Undetectable dystrophin can still result in a relatively benign phenotype of dystrophinopathy

Duchenne Muscular Dystrophy and Becker Muscular Dystrophy Confirmed by Multiplex Ligation-Dependent Probe Amplification: Genotype-Phenotype Correlation in a Large Cohort

Background and Purpose

Studies of cases of Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) confirmed by multiplex ligation-dependent probe amplification (MLPA) have determined the clinical characteristics, genotype, and relations between the reading frame and phenotype for different countries. This is the first such study from India.

Methods

A retrospective genotype-phenotype analysis of 317 MLPA-confirmed patients with DMD or BMD who visited the neuromuscular clinic of a quaternary referral center in southern India.

Results

The 317 patients comprised 279 cases of DMD (88%), 32 of BMD (10.1%), and 6 of intermediate phenotype (1.9%). Deletions accounted for 91.8% of cases, with duplications causing the remaining 8.2%. There were 254 cases of DMD (91%) with deletions and 25 (9%) due to duplications, and 31 cases (96.8%) of BMD with deletions and 1 (3.2%) due to duplication. All six cases of intermediate type were due to deletions. The most-common mutation was a single-exon deletion. Deletions of six or fewer exons constituted 68.8% of cases. The deletion of exon 50 was the most common. The reading-frame rule held in 90% of DMD and 94% of BMD cases. A tendency toward a lower IQ and earlier wheelchair dependence was observed with distal exon deletions, though a significant correlation was not found.

Conclusions

The reading-frame rule held in 90% to 94% of children, which is consistent with reports from other parts of the world. However, testing by MLPA is a limitation, and advanced sequencing methods including analysis of the structure of mutant dystrophin is needed for more-accurate assessments of the genotype-phenotype correlation.

Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy

Background

Duchenne muscular dystrophy (DMD) causes progressive muscle degeneration, cardiomyopathy and respiratory failure in approximately 1/5,000 boys. Golden Retriever muscular dystrophy (GRMD) resembles DMD both clinically and pathologically. Like DMD, GRMD exhibits remarkable phenotypic variation among affected dogs, suggesting the influence of modifiers. Understanding the role(s) of genetic modifiers of GRMD may identify genes and pathways that also modify phenotypes in DMD and reveal novel therapies. Therefore, our objective in this study was to identify genetic modifiers that affect discrete GRMD phenotypes.

Results

We performed a linear mixed-model (LMM) analysis using 16 variably-affected dogs from our GRMD colony (8 dystrophic, 8 non-dystrophic). All of these dogs were either full or half-siblings, and phenotyped for 19 objective, quantitative biomarkers at ages 6 and 12 months. Each biomarker was individually assessed. Gene expression profiles of 59 possible candidate genes were generated for two muscle types: the cranial tibialis and medial head of the gastrocnemius. SNPs significantly associated with GRMD biomarkers were identified on multiple chromosomes (including the X chromosome). Gene expression levels for candidate genes located near these SNPs correlated with biomarker values, suggesting possible roles as GRMD modifiers.

Conclusions

The results of this study enhance our understanding of GRMD pathology and represent a first step toward the characterization of GRMD modifiers that may be relevant to DMD pathology. Such modifiers are likely to be useful for DMD treatment development based on their relationships to GRMD phenotypes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2948-z) contains supplementary material, which is available to authorized users.

Animal models of Duchenne muscular dystrophy: from basic mechanisms to gene therapy

Duchenne muscular dystrophy (DMD) is a progressive muscle-wasting disorder. It is caused by loss-of-function mutations in the dystrophin gene. Currently, there is no cure. A highly promising therapeutic strategy is to replace or repair the defective dystrophin gene by gene therapy. Numerous animal models of DMD have been developed over the last 30 years, ranging from invertebrate to large mammalian models. mdx mice are the most commonly employed models in DMD research and have been used to lay the groundwork for DMD gene therapy. After ~30 years of development, the field has reached the stage at which the results in mdx mice can be validated and scaled-up in symptomatic large animals. The canine DMD (cDMD) model will be excellent for these studies. In this article, we review the animal models for DMD, the pros and cons of each model system, and the history and progress of preclinical DMD gene therapy research in the animal models. We also discuss the current and emerging challenges in this field and ways to address these challenges using animal models, in particular cDMD dogs.

New developments in the use of gene therapy to treat Duchenne muscular dystrophy

INTRODUCTION

Duchenne muscular dystrophy (DMD) is a lethal X-linked inherited disorder characterised by progressive muscle weakness, wasting and degeneration. Although the gene affected in DMD was identified over 25 years ago, there is still no effective treatment.

AREAS COVERED

Here we review some of the genetic-based strategies aimed at amelioration of the DMD phenotype. A number of Phase II/III clinical trials of antisense oligonucleotide-induced exon skipping for restoration of the open reading frame (ORF) of the DMD gene have recently been completed. The potential strategies for overcoming the hurdles that appear to prevent exon skipping becoming an effective treatment for DMD currently are discussed.

EXPERT OPINION

The applicability of exon skipping as a therapy to DMD is restricted and the development of alternative strategies that are more encompassing is needed. The rapid pre-clinical advances that are being made in the field of adeno-associated virus (AAV)-based delivery of micro-dystrophin would address this. The obstacles to be faced with gene replacement strategies would include the need for high viral titres, efficient muscle targeting and avoidance of immune response to vector and transgene. The new emerging field of gene editing could potentially provide permanent correction of the DMD gene and the feasibility of such an approach to DMD is discussed.

Modifying muscular dystrophy through transforming growth factor-β

Muscular dystrophy arises from ongoing muscle degeneration and insufficient regeneration. This imbalance leads to loss of muscle, with replacement by scar or fibrotic tissue, resulting in muscle weakness and, eventually, loss of muscle function. Human muscular dystrophy is characterized by a wide range of disease severity, even when the same genetic mutation is present. This variability implies that other factors, both genetic and environmental, modify the disease outcome. There has been an ongoing effort to define the genetic and molecular bases that influence muscular dystrophy onset and progression. Modifier genes for muscle disease have been identified through both candidate gene approaches and genome-wide surveys. Multiple lines of experimental evidence have now converged on the transforming growth factor-β (TGF-β) pathway as a modifier for muscular dystrophy. TGF-β signaling is upregulated in dystrophic muscle as a result of a destabilized plasma membrane and/or an altered extracellular matrix. Given the important biological role of the TGF-β pathway, and its role beyond muscle homeostasis, we review modifier genes that alter the TGF-β pathway and approaches to modulate TGF-β activity to ameliorate muscle disease.

Assessment of the structural and functional impact of in-frame mutations of the DMD gene, using the tools included in the eDystrophin online database

Background

Dystrophin is a large essential protein of skeletal and heart muscle. It is a filamentous scaffolding protein with numerous binding domains. Mutations in the DMD gene, which encodes dystrophin, mostly result in the deletion of one or several exons and cause Duchenne (DMD) and Becker (BMD) muscular dystrophies. The most common DMD mutations are frameshift mutations resulting in an absence of dystrophin from tissues. In-frame DMD mutations are less frequent and result in a protein with partial wild-type dystrophin function. The aim of this study was to highlight structural and functional modifications of dystrophin caused by in-frame mutations.

Methods and results

We developed a dedicated database for dystrophin, the eDystrophin database. It contains 209 different non frame-shifting mutations found in 945 patients from a French cohort and previous studies. Bioinformatics tools provide models of the three-dimensional structure of the protein at deletion sites, making it possible to determine whether the mutated protein retains the typical filamentous structure of dystrophin. An analysis of the structure of mutated dystrophin molecules showed that hybrid repeats were reconstituted at the deletion site in some cases. These hybrid repeats harbored the typical triple coiled-coil structure of native repeats, which may be correlated with better function in muscle cells.

Conclusion

This new database focuses on the dystrophin protein and its modification due to in-frame deletions in BMD patients. The observation of hybrid repeat reconstitution in some cases provides insight into phenotype-genotype correlations in dystrophin diseases and possible strategies for gene therapy. The eDystrophin database is freely available: http://edystrophin.genouest.org/.

Petri net modelling of gene regulation of the Duchenne muscular dystrophy

Searching for therapeutic strategies for Duchenne muscular dystrophy, it is of great interest to understand the responsible molecular pathways down-stream of dystrophin completely. For this reason we have performed real-time PCR experiments to compare mRNA expression levels of relevant genes in tissues of affected patients and controls. To bring experimental data in context with the underlying pathway theoretical models are needed. Modelling of biological processes in the cell at higher description levels is still an open problem in the field of systems biology. In this paper, a new application of Petri net theory is presented to model gene regulatory processes of Duchenne muscular dystrophy. We have developed a Petri net model, which is based mainly on own experimental and literature data. We distinguish between up- and down-regulated states of gene expression. The analysis of the model comprises the computation of structural and dynamic properties with focus on a thorough T-invariant analysis, including clustering techniques and the decomposition of the network into maximal common transition sets (MCT-sets), which can be interpreted as functionally related building blocks. All possible pathways, which reflect the complex net behaviour in dependence of different gene expression patterns, are discussed. We introduce Mauritius maps of T-invariants, which enable, for example, theoretical knockout analysis. The resulted model serves as basis for a better understanding of pathological processes, and thereby for planning next experimental steps in searching for new therapeutic possibilities.

AVAILABILITY

Free availability of the Petri net editor and animator Snoopy and the clustering tool PInA via http://www-dssz.informatik.tu-cottbus.de/~ wwwdssz/. The Petri net models used can be accessed via http://www.tfh-berlin.de/bi/duchenne/.

Two novel missense mutations in the myostatin gene identified in Japanese patients with Duchenne muscular dystrophy

Background

Myostatin is a negative regulator of skeletal muscle growth. Truncating mutations in the myostatin gene have been reported to result in gross muscle hypertrophy. Duchenne muscular dystrophy (DMD), the most common lethal muscle wasting disease, is a result of an absence of muscle dystrophin. Although this disorder causes a rather uniform pattern of muscle wasting, afflicted patients display phenotypic variability. We hypothesized that genetic variation in myostatin is a modifier of the DMD phenotype.

Methods

We analyzed 102 Japanese DMD patients for mutations in the myostatin gene.

Results

Two polymorphisms that are commonly observed in Western countries, p.55A>T and p.153K>R, were not observed in these Japanese patients. An uncommon polymorphism of p.164E>K was uncovered in four cases; each patient was found to be heterozygous for this polymorphism, which had the highest frequency of the polymorphism observed in the Japanese patients. Remarkably, two patients were found to be heterozygous for one of two novel missense mutations (p.95D>H and p.156L>I). One DMD patient carrying a novel missense mutation of p.95D>H was not phenotypically different from the non-carriers. The other DMD patient was found to carry both a novel mutation (p.156L>I) and a known polymorphism (p.164E>K) in one allele, although his phenotype was not significantly modified. Any nucleotide change creating a target site for micro RNAs was not disclosed in the 3' untranslated region.

Conclusion

Our results indicate that heterozygous missense mutations including two novel mutations did not produce an apparent increase in muscle strength in Japanese DMD cases, even in a patient carrying two missense mutations.

Calcium misregulation and the pathogenesis of muscular dystrophy

Although the exact nature of the relationship between calcium and the pathogenesis of Duchenne muscular dystrophy (DMD) is not fully understood, this is an important issue which has been addressed in several recent reviews (Alderton and Steinhardt, 2000a, Gailly, 2002, Allen et al., 2005). A key question when trying to understand the cellular basis of DMD is how the absence or low level of expression of dystrophin, a cytoskeletal protein, results in the slow but progressive necrosis of muscle fibres. Although loss of cytoskeletal and sarcolemmal integrity which results from the absence of dystrophin clearly plays a key role in the pathogenesis associated with DMD, a number of lines of evidence also establish a role for misregulation of calcium ions in the DMD pathology, particularly in the cytoplasmic space just under the sarcolemma. A number of calcium-permeable channels have been identified which can exhibit greater activity in dystrophic muscle cells, and exIsting evidence suggests that these may represent different variants of the same channel type (perhaps the transient receptor potential channel, TRPC). In addition, a prominent role for calcium-activated proteases in the DMD pathology has been established, as well as modulation of other intracellular regulatory proteins and signaling pathways. Whether dystrophin and its associated proteins have a direct role in the regulation of calcium ions, calcium channels or intracellular calcium stores, or indirectly alters calcium regulation through enhancement of membrane tearing, remains unclear. Here we focus on areas of consensus or divergence amongst the existing literature, and propose areas where future research would be especially valuable.

C-terminal truncated dystrophin identified in skeletal muscle of an asymptomatic boy with a novel nonsense mutation of the dystrophin gene

Mutations that cause premature stop codons in the dystrophin gene lead to a complete loss of dystrophin from skeletal muscle, resulting in severe Duchenne muscular dystrophy. Here, a C-terminally truncated dystrophin resulting from a novel nonsense mutation is shown for the first time to be localized to the muscle plasma membrane. An asymptomatic 8-y-old boy was examined for dystrophin in skeletal muscle because of high serum creatine kinase activity. Remarkably, no dystrophin labeling was seen with an MAb against the C-terminal domain, suggesting the presence of an early stop codon in the dystrophin gene. Labeling with an antibody specific to the N-terminal domain, however, revealed weak, patchy, and discontinuous staining, suggesting limited production of a truncated form of the protein. Molecular analysis revealed a novel nonsense mutation (Q3625X) as a result of a single nucleotide change in the patient's genomic DNA (C10873T), leaving 1.6% of dystrophin gene product unsynthesized at the C terminus. Dystrophin mRNA analysis did not show rescue of the nonsense mutation as a result of exon-skipping by an alternative splicing mechanism. This is the first report of an asymptomatic dystrophinopathy with a nonsense mutation in the dystrophin gene.

Identification of transcripts from a subtraction library which might be responsible for the mild phenotype in an intrafamilially variable course of Duchenne muscular dystrophy

While frame-shift mutations are usually found in Duchenne muscular dystrophy (DMD), in-frame mutations are associated with the less severe phenotype of Becker's muscular dystrophy. Exceptions have been reported in both directions suggesting the existence of modifying genes, which might be helpful for innovation of new therapeutic strategies. We report on the very rare case of an intrafamilially different course of DMD, with the younger brother being far less affected than the older one when compared at the same age. In this context, we constructed a subtraction library enriched for transcripts over-expressed in the patient with the milder phenotype. Twelve random clones were sequenced, followed by database analysis. Six of them, casein kinase 1 alpha 1, RAP2B, dynactin 3 light chain, core binding factor beta, myosin light polypeptide 2 and one hypothetical gene, were further analysed by real-time RT-PCR. All these genes were over-expressed 3-20 times in the less affected patient compared with the more severely affected one. Casein kinase 1 and the hypothetical gene showed even a slightly higher expression than the control. Up-regulation of myosin light polypeptide 2, one of the most sensitive markers of muscle fibre regeneration, obviously reflects the milder phenotype. Casein kinase 1, dynactin and core binding factor are supposed to be involved in cell cycle pathways. RAP is a component of the signalling network which controls fundamental cellular processes such as proliferation and differentiation. All four might be interesting candidates for a therapeutic approach to diminish progression of dystrophy in DMD.

Function and genetics of dystrophin and dystrophin-related proteins in muscle

The X-linked muscle-wasting disease Duchenne muscular dystrophy is caused by mutations in the gene encoding dystrophin. There is currently no effective treatment for the disease; however, the complex molecular pathology of this disorder is now being unravelled. Dystrophin is located at the muscle sarcolemma in a membrane-spanning protein complex that connects the cytoskeleton to the basal lamina. Mutations in many components of the dystrophin protein complex cause other forms of autosomally inherited muscular dystrophy, indicating the importance of this complex in normal muscle function. Although the precise function of dystrophin is unknown, the lack of protein causes membrane destabilization and the activation of multiple pathophysiological processes, many of which converge on alterations in intracellular calcium handling. Dystrophin is also the prototype of a family of dystrophin-related proteins, many of which are found in muscle. This family includes utrophin and alpha-dystrobrevin, which are involved in the maintenance of the neuromuscular junction architecture and in muscle homeostasis. New insights into the pathophysiology of dystrophic muscle, the identification of compensating proteins, and the discovery of new binding partners are paving the way for novel therapeutic strategies to treat this fatal muscle disease. This review discusses the role of the dystrophin complex and protein family in muscle and describes the physiological processes that are affected in Duchenne muscular dystrophy.

The muscular dystrophies

The muscular dystrophies are inherited myogenic disorders characterised by progressive muscle wasting and weakness of variable distribution and severity. They can be subdivided into several groups, including congenital forms, in accordance with the distribution of predominant muscle weakness: Duchenne and Becker; Emery-Dreifuss; distal; facioscapulohumeral; oculopharyngeal; and limb-girdle which is the most heterogeneous group. In several dystrophies the heart can be seriously affected, sometimes in the absence of clinically significant weakness. The genes and their protein products that cause most of these disorders have now been identified. This information is essential to establish an accurate diagnosis and for reliable genetic counselling and prenatal diagnosis. There is, as yet, no way of greatly affecting the long-term course of any of these diseases. However, advances in gene manipulation and stem-cell therapy suggest cautious optimism for finding an effective treatment in the not-too-distant future.

Heterozygous myogenic factor 6 mutation associated with myopathy and severe course of Becker muscular dystrophy

Myogenic factors (MYF) belong to the basic helix-loop-helix (bHLH) transcription factor family and regulate myogenesis and muscle regeneration. The physiological importance of both functions was demonstrated in homozygous Myf knockout mice and mdx mice. Myf5 and Myod are predominantly expressed in proliferating myoblasts while Myf4 and Myf6 are involved in differentiation of myotubes. In a boy with myopathy and an increase of muscle fibres with central nuclei we detected a heterozygous 387G-->T nucleotide transversion in the MYF6 gene (MIM*159991). Protein-protein interaction of mutant MYF6 was reduced, and DNA-binding potential and transactivation capacity were abolished, thus demonstrating MYF6 haploinsufficiency. The boy's father carried the identical mutation and, in addition, an in-frame deletion of exons 45-47 in his dystrophin gene. This mutation is normally associated with a mild to moderate course of Becker muscular dystrophy but the father suffered from a severe course of Becker muscular dystrophy suggesting MYF6 as a modifier.

Dystrophin mutations predict cellular susceptibility to oxidative stress

Mutations in the dystrophin gene that lead to the expression of truncated forms of the dystrophin protein cause muscular dystrophies of varying severities both in humans and in mice. We have shown previously that dystrophin-deficient muscle is more susceptible to oxidative injury than is normal muscle. In this report, we have used muscle cells derived from mdx mice, which express no dystrophin, and mdx-transgenic strains that express full-length dystrophin or truncated forms of dystrophin to explore further the relationship between dystrophin expression and susceptibility of muscle to oxidative injury. We show that, when differentiated into myotubes, the relative susceptibility of the cell populations to oxidative stress correlates with the severity of the dystrophy in the strain from which the cells were isolated. The most susceptible populations exhibited the greatest oxidative damage as assessed by protein oxidation. Thus, the relative efficacy of truncated dystrophin proteins to protect muscle from necrotic degeneration in vivo is predicted by their ability to protect muscle cells from free radical mediated injury. These findings support the hypothesis that the dystrophin protein complex may have important regulatory or signaling properties in terms of cell survival and antioxidant defense mechanisms.