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      Defining and identifying satellite cell-opathies within muscular dystrophies and myopathies

      research-article
      a , ∗∗ , b , c , a , , 1
      Experimental Cell Research
      Academic Press
      Muscle stem cell, Satellite cell, Satellite Cell-opathy, Skeletal muscle, Congenital myopathy, Muscular dystrophy, PAX7, Myopathogene, Carey-Fineman-Ziter Syndrome, CFZS, Creatine Kinase, CK, Duchenne muscular dystrophy, DMD, Dystrophin-Associated Protein Complex, DAPC, Facioscapulohumeral muscular dystrophy, FSHD, Gene Ontologies Satellite Cells, GOSC, Glycogen Storage Disease II, GSD2, Limb-Girdle Muscular Dystrophy Recessive 1, LGMDR1, Myopathy, Areflexia, Respiratory Distress, And Dysphagia, Early-Onset, EMARDD, Myopathy, Congenital, With Diaphragmatic Defects, Respiratory Insufficiency, And Dysmorphic Facies, MYODRIF , Myopathy, Congenital, With Fiber-Type Disproportion, CFTD, Muscular Dystrophy, Congenital, Lmna-Related, MDCL, Muscular Dystrophy, Congenital Merosin-Deficient, 1a MDC1A, Progressive Congenital Myopathy with Scoliosis, MYOSCO, Rigid Spine Muscular Dystrophy 1, RSMD1, Ulrich congenital muscular dystrophy, UCMD

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          Abstract

          Muscular dystrophies and congenital myopathies arise from specific genetic mutations causing skeletal muscle weakness that reduces quality of life. Muscle health relies on resident muscle stem cells called satellite cells, which enable life-course muscle growth, maintenance, repair and regeneration. Such tuned plasticity gradually diminishes in muscle diseases, suggesting compromised satellite cell function. A central issue however, is whether the pathogenic mutation perturbs satellite cell function directly and/or indirectly via an increasingly hostile microenvironment as disease progresses. Here, we explore the effects on satellite cell function of pathogenic mutations in genes (myopathogenes) that associate with muscle disorders, to evaluate clinical and muscle pathological hallmarks that define dysfunctional satellite cells. We deploy transcriptomic analysis and comparison between muscular dystrophies and myopathies to determine the contribution of satellite cell dysfunction using literature, expression dynamics of myopathogenes and their response to the satellite cell regulator PAX7. Our multimodal approach extends current pathological classifications to define Satellite Cell-opathies: muscle disorders in which satellite cell dysfunction contributes to pathology. Primary Satellite Cell-opathies are conditions where mutations in a myopathogene directly affect satellite cell function, such as in Progressive Congenital Myopathy with Scoliosis (MYOSCO) and Carey-Fineman-Ziter Syndrome (CFZS). Primary satellite cell-opathies are generally characterised as being congenital with general hypotonia, and specific involvement of respiratory, trunk and facial muscles, although serum CK levels are usually within the normal range. Secondary Satellite Cell-opathies have mutations in myopathogenes that affect both satellite cells and muscle fibres. Such classification aids diagnosis and predicting probable disease course, as well as informing on treatment and therapeutic development.

          Highlights

          • Muscle homeostasis, growth and repair are impaired in muscular dystrophies and myopathies, exposing satellite cell dysfunction.

          • Our multimodal approach identifies ‘myopathogenes’ in muscle disorders that could directly alter satellite cell function.

          • In ‘Primary Satellite Cell-opathies’ the myopathogene directly affects satellite cell function.

          • In ‘Secondary Satellite Cell-opathies’ the myopathogene affects both the function of satellite cells and muscle fibres.

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          Most cited references241

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          Cytoscape: a software environment for integrated models of biomolecular interaction networks.

          Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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            Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

            A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Successful analysis requires the integration of a broad set of current biological databases and the application of a robust analytical pipeline to produce readily interpretable results. Metascape is a web-based portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists. In terms of design features, Metascape combines functional enrichment, interactome analysis, gene annotation, and membership search to leverage over 40 independent knowledgebases within one integrated portal. Additionally, it facilitates comparative analyses of datasets across multiple independent and orthogonal experiments. Metascape provides a significantly simplified user experience through a one-click Express Analysis interface to generate interpretable outputs. Taken together, Metascape is an effective and efficient tool for experimental biologists to comprehensively analyze and interpret OMICs-based studies in the big data era.
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              PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

              Abstract PANTHER (Protein Analysis Through Evolutionary Relationships, http://pantherdb.org) is a resource for the evolutionary and functional classification of genes from organisms across the tree of life. We report the improvements we have made to the resource during the past two years. For evolutionary classifications, we have added more prokaryotic and plant genomes to the phylogenetic gene trees, expanding the representation of gene evolution in these lineages. We have refined many protein family boundaries, and have aligned PANTHER with the MEROPS resource for protease and protease inhibitor families. For functional classifications, we have developed an entirely new PANTHER GO-slim, containing over four times as many Gene Ontology terms as our previous GO-slim, as well as curated associations of genes to these terms. Lastly, we have made substantial improvements to the enrichment analysis tools available on the PANTHER website: users can now analyze over 900 different genomes, using updated statistical tests with false discovery rate corrections for multiple testing. The overrepresentation test is also available as a web service, for easy addition to third-party sites.
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                Author and article information

                Contributors
                Journal
                Exp Cell Res
                Exp Cell Res
                Experimental Cell Research
                Academic Press
                0014-4827
                1090-2422
                01 February 2022
                01 February 2022
                : 411
                : 1
                : 112906
                Affiliations
                [a ]Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
                [b ]Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, United Kingdom
                [c ]NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, United Kingdom
                Author notes
                []Corresponding author. peter.zammit@ 123456kcl.ac.uk
                [∗∗ ]Corresponding author. massimo.ganassi@ 123456kcl.ac.uk
                [1]

                Lead author for Correspondence

                Article
                S0014-4827(21)00462-6 112906
                10.1016/j.yexcr.2021.112906
                8784828
                34740639
                771a7947-bc9b-4768-9fda-d964f7033835
                © 2021 The Author(s)

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 22 April 2021
                : 12 October 2021
                : 29 October 2021
                Categories
                Article

                Cell biology
                muscle stem cell,satellite cell,satellite cell-opathy,skeletal muscle,congenital myopathy,muscular dystrophy,pax7,myopathogene,carey-fineman-ziter syndrome, cfzs,creatine kinase, ck,duchenne muscular dystrophy, dmd,dystrophin-associated protein complex, dapc,facioscapulohumeral muscular dystrophy, fshd,gene ontologies satellite cells, gosc,glycogen storage disease ii, gsd2,limb-girdle muscular dystrophy recessive 1, lgmdr1,myopathy, areflexia, respiratory distress, and dysphagia, early-onset, emardd,myopathy, congenital, with diaphragmatic defects, respiratory insufficiency, and dysmorphic facies, myodrif,myopathy, congenital, with fiber-type disproportion, cftd,muscular dystrophy, congenital, lmna-related, mdcl,muscular dystrophy, congenital merosin-deficient, 1a mdc1a,progressive congenital myopathy with scoliosis, myosco,rigid spine muscular dystrophy 1, rsmd1,ulrich congenital muscular dystrophy, ucmd

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