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Porcu C, Dobrowolny G, Scicchitano BM. Exploring the Role of Extracellular Vesicles in Skeletal Muscle Regeneration. Int J Mol Sci 2024; 25:5811. [PMID: 38892005 PMCID: PMC11171935 DOI: 10.3390/ijms25115811] [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: 04/30/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Skeletal muscle regeneration entails a multifaceted process marked by distinct phases, encompassing inflammation, regeneration, and remodeling. The coordination of these phases hinges upon precise intercellular communication orchestrated by diverse cell types and signaling molecules. Recent focus has turned towards extracellular vesicles (EVs), particularly small EVs, as pivotal mediators facilitating intercellular communication throughout muscle regeneration. Notably, injured muscle provokes the release of EVs originating from myofibers and various cell types, including mesenchymal stem cells, satellite cells, and immune cells such as M2 macrophages, which exhibit anti-inflammatory and promyogenic properties. EVs harbor a specific cargo comprising functional proteins, lipids, and nucleic acids, including microRNAs (miRNAs), which intricately regulate gene expression in target cells and activate downstream pathways crucial for skeletal muscle homeostasis and repair. Furthermore, EVs foster angiogenesis, muscle reinnervation, and extracellular matrix remodeling, thereby modulating the tissue microenvironment and promoting effective tissue regeneration. This review consolidates the current understanding on EVs released by cells and damaged tissues throughout various phases of muscle regeneration with a focus on EV cargo, providing new insights on potential therapeutic interventions to mitigate muscle-related pathologies.
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Affiliation(s)
- Cristiana Porcu
- DAHFMO-Unità di Istologia ed Embriologia Medica, Sapienza Università di Roma, 00161 Roma, Italy;
| | - Gabriella Dobrowolny
- DAHFMO-Unità di Istologia ed Embriologia Medica, Sapienza Università di Roma, 00161 Roma, Italy;
| | - Bianca Maria Scicchitano
- Sezione di Istologia ed Embriologia, Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Roma, Italy
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2
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Beiter T, Zügel M, Hudemann J, Schild M, Fragasso A, Burgstahler C, Krüger K, Mooren FC, Steinacker JM, Nieß AM. The Acute, Short-, and Long-Term Effects of Endurance Exercise on Skeletal Muscle Transcriptome Profiles. Int J Mol Sci 2024; 25:2881. [PMID: 38474128 DOI: 10.3390/ijms25052881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
A better understanding of the cellular and molecular mechanisms that are involved in skeletal muscle adaptation to exercise is fundamentally important to take full advantage of the enormous benefits that exercise training offers in disease prevention and therapy. The aim of this study was to elucidate the transcriptional signatures that distinguish the endurance-trained and untrained muscles in young adult males (24 ± 3.5 years). We characterized baseline differences as well as acute exercise-induced transcriptome responses in vastus lateralis biopsy specimens of endurance-trained athletes (ET; n = 8; VO2max, 67.2 ± 8.9 mL/min/kg) and sedentary healthy volunteers (SED; n = 8; VO2max, 40.3 ± 7.6 mL/min/kg) using microarray technology. A second cohort of SED volunteers (SED-T; n = 10) followed an 8-week endurance training program to assess expression changes of selected marker genes in the course of skeletal muscle adaptation. We deciphered differential baseline signatures that reflected major differences in the oxidative and metabolic capacity of the endurance-trained and untrained muscles. SED-T individuals in the training group displayed an up-regulation of nodal regulators of oxidative adaptation after 3 weeks of training and a significant shift toward the ET signature after 8 weeks. Transcriptome changes provoked by 1 h of intense cycling exercise only poorly overlapped with the genes that constituted the differential baseline signature of ETs and SEDs. Overall, acute exercise-induced transcriptional responses were connected to pathways of contractile, oxidative, and inflammatory stress and revealed a complex and highly regulated framework of interwoven signaling cascades to cope with exercise-provoked homeostatic challenges. While temporal transcriptional programs that were activated in SEDs and ETs were quite similar, the quantitative divergence in the acute response transcriptomes implicated divergent kinetics of gene induction and repression following an acute bout of exercise. Together, our results provide an extensive examination of the transcriptional framework that underlies skeletal muscle plasticity.
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Affiliation(s)
- Thomas Beiter
- Department of Sports Medicine, Medical Clinic, Eberhard-Karls-University of Tübingen, 72076 Tübingen, Germany
| | - Martina Zügel
- Department of Sport and Rehabilitation Medicine, University of Ulm, 89075 Ulm, Germany
| | - Jens Hudemann
- Department of Sports Medicine, Medical Clinic, Eberhard-Karls-University of Tübingen, 72076 Tübingen, Germany
| | - Marius Schild
- Department of Exercise Physiology and Sports Therapy, University of Gießen, 35394 Gießen, Germany
| | - Annunziata Fragasso
- Department of Sports Medicine, Medical Clinic, Eberhard-Karls-University of Tübingen, 72076 Tübingen, Germany
| | - Christof Burgstahler
- Department of Sports Medicine, Medical Clinic, Eberhard-Karls-University of Tübingen, 72076 Tübingen, Germany
| | - Karsten Krüger
- Department of Exercise Physiology and Sports Therapy, University of Gießen, 35394 Gießen, Germany
| | - Frank C Mooren
- Department of Medicine, Faculty of Health, University of Witten/Herdecke, 58455 Witten, Germany
| | - Jürgen M Steinacker
- Department of Sport and Rehabilitation Medicine, University of Ulm, 89075 Ulm, Germany
| | - Andreas M Nieß
- Department of Sports Medicine, Medical Clinic, Eberhard-Karls-University of Tübingen, 72076 Tübingen, Germany
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3
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Reggiani C, Murgia M. Comment on "Fiber-type traps: revisiting common misconceptions about skeletal muscle fiber types with application to motor control, biomechanics, physiology, and biology". J Appl Physiol (1985) 2024; 136:437-438. [PMID: 38353629 DOI: 10.1152/japplphysiol.00008.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 02/16/2024] Open
Affiliation(s)
- Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- Science and Research Center Koper, Institute for Kinesiology Research, Koper, Slovenia
| | - Marta Murgia
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
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Rodríguez MP, Cabello-Verrugio C. Soluble Factors Associated with Denervation-induced Skeletal Muscle Atrophy. Curr Protein Pept Sci 2024; 25:189-199. [PMID: 38018212 DOI: 10.2174/0113892037189827231018092036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/22/2023] [Accepted: 09/03/2023] [Indexed: 11/30/2023]
Abstract
Skeletal muscle tissue has the critical function of mechanical support protecting the body. In addition, its functions are strongly influenced by the balanced synthesis and degradation processes of structural and regulatory proteins. The inhibition of protein synthesis and/or the activation of catabolism generally determines a pathological state or condition called muscle atrophy, a reduction in muscle mass that results in partial or total loss of function. It has been established that many pathophysiological conditions can cause a decrease in muscle mass. Skeletal muscle innervation involves stable and functional neural interactions with muscles via neuromuscular junctions and is essential for maintaining normal muscle structure and function. Loss of motor innervation induces rapid skeletal muscle fiber degeneration with activation of atrophy-related signaling and subsequent disassembly of sarcomeres, altering normal muscle function. After denervation, an inflammation stage is characterized by the increased expression of pro-inflammatory cytokines that determine muscle atrophy. In this review, we highlighted the impact of some soluble factors on the development of muscle atrophy by denervation.
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Affiliation(s)
- Marianny Portal Rodríguez
- Laboratory of Muscle Pathology, Fragility, and Aging, Faculty of Life Sciences, Universidad Andres Bello, Santiago, 8370146, Chile
- Millennium Institute on Immunology and Immunotherapy, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Claudio Cabello-Verrugio
- Laboratory of Muscle Pathology, Fragility, and Aging, Faculty of Life Sciences, Universidad Andres Bello, Santiago, 8370146, Chile
- Millennium Institute on Immunology and Immunotherapy, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
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Wu L, Shi M, Liang Y, Huang J, Xia W, Bian H, Zhuo Q, Zhao C. The profiles and clinical significance of extraocular muscle-expressed lncRNAs and mRNAs in oculomotor nerve palsy. Front Mol Neurosci 2023; 16:1293344. [PMID: 38173464 PMCID: PMC10761543 DOI: 10.3389/fnmol.2023.1293344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction Oculomotor nerve palsy (ONP) arises from primary abnormalities in the central neural pathways that control the extraocular muscles (EOMs). Long non-coding RNAs (lncRNAs) have been found to be involved in the pathogenesis of various neuroparalytic diseases. However, little is known about the role of lncRNAs in ONP. Methods We collected medial rectus muscle tissue from ONP and constant exotropia (CXT) patients during strabismus surgeries for RNA sequencing analysis. Differentially expressed mRNAs and lncRNAs were revealed and included in the functional enrichment analysis. Co-expression analysis was conducted between these differentially expressed mRNAs and lncRNAs, followed by target gene prediction of differentially expressed lncRNAs. In addition, lncRNA-microRNA and lncRNA-transcription factor-mRNA interaction networks were constructed to further elaborate the pathological changes in medial rectus muscle of ONP. Furthermore, RT-qPCR was applied to further validate the expression levels of important lncRNAs and mRNAs, whose clinical significance was examined by receiver operating characteristic (ROC) curve analysis. Results A total of 618 differentially expressed lncRNAs and 322 differentially expressed mRNAs were identified. The up-regulated mRNAs were significantly related to cholinergic synaptic transmission (such as CHRM3 and CHRND) and the components and metabolism of extracellular matrix (such as CHI3L1 and COL19A1), while the down-regulated mRNAs were significantly correlated with the composition (such as MYH7 and MYL3) and contraction force (such as MYH7 and TNNT1) of muscle fibers. Co-expression analysis and target gene prediction revealed the strong correlation between MYH7 and NR_126491.1 as well as MYOD1 and ENST00000524479. Moreover, the differential expressions of lncRNAs (XR_001739409.1, NR_024160.1 and XR_001738373.1) and mRNAs (CDKN1A, MYOG, MYOD1, MYBPH, TMEM64, STATH, and MYL3) were validated by RT-qPCR. ROC curve analysis showed that lncRNAs (XR_001739409.1, NR_024160.1, and NR_002766.2) and mRNAs (CDKN1A, MYOG, MYOD1, MYBPH, TMEM64, and STATH) might be promising biomarkers of ONP. Conclusions These results may shed light on the molecular biology of EOMs of ONP, as well as the possible correlation of lncRNAs and mRNAs with clinical practice.
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Affiliation(s)
- Lianqun Wu
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Mingsu Shi
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Yu Liang
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Jiaqiu Huang
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Weiyi Xia
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Hewei Bian
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Qiao Zhuo
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Chen Zhao
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
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Rubenstein AB, Smith GR, Zhang Z, Chen X, Chambers TL, Ruf-Zamojski F, Mendelev N, Cheng WS, Zamojski M, Amper MAS, Nair VD, Marderstein AR, Montgomery SB, Troyanskaya OG, Zaslavsky E, Trappe T, Trappe S, Sealfon SC. Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.558914. [PMID: 37808658 PMCID: PMC10557702 DOI: 10.1101/2023.09.26.558914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Endurance exercise is an important health modifier. We studied cell-type specific adaptations of human skeletal muscle to acute endurance exercise using single-nucleus (sn) multiome sequencing in human vastus lateralis samples collected before and 3.5 hours after 40 min exercise at 70% VO2max in four subjects, as well as in matched time of day samples from two supine resting circadian controls. High quality same-cell RNA-seq and ATAC-seq data were obtained from 37,154 nuclei comprising 14 cell types. Among muscle fiber types, both shared and fiber-type specific regulatory programs were identified. Single-cell circuit analysis identified distinct adaptations in fast, slow and intermediate fibers as well as LUM-expressing FAP cells, involving a total of 328 transcription factors (TFs) acting at altered accessibility sites regulating 2,025 genes. These data and circuit mapping provide single-cell insight into the processes underlying tissue and metabolic remodeling responses to exercise.
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Affiliation(s)
- Aliza B. Rubenstein
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Gregory R. Smith
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Zidong Zhang
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Xi Chen
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Toby L. Chambers
- Human Performance Laboratory, Ball State University, Muncie, IN 47306, USA
| | - Frederique Ruf-Zamojski
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Natalia Mendelev
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Wan Sze Cheng
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Michel Zamojski
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mary Anne S. Amper
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Venugopalan D. Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Andrew R. Marderstein
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Olga G. Troyanskaya
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Todd Trappe
- Human Performance Laboratory, Ball State University, Muncie, IN 47306, USA
| | - Scott Trappe
- Human Performance Laboratory, Ball State University, Muncie, IN 47306, USA
- Senior author
| | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
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7
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Lloyd EM, Pinniger GJ, Murphy RM, Grounds MD. Slow or fast: Implications of myofibre type and associated differences for manifestation of neuromuscular disorders. Acta Physiol (Oxf) 2023; 238:e14012. [PMID: 37306196 DOI: 10.1111/apha.14012] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Many neuromuscular disorders can have a differential impact on a specific myofibre type, forming the central premise of this review. The many different skeletal muscles in mammals contain a spectrum of slow- to fast-twitch myofibres with varying levels of protein isoforms that determine their distinctive contractile, metabolic, and other properties. The variations in functional properties across the range of classic 'slow' to 'fast' myofibres are outlined, combined with exemplars of the predominantly slow-twitch soleus and fast-twitch extensor digitorum longus muscles, species comparisons, and techniques used to study these properties. Other intrinsic and extrinsic differences are discussed in the context of slow and fast myofibres. These include inherent susceptibility to damage, myonecrosis, and regeneration, plus extrinsic nerves, extracellular matrix, and vasculature, examined in the context of growth, ageing, metabolic syndrome, and sexual dimorphism. These many differences emphasise the importance of carefully considering the influence of myofibre-type composition on manifestation of various neuromuscular disorders across the lifespan for both sexes. Equally, understanding the different responses of slow and fast myofibres due to intrinsic and extrinsic factors can provide deep insight into the precise molecular mechanisms that initiate and exacerbate various neuromuscular disorders. This focus on the influence of different myofibre types is of fundamental importance to enhance translation for clinical management and therapies for many skeletal muscle disorders.
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Affiliation(s)
- Erin M Lloyd
- Department of Anatomy, Physiology and Human Biology, School of Human Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Curtin Health Innovation Research Institute, Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
| | - Gavin J Pinniger
- Department of Anatomy, Physiology and Human Biology, School of Human Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Robyn M Murphy
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
| | - Miranda D Grounds
- Department of Anatomy, Physiology and Human Biology, School of Human Sciences, The University of Western Australia, Perth, Western Australia, Australia
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Vianello C, Dal Bello F, Shin SH, Schiavon S, Bean C, Magalhães Rebelo AP, Knedlík T, Esfahani EN, Costiniti V, Lacruz RS, Covello G, Munari F, Scolaro T, Viola A, Rampazzo E, Persano L, Zumerle S, Scorrano L, Gianelle A, Giacomello M. High-Throughput Microscopy Analysis of Mitochondrial Membrane Potential in 2D and 3D Models. Cells 2023; 12:cells12071089. [PMID: 37048162 PMCID: PMC10093082 DOI: 10.3390/cells12071089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/24/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
Recent proteomic, metabolomic, and transcriptomic studies have highlighted a connection between changes in mitochondria physiology and cellular pathophysiological mechanisms. Secondary assays to assess the function of these organelles appear fundamental to validate these -omics findings. Although mitochondrial membrane potential is widely recognized as an indicator of mitochondrial activity, high-content imaging-based approaches coupled to multiparametric to measure it have not been established yet. In this paper, we describe a methodology for the unbiased high-throughput quantification of mitochondrial membrane potential in vitro, which is suitable for 2D to 3D models. We successfully used our method to analyze mitochondrial membrane potential in monolayers of human fibroblasts, neural stem cells, spheroids, and isolated muscle fibers. Moreover, by combining automated image analysis and machine learning, we were able to discriminate melanoma cells from macrophages in co-culture and to analyze the subpopulations separately. Our data demonstrated that our method is a widely applicable strategy for large-scale profiling of mitochondrial activity.
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Affiliation(s)
- Caterina Vianello
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35131 Padova, Italy
| | - Federica Dal Bello
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35131 Padova, Italy
| | - Sang Hun Shin
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35131 Padova, Italy
| | - Sara Schiavon
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35131 Padova, Italy
| | - Camilla Bean
- Department of Medicine, University of Udine, Piazzale Kolbe, 33100 Udine, Italy
| | | | - Tomáš Knedlík
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35131 Padova, Italy
| | | | - Veronica Costiniti
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA
| | - Rodrigo S. Lacruz
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA
| | - Giuseppina Covello
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35131 Padova, Italy
| | - Fabio Munari
- Department of Biomedical Sciences, Via Ugo Bassi 58B, 35131 Padova, Italy
- Pediatric Research Institute, Città della Speranza Foundation, Corso Stati Uniti 4 F, 35127 Padova, Italy
| | - Tommaso Scolaro
- Pediatric Research Institute, Città della Speranza Foundation, Corso Stati Uniti 4 F, 35127 Padova, Italy
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, B3000 Leuven, Belgium
| | - Antonella Viola
- Department of Biomedical Sciences, Via Ugo Bassi 58B, 35131 Padova, Italy
- Pediatric Research Institute, Città della Speranza Foundation, Corso Stati Uniti 4 F, 35127 Padova, Italy
| | - Elena Rampazzo
- Pediatric Research Institute, Città della Speranza Foundation, Corso Stati Uniti 4 F, 35127 Padova, Italy
- Oncohematology, Department of Women’s and Children’s Health, University of Padova, Via Giustiniani 3, 35128 Padova, Italy
| | - Luca Persano
- Pediatric Research Institute, Città della Speranza Foundation, Corso Stati Uniti 4 F, 35127 Padova, Italy
- Oncohematology, Department of Women’s and Children’s Health, University of Padova, Via Giustiniani 3, 35128 Padova, Italy
| | - Sara Zumerle
- Department of Medicine, University of Padova, Via Giustiniani 2, 35128 Padova, Italy
- Veneto Institute of Molecular Medicine, Via Giuseppe Orus 2, 35128 Padova, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35131 Padova, Italy
- Veneto Institute of Molecular Medicine, Via Giuseppe Orus 2, 35128 Padova, Italy
| | - Alessio Gianelle
- National Institute for Nuclear Physics, Padova Division, Via Marzolo 8, 35131 Padova, Italy
| | - Marta Giacomello
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35131 Padova, Italy
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9
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Łoboda A, Dulak J. Nuclear Factor Erythroid 2-Related Factor 2 and Its Targets in Skeletal Muscle Repair and Regeneration. Antioxid Redox Signal 2023; 38:619-642. [PMID: 36597355 DOI: 10.1089/ars.2022.0208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Significance: Skeletal muscles have a robust regenerative capacity in response to acute and chronic injuries. Muscle repair and redox homeostasis are intimately linked; increased generation of reactive oxygen species leads to cellular dysfunction and contributes to muscle wasting and progression of muscle diseases. In exemplary muscle disease, Duchenne muscular dystrophy (DMD), caused by mutations in the DMD gene that encodes the muscle structural protein dystrophin, the regeneration machinery is severely compromised, while oxidative stress contributes to the progression of the disease. The nuclear factor erythroid 2-related factor 2 (NRF2) and its target genes, including heme oxygenase-1 (HO-1), provide protective mechanisms against oxidative insults. Recent Advances: Relevant advances have been evolving in recent years in understanding the mechanisms by which NRF2 regulates processes that contribute to effective muscle regeneration. To this end, pathways related to muscle satellite cell differentiation, oxidative stress, mitochondrial metabolism, inflammation, fibrosis, and angiogenesis have been studied. The regulatory role of NRF2 in skeletal muscle ferroptosis has been also suggested. Animal studies have shown that NRF2 pathway activation can stop or reverse skeletal muscle pathology, especially when endogenous stress defence mechanisms are imbalanced. Critical Issues: Despite the growing recognition of NRF2 as a factor that regulates various aspects of muscle regeneration, the mechanistic impact on muscle pathology in various models of muscle injury remains imprecise. Future Directions: Further studies are necessary to fully uncover the role of NRF2 in muscle regeneration, both in physiological and pathological conditions, and to investigate the possibilities for development of new therapeutic modalities. Antioxid. Redox Signal. 38, 619-642.
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Affiliation(s)
- Agnieszka Łoboda
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
| | - Józef Dulak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
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10
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Dysfunctional mitochondria accumulate in a skeletal muscle knockout model of Smn1, the causal gene of spinal muscular atrophy. Cell Death Dis 2023; 14:162. [PMID: 36849544 PMCID: PMC9971247 DOI: 10.1038/s41419-023-05573-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 03/01/2023]
Abstract
The approved gene therapies for spinal muscular atrophy (SMA), caused by loss of survival motor neuron 1 (SMN1), greatly ameliorate SMA natural history but are not curative. These therapies primarily target motor neurons, but SMN1 loss has detrimental effects beyond motor neurons and especially in muscle. Here we show that SMN loss in mouse skeletal muscle leads to accumulation of dysfunctional mitochondria. Expression profiling of single myofibers from a muscle specific Smn1 knockout mouse model revealed down-regulation of mitochondrial and lysosomal genes. Albeit levels of proteins that mark mitochondria for mitophagy were increased, morphologically deranged mitochondria with impaired complex I and IV activity and respiration and that produced excess reactive oxygen species accumulated in Smn1 knockout muscles, because of the lysosomal dysfunction highlighted by the transcriptional profiling. Amniotic fluid stem cells transplantation that corrects the SMN knockout mouse myopathic phenotype restored mitochondrial morphology and expression of mitochondrial genes. Thus, targeting muscle mitochondrial dysfunction in SMA may complement the current gene therapy.
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11
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Chen M, Wang Y, Deng S, Lian Z, Yu K. Skeletal muscle oxidative stress and inflammation in aging: Focus on antioxidant and anti-inflammatory therapy. Front Cell Dev Biol 2022; 10:964130. [PMID: 36111339 PMCID: PMC9470179 DOI: 10.3389/fcell.2022.964130] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/10/2022] [Indexed: 12/06/2022] Open
Abstract
With aging, the progressive loss of skeletal muscle will have negative effect on multiple physiological parameters, such as exercise, respiration, thermoregulation, and metabolic homeostasis. Accumulating evidence reveals that oxidative stress and inflammation are the main pathological characteristics of skeletal muscle during aging. Here, we focus on aging-related sarcopenia, summarize the relationship between aging and sarcopenia, and elaborate on aging-mediated oxidative stress and oxidative damage in skeletal muscle and its critical role in the occurrence and development of sarcopenia. In addition, we discuss the production of excessive reactive oxygen species in aging skeletal muscle, which reduces the ability of skeletal muscle satellite cells to participate in muscle regeneration, and analyze the potential molecular mechanism of ROS-mediated mitochondrial dysfunction in aging skeletal muscle. Furthermore, we have also paid extensive attention to the possibility and potential regulatory pathways of skeletal muscle aging and oxidative stress mediate inflammation. Finally, in response to the abnormal activity of oxidative stress and inflammation during aging, we summarize several potential antioxidant and anti-inflammatory strategies for the treatment of sarcopenia, which may provide beneficial help for improving sarcopenia during aging.
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Affiliation(s)
- Mingming Chen
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yiyi Wang
- Zhejiang A&F University, Zhejiang Provincial Key Laboratory of Characteristic Traditional Chinese Medicine Resources Protection and Innovative Utilization, Lin’an, China
| | - Shoulong Deng
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Zhengxing Lian
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Zhengxing Lian, ; Kun Yu,
| | - Kun Yu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Zhengxing Lian, ; Kun Yu,
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12
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Manno C, Tammineni E, Figueroa L, Oropeza-Almazán Y, Rios E. A novel method for determining murine skeletal muscle fiber type using autofluorescence lifetimes. J Gen Physiol 2022; 154:213341. [PMID: 35796671 PMCID: PMC9272018 DOI: 10.1085/jgp.202213143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/13/2022] [Indexed: 01/09/2023] Open
Abstract
This work describes a simple way to identify fiber types in living muscles by fluorescence lifetime imaging microscopy (FLIM). We quantified the mean values of lifetimes τ1 and τ2 derived from a two-exponential fit in freshly dissected mouse flexor digitorum brevis (FDB) and soleus muscles. While τ1 values changed following a bimodal behavior between muscles, the distribution of τ2 is shifted to higher values in FDB. To understand the origin of this difference, we obtained maps of autofluorescence lifetimes of flavin mononucleotide and dinucleotide (FMN/FAD) in cryosections, where excitation was set at 440 nm and emission at a bandwidth of between 500 and 570 nm, and paired them with immunofluorescence images of myosin heavy chain isoforms, which allowed identification of fiber types. In soleus, τ2 was 3.16 ns for type I (SD 0.11, 97 fibers), 3.45 ns for IIA (0.10, 69), and 3.46 ns for IIX (0.12, 65). In FDB muscle, τ2 was 3.17 ns for type I (0.08, 22), 3.46 ns for IIA (0.16, 48), and 3.66 ns for IIX (0.15, 43). From τ2 distributions, it follows that an FDB fiber with τ2 > 3.3 ns is expected to be of type II, and of type I otherwise. This simple classification method has first and second kind errors estimated at 0.02 and 0.10, which can be lowered by reducing the threshold for identification of type I and increasing it for type II. Lifetime maps of autofluorescence, therefore, constitute a tool to identify fiber types that, for being practical, fast, and noninvasive, can be applied in living tissue without compromising other experimental interventions.
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Affiliation(s)
- Carlo Manno
- Department of Physiology and Biophysics, Rush University, Chicago, IL,Correspondence to Carlo Manno:
| | - Eshwar Tammineni
- Department of Physiology and Biophysics, Rush University, Chicago, IL
| | - Lourdes Figueroa
- Department of Physiology and Biophysics, Rush University, Chicago, IL
| | | | - Eduardo Rios
- Department of Physiology and Biophysics, Rush University, Chicago, IL
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13
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Macchi C, Bonalume V, Greco MF, Mozzo M, Melfi V, Sirtori CR, Magnaghi V, Corsini A, Ruscica M. Impact of Atorvastatin on Skeletal Muscle Mitochondrial Activity, Locomotion and Axonal Excitability-Evidence from ApoE-/- Mice. Int J Mol Sci 2022; 23:ijms23105415. [PMID: 35628225 PMCID: PMC9141374 DOI: 10.3390/ijms23105415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 02/04/2023] Open
Abstract
The cardiovascular benefit of statins is well established. However, only 20% of high-risk patients remain adequately adherent after 5 years of treatment. Among reasons for discontinuation, statin associated-muscle pain symptoms are the most prevalent. Aim of the present study was to evaluate the impact of high dose atorvastatin on skeletal muscle mitochondrial activity, aerobic and anaerobic exercise, and axonal excitability in a murine model of atherosclerosis. ApoE-/- mice were fed 12 weeks a high-fat high-cholesterol diet alone or containing atorvastatin (40 mg/Kg/day). Outcomes were the evaluation of muscle mitochondrial functionality, locomotion, grip test, and axonal excitability (compound action potential recording analysis of Aα motor propioceptive, Aβ mechanoceptive and C nociceptive fibres). Atorvastatin led to a reduction in muscle mitochondrial biogenesis and mitochondrial ATP production. It did not affect muscular strength but led to a time-dependent motor impairment. Atorvastatin altered the responsiveness of mechanoceptive and nociceptive fibres, respectively, the Aβ and C fibres. These findings point out to a mild sensitization on mechanical, tactile and pain sensitivity. In conclusion, although the prevalence of muscular side effects from statins may be overestimated, understanding of the underlying mechanisms can help improve the therapeutic approach and reassure adherence in patients needing-to-be-treated.
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14
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Pereyra AS, Lin CT, Sanchez DM, Laskin J, Spangenburg EE, Neufer PD, Fisher-Wellman K, Ellis JM. Skeletal muscle undergoes fiber type metabolic switch without myosin heavy chain switch in response to defective fatty acid oxidation. Mol Metab 2022; 59:101456. [PMID: 35150906 PMCID: PMC8898976 DOI: 10.1016/j.molmet.2022.101456] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 11/20/2022] Open
Abstract
Objective Skeletal muscle is a heterogeneous and dynamic tissue that adapts to functional demands and substrate availability by modulating muscle fiber size and type. The concept of muscle fiber type relates to its contractile (slow or fast) and metabolic (glycolytic or oxidative) properties. Here, we tested whether disruptions in muscle oxidative catabolism are sufficient to prompt parallel adaptations in energetics and contractile protein composition. Methods Mice with defective mitochondrial long-chain fatty acid oxidation (mLCFAO) in the skeletal muscle due to loss of carnitine palmitoyltransferase 2 (Cpt2Sk−/−) were used to model a shift in muscle macronutrient catabolism. Glycolytic and oxidative muscles of Cpt2Sk−/− mice and control littermates were compared for the expression of energy metabolism-related proteins, mitochondrial respiratory capacity, and myosin heavy chain isoform composition. Results Differences in bioenergetics and macronutrient utilization in response to energy demands between control muscles were intrinsic to the mitochondria, allowing for a clear distinction of muscle types. Loss of CPT2 ablated mLCFAO and resulted in mitochondrial biogenesis occurring most predominantly in oxidative muscle fibers. The metabolism-related proteomic signature of Cpt2Sk−/− oxidative muscle more closely resembled that of glycolytic muscle than of control oxidative muscle. Respectively, intrinsic substrate-supported mitochondrial respiration of CPT2 deficient oxidative muscles shifted to closely match that of glycolytic muscles. Despite this shift in mitochondrial metabolism, CPT2 deletion did not result in contractile-based fiber type switching according to myosin heavy chain composition analysis. Conclusion The loss of mitochondrial long-chain fatty acid oxidation elicits an adaptive response involving conversion of oxidative muscle toward a metabolic profile that resembles a glycolytic muscle, but this is not accompanied by changes in myosin heavy chain isoforms. These data suggest that shifts in muscle catabolism are not sufficient to drive shifts in the contractile apparatus but are sufficient to drive adaptive changes in metabolic properties. Fuel oxidation in glycolytic compared to oxidative muscles are different and intrinsic to the mitochondria. Muscle CPT2 loss elicits fiber-type dependent mitochondrial biogenesis. Muscle CPT2 loss elicits an oxidative-to-glycolytic shift in mitochondrial and metabolic properties. Muscle CPT2 loss does not alter myosin heavy chain isoform composition. CPT2 deficient muscles demonstrate a metabolic-contractile apparatus mismatch.
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Affiliation(s)
- Andrea S Pereyra
- Brody School of Medicine at East Carolina University, Department of Physiology and East Carolina Diabetes and Obesity Institute, Greenville, NC, 27834, USA.
| | - Chien-Te Lin
- Brody School of Medicine at East Carolina University, Department of Physiology and East Carolina Diabetes and Obesity Institute, Greenville, NC, 27834, USA
| | | | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Espen E Spangenburg
- Brody School of Medicine at East Carolina University, Department of Physiology and East Carolina Diabetes and Obesity Institute, Greenville, NC, 27834, USA
| | - P Darrell Neufer
- Brody School of Medicine at East Carolina University, Department of Physiology and East Carolina Diabetes and Obesity Institute, Greenville, NC, 27834, USA
| | - Kelsey Fisher-Wellman
- Brody School of Medicine at East Carolina University, Department of Physiology and East Carolina Diabetes and Obesity Institute, Greenville, NC, 27834, USA
| | - Jessica M Ellis
- Brody School of Medicine at East Carolina University, Department of Physiology and East Carolina Diabetes and Obesity Institute, Greenville, NC, 27834, USA.
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15
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Skeletal muscle phenotyping of Hippo gene-mutated mice reveals that Lats1 deletion increases the percentage of type I muscle fibers. Transgenic Res 2022; 31:227-237. [PMID: 34984591 PMCID: PMC8993742 DOI: 10.1007/s11248-021-00293-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 12/02/2021] [Indexed: 12/04/2022]
Abstract
The Hippo signal transduction network regulates transcription through Yap/Taz-Tead1-4 in many tissues including skeletal muscle. Whilst transgenic mice have been generated for many Hippo genes, the resultant skeletal muscle phenotypes were not always characterized. Here, we aimed to phenotype the hindlimb muscles of Hippo gene-mutated Lats1−/−, Mst2−/−, Vgll3−/−, and Vgll4+/− mice. This analysis revealed that Lats1−/− mice have 11% more slow type I fibers than age and sex-matched wild-type controls. Moreover, the mRNA expression of slow Myh7 increased by 50%, and the concentration of type I myosin heavy chain is 80% higher in Lats1−/− mice than in age and sex-matched wild-type controls. Second, to find out whether exercise-related stimuli affect Lats1, we stimulated C2C12 myotubes with the hypertrophy agent clenbuterol or the energy stress agent AICAR. We found that both stimulated Lats1 expression by 1.2 and 1.3 fold respectively. Third, we re-analyzed published datasets and found that Lats1 mRNA in muscle is 63% higher in muscular dystrophy, increases by 17–77% after cardiotoxin-induced muscle injury, by 41–71% in muscles during overload-induced hypertrophy, and by 19–21% after endurance exercise when compared to respective controls. To conclude, Lats1 contributes to the regulation of muscle fiber type proportions, and its expression is regulated by physiological and pathological situations in skeletal muscle.
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16
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Merz KE, Tunduguru R, Ahn M, Salunkhe VA, Veluthakal R, Hwang J, Bhattacharya S, McCown EM, Garcia PA, Zhou C, Oh E, Yoder SM, Elmendorf JS, Thurmond DC. Changes in Skeletal Muscle PAK1 Levels Regulate Tissue Crosstalk to Impact Whole Body Glucose Homeostasis. Front Endocrinol (Lausanne) 2022; 13:821849. [PMID: 35222279 PMCID: PMC8881144 DOI: 10.3389/fendo.2022.821849] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
Skeletal muscle accounts for ~80% of insulin-stimulated glucose uptake. The Group I p21-activated kinase 1 (PAK1) is required for the non-canonical insulin-stimulated GLUT4 vesicle translocation in skeletal muscle cells. We found that the abundances of PAK1 protein and its downstream effector in muscle, ARPC1B, are significantly reduced in the skeletal muscle of humans with type 2 diabetes, compared to the non-diabetic controls, making skeletal muscle PAK1 a candidate regulator of glucose homeostasis. Although whole-body PAK1 knockout mice exhibit glucose intolerance and are insulin resistant, the contribution of skeletal muscle PAK1 in particular was unknown. As such, we developed inducible skeletal muscle-specific PAK1 knockout (skmPAK1-iKO) and overexpression (skmPAK1-iOE) mouse models to evaluate the role of PAK1 in skeletal muscle insulin sensitivity and glucose homeostasis. Using intraperitoneal glucose tolerance and insulin tolerance testing, we found that skeletal muscle PAK1 is required for maintaining whole body glucose homeostasis. Moreover, PAK1 enrichment in GLUT4-myc-L6 myoblasts preserves normal insulin-stimulated GLUT4 translocation under insulin resistance conditions. Unexpectedly, skmPAK1-iKO also showed aberrant plasma insulin levels following a glucose challenge. By applying conditioned media from PAK1-enriched myotubes or myoblasts to β-cells in culture, we established that a muscle-derived circulating factor(s) could enhance β-cell function. Taken together, these data suggest that PAK1 levels in the skeletal muscle can regulate not only skeletal muscle insulin sensitivity, but can also engage in tissue crosstalk with pancreatic β-cells, unveiling a new molecular mechanism by which PAK1 regulates whole-body glucose homeostasis.
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Affiliation(s)
- Karla E. Merz
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute of City of Hope, Duarte, CA, United States
| | - Ragadeepthi Tunduguru
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute of City of Hope, Duarte, CA, United States
| | - Miwon Ahn
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute of City of Hope, Duarte, CA, United States
| | - Vishal A. Salunkhe
- Sahlgrenska Academy, Institute of Neuroscience and Physiology, Metabolism Research Unit, University of Gothenburg, Gothenburg, Sweden
| | - Rajakrishnan Veluthakal
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute of City of Hope, Duarte, CA, United States
| | - Jinhee Hwang
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute of City of Hope, Duarte, CA, United States
| | - Supriyo Bhattacharya
- Division of Translational Bioinformatics, City of Hope, Duarte, CA, United States
| | - Erika M. McCown
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute of City of Hope, Duarte, CA, United States
| | - Pablo A. Garcia
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute of City of Hope, Duarte, CA, United States
| | - Chunxue Zhou
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute of City of Hope, Duarte, CA, United States
| | - Eunjin Oh
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute of City of Hope, Duarte, CA, United States
| | - Stephanie M. Yoder
- Global Scientific Communications, Eli Lilly & Company, Indianapolis, IN, United States
| | - Jeffrey S. Elmendorf
- Department of Anatomy, Cell Biology and Physiology, Center for Diabetes and Metabolic Disease, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Debbie C. Thurmond
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute of City of Hope, Duarte, CA, United States
- *Correspondence: Debbie C. Thurmond,
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17
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Orchard P, Manickam N, Ventresca C, Vadlamudi S, Varshney A, Rai V, Kaplan J, Lalancette C, Mohlke KL, Gallagher K, Burant CF, Parker SCJ. Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits. Genome Res 2021; 31:2258-2275. [PMID: 34815310 PMCID: PMC8647829 DOI: 10.1101/gr.268482.120] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/16/2021] [Indexed: 12/12/2022]
Abstract
Skeletal muscle accounts for the largest proportion of human body mass, on average, and is a key tissue in complex diseases and mobility. It is composed of several different cell and muscle fiber types. Here, we optimize single-nucleus ATAC-seq (snATAC-seq) to map skeletal muscle cell-specific chromatin accessibility landscapes in frozen human and rat samples, and single-nucleus RNA-seq (snRNA-seq) to map cell-specific transcriptomes in human. We additionally perform multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 33,862 nuclei and identify seven cell types ranging in abundance from 59.6% to 1.0% of all nuclei. We introduce a regression-based approach to infer cell types by comparing transcription start site-distal ATAC-seq peaks to reference enhancer maps and show consistency with RNA-based marker gene cell type assignments. We find heterogeneity in enrichment of genetic variants linked to complex phenotypes from the UK Biobank and diabetes genome-wide association studies in cell-specific ATAC-seq peaks, with the most striking enrichment patterns in muscle mesenchymal stem cells (∼3.5% of nuclei). Finally, we overlay these chromatin accessibility maps on GWAS data to nominate causal cell types, SNPs, transcription factor motifs, and target genes for type 2 diabetes signals. These chromatin accessibility profiles for human and rat skeletal muscle cell types are a useful resource for nominating causal GWAS SNPs and cell types.
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Affiliation(s)
- Peter Orchard
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Nandini Manickam
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Christa Ventresca
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Swarooparani Vadlamudi
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Arushi Varshney
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Vivek Rai
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jeremy Kaplan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Claudia Lalancette
- Epigenomics Core, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Katherine Gallagher
- Department of Surgery, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
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18
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Verbrugge SAJ, Alhusen JA, Kempin S, Pillon NJ, Rozman J, Wackerhage H, Kleinert M. Genes controlling skeletal muscle glucose uptake and their regulation by endurance and resistance exercise. J Cell Biochem 2021; 123:202-214. [PMID: 34812516 DOI: 10.1002/jcb.30179] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/27/2021] [Accepted: 11/04/2021] [Indexed: 12/25/2022]
Abstract
Exercise improves the insulin sensitivity of glucose uptake in skeletal muscle. Due to that, exercise has become a cornerstone treatment for type 2 diabetes mellitus (T2DM). The mechanisms by which exercise improves skeletal muscle insulin sensitivity are, however, incompletely understood. We conducted a systematic review to identify all genes whose gain or loss of function alters skeletal muscle glucose uptake. We subsequently cross-referenced these genes with recently generated data sets on exercise-induced gene expression and signaling. Our search revealed 176 muscle glucose-uptake genes, meaning that their genetic manipulation altered glucose uptake in skeletal muscle. Notably, exercise regulates the expression or phosphorylation of more than 50% of the glucose-uptake genes or their protein products. This included many genes that previously have not been associated with exercise-induced insulin sensitivity. Interestingly, endurance and resistance exercise triggered some common but mostly unique changes in expression and phosphorylation of glucose-uptake genes or their protein products. Collectively, our work provides a resource of potentially new molecular effectors that play a role in the incompletely understood regulation of muscle insulin sensitivity by exercise.
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Affiliation(s)
- Sander A J Verbrugge
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, Neuherberg, Germany.,Exercise Biology Group, Department for Sport and Health Sciences, Technical University of Munich, Munich, Germany
| | - Julia A Alhusen
- Molecular Endocrinology, Institute for Diabetes and Cancer (IDC), Helmholtz Zentrum Munich, Helmholtz Diabetes Center (HMGU), Munich, Germany
| | - Shimon Kempin
- Exercise Biology Group, Department for Sport and Health Sciences, Technical University of Munich, Munich, Germany
| | - Nicolas J Pillon
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Rozman
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Henning Wackerhage
- Exercise Biology Group, Department for Sport and Health Sciences, Technical University of Munich, Munich, Germany
| | - Maximilian Kleinert
- Muscle Physiology and Metabolism Group, German Institute of Human Nutrition, Potsdam - Rehbrücke, Nuthetal, Germany.,Department of Nutrition, Exercise and Sports, Faculty of Science, Section of Molecular Physiology, University of Copenhagen, Copenhagen, Denmark
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19
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Bengtsen M, Winje IM, Eftestøl E, Landskron J, Sun C, Nygård K, Domanska D, Millay DP, Meza-Zepeda LA, Gundersen K. Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle. PLoS Genet 2021; 17:e1009907. [PMID: 34752468 PMCID: PMC8604348 DOI: 10.1371/journal.pgen.1009907] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 11/19/2021] [Accepted: 10/23/2021] [Indexed: 01/04/2023] Open
Abstract
Muscle cells have different phenotypes adapted to different usage, and can be grossly divided into fast/glycolytic and slow/oxidative types. While most muscles contain a mixture of such fiber types, we aimed at providing a genome-wide analysis of the epigenetic landscape by ChIP-Seq in two muscle extremes, the fast/glycolytic extensor digitorum longus (EDL) and slow/oxidative soleus muscles. Muscle is a heterogeneous tissue where up to 60% of the nuclei can be of a different origin. Since cellular homogeneity is critical in epigenome-wide association studies we developed a new method for purifying skeletal muscle nuclei from whole tissue, based on the nuclear envelope protein Pericentriolar material 1 (PCM1) being a specific marker for myonuclei. Using antibody labelling and a magnetic-assisted sorting approach, we were able to sort out myonuclei with 95% purity in muscles from mice, rats and humans. The sorting eliminated influence from the other cell types in the tissue and improved the myo-specific signal. A genome-wide comparison of the epigenetic landscape in EDL and soleus reflected the differences in the functional properties of the two muscles, and revealed distinct regulatory programs involving distal enhancers, including a glycolytic super-enhancer in the EDL. The two muscles were also regulated by different sets of transcription factors; e.g. in soleus, binding sites for MEF2C, NFATC2 and PPARA were enriched, while in EDL MYOD1 and SIX1 binding sites were found to be overrepresented. In addition, more novel transcription factors for muscle regulation such as members of the MAF family, ZFX and ZBTB14 were identified. Complex tissues like skeletal muscle contain a variety of cells which confound the analysis of each cell type when based on homogenates, thus only about half of the cell nuclei in muscles reside inside the muscle cells. We here describe a labelling and sorting technique that allowed us to study the epigenetic landscape in purified muscle cell nuclei leaving the other cell types out. Differences between a fast/glycolytic and a slow/oxidative muscle were studied. While all skeletal muscle fibers have a similar make up and basic function, they differ in their physiology and the way they are used. Thus, some fibers are fast contracting but fatigable, and are used for short lasting explosive tasks such as sprinting. Other fibers are slow and are used for more prolonged tasks such as standing or long distance running. Since fiber type correlate with metabolic profile these features can also be related to metabolic diseases. We here show that the epigenetic landscape differed in gene loci corresponding to the differences in functional properties, and revealed that the two types are enriched in different gene regulatory networks. Exercise can alter muscle phenotype, and the epigenetic landscape might be related to how plastic different properties are.
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Affiliation(s)
- Mads Bengtsen
- Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Einar Eftestøl
- Department of Biosciences, University of Oslo, Oslo, Norway
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | | | - Chengyi Sun
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Kamilla Nygård
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Diana Domanska
- Department of Pathology, University of Oslo, Oslo, Norway
| | - Douglas P. Millay
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Leonardo A. Meza-Zepeda
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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Yin L, Li N, Jia W, Wang N, Liang M, Yang X, Du G. Skeletal muscle atrophy: From mechanisms to treatments. Pharmacol Res 2021; 172:105807. [PMID: 34389456 DOI: 10.1016/j.phrs.2021.105807] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/03/2021] [Accepted: 08/07/2021] [Indexed: 02/07/2023]
Abstract
Skeletal muscle is a crucial tissue for movement, gestural assistance, metabolic homeostasis, and thermogenesis. It makes up approximately 40% of the total body weight and 50% of total protein. However, several pathological abnormalities (e.g., chronic diseases, cancer, long-term infection, aging) can induce an imbalance in skeletal muscle protein synthesis and degradation, which triggers muscle wasting and even leads to atrophy. Skeletal muscle atrophy is characterized by weakening, shrinking, and decreasing muscle mass and fiber cross-sectional area at the histological level. It manifests as a reduction in force production, easy fatigue and decreased exercise capability, along with a lower quality of life. Mechanistically, there are several pathophysiological processes involved in skeletal muscle atrophy, including oxidative stress and inflammation, which then activate signal transduction, such as the ubiquitin proteasome system, autophagy lysosome system, and mTOR. Considering the great economic and social burden that muscle atrophy can inflict, effective prevention and treatment strategies are essential but still limited. Exercise is widely acknowledged as the most effective therapy for skeletal muscle atrophy; unfortunately, it is not applicable for all patients. Several active substances for skeletal muscle atrophy have been discovered and evaluated in clinical trials, however, they have not been marketed to date. Knowledge is being gained on the underlying mechanisms, highlighting more promising treatment strategies in the future. In this paper, the mechanisms and treatment strategies for skeletal muscle atrophy are briefly reviewed.
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Affiliation(s)
- Lin Yin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Drug Target and Screening Research, Institute of Materia Medica of Peking Union Medical College, 1 Xian Nong Tan Street, Beijing 100050, PR China
| | - Na Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Drug Target and Screening Research, Institute of Materia Medica of Peking Union Medical College, 1 Xian Nong Tan Street, Beijing 100050, PR China
| | - Weihua Jia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Drug Target and Screening Research, Institute of Materia Medica of Peking Union Medical College, 1 Xian Nong Tan Street, Beijing 100050, PR China
| | - Nuoqi Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Drug Target and Screening Research, Institute of Materia Medica of Peking Union Medical College, 1 Xian Nong Tan Street, Beijing 100050, PR China
| | - Meidai Liang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Drug Target and Screening Research, Institute of Materia Medica of Peking Union Medical College, 1 Xian Nong Tan Street, Beijing 100050, PR China
| | - Xiuying Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Drug Target and Screening Research, Institute of Materia Medica of Peking Union Medical College, 1 Xian Nong Tan Street, Beijing 100050, PR China.
| | - Guanhua Du
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Beijing Key Laboratory of Drug Target and Screening Research, Institute of Materia Medica of Peking Union Medical College, 1 Xian Nong Tan Street, Beijing 100050, PR China.
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21
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Jin L, Tang Q, Hu S, Chen Z, Zhou X, Zeng B, Wang Y, He M, Li Y, Gui L, Shen L, Long K, Ma J, Wang X, Chen Z, Jiang Y, Tang G, Zhu L, Liu F, Zhang B, Huang Z, Li G, Li D, Gladyshev VN, Yin J, Gu Y, Li X, Li M. A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription. Nat Commun 2021; 12:3715. [PMID: 34140474 PMCID: PMC8211698 DOI: 10.1038/s41467-021-23560-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
A comprehensive transcriptomic survey of pigs can provide a mechanistic understanding of tissue specialization processes underlying economically valuable traits and accelerate their use as a biomedical model. Here we characterize four transcript types (lncRNAs, TUCPs, miRNAs, and circRNAs) and protein-coding genes in 31 adult pig tissues and two cell lines. We uncover the transcriptomic variability among 47 skeletal muscles, and six adipose depots linked to their different origins, metabolism, cell composition, physical activity, and mitochondrial pathways. We perform comparative analysis of the transcriptomes of seven tissues from pigs and nine other vertebrates to reveal that evolutionary divergence in transcription potentially contributes to lineage-specific biology. Long-range promoter–enhancer interaction analysis in subcutaneous adipose tissues across species suggests evolutionarily stable transcription patterns likely attributable to redundant enhancers buffering gene expression patterns against perturbations, thereby conferring robustness during speciation. This study can facilitate adoption of the pig as a biomedical model for human biology and disease and uncovers the molecular bases of valuable traits. A comprehensive transcriptomic survey of the pig could enable mechanistic understanding of tissue specialization and accelerate its use as a biomedical model. Here the authors characterize four distinct transcript types in 31 adult pig tissues to dissect their distinct structural and transcriptional features and uncover transcriptomic variability related to tissue physiology.
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Affiliation(s)
- Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhongxu Chen
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan, China
| | - Xuming Zhou
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bo Zeng
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuhao Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lixuan Gui
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan, China
| | - Linyuan Shen
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhengli Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanzhi Jiang
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Guoqing Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Li Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fei Liu
- Information and Educational Technology Center, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Zhang
- Ya'an Digital Economy Operation Company, Ya'an, Sichuan, China
| | - Zhiqing Huang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guisen Li
- Renal Department and Nephrology Institute, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jingdong Yin
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
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22
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Eggers B, Schork K, Turewicz M, Barkovits K, Eisenacher M, Schröder R, Clemen CS, Marcus K. Advanced Fiber Type-Specific Protein Profiles Derived from Adult Murine Skeletal Muscle. Proteomes 2021; 9:proteomes9020028. [PMID: 34201234 PMCID: PMC8293376 DOI: 10.3390/proteomes9020028] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
Skeletal muscle is a heterogeneous tissue consisting of blood vessels, connective tissue, and muscle fibers. The last are highly adaptive and can change their molecular composition depending on external and internal factors, such as exercise, age, and disease. Thus, examination of the skeletal muscles at the fiber type level is essential to detect potential alterations. Therefore, we established a protocol in which myosin heavy chain isoform immunolabeled muscle fibers were laser microdissected and separately investigated by mass spectrometry to develop advanced proteomic profiles of all murine skeletal muscle fiber types. All data are available via ProteomeXchange with the identifier PXD025359. Our in-depth mass spectrometric analysis revealed unique fiber type protein profiles, confirming fiber type-specific metabolic properties and revealing a more versatile function of type IIx fibers. Furthermore, we found that multiple myopathy-associated proteins were enriched in type I and IIa fibers. To further optimize the assignment of fiber types based on the protein profile, we developed a hypothesis-free machine-learning approach, identified a discriminative peptide panel, and confirmed our panel using a public data set.
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Affiliation(s)
- Britta Eggers
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany; (K.S.); (M.T.); (K.B.); (M.E.)
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI), Ruhr-University Bochum, 44801 Bochum, Germany
- Correspondence: (B.E.); (K.M.)
| | - Karin Schork
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany; (K.S.); (M.T.); (K.B.); (M.E.)
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI), Ruhr-University Bochum, 44801 Bochum, Germany
| | - Michael Turewicz
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany; (K.S.); (M.T.); (K.B.); (M.E.)
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI), Ruhr-University Bochum, 44801 Bochum, Germany
| | - Katalin Barkovits
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany; (K.S.); (M.T.); (K.B.); (M.E.)
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI), Ruhr-University Bochum, 44801 Bochum, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany; (K.S.); (M.T.); (K.B.); (M.E.)
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI), Ruhr-University Bochum, 44801 Bochum, Germany
| | - Rolf Schröder
- Institute of Neuropathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany;
| | - Christoph S. Clemen
- German Aerospace Center, Institute of Aerospace Medicine, 51147 Cologne, Germany;
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany; (K.S.); (M.T.); (K.B.); (M.E.)
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI), Ruhr-University Bochum, 44801 Bochum, Germany
- Correspondence: (B.E.); (K.M.)
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23
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Bindellini D, Voortman LM, Olie CS, van Putten M, van den Akker E, Raz V. Discovering fiber type architecture over the entire muscle using data-driven analysis. Cytometry A 2021; 99:1240-1249. [PMID: 34089298 PMCID: PMC9545503 DOI: 10.1002/cyto.a.24465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/06/2021] [Accepted: 05/25/2021] [Indexed: 11/16/2022]
Abstract
Skeletal muscle function is inferred from the spatial arrangement of muscle fiber architecture, which corresponds to myofiber molecular and metabolic features. Myofiber features are often determined using immunofluorescence on a local sampling, typically obtained from a median region. This median region is assumed to represent the entire muscle. However, it remains largely unknown to what extent this local sampling represents the entire muscle. We present a pipeline to study the architecture of muscle fiber features over the entire muscle, including sectioning, staining, imaging to image quantification and data‐driven analysis with Myofiber type were identified by the expression of myosin heavy chain (MyHC) isoforms, representing contraction properties. We reconstructed muscle architecture from consecutive cross‐sections stained for laminin and MyHC isoforms. Examining the entire muscle using consecutive cross‐sections is extremely laborious, we provide consideration to reduce the dataset without loosing spatial information. Data‐driven analysis with over 150,000 myofibers showed spatial variations in myofiber geometric features, myofiber type, and the distribution of neuromuscular junctions over the entire muscle. We present a workflow to study histological changes over the entire muscle using high‐throughput imaging, image quantification, and data‐driven analysis. Our results suggest that asymmetric spatial distribution of these features over the entire muscle could impact muscle function. Therefore, instead of a single sampling from a median region, representative regions covering the entire muscle should be investigated in future studies.
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Affiliation(s)
- Davide Bindellini
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Lennard M Voortman
- Department of Chemical Cell Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Cyriel S Olie
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Maaike van Putten
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Erik van den Akker
- Biomedical Data Science, Leiden University Medical Centre, Leiden, The Netherlands
| | - Vered Raz
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
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24
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Verma RX, Kannan S, Lin BL, Fomchenko KM, Nieuwenhuis TO, Patil AH, Lukban C, Yang X, Fox-Talbot K, McCall MN, Kwon C, Kass DA, Rosenberg AZ, Halushka MK. Single cell RNA-seq analysis of the flexor digitorum brevis mouse myofibers. Skelet Muscle 2021; 11:13. [PMID: 34001262 PMCID: PMC8127317 DOI: 10.1186/s13395-021-00269-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/28/2021] [Indexed: 01/23/2023] Open
Abstract
Background Skeletal muscle myofibers can be separated into functionally distinct cell types that differ in gene and protein expression. Current single cell expression data is generally based upon single nucleus RNA, rather than whole myofiber material. We examined if a whole-cell flow sorting approach could be applied to perform single cell RNA-seq (scRNA-seq) in a single muscle type. Methods We performed deep, whole cell, scRNA-seq on intact and fragmented skeletal myofibers from the mouse fast-twitch flexor digitorum brevis muscle utilizing a flow-gated method of large cell isolation. We performed deep sequencing of 763 intact and fragmented myofibers. Results Quality control metrics across the different gates indicated only 171 of these cells were optimal, with a median read count of 239,252 and an average of 12,098 transcripts per cell. scRNA-seq identified three clusters of myofibers (a slow/fast 2A cluster and two fast 2X clusters). Comparison to a public skeletal nuclear RNA-seq dataset demonstrated a diversity in transcript abundance by method. RISH validated multiple genes across fast and slow twitch skeletal muscle types. Conclusion This study introduces and validates a method to isolate intact skeletal muscle myofibers to generate deep expression patterns and expands the known repertoire of fiber-type-specific genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13395-021-00269-2.
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Affiliation(s)
- Rohan X Verma
- Department of Pathology, Johns Hopkins University School of Medicine, Ross Bldg. Rm 632B, 720 Rutland Avenue, Baltimore, MD, 21205, USA
| | - Suraj Kannan
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brian L Lin
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Katherine M Fomchenko
- Department of Pathology, Johns Hopkins University School of Medicine, Ross Bldg. Rm 632B, 720 Rutland Avenue, Baltimore, MD, 21205, USA
| | - Tim O Nieuwenhuis
- Department of Pathology, Johns Hopkins University School of Medicine, Ross Bldg. Rm 632B, 720 Rutland Avenue, Baltimore, MD, 21205, USA
| | - Arun H Patil
- Department of Pathology, Johns Hopkins University School of Medicine, Ross Bldg. Rm 632B, 720 Rutland Avenue, Baltimore, MD, 21205, USA
| | - Clarisse Lukban
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xiaoping Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Ross Bldg. Rm 632B, 720 Rutland Avenue, Baltimore, MD, 21205, USA
| | - Karen Fox-Talbot
- Department of Pathology, Johns Hopkins University School of Medicine, Ross Bldg. Rm 632B, 720 Rutland Avenue, Baltimore, MD, 21205, USA
| | - Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Chulan Kwon
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David A Kass
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Ross Bldg. Rm 632B, 720 Rutland Avenue, Baltimore, MD, 21205, USA
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Ross Bldg. Rm 632B, 720 Rutland Avenue, Baltimore, MD, 21205, USA.
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25
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Muscle Diversity, Heterogeneity, and Gradients: Learning from Sarcoglycanopathies. Int J Mol Sci 2021; 22:ijms22052502. [PMID: 33801487 PMCID: PMC7958856 DOI: 10.3390/ijms22052502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/25/2022] Open
Abstract
Skeletal muscle, the most abundant tissue in the body, is heterogeneous. This heterogeneity forms the basis of muscle diversity, which is reflected in the specialized functions of muscles in different parts of the body. However, these different parts are not always clearly delimitated, and this often gives rise to gradients within the same muscle and even across the body. During the last decade, several studies on muscular disorders both in mice and in humans have observed particular distribution patterns of muscle weakness during disease, indicating that the same mutation can affect muscles differently. Moreover, these phenotypical differences reveal gradients of severity, existing alongside other architectural gradients. These two factors are especially prominent in sarcoglycanopathies. Nevertheless, very little is known about the mechanism(s) driving the phenotypic diversity of the muscles affected by these diseases. Here, we will review the available literature on sarcoglycanopathies, focusing on phenotypic differences among affected muscles and gradients, characterization techniques, molecular signatures, and cell population heterogeneity, highlighting the possibilities opened up by new technologies. This review aims to revive research interest in the diverse disease phenotype affecting different muscles, in order to pave the way for new therapeutic interventions.
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26
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Oe M, Ojima K, Muroya S. Difference in potential DNA methylation impact on gene expression between fast- and slow-type myofibers. Physiol Genomics 2021; 53:69-83. [PMID: 33459151 DOI: 10.1152/physiolgenomics.00099.2020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Skeletal muscles are comprised of two major types of myofibers, fast and slow. It is hypothesized that once myofiber type is determined, muscle fiber-type specificity is maintained by an epigenetic mechanism, however, this remains poorly understood. To address this, we conducted a comprehensive CpG methylation analysis with a reduced representation of bisulfite sequencing (RRBS). Using GFP-myh7 mouse, we visually distinguished and separately pooled slow-type and myh7-negative fast-type fibers for analyses. A total of 31,967 and 26,274 CpGs were hypermethylated by ≥10% difference in the fast- and slow-type fibers, respectively. Notably, the number of promoter-hypermethylated genes with downregulated expression in the slow-type fibers was 3.5 times higher than that in the fast-type fibers. Gene bodies of the fast-type-specific myofibrillar genes Actn3, Tnnt3, Tnni2, Tnnc2, and Tpm1 were hypermethylated in the slow-type fibers, whereas those of the slow-type-specific genes Myh7, Tnnt1, and Tpm3 were hypermethylated in the fast-type fibers. Each of the instances of gene hypermethylation was associated with the respective downregulated expression. In particular, a relationship between CpG methylation sites and the transcription variant distribution of Tpm1 was observed, suggesting a regulation of Tpm1 alternative promoter usage by gene body CpG methylation. An association of hypermethylation with the regulation of gene expression was also observed in the transcription factors Sim2 and Tbx1. These results suggest not only a myofiber type-specific regulation of gene expression and alternative promoter usage by gene body CpG methylation but also a dominant effect of promoter-hypermethylation on the gene expressions in slow myofibers.
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Affiliation(s)
- Mika Oe
- Muscle Biology Research Unit, Division of Animal Products Research, NARO Institute of Livestock and Grassland Science, Tsukuba, Japan
| | - Koichi Ojima
- Muscle Biology Research Unit, Division of Animal Products Research, NARO Institute of Livestock and Grassland Science, Tsukuba, Japan
| | - Susumu Muroya
- Muscle Biology Research Unit, Division of Animal Products Research, NARO Institute of Livestock and Grassland Science, Tsukuba, Japan
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27
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Wei X, Franke J, Ost M, Wardelmann K, Börno S, Timmermann B, Meierhofer D, Kleinridders A, Klaus S, Stricker S. Cell autonomous requirement of neurofibromin (Nf1) for postnatal muscle hypertrophic growth and metabolic homeostasis. J Cachexia Sarcopenia Muscle 2020; 11:1758-1778. [PMID: 33078583 PMCID: PMC7749575 DOI: 10.1002/jcsm.12632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/09/2020] [Accepted: 09/10/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Neurofibromatosis type 1 (NF1) is a multi-organ disease caused by mutations in neurofibromin 1 (NF1). Amongst other features, NF1 patients frequently show reduced muscle mass and strength, impairing patients' mobility and increasing the risk of fall. The role of Nf1 in muscle and the cause for the NF1-associated myopathy are mostly unknown. METHODS To dissect the function of Nf1 in muscle, we created muscle-specific knockout mouse models for NF1, inactivating Nf1 in the prenatal myogenic lineage either under the Lbx1 promoter or under the Myf5 promoter. Mice were analysed during prenatal and postnatal myogenesis and muscle growth. RESULTS Nf1Lbx1 and Nf1Myf5 animals showed only mild defects in prenatal myogenesis. Nf1Lbx1 animals were perinatally lethal, while Nf1Myf5 animals survived only up to approximately 25 weeks. A comprehensive phenotypic characterization of Nf1Myf5 animals showed decreased postnatal growth, reduced muscle size, and fast fibre atrophy. Proteome and transcriptome analyses of muscle tissue indicated decreased protein synthesis and increased proteasomal degradation, and decreased glycolytic and increased oxidative activity in muscle tissue. High-resolution respirometry confirmed enhanced oxidative metabolism in Nf1Myf5 muscles, which was concomitant to a fibre type shift from type 2B to type 2A and type 1. Moreover, Nf1Myf5 muscles showed hallmarks of decreased activation of mTORC1 and increased expression of atrogenes. Remarkably, loss of Nf1 promoted a robust activation of AMPK with a gene expression profile indicative of increased fatty acid catabolism. Additionally, we observed a strong induction of genes encoding catabolic cytokines in muscle Nf1Myf5 animals, in line with a drastic reduction of white, but not brown adipose tissue. CONCLUSIONS Our results demonstrate a cell autonomous role for Nf1 in myogenic cells during postnatal muscle growth required for metabolic and proteostatic homeostasis. Furthermore, Nf1 deficiency in muscle drives cross-tissue communication and mobilization of lipid reserves.
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Affiliation(s)
- Xiaoyan Wei
- Musculoskeletal Development and Regeneration Group, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.,Development and Disease Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Julia Franke
- Musculoskeletal Development and Regeneration Group, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.,Development and Disease Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Mario Ost
- Department of Physiology of Energy Metabolism, German Institute for Human Nutrition, Nuthetal, Germany.,Department of Neuropathology, University Hospital Leipzig, Leipzig, Germany
| | - Kristina Wardelmann
- Junior Research Group Central Regulation of Metabolism, German Institute for Human Nutrition, Nuthetal, Germany.,Institute of Nutritional Science, Department of Molecular and Experimental Nutritional Medicine, University of Potsdam, Potsdam, Germany
| | - Stefan Börno
- Sequencing Core Unit, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Unit, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - David Meierhofer
- Mass Spectrometry Core Unit, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Andre Kleinridders
- Junior Research Group Central Regulation of Metabolism, German Institute for Human Nutrition, Nuthetal, Germany.,Institute of Nutritional Science, Department of Molecular and Experimental Nutritional Medicine, University of Potsdam, Potsdam, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Susanne Klaus
- Department of Physiology of Energy Metabolism, German Institute for Human Nutrition, Nuthetal, Germany.,Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Sigmar Stricker
- Musculoskeletal Development and Regeneration Group, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.,Development and Disease Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
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28
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Chemello F, Grespi F, Zulian A, Cancellara P, Hebert-Chatelain E, Martini P, Bean C, Alessio E, Buson L, Bazzega M, Armani A, Sandri M, Ferrazza R, Laveder P, Guella G, Reggiani C, Romualdi C, Bernardi P, Scorrano L, Cagnin S, Lanfranchi G. Transcriptomic Analysis of Single Isolated Myofibers Identifies miR-27a-3p and miR-142-3p as Regulators of Metabolism in Skeletal Muscle. Cell Rep 2020; 26:3784-3797.e8. [PMID: 30917329 DOI: 10.1016/j.celrep.2019.02.105] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/29/2018] [Accepted: 02/26/2019] [Indexed: 12/27/2022] Open
Abstract
Skeletal muscle is composed of different myofiber types that preferentially use glucose or lipids for ATP production. How fuel preference is regulated in these post-mitotic cells is largely unknown, making this issue a key question in the fields of muscle and whole-body metabolism. Here, we show that microRNAs (miRNAs) play a role in defining myofiber metabolic profiles. mRNA and miRNA signatures of all myofiber types obtained at the single-cell level unveiled fiber-specific regulatory networks and identified two master miRNAs that coordinately control myofiber fuel preference and mitochondrial morphology. Our work provides a complete and integrated mouse myofiber type-specific catalog of gene and miRNA expression and establishes miR-27a-3p and miR-142-3p as regulators of lipid use in skeletal muscle.
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Affiliation(s)
- Francesco Chemello
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Francesca Grespi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Alessandra Zulian
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Pasqua Cancellara
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Etienne Hebert-Chatelain
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Paolo Martini
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Camilla Bean
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Enrico Alessio
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Lisa Buson
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Martina Bazzega
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Andrea Armani
- Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Marco Sandri
- Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy; Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Ruggero Ferrazza
- Department of Physics, University of Trento, Via Sommarive 14, 38123 Povo (Trento), Italy
| | - Paolo Laveder
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Graziano Guella
- Department of Physics, University of Trento, Via Sommarive 14, 38123 Povo (Trento), Italy
| | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Chiara Romualdi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Paolo Bernardi
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35131 Padova, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; CIR-Myo Myology Center, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.
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29
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Rubenstein AB, Smith GR, Raue U, Begue G, Minchev K, Ruf-Zamojski F, Nair VD, Wang X, Zhou L, Zaslavsky E, Trappe TA, Trappe S, Sealfon SC. Single-cell transcriptional profiles in human skeletal muscle. Sci Rep 2020; 10:229. [PMID: 31937892 PMCID: PMC6959232 DOI: 10.1038/s41598-019-57110-6] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 12/18/2019] [Indexed: 12/22/2022] Open
Abstract
Skeletal muscle is a heterogeneous tissue comprised of muscle fiber and mononuclear cell types that, in addition to movement, influences immunity, metabolism and cognition. We investigated the gene expression patterns of skeletal muscle cells using RNA-seq of subtype-pooled single human muscle fibers and single cell RNA-seq of mononuclear cells from human vastus lateralis, mouse quadriceps, and mouse diaphragm. We identified 11 human skeletal muscle mononuclear cell types, including two fibro-adipogenic progenitor (FAP) cell subtypes. The human FBN1+ FAP cell subtype is novel and a corresponding FBN1+ FAP cell type was also found in single cell RNA-seq analysis in mouse. Transcriptome exercise studies using bulk tissue analysis do not resolve changes in individual cell-type proportion or gene expression. The cell-type gene signatures provide the means to use computational methods to identify cell-type level changes in bulk studies. As an example, we analyzed public transcriptome data from an exercise training study and revealed significant changes in specific mononuclear cell-type proportions related to age, sex, acute exercise and training. Our single-cell expression map of skeletal muscle cell types will further the understanding of the diverse effects of exercise and the pathophysiology of muscle disease.
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Affiliation(s)
- Aliza B Rubenstein
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA.,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Gregory R Smith
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA.,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Ulrika Raue
- Human Performance Laboratory, Ball State University, Muncie, Indiana, 47306, USA
| | - Gwénaëlle Begue
- Human Performance Laboratory, Ball State University, Muncie, Indiana, 47306, USA
| | - Kiril Minchev
- Human Performance Laboratory, Ball State University, Muncie, Indiana, 47306, USA
| | - Frederique Ruf-Zamojski
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA.,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Venugopalan D Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA.,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Xingyu Wang
- Department of Neurology, Boston University Medical Center, Boston, MA, 02118, USA
| | - Lan Zhou
- Department of Neurology, Boston University Medical Center, Boston, MA, 02118, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA.,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Todd A Trappe
- Human Performance Laboratory, Ball State University, Muncie, Indiana, 47306, USA
| | - Scott Trappe
- Human Performance Laboratory, Ball State University, Muncie, Indiana, 47306, USA
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA. .,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA.
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30
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Singh V, Kumar R, Ojha K, Kushwaha P. Muscle biopsies differ in relation to expression of fiber-type specific genes. JOURNAL OF DIABETOLOGY 2020. [DOI: 10.4103/jod.jod_6_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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31
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Tosetti B, Brodesser S, Brunn A, Deckert M, Blüher M, Doehner W, Anker SD, Wenzel D, Fleischmann B, Pongratz C, Peters F, Utermöhlen O, Krönke M. A tissue-specific screen of ceramide expression in aged mice identifies ceramide synthase-1 and ceramide synthase-5 as potential regulators of fiber size and strength in skeletal muscle. Aging Cell 2020; 19:e13049. [PMID: 31692231 PMCID: PMC6974707 DOI: 10.1111/acel.13049] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 09/02/2019] [Accepted: 09/20/2019] [Indexed: 12/14/2022] Open
Abstract
Loss of skeletal muscle mass is one of the most widespread and deleterious processes in aging humans. However, the mechanistic metabolic principles remain poorly understood. In the framework of a multi‐organ investigation of age‐associated changes of ceramide species, a unique and distinctive change pattern of C16:0 and C18:0 ceramide species was detected in aged skeletal muscle. Consistently, the expression of CerS1 and CerS5 mRNA, encoding the ceramide synthases (CerS) with substrate preference for C16:0 and C18:0 acyl chains, respectively, was down‐regulated in skeletal muscle of aged mice. Similarly, an age‐dependent decline of both CerS1 and CerS5 mRNA expression was observed in skeletal muscle biopsies of humans. Moreover, CerS1 and CerS5 mRNA expression was also reduced in muscle biopsies from patients in advanced stage of chronic heart failure (CHF) suffering from muscle wasting and frailty. The possible impact of CerS1 and CerS5 on muscle function was addressed by reversed genetic analysis using CerS1Δ/Δ and CerS5Δ/Δ knockout mice. Skeletal muscle from mice deficient of either CerS1 or CerS5 showed reduced caliber sizes of both slow (type 1) and fast (type 2) muscle fibers, fiber grouping, and fiber switch to type 1 fibers. Moreover, CerS1‐ and CerS5‐deficient mice exhibited reduced twitch and tetanus forces of musculus extensor digitorum longus. The findings of this study link CerS1 and CerS5 to histopathological changes and functional impairment of skeletal muscle in mice that might also play a functional role for the aging skeletal muscle and for age‐related muscle wasting disorders in humans.
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Affiliation(s)
- Bettina Tosetti
- Institute for Medical Microbiology, Immunology and Hygiene University Hospital Cologne Cologne Germany
- Cologne Cluster of Excellence on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) Cologne Germany
| | - Susanne Brodesser
- Cologne Cluster of Excellence on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) Cologne Germany
| | - Anna Brunn
- Department of Neuropathology Faculty of Medicine University of Cologne Cologne Germany
| | - Martina Deckert
- Department of Neuropathology Faculty of Medicine University of Cologne Cologne Germany
| | - Matthias Blüher
- Department of Medicine University of Leipzig Leipzig Germany
| | - Wolfram Doehner
- Department of Cardiology (Campus Virchow Klinikum) German Centre for Cardiovascular Research Berlin Germany
- BIH Center for Regenerative Therapies (BCRT) Charité Universitätsmedizin Berlin Berlin Germany
| | - Stefan D. Anker
- Division of Cardiology and Metabolism Department of Cardiology (Campus Virchow Klinikum) Charité Universitätsmedizin Berlin Berlin Germany
- Berlin‐Brandenburg Center for Regenerative Therapies (BCRT) Charité Universitätsmedizin Berlin Berlin Germany
| | - Daniela Wenzel
- Institute of Physiology I Medical Faculty University of Bonn Bonn Germany
| | - Bernd Fleischmann
- Institute of Physiology I Medical Faculty University of Bonn Bonn Germany
| | - Carola Pongratz
- Institute for Medical Microbiology, Immunology and Hygiene University Hospital Cologne Cologne Germany
- Cologne Cluster of Excellence on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) Cologne Germany
| | - Franziska Peters
- Institute for Medical Microbiology, Immunology and Hygiene University Hospital Cologne Cologne Germany
- Cologne Cluster of Excellence on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) Cologne Germany
| | - Olaf Utermöhlen
- Institute for Medical Microbiology, Immunology and Hygiene University Hospital Cologne Cologne Germany
- Center for Molecular Medicine Cologne (CMMC) Cologne Germany
| | - Martin Krönke
- Institute for Medical Microbiology, Immunology and Hygiene University Hospital Cologne Cologne Germany
- Cologne Cluster of Excellence on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) Cologne Germany
- Center for Molecular Medicine Cologne (CMMC) Cologne Germany
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32
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Klaus S, Ost M. Mitochondrial uncoupling and longevity - A role for mitokines? Exp Gerontol 2019; 130:110796. [PMID: 31786315 DOI: 10.1016/j.exger.2019.110796] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022]
Abstract
Aging has been viewed both as a random process due to accumulation of molecular and cellular damage over time and as a programmed process linked to cellular pathway important for growth and maturation. These views converge on mitochondria as both the major producer of damaging reactive oxidant species (ROS) and as signaling organelles. A finite proton leak across the inner mitochondrial membrane leading to a slight uncoupling of oxidative phosphorylation and respiration is an intrinsic property of all mitochondria and according to the "uncoupling to survive" hypothesis it has evolved to protect against ROS production to minimize oxidative damage. This hypothesis is supported by evidence linking an increased endogenous, uncoupling protein (UCP1) mediated, as well as experimentally induced mitochondrial uncoupling to an increased lifespan in rodents. This is possibly due to the synergistic activation of molecular pathways linked to life extending effects of caloric restriction as well as a mitohormetic response. Mitohormesis is an adaptive stress response through mitonuclear signaling which increases stress resistance resulting in health promoting effects. Part of this response is the induction of fibroblast growth factor 21 (FGF21) and growth and differentiation factor 15 (GDF15), two stress-induced mitokines which elicit beneficial systemic metabolic effects via endocrine action.
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Affiliation(s)
- Susanne Klaus
- German Institute of Human Nutrition in Potsdam Rehbrücke, Nuthetal, Germany; University of Potsdam, Institute of Nutritional Science, Potsdam, Germany.
| | - Mario Ost
- German Institute of Human Nutrition in Potsdam Rehbrücke, Nuthetal, Germany
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33
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Schiaffino S, Reggiani C, Murgia M. Fiber type diversity in skeletal muscle explored by mass spectrometry-based single fiber proteomics. Histol Histopathol 2019; 35:239-246. [PMID: 31612964 DOI: 10.14670/hh-18-170] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mammalian skeletal muscles are composed of a variety of muscle fibers with specialized functional properties. Slow fibers are suited for long lasting and low intensity contractile activity, while various subtypes of fast fibers are optimized to produce high force and power even with a significant fatigue. The functional specialization of muscle fibers is based on selective gene expression regulation, which provides each fiber with a specific protein complement. The recent refinement of small-scale sample preparation, combined with the development of mass spectrometers characterized by high sensitivity, sequencing speed and mass accuracy, has allowed the characterization of the proteome of single muscle fibers with an unprecedented resolution. In the last few years, the first studies on the global proteomics of individual fibers of different types have been published. In this short review we discuss the methodological advancements which have opened the way to single fiber proteomics and the discovery power of this approach. We provide examples of how specific features of single fibers can be overlooked when whole muscle or multi-fiber samples are analyzed and can only be detected when a single fiber proteome is analyzed. Thus, novel subtype-specific metabolic features, most prominently mitochondrial specialization of fiber types have been revealed by single fiber proteomics. In the same way, specific adaptive responses of single fibers to aging or loss of neural input have been detected when single fibers were individually analyzed. We conclude that the fiber type-resolved proteomes represent a powerful tool which can be applied to a variety of physiological and pathological conditions.
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Affiliation(s)
| | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Institute for Kinesiology Research, Science and Research Center of Koper, Koper, Slovenia
| | - Marta Murgia
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Max-Planck-Institute of Biochemistry, Martinsried, Germany
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34
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Chemello F, Alessio E, Buson L, Pacchioni B, Millino C, Lanfranchi G, Cagnin S. Isolation and Transcriptomic Profiling of Single Myofibers from Mice. Bio Protoc 2019; 9:e3378. [PMID: 33654874 DOI: 10.21769/bioprotoc.3378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 11/02/2022] Open
Abstract
Skeletal muscle is composed of different cells and myofiber types, with distinct metabolic and structural features. Generally, transcriptomic analysis of skeletal muscle is performed using whole muscle, resulting in average information as all cells composing the organ contribute to the expression value detected for each gene with the loss of information about the distinctive features of each specific myofiber type. Since myofibers are the smallest complete contractile system of skeletal muscle influencing its contraction velocity and metabolism, it would be beneficial to have fiber-specific information about gene expression. Here, we describe a protocol for the isolation and the transcriptomic analysis of single individual myofibers. The protocol was set up using single myofibers isolated from soleus and Extensor Digitorum Longus (EDL) muscles, but it can be applied to all skeletal muscles. Briefly, muscles are enzymatically dissociated and individually collected. Long RNAs (> 200 nt) and short RNAs (< 200 nt) are separately purified from each myofiber and used to produce libraries for microarray or sequencing analysis. Through this approach, myofiber-specific transcriptional profiles can be produced, free from transcripts from other non-contractile cell types, in order to identify mRNA-miRNA-lncRNA regulatory networks specific for each myofiber type.
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Affiliation(s)
| | - Enrico Alessio
- Department of Biology, University of Padova, Padova, Italy
| | - Lisa Buson
- Department of Biology, University of Padova, Padova, Italy
| | - Beniamina Pacchioni
- Department of Biology, University of Padova, Padova, Italy.,CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Caterina Millino
- Department of Biology, University of Padova, Padova, Italy.,CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, Padova, Italy.,CRIBI Biotechnology Center, University of Padova, Padova, Italy.,CIR-Myo Myology Center, University of Padova, Padova, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Padova, Italy.,CRIBI Biotechnology Center, University of Padova, Padova, Italy.,CIR-Myo Myology Center, University of Padova, Padova, Italy
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35
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Randazzo D, Khalique U, Belanto JJ, Kenea A, Talsness DM, Olthoff JT, Tran MD, Zaal KJ, Pak K, Pinal-Fernandez I, Mammen AL, Sackett D, Ervasti JM, Ralston E. Persistent upregulation of the β-tubulin tubb6, linked to muscle regeneration, is a source of microtubule disorganization in dystrophic muscle. Hum Mol Genet 2019; 28:1117-1135. [PMID: 30535187 DOI: 10.1093/hmg/ddy418] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/26/2018] [Accepted: 12/02/2018] [Indexed: 12/20/2022] Open
Abstract
In healthy adult skeletal muscle fibers microtubules form a three-dimensional grid-like network. In the mdx mouse, a model of Duchenne muscular dystrophy (DMD), microtubules are mostly disordered, without periodicity. These microtubule defects have been linked to the mdx mouse pathology. We now report that increased expression of the beta 6 class V β-tubulin (tubb6) contributes to the microtubule changes of mdx muscles. Wild-type muscle fibers overexpressing green fluorescent protein (GFP)-tubb6 (but not GFP-tubb5) have disorganized microtubules whereas mdx muscle fibers depleted of tubb6 (but not of tubb5) normalize their microtubules, suggesting that increasing tubb6 is toxic. However, tubb6 increases spontaneously during differentiation of mouse and human muscle cultures. Furthermore, endogenous tubb6 is not uniformly expressed in mdx muscles but is selectively increased in fiber clusters, which we identify as regenerating. Similarly, mdx-based rescued transgenic mice that retain a higher than expected tubb6 level show focal expression of tubb6 in subsets of fibers. Tubb6 is also upregulated in cardiotoxin-induced mouse muscle regeneration, in human myositis and DMD biopsies, and the tubb6 level correlates with that of embryonic myosin heavy chain, a regeneration marker. In conclusion, modulation of a β-tubulin isotype plays a role in muscle differentiation and regeneration. Increased tubb6 expression and microtubule reorganization are not pathological per se but reflect a return to an earlier developmental stage. However, chronic elevation of tubb6, as occurs in the mdx mouse, may contribute to the repeated cycles of regeneration and to the pathology of the disease.
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Affiliation(s)
- Davide Randazzo
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Umara Khalique
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Joseph J Belanto
- Department of Biochemistry, Molecular Biology, and Biophysics, and Program in Molecular, Cellular, Developmental Biology, and Genetics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Aster Kenea
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Dana M Talsness
- Department of Biochemistry, Molecular Biology, and Biophysics, and Program in Molecular, Cellular, Developmental Biology, and Genetics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - John T Olthoff
- Department of Biochemistry, Molecular Biology, and Biophysics, and Program in Molecular, Cellular, Developmental Biology, and Genetics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Michelle D Tran
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kristien J Zaal
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Katherine Pak
- Laboratory of Muscle Stem Cells and Gene Regulation, Muscle Disease Unit, NIAMS, NIH, Bethesda, MD, USA
| | - Iago Pinal-Fernandez
- Laboratory of Muscle Stem Cells and Gene Regulation, Muscle Disease Unit, NIAMS, NIH, Bethesda, MD, USA.,Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew L Mammen
- Laboratory of Muscle Stem Cells and Gene Regulation, Muscle Disease Unit, NIAMS, NIH, Bethesda, MD, USA.,Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dan Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, USA
| | - James M Ervasti
- Department of Biochemistry, Molecular Biology, and Biophysics, and Program in Molecular, Cellular, Developmental Biology, and Genetics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Evelyn Ralston
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
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36
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EGF receptor (EGFR) inhibition promotes a slow-twitch oxidative, over a fast-twitch, muscle phenotype. Sci Rep 2019; 9:9218. [PMID: 31239465 PMCID: PMC6592914 DOI: 10.1038/s41598-019-45567-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 04/10/2019] [Indexed: 11/17/2022] Open
Abstract
A low quadriceps slow-twitch (ST), oxidative (relative to fast-twitch) fiber proportion is prevalent in chronic diseases such Chronic Obstructive Pulmonary Disease (COPD) and is associated with exercise limitation and poor outcomes. Benefits of an increased ST fiber proportion are demonstrated in genetically modified animals. Pathway analysis of published data of differentially expressed genes in mouse ST and FT fibers, mining of our microarray data and a qPCR analysis of quadriceps specimens from COPD patients and controls were performed. ST markers were quantified in C2C12 myotubes with EGF-neutralizing antibody, EGFR inhibitor or an EGFR-silencing RNA added. A zebrafish egfra mutant was generated by genome editing and ST fibers counted. EGF signaling was (negatively) associated with the ST muscle phenotype in mice and humans, and muscle EGF transcript levels were raised in COPD. In C2C12 myotubes, EGFR inhibition/silencing increased ST, including mitochondrial, markers. In zebrafish, egfra depletion increased ST fibers and mitochondrial content. EGF is negatively associated with ST muscle phenotype in mice, healthy humans and COPD patients. EGFR blockade promotes the ST phenotype in myotubes and zebrafish embryos. EGF signaling suppresses the ST phenotype, therefore EGFR inhibitors may be potential treatments for COPD-related muscle ST fiber loss.
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37
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Alessio E, Buson L, Chemello F, Peggion C, Grespi F, Martini P, Massimino ML, Pacchioni B, Millino C, Romualdi C, Bertoli A, Scorrano L, Lanfranchi G, Cagnin S. Single cell analysis reveals the involvement of the long non-coding RNA Pvt1 in the modulation of muscle atrophy and mitochondrial network. Nucleic Acids Res 2019; 47:1653-1670. [PMID: 30649422 PMCID: PMC6393313 DOI: 10.1093/nar/gkz007] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/05/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as important players in the regulation of several aspects of cellular biology. For a better comprehension of their function, it is fundamental to determine their tissue or cell specificity and to identify their subcellular localization. In fact, the activity of lncRNAs may vary according to cell and tissue specificity and subcellular compartmentalization. Myofibers are the smallest complete contractile system of skeletal muscle influencing its contraction velocity and metabolism. How lncRNAs are expressed in different myofibers, participate in metabolism regulation and muscle atrophy or how they are compartmentalized within a single myofiber is still unknown. We compiled a comprehensive catalog of lncRNAs expressed in skeletal muscle, associating the fiber-type specificity and subcellular location to each of them, and demonstrating that many lncRNAs can be involved in the biological processes de-regulated during muscle atrophy. We demonstrated that the lncRNA Pvt1, activated early during muscle atrophy, impacts mitochondrial respiration and morphology and affects mito/autophagy, apoptosis and myofiber size in vivo. This work corroborates the importance of lncRNAs in the regulation of metabolism and neuromuscular pathologies and offers a valuable resource to study the metabolism in single cells characterized by pronounced plasticity.
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Affiliation(s)
- Enrico Alessio
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Lisa Buson
- Department of Biology, University of Padova, 35131 Padova, Italy
| | | | - Caterina Peggion
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Francesca Grespi
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Paolo Martini
- Department of Biology, University of Padova, 35131 Padova, Italy
| | | | - Beniamina Pacchioni
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
| | - Caterina Millino
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
| | - Chiara Romualdi
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Alessandro Bertoli
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Padova Neuroscience Center, University of Padova, 35131 Padova, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, 35131 Padova, Italy
- Venetian Institute of Molecular Medicine, 35131 Padova, Italy
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
- CIR-Myo Myology Center, University of Padova, 35131 Padova, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
- CIR-Myo Myology Center, University of Padova, 35131 Padova, Italy
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38
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Lee JH, Lewis KM, Moural TW, Kirilenko B, Borgonovo B, Prange G, Koessl M, Huggenberger S, Kang C, Hiller M. Molecular parallelism in fast-twitch muscle proteins in echolocating mammals. SCIENCE ADVANCES 2018; 4:eaat9660. [PMID: 30263960 PMCID: PMC6157964 DOI: 10.1126/sciadv.aat9660] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
Abstract
Detecting associations between genomic changes and phenotypic differences is fundamental to understanding how phenotypes evolved. By systematically screening for parallel amino acid substitutions, we detected known as well as novel cases (Strc, Tecta, and Cabp2) of parallelism between echolocating bats and toothed whales in proteins that could contribute to high-frequency hearing adaptations. Our screen also showed that echolocating mammals exhibit an unusually high number of parallel substitutions in fast-twitch muscle fiber proteins. Both echolocating bats and toothed whales produce an extremely rapid call rate when homing in on their prey, which was shown in bats to be powered by specialized superfast muscles. We show that these genes with parallel substitutions (Casq1, Atp2a1, Myh2, and Myl1) are expressed in the superfast sound-producing muscle of bats. Furthermore, we found that the calcium storage protein calsequestrin 1 of the little brown bat and the bottlenose dolphin functionally converged in its ability to form calcium-sequestering polymers at lower calcium concentrations, which may contribute to rapid calcium transients required for superfast muscle physiology. The proteins that our genomic screen detected could be involved in the convergent evolution of vocalization in echolocating mammals by potentially contributing to both rapid Ca2+ transients and increased shortening velocities in superfast muscles.
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Affiliation(s)
- Jun-Hoe Lee
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Kevin M. Lewis
- Department of Chemistry, Washington State University, Pullman, WA 99164–4630, USA
| | - Timothy W. Moural
- Department of Chemistry, Washington State University, Pullman, WA 99164–4630, USA
| | - Bogdan Kirilenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Barbara Borgonovo
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Gisa Prange
- Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Manfred Koessl
- Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Stefan Huggenberger
- Department II of Anatomy—Neuroanatomy, University of Cologne, Cologne, Germany
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, WA 99164–4630, USA
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
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39
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Motohashi N, Uezumi A, Asakura A, Ikemoto-Uezumi M, Mori S, Mizunoe Y, Takashima R, Miyagoe-Suzuki Y, Takeda S, Shigemoto K. Tbx1 regulates inherited metabolic and myogenic abilities of progenitor cells derived from slow- and fast-type muscle. Cell Death Differ 2018; 26:1024-1036. [PMID: 30154444 DOI: 10.1038/s41418-018-0186-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/18/2018] [Accepted: 07/27/2018] [Indexed: 11/09/2022] Open
Abstract
Skeletal muscle is divided into slow- and fast-type muscles, which possess distinct contractile and metabolic properties. Myogenic progenitors associated with each muscle fiber type are known to intrinsically commit to specific muscle fiber lineage during embryonic development. However, it is still unclear whether the functionality of postnatal adult myogenic cells is attributable to the muscle fiber in which they reside, and whether the characteristics of myogenic cells derived from slow- and fast-type fibers can be distinguished at the genetic level. In this study, we isolated adult satellite cells from slow- and fast-type muscle individually and observed that satellite cells from each type of muscle generated myotubes expressing myosin heavy chain isoforms similar to their original muscle, and showed different metabolic features. Notably, we discovered that slow muscle-derived cells had low potential to differentiate but high potential to self-renew compared with fast muscle-derived cells. Additionally, cell transplantation experiments of slow muscle-derived cells into fast-type muscle revealed that slow muscle-derived cells could better contribute to myofiber formation and satellite cell constitution than fast muscle-derived cells, suggesting that the recipient muscle fiber type may not affect the predetermined abilities of myogenic cells. Gene expression analyses identified T-box transcriptional factor Tbx1 as a highly expressed gene in fast muscle-derived myoblasts. Gain- and loss-of-function experiments revealed that Tbx1 modulated muscle fiber types and oxidative metabolism in myotubes, and that Tbx1 stimulated myoblast differentiation, but did not regulate myogenic cell self-renewal. Our data suggest that metabolic and myogenic properties of myogenic progenitor cells vary depending on the type of muscle from which they originate, and that Tbx1 expression partially explains the functional differences of myogenic cells derived from fast-type and slow-type muscles.
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Affiliation(s)
- Norio Motohashi
- Department of Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, 173-0015, Japan. .,Stem Cell Institute, Paul and Sheila Wellstone Muscular Dystrophy Center, Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
| | - Akiyoshi Uezumi
- Department of Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, 173-0015, Japan
| | - Atsushi Asakura
- Stem Cell Institute, Paul and Sheila Wellstone Muscular Dystrophy Center, Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Madoka Ikemoto-Uezumi
- Department of Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, 173-0015, Japan
| | - Shuuichi Mori
- Department of Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, 173-0015, Japan
| | - Yuhei Mizunoe
- Department of Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, 173-0015, Japan
| | - Rumi Takashima
- Department of Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, 173-0015, Japan
| | - Yuko Miyagoe-Suzuki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8502, Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8502, Japan
| | - Kazuhiro Shigemoto
- Department of Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, 173-0015, Japan
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40
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Lang F, Khaghani S, Türk C, Wiederstein JL, Hölper S, Piller T, Nogara L, Blaauw B, Günther S, Müller S, Braun T, Krüger M. Single Muscle Fiber Proteomics Reveals Distinct Protein Changes in Slow and Fast Fibers during Muscle Atrophy. J Proteome Res 2018; 17:3333-3347. [DOI: 10.1021/acs.jproteome.8b00093] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Franziska Lang
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Solmaz Khaghani
- Max Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231 Bad Nauheim, Germany
| | - Clara Türk
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Janica Lea Wiederstein
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Soraya Hölper
- Sanofi-Aventis Deutschland GmbH, Biologics Research, Protein Therapeutics, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Tanja Piller
- Institute of Biochemistry II, Goethe University Medical School, 60590 Frankfurt, Germany
| | - Leonardo Nogara
- Venetian Institute of Molecular Medicine (VIMM), Department of Biomedical Sciences Padova, University of Padova, 2-35129 Padova, Italy
| | - Bert Blaauw
- Venetian Institute of Molecular Medicine (VIMM), Department of Biomedical Sciences Padova, University of Padova, 2-35129 Padova, Italy
| | - Stefan Günther
- Max Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231 Bad Nauheim, Germany
| | - Stefan Müller
- Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231 Bad Nauheim, Germany
| | - Marcus Krüger
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany
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41
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Lack of cyclin D3 induces skeletal muscle fiber-type shifting, increased endurance performance and hypermetabolism. Sci Rep 2018; 8:12792. [PMID: 30143714 PMCID: PMC6109157 DOI: 10.1038/s41598-018-31090-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 08/10/2018] [Indexed: 12/25/2022] Open
Abstract
The mitogen-induced D-type cyclins (D1, D2 and D3) are regulatory subunits of the cyclin-dependent kinases CDK4 and CDK6 that drive progression through the G1 phase of the cell cycle. In skeletal muscle, cyclin D3 plays a unique function in controlling the proliferation/differentiation balance of myogenic progenitor cells. Here, we show that cyclin D3 also performs a novel function, regulating muscle fiber type-specific gene expression. Mice lacking cyclin D3 display an increased number of myofibers with higher oxidative capacity in fast-twitch muscle groups, primarily composed of myofibers that utilize glycolytic metabolism. The remodeling of myofibers toward a slower, more oxidative phenotype is accompanied by enhanced running endurance and increased energy expenditure and fatty acid oxidation. In addition, gene expression profiling of cyclin D3-/- muscle reveals the upregulation of genes encoding proteins involved in the regulation of contractile function and metabolic markers specifically expressed in slow-twitch and fast-oxidative myofibers, many of which are targets of MEF2 and/or NFAT transcription factors. Furthermore, cyclin D3 can repress the calcineurin- or MEF2-dependent activation of a slow fiber-specific promoter in cultured muscle cells. These data suggest that cyclin D3 regulates muscle fiber type phenotype, and consequently whole body metabolism, by antagonizing the activity of MEF2 and/or NFAT.
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42
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Terry EE, Zhang X, Hoffmann C, Hughes LD, Lewis SA, Li J, Wallace MJ, Riley LA, Douglas CM, Gutierrez-Monreal MA, Lahens NF, Gong MC, Andrade F, Esser KA, Hughes ME. Transcriptional profiling reveals extraordinary diversity among skeletal muscle tissues. eLife 2018; 7:34613. [PMID: 29809149 PMCID: PMC6008051 DOI: 10.7554/elife.34613] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 05/15/2018] [Indexed: 11/24/2022] Open
Abstract
Skeletal muscle comprises a family of diverse tissues with highly specialized functions. Many acquired diseases, including HIV and COPD, affect specific muscles while sparing others. Even monogenic muscular dystrophies selectively affect certain muscle groups. These observations suggest that factors intrinsic to muscle tissues influence their resistance to disease. Nevertheless, most studies have not addressed transcriptional diversity among skeletal muscles. Here we use RNAseq to profile mRNA expression in skeletal, smooth, and cardiac muscle tissues from mice and rats. Our data set, MuscleDB, reveals extensive transcriptional diversity, with greater than 50% of transcripts differentially expressed among skeletal muscle tissues. We detect mRNA expression of hundreds of putative myokines that may underlie the endocrine functions of skeletal muscle. We identify candidate genes that may drive tissue specialization, including Smarca4, Vegfa, and Myostatin. By demonstrating the intrinsic diversity of skeletal muscles, these data provide a resource for studying the mechanisms of tissue specialization. About 40% of our weight is formed of skeletal muscles, the hundreds of muscles in our bodies that can be voluntarily controlled by our nervous system. At the moment, the research community largely sees all these muscles as a single group whose tissues are virtually interchangeable. Yet, skeletal muscles have highly diverse origins, shapes and roles. For example, our diaphragm is a long muscle that contracts slowly and rhythmically so we can draw breaths, while tiny muscles in our eyes generate the short and precise movements of our eyeballs. Different skeletal muscles also respond in distinct ways to injuries, drugs and diseases. This suggests that these muscles may be diverse at the genetic level. While all the cells in our body have the same genetic information, exactly which genes are turned on and off (or ‘expressed’) changes between types of cells. On top of this ‘on or off’ regulation, the level of expression of a gene – how active it is – can also differ. However, the studies that examine the differences in gene expression between tissues usually overlook skeletal muscles. Here, Terry et al. use genetic techniques to measure how genes are expressed in over 20 types of muscle in mice and rats. The results show that the expression levels of over 50% of all the animals’ genes vary between muscles. In fact, any two types of muscles express on average 13% of their genes differently from each other. The analyses yield further unexpected findings. For example, the expression levels in a muscle in the foot that helps to flex the rodents’ toes are more similar to those found in eye muscles than to the ones observed in limb muscles. These conclusions indicate that skeletal muscles are a widely diverse family of tissues. The research community will be able to use the data collected by Terry et al. to explore further the origins and the consequences of the differences between skeletal muscles. This could help researchers to understand why specific groups of muscles are more susceptible to disease, or react differently to a drug. This knowledge could also be exploited to refine approaches in tissue engineering, which aims to replace damaged muscles in the body.
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Affiliation(s)
- Erin E Terry
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, United States
| | - Xiping Zhang
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, United States
| | - Christy Hoffmann
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, United States
| | - Laura D Hughes
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
| | - Scott A Lewis
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, United States
| | - Jiajia Li
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, United States
| | - Matthew J Wallace
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, United States
| | - Lance A Riley
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, United States
| | - Collin M Douglas
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, United States
| | - Miguel A Gutierrez-Monreal
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, United States
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Ming C Gong
- Department of Physiology, University of Kentucky School of Medicine, Lexington, United States
| | - Francisco Andrade
- Department of Physiology, University of Kentucky School of Medicine, Lexington, United States
| | - Karyn A Esser
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, United States
| | - Michael E Hughes
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, United States
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43
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Verbrugge SAJ, Schönfelder M, Becker L, Yaghoob Nezhad F, Hrabě de Angelis M, Wackerhage H. Genes Whose Gain or Loss-Of-Function Increases Skeletal Muscle Mass in Mice: A Systematic Literature Review. Front Physiol 2018; 9:553. [PMID: 29910734 PMCID: PMC5992403 DOI: 10.3389/fphys.2018.00553] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/30/2018] [Indexed: 12/20/2022] Open
Abstract
Skeletal muscle mass differs greatly in mice and humans and this is partially inherited. To identify muscle hypertrophy candidate genes we conducted a systematic review to identify genes whose experimental loss or gain-of-function results in significant skeletal muscle hypertrophy in mice. We found 47 genes that meet our search criteria and cause muscle hypertrophy after gene manipulation. They are from high to small effect size: Ski, Fst, Acvr2b, Akt1, Mstn, Klf10, Rheb, Igf1, Pappa, Ppard, Ikbkb, Fstl3, Atgr1a, Ucn3, Mcu, Junb, Ncor1, Gprasp1, Grb10, Mmp9, Dgkz, Ppargc1a (specifically the Ppargc1a4 isoform), Smad4, Ltbp4, Bmpr1a, Crtc2, Xiap, Dgat1, Thra, Adrb2, Asb15, Cast, Eif2b5, Bdkrb2, Tpt1, Nr3c1, Nr4a1, Gnas, Pld1, Crym, Camkk1, Yap1, Inhba, Tp53inp2, Inhbb, Nol3, Esr1. Knock out, knock down, overexpression or a higher activity of these genes causes overall muscle hypertrophy as measured by an increased muscle weight or cross sectional area. The mean effect sizes range from 5 to 345% depending on the manipulated gene as well as the muscle size variable and muscle investigated. Bioinformatical analyses reveal that Asb15, Klf10, Tpt1 are most highly expressed hypertrophy genes in human skeletal muscle when compared to other tissues. Many of the muscle hypertrophy-regulating genes are involved in transcription and ubiquitination. Especially genes belonging to three signaling pathways are able to induce hypertrophy: (a) Igf1-Akt-mTOR pathway, (b) myostatin-Smad signaling, and (c) the angiotensin-bradykinin signaling pathway. The expression of several muscle hypertrophy-inducing genes and the phosphorylation of their protein products changes after human resistance and high intensity exercise, in maximally stimulated mouse muscle or in overloaded mouse plantaris.
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Affiliation(s)
- Sander A. J. Verbrugge
- Exercise Biology Group, Faculty of Sport and Health Sciences, Technical University of Munich, Munich, Germany
| | - Martin Schönfelder
- Exercise Biology Group, Faculty of Sport and Health Sciences, Technical University of Munich, Munich, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Fakhreddin Yaghoob Nezhad
- Exercise Biology Group, Faculty of Sport and Health Sciences, Technical University of Munich, Munich, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Freising, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Henning Wackerhage
- Exercise Biology Group, Faculty of Sport and Health Sciences, Technical University of Munich, Munich, Germany
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44
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Murgia M, Toniolo L, Nagaraj N, Ciciliot S, Vindigni V, Schiaffino S, Reggiani C, Mann M. Single Muscle Fiber Proteomics Reveals Fiber-Type-Specific Features of Human Muscle Aging. Cell Rep 2018; 19:2396-2409. [PMID: 28614723 DOI: 10.1016/j.celrep.2017.05.054] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/10/2017] [Accepted: 05/17/2017] [Indexed: 12/20/2022] Open
Abstract
Skeletal muscle is a key tissue in human aging, which affects different muscle fiber types unequally. We developed a highly sensitive single muscle fiber proteomics workflow to study human aging and show that the senescence of slow and fast muscle fibers is characterized by diverging metabolic and protein quality control adaptations. Whereas mitochondrial content declines with aging in both fiber types, glycolysis and glycogen metabolism are upregulated in slow but downregulated in fast muscle fibers. Aging mitochondria decrease expression of the redox enzyme monoamine oxidase A. Slow fibers upregulate a subset of actin and myosin chaperones, whereas an opposite change happens in fast fibers. These changes in metabolism and sarcomere quality control may be related to the ability of slow, but not fast, muscle fibers to maintain their mass during aging. We conclude that single muscle fiber analysis by proteomics can elucidate pathophysiology in a sub-type-specific manner.
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Affiliation(s)
- Marta Murgia
- Max-Planck-Institute of Biochemistry, Martinsried 82152, Germany; Department of Biomedical Science, University of Padova, Padua 35121, Italy.
| | - Luana Toniolo
- Department of Biomedical Science, University of Padova, Padua 35121, Italy
| | | | - Stefano Ciciliot
- Venetian Institute of Molecular Medicine, Padua 35129, Italy; Department of Medicine, University of Padua, Padua 35128, Italy
| | - Vincenzo Vindigni
- Department of Neurosciences, University of Padova, Padua 35128, Italy
| | | | - Carlo Reggiani
- Department of Biomedical Science, University of Padova, Padua 35121, Italy
| | - Matthias Mann
- Max-Planck-Institute of Biochemistry, Martinsried 82152, Germany.
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45
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Ruiz A, Dror E, Handschin C, Furrer R, Perez-Schindler J, Bachmann C, Treves S, Zorzato F. Over-expression of a retinol dehydrogenase (SRP35/DHRS7C) in skeletal muscle activates mTORC2, enhances glucose metabolism and muscle performance. Sci Rep 2018; 8:636. [PMID: 29330505 PMCID: PMC5766524 DOI: 10.1038/s41598-017-18844-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/18/2017] [Indexed: 12/31/2022] Open
Abstract
SRP-35 is a short-chain dehydrogenase/reductase belonging to the DHRS7C dehydrogenase/ reductase family 7. Here we show that its over-expression in mouse skeletal muscles induces enhanced muscle performance in vivo, which is not related to alterations in excitation-contraction coupling but rather linked to enhanced glucose metabolism. Over-expression of SRP-35 causes increased phosphorylation of AktS473, triggering plasmalemmal targeting of GLUT4 and higher glucose uptake into muscles. SRP-35 signaling involves RARα and RARγ (non-genomic effect), PI3K and mTORC2. We also demonstrate that all-trans retinoic acid, a downstream product of the enzymatic activity of SRP-35, mimics the effect of SRP-35 in skeletal muscle, inducing a synergistic effect with insulin on AKTS473 phosphorylation. These results indicate that SRP-35 affects skeletal muscle metabolism and may represent an important target for the treatment of metabolic diseases.
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Affiliation(s)
- Alexis Ruiz
- Departments of Anesthesia and of Biomedicine, Basel University Hospital, Hebelstrasse 20, 4031, Basel, Switzerland
| | - Erez Dror
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | | | - Regula Furrer
- Biozentrum, University of Basel, CH-4056, Basel, Switzerland
| | | | - Christoph Bachmann
- Departments of Anesthesia and of Biomedicine, Basel University Hospital, Hebelstrasse 20, 4031, Basel, Switzerland
| | - Susan Treves
- Departments of Anesthesia and of Biomedicine, Basel University Hospital, Hebelstrasse 20, 4031, Basel, Switzerland.,Department of Life Sciences, General Pathology section, University of Ferrara, Via Borsari 46, 44100, Ferrara, Italy
| | - Francesco Zorzato
- Departments of Anesthesia and of Biomedicine, Basel University Hospital, Hebelstrasse 20, 4031, Basel, Switzerland. .,Department of Life Sciences, General Pathology section, University of Ferrara, Via Borsari 46, 44100, Ferrara, Italy.
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46
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Cretoiu D, Pavelescu L, Duica F, Radu M, Suciu N, Cretoiu SM. Myofibers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1088:23-46. [PMID: 30390246 DOI: 10.1007/978-981-13-1435-3_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Muscle tissue is a highly specialized type of tissue, made up of cells that have as their fundamental properties excitability and contractility. The cellular elements that make up this type of tissue are called muscle fibers, or myofibers, because of the elongated shape they have. Contractility is due to the presence of myofibrils in the muscle fiber cytoplasm, as large cellular assemblies. Also, myofibers are responsible for the force that the muscle generates which represents a countless aspect of human life. Movements due to muscles are based on the ability of muscle fibers to use the chemical energy procured in metabolic processes, to shorten and then to return to the original dimensions. We describe in detail the levels of organization for the myofiber, and we correlate the structural aspects with the functional ones, beginning with neuromuscular transmission down to the biochemical reactions achieved in the sarcoplasmic reticulum by the release of Ca2+ and the cycling of crossbridges. Furthermore, we are reviewing the types of muscle contractions and the fiber-type classification.
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Affiliation(s)
- Dragos Cretoiu
- Alessandrescu-Rusescu National Institute of Mother and Child Health, Fetal Medicine Excellence Research Center Bucharest, Bucharest, Romania.,Division of Cell and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Luciana Pavelescu
- Division of Cell and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Florentina Duica
- Alessandrescu-Rusescu National Institute of Mother and Child Health, Fetal Medicine Excellence Research Center Bucharest, Bucharest, Romania
| | - Mihaela Radu
- Alessandrescu-Rusescu National Institute of Mother and Child Health, Fetal Medicine Excellence Research Center Bucharest, Bucharest, Romania
| | - Nicolae Suciu
- Alessandrescu-Rusescu National Institute of Mother and Child Health, Fetal Medicine Excellence Research Center Bucharest, Bucharest, Romania
| | - Sanda Maria Cretoiu
- Division of Cell and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.
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47
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Mechanical isolation, and measurement of force and myoplasmic free [Ca 2+] in fully intact single skeletal muscle fibers. Nat Protoc 2017; 12:1763-1776. [PMID: 28771237 DOI: 10.1038/nprot.2017.056] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mechanical dissection of single intact mammalian skeletal muscle fibers permits real-time measurement of intracellular properties and contractile function of living fibers. A major advantage of mechanical over enzymatic fiber dissociation is that single fibers can be isolated with their tendons remaining attached, which allows contractile forces (in the normal expected range of 300-450 kN/m2) to be measured during electrical stimulation. Furthermore, the sarcolemma of single fibers remains fully intact after mechanical dissection, and hence the living fibers can be studied with intact intracellular milieu and normal function and metabolic properties, as well as ionic control. Given that Ca2+ is the principal regulator of the contractile force, measurements of myoplasmic free [Ca2+] ([Ca2+]i) can be used to further delineate the intrinsic mechanisms underlying changes in skeletal muscle function. [Ca2+]i measurements are most commonly performed in intact single fibers using ratiometric fluorescent indicators such as indo-1 or fura-2. These Ca2+ indicators are introduced into the fiber by pressure injection or by using the membrane-permeable indo-1 AM, and [Ca2+]i is measured by calculating a ratio of the fluorescence at specific wavelengths emitted for the Ca2+-free and Ca2+-bound forms of the dye. We describe here the procedures for mechanical dissection, and for force and [Ca2+]i measurement in intact single fibers from mouse flexor digitorum brevis (FDB) muscle, which is the most commonly used muscle in studies using intact single fibers. This technique can also be used to isolate intact single fibers from various muscles and from various species. As an alternative to Ca2+ indicators, single fibers can also be loaded with fluorescent indicators to measure, for instance, reactive oxygen species, pH, and [Mg2+], or they can be injected with proteins to change functional properties. The entire protocol, from dissection to the start of an experiment on a single fiber, takes ∼3 h.
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Wu CL, Satomi Y, Walsh K. RNA-seq and metabolomic analyses of Akt1-mediated muscle growth reveals regulation of regenerative pathways and changes in the muscle secretome. BMC Genomics 2017; 18:181. [PMID: 28209124 PMCID: PMC5314613 DOI: 10.1186/s12864-017-3548-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 02/02/2017] [Indexed: 12/20/2022] Open
Abstract
Background Skeletal muscle is a major regulator of systemic metabolism as it serves as the major site for glucose disposal and the main reservoir for amino acids. With aging, cachexia, starvation, and myositis, there is a preferential loss of fast glycolytic muscle fibers. We previously reported a mouse model in which a constitutively-active Akt transgene is induced to express in a subset of muscle groups leading to the hypertrophy of type IIb myofibers with an accompanying increase in strength. This muscle growth protects mice in various cardio-metabolic disease models, but little is known about the underlying cellular and molecular mechanisms by which fast-twitch muscle impacts disease processes and regulates distant tissues. In the present study, poly (A) + tail mRNA-seq and non-targeted metabolomics were performed to characterize the transcriptome and metabolome of the hypertrophic gastrocnemius muscle from Akt1-transgenic mice. Results Combined metabolomics and transcriptomic analyses revealed that Akt1-induced muscle growth mediated a metabolic shift involving reductions in glycolysis and oxidative phosphorylation, but enhanced pentose phosphate pathway activation and increased branch chain amino acid accumulation. Pathway analysis for the 4,027 differentially expressed genes in muscle identified enriched signaling pathways involving growth, cell cycle regulation, and inflammation. Consistent with a regenerative transcriptional signature, the transgenic muscle tissue was found to be comprised of fibers with centralized nuclei that are positive for embryonic myosin heavy chain. Immunohistochemical analysis also revealed the presence of inflammatory cells associated with the regenerating fibers. Signal peptide prediction analysis revealed 240 differentially expressed in muscle transcripts that potentially encode secreted proteins. A number of these secreted factors have signaling properties that are consistent with the myogenic, metabolic and cardiovascular-protective properties that have previously been associated with type IIb muscle growth. Conclusions This study provides the first extensive transcriptomic sequencing/metabolomics analysis for a model of fast-twitch myofiber growth. These data reveal that enhanced Akt signaling promotes the activation of pathways that are important for the production of proteins and nucleic acids. Numerous transcripts potentially encoding muscle secreted proteins were identified, indicating the importance of fast-twitch muscle in inter-tissue communication. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3548-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chia-Ling Wu
- Molecular Cardiology, Whitaker Cardiovascular Institute, Boston University School of Medicine, 715 Albany Street, W-611, Boston, MA, 02118, USA
| | - Yoshinori Satomi
- Integrated Technology Research Laboratories, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Kenneth Walsh
- Molecular Cardiology, Whitaker Cardiovascular Institute, Boston University School of Medicine, 715 Albany Street, W-611, Boston, MA, 02118, USA.
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Hagihara H, Horikawa T, Nakamura HK, Umemori J, Shoji H, Kamitani Y, Miyakawa T. Circadian Gene Circuitry Predicts Hyperactive Behavior in a Mood Disorder Mouse Model. Cell Rep 2016; 14:2784-96. [PMID: 27028761 DOI: 10.1016/j.celrep.2016.02.067] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/07/2016] [Accepted: 02/22/2016] [Indexed: 11/26/2022] Open
Abstract
Bipolar disorder, also known as manic-depressive illness, causes swings in mood and activity levels at irregular intervals. Such changes are difficult to predict, and their molecular basis remains unknown. Here, we use infradian (longer than a day) cyclic activity levels in αCaMKII (Camk2a) mutant mice as a proxy for such mood-associated changes. We report that gene-expression patterns in the hippocampal dentate gyrus could retrospectively predict whether the mice were in a state of high or low locomotor activity (LA). Expression of a subset of circadian genes, as well as levels of cAMP and pCREB, possible upstream regulators of circadian genes, were correlated with LA states, suggesting that the intrinsic molecular circuitry changes concomitant with infradian oscillatory LA. Taken together, these findings shed light onto the molecular basis of how irregular biological rhythms and behavior are controlled by the brain.
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Affiliation(s)
- Hideo Hagihara
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Tomoyasu Horikawa
- ATR Computational Neuroscience Laboratories, Soraku-gun, Kyoto 619-0288, Japan
| | - Hironori K Nakamura
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Juzoh Umemori
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Hirotaka Shoji
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Yukiyasu Kamitani
- ATR Computational Neuroscience Laboratories, Soraku-gun, Kyoto 619-0288, Japan; Graduate School of Informatics, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Tsuyoshi Miyakawa
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan; Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan.
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The High Level of Aberrant Splicing of ISCU in Slow-Twitch Muscle May Involve the Splicing Factor SRSF3. PLoS One 2016; 11:e0165453. [PMID: 27783661 PMCID: PMC5081167 DOI: 10.1371/journal.pone.0165453] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 10/12/2016] [Indexed: 01/08/2023] Open
Abstract
Hereditary myopathy with lactic acidosis (HML) is an autosomal recessive disease caused by an intronic one-base mutation in the iron-sulfur cluster assembly (ISCU) gene, resulting in aberrant splicing. The incorrectly spliced transcripts contain a 100 or 86 bp intron sequence encoding a non-functional ISCU protein, which leads to defects in several Fe-S containing proteins in the respiratory chain and the TCA cycle. The symptoms in HML are restricted to skeletal muscle, and it has been proposed that this effect is due to higher levels of incorrectly spliced ISCU in skeletal muscle compared with other energy-demanding tissues. In this study, we confirm that skeletal muscle contains the highest levels of incorrect ISCU splice variants compared with heart, brain, liver and kidney using a transgenic mouse model expressing human HML mutated ISCU. We also show that incorrect splicing occurs to a significantly higher extent in the slow-twitch soleus muscle compared with the gastrocnemius and quadriceps. The splicing factor serine/arginine-rich splicing factor 3 (SRSF3) was identified as a potential candidate for the slow fiber specific regulation of ISCU splicing since this factor was expressed at higher levels in the soleus compared to the gastrocnemius and quadriceps. We identified an interaction between SRSF3 and the ISCU transcript, and by overexpressing SRSF3 in human myoblasts we observed increased levels of incorrectly spliced ISCU, while knockdown of SRSF3 resulted in decreased levels. We therefore suggest that SRSF3 may participate in the regulation of the incorrect splicing of mutant ISCU and may, at least partially, explain the muscle-specific symptoms of HML.
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