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Szwec S, Kapłucha Z, Chamberlain JS, Konieczny P. Dystrophin- and Utrophin-Based Therapeutic Approaches for Treatment of Duchenne Muscular Dystrophy: A Comparative Review. BioDrugs 2024; 38:95-119. [PMID: 37917377 PMCID: PMC10789850 DOI: 10.1007/s40259-023-00632-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2023] [Indexed: 11/04/2023]
Abstract
Duchenne muscular dystrophy is a devastating disease that leads to progressive muscle loss and premature death. While medical management focuses mostly on symptomatic treatment, decades of research have resulted in first therapeutics able to restore the affected reading frame of dystrophin transcripts or induce synthesis of a truncated dystrophin protein from a vector, with other strategies based on gene therapy and cell signaling in preclinical or clinical development. Nevertheless, recent reports show that potentially therapeutic dystrophins can be immunogenic in patients. This raises the question of whether a dystrophin paralog, utrophin, could be a more suitable therapeutic protein. Here, we compare dystrophin and utrophin amino acid sequences and structures, combining published data with our extended in silico analyses. We then discuss these results in the context of therapeutic approaches for Duchenne muscular dystrophy. Specifically, we focus on strategies based on delivery of micro-dystrophin and micro-utrophin genes with recombinant adeno-associated viral vectors, exon skipping of the mutated dystrophin pre-mRNAs, reading through termination codons with small molecules that mask premature stop codons, dystrophin gene repair by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated genetic engineering, and increasing utrophin levels. Our analyses highlight the importance of various dystrophin and utrophin domains in Duchenne muscular dystrophy treatment, providing insights into designing novel therapeutic compounds with improved efficacy and decreased immunoreactivity. While the necessary actin and β-dystroglycan binding sites are present in both proteins, important functional distinctions can be identified in these domains and some other parts of truncated dystrophins might need redesigning due to their potentially immunogenic qualities. Alternatively, therapies based on utrophins might provide a safer and more effective approach.
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Affiliation(s)
- Sylwia Szwec
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Zuzanna Kapłucha
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Jeffrey S Chamberlain
- Department of Neurology, University of Washington School of Medicine, Seattle, WA, 98109-8055, USA
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Washington School of Medicine, Seattle, WA, 98109-8055, USA
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA, 98109-8055, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98109-8055, USA
| | - Patryk Konieczny
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
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Boehler JF, Brown KJ, Beatka M, Gonzalez JP, Donisa Dreghici R, Soustek-Kramer M, McGonigle S, Ganot A, Palmer T, Lowie C, Chamberlain JS, Lawlor MW, Morris CA. Clinical potential of microdystrophin as a surrogate endpoint. Neuromuscul Disord 2023; 33:40-49. [PMID: 36575103 DOI: 10.1016/j.nmd.2022.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/28/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Accelerated approval based on a likely surrogate endpoint can be life-changing for patients suffering from a rare progressive disease with unmet medical need, as it substantially hastens access to potentially lifesaving therapies. In one such example, antisense morpholinos were approved to treat Duchenne muscular dystrophy (DMD) based on measurement of shortened dystrophin in skeletal muscle biopsies as a surrogate biomarker. New, promising therapeutics for DMD include AAV gene therapy to restore another form of dystrophin termed mini- or microdystrophin. AAV-microdystrophins are currently in clinical trials but have yet to be accepted by regulatory agencies as reasonably likely surrogate endpoints. To evaluate microdystrophin expression as a reasonably likely surrogate endpoint for DMD, this review highlights dystrophin biology in the context of functional and clinical benefit to support the argument that microdystrophin proteins have a high probability of providing clinical benefit based on their rational design. Unlike exon-skipping based strategies, the approach of rational design allows for functional capabilities (i.e. quality) of the protein to be maximized with every patient receiving the same optimized microdystrophin. Therefore, the presence of rationally designed microdystrophin in a muscle biopsy is likely to predict clinical benefit and is consequently a strong candidate for a surrogate endpoint analysis to support accelerated approval.
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Affiliation(s)
- Jessica F Boehler
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States
| | - Kristy J Brown
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States
| | - Margaret Beatka
- Diverge TSL, 247 Freshwater Way Suite 610, Milwaukee, WI 53204, United States
| | - J Patrick Gonzalez
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States
| | | | | | - Sharon McGonigle
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States
| | - Annie Ganot
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States
| | - Timothy Palmer
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States
| | - Caitlin Lowie
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States
| | - Jeffrey S Chamberlain
- Department of Neurology, University of Washington School of Medicine, Seattle, United States
| | - Michael W Lawlor
- Diverge TSL, 247 Freshwater Way Suite 610, Milwaukee, WI 53204, United States
| | - Carl A Morris
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA 02129, United States.
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Gaina G, Vossen RHAM, Manole E, Plesca DA, Ionica E. Combining Protein Expression and Molecular Data Improves Mutation Characterization of Dystrophinopathies. Front Neurol 2021; 12:718396. [PMID: 34950096 PMCID: PMC8689184 DOI: 10.3389/fneur.2021.718396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Duchenne and Becker muscular dystrophy are X-linked recessive inherited disorders characterized by progressive weakness due to skeletal muscle degeneration. Different mutations in the DMD gene, which encodes for dystrophin protein, are responsible for these disorders. The aim of our study was to investigate the relationship between type, size, and location of the mutation that occurs in the DMD gene and their effect on dystrophin protein expression in a cohort of 40 male dystrophinopathy patients and nine females, possible carriers. We evaluated the expression of dystrophin by immunofluorescence and immunoblotting. The mutational spectrum of the DMD gene was established by MLPA for large copy number variants, followed by HRM analysis for point mutations and sequencing of samples with an abnormal melting profile. MLPA revealed 30 deletions (75%) and three duplications (7.5%). HRM analysis accounted for seven-point mutations (17.5%). We also report four novel small mutations (c. 8507G>T, c.3021delG, c.9563_9563+1insAGCATGTTTATGATACAGCA, c.7661-60T>A) in DMD gene. Our work shows that the DNA translational open reading frame and the location of the mutation both influence the expression of dystrophin and disease severity phenotype. The proposed algorithm used in this study demonstrates its accuracy for the characterization of dystrophinopathy patients.
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Affiliation(s)
- Gisela Gaina
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest, Romania
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, Bucharest, Romania
- *Correspondence: Gisela Gaina ;
| | - Rolf H. A. M. Vossen
- Center for Human and Clinical Genetics, Leiden Genome Technology Center, Leiden, Netherlands
| | - Emilia Manole
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, Bucharest, Romania
- Colentina Clinical Hospital, Bucharest, Romania
| | - Doina Anca Plesca
- Department of Pediatrics, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- Department of Clinical Pediatrics, Victor Gomoiu Children Clinical Hospital, Bucharest, Romania
| | - Elena Ionica
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest, Romania
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Transcriptomic Analysis Reveals Involvement of the Macrophage Migration Inhibitory Factor Gene Network in Duchenne Muscular Dystrophy. Genes (Basel) 2019; 10:genes10110939. [PMID: 31752120 PMCID: PMC6896047 DOI: 10.3390/genes10110939] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/11/2019] [Accepted: 11/15/2019] [Indexed: 01/04/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a progressive hereditary muscular disease with X-linked recessive inheritance, that leads patients to premature death. The loss of dystrophin determines membrane instability, causing cell damage and inflammatory response. Macrophage migration inhibitory factor (MIF) is a cytokine that exerts pleiotropic properties and is implicated in the pathogenesis of a variety of diseases. Recently, converging data from independent studies have pointed to a possible role of MIF in dystrophic muscle disorders, including DMD. In the present study, we have investigated the modulation of MIF and MIF-related genes in degenerative muscle disorders, by making use of publicly available whole-genome expression datasets. We show here a significant enrichment of MIF and related genes in muscle samples from DMD patients, as well as from patients suffering from Becker’s disease and limb-girdle muscular dystrophy type 2B. On the other hand, transcriptomic analysis of in vitro differentiated myotubes from healthy controls and DMD patients revealed no significant alteration in the expression levels of MIF-related genes. Finally, by analyzing DMD samples as a time series, we show that the modulation of the genes belonging to the MIF network is an early event in the DMD muscle and does not change with the increasing age of the patients, Overall, our analysis suggests that MIF may play a role in vivo during muscle degeneration, likely promoting inflammation and local microenvironment reaction.
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Deepha S, Vengalil S, Preethish-Kumar V, Polavarapu K, Nalini A, Gayathri N, Purushottam M. MLPA identification of dystrophin mutations and in silico evaluation of the predicted protein in dystrophinopathy cases from India. BMC MEDICAL GENETICS 2017; 18:67. [PMID: 28610567 PMCID: PMC5470271 DOI: 10.1186/s12881-017-0431-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/31/2017] [Indexed: 11/18/2022]
Abstract
Background Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are X-linked recessive disorders caused by mutations in the DMD gene. The aim of this study was to predict the effect of gene mutations on the dystrophin protein and study its impact on clinical phenotype. Methods In this study, 415 clinically diagnosed patients were tested for mutations by Multiplex ligation dependent probe amplification (MLPA). Muscle biopsy was performed in 34 patients with negative MLPA. Phenotype-genotype correlation was done using PROVEAN, hydrophobicity and eDystrophin analysis. We have utilized bioinformatics tools in order to evaluate the observed mutations both at the level of primary as well as secondary structure. Results Mutations were identified in 75.42% cases, of which there were deletions in 91.6% and duplications in 8.30%. As per the reading frame rule, 84.6% out-of frame and 15.3% in-frame mutations were noted. Exon 50 was the most frequently deleted exon and the exon 45–52 region was the hot-spot for deletions in this cohort. There was no correlation noted between age of onset or creatine kinase (CK) values with extent of gene mutation. The PROVEAN analysis showed a deleterious effect in 94.5% cases and a neutral effect in 5.09% cases. Mutations in exon 45–54 (out of frame) and exon 46–54 (in-frame) regions in the central rod domain of dystrophin showed more negative scores compared to other domains in the present study. Hydrophobicity profile analysis showed that the hydrophobic regions I & III were equally affected. Analysis of deletions in hinge III hydrophobic region by the eDystrophin programme also predicted a hybrid repeat seen to be associated with a BMD like disease progression, thus making the hinge III region relatively tolerant to mutations. Conclusions We found that, while the predictions made by the software utilized might have overall significance, the results were not convincing on a case by case basis. This reflects the inadequacy of the currently available tools and also underlines the possible inadequacy of MLPA to detect other minor mutations that might enhance or suppress the effect of the primary mutation in this large gene. Next Generation Sequencing or targeted Sanger sequencing on a case by case basis might improve phenotype- genotype correlation. Electronic supplementary material The online version of this article (doi:10.1186/s12881-017-0431-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sekar Deepha
- Department of Neuropathology, Neuromuscular Laboratory, Bengaluru, Karnataka, India
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Veeramani Preethish-Kumar
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Kiran Polavarapu
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Narayanappa Gayathri
- Department of Neuropathology, Neuromuscular Laboratory, Bengaluru, Karnataka, India
| | - Meera Purushottam
- Molecular Genetics Laboratory, Neurobiology Research Centre, Department of Psychiatry, National Institute of Mental Health and Neurosciences, Hosur Road, Bangalore, 560029, Karnataka, India.
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