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Akbar F, Saleem SM, Khalid E, Ibrahim S, Afroze B, Kirmani S, Khan S. The spectrum of hereditary neuromuscular disorders in the Pakistani population. Am J Med Genet A 2023; 191:2536-2550. [PMID: 37366078 DOI: 10.1002/ajmg.a.63332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/21/2023] [Accepted: 06/07/2023] [Indexed: 06/28/2023]
Abstract
Hereditary neuromuscular disorders (NMDs) are a broad group of clinically heterogeneous disorders with varying inheritance patterns, that are associated with over 500 implicated genes. In the context of a highly consanguineous Pakistani population, we expect that autosomal recessive NMDs may have a higher prevalence compared with patients of European descent. This is the first study to offer a detailed description of the spectrum of genes causing hereditary NMDs in the Pakistani population using NGS testing. To study the clinical and genetic profiles of patients presenting for evaluation of a hereditary neuromuscular disorder. This is a retrospective chart review of patients seen in the Neuromuscular Disorders Clinic and referred to the Genetics Clinic with a suspected hereditary neuromuscular disorder, between 2016 and 2020 at the Aga Khan University Hospital, Karachi and Mukhtiar A. Sheikh Hospital, Multan, Pakistan. The genetic testing for these patients included NGS-based single gene sequencing, NGS-based multi-gene panel and whole exome sequencing. In a total of 112 patients studied, 35 (31.3%) were female. The mean age of onset in all patients was 14.6 years (SD ±12.1 years), with the average age at presentation to the clinic of 22.4 years (SD ±14.10 years). Forty-seven (41.9%) patients had a positive genetic test result, 53 (47.3%) had one or more variants of uncertain significance (VUS), and 12 (10.7%) had a negative result. Upon further genotype-phenotype correlation and family segregation analysis, the diagnostic yield improved, with 59 (52.7%) patients reaching a diagnosis of a hereditary NMD. We also report probable founder variants in COL6A2, FKTN, GNE, and SGCB, previously reported in populations that have possible shared ancestry with the Pakistani population. Our findings reemphasizes that the rate of VUSs can be reduced by clinical correlation and family segregation studies.
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Affiliation(s)
- Fizza Akbar
- Division of Women and Child Health, The Aga Khan University, Karachi, Pakistan
| | | | | | - Shahnaz Ibrahim
- Department of Paediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Bushra Afroze
- Department of Paediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Salman Kirmani
- Division of Women and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Sara Khan
- Department of Neurology, The Aga Khan University, Karachi, Pakistan
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2
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Barthélémy F, Santoso JW, Rabichow L, Jin R, Little I, Nelson SF, McCain ML, Miceli MC. Modeling Patient-Specific Muscular Dystrophy Phenotypes and Therapeutic Responses in Reprogrammed Myotubes Engineered on Micromolded Gelatin Hydrogels. Front Cell Dev Biol 2022; 10:830415. [PMID: 35465312 PMCID: PMC9020228 DOI: 10.3389/fcell.2022.830415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/22/2022] [Indexed: 11/24/2022] Open
Abstract
In vitro models of patient-derived muscle allow for more efficient development of genetic medicines for the muscular dystrophies, which often present mutation-specific pathologies. One popular strategy to generate patient-specific myotubes involves reprogramming dermal fibroblasts to a muscle lineage through MyoD induction. However, creating physiologically relevant, reproducible tissues exhibiting multinucleated, aligned myotubes with organized striations is dependent on the introduction of physicochemical cues that mimic the native muscle microenvironment. Here, we engineered patient-specific control and dystrophic muscle tissues in vitro by culturing and differentiating MyoD–directly reprogrammed fibroblasts isolated from one healthy control subject, three patients with Duchenne muscular dystrophy (DMD), and two Limb Girdle 2A/R1 (LGMD2A/R1) patients on micromolded gelatin hydrogels. Engineered DMD and LGMD2A/R1 tissues demonstrated varying levels of defects in α-actinin expression and organization relative to control, depending on the mutation. In genetically relevant DMD tissues amenable to mRNA reframing by targeting exon 44 or 45 exclusion, exposure to exon skipping antisense oligonucleotides modestly increased myotube coverage and alignment and rescued dystrophin protein expression. These findings highlight the value of engineered culture substrates in guiding the organization of reprogrammed patient fibroblasts into aligned muscle tissues, thereby extending their value as tools for exploration and dissection of the cellular and molecular basis of genetic muscle defects, rescue, and repair.
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Affiliation(s)
- Florian Barthélémy
- Department of Microbiology Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jeffrey W. Santoso
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, United States
| | - Laura Rabichow
- Department of Microbiology Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, United States
| | - Rongcheng Jin
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, United States
| | - Isaiah Little
- Department of Microbiology Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, United States
| | - Stanley F. Nelson
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Megan L. McCain
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, United States
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, United States
- *Correspondence: M. Carrie Miceli, ; Megan L. McCain,
| | - M. Carrie Miceli
- Department of Microbiology Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, United States
- *Correspondence: M. Carrie Miceli, ; Megan L. McCain,
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3
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Chakravorty S, Nallamilli BRR, Khadilkar SV, Singla MB, Bhutada A, Dastur R, Gaitonde PS, Rufibach LE, Gloster L, Hegde M. Clinical and Genomic Evaluation of 207 Genetic Myopathies in the Indian Subcontinent. Front Neurol 2020; 11:559327. [PMID: 33250842 PMCID: PMC7674836 DOI: 10.3389/fneur.2020.559327] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Objective: Inherited myopathies comprise more than 200 different individually rare disease-subtypes, but when combined together they have a high prevalence of 1 in 6,000 individuals across the world. Our goal was to determine for the first time the clinical- and gene-variant spectrum of genetic myopathies in a substantial cohort study of the Indian subcontinent. Methods: In this cohort study, we performed the first large clinical exome sequencing (ES) study with phenotype correlation on 207 clinically well-characterized inherited myopathy-suspected patients from the Indian subcontinent with diverse ethnicities. Results: Clinical-correlation driven definitive molecular diagnosis was established in 49% (101 cases; 95% CI, 42–56%) of patients with the major contributing pathogenicity in either of three genes, GNE (28%; GNE-myopathy), DYSF (25%; Dysferlinopathy), and CAPN3 (19%; Calpainopathy). We identified 65 variant alleles comprising 37 unique variants in these three major genes. Seventy-eight percent of the DYSF patients were homozygous for the detected pathogenic variant, suggesting the need for carrier-testing for autosomal-recessive disorders like Dysferlinopathy that are common in India. We describe the observed clinical spectrum of myopathies including uncommon and rare subtypes in India: Sarcoglycanopathies (SGCA/B/D/G), Collagenopathy (COL6A1/2/3), Anoctaminopathy (ANO5), telethoninopathy (TCAP), Pompe-disease (GAA), Myoadenylate-deaminase-deficiency-myopathy (AMPD1), myotilinopathy (MYOT), laminopathy (LMNA), HSP40-proteinopathy (DNAJB6), Emery-Dreifuss-muscular-dystrophy (EMD), Filaminopathy (FLNC), TRIM32-proteinopathy (TRIM32), POMT1-proteinopathy (POMT1), and Merosin-deficiency-congenital-muscular-dystrophy-type-1 (LAMA2). Thirteen patients harbored pathogenic variants in >1 gene and had unusual clinical features suggesting a possible role of synergistic-heterozygosity/digenic-contribution to disease presentation and progression. Conclusions: Application of clinically correlated ES to myopathy diagnosis has improved our understanding of the clinical and genetic spectrum of different subtypes and their overlaps in Indian patients. This, in turn, will enhance the global gene-variant-disease databases by including data from developing countries/continents for more efficient clinically driven molecular diagnostics.
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Affiliation(s)
- Samya Chakravorty
- Emory University Department of Pediatrics, Atlanta, GA, United States.,Emory University Department of Human Genetics, Atlanta, GA, United States.,Division of Neurosciences, Children's Healthcare of Atlanta, Atlanta, GA, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | | | - Satish Vasant Khadilkar
- Department of Neurology, Bombay Hospital, Mumbai, India.,Department of Neurology, Sir J J Group of Hospitals, Grant Medical College, Mumbai, India.,Bombay Hospital Institute of Medical Sciences, Mumbai, India
| | - Madhu Bala Singla
- Department of Neurology, Bombay Hospital, Mumbai, India.,Department of Neurology, Sir J J Group of Hospitals, Grant Medical College, Mumbai, India.,Bombay Hospital Institute of Medical Sciences, Mumbai, India
| | | | - Rashna Dastur
- Centre for Advanced Molecular Diagnostics in Neuromuscular Disorders (CAMDND), Mumbai, India
| | - Pradnya Satish Gaitonde
- Centre for Advanced Molecular Diagnostics in Neuromuscular Disorders (CAMDND), Mumbai, India
| | | | - Logan Gloster
- Emory University Department of Pediatrics, Atlanta, GA, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Madhuri Hegde
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,PerkinElmer Genomics, Global Laboratory Services, Waltham, MA, United States
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European muscle MRI study in limb girdle muscular dystrophy type R1/2A (LGMDR1/LGMD2A). J Neurol 2019; 267:45-56. [PMID: 31555977 DOI: 10.1007/s00415-019-09539-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Limb girdle muscular dystrophy type R1/2A (LGMDR1/LGMD2A) is a progressive myopathy caused by deficiency of calpain 3, a calcium-dependent cysteine protease of skeletal muscle, and it represents the most frequent type of LGMD worldwide. In the last few years, muscle magnetic resonance imaging (MRI) has been proposed as a tool for identifying patterns of muscular involvement in genetic disorders and as a biomarker of disease progression in muscle diseases. In this study, 57 molecularly confirmed LGMDR1 patients from a European cohort (age range 7-78 years) underwent muscle MRI and a global evaluation of functional status (Gardner-Medwin and Walton score and ability to raise the arms). RESULTS We confirmed a specific pattern of fatty substitution involving predominantly the hip adductors and hamstrings in lower limbs. Spine extensors were more severely affected than spine rotators, in agreement with higher incidence of lordosis than scoliosis in LGMDR1. Hierarchical clustering of lower limb MRI scores showed that involvement of anterior thigh muscles discriminates between classes of disease progression. Severity of muscle fatty substitution was significantly correlated with CAPN3 mutations: in particular, patients with no or one "null" alleles showed a milder involvement, compared to patients with two null alleles (i.e., predicting absence of calpain-3 protein). Expectedly, fat infiltration scores strongly correlated with functional measures. The "pseudocollagen" sign (central areas of sparing in some muscle) was associated with longer and more severe disease course. CONCLUSIONS We conclude that skeletal muscle MRI represents a useful tool in the diagnostic workup and clinical management of LGMDR1.
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Angelini C, Fanin M. Limb girdle muscular dystrophies: clinical-genetical diagnostic update and prospects for therapy. Expert Opin Orphan Drugs 2017. [DOI: 10.1080/21678707.2017.1367283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Corrado Angelini
- Department of Neurodegenerative Disorders, Neuromuscular Center, San Camillo Hospital IRCCS, Venice, Italy
| | - Marina Fanin
- Department of Neurosciences, University of Padova, Padova, Italy
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6
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Redox state and mitochondrial respiratory chain function in skeletal muscle of LGMD2A patients. PLoS One 2014; 9:e102549. [PMID: 25079074 PMCID: PMC4117472 DOI: 10.1371/journal.pone.0102549] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 06/19/2014] [Indexed: 11/30/2022] Open
Abstract
Background Calpain-3 deficiency causes oxidative and nitrosative stress-induced damage in skeletal muscle of LGMD2A patients, but mitochondrial respiratory chain function and anti-oxidant levels have not been systematically assessed in this clinical population previously. Methods We identified 14 patients with phenotypes consistent with LGMD2A and performed CAPN3 gene sequencing, CAPN3 expression/autolysis measurements, and insilico predictions of pathogenicity. Oxidative damage, anti-oxidant capacity, and mitochondrial enzyme activities were determined in a subset of muscle biopsies. Results Twenty-one disease-causing variants were detected along the entire CAPN3 gene, five of which were novel (c.338 T>C, c.500 T>C, c.1525-1 G>T, c.2115+4 T>G, c.2366 T>A). Protein- and mRNA-based tests confirmed insilico predictions and the clinical diagnosis in 75% of patients. Reductions in antioxidant defense mechanisms (SOD-1 and NRF-2, but not SOD-2), coupled with increased lipid peroxidation and protein ubiquitination, were observed in calpain-3 deficient muscle, indicating a redox imbalance primarily affecting non-mitochondrial compartments. Although ATP synthase levels were significantly lower in LGMD2A patients, citrate synthase, cytochrome c oxidase, and complex I+III activities were not different from controls. Conclusions Despite significant oxidative damage and redox imbalance in cytosolic/myofibrillar compartments, mitochondrial respiratory chain function is largely maintained in skeletal muscle of LGMD2A patients.
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Gallardo E, Saenz A, Illa I. Limb-girdle muscular dystrophy 2A. HANDBOOK OF CLINICAL NEUROLOGY 2011; 101:97-110. [PMID: 21496626 DOI: 10.1016/b978-0-08-045031-5.00006-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Limb-girdle muscular dystrophy type 2A (LGMD2A) is caused by mutations in the gene CAPN3 located in the chromosome region 15q15.1-q21.1. To date more than 300 mutations have been described. This gene encodes for a 94-kDa nonlysosomal calcium-dependent cysteine protease and its function in skeletal muscle is not fully understood. It seems that calpain-3 has an unusual zymogenic activation that involves, among other substrates, cytoskeletal proteins. Calpain-3 is thought to interact with titin and dysferlin. Calpain-3 deficiency produces abnormal sarcomeres that lead eventually to muscle fiber death. Hip adductors and gluteus maximus are the earliest clinically affected muscles. No clinical differences have been reported depending on the type of mutation in the CAPN3 gene. The muscle biopsy shows variability of fiber size, interstitial fibrosis, internal nuclei, lobulated fibers, and, in some cases, presence of eosinophils. Recent gene expression profiling studies have shown upregulation of interleukin-32 and immunoglobulin genes, which may explain the eosinophilic infiltration. Two mouse knockout models of CAPN3 have been characterized. There are no curative treatments for this disease. However, experimental therapeutics using mouse models conclude that adeno-associated virus (AAV) vectors seem to be one of the best approaches because of their efficiency and persistency of gene transfer.
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Affiliation(s)
- Eduard Gallardo
- Department of Neurology and Laboratory of Experimental Neurology, Hospital de la Santa Creu i Sant Pau and Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
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8
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Papić L, Fischer D, Trajanoski S, Höftberger R, Fischer C, Ströbel T, Schmidt WM, Bittner RE, Schabhüttl M, Gruber K, Pieber TR, Janecke AR, Auer-Grumbach M. SNP-array based whole genome homozygosity mapping: a quick and powerful tool to achieve an accurate diagnosis in LGMD2 patients. Eur J Med Genet 2010; 54:214-9. [PMID: 21172462 PMCID: PMC3085821 DOI: 10.1016/j.ejmg.2010.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 12/04/2010] [Indexed: 12/20/2022]
Abstract
A large number of novel disease genes have been identified by homozygosity mapping and the positional candidate approach. In this study we used single nucleotide polymorphism (SNP) array-based, whole genome homozygosity mapping as the first step to a molecular diagnosis in the highly heterogeneous muscle disease, limb girdle muscular dystrophy (LGMD). In a consanguineous family, both affected siblings showed homozygous blocks on chromosome 15 corresponding to the LGMD2A locus. Direct sequencing of CAPN3, encoding calpain-3, identified a homozygous deletion c.483delG (p.Ile162SerfsX17). In a sporadic LGMD patient complete absence of caveolin-3 on Western blot was observed. However, a mutation in CAV3 could not be detected. Homozygosity mapping revealed a large homozygous block at the LGMD2I locus, and direct sequencing of FKRP encoding fukutin-related-protein detected the common homozygous c.826 C > A (p.Leu276Ile) mutation. Subsequent re-examination of this patient's muscle biopsy showed aberrant α-dystroglycan glycosylation. In summary, we show that whole-genome homozygosity mapping using low cost SNP arrays provides a fast and non-invasive method to identify disease-causing mutations in sporadic patients or sibs from consanguineous families in LGMD2. Furthermore, this is the first study describing that in addition to PTRF, encoding polymerase I and transcript release factor, FKRP mutations may cause secondary caveolin-3 deficiency.
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Affiliation(s)
- Lea Papić
- Department of Internal Medicine, Division of Diabetes and Metabolism, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
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9
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Nascimbeni AC, Fanin M, Tasca E, Angelini C. Transcriptional and translational effects of intronic CAPN3 gene mutations. Hum Mutat 2010; 31:E1658-69. [PMID: 20635405 PMCID: PMC2966865 DOI: 10.1002/humu.21320] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Variants of unknown significance in the CAPN3 gene constitute a significant challenge for genetic counselling. Despite the frequency of intronic nucleotide changes in this gene (15-25% of all mutations), so far their pathogenicity has only been inferred by in-silico analysis, and occasionally, proven by RNA analysis. In this study, 5 different intronic variants (one novel) that bioinformatic tools predicted would affect RNA splicing, underwent comprehensive studies which were designed to prove they are disease-causing. Muscle mRNA from 15 calpainopathy patients was analyzed by RT-PCR and splicing-specific-PCR tests. We established the previously unrecognized pathogenicity of these mutations, which caused aberrant splicing, most frequently by the activation of cryptic splicing sites or, occasionally, by exon skipping. The absence or severe reduction of protein demonstrated their deleterious effect at translational level. We concluded that bioinformatic tools are valuable to suggest the potential effects of intronic variants; however, the experimental demonstration of the pathogenicity is not always easy to do even when using RNA analysis (low abundance, degradation mechanisms), and it might not be successful unless splicing-specific-PCR tests are used. A comprehensive approach is therefore recommended to identify and describe unclassified variants in order to offer essential data for basic and clinical geneticists.
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10
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de Morrée A, Lutje Hulsik D, Impagliazzo A, van Haagen HHHBM, de Galan P, van Remoortere A, 't Hoen PAC, van Ommen GB, Frants RR, van der Maarel SM. Calpain 3 is a rapid-action, unidirectional proteolytic switch central to muscle remodeling. PLoS One 2010; 5:e11940. [PMID: 20694146 PMCID: PMC2915920 DOI: 10.1371/journal.pone.0011940] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 06/16/2010] [Indexed: 11/24/2022] Open
Abstract
Calpain 3 (CAPN3) is a cysteine protease that when mutated causes Limb Girdle Muscular Dystrophy 2A. It is thereby the only described Calpain family member that genetically causes a disease. Due to its inherent instability little is known of its substrates or its mechanism of activity and pathogenicity. In this investigation we define a primary sequence motif underlying CAPN3 substrate cleavage. This motif can transform non-related proteins into substrates, and identifies >300 new putative CAPN3 targets. Bioinformatic analyses of these targets demonstrate a critical role in muscle cytoskeletal remodeling and identify novel CAPN3 functions. Among the new CAPN3 substrates are three E3 SUMO ligases of the Protein Inhibitor of Activated Stats (PIAS) family. CAPN3 can cleave PIAS proteins and negatively regulates PIAS3 sumoylase activity. Consequently, SUMO2 is deregulated in patient muscle tissue. Our study thus uncovers unexpected crosstalk between CAPN3 proteolysis and protein sumoylation, with strong implications for muscle remodeling.
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Affiliation(s)
- Antoine de Morrée
- Center for Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - David Lutje Hulsik
- Department of Cellular Architecture and Dynamics, Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
| | | | | | - Paula de Galan
- Center for Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Peter A. C. 't Hoen
- Center for Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - GertJan B. van Ommen
- Center for Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rune R. Frants
- Center for Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Guédard-Méreuze SL, Vaché C, Molinari N, Vaudaine J, Claustres M, Roux AF, Tuffery-Giraud S. Sequence contexts that determine the pathogenicity of base substitutions at position +3 of donor splice-sites. Hum Mutat 2009; 30:1329-39. [DOI: 10.1002/humu.21070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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Blázquez L, Azpitarte M, Sáenz A, Goicoechea M, Otaegui D, Ferrer X, Illa I, Gutierrez-Rivas E, Vilchez JJ, López de Munain A. Characterization of novel CAPN3 isoforms in white blood cells: an alternative approach for limb-girdle muscular dystrophy 2A diagnosis. Neurogenetics 2008; 9:173-82. [PMID: 18563459 DOI: 10.1007/s10048-008-0129-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Accepted: 03/26/2008] [Indexed: 10/21/2022]
Abstract
Limb-girdle muscular dystrophy type 2A (LGMD2A) is an autosomal recessive disorder caused by mutations in the CAPN3 gene. Its definitive diagnosis is laborious, since the clinical phenotype is often similar to other types of muscular dystrophy and since the CAPN3 gene encompasses a large genomic region with more than 300 pathogenic mutations described to date. In fact, it is estimated that nearly 25% of the cases with a phenotype suggestive of LGMD2A do not have mutations in the CAPN3 gene and that, in up to 22% of the cases, only one mutation is identified. In the present work, we have characterised CAPN3 messenger RNA (mRNA) expression in peripheral blood, and we have performed a retrospective diagnostic study with 26 LGMD2A patients, sequencing a transcript of CAPN3 present in white blood cells (WBCs). The 25% of the mutations presented in this paper (7/28) act modifying pre-mRNA splicing of the CAPN3 transcript, including the first deep-intronic mutation described to date in the CAPN3 gene. Our results determine that the sequencing of CAPN3 transcripts present in WBCs could be applied as a new approach for LGMD2A diagnosis. This method improves and simplifies diagnosis, since it combines the advantages of mRNA analysis in a more accessible and rapidly regenerated tissue. However, the lack of exon 15 in the CAPN3 isoforms present in blood, and the presence of mRNA degradation make it necessary to combine mRNA and DNA analyses in some specific cases.
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Affiliation(s)
- L Blázquez
- Experimental Unit, Hospital Donostia, San Sebastián, Spain.
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13
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cDNA analyses of CAPN3 enhance mutation detection and reveal a low prevalence of LGMD2A patients in Denmark. Eur J Hum Genet 2008; 16:935-40. [PMID: 18337726 DOI: 10.1038/ejhg.2008.47] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Calpainopathy or limb-girdle muscular dystrophy type 2A (LGMD2A) is generally recognized as the most prevalent form of recessive LGMD and is caused by mutations in the CAPN3 gene. Out of a cohort of 119 patients fulfilling clinical criteria for LGMD2, referred to our neuromuscular clinic, 46 were suspected to have LGMD2A, based on western blot results. Four of these patients were shown to have LGMD2I upon molecular analysis, whereas 16 of the remaining 42 patients harbored mutations in CAPN3 by both direct genomic sequencing and cDNA analyses. In 10 patients, we identified both mutant alleles. In three other, only one heterozygous mutation could be identified on the genomic level; however, CAPN3 cDNA analyses demonstrated homozygosity for the mutant allele, indicating the presence of an unidentified allele that somehow compromise correct CAPN3 RNA processing. In the three remaining patients, only a single heterozygous mutation could be identified both at the genomic level and on full-length CAPN3 cDNA. All three patients exhibited a highly abnormal western blot for calpain-3 and clinical characteristics of LGMD2A. Only three of the genetically confirmed LGMD2A patients were of Danish origin, indicating a five- to sixfold lower prevalence in Denmark compared to other European countries. A total of 16 different CAPN3 mutations were identified, of which 5 were novel. The present study demonstrates the value of cDNA analysis for CAPN3 in LGMD2A patients and indicates that calpainopathy is an uncommon cause of LGMD in the Denmark.
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Abstract
The backbone of the third filament system of the sarcomere is the huge titin molecule, spanning from the sarcomeric Z-disc to the M-line. Proteins in direct interaction and functionally integrated with titin, such as calpain 3 and telethonin, are part of the third filament system. The third filament system provides support to the contractile filament systems during development and mature states including mechanical properties and regulatory signaling functions. The first mutations in the third filament system causing human muscle disease were identified in calpain 3 in 1995, followed by telethonin and titin. In spite of some early ideas on what is going wrong in the muscle cells based on the defective proteins, the exact molecular pathomechanisms leading to muscle atrophy in patients with these disorders are still unknown. However, preparations for direct trials of gene therapy have already been launched, at least for calpainopathy.
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Affiliation(s)
- Bjarne Udd
- Department of Neurology, Tampere University Hospital and Medical School, Tampere, Finland.
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15
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Krahn M, Pécheux C, Chapon F, Béroud C, Drouin-Garraud V, Laforet P, Romero NB, Penisson-Besnier I, Bernard R, Urtizberea JA, Leturcq F, Lévy N. Transcriptional explorations of CAPN3 identify novel splicing mutations, a large-sized genomic deletion and evidence for messenger RNA decay. Clin Genet 2007; 72:582-92. [PMID: 17979987 DOI: 10.1111/j.1399-0004.2007.00906.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mutations in the gene encoding calpain-3 (CAPN3) cause autosomal recessive limb-girdle muscular dystrophy type 2A (LGMD2A) and idiopathic eosinophilic myositis. Accurate diagnosis and genetic counselling are based on the identification of disease-causing mutations on both alleles of CAPN3 in the patients. In the present study, we used transcriptional analysis as a complementary approach for patients suspected of being affected with LGMD2A, in whom initial denaturing high-performance liquid chromatography genomic mutation screening evidenced no or only one CAPN3 mutation obviously considered as disease causing. This allowed to identify and characterize cDNA deletions. Further genomic analysis allowed to determine the origin of these deletions, either as splicing defects caused by intronic mutations or as an internal multi-exonic deletion. In particular, we report two novel CAPN3 mutations (c.1745 + 4_1745 + 7delAGTG in IVS13 and c.2185-16A>G in IVS20) and a recurrent large-sized genomic deletion including exons 2-8 for which genomic breakpoints have been characterized. In addition, our results indicate nonsense-mediated messenger RNA decay as a mechanism for under-expression of CAPN3 associated to some specific variations.
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Affiliation(s)
- M Krahn
- Département de Génétique Médicale, Hôpital d'enfants de la Timone, Marseille, France
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Fanin M, Nardetto L, Nascimbeni AC, Tasca E, Spinazzi M, Padoan R, Angelini C. Correlations between clinical severity, genotype and muscle pathology in limb girdle muscular dystrophy type 2A. J Med Genet 2007; 44:609-14. [PMID: 17526799 PMCID: PMC2597960 DOI: 10.1136/jmg.2007.050328] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Limb girdle muscular dystrophy type 2A (LGMD2A) is characterised by wide variability in clinical features and rate of progression. Patients with two null mutations usually have a rapid course, but in the remaining cases (two missense mutations or compound heterozygote mutations) prognosis is uncertain. METHODS We conducted what is to our knowledge the first systematic histopathological, biochemical and molecular investigation of 24 LGMD2A patients, subdivided according to rapid or slow disease progression, to determine if some parameters could correlate with disease progression. RESULTS We found that muscle histopathology score and the extent of regenerating and degenerating fibres could be correlated with the rate of disease course when the biochemical and molecular data do not offer sufficient information. Comparison of clinical and muscle histopathological data between LGMD2A and four other types of LGMD (LGMD2B-E) also gave another important and novel result. We found that LGMD2A has significantly lower levels of dystrophic features (ie degenerating and regenerating fibres) and higher levels of chronic changes (ie lobulated fibres) compared with other LGMDs, particularly LGMD2B. These results might explain the observation that atrophic muscle involvement seems to be a clinical feature peculiar to LGMD2A patients. CONCLUSIONS Distinguishing patterns of muscle histopathological changes in LGMD2A might reflect the effects of a disease-specific pathogenetic mechanism and provide clues complementary to genetic data.
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Affiliation(s)
- M Fanin
- Venetian Institute of Molecular Medicine, via G. Orus 2, 35129 Padova, Italy.
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Milic A, Daniele N, Lochmüller H, Mora M, Comi GP, Moggio M, Noulet F, Walter MC, Morandi L, Poupiot J, Roudaut C, Bittner RE, Bartoli M, Richard I. A third of LGMD2A biopsies have normal calpain 3 proteolytic activity as determined by an in vitro assay. Neuromuscul Disord 2007; 17:148-56. [PMID: 17236769 DOI: 10.1016/j.nmd.2006.11.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 11/06/2006] [Accepted: 11/21/2006] [Indexed: 10/23/2022]
Abstract
Limb-girdle muscular dystrophy type 2A (LGMD2A) is an autosomal recessive muscular disorder caused by mutations in the gene coding for calpain 3, a calcium-dependent protease. We developed an in vitro assay that can detect the proteolytic activity of calpain 3 in a muscle sample. This assay is based on the use of an inactive calpain 3 as a substrate for active calpain 3 molecules. A total of 79 human biopsies have been analysed using an unbiased single blind method. Results were confronted with the molecular diagnosis for confirmation. Proteolytic activity was either reduced or absent in 68% of LGMD2A biopsies. In the remaining 32%, normal proteolytic activity was found despite the presence of calpain 3 mutation(s), suggesting that other calpain 3 properties might be impaired to give rise to the LGMD2A phenotype. Our assay is easily adaptable to routine and appears to be more sensitive than common analysis by immunodetection.
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Affiliation(s)
- Astrid Milic
- Laboratory of Clinical Neurogenetics and Muscular Disorders, Zagreb University School of Medicine, Croatian Institute for Brain Research, Salata 12, 10000 Zagreb, Croatia
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