel antisense compounds and enhance oligonucleotide delivery in order to further improve efficacy and accelerate implementation of antisense therapeutics for human disease.
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Affiliation(s)
| | - Loren L Flynn
- Murdoch University, Murdoch, WA, 6150, Australia.,The University of Western Australia, Nedlands, WA, 6009, Australia.,Perron Institute, Nedlands, WA, 6009, Australia
| | - Steve D Wilton
- Murdoch University, Murdoch, WA, 6150, Australia.,The University of Western Australia, Nedlands, WA, 6009, Australia.,Perron Institute, Nedlands, WA, 6009, Australia
| | - Sue Fletcher
- Murdoch University, Murdoch, WA, 6150, Australia.,The University of Western Australia, Nedlands, WA, 6009, Australia.,Perron Institute, Nedlands, WA, 6009, Australia
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6
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Systematic evaluation of 2'-Fluoro modified chimeric antisense oligonucleotide-mediated exon skipping in vitro. Sci Rep 2019; 9:6078. [PMID: 30988454 PMCID: PMC6465270 DOI: 10.1038/s41598-019-42523-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/02/2019] [Indexed: 01/16/2023] Open
Abstract
Antisense oligonucleotide (AO)-mediated splice modulation has been established as a therapeutic approach for tackling genetic diseases. Recently, Exondys51, a drug that aims to correct splicing defects in the dystrophin gene was approved by the US Food and Drug Administration (FDA) for the treatment of Duchenne muscular dystrophy (DMD). However, Exondys51 has relied on phosphorodiamidate morpholino oligomer (PMO) chemistry which poses challenges in the cost of production and compatibility with conventional oligonucleotide synthesis procedures. One approach to overcome this problem is to construct the AO with alternative nucleic acid chemistries using solid-phase oligonucleotide synthesis via standard phosphoramidite chemistry. 2′-Fluoro (2′-F) is a potent RNA analogue that possesses high RNA binding affinity and resistance to nuclease degradation with good safety profile, and an approved drug Macugen containing 2′-F-modified pyrimidines was approved for the treatment of age-related macular degeneration (AMD). In the present study, we investigated the scope of 2′-F nucleotides to construct mixmer and gapmer exon skipping AOs with either 2′-O-methyl (2′-OMe) or locked nucleic acid (LNA) nucleotides on a phosphorothioate (PS) backbone, and evaluated their efficacy in inducing exon-skipping in mdx mouse myotubes in vitro. Our results showed that all AOs containing 2′-F nucleotides induced efficient exon-23 skipping, with LNA/2′-F chimeras achieving better efficiency than the AOs without LNA modification. In addition, LNA/2′-F chimeric AOs demonstrated higher exonuclease stability and lower cytotoxicity than the 2′-OMe/2′-F chimeras. Overall, our findings certainly expand the scope of constructing 2′-F modified AOs in splice modulation by incorporating 2′-OMe and LNA modifications.
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7
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Schnell FJ, Frank D, Fletcher S, Johnsen RD, Wilton SD. Challenges of Interpreting Dystrophin Content by Western Blot. ACTA ACUST UNITED AC 2019. [DOI: 10.17925/usn.2019.15.1.40] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Duchenne muscular dystrophy community has recently seen the first approved therapy for the restoration of dystrophin, based on its ability to increase levels of dystrophin protein, as determined by western blot. The approval, along with the initiation of clinical trials evaluating other dystrophin-restoring therapies, highlights the importance of accurate dystrophin quantitation. Nonoptimized western blot methods can reflect inaccurate results, especially in the quantitation of low dystrophin levels. A few key changes to standards and data analysis parameters can result in a low level of dystrophin (<0.5% of a healthy biopsy) being inaccurately interpreted as >20% of the levels reported in healthy human muscle. A review of the dystrophin western blot data on Duchenne and Becker muscular dystrophy biopsies is conducted, along with a thorough investigation of methodologies to quantify dystrophin.
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8
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Li D, Mastaglia FL, Fletcher S, Wilton SD. Precision Medicine through Antisense Oligonucleotide-Mediated Exon Skipping. Trends Pharmacol Sci 2018; 39:982-994. [PMID: 30282590 DOI: 10.1016/j.tips.2018.09.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/30/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022]
Abstract
Clinical implementation of two recently approved antisense RNA therapeutics - Exondys51® to treat Duchenne muscular dystrophy (Duchenne MD) and Spinraza® as a treatment for spinal muscular atrophy (SMA) - highlights the therapeutic potential of antisense oligonucleotides (ASOs). As shown in the Duchenne and Becker cases, the identification and specific removal of 'dispensable' exons by exon-skipping ASOs could potentially bypass lethal mutations in other genes and bring clinical benefits to affected individuals carrying amenable mutations. In this review, we discuss the potential of therapeutic alternative splicing, with a particular focus on targeted exon skipping using Duchenne MD as an example, and speculate on new applications for other inherited rare diseases where redundant or dispensable exons may be amenable to exon-skipping ASO intervention as precision medicine.
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Affiliation(s)
- Dunhui Li
- Centre for Comparative Genomics, Murdoch University, Perth 6050, Australia; Perron Institute for Neurological and Translational Science, University of Western Australia, Perth 6000, Australia
| | - Frank L Mastaglia
- Perron Institute for Neurological and Translational Science, University of Western Australia, Perth 6000, Australia
| | - Sue Fletcher
- Centre for Comparative Genomics, Murdoch University, Perth 6050, Australia; Perron Institute for Neurological and Translational Science, University of Western Australia, Perth 6000, Australia
| | - Steve D Wilton
- Centre for Comparative Genomics, Murdoch University, Perth 6050, Australia; Perron Institute for Neurological and Translational Science, University of Western Australia, Perth 6000, Australia.
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9
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Viola HM, Johnstone VP, Adams AM, Fletcher S, Hool LC. A Morpholino Oligomer Therapy Regime That Restores Mitochondrial Function and Prevents mdx Cardiomyopathy. JACC Basic Transl Sci 2018; 3:391-402. [PMID: 30062225 PMCID: PMC6059013 DOI: 10.1016/j.jacbts.2018.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/15/2018] [Indexed: 02/07/2023]
Abstract
Current clinical trials demonstrate Duchenne muscular dystrophy (DMD) patients receiving phosphorodiamidate morpholino oligomer (PMO) therapy exhibit improved ambulation and stable pulmonary function; however, cardiac abnormalities remain. Utilizing the same PMO chemistry as current clinical trials, we have identified a non-toxic PMO treatment regimen that restores metabolic activity and prevents DMD cardiomyopathy. We propose that a treatment regimen of this nature may have the potential to significantly improve morbidity and mortality from DMD by improving ambulation, stabilizing pulmonary function, and preventing the development of cardiomyopathy.
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Key Words
- DMD, Duchenne muscular dystrophy
- ICa-L, L-type Ca2+ channel
- JC-1, 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolylcarbocyanine iodide
- L-type calcium channels
- PMO, phosphorodiamidate morpholino oligomer
- RT-PCR, reverse transcriptase polymerase chain reaction
- cardiomyopathy
- mdx, murine model of Duchenne muscular dystrophy
- mitochondria
- wt, wild type
- Ψm, mitochondrial membrane potential
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Affiliation(s)
- Helena M. Viola
- School of Human Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Victoria P.A. Johnstone
- School of Human Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Abbie M. Adams
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia, Australia
| | - Susan Fletcher
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia, Australia
- Perron Institute for Neuroscience and Translational Science, and Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Livia C. Hool
- School of Human Sciences, The University of Western Australia, Crawley, Western Australia, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
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10
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Dowling JJ, D. Gonorazky H, Cohn RD, Campbell C. Treating pediatric neuromuscular disorders: The future is now. Am J Med Genet A 2018; 176:804-841. [PMID: 28889642 PMCID: PMC5900978 DOI: 10.1002/ajmg.a.38418] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 12/12/2022]
Abstract
Pediatric neuromuscular diseases encompass all disorders with onset in childhood and where the primary area of pathology is in the peripheral nervous system. These conditions are largely genetic in etiology, and only those with a genetic underpinning will be presented in this review. This includes disorders of the anterior horn cell (e.g., spinal muscular atrophy), peripheral nerve (e.g., Charcot-Marie-Tooth disease), the neuromuscular junction (e.g., congenital myasthenic syndrome), and the muscle (myopathies and muscular dystrophies). Historically, pediatric neuromuscular disorders have uniformly been considered to be without treatment possibilities and to have dire prognoses. This perception has gradually changed, starting in part with the discovery and widespread application of corticosteroids for Duchenne muscular dystrophy. At present, several exciting therapeutic avenues are under investigation for a range of conditions, offering the potential for significant improvements in patient morbidities and mortality and, in some cases, curative intervention. In this review, we will present the current state of treatment for the most common pediatric neuromuscular conditions, and detail the treatment strategies with the greatest potential for helping with these devastating diseases.
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Affiliation(s)
- James J. Dowling
- Division of NeurologyHospital for Sick ChildrenTorontoOntarioCanada
- Program for Genetics and Genome BiologyHospital for Sick ChildrenTorontoOntarioCanada
- Departments of Paediatrics and Molecular GeneticsUniversity of TorontoTorontoOntarioCanada
| | | | - Ronald D. Cohn
- Program for Genetics and Genome BiologyHospital for Sick ChildrenTorontoOntarioCanada
- Departments of Paediatrics and Molecular GeneticsUniversity of TorontoTorontoOntarioCanada
| | - Craig Campbell
- Department of PediatricsClinical Neurological SciencesEpidemiologyWestern UniversityLondonOntarioCanada
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11
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Delalande O, Molza AE, Dos Santos Morais R, Chéron A, Pollet É, Raguenes-Nicol C, Tascon C, Giudice E, Guilbaud M, Nicolas A, Bondon A, Leturcq F, Férey N, Baaden M, Perez J, Roblin P, Piétri-Rouxel F, Hubert JF, Czjzek M, Le Rumeur E. Dystrophin's central domain forms a complex filament that becomes disorganized by in-frame deletions. J Biol Chem 2018. [PMID: 29535188 DOI: 10.1074/jbc.m117.809798] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Dystrophin, encoded by the DMD gene, is critical for maintaining plasma membrane integrity during muscle contraction events. Mutations in the DMD gene disrupting the reading frame prevent dystrophin production and result in severe Duchenne muscular dystrophy (DMD); in-frame internal deletions allow production of partly functional internally deleted dystrophin and result in less severe Becker muscular dystrophy (BMD). Many known BMD deletions occur in dystrophin's central domain, generally considered to be a monotonous rod-shaped domain based on the knowledge of spectrin family proteins. However, the effects caused by these deletions, ranging from asymptomatic to severe BMD, argue against the central domain serving only as a featureless scaffold. We undertook structural studies combining small-angle X-ray scattering and molecular modeling in an effort to uncover the structure of the central domain, as dystrophin has been refractory to characterization. We show that this domain appears to be a tortuous and complex filament that is profoundly disorganized by the most severe BMD deletion (loss of exons 45-47). Despite the preservation of large parts of the binding site for neuronal nitric oxide synthase (nNOS) in this deletion, computational approaches failed to recreate the association of dystrophin with nNOS. This observation is in agreement with a strong decrease of nNOS immunolocalization in muscle biopsies, a parameter related to the severity of BMD phenotypes. The structural description of the whole dystrophin central domain we present here is a first necessary step to improve the design of microdystrophin constructs toward the goal of a successful gene therapy for DMD.
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Affiliation(s)
- Olivier Delalande
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France,
| | - Anne-Elisabeth Molza
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Raphael Dos Santos Morais
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France.,the Synchrotron SOLEIL, 91190 Saint Aubin, France.,the Laboratoire Léon-Brillouin, UMR 12 CEA-CNRS, Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Angélique Chéron
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Émeline Pollet
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Céline Raguenes-Nicol
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Christophe Tascon
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Emmanuel Giudice
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Marine Guilbaud
- the Sorbonne Universités UPMC-INSERM-UMRS 97-CNRS FRE 3617, Institut de Myologie, 75013 Paris, France
| | - Aurélie Nicolas
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Arnaud Bondon
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France.,the Université Rennes, CNRS, Institut des Sciences Chimiques de Rennes-UMR 6226, PRISM, 35000 Rennes, France
| | - France Leturcq
- the Sorbonne Universités UPMC-INSERM-UMRS 97-CNRS FRE 3617, Institut de Myologie, 75013 Paris, France.,the AP-HP, Groupe Hospitalier Cochin-Broca-Hôtel Dieu, Laboratoire de Biochimie et Génétique Moléculaire, 75014 Paris, France
| | - Nicolas Férey
- the CNRS UPR3251, Université Paris XI, 91403 Orsay Cedex, France
| | - Marc Baaden
- the CNRS UPR9080, Université Paris Diderot, Sorbonne Paris Cité, 75005 Paris, France
| | - Javier Perez
- the Synchrotron SOLEIL, 91190 Saint Aubin, France
| | - Pierre Roblin
- the Synchrotron SOLEIL, 91190 Saint Aubin, France.,the INRA-Biopolymères, Interaction et Assemblages, 44000 Nantes, France
| | - France Piétri-Rouxel
- the Sorbonne Universités UPMC-INSERM-UMRS 97-CNRS FRE 3617, Institut de Myologie, 75013 Paris, France
| | - Jean-François Hubert
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Mirjam Czjzek
- the Sorbonne Universités, UPMC Université Paris 06, 75006 Paris, France, and.,the CNRS UMR 8227, Integrative Biology of Marine Models, 29688 Roscoff Cedex, France
| | - Elisabeth Le Rumeur
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
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12
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Le BT, Adams AM, Fletcher S, Wilton SD, Veedu RN. Rational Design of Short Locked Nucleic Acid-Modified 2'-O-Methyl Antisense Oligonucleotides for Efficient Exon-Skipping In Vitro. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 9:155-161. [PMID: 29246294 PMCID: PMC5633351 DOI: 10.1016/j.omtn.2017.09.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/04/2017] [Accepted: 09/06/2017] [Indexed: 01/16/2023]
Abstract
Locked nucleic acid is a prominent nucleic acid analog with unprecedented target binding affinity to cDNA and RNA oligonucleotides and shows remarkable stability against nuclease degradation. Incorporation of locked nucleic acid nucleotides into an antisense oligonucleotide (AO) sequence can reduce the length required without compromising the efficacy. In this study, we synthesized a series of systematically truncated locked nucleic acid-modified 2′-O-methyl AOs on a phosphorothioate (PS) backbone that were designed to induce skipping exon 23 from the dystrophin transcript in H-2Kb-tsA58 mdx mouse myotubes in vitro. The results clearly demonstrated that shorter AOs (16- to 14-mer) containing locked nucleic acid nucleotides efficiently induced dystrophin exon 23 skipping compared with the corresponding 2′-O-methyl AOs. Our remarkable findings contribute significantly to the existing knowledge about the designing of short LNA-modified oligonucleotides for exon-skipping applications, which will help reduce the cost of exon-skipping AOs and potential toxicities, particularly the 2′-OMe-based oligos, by further reducing the length of AOs.
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Affiliation(s)
- Bao T Le
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150, Australia; Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Abbie M Adams
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150, Australia
| | - Susan Fletcher
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150, Australia; Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Stephen D Wilton
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150, Australia; Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Rakesh N Veedu
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150, Australia; Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.
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13
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Irwin AN, Herink MC. Eteplirsen for the Treatment of Duchenne Muscular Dystrophy: Quality of Evidence Concerns-an Alternative Viewpoint. Pharmacotherapy 2017; 37:e109-e111. [PMID: 28741800 DOI: 10.1002/phar.1996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Adriane N Irwin
- College of Pharmacy, Oregon State University/Oregon Health and Science University, Corvallis, Oregon
| | - Megan C Herink
- College of Pharmacy, Oregon State University/Oregon Health and Science University, Portland, Oregon
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14
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Huang D, Fletcher S, Wilton SD, Palmer N, McLenachan S, Mackey DA, Chen FK. Inherited Retinal Disease Therapies Targeting Precursor Messenger Ribonucleic Acid. Vision (Basel) 2017; 1:vision1030022. [PMID: 31740647 PMCID: PMC6836112 DOI: 10.3390/vision1030022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 07/24/2017] [Accepted: 08/24/2017] [Indexed: 02/07/2023] Open
Abstract
Inherited retinal diseases are an extremely diverse group of genetically and phenotypically heterogeneous conditions characterized by variable maturation of retinal development, impairment of photoreceptor cell function and gradual loss of photoreceptor cells and vision. Significant progress has been made over the last two decades in identifying the many genes implicated in inherited retinal diseases and developing novel therapies to address the underlying genetic defects. Approximately one-quarter of exonic mutations related to human inherited diseases are likely to induce aberrant splicing products, providing opportunities for the development of novel therapeutics that target splicing processes. The feasibility of antisense oligomer mediated splice intervention to treat inherited diseases has been demonstrated in vitro, in vivo and in clinical trials. In this review, we will discuss therapeutic approaches to treat inherited retinal disease, including strategies to correct splicing and modify exon selection at the level of pre-mRNA. The challenges of clinical translation of this class of emerging therapeutics will also be discussed.
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Affiliation(s)
- Di Huang
- Molecular Therapy Laboratory, Murdoch University, Murdoch 6150, Australia
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Sue Fletcher
- Molecular Therapy Laboratory, Murdoch University, Murdoch 6150, Australia
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Steve D. Wilton
- Molecular Therapy Laboratory, Murdoch University, Murdoch 6150, Australia
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Norman Palmer
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
| | - David A. Mackey
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
| | - Fred K. Chen
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth 6000, Australia
- Correspondence: ; Tel.: +61-8-9381-0817
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15
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Normal and altered pre-mRNA processing in the DMD gene. Hum Genet 2017; 136:1155-1172. [DOI: 10.1007/s00439-017-1820-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/02/2017] [Indexed: 12/11/2022]
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16
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Johnstone VPA, Viola HM, Hool LC. Dystrophic Cardiomyopathy-Potential Role of Calcium in Pathogenesis, Treatment and Novel Therapies. Genes (Basel) 2017; 8:genes8040108. [PMID: 28338606 PMCID: PMC5406855 DOI: 10.3390/genes8040108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/16/2017] [Accepted: 03/21/2017] [Indexed: 01/06/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is caused by defects in the DMD gene and results in progressive wasting of skeletal and cardiac muscle due to an absence of functional dystrophin. Cardiomyopathy is prominent in DMD patients, and contributes significantly to mortality. This is particularly true following respiratory interventions that reduce death rate and increase ambulation and consequently cardiac load. Cardiomyopathy shows an increasing prevalence with age and disease progression, and over 95% of patients exhibit dilated cardiomyopathy by the time they reach adulthood. Development of the myopathy is complex, and elevations in intracellular calcium, functional muscle ischemia, and mitochondrial dysfunction characterise the pathophysiology. Current therapies are limited to treating symptoms of the disease and there is therefore an urgent need to treat the underlying genetic defect. Several novel therapies are outlined here, and the unprecedented success of phosphorodiamidate morpholino oligomers (PMOs) in preclinical and clinical studies is overviewed.
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Affiliation(s)
- Victoria P A Johnstone
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia.
| | - Helena M Viola
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia.
| | - Livia C Hool
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia.
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia.
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17
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Correction of the Exon 2 Duplication in DMD Myoblasts by a Single CRISPR/Cas9 System. MOLECULAR THERAPY. NUCLEIC ACIDS 2017. [PMID: 28624187 PMCID: PMC5363679 DOI: 10.1016/j.omtn.2017.02.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Exonic duplications account for 10%-15% of all mutations in Duchenne muscular dystrophy (DMD), a severe hereditary neuromuscular disorder. We report a CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9-based strategy to correct the most frequent (exon 2) duplication in the DMD gene by targeted deletion, and tested the efficacy of such an approach in patient-derived myogenic cells. We demonstrate restoration of wild-type dystrophin expression at transcriptional and protein level in myotubes derived from genome-edited myoblasts in the absence of selection. Removal of the duplicated exon was achieved by the use of only one guide RNA (gRNA) directed against an intronic duplicated region, thereby increasing editing efficiency and reducing the risk of off-target effects. This study opens a novel therapeutic perspective for patients carrying disease-causing duplications.
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18
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Lee T, Awano H, Yagi M, Matsumoto M, Watanabe N, Goda R, Koizumi M, Takeshima Y, Matsuo M. 2'-O-Methyl RNA/Ethylene-Bridged Nucleic Acid Chimera Antisense Oligonucleotides to Induce Dystrophin Exon 45 Skipping. Genes (Basel) 2017; 8:genes8020067. [PMID: 28208626 PMCID: PMC5333056 DOI: 10.3390/genes8020067] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/02/2017] [Accepted: 02/07/2017] [Indexed: 12/17/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal muscle-wasting disease characterized by dystrophin deficiency from mutations in the dystrophin gene. Antisense oligonucleotide (AO)-mediated exon skipping targets restoration of the dystrophin reading frame to allow production of an internally deleted dystrophin protein with functional benefit for DMD patients who have out-of-frame deletions. After accelerated US approval of eteplirsen (Exondys 51), which targets dystrophin exon 51 for skipping, efforts are now focused on targeting other exons. For improved clinical benefits, this strategy requires more studies of the delivery method and modification of nucleic acids. We studied a nucleotide with a 2′-O,4′-C-ethylene-bridged nucleic acid (ENA), which shows high nuclease resistance and high affinity for complementary RNA strands. Here, we describe the process of developing a 2′-O-methyl RNA(2′-OMeRNA)/ENA chimera AO to induce dystrophin exon 45 skipping. One 18-mer 2′-OMeRNA/ENA chimera (AO85) had the most potent activity for inducing exon 45 skipping in cultured myotubes. AO85 was administered to mdx mice without significant side effects. AO85 transfection into cultured myotubes from 13 DMD patients induced exon 45 skipping in all samples at different levels and dystrophin expression in 11 patients. These results suggest the possible efficacy of AO-mediated exon skipping changes in individual patients and highlight the 2′-OMeRNA/ENA chimera AO as a potential fundamental treatment for DMD.
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Affiliation(s)
- Tomoko Lee
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya 6638501, Japan.
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 6500017, Japan.
| | - Mariko Yagi
- Nikoniko House Medical and Welfare Center, Kobe 6511102, Japan.
| | - Masaaki Matsumoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 6500017, Japan.
| | - Nobuaki Watanabe
- Drug Metabolism & Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., Tokyo 1408710, Japan.
| | - Ryoya Goda
- Drug Metabolism & Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., Tokyo 1408710, Japan.
| | - Makoto Koizumi
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd., Tokyo 1408710, Japan.
| | - Yasuhiro Takeshima
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya 6638501, Japan.
| | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, Kobe 6512180, Japan.
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19
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Delalande O, Czogalla A, Hubert JF, Sikorski A, Le Rumeur E. Dystrophin and Spectrin, Two Highly Dissimilar Sisters of the Same Family. Subcell Biochem 2017; 82:373-403. [PMID: 28101868 DOI: 10.1007/978-3-319-49674-0_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Dystrophin and Spectrin are two proteins essential for the organization of the cytoskeleton and for the stabilization of membrane cells. The comparison of these two sister proteins, and with the dystrophin homologue utrophin, enables us to emphasise that, despite a similar topology with common subdomains and a common structural basis of a three-helix coiled-coil, they show a large range of dissimilarities in terms of genetics, cell expression and higher level structural organisation. Interactions with cellular partners, including proteins and membrane phospholipids, also show both strikingly similar and very different behaviours. The differences between dystrophin and spectrin are also illustrated by the large variety of pathological anomalies emerging from the dysfunction or the absence of these proteins, showing that they are keystones in their function of providing a scaffold that sustains cell structure.
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Affiliation(s)
- Olivier Delalande
- Institut de Génétique et Développement de Rennes, UMR CNRS 6290, Université de Rennes 1, Rennes, France.
| | - Aleksander Czogalla
- Biotechnology Faculty, Department of Cytobiochemistry, University of Wrocław, ul. joliot-Curie 14a, 50-383, Wroclaw, Poland
| | - Jean-François Hubert
- Institut de Génétique et Développement de Rennes, UMR CNRS 6290, Université de Rennes 1, Rennes, France
| | - Aleksander Sikorski
- Biotechnology Faculty, Department of Cytobiochemistry, University of Wrocław, ul. joliot-Curie 14a, 50-383, Wroclaw, Poland
| | - Elisabeth Le Rumeur
- Institut de Génétique et Développement de Rennes, UMR CNRS 6290, Université de Rennes 1, Rennes, France
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20
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Le BT, Murayama K, Shabanpoor F, Asanuma H, Veedu RN. Antisense oligonucleotide modified with serinol nucleic acid (SNA) induces exon skipping in mdx myotubes. RSC Adv 2017. [DOI: 10.1039/c7ra06091b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We investigated the potential of SNA-modified antisense oligonucleotide (AO) for exon-skipping. We found that a 20-mer SNA-AO induced efficient exon-23 skipping in the mouse dystrophin gene transcript.
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Affiliation(s)
- Bao T. Le
- Centre for Comparative Genomics
- Murdoch University
- Perth
- Australia-6150
- Perron Institute for Neurological and Translational Science
| | - Keiji Murayama
- Department of Biomolecular Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
| | - Fazel Shabanpoor
- Florey Department of Neuroscience and Mental Health
- University of Melbourne
- Australia
| | - Hiroyuki Asanuma
- Department of Biomolecular Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
| | - Rakesh N. Veedu
- Centre for Comparative Genomics
- Murdoch University
- Perth
- Australia-6150
- Perron Institute for Neurological and Translational Science
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21
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Le BT, Hornum M, Sharma PK, Nielsen P, Veedu RN. Nucleobase-modified antisense oligonucleotides containing 5-(phenyltriazol)-2′-deoxyuridine nucleotides induce exon-skipping in vitro. RSC Adv 2017. [DOI: 10.1039/c7ra10964d] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We investigated the potential of nucleobase-modified antisense oligonucleotides to induce exon-skipping, and found that 5-(phenyltriazol)-2′-deoxyuridine-modified antisense oligonucleotides induced efficient exon-skipping in vitro.
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Affiliation(s)
- Bao T. Le
- Centre for Comparative Genomics
- Murdoch University
- Perth
- Australia-6150
- Perron Institute for Neurological and Translational Science
| | - Mick Hornum
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- DK-5230 Odense M
- Denmark
| | - Pawan K. Sharma
- Department of Chemistry
- Kurukshetra University
- Kurukshetra-113-119
- India
| | - Poul Nielsen
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- DK-5230 Odense M
- Denmark
| | - Rakesh N. Veedu
- Centre for Comparative Genomics
- Murdoch University
- Perth
- Australia-6150
- Perron Institute for Neurological and Translational Science
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22
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Chen S, Le BT, Rahimizadeh K, Shaikh K, Mohal N, Veedu RN. Synthesis of a Morpholino Nucleic Acid (MNA)-Uridine Phosphoramidite, and Exon Skipping Using MNA/2'-O-Methyl Mixmer Antisense Oligonucleotide. Molecules 2016; 21:molecules21111582. [PMID: 27879669 PMCID: PMC6274534 DOI: 10.3390/molecules21111582] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/11/2016] [Accepted: 11/16/2016] [Indexed: 01/14/2023] Open
Abstract
In this study, we synthesised a morpholino nucleoside-uridine (MNA-U) phosphoramidite and evaluated the potential of a MNA-modified antisense oligonucleotide (AO) sequences to induce exon 23 skipping in mdx mouse myotubes in vitro towards extending the applicability of morpholino chemistry with other nucleotide monomers. We designed, synthesised, and compared exon skipping efficiencies of 20 mer MNA-modified 2'-O-methyl RNA mixmer AO on a phosphorothioate backbone (MNA/2'-OMePS) to the corresponding fully modified 2'-O-methyl RNA AO (2'-OMePS) as a control. Our results showed that the MNA/2'-OMePS efficiently induced exon 23 skipping. As expected, the 2'-OMePS AO control yielded efficient exon 23 skipping. Under the applied conditions, both the AOs showed minor products corresponding to exon 22/23 dual exon skipping in low yield. As these are very preliminary data, more detailed studies are necessary; however, based on the preliminary results, MNA nucleotides might be useful in constructing antisense oligonucleotides.
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Affiliation(s)
- Suxiang Chen
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia.
- Western Australian Neuroscience Research Institute, Perth 6150, Australia.
| | - Bao T Le
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia.
- Western Australian Neuroscience Research Institute, Perth 6150, Australia.
| | - Kamal Rahimizadeh
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia.
| | - Khalil Shaikh
- GMK Research Laboratories Pvt. Ltd., Mallapur, Hyderabad 500 076, India.
| | - Narinder Mohal
- GMK Research Laboratories Pvt. Ltd., Mallapur, Hyderabad 500 076, India.
| | - Rakesh N Veedu
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia.
- Western Australian Neuroscience Research Institute, Perth 6150, Australia.
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23
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24
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Fletcher S, Bellgard MI, Price L, Akkari AP, Wilton SD. Translational development of splice-modifying antisense oligomers. Expert Opin Biol Ther 2016; 17:15-30. [PMID: 27805416 DOI: 10.1080/14712598.2017.1250880] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Antisense nucleic acid analogues can interact with pre-mRNA motifs and influence exon or splice site selection and thereby alter gene expression. Design of antisense molecules to target specific motifs can result in either exon exclusion or exon inclusion during splicing. Novel drugs exploiting the antisense concept are targeting rare, life-limiting diseases; however, the potential exists to treat a wide range of conditions by antisense-mediated splice intervention. Areas covered: In this review, the authors discuss the clinical translation of novel molecular therapeutics to address the fatal neuromuscular disorders Duchenne muscular dystrophy and spinal muscular atrophy. The review also highlights difficulties posed by issues pertaining to restricted participant numbers, variable phenotype and disease progression, and the identification and validation of study endpoints. Expert opinion: Translation of novel therapeutics for Duchenne muscular dystrophy and spinal muscular atrophy has been greatly advanced by multidisciplinary research, academic-industry partnerships and in particular, the engagement and support of the patient community. Sponsors, supporters and regulators are cooperating to deliver new drugs and identify and define meaningful outcome measures. Non-conventional and adaptive trial design could be particularly suited to clinical evaluation of novel therapeutics and strategies to treat serious, rare diseases that may be problematic to study using more conventional clinical trial structures.
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Affiliation(s)
- S Fletcher
- a Centre for Neuromuscular and Neurological Disorders , University of Western Australia , Nedlands , Western Australia , Australia.,b Western Australian Neuroscience Research Institute , Nedlands , Western Australia , Australia.,c Centre for Comparative Genomics , Murdoch University , Western Australia , Australia
| | - M I Bellgard
- b Western Australian Neuroscience Research Institute , Nedlands , Western Australia , Australia.,c Centre for Comparative Genomics , Murdoch University , Western Australia , Australia
| | - L Price
- a Centre for Neuromuscular and Neurological Disorders , University of Western Australia , Nedlands , Western Australia , Australia.,b Western Australian Neuroscience Research Institute , Nedlands , Western Australia , Australia.,c Centre for Comparative Genomics , Murdoch University , Western Australia , Australia
| | - A P Akkari
- b Western Australian Neuroscience Research Institute , Nedlands , Western Australia , Australia.,c Centre for Comparative Genomics , Murdoch University , Western Australia , Australia.,d Shiraz Pharmaceuticals, Inc , Chapel Hill , NC , USA
| | - S D Wilton
- a Centre for Neuromuscular and Neurological Disorders , University of Western Australia , Nedlands , Western Australia , Australia.,b Western Australian Neuroscience Research Institute , Nedlands , Western Australia , Australia.,c Centre for Comparative Genomics , Murdoch University , Western Australia , Australia
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25
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Verheul RC, van Deutekom JCT, Datson NA. Digital Droplet PCR for the Absolute Quantification of Exon Skipping Induced by Antisense Oligonucleotides in (Pre-)Clinical Development for Duchenne Muscular Dystrophy. PLoS One 2016; 11:e0162467. [PMID: 27612288 PMCID: PMC5017733 DOI: 10.1371/journal.pone.0162467] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/23/2016] [Indexed: 01/15/2023] Open
Abstract
Antisense oligonucleotides (AONs) in clinical development for Duchenne muscular dystrophy (DMD) aim to induce skipping of a specific exon of the dystrophin transcript during pre-mRNA splicing. This results in restoration of the open reading frame and consequently synthesis of a dystrophin protein with a shorter yet functional central rod domain. To monitor the molecular therapeutic effect of exon skip-inducing AONs in clinical studies, accurate quantification of pre- and post-treatment exon skip levels is required. With the recent introduction of 3rd generation digital droplet PCR (ddPCR), a state-of-the-art technology became available which allows absolute quantification of transcript copy numbers with and without specific exon skip with high precision, sensitivity and reproducibility. Using Taqman assays with probes targeting specific exon-exon junctions, we here demonstrate that ddPCR reproducibly quantified cDNA fragments with and without exon 51 of the DMD gene over a 4-log dynamic range. In a comparison of conventional nested PCR, qPCR and ddPCR using cDNA constructs with and without exon 51 mixed in different molar ratios using, ddPCR quantification came closest to the expected outcome over the full range of ratios (0–100%), while qPCR and in particular nested PCR overestimated the relative percentage of the construct lacking exon 51. Highest accuracy was similarly obtained with ddPCR in DMD patient-derived muscle cells treated with an AON inducing exon 51 skipping. We therefore recommend implementation of ddPCR for quantification of exon skip efficiencies of AONs in (pre)clinical development for DMD.
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26
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Duchenne muscular dystrophy drugs at the crossroads, as newer agents advance. Nat Biotechnol 2016; 34:675-6. [DOI: 10.1038/nbt0716-675] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Circulating miRNAs are generic and versatile therapeutic monitoring biomarkers in muscular dystrophies. Sci Rep 2016; 6:28097. [PMID: 27323895 PMCID: PMC4914855 DOI: 10.1038/srep28097] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/26/2016] [Indexed: 12/29/2022] Open
Abstract
The development of medical approaches requires preclinical and clinical trials for assessment of therapeutic efficacy. Such evaluation entails the use of biomarkers, which provide information on the response to the therapeutic intervention. One newly-proposed class of biomarkers is the microRNA (miRNA) molecules. In muscular dystrophies (MD), the dysregulation of miRNAs was initially observed in muscle biopsy and later extended to plasma samples, suggesting that they may be of interest as biomarkers. First, we demonstrated that dystromiRs dysregulation occurs in MD with either preserved or disrupted expression of the dystrophin-associated glycoprotein complex, supporting the utilization of dystromiRs as generic biomarkers in MD. Then, we aimed at evaluation of the capacity of miRNAs as monitoring biomarkers for experimental therapeutic approach in MD. To this end, we took advantage of our previously characterized gene therapy approach in a mouse model for α-sarcoglycanopathy. We identified a dose-response correlation between the expression of miRNAs on both muscle tissue and blood serum and the therapeutic benefit as evaluated by a set of new and classically-used evaluation methods. This study supports the utility of profiling circulating miRNAs for the evaluation of therapeutic outcome in medical approaches for MD.
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Toh ZYC, Thandar Aung-Htut M, Pinniger G, Adams AM, Krishnaswarmy S, Wong BL, Fletcher S, Wilton SD. Deletion of Dystrophin In-Frame Exon 5 Leads to a Severe Phenotype: Guidance for Exon Skipping Strategies. PLoS One 2016; 11:e0145620. [PMID: 26745801 PMCID: PMC4706350 DOI: 10.1371/journal.pone.0145620] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 12/07/2015] [Indexed: 12/03/2022] Open
Abstract
Duchenne and Becker muscular dystrophy severity depends upon the nature and location of the DMD gene lesion and generally correlates with the dystrophin open reading frame. However, there are striking exceptions where an in-frame genomic deletion leads to severe pathology or protein-truncating mutations (nonsense or frame-shifting indels) manifest as mild disease. Exceptions to the dystrophin reading frame rule are usually resolved after molecular diagnosis on muscle RNA. We report a moderate/severe Becker muscular dystrophy patient with an in-frame genomic deletion of DMD exon 5. This mutation has been reported by others as resulting in Duchenne or Intermediate muscular dystrophy, and the loss of this in-frame exon in one patient led to multiple splicing events, including omission of exon 6, that disrupts the open reading frame and is consistent with a severe phenotype. The patient described has a deletion of dystrophin exon 5 that does not compromise recognition of exon 6, and although the deletion does not disrupt the reading frame, his clinical presentation is more severe than would be expected for classical Becker muscular dystrophy. We suggest that the dystrophin isoform lacking the actin-binding sequence encoded by exon 5 is compromised, reflected by the phenotype resulting from induction of this dystrophin isoform in mouse muscle in vivo. Hence, exon skipping to address DMD-causing mutations within DMD exon 5 may not yield an isoform that confers marked clinical benefit. Additional studies will be required to determine whether multi-exon skipping strategies could yield more functional dystrophin isoforms, since some BMD patients with larger in-frame deletions in this region have been reported with mild phenotypes.
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Affiliation(s)
- Zhi Yon Charles Toh
- Western Australian Neuroscience Research Institute, Perth, Australia
- University of Western Australia, Perth, Australia
| | | | - Gavin Pinniger
- School of Anatomy, Physiology and Human Biology, University of Western Australia, Perth, Australia
| | - Abbie M. Adams
- Western Australian Neuroscience Research Institute, Perth, Australia
- University of Western Australia, Perth, Australia
- Centre for Comparative Genomics, Murdoch University, Perth, Australia
| | | | - Brenda L. Wong
- Department of Paediatrics, Department of Neurology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Sue Fletcher
- Western Australian Neuroscience Research Institute, Perth, Australia
- University of Western Australia, Perth, Australia
- Centre for Comparative Genomics, Murdoch University, Perth, Australia
| | - Steve D. Wilton
- Western Australian Neuroscience Research Institute, Perth, Australia
- University of Western Australia, Perth, Australia
- Centre for Comparative Genomics, Murdoch University, Perth, Australia
- * E-mail:
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Bao TL, Veedu RN, Fletcher S, Wilton SD. Antisense oligonucleotide development for the treatment of muscular dystrophies. Expert Opin Orphan Drugs 2015. [DOI: 10.1517/21678707.2016.1122517] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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LoMauro A, D'Angelo MG, Aliverti A. Assessment and management of respiratory function in patients with Duchenne muscular dystrophy: current and emerging options. Ther Clin Risk Manag 2015; 11:1475-88. [PMID: 26451113 PMCID: PMC4592047 DOI: 10.2147/tcrm.s55889] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked myopathy resulting in progressive weakness and wasting of all the striated muscles including the respiratory muscles. The consequences are loss of ambulation before teen ages, cardiac involvement and breathing difficulties, the main cause of death. A cure for DMD is not currently available. In the last decades the survival of patients with DMD has improved because the natural history of the disease can be changed thanks to a more comprehensive therapeutic approach. This comprises interventions targeted to the manifestations and complications of the disease, particularly in the respiratory care. These include: 1) pharmacological intervention, namely corticosteroids and idebenone that significantly reduce the decline of spirometric parameters; 2) rehabilitative intervention, namely lung volume recruitment techniques that help prevent atelectasis and slows the rate of decline of pulmonary function; 3) scoliosis treatment, namely steroid therapy that is used to reduce muscle inflammation/degeneration and prolong ambulation in order to delay the onset of scoliosis, being an additional contribution to the restrictive lung pattern; 4) cough assisted devices that improve airway clearance thus reducing the risk of pulmonary infections; and 5) non-invasive mechanical ventilation that is essential to treat nocturnal hypoventilation, sleep disordered breathing, and ultimately respiratory failure. Without any intervention death occurs within the first 2 decades, however, thanks to this multidisciplinary therapeutic approach life expectancy of a newborn with DMD nowadays can be significantly prolonged up to his fourth decade. This review is aimed at providing state-of-the-art methods and techniques for the assessment and management of respiratory function in DMD patients.
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Affiliation(s)
- Antonella LoMauro
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, Italy
| | | | - Andrea Aliverti
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, Italy
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Merlini L, Sabatelli P. Improving clinical trial design for Duchenne muscular dystrophy. BMC Neurol 2015; 15:153. [PMID: 26306629 PMCID: PMC4549867 DOI: 10.1186/s12883-015-0408-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 08/14/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Currently, the most promising therapies for Duchenne muscular dystrophy (DMD) are exon skipping and stop codon read-through, two strategies aimed at restoring the expression of dystrophin. A phase 3 clinical trial with drisapersen, a drug designed to induce exon 51-skipping, has failed to show significant improvement of the primary outcome measure, the six-minute walk test. DISCUSSION Here, we review some key points that should be considered when designing clinical trials for these new therapies. First, younger patients have more functional abilities and more muscle fibers to preserve than older patients and therefore are better subjects for trials designed to demonstrate the success of new treatments. Second, the inclusion of patients on corticosteroids both in the treatment and placebo groups is of concern because the positive effect of corticosteroids might mask the effect of the treatment being tested. Additionally, the reasonable expectation from these therapies is the slowing of disease progression rather than improvement. Therefore, the appropriate clinical endpoints are the prolongation of the ability to stand from the floor, climb stairs, and walk, not an increase in muscle strength or function. Hence, the time frames for the detection of new dystrophin, which occurs within months, and the ability to demonstrate a slowing of disease progression, which requires years, are strikingly different. Finally, placebo-controlled trials are difficult to manage if years of blindness are required to demonstrate a slowing of disease progression. Thus, accelerated/conditional approval for new therapies should be based on surrogate biochemical outcomes: the demonstration of de novo dystrophin production and of its beneficial effect on the functional recovery of muscle fiber. These data suggest that clinical trials for DMD patients must be adapted to the particular characteristics of the disease in order to demonstrate the expected positive effect of new treatments.
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Affiliation(s)
- Luciano Merlini
- Laboratory of Musculoskeletal Cell Biology, Istituto Ortopedico Rizzoli, IRCCS, Via Di Barbiano 1/10, 40136, Bologna, Italy.
| | - Patrizia Sabatelli
- Laboratory of Musculoskeletal Cell Biology, Istituto Ortopedico Rizzoli, IRCCS, Via Di Barbiano 1/10, 40136, Bologna, Italy. .,CNR National Research Council of Italy, Institute of Molecular Genetics, Bologna, Italy.
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Le Rumeur E. Dystrophin and the two related genetic diseases, Duchenne and Becker muscular dystrophies. Bosn J Basic Med Sci 2015; 15:14-20. [PMID: 26295289 DOI: 10.17305/bjbms.2015.636] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 07/20/2015] [Indexed: 01/01/2023] Open
Abstract
Mutations of the dystrophin DMD gene, essentially deletions of one or several exons, are the cause of two devastating and to date incurable diseases, Duchenne (DMD) and Becker (BMD) muscular dystrophies. Depending upon the preservation or not of the reading frame, dystrophin is completely absent in DMD, or present in either a mutated or a truncated form in BMD. DMD is a severe disease which leads to a premature death of the patients. Therapy approaches are evolving with the aim to transform the severe DMD in the BMD form of the disease by restoring the expression of a mutated or truncated dystrophin. These therapies are based on the assumption that BMD is a mild disease. However, this is not completely true as BMD patients are more or less severely affected and no molecular basis of this heterogeneity of the BMD form of the disease is yet understood. The aim of this review is to report for the correlation between dystrophin structures in BMD deletions in view of this heterogeneity and to emphasize that examining BMD patients in details is highly relevant to anticipate for DMD therapy effects.
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Affiliation(s)
- Elisabeth Le Rumeur
- Institut de Génétique et Développement de Rennes (IGDR), Faculté de Médecine, Rennes Cedex.
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