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Silverstein S, Orbach R, Syeda S, Foley AR, Gorokhova S, Meilleur KG, Leach ME, Uapinyoying P, Chao KR, Donkervoort S, Bönnemann CG. Differential inclusion of NEB exons 143 and 144 provides insight into NEB-related myopathy variant interpretation and disease manifestation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.25.24304535. [PMID: 38585796 PMCID: PMC10996755 DOI: 10.1101/2024.03.25.24304535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Biallelic pathogenic variants in the gene encoding nebulin (NEB) are a known cause of congenital myopathy. We present two individuals with congenital myopathy and compound heterozygous variants (NM_001271208.2: c.2079C>A; p.(Cys693Ter) and c.21522+3A>G ) in NEB. Transcriptomic sequencing on patient muscle revealed that the extended splice variant c.21522+3A>G causes exon 144 skipping. Nebulin isoforms containing exon 144 are known to be mutually exclusive with isoforms containing exon 143, and these isoforms are differentially expressed during development and in adult skeletal muscles. Patients MRIs were compared to the known pattern of relative abundance of these two isoforms in muscle. We propose that the pattern of muscle involvement in these patients better fits the distribution of exon 144-containing isoforms in muscle than with previously published MRI findings in NEB-related disease due to other variants. To our knowledge this is the first report hypothesizing disease pathogenesis through the alteration of isoform distributions in muscle.
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Affiliation(s)
- Sarah Silverstein
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
- Rutgers New Jersey School of Medicine, 185 S Orange Ave Newark NJ 07103 USA
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland 20892, USA
| | - Rotem Orbach
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Safoora Syeda
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Svetlana Gorokhova
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
- Department of Medical Genetics, Timone Children’s Hospital, APHM, Marseille, France
| | - Katherine G. Meilleur
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
- Biogen, Boston MA
| | - Meganne E. Leach
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
- Division of Neurology, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd, Portland, OR
| | - Prech Uapinyoying
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
- Research Center for Genetic Medicine, Children’s National Research Institute, Children’s National Medical Center, Washington DC 20010
| | - Katherine R Chao
- Broad Institute of MIT and Harvard, 415 Main St. Cambridge MA 02142
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Carsten G. Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
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Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflight. Skelet Muscle 2022; 12:11. [PMID: 35642060 PMCID: PMC9153194 DOI: 10.1186/s13395-022-00294-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As the interest in manned spaceflight increases, so does the requirement to understand the transcriptomic mechanisms that underlay the detrimental physiological adaptations of skeletal muscle to microgravity. While microgravity-induced differential gene expression (DGE) has been extensively investigated, the contribution of differential alternative splicing (DAS) to the plasticity and functional status of the skeletal muscle transcriptome has not been studied in an animal model. Therefore, by evaluating both DGE and DAS across spaceflight, we set out to provide the first comprehensive characterization of the transcriptomic landscape of skeletal muscle during exposure to microgravity. METHODS RNA-sequencing, immunohistochemistry, and morphological analyses were conducted utilizing total RNA and tissue sections isolated from the gastrocnemius and quadriceps muscles of 30-week-old female BALB/c mice exposed to microgravity or ground control conditions for 9 weeks. RESULTS In response to microgravity, the skeletal muscle transcriptome was remodeled via both DGE and DAS. Importantly, while DGE showed variable gene network enrichment, DAS was enriched in structural and functional gene networks of skeletal muscle, resulting in the expression of alternatively spliced transcript isoforms that have been associated with the physiological changes to skeletal muscle in microgravity, including muscle atrophy and altered fiber type function. Finally, RNA-binding proteins, which are required for regulation of pre-mRNA splicing, were themselves differentially spliced but not differentially expressed, an upstream event that is speculated to account for the downstream splicing changes identified in target skeletal muscle genes. CONCLUSIONS Our work serves as the first investigation of coordinate changes in DGE and DAS in large limb muscles across spaceflight. It opens up a new opportunity to understand (i) the molecular mechanisms by which splice variants of skeletal muscle genes regulate the physiological adaptations of skeletal muscle to microgravity and (ii) how small molecule splicing regulator therapies might thwart muscle atrophy and alterations to fiber type function during prolonged spaceflight.
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3
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Laflamme N, Lace B, Thonta Setty S, Rioux N, Labrie Y, Droit A, Chrestian N, Rivest S. A Homozygous Deep Intronic Mutation Alters the Splicing of Nebulin Gene in a Patient With Nemaline Myopathy. Front Neurol 2021; 12:660113. [PMID: 34211429 PMCID: PMC8239344 DOI: 10.3389/fneur.2021.660113] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
Nemaline myopathy is a rare disorder affecting the muscle sarcomere. Mutations in nebulin gene (NEB) are known to be responsible for about 50% of nemaline myopathy cases. Nebulin is a giant protein which is formed integrally with the sarcomeric thin filament. This complex gene is under extensive alternative splicing giving rise to multiple isoforms. In this study, we report a 6-year-old boy presenting with general muscular weaknesses. Identification of rod-shaped structures in the patient' biopsy raised doubt about the presence of a nemaline myopathy. Next-generation sequencing was used to identify a causative mutation for the patient syndrome. A homozygous deep intronic substitution was found in the intron 144 of the NEB. The variant was predicted by in silico tools to create a new donor splice site. Molecular analysis has shown that the mutation could alter splicing events of the nebulin gene leading to a significant decrease of isoforms level. This change in the expression level of nebulin could give rise to functional consequences in the sarcomere. These results are consistent with the phenotypes observed in the patient. Such a discovery of variants in this gene will allow a better understanding of the involvement of nebulin in neuromuscular diseases and help find new treatments for the nemaline myopathy.
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Affiliation(s)
- Nathalie Laflamme
- Centre de recherche CHU de Québec- Laval University, Quebec City, QC, Canada
| | - Baiba Lace
- Department of Medical Genetics, Centre Mère Enfant Soleil, Laval University, Quebec City, QC, Canada
| | | | - Nadie Rioux
- Centre de recherche CHU de Québec- Laval University, Quebec City, QC, Canada
| | - Yvan Labrie
- Centre de recherche CHU de Québec- Laval University, Quebec City, QC, Canada
| | - Arnaud Droit
- Centre de recherche CHU de Québec- Laval University, Quebec City, QC, Canada
| | - Nicolas Chrestian
- Department of Pediatric Neurology, Pediatric Neuromuscular Disorder, Centre Mère Enfant Soleil, Laval University, Quebec City, QC, Canada
| | - Serge Rivest
- Centre de recherche CHU de Québec- Laval University, Quebec City, QC, Canada
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4
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Kiss B, Gohlke J, Tonino P, Hourani Z, Kolb J, Strom J, Alekhina O, Smith JE, Ottenheijm C, Gregorio C, Granzier H. Nebulin and Lmod2 are critical for specifying thin-filament length in skeletal muscle. SCIENCE ADVANCES 2020; 6:6/46/eabc1992. [PMID: 33177085 PMCID: PMC7673738 DOI: 10.1126/sciadv.abc1992] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 09/23/2020] [Indexed: 06/07/2023]
Abstract
Regulating the thin-filament length in muscle is crucial for controlling the number of myosin motors that generate power. The giant protein nebulin forms a long slender filament that associates along the length of the thin filament in skeletal muscle with functions that remain largely obscure. Here nebulin's role in thin-filament length regulation was investigated by targeting entire super-repeats in the Neb gene; nebulin was either shortened or lengthened by 115 nm. Its effect on thin-filament length was studied using high-resolution structural and functional techniques. Results revealed that thin-filament length is strictly regulated by the length of nebulin in fast muscles. Nebulin's control is less tight in slow muscle types where a distal nebulin-free thin-filament segment exists, the length of which was found to be regulated by leiomodin-2 (Lmod2). We propose that strict length control by nebulin promotes high-speed shortening and that dual-regulation by nebulin/Lmod2 enhances contraction efficiency.
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Affiliation(s)
- Balázs Kiss
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Jochen Gohlke
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Paola Tonino
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Zaynab Hourani
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Justin Kolb
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Joshua Strom
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Olga Alekhina
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - John E Smith
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Coen Ottenheijm
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Carol Gregorio
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Henk Granzier
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85721, USA.
- Allan and Alfie Endowed Chair for Heart Disease in Women Research, Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ 85721, USA
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5
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Uapinyoying P, Goecks J, Knoblach SM, Panchapakesan K, Bonnemann CG, Partridge TA, Jaiswal JK, Hoffman EP. A long-read RNA-seq approach to identify novel transcripts of very large genes. Genome Res 2020; 30:885-897. [PMID: 32660935 PMCID: PMC7370890 DOI: 10.1101/gr.259903.119] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/22/2020] [Indexed: 12/15/2022]
Abstract
RNA-seq is widely used for studying gene expression, but commonly used sequencing platforms produce short reads that only span up to two exon junctions per read. This makes it difficult to accurately determine the composition and phasing of exons within transcripts. Although long-read sequencing improves this issue, it is not amenable to precise quantitation, which limits its utility for differential expression studies. We used long-read isoform sequencing combined with a novel analysis approach to compare alternative splicing of large, repetitive structural genes in muscles. Analysis of muscle structural genes that produce medium (Nrap: 5 kb), large (Neb: 22 kb), and very large (Ttn: 106 kb) transcripts in cardiac muscle, and fast and slow skeletal muscles identified unannotated exons for each of these ubiquitous muscle genes. This also identified differential exon usage and phasing for these genes between the different muscle types. By mapping the in-phase transcript structures to known annotations, we also identified and quantified previously unannotated transcripts. Results were confirmed by endpoint PCR and Sanger sequencing, which revealed muscle-type-specific differential expression of these novel transcripts. The improved transcript identification and quantification shown by our approach removes previous impediments to studies aimed at quantitative differential expression of ultralong transcripts.
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Affiliation(s)
- Prech Uapinyoying
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA.,Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, D.C. 20052, USA.,Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jeremy Goecks
- Computational Biology Program, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Susan M Knoblach
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA.,Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, D.C. 20052, USA
| | - Karuna Panchapakesan
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA
| | - Carsten G Bonnemann
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA.,Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Terence A Partridge
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA.,Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, D.C. 20052, USA
| | - Jyoti K Jaiswal
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA.,Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, D.C. 20052, USA
| | - Eric P Hoffman
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA.,Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, New York 13902, USA
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6
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Cox DC, Guan X, Xia Z, Cooper TA. Increased nuclear but not cytoplasmic activities of CELF1 protein leads to muscle wasting. Hum Mol Genet 2020; 29:1729-1744. [PMID: 32412585 PMCID: PMC7322576 DOI: 10.1093/hmg/ddaa095] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/16/2020] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
mRNA processing is highly regulated during development through changes in RNA-binding protein (RBP) activities. CUG-BP, Elav-like family member 1 (CELF1, also called CUGBP1) is an RBP, the expression of which decreases in skeletal muscle soon after birth. CELF1 regulates multiple nuclear and cytoplasmic RNA processing events. In the nucleus, CELF1 regulates networks of postnatal alternative splicing (AS) transitions, while in the cytoplasm, CELF1 regulates mRNA stability and translation. Stabilization and misregulation of CELF1 has been implicated in human diseases including myotonic dystrophy type 1, Alzheimer's disease and multiple cancers. To understand the contribution of nuclear and cytoplasmic CELF1 activity to normal and pathogenic skeletal muscle biology, we generated transgenic mice for doxycycline-inducible and skeletal muscle-specific expression of active CELF1 mutants engineered to be localized predominantly to either the nucleus or the cytoplasm. Adult mice expressing nuclear, but not cytoplasmic, CELF1 are characterized by strong histopathological defects, muscle loss within 10 days and changes in AS. In contrast, mice expressing cytoplasmic CELF1 display changes in protein levels of targets known to be regulated at the level of translation by CELF1, with minimal changes in AS. These changes are in the absence of overt histopathological changes or muscle loss. RNA-sequencing revealed extensive gene expression and AS changes in mice overexpressing nuclear and naturally localized CELF1 protein, with affected genes involved in cytoskeleton dynamics, membrane dynamics, RNA processing and zinc ion binding. These results support a stronger role for nuclear CELF1 functions as compared to cytoplasmic CELF1 functions in skeletal muscle wasting.
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Affiliation(s)
- Diana C Cox
- Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Biochemistry & Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Xiangnan Guan
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239 USA
| | - Zheng Xia
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239 USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Thomas A Cooper
- Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular Physiology & Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular & Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston TX, 77030 USA
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7
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Lam LT, Holt I, Laitila J, Hanif M, Pelin K, Wallgren-Pettersson C, Sewry CA, Morris GE. Two alternatively-spliced human nebulin isoforms with either exon 143 or exon 144 and their developmental regulation. Sci Rep 2018; 8:15728. [PMID: 30356055 PMCID: PMC6200726 DOI: 10.1038/s41598-018-33281-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/07/2018] [Indexed: 11/09/2022] Open
Abstract
Nebulin is a very large protein required for assembly of the contractile machinery in muscle. Mutations in the nebulin gene NEB are a common cause of nemaline myopathy. Nebulin mRNA is alternatively-spliced so that each mRNA contains either exon 143 or exon 144. We have produced monoclonal antibodies specific for the regions of nebulin encoded by these two exons, enabling analysis of expression of isoforms at the protein level for the first time. All antibodies recognized a protein of the expected size (600–900 kD) and stained cross-striations of sarcomeres in muscle sections. Expression of exon 143 is developmentally-regulated since newly-formed myotubes in cell culture expressed nebulin with exon 144 only; this was confirmed at the mRNA level by qPCR. In fetal muscle, nebulin with exon 143 was expressed in some myotubes by 12-weeks of gestation and strongly-expressed in most myotubes by 17-weeks. In mature human muscle, the exon 144 antibody stained all fibres, but the exon 143 antibody staining varied from very strong in some fibres to almost-undetectable in other fibres. The results show that nebulin containing exon 144 is the default isoform early in myogenesis, while regulated expression of nebulin containing exon 143 occurs at later stages of muscle development.
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Affiliation(s)
- Le Thanh Lam
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK
| | - Ian Holt
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK.,Institute for Science and Technology in Medicine, Keele University, Keele, UK
| | - Jenni Laitila
- The Folkhälsan Institute of Genetics, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Mubashir Hanif
- The Folkhälsan Institute of Genetics, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Katarina Pelin
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Carina Wallgren-Pettersson
- The Folkhälsan Institute of Genetics, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Caroline A Sewry
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK.,Dubowitz Neuromuscular Centre, Institute for Child Health and Great Ormond Street Hospital, London, UK
| | - Glenn E Morris
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK. .,Institute for Science and Technology in Medicine, Keele University, Keele, UK.
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Abstract
In this review we discuss the history and the current state of ideas related to the mechanism of size regulation of the thick (myosin) and thin (actin) filaments in vertebrate striated muscles. Various hypotheses have been considered during of more than half century of research, recently mostly involving titin and nebulin acting as templates or 'molecular rulers', terminating exact assembly. These two giant, single-polypeptide, filamentous proteins are bound in situ along the thick and thin filaments, respectively, with an almost perfect match in the respective lengths and structural periodicities. However, evidence still questions the possibility that the proteins function as templates, or scaffolds, on which the thin and thick filaments could be assembled. In addition, the progress in muscle research during the last decades highlighted a number of other factors that could potentially be involved in the mechanism of length regulation: molecular chaperones that may guide folding and assembly of actin and myosin; capping proteins that can influence the rates of assembly-disassembly of the myofilaments; Ca2+ transients that can activate or deactivate protein interactions, etc. The entire mechanism of sarcomere assembly appears complex and highly dynamic. This mechanism is also capable of producing filaments of about the correct size without titin and nebulin. What then is the role of these proteins? Evidence points to titin and nebulin stabilizing structures of the respective filaments. This stabilizing effect, based on linear proteins of a fixed size, implies that titin and nebulin are indeed molecular rulers of the filaments. Although the proteins may not function as templates in the assembly of the filaments, they measure and stabilize exactly the same size of the functionally important for the muscles segments in each of the respective filaments.
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9
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Lehtokari VL, Kiiski K, Sandaradura SA, Laporte J, Repo P, Frey JA, Donner K, Marttila M, Saunders C, Barth PG, den Dunnen JT, Beggs AH, Clarke NF, North KN, Laing NG, Romero NB, Winder TL, Pelin K, Wallgren-Pettersson C. Mutation update: the spectra of nebulin variants and associated myopathies. Hum Mutat 2015; 35:1418-26. [PMID: 25205138 DOI: 10.1002/humu.22693] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 08/29/2014] [Indexed: 12/23/2022]
Abstract
A mutation update on the nebulin gene (NEB) is necessary because of recent developments in analysis methodology, the identification of increasing numbers and novel types of variants, and a widening in the spectrum of clinical and histological phenotypes associated with this gigantic, 183 exons containing gene. Recessive pathogenic variants in NEB are the major cause of nemaline myopathy (NM), one of the most common congenital myopathies. Moreover, pathogenic NEB variants have been identified in core-rod myopathy and in distal myopathies. In this update, we present the disease-causing variants in NEB in 159 families, 143 families with NM, and 16 families with NM-related myopathies. Eighty-eight families are presented here for the first time. We summarize 86 previously published and 126 unpublished variants identified in NEB. Furthermore, we have analyzed the NEB variants deposited in the Exome Variant Server (http://evs.gs.washington.edu/EVS/), identifying that pathogenic variants are a minor fraction of all coding variants (∼7%). This indicates that nebulin tolerates substantial changes in its amino acid sequence, providing an explanation as to why variants in such a large gene result in relatively rare disorders. Lastly, we discuss the difficulties of drawing reliable genotype-phenotype correlations in NEB-associated disease.
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Affiliation(s)
- Vilma-Lotta Lehtokari
- The Folkhälsan Institute of Genetics and the Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland
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10
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A reply to a commentary on identification of the rare compound heterozygous variants in the NEB gene in a Korean family with intellectual disability, epilepsy and early-childhood-onset generalized muscle weakness. J Hum Genet 2015; 60:163-4. [DOI: 10.1038/jhg.2014.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Identification of the rare compound heterozygous variants in the NEB gene in a Korean family with intellectual disability, epilepsy and early-childhood-onset generalized muscle weakness. J Hum Genet 2014; 59:643-7. [PMID: 25296583 DOI: 10.1038/jhg.2014.87] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/03/2014] [Accepted: 09/13/2014] [Indexed: 11/08/2022]
Abstract
We examined a Korean family with complex phenotypes characterized by intellectual disability, epilepsy and early-childhood-onset generalized muscle weakness. Since we did not find any abnormality using several conventional genetic tests for detection of chromosomal aberrations, gene copy number variations and mitochondrial gene mutations, we aimed to identify disease-causing genetic alteration(s) in this family. We conducted whole-exome sequencing (WES) in this family. After filtering the WES data, we compared five exome sequences of two affected siblings, one unaffected sibling and the unaffected parents, and we determined the allele frequency of the identified variants in an Asian population. Finally, we selected one candidate variant pair which is unique in the patients and corresponds to an autosomal recessive genetic model. The two affected siblings had the same compound heterozygous variation in the NEB gene encoding nebulin, which was composed of two different missense variants: c.2603T>C (p.L868P) in exon 27 and c.21340C>T (p.R7114W) in exon 143. We confirmed these variations by Sanger sequencing. On the basis of the fundamental role of nebulin in the brain and skeletal muscles, we concluded that this compound heterozygous NEB variation may be a sound candidate for the disease-causing mutation in this family. Since the patients are characterized by generalized muscle weakness together with neurodevelopmental phenotypes, it is suggested that NEB mutations could manifest more diverse phenotypes than those previously described.
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Laitila J, Hanif M, Paetau A, Hujanen S, Keto J, Somervuo P, Huovinen S, Udd B, Wallgren-Pettersson C, Auvinen P, Hackman P, Pelin K. Expression of multiple nebulin isoforms in human skeletal muscle and brain. Muscle Nerve 2012; 46:730-7. [PMID: 22941678 DOI: 10.1002/mus.23380] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2012] [Indexed: 11/11/2022]
Abstract
INTRODUCTION Nebulin is a large actin-binding protein of the skeletal muscle sarcomere. Multiple isoforms of nebulin are produced from the 183-exon-containing nebulin gene (NEB). Mutations in NEB cause nemaline myopathy, distal myopathy, and core-rod myopathy. METHODS Nebulin mRNA expression was assessed by microarrays and RT-PCR in 21 human leg muscle and 2 brain samples. Protein expression was assessed by immunohistochemistry in 5 regions of 1 brain sample. RESULTS Nebulin isoform diversity is as high in brain as in skeletal muscle. Isoforms with more than 22 super repeats seem to be more common than previously anticipated. Immunohistochemistry showed nebulin expression predominantly in the cytoplasm of pyramidal neurons but also in the cytoplasm of mainly subcortical endothelial cells. CONCLUSIONS Nebulin, as in skeletal muscle, may have a role as an actin filament stabilizer or length regulator in neurons of the human brain, although patients with NEB mutations usually have normal cognition.
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Affiliation(s)
- Jenni Laitila
- Department of Biosciences, Division of Genetics, PO Box 56, University of Helsinki, Helsinki FI-00014, Finland
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13
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Buck D, Hudson BD, Ottenheijm CA, Labeit S, Granzier H. Differential splicing of the large sarcomeric protein nebulin during skeletal muscle development. J Struct Biol 2010; 170:325-33. [PMID: 20176113 PMCID: PMC2856706 DOI: 10.1016/j.jsb.2010.02.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 02/15/2010] [Accepted: 02/16/2010] [Indexed: 01/08/2023]
Abstract
We studied differential splicing of nebulin, a giant filamentous F-actin binding protein (M(r) approximately 700-800kDa) that is found in skeletal muscle. Nebulin spans the thin filament length, its C-terminus is anchored in the Z-disc, and its N-terminal region is located toward the thin filament pointed end. Various lines of evidence indicate that nebulin plays important roles in thin filament and Z-disc structure in skeletal muscle. In the present work we studied nebulin in a range of muscle types during postnatal development and performed transcript studies with a mouse nebulin exon microarray, developed by us, whose results were confirmed by RT-PCR. We also performed protein studies with high-resolution SDS-agarose gels and Western blots, and structural studies with electron microscopy. We found during postnatal development of the soleus muscle major changes in splicing in both the super-repeat region and the Z-disc region of nebulin; interestingly, these changes were absent in other muscle types. Three novel Z-disc exons, previously described in the mouse gene, were upregulated during postnatal development of soleus muscle and this was correlated with a significant increase in Z-disc width. These findings support the view that nebulin plays an important role in Z-disc width regulation. In summary, we discovered changes in both the super-repeat region and the Z-disc region of nebulin, that these changes are muscle-type specific, and that they correlate with differences in sarcomere structure.
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Affiliation(s)
- Danielle Buck
- Depts of Physiology and Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85724, USA
| | - Bryan D. Hudson
- Depts of Physiology and Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85724, USA
| | - Coen A.C. Ottenheijm
- Depts of Physiology and Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85724, USA
- Laboratory for Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam 1081 BT, the Netherlands
| | - Siegfried Labeit
- Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Henk Granzier
- Depts of Physiology and Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85724, USA
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14
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Kontrogianni-Konstantopoulos A, Ackermann MA, Bowman AL, Yap SV, Bloch RJ. Muscle giants: molecular scaffolds in sarcomerogenesis. Physiol Rev 2009; 89:1217-67. [PMID: 19789381 PMCID: PMC3076733 DOI: 10.1152/physrev.00017.2009] [Citation(s) in RCA: 186] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Myofibrillogenesis in striated muscles is a highly complex process that depends on the coordinated assembly and integration of a large number of contractile, cytoskeletal, and signaling proteins into regular arrays, the sarcomeres. It is also associated with the stereotypical assembly of the sarcoplasmic reticulum and the transverse tubules around each sarcomere. Three giant, muscle-specific proteins, titin (3-4 MDa), nebulin (600-800 kDa), and obscurin (approximately 720-900 kDa), have been proposed to play important roles in the assembly and stabilization of sarcomeres. There is a large amount of data showing that each of these molecules interacts with several to many different protein ligands, regulating their activity and localizing them to particular sites within or surrounding sarcomeres. Consistent with this, mutations in each of these proteins have been linked to skeletal and cardiac myopathies or to muscular dystrophies. The evidence that any of them plays a role as a "molecular template," "molecular blueprint," or "molecular ruler" is less definitive, however. Here we review the structure and function of titin, nebulin, and obscurin, with the literature supporting a role for them as scaffolding molecules and the contradictory evidence regarding their roles as molecular guides in sarcomerogenesis.
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15
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Mourkioti F, Slonimsky E, Huth M, Berno V, Rosenthal N. Analysis of CRE-mediated recombination driven by myosin light chain 1/3 regulatory elements in embryonic and adult skeletal muscle: a tool to study fiber specification. Genesis 2008; 46:424-30. [PMID: 18693277 DOI: 10.1002/dvg.20419] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An increasing number of genes have been implicated in skeletal muscle fiber diversity. To study the contribution of diverse genetic elements to the regulation of fiber-type composition, we generated a transgenic mouse in which CRE recombinase expression is driven by muscle-specific regulatory sequences of the myosin light chain 1/3 locus (MLC). Using ROSA26 conditional reporter mice, we detected expression of the MLC-Cre transgene starting from embryonic day 12.5 (E12.5). By E15, recombination was detected in all muscle-derived structures. Immunohistochemical analysis revealed CRE activity was restricted to fast-twitch (type II) and excluded from slow-twitch (type I) fibers of skeletal muscle. The MLC-Cre transgenic mouse can be used in conjunction with conditional alleles to study both developmental patterning and maintenance of fast fiber-type phenotypes.
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16
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Pelin K, Wallgren-Pettersson C. Nebulin—A Giant Chameleon. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008. [DOI: 10.1007/978-0-387-84847-1_3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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