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Tran MP, Ochoa Reyes D, Weitzel AJ, Saxena A, Hiller M, Cooper KL. Gene expression differences associated with intrinsic hindfoot muscle loss in the jerboa, Jaculus jaculus. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024. [PMID: 38946691 DOI: 10.1002/jez.b.23268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/16/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
Vertebrate animals that run or jump across sparsely vegetated habitats, such as horses and jerboas, have reduced the number of distal limb bones, and many have lost most or all distal limb muscle. We previously showed that nascent muscles are present in the jerboa hindfoot at birth and that these myofibers are rapidly and completely lost soon after by a process that shares features with pathological skeletal muscle atrophy. Here, we apply an intra- and interspecies differential RNA-Seq approach, comparing jerboa and mouse muscles, to identify gene expression differences associated with the initiation and progression of jerboa hindfoot muscle loss. We show evidence for reduced hepatocyte growth factor and fibroblast growth factor signaling and an imbalance in nitric oxide signaling; all are pathways that are necessary for skeletal muscle development and regeneration. We also find evidence for phagosome formation, which hints at how myofibers may be removed by autophagy or by nonprofessional phagocytes without evidence for cell death or immune cell activation. Last, we show significant overlap between genes associated with jerboa hindfoot muscle loss and genes that are differentially expressed in a variety of human muscle pathologies and rodent models of muscle loss disorders. All together, these data provide molecular insight into the process of evolutionary and developmental muscle loss in jerboa hindfeet.
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Affiliation(s)
- Mai P Tran
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, California, USA
| | - Daniel Ochoa Reyes
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, California, USA
| | - Alexander J Weitzel
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, California, USA
| | - Aditya Saxena
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, California, USA
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Research Institute, Frankfurt, Germany
- Faculty of Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Kimberly L Cooper
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, California, USA
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Wu P, Wang J, Ji X, Chai J, Chen L, Zhang T, Long X, Tu Z, Chen S, Zhang L, Wang K, Zhang L, Guo Z, Wang J. Maternal Hypermethylated Genes Contribute to Intrauterine Growth Retardation of Piglets in Rongchang Pigs. Int J Mol Sci 2024; 25:6462. [PMID: 38928167 PMCID: PMC11203632 DOI: 10.3390/ijms25126462] [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: 04/16/2024] [Revised: 06/04/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
The placenta is a crucial determinant of fetal survival, growth, and development. Deficiency in placental development directly causes intrauterine growth retardation (IUGR). IUGR can lead to fetal growth restriction and an increase in the mortality rate. The genetic mechanisms underlying IUGR development, however, remain unclear. In the present study, we integrated whole-genome DNA methylation and transcriptomic analyses to determine distinct gene expression patterns in various placental tissues to identify pivotal genes that are implicated with IUGR development. By performing RNA-sequencing analysis, 1487 differentially expressed genes (DEGs), with 737 upregulated and 750 downregulated genes, were identified in IUGR pigs (H_IUGR) compared with that in normal birth weight pigs (N_IUGR) (p < 0.05); furthermore, 77 miRNAs, 1331 lncRNAs, and 61 circRNAs were differentially expressed. The protein-protein interaction network analysis revealed that among these DEGs, the genes GNGT1, ANXA1, and CDC20 related to cellular developmental processes and blood vessel development were the key genes associated with the development of IUGR. A total of 495,870 differentially methylated regions were identified between the N_IUGR and H_IUGR groups, which included 25,053 differentially methylated genes (DMEs); moreover, the overall methylation level was higher in the H_IUGR group than in the N_IUGR group. Combined analysis showed an inverse correlation between methylation levels and gene expression. A total of 1375 genes involved in developmental processes, tissue development, and immune system regulation exhibited methylation differences in gene expression levels in the promoter regions and gene ontology regions. Five genes, namely, ANXA1, ADM, NRP2, SHH, and SMAD1, with high methylation levels were identified as potential contributors to IUGR development. These findings provide valuable insights that DNA methylation plays a crucial role in the epigenetic regulation of gene expression and mammalian development and that DNA-hypermethylated genes contribute to IUGR development in Rongchang pigs.
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Affiliation(s)
- Pingxian Wu
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing 402460, China (S.C.)
- National Center of Technology Innovation for Pigs, Rongchang, Chongqing 402460, China
- Chongqing Modern Agricultural Industry Technology System, Chongqing 401120, China
| | - Junge Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiang Ji
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jie Chai
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing 402460, China (S.C.)
- National Center of Technology Innovation for Pigs, Rongchang, Chongqing 402460, China
- Chongqing Modern Agricultural Industry Technology System, Chongqing 401120, China
| | - Li Chen
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing 402460, China (S.C.)
- National Center of Technology Innovation for Pigs, Rongchang, Chongqing 402460, China
- Chongqing Modern Agricultural Industry Technology System, Chongqing 401120, China
| | - Tinghuan Zhang
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing 402460, China (S.C.)
- National Center of Technology Innovation for Pigs, Rongchang, Chongqing 402460, China
| | - Xi Long
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing 402460, China (S.C.)
- National Center of Technology Innovation for Pigs, Rongchang, Chongqing 402460, China
- Chongqing Modern Agricultural Industry Technology System, Chongqing 401120, China
| | - Zhi Tu
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing 402460, China (S.C.)
- National Center of Technology Innovation for Pigs, Rongchang, Chongqing 402460, China
- Chongqing Modern Agricultural Industry Technology System, Chongqing 401120, China
| | - Siqing Chen
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing 402460, China (S.C.)
- National Center of Technology Innovation for Pigs, Rongchang, Chongqing 402460, China
| | - Lijuan Zhang
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing 402460, China (S.C.)
- National Center of Technology Innovation for Pigs, Rongchang, Chongqing 402460, China
| | - Ketian Wang
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing 402460, China (S.C.)
- National Center of Technology Innovation for Pigs, Rongchang, Chongqing 402460, China
| | - Liang Zhang
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing 402460, China (S.C.)
- National Center of Technology Innovation for Pigs, Rongchang, Chongqing 402460, China
| | - Zongyi Guo
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing 402460, China (S.C.)
- National Center of Technology Innovation for Pigs, Rongchang, Chongqing 402460, China
- Chongqing Modern Agricultural Industry Technology System, Chongqing 401120, China
| | - Jinyong Wang
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing 402460, China (S.C.)
- National Center of Technology Innovation for Pigs, Rongchang, Chongqing 402460, China
- Chongqing Modern Agricultural Industry Technology System, Chongqing 401120, China
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Kolonay DW, Sattler KM, Strawser C, Rafael-Fortney J, Mihaylova MM, Miller KE, Lepper C, Baskin KK. Temporal regulation of the Mediator complex during muscle proliferation, differentiation, regeneration, aging, and disease. Front Cell Dev Biol 2024; 12:1331563. [PMID: 38690566 PMCID: PMC11058648 DOI: 10.3389/fcell.2024.1331563] [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: 11/01/2023] [Accepted: 03/26/2024] [Indexed: 05/02/2024] Open
Abstract
Genesis of skeletal muscle relies on the differentiation and fusion of mono-nucleated muscle progenitor cells into the multi-nucleated muscle fiber syncytium. The temporally-controlled cellular and morphogenetic changes underlying this process are initiated by a series of highly coordinated transcription programs. At the core, the myogenic differentiation cascade is driven by muscle-specific transcription factors, i.e., the Myogenic Regulatory Factors (MRFs). Despite extensive knowledge on the function of individual MRFs, very little is known about how they are coordinated. Ultimately, highly specific coordination of these transcription programs is critical for their masterfully timed transitions, which in turn facilitates the intricate generation of skeletal muscle fibers from a naïve pool of progenitor cells. The Mediator complex links basal transcriptional machinery and transcription factors to regulate transcription and could be the integral component that coordinates transcription factor function during muscle differentiation, growth, and maturation. In this study, we systematically deciphered the changes in Mediator complex subunit expression in skeletal muscle development, regeneration, aging, and disease. We incorporated our in vitro and in vivo experimental results with analysis of publicly available RNA-seq and single nuclei RNA-seq datasets and uncovered the regulation of Mediator subunits in different physiological and temporal contexts. Our experimental results revealed that Mediator subunit expression during myogenesis is highly dynamic. We also discovered unique temporal patterns of Mediator expression in muscle stem cells after injury and during the early regeneration period, suggesting that Mediator subunits may have unique contributions to directing muscle stem cell fate. Although we observed few changes in Mediator subunit expression in aging muscles compared to younger muscles, we uncovered extensive heterogeneity of Mediator subunit expression in dystrophic muscle nuclei, characteristic of chronic muscle degeneration and regeneration cycles. Taken together, our study provides a glimpse of the complex regulation of Mediator subunit expression in the skeletal muscle cell lineage and serves as a springboard for mechanistic studies into the function of individual Mediator subunits in skeletal muscle.
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Affiliation(s)
- Dominic W. Kolonay
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Kristina M. Sattler
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Corinne Strawser
- Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Jill Rafael-Fortney
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Maria M. Mihaylova
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Katherine E. Miller
- Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Christoph Lepper
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Kedryn K. Baskin
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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Najm A, Niculescu AG, Grumezescu AM, Beuran M. Emerging Therapeutic Strategies in Sarcopenia: An Updated Review on Pathogenesis and Treatment Advances. Int J Mol Sci 2024; 25:4300. [PMID: 38673885 PMCID: PMC11050002 DOI: 10.3390/ijms25084300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Sarcopenia is a prevalent degenerative skeletal muscle condition in the elderly population, posing a tremendous burden on diseased individuals and healthcare systems worldwide. Conventionally, sarcopenia is currently managed through nutritional interventions, physical therapy, and lifestyle modification, with no pharmaceutical agents being approved for specific use in this disease. As the pathogenesis of sarcopenia is still poorly understood and there is no treatment recognized as universally effective, recent research efforts have been directed at better comprehending this illness and diversifying treatment strategies. In this respect, this paper overviews the new advances in sarcopenia treatment in correlation with its underlying mechanisms. Specifically, this review creates an updated framework for sarcopenia, describing its etiology, pathogenesis, risk factors, and conventional treatments, further discussing emerging therapeutic approaches like new drug formulations, drug delivery systems, stem cell therapies, and tissue-engineered scaffolds in more detail.
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Affiliation(s)
- Alfred Najm
- Department of Surgery, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari, Sector 5, 050474 Bucharest, Romania; (A.N.); (M.B.)
- Emergency Hospital Floreasca Bucharest, 8 Calea Floresca, Sector 1, 014461 Bucharest, Romania
| | - Adelina-Gabriela Niculescu
- Research Institute of the University of Bucharest—ICUB, University of Bucharest, 050657 Bucharest, Romania;
- Department of Science and Engineering of Oxide Materials and Nanomaterials, National University of Science and Technology Politehnica Bucharest, 011061 Bucharest, Romania
| | - Alexandru Mihai Grumezescu
- Research Institute of the University of Bucharest—ICUB, University of Bucharest, 050657 Bucharest, Romania;
- Department of Science and Engineering of Oxide Materials and Nanomaterials, National University of Science and Technology Politehnica Bucharest, 011061 Bucharest, Romania
| | - Mircea Beuran
- Department of Surgery, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari, Sector 5, 050474 Bucharest, Romania; (A.N.); (M.B.)
- Emergency Hospital Floreasca Bucharest, 8 Calea Floresca, Sector 1, 014461 Bucharest, Romania
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5
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Ducommun S, Jannig PR, Cervenka I, Murgia M, Mittenbühler MJ, Chernogubova E, Dias JM, Jude B, Correia JC, Van Vranken JG, Ocana-Santero G, Porsmyr-Palmertz M, McCann Haworth S, Martínez-Redondo V, Liu Z, Carlström M, Mann M, Lanner JT, Teixeira AI, Maegdefessel L, Spiegelman BM, Ruas JL. Mustn1 is a smooth muscle cell-secreted microprotein that modulates skeletal muscle extracellular matrix composition. Mol Metab 2024; 82:101912. [PMID: 38458566 PMCID: PMC10950823 DOI: 10.1016/j.molmet.2024.101912] [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] [Received: 12/19/2023] [Revised: 02/21/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024] Open
Abstract
OBJECTIVE Skeletal muscle plasticity and remodeling are critical for adapting tissue function to use, disuse, and regeneration. The aim of this study was to identify genes and molecular pathways that regulate the transition from atrophy to compensatory hypertrophy or recovery from injury. Here, we have used a mouse model of hindlimb unloading and reloading, which causes skeletal muscle atrophy, and compensatory regeneration and hypertrophy, respectively. METHODS We analyzed mouse skeletal muscle at the transition from hindlimb unloading to reloading for changes in transcriptome and extracellular fluid proteome. We then used qRT-PCR, immunohistochemistry, and bulk and single-cell RNA sequencing data to determine Mustn1 gene and protein expression, including changes in gene expression in mouse and human skeletal muscle with different challenges such as exercise and muscle injury. We generated Mustn1-deficient genetic mouse models and characterized them in vivo and ex vivo with regard to muscle function and whole-body metabolism. We isolated smooth muscle cells and functionally characterized them, and performed transcriptomics and proteomics analysis of skeletal muscle and aorta of Mustn1-deficient mice. RESULTS We show that Mustn1 (Musculoskeletal embryonic nuclear protein 1, also known as Mustang) is highly expressed in skeletal muscle during the early stages of hindlimb reloading. Mustn1 expression is transiently elevated in mouse and human skeletal muscle in response to intense exercise, resistance exercise, or injury. We find that Mustn1 expression is highest in smooth muscle-rich tissues, followed by skeletal muscle fibers. Muscle from heterozygous Mustn1-deficient mice exhibit differences in gene expression related to extracellular matrix and cell adhesion, compared to wild-type littermates. Mustn1-deficient mice have normal muscle and aorta function and whole-body glucose metabolism. We show that Mustn1 is secreted from smooth muscle cells, and that it is present in arterioles of the muscle microvasculature and in muscle extracellular fluid, particularly during the hindlimb reloading phase. Proteomics analysis of muscle from Mustn1-deficient mice confirms differences in extracellular matrix composition, and female mice display higher collagen content after chemically induced muscle injury compared to wild-type littermates. CONCLUSIONS We show that, in addition to its previously reported intracellular localization, Mustn1 is a microprotein secreted from smooth muscle cells into the muscle extracellular space. We explore its role in muscle ECM deposition and remodeling in homeostasis and upon muscle injury. The role of Mustn1 in fibrosis and immune infiltration upon muscle injury and dystrophies remains to be investigated, as does its potential for therapeutic interventions.
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Affiliation(s)
- Serge Ducommun
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Paulo R Jannig
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Igor Cervenka
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Marta Murgia
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B, 35131 Padua, Italy; Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Melanie J Mittenbühler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ekaterina Chernogubova
- Department of Medicine, Cardiovascular Unit, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - José M Dias
- Department of Cell and Molecular Biology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden; Nanomedicine and Spatial Biology, Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Baptiste Jude
- Molecular Muscle Physiology and Pathophysiology, Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Jorge C Correia
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden
| | | | - Gabriel Ocana-Santero
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Margareta Porsmyr-Palmertz
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sarah McCann Haworth
- Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Vicente Martínez-Redondo
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Zhengye Liu
- Molecular Muscle Physiology and Pathophysiology, Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Mattias Carlström
- Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Matthias Mann
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Johanna T Lanner
- Molecular Muscle Physiology and Pathophysiology, Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ana I Teixeira
- Nanomedicine and Spatial Biology, Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Lars Maegdefessel
- Department of Medicine, Cardiovascular Unit, Karolinska Institutet, 171 77 Stockholm, Sweden; Institute of Molecular Vascular Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; German Center for Cardiovascular Research DZHK, Partner Site Munich Heart Alliance, 10785 Berlin, Germany
| | - Bruce M Spiegelman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jorge L Ruas
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Biomedicum, Karolinska Institutet, 171 77 Stockholm, Sweden; Department of Pharmacology and Stanley and Judith Frankel Institute for Heart & Brain Health, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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6
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Girolamo DD, Benavente-Diaz M, Murolo M, Grimaldi A, Lopes PT, Evano B, Kuriki M, Gioftsidi S, Laville V, Tinevez JY, Letort G, Mella S, Tajbakhsh S, Comai G. Extraocular muscle stem cells exhibit distinct cellular properties associated with non-muscle molecular signatures. Development 2024; 151:dev202144. [PMID: 38240380 DOI: 10.1242/dev.202144] [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: 06/29/2023] [Accepted: 12/27/2023] [Indexed: 02/22/2024]
Abstract
Skeletal muscle stem cells (MuSCs) are recognised as functionally heterogeneous. Cranial MuSCs are reported to have greater proliferative and regenerative capacity when compared with those in the limb. A comprehensive understanding of the mechanisms underlying this functional heterogeneity is lacking. Here, we have used clonal analysis, live imaging and single cell transcriptomic analysis to identify crucial features that distinguish extraocular muscle (EOM) from limb muscle stem cell populations. A MyogeninntdTom reporter showed that the increased proliferation capacity of EOM MuSCs correlates with deferred differentiation and lower expression of the myogenic commitment gene Myod. Unexpectedly, EOM MuSCs activated in vitro expressed a large array of extracellular matrix components typical of mesenchymal non-muscle cells. Computational analysis underscored a distinct co-regulatory module, which is absent in limb MuSCs, as driver of these features. The EOM transcription factor network, with Foxc1 as key player, appears to be hardwired to EOM identity as it persists during growth, disease and in vitro after several passages. Our findings shed light on how high-performing MuSCs regulate myogenic commitment by remodelling their local environment and adopting properties not generally associated with myogenic cells.
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Affiliation(s)
- Daniela Di Girolamo
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Maria Benavente-Diaz
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Sorbonne Universités, Complexité du Vivant, F-75005 Paris, France
| | - Melania Murolo
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Alexandre Grimaldi
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Sorbonne Universités, Complexité du Vivant, F-75005 Paris, France
| | - Priscilla Thomas Lopes
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Brendan Evano
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Mao Kuriki
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Stamatia Gioftsidi
- Université Paris-Est, 77420 Champs-sur- Marne, France
- Freie Universität Berlin, 14195 Berlin, Germany
- Inserm, IMRB U955-E10, 94000 Créteil, France
| | - Vincent Laville
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, 75015 Paris, France
| | - Gaëlle Letort
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 rue du Dr Roux, 75015 Paris, France
| | - Sebastian Mella
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Shahragim Tajbakhsh
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Glenda Comai
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
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7
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Habiballa L, Hruby A, Granic A, Dodds RM, Hillman SJ, Jurk D, Passos JF, Sayer AA. Determining the feasibility of characterising cellular senescence in human skeletal muscle and exploring associations with muscle morphology and physical function at different ages: findings from the MASS_Lifecourse Study. GeroScience 2024; 46:1141-1158. [PMID: 37434081 PMCID: PMC10828484 DOI: 10.1007/s11357-023-00869-4] [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: 04/13/2023] [Accepted: 07/05/2023] [Indexed: 07/13/2023] Open
Abstract
Cellular senescence may be associated with morphological changes in skeletal muscle and changes in physical function with age although there have been few human studies. We aimed to determine the feasibility of characterising cellular senescence in skeletal muscle and explored sex-specific associations between markers of cellular senescence, muscle morphology, and physical function in participants from the MASS_Lifecourse Study. Senescence markers (p16, TAF (Telomere-Associated DNA Damage Foci), HMGB1 (High Mobility Group Box 1), and Lamin B1) and morphological characteristics (fibre size, number, fibrosis, and centrally nucleated fibres) were assessed in muscle biopsies from 40 men and women (age range 47-84) using spatially-resolved methods (immunohistochemistry, immunofluorescence, and RNA and fluorescence in situ hybridisation). The associations between senescence, morphology, and physical function (muscle strength, mass, and physical performance) at different ages were explored. We found that most senescence markers and morphological characteristics were weakly associated with age in men but more strongly, although non-significantly, associated with age in women. Associations between senescence markers, morphology, and physical function were also stronger in women for HMGB1 and grip strength (r = 0.52); TAF, BMI, and muscle mass (r > 0.4); Lamin B1 and fibrosis (r = - 0.5); fibre size and muscle mass (r ≥ 0.4); and gait speed (r = - 0.5). However, these associations were non-significant. In conclusion, we have demonstrated that it is feasible to characterise cellular senescence in human skeletal muscle and to explore associations with morphology and physical function in women and men of different ages. The findings require replication in larger studies.
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Affiliation(s)
- Leena Habiballa
- AGE Research Group, Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry Psychology and Neuroscience, King's College London, London, UK
| | - Adam Hruby
- Robert and Arlene Kogod Center On Aging, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- University of Southern California, Los Angeles, CA, USA
| | - Antoneta Granic
- AGE Research Group, Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK.
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK.
| | - Richard M Dodds
- AGE Research Group, Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Susan J Hillman
- AGE Research Group, Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Diana Jurk
- Robert and Arlene Kogod Center On Aging, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - João F Passos
- Robert and Arlene Kogod Center On Aging, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Avan A Sayer
- AGE Research Group, Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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8
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Housley SN, Gardolinski EA, Nardelli P, Reed J, Rich MM, Cope TC. Mechanosensory encoding in ex vivo muscle-nerve preparations. Exp Physiol 2024; 109:35-44. [PMID: 37119460 PMCID: PMC10613129 DOI: 10.1113/ep090763] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/12/2023] [Indexed: 05/01/2023]
Abstract
Our objective was to evaluate an ex vivo muscle-nerve preparation used to study mechanosensory signalling by low threshold mechanosensory receptors (LTMRs). Specifically, we aimed to assess how well the ex vivo preparation represents in vivo firing behaviours of the three major LTMR subtypes of muscle primary sensory afferents, namely type Ia and II muscle spindle (MS) afferents and type Ib tendon organ afferents. Using published procedures for ex vivo study of LTMRs in mouse hindlimb muscles, we replicated earlier reports on afferent firing in response to conventional stretch paradigms applied to non-contracting, that is passive, muscle. Relative to in vivo studies, stretch-evoked firing for confirmed MS afferents in the ex vivo preparation was markedly reduced in firing rate and deficient in encoding dynamic features of muscle stretch. These deficiencies precluded conventional means of discriminating type Ia and II afferents. Muscle afferents, including confirmed Ib afferents were often indistinguishable based on their similar firing responses to the same physiologically relevant stretch paradigms. These observations raise uncertainty about conclusions drawn from earlier ex vivo studies that either attribute findings to specific afferent types or suggest an absence of treatment effects on dynamic firing. However, we found that replacing the recording solution with bicarbonate buffer resulted in afferent firing rates and profiles more like those seen in vivo. Improving representation of the distinctive sensory encoding properties in ex vivo muscle-nerve preparations will promote accuracy in assigning molecular markers and mechanisms to heterogeneous types of muscle mechanosensory neurons.
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Affiliation(s)
- Stephen N. Housley
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaGAUSA
| | | | - Paul Nardelli
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaGAUSA
| | - J'Ana Reed
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaGAUSA
| | - Mark M. Rich
- Department of Neuroscience, Cell Biology and PhysiologyWright State UniversityDaytonOHUSA
| | - Timothy C. Cope
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaGAUSA
- W.H. Coulter Department of Biomedical EngineeringEmory University and Georgia Institute of Technology, Georgia Institute of TechnologyAtlantaGAUSA
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9
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Singh NP, Wu EY, Fan J, Love MI, Patro R. Tree-based differential testing using inferential uncertainty for RNA-Seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.25.573288. [PMID: 38234739 PMCID: PMC10793400 DOI: 10.1101/2023.12.25.573288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Identifying differentially expressed transcripts poses a crucial yet challenging problem in transcriptomics. Substantial uncertainty is associated with the abundance estimates of certain transcripts which, if ignored, can lead to the exaggeration of false positives and, if included, may lead to reduced power. For a given set of RNA-Seq samples, TreeTerminus arranges transcripts in a hierarchical tree structure that encodes different layers of resolution for interpretation of the abundance of transcriptional groups, with uncertainty generally decreasing as one ascends the tree from the leaves. We introduce trenDi, which utilizes the tree structure from TreeTerminus for differential testing. The candidate nodes are determined in a data-driven manner to maximize the signal that can be extracted from the data while controlling for the uncertainty associated with estimating the transcript abundances. The identified candidate nodes can include transcripts and inner nodes, with no two nodes having an ancestor/descendant relationship. We evaluated our method on both simulated and experimental datasets, comparing its performance with other tree-based differential methods as well as with uncertainty-aware differential transcript/gene expression methods. Our method detects inner nodes that show a strong signal for differential expression, which would have been overlooked when analyzing the transcripts alone.
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Affiliation(s)
- Noor Pratap Singh
- Department of Computer Science, University of Maryland, College Park
| | - Euphy Y. Wu
- Department of Biostatistics, University of North Carolina-Chapel Hill
| | - Jason Fan
- Department of Computer Science, University of Maryland, College Park
| | - Michael I. Love
- Department of Biostatistics, University of North Carolina-Chapel Hill
- Department of Genetics, University of North Carolina-Chapel Hill
| | - Rob Patro
- Department of Computer Science, University of Maryland, College Park
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10
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Savary C, Luciana L, Huchedé P, Tourbez A, Coquet C, Broustal M, Lopez Gonzalez A, Deligne C, Diot T, Naret O, Costa M, Meynard N, Barbet V, Müller K, Tonon L, Gadot N, Degletagne C, Attignon V, Léon S, Vanbelle C, Bomane A, Rochet I, Mournetas V, Oliveira L, Rinaudo P, Bergeron C, Dutour A, Cordier-Bussat M, Roch A, Brandenberg N, El Zein S, Watson S, Orbach D, Delattre O, Dijoud F, Corradini N, Picard C, Maucort-Boulch D, Le Grand M, Pasquier E, Blay JY, Castets M, Broutier L. Fusion-negative rhabdomyosarcoma 3D organoids to predict effective drug combinations: A proof-of-concept on cell death inducers. Cell Rep Med 2023; 4:101339. [PMID: 38118405 PMCID: PMC10772578 DOI: 10.1016/j.xcrm.2023.101339] [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: 04/13/2023] [Revised: 09/29/2023] [Accepted: 11/22/2023] [Indexed: 12/22/2023]
Abstract
Rhabdomyosarcoma (RMS) is the main form of pediatric soft-tissue sarcoma. Its cure rate has not notably improved in the last 20 years following relapse, and the lack of reliable preclinical models has hampered the design of new therapies. This is particularly true for highly heterogeneous fusion-negative RMS (FNRMS). Although methods have been proposed to establish FNRMS organoids, their efficiency remains limited to date, both in terms of derivation rate and ability to accurately mimic the original tumor. Here, we present the development of a next-generation 3D organoid model derived from relapsed adult and pediatric FNRMS. This model preserves the molecular features of the patients' tumors and is expandable for several months in 3D, reinforcing its interest to drug combination screening with longitudinal efficacy monitoring. As a proof-of-concept, we demonstrate its preclinical relevance by reevaluating the therapeutic opportunities of targeting apoptosis in FNRMS from a streamlined approach based on transcriptomic data exploitation.
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Affiliation(s)
- Clara Savary
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Léa Luciana
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Paul Huchedé
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Arthur Tourbez
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Claire Coquet
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Maëlle Broustal
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Alejandro Lopez Gonzalez
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Clémence Deligne
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Thomas Diot
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Olivier Naret
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Mariana Costa
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Nina Meynard
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Virginie Barbet
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Kevin Müller
- Université Aix-Marseille, CNRS 7258, INSERM 1068, Institute Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), 13009 Marseille, France
| | - Laurie Tonon
- Synergie Lyon Cancer, Gilles Thomas' Bioinformatics Platform, Centre Léon Bérard, 69008 Lyon, France
| | - Nicolas Gadot
- Anatomopathology Research Platform, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Cyril Degletagne
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Valéry Attignon
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Sophie Léon
- EX-VIVO Platform, Centre de recherche en cancérologie de Lyon (CRCL), Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Christophe Vanbelle
- Plateforme d'Imagerie cellulaire, Centre de recherche en cancérologie de Lyon (CRCL), Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Alexandra Bomane
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Isabelle Rochet
- Multisite Institute of Pathology, Groupement Hospitalier Est du CHU de Lyon, Hôpital Femme-Mère-Enfant, 69677 Bron, France; Department of Pediatric Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, Centre Léon Bérard, 69008 Lyon, France
| | | | | | | | - Christophe Bergeron
- Department of Pediatric Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, Centre Léon Bérard, 69008 Lyon, France
| | - Aurélie Dutour
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Martine Cordier-Bussat
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Aline Roch
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Nathalie Brandenberg
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Sophie El Zein
- Department of Biopathology, Institut Curie, Paris, France
| | - Sarah Watson
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France; INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie, PSL Research University, Paris, France; Medical Oncology Department, Institut Curie, PSL Research University, Paris, France
| | - Daniel Orbach
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France
| | - Olivier Delattre
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France; INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie, PSL Research University, Paris, France
| | - Frédérique Dijoud
- Multisite Institute of Pathology, Groupement Hospitalier Est du CHU de Lyon, Hôpital Femme-Mère-Enfant, 69677 Bron, France
| | - Nadège Corradini
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Pediatric Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, Centre Léon Bérard, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France
| | - Cécile Picard
- Multisite Institute of Pathology, Groupement Hospitalier Est du CHU de Lyon, Hôpital Femme-Mère-Enfant, 69677 Bron, France
| | - Delphine Maucort-Boulch
- Université Lyon 1, 69100 Villeurbanne, France; Hospices Civils de Lyon, Pôle Santé Publique, Service de Biostatistique et Bioinformatique, 69003 Lyon, France; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, Équipe Biostatistique-Santé, 69100 Villeurbanne, France
| | - Marion Le Grand
- Université Aix-Marseille, CNRS 7258, INSERM 1068, Institute Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), 13009 Marseille, France
| | - Eddy Pasquier
- Université Aix-Marseille, CNRS 7258, INSERM 1068, Institute Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), 13009 Marseille, France
| | - Jean-Yves Blay
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France
| | - Marie Castets
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France.
| | - Laura Broutier
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France.
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11
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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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12
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Andreoletti G, Romano O, Chou HJ, Sefid-Dashti MJ, Grilli A, Chen C, Lakshman N, Purushothaman P, Varfaj F, Mavilio F, Bicciato S, Urbinati F. High-throughput transcriptome analyses from ASPIRO, a phase 1/2/3 study of gene replacement therapy for X-linked myotubular myopathy. Am J Hum Genet 2023; 110:1648-1660. [PMID: 37673065 PMCID: PMC10577074 DOI: 10.1016/j.ajhg.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023] Open
Abstract
X-linked myotubular myopathy (XLMTM) is a severe congenital disease characterized by profound muscle weakness, respiratory failure, and early death. No approved therapy for XLMTM is currently available. Adeno-associated virus (AAV)-mediated gene replacement therapy has shown promise as an investigational therapeutic strategy. We aimed to characterize the transcriptomic changes in muscle biopsies of individuals with XLMTM who received resamirigene bilparvovec (AT132; rAAV8-Des-hMTM1) in the ASPIRO clinical trial and to identify potential biomarkers that correlate with therapeutic outcome. We leveraged RNA-sequencing data from the muscle biopsies of 15 study participants and applied differential expression analysis, gene co-expression analysis, and machine learning to characterize the transcriptomic changes at baseline (pre-dose) and at 24 and 48 weeks after resamirigene bilparvovec dosing. As expected, MTM1 expression levels were significantly increased after dosing (p < 0.0001). Differential expression analysis identified upregulated genes after dosing that were enriched in several pathways, including lipid metabolism and inflammatory response pathways, and downregulated genes were enriched in cell-cell adhesion and muscle development pathways. Genes involved in inflammatory and immune pathways were differentially expressed between participants exhibiting ventilator support reduction of either greater or less than 6 h/day after gene therapy compared to pre-dosing. Co-expression analysis identified similarly regulated genes, which were grouped into modules. Finally, the machine learning model identified five genes, including MTM1, as potential RNA biomarkers to monitor the progress of AAV gene replacement therapy. These findings further extend our understanding of AAV-mediated gene therapy in individuals with XLMTM at the transcriptomic level.
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Affiliation(s)
- Gaia Andreoletti
- Astellas Gene Therapies (formerly Audentes Therapeutics), San Francisco, CA, USA.
| | - Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Hsin-Jung Chou
- Astellas Gene Therapies (formerly Audentes Therapeutics), San Francisco, CA, USA
| | | | - Andrea Grilli
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Clarice Chen
- Astellas Gene Therapies (formerly Audentes Therapeutics), San Francisco, CA, USA; Tox and Text Solutions, LLC, Anaheim, CA 92807, USA
| | - Neema Lakshman
- Astellas Gene Therapies (formerly Audentes Therapeutics), San Francisco, CA, USA
| | - Pravin Purushothaman
- Astellas Gene Therapies (formerly Audentes Therapeutics), San Francisco, CA, USA
| | - Fatbardha Varfaj
- Astellas Gene Therapies (formerly Audentes Therapeutics), San Francisco, CA, USA
| | - Fulvio Mavilio
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Fabrizia Urbinati
- Astellas Gene Therapies (formerly Audentes Therapeutics), San Francisco, CA, USA.
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13
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Lin X, Wang P, Wang W, Zhou H, Zhu S, Feng S, Chen Y, Zhou H, Wang Q, Xin H, Shao X, Wang J. Suppressed Akt/GSK-3β/β-catenin signaling contributes to excessive adipogenesis of fibro-adipogenic progenitors after rotator cuff tears. Cell Death Discov 2023; 9:312. [PMID: 37626040 PMCID: PMC10457376 DOI: 10.1038/s41420-023-01618-4] [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: 04/18/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Muscular fatty infiltration is a common and troublesome pathology after rotator cuff tears (RCT), which mainly derives from fibro-adipogenic progenitors (FAPs). Compared to the RCT, fatty infiltration is not so severe in Achilles tendon tears (ATT). The knowledge of why fatty infiltration is more likely to occur after RCT is limited. In this study, more severe fatty infiltration was verified in supraspinatus than gastrocnemius muscles after tendon injury. Additionally, we revealed higher adipogenic differentiation ability of RCT-FAPs in vitro. Activation of Akt significantly stimulated GSK-3β/β-catenin signaling and thus decreased PPARγ expression and adipogenesis of RCT-FAPs, while the inhibition effect was attenuated by β-catenin inhibitor. Furthermore, Wnt signaling activator BML-284 limited adipogenesis of RCT-FAPs, alleviated muscular fatty infiltration, and improved parameters in gait analysis and treadmill test for RCT model. In conclusion, our study demonstrated that suppressed Akt/GSK-3β/β-catenin signaling increased PPARγ expression and thus contributed to excessive adipogenesis in RCT-FAPs. Modulation of Akt/GSK-3β/β-catenin signaling ameliorated excessive fatty infiltration of rotator cuff muscles and improved shoulder function after RCT.
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Affiliation(s)
- Xingzuan Lin
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peng Wang
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Wang
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
| | - Hao Zhou
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siyuan Zhu
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Yuzhou Chen
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Han Zhou
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qichao Wang
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hanlong Xin
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, China.
| | - Xiexiang Shao
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jianhua Wang
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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14
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Nieves-Rodriguez S, Barthélémy F, Woods JD, Douine ED, Wang RT, Scripture-Adams DD, Chesmore KN, Galasso F, Miceli MC, Nelson SF. Transcriptomic analysis of paired healthy human skeletal muscles to identify modulators of disease severity in DMD. Front Genet 2023; 14:1216066. [PMID: 37576554 PMCID: PMC10415210 DOI: 10.3389/fgene.2023.1216066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023] Open
Abstract
Muscle damage and fibro-fatty replacement of skeletal muscles is a main pathologic feature of Duchenne muscular dystrophy (DMD) with more proximal muscles affected earlier and more distal affected later in the disease course, suggesting that different skeletal muscle groups possess distinctive characteristics that influence their susceptibility to disease. To explore transcriptomic factors driving differential gene expression and modulating DMD skeletal muscle severity, we characterized the transcriptome of vastus lateralis (VL), a more proximal and susceptible muscle, relative to tibialis anterior (TA), a more distal and protected muscle, in 15 healthy individuals using bulk RNA sequencing to identify gene expression differences that may mediate their relative susceptibility to damage with loss of dystrophin. Matching single nuclei RNA sequencing data was generated for 3 of the healthy individuals, to infer cell composition in the bulk RNA sequencing dataset and to improve mapping of differentially expressed genes to their cell source of expression. A total of 3,410 differentially expressed genes were identified and mapped to cell type using single nuclei RNA sequencing of muscle, including long non-coding RNAs and protein coding genes. There was an enrichment of genes involved in calcium release from the sarcoplasmic reticulum, particularly in the myofibers and these myofiber genes were higher in the VL. There was an enrichment of genes in "Collagen-Containing Extracellular Matrix" expressed by fibroblasts, endothelial, smooth muscle and pericytes, with most genes higher in the TA, as well as genes in "Regulation Of Apoptotic Process" expressed across all cell types. Previously reported genetic modifiers were also enriched within the differentially expressed genes. We also identify 6 genes with differential isoform usage between the VL and TA. Lastly, we integrate our findings with DMD RNA sequencing data from the TA, and identify "Collagen-Containing Extracellular Matrix" and "Negative Regulation Of Apoptotic Process" as differentially expressed between DMD compared to healthy. Collectively, these findings propose novel candidate mechanisms that may mediate differential muscle susceptibility in muscular dystrophies and provide new insight into potential therapeutic targets.
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Affiliation(s)
- Shirley Nieves-Rodriguez
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
| | - Florian Barthélémy
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Microbiology, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jeremy D. Woods
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Emilie D. Douine
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Richard T. Wang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
| | - Deirdre D. Scripture-Adams
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Microbiology, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kevin N. Chesmore
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
| | - Francesca Galasso
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - M. Carrie Miceli
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Microbiology, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Stanley F. Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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15
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Hildyard JCW, Piercy RJ. When Size Really Matters: The Eccentricities of Dystrophin Transcription and the Hazards of Quantifying mRNA from Very Long Genes. Biomedicines 2023; 11:2082. [PMID: 37509720 PMCID: PMC10377302 DOI: 10.3390/biomedicines11072082] [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: 06/27/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
At 2.3 megabases in length, the dystrophin gene is enormous: transcription of a single mRNA requires approximately 16 h. Principally expressed in skeletal muscle, the dystrophin protein product protects the muscle sarcolemma against contraction-induced injury, and dystrophin deficiency results in the fatal muscle-wasting disease, Duchenne muscular dystrophy. This gene is thus of key clinical interest, and therapeutic strategies aimed at eliciting dystrophin restoration require quantitative analysis of its expression. Approaches for quantifying dystrophin at the protein level are well-established, however study at the mRNA level warrants closer scrutiny: measured expression values differ in a sequence-dependent fashion, with significant consequences for data interpretation. In this manuscript, we discuss these nuances of expression and present evidence to support a transcriptional model whereby the long transcription time is coupled to a short mature mRNA half-life, with dystrophin transcripts being predominantly nascent as a consequence. We explore the effects of such a model on cellular transcriptional dynamics and then discuss key implications for the study of dystrophin gene expression, focusing on both conventional (qPCR) and next-gen (RNAseq) approaches.
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Affiliation(s)
- John C. W. Hildyard
- Comparative Neuromuscular Disease Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London NW1 0TU, UK;
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16
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Singh NP, Love MI, Patro R. TreeTerminus -creating transcript trees using inferential replicate counts. iScience 2023; 26:106961. [PMID: 37378336 PMCID: PMC10291472 DOI: 10.1016/j.isci.2023.106961] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/18/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
A certain degree of uncertainty is always associated with the transcript abundance estimates. The uncertainty may make many downstream analyses, such as differential testing, difficult for certain transcripts. Conversely, gene-level analysis, though less ambiguous, is often too coarse-grained. We introduce TreeTerminus, a data-driven approach for grouping transcripts into a tree structure where leaves represent individual transcripts and internal nodes represent an aggregation of a transcript set. TreeTerminus constructs trees such that, on average, the inferential uncertainty decreases as we ascend the tree topology. The tree provides the flexibility to analyze data at nodes that are at different levels of resolution in the tree and can be tuned depending on the analysis of interest. We evaluated TreeTerminus on two simulated and two experimental datasets and observed an improved performance compared to transcripts (leaves) and other methods under several different metrics.
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Affiliation(s)
- Noor Pratap Singh
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Michael I. Love
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Rob Patro
- Department of Computer Science, University of Maryland, College Park, MD, USA
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17
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You JS, Kim Y, Lee S, Bashir R, Chen J. RhoA/ROCK signalling activated by ARHGEF3 promotes muscle weakness via autophagy in dystrophic mdx mice. J Cachexia Sarcopenia Muscle 2023. [PMID: 37311604 PMCID: PMC10401546 DOI: 10.1002/jcsm.13278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/16/2023] [Accepted: 05/01/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD), caused by dystrophin deficiency, leads to progressive and fatal muscle weakness through yet-to-be-fully deciphered molecular perturbations. Emerging evidence implicates RhoA/Rho-associated protein kinase (ROCK) signalling in DMD pathology, yet its direct role in DMD muscle function, and related mechanisms, are unknown. METHODS Three-dimensionally engineered dystrophin-deficient mdx skeletal muscles and mdx mice were used to test the role of ROCK in DMD muscle function in vitro and in situ, respectively. The role of ARHGEF3, one of the RhoA guanine nucleotide exchange factors (GEFs), in RhoA/ROCK signalling and DMD pathology was examined by generating Arhgef3 knockout mdx mice. The role of RhoA/ROCK signalling in mediating the function of ARHGEF3 was determined by evaluating the effects of wild-type or GEF-inactive ARHGEF3 overexpression with ROCK inhibitor treatment. To gain more mechanistic insights, autophagy flux and the role of autophagy were assessed in various conditions with chloroquine. RESULTS Inhibition of ROCK with Y-27632 improved muscle force production in 3D-engineered mdx muscles (+25% from three independent experiments, P < 0.05) and in mice (+25%, P < 0.001). Unlike suggested by previous studies, this improvement was independent of muscle differentiation or quantity and instead related to increased muscle quality. We found that ARHGEF3 was elevated and responsible for RhoA/ROCK activation in mdx muscles, and that depleting ARHGEF3 in mdx mice restored muscle quality (up to +36%, P < 0.01) and morphology without affecting regeneration. Conversely, overexpressing ARHGEF3 further compromised mdx muscle quality (-13% vs. empty vector control, P < 0.01) in GEF activity- and ROCK-dependent manner. Notably, ARHGEF3/ROCK inhibition exerted the effects by rescuing autophagy which is commonly impaired in dystrophic muscles. CONCLUSIONS Our findings uncover a new pathological mechanism of muscle weakness in DMD involving the ARHGEF3-ROCK-autophagy pathway and the therapeutic potential of targeting ARHGEF3 in DMD.
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Affiliation(s)
- Jae-Sung You
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Nick J. Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yongdeok Kim
- Nick J. Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Soohyun Lee
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Nick J. Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, Illinois, USA
| | - Jie Chen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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18
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Abbassi-Daloii T, el Abdellaoui S, Voortman LM, Veeger TTJ, Cats D, Mei H, Meuffels DE, van Arkel E, 't Hoen PAC, Kan HE, Raz V. A transcriptome atlas of leg muscles from healthy human volunteers reveals molecular and cellular signatures associated with muscle location. eLife 2023; 12:80500. [PMID: 36744868 PMCID: PMC9988256 DOI: 10.7554/elife.80500] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 02/03/2023] [Indexed: 02/07/2023] Open
Abstract
Skeletal muscles support the stability and mobility of the skeleton but differ in biomechanical properties and physiological functions. The intrinsic factors that regulate muscle-specific characteristics are poorly understood. To study these, we constructed a large atlas of RNA-seq profiles from six leg muscles and two locations from one muscle, using biopsies from 20 healthy young males. We identified differential expression patterns and cellular composition across the seven tissues using three bioinformatics approaches confirmed by large-scale newly developed quantitative immune-histology procedures. With all three procedures, the muscle samples clustered into three groups congruent with their anatomical location. Concomitant with genes marking oxidative metabolism, genes marking fast- or slow-twitch myofibers differed between the three groups. The groups of muscles with higher expression of slow-twitch genes were enriched in endothelial cells and showed higher capillary content. In addition, expression profiles of Homeobox (HOX) transcription factors differed between the three groups and were confirmed by spatial RNA hybridization. We created an open-source graphical interface to explore and visualize the leg muscle atlas (https://tabbassidaloii.shinyapps.io/muscleAtlasShinyApp/). Our study reveals the molecular specialization of human leg muscles, and provides a novel resource to study muscle-specific molecular features, which could be linked with (patho)physiological processes.
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Affiliation(s)
| | - Salma el Abdellaoui
- Department of Human Genetics, Leiden University Medical CenterLeidenNetherlands
| | - Lenard M Voortman
- Division of Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Thom TJ Veeger
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical CenterLeidenNetherlands
| | - Davy Cats
- Sequencing Analysis Support Core, Leiden University Medical CenterLeidenNetherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical CenterLeidenNetherlands
| | - Duncan E Meuffels
- Orthopedic and Sport Medicine Department, Erasmus MC, University Medical Center RotterdamRotterdamNetherlands
| | | | - Peter AC 't Hoen
- Department of Human Genetics, Leiden University Medical CenterLeidenNetherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical CenterRadboudNetherlands
| | - Hermien E Kan
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical CenterLeidenNetherlands
- Duchenne Center NetherlandsLeidenNetherlands
| | - Vered Raz
- Department of Human Genetics, Leiden University Medical CenterLeidenNetherlands
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19
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Distinctive chaperonopathy in skeletal muscle associated with the dominant variant in DNAJB4. Acta Neuropathol 2023; 145:235-255. [PMID: 36512060 DOI: 10.1007/s00401-022-02530-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/15/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
DnaJ homolog, subfamily B, member 4, a member of the heat shock protein 40 chaperones encoded by DNAJB4, is highly expressed in myofibers. We identified a heterozygous c.270 T > A (p.F90L) variant in DNAJB4 in a family with a dominantly inherited distal myopathy, in which affected members have specific features on muscle pathology represented by the presence of cytoplasmic inclusions and the accumulation of desmin, p62, HSP70, and DNAJB4 predominantly in type 1 fibers. Both Dnajb4F90L knockin and knockout mice developed muscle weakness and recapitulated the patient muscle pathology in the soleus muscle, where DNAJB4 has the highest expression. These data indicate that the identified variant is causative, resulting in defective chaperone function and selective muscle degeneration in specific muscle fibers. This study demonstrates the importance of DNAJB4 in skeletal muscle proteostasis by identifying the associated chaperonopathy.
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20
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Wolff CA, Gutierrez-Monreal MA, Meng L, Zhang X, Douma LG, Costello HM, Douglas CM, Ebrahimi E, Pham A, Oliveira AC, Fu C, Nguyen A, Alava BR, Hesketh SJ, Morris AR, Endale MM, Crislip GR, Cheng KY, Schroder EA, Delisle BP, Bryant AJ, Gumz ML, Huo Z, Liu AC, Esser KA. Defining the age-dependent and tissue-specific circadian transcriptome in male mice. Cell Rep 2023; 42:111982. [PMID: 36640301 PMCID: PMC9929559 DOI: 10.1016/j.celrep.2022.111982] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/01/2022] [Accepted: 12/23/2022] [Indexed: 01/10/2023] Open
Abstract
Cellular circadian clocks direct a daily transcriptional program that supports homeostasis and resilience. Emerging evidence has demonstrated age-associated changes in circadian functions. To define age-dependent changes at the systems level, we profile the circadian transcriptome in the hypothalamus, lung, heart, kidney, skeletal muscle, and adrenal gland in three age groups. We find age-dependent and tissue-specific clock output changes. Aging reduces the number of rhythmically expressed genes (REGs), indicative of weakened circadian control. REGs are enriched for the hallmarks of aging, adding another dimension to our understanding of aging. Analyzing differential gene expression within a tissue at four different times of day identifies distinct clusters of differentially expressed genes (DEGs). Increased variability of gene expression across the day is a common feature of aged tissues. This analysis extends the landscape for understanding aging and highlights the impact of aging on circadian clock function and temporal changes in gene expression.
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Affiliation(s)
- Christopher A Wolff
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA
| | - Miguel A Gutierrez-Monreal
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA; Claude D. Pepper Older Americans Independence Center, University of Florida, Gainesville, FL 32610, USA
| | - Lingsong Meng
- Department of Biostatistics, University of Florida, Gainesville, FL 32610, USA
| | - Xiping Zhang
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA
| | - Lauren G Douma
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Hannah M Costello
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Collin M Douglas
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA
| | - Elnaz Ebrahimi
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Ann Pham
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Aline C Oliveira
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Chunhua Fu
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Amy Nguyen
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Bryan R Alava
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Stuart J Hesketh
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA
| | - Andrew R Morris
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mehari M Endale
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - G Ryan Crislip
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Kit-Yan Cheng
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Elizabeth A Schroder
- Internal Medicine, Pulmonary, University of Kentucky, Lexington, KY 40506, USA; Department of Physiology, University of Kentucky, Lexington, KY 40506, USA
| | - Brian P Delisle
- Department of Physiology, University of Kentucky, Lexington, KY 40506, USA
| | - Andrew J Bryant
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Michelle L Gumz
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; Center for Integrative Cardiovascular and Metabolic Disease, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, Gainesville, FL 32610, USA.
| | - Andrew C Liu
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
| | - Karyn A Esser
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Myology Institute, University of Florida, Gainesville, FL 32610, USA; Claude D. Pepper Older Americans Independence Center, University of Florida, Gainesville, FL 32610, USA.
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21
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Promoter-Adjacent DNA Hypermethylation Can Downmodulate Gene Expression: TBX15 in the Muscle Lineage. EPIGENOMES 2022; 6:epigenomes6040043. [PMID: 36547252 PMCID: PMC9778270 DOI: 10.3390/epigenomes6040043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
TBX15, which encodes a differentiation-related transcription factor, displays promoter-adjacent DNA hypermethylation in myoblasts and skeletal muscle (psoas) that is absent from non-expressing cells in other lineages. By whole-genome bisulfite sequencing (WGBS) and enzymatic methyl-seq (EM-seq), these hypermethylated regions were found to border both sides of a constitutively unmethylated promoter. To understand the functionality of this DNA hypermethylation, we cloned the differentially methylated sequences (DMRs) in CpG-free reporter vectors and tested them for promoter or enhancer activity upon transient transfection. These cloned regions exhibited strong promoter activity and, when placed upstream of a weak promoter, strong enhancer activity specifically in myoblast host cells. In vitro CpG methylation targeted to the DMR sequences in the plasmids resulted in 86−100% loss of promoter or enhancer activity, depending on the insert sequence. These results as well as chromatin epigenetic and transcription profiles for this gene in various cell types support the hypothesis that DNA hypermethylation immediately upstream and downstream of the unmethylated promoter region suppresses enhancer/extended promoter activity, thereby downmodulating, but not silencing, expression in myoblasts and certain kinds of skeletal muscle. This promoter-border hypermethylation was not found in cell types with a silent TBX15 gene, and these cells, instead, exhibit repressive chromatin in and around the promoter. TBX18, TBX2, TBX3 and TBX1 display TBX15-like hypermethylated DMRs at their promoter borders and preferential expression in myoblasts. Therefore, promoter-adjacent DNA hypermethylation for downmodulating transcription to prevent overexpression may be used more frequently for transcription regulation than currently appreciated.
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22
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Jengelley DHA, Wang M, Narasimhan A, Rupert JE, Young AR, Zhong X, Horan DJ, Robling AG, Koniaris LG, Zimmers TA. Exogenous Oncostatin M induces Cardiac Dysfunction, Musculoskeletal Atrophy, and Fibrosis. Cytokine 2022; 159:155972. [PMID: 36054964 PMCID: PMC10468097 DOI: 10.1016/j.cyto.2022.155972] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 01/21/2023]
Abstract
Musculoskeletal diseases such as muscular dystrophy, cachexia, osteoarthritis, and rheumatoid arthritis impair overall physical health and reduce survival. Patients suffer from pain, dysfunction, and dysmobility due to inflammation and fibrosis in bones, muscles, and joints, both locally and systemically. The Interleukin-6 (IL-6) family of cytokines, most notably IL-6, is implicated in musculoskeletal disorders and cachexia. Here we show elevated circulating levels of OSM in murine pancreatic cancer cachexia and evaluate the effects of the IL-6 family member, Oncostatin M (OSM), on muscle and bone using adeno-associated virus (AAV) mediated over-expression of murine OSM in wildtype and IL-6 deficient mice. Initial studies with high titer AAV-OSM injection yielded high circulating OSM and IL-6, thrombocytosis, inflammation, and 60% mortality without muscle loss within 4 days. Subsequently, to mimic OSM levels in cachexia, a lower titer of AAV-OSM was used in wildtype and Il6 null mice, observing effects out to 4 weeks and 12 weeks. AAV-OSM caused muscle atrophy and fibrosis in the gastrocnemius, tibialis anterior, and quadriceps of the injected limb, but these effects were not observed on the non-injected side. In contrast, OSM induced both local and distant trabecular bone loss as shown by reduced bone volume, trabecular number, and thickness, and increased trabecular separation. OSM caused cardiac dysfunction including reduced ejection fraction and reduced fractional shortening. RNA-sequencing of cardiac muscle revealed upregulation of genes related to inflammation and fibrosis. None of these effects were different in IL-6 knockout mice. Thus, OSM induces local muscle atrophy, systemic bone loss, tissue fibrosis, and cardiac dysfunction independently of IL-6, suggesting a role for OSM in musculoskeletal conditions with these characteristics, including cancer cachexia.
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Affiliation(s)
- Daenique H A Jengelley
- Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, IN 46202, USA
| | - Meijing Wang
- Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, IN 46202, USA
| | - Ashok Narasimhan
- Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, IN 46202, USA
| | - Joseph E Rupert
- Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, IN 46202, USA
| | - Andrew R Young
- Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Xiaoling Zhong
- Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA; Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, IN 46202, USA
| | - Daniel J Horan
- Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, IN 46202, USA
| | - Alexander G Robling
- Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, IN 46202, USA
| | - Leonidas G Koniaris
- Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA; Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, IN 46202, USA
| | - Teresa A Zimmers
- Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Otolaryngology, Head & Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA; Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, IN 46202, USA.
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23
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Blazev R, Carl CS, Ng YK, Molendijk J, Voldstedlund CT, Zhao Y, Xiao D, Kueh AJ, Miotto PM, Haynes VR, Hardee JP, Chung JD, McNamara JW, Qian H, Gregorevic P, Oakhill JS, Herold MJ, Jensen TE, Lisowski L, Lynch GS, Dodd GT, Watt MJ, Yang P, Kiens B, Richter EA, Parker BL. Phosphoproteomics of three exercise modalities identifies canonical signaling and C18ORF25 as an AMPK substrate regulating skeletal muscle function. Cell Metab 2022; 34:1561-1577.e9. [PMID: 35882232 DOI: 10.1016/j.cmet.2022.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/31/2022] [Accepted: 07/08/2022] [Indexed: 11/03/2022]
Abstract
Exercise induces signaling networks to improve muscle function and confer health benefits. To identify divergent and common signaling networks during and after different exercise modalities, we performed a phosphoproteomic analysis of human skeletal muscle from a cross-over intervention of endurance, sprint, and resistance exercise. This identified 5,486 phosphosites regulated during or after at least one type of exercise modality and only 420 core phosphosites common to all exercise. One of these core phosphosites was S67 on the uncharacterized protein C18ORF25, which we validated as an AMPK substrate. Mice lacking C18ORF25 have reduced skeletal muscle fiber size, exercise capacity, and muscle contractile function, and this was associated with reduced phosphorylation of contractile and Ca2+ handling proteins. Expression of C18ORF25 S66/67D phospho-mimetic reversed the decreased muscle force production. This work defines the divergent and canonical exercise phosphoproteome across different modalities and identifies C18ORF25 as a regulator of exercise signaling and muscle function.
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Affiliation(s)
- Ronnie Blazev
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Christian S Carl
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Yaan-Kit Ng
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Jeffrey Molendijk
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Christian T Voldstedlund
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Yuanyuan Zhao
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Di Xiao
- Children's Medical Research Institute, The University of Sydney, Camperdown, NSW, Australia; School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
| | - Andrew J Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Paula M Miotto
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Vanessa R Haynes
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Justin P Hardee
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Jin D Chung
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - James W McNamara
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia; Murdoch Children's Research Institute and Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Hongwei Qian
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Paul Gregorevic
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | | | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Thomas E Jensen
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Leszek Lisowski
- Children's Medical Research Institute, The University of Sydney, Camperdown, NSW, Australia; Military Institute of Medicine, Warsaw, Poland
| | - Gordon S Lynch
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Garron T Dodd
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Matthew J Watt
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Pengyi Yang
- Children's Medical Research Institute, The University of Sydney, Camperdown, NSW, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Bente Kiens
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark.
| | - Erik A Richter
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark.
| | - Benjamin L Parker
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia.
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24
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Kui H, Ran B, Yang M, Shi X, Luo Y, Wang Y, Wang T, Li D, Shuai S, Li M. Gene expression profiles of specific chicken skeletal muscles. Sci Data 2022; 9:552. [PMID: 36075978 PMCID: PMC9458719 DOI: 10.1038/s41597-022-01668-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/24/2022] [Indexed: 12/03/2022] Open
Abstract
The chicken provides large amounts of protein for the human diet and is also used as a model organism for biomedical research. Increasing meat production is an important goal in the poultry industry and skeletal muscles have highly diverse origins, shapes, metabolic features, and physical functions. Previous gene expression atlases have largely ignored the differences among diverse types of skeletal muscles; therefore, comprehensive transcriptional maps of all skeletal muscles are needed to improve meat production traits. In this study, we sequenced 58 samples from 10 different skeletal muscles of 42-day-old White Plymouth Rock chickens. We also measured myofiber diameter and generated myofiber-type datasets of these 10 tissues. We generated 418.4 Gb high-quality bulk RNA-Seq data from four or six biological replicates of each skeletal muscle (four replicates from extraocular samples) (approximately 7.4 Gb per sample). This dataset provides valuable information for understanding the muscle fiber characteristics of White Plymouth Rock chickens. Furthermore, our data can be used as a model for heterogeneity analysis between tissues with similar properties. Measurement(s) | Gene expression profiles of specific chicken skeletal muscles • cross section area of chicken skeletal muscles and type I muscle fiber quantity | Technology Type(s) | RNA sequence • Histological Procedure | Factor Type(s) | different skeletal muscles | Sample Characteristic - Organism | Gallus gallus | Sample Characteristic - Environment | farm |
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Affiliation(s)
- Hua Kui
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Bo Ran
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Maosen Yang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xin Shi
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yingyu Luo
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yujie Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Tao Wang
- School of Pharmacy, Chengdu University, Chengdu, 610106, Sichuan, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu, 610106, Sichuan, China
| | - Surong Shuai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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25
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Zhang Y, Chen J, He S, Xiao Y, Liu A, Zhang D, Li X. Systematic identification of aberrant non-coding RNAs and their mediated modules in rotator cuff tears. Front Mol Biosci 2022; 9:940290. [PMID: 36111133 PMCID: PMC9470226 DOI: 10.3389/fmolb.2022.940290] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/05/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Rotator cuff tears (RCT) is the most common cause of shoulder dysfunction, however, its molecular mechanisms remain unclear. Non-coding RNAs(ncRNAs), such as long ncRNA (lncRNA), microRNA (miRNA) and circular RNA (circRNA), are involved in a variety of diseases, but little is known about their roles in RCT. Therefore, the purpose of this study is to identify dysregulated ncRNAs and understand how they influence RCT. Methods: We performed RNA sequencing and miRNA sequencing on five pairs of torn supraspinatus muscles and matched unharmed subscapularis muscles to identify RNAs dysregulated in RCT patients. To better comprehend the fundamental biological processes, we carried out enrichment analysis of these dysregulated mRNAs or the co-expressed genes of dysregulated ncRNAs. According to the competing endogenous RNA (ceRNA) theory, we finally established ceRNA networks to explore the relationship among dysregulated RNAs in RCT. Results: A total of 151 mRNAs, 38 miRNAs, 20 lncRNAs and 90 circRNAs were differentially expressed between torn supraspinatus muscles and matched unharmed subscapularis muscles, respectively. We found that these dysregulated mRNAs, the target mRNAs of these dysregulated miRNAs or the co-expressed mRNAs of these dysregulated ncRNAs were enriched in muscle structure development, actin-mediated cell contraction and actin binding. Then we constructed and analyzed the ceRNA network and found that the largest module in the ceRNA network was associated with vasculature development. Based on the topological properties of the largest module, we identified several important ncRNAs including hsa_circ_0000722, hsa-miR-129-5p and hsa-miR-30c-5p, whose interacting mRNAs related to muscle diseases, fat and inflammation. Conclusion: This study presented a systematic dissection of the expression profile of mRNAs and ncRNAs in RCT patients and revealed some important ncRNAs which may contribute to the development of RCT. Such results could provide new insights for further research on RCT.
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Affiliation(s)
- Yichong Zhang
- Department of Orthopedics and Trauma, Key Laboratory of Trauma and Neural Regeneration (Ministry of Education/Peking University), Peking University People’s Hospital, Beijing, China
| | - Jianhai Chen
- Department of Orthopedics and Trauma, Key Laboratory of Trauma and Neural Regeneration (Ministry of Education/Peking University), Peking University People’s Hospital, Beijing, China
| | - Shengyuan He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Aiyu Liu
- Central Laboratory, Peking University People’s Hospital, Beijing, China
| | - Dianying Zhang
- Department of Orthopedics and Trauma, Key Laboratory of Trauma and Neural Regeneration (Ministry of Education/Peking University), Peking University People’s Hospital, Beijing, China
- *Correspondence: Dianying Zhang, ; Xia Li,
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
- *Correspondence: Dianying Zhang, ; Xia Li,
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26
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Zhou C, Zhang L, Xu D, Ding H, Zheng S, Liu M. MeDIP-seq and RNA-seq analysis during porcine testis development reveals functional DMRs at the promoter of LDHC. Genomics 2022; 114:110467. [PMID: 36041633 DOI: 10.1016/j.ygeno.2022.110467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/09/2022] [Accepted: 08/26/2022] [Indexed: 11/04/2022]
Abstract
Testis development requires tight regulation of gene expression programmed by epigenetic modifiers. However, their mechanism remains to be elucidated. Here, we investigated the genome-wide DNA methylation landscape in the Duroc and Meishan boar testes using methylated DNA immunoprecipitation sequencing (MeDIP-seq). We identified over 1100 promoter differential methylation genes (DMGs) before and after puberty, most of which are associated with testis development. Furthermore, we discovered that the expression of lactate dehydrogenase C (LDHC) gene during testis development is regulated by DNA methylation. The promoter of LDHC in pre-pubertal testes is substantially methylated, whereas considerably demethylated in post-pubertal testes. Artificial demethylation with the demethylating agent 5-Aza-CdR induced LDHC expression in immature Sertoli cells (SCs). Mechanistically, we confirmed the transcription factor SP1 was recruited to bind in hypomethylated differentially methylated regions (DMRs) in LDHC promoter, which upregulated the expression of LDHC. Functionally, we demonstrated that LDHC gene was activated in mature SCs (mSCs) and its overexpression significantly increases lactate secretion in SCs. In conclusion, our results highlight the function and regulation of dynamic DNA methylation in testis development.
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Affiliation(s)
- Changfan Zhou
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Long Zhang
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Dequan Xu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Haisheng Ding
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Shuailong Zheng
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Min Liu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
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27
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Vicente-García C, Hernández-Camacho JD, Carvajal JJ. Regulation of myogenic gene expression. Exp Cell Res 2022; 419:113299. [DOI: 10.1016/j.yexcr.2022.113299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/22/2022]
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28
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Hamilton MT, Hamilton DG, Zderic TW. A potent physiological method to magnify and sustain soleus oxidative metabolism improves glucose and lipid regulation. iScience 2022; 25:104869. [PMID: 36034224 PMCID: PMC9404652 DOI: 10.1016/j.isci.2022.104869] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/29/2022] [Accepted: 07/28/2022] [Indexed: 11/24/2022] Open
Abstract
Slow oxidative muscle, most notably the soleus, is inherently well equipped with the molecular machinery for regulating blood-borne substrates. However, the entire human musculature accounts for only ∼15% of the body’s oxidative metabolism of glucose at the resting energy expenditure, despite being the body’s largest lean tissue mass. We found the human soleus muscle could raise local oxidative metabolism to high levels for hours without fatigue, during a type of soleus-dominant activity while sitting, even in unfit volunteers. Muscle biopsies revealed there was minimal glycogen use. Magnifying the otherwise negligible local energy expenditure with isolated contractions improved systemic VLDL-triglyceride and glucose homeostasis by a large magnitude, e.g., 52% less postprandial glucose excursion (∼50 mg/dL less between ∼1 and 2 h) with 60% less hyperinsulinemia. Targeting a small oxidative muscle mass (∼1% body mass) with local contractile activity is a potent method for improving systemic metabolic regulation while prolonging the benefits of oxidative metabolism. We developed a method to capitalize upon the unique phenotype of the soleus “A high quality versus large quantity perspective” for muscle activation Singular movement targeting the 1 kg soleus easily sustains oxidative metabolism This method provides a distinct muscular activity stimulus for metabolic control
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Affiliation(s)
- Marc T. Hamilton
- Department Health and Human Performance, University of Houston, Houston, TX 77204, USA
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
- Corresponding author
| | - Deborah G. Hamilton
- Department Health and Human Performance, University of Houston, Houston, TX 77204, USA
| | - Theodore W. Zderic
- Department Health and Human Performance, University of Houston, Houston, TX 77204, USA
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29
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McDonough AA, Fenton RA. Potassium homeostasis: sensors, mediators, and targets. Pflugers Arch 2022; 474:853-867. [PMID: 35727363 PMCID: PMC10163916 DOI: 10.1007/s00424-022-02718-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/08/2022] [Accepted: 06/12/2022] [Indexed: 12/16/2022]
Abstract
Transmembrane potassium (K) gradients are key determinants of membrane potential that can modulate action potentials, control muscle contractility, and influence ion channel and transporter activity. Daily K intake is normally equal to the amount of K in the entire extracellular fluid (ECF) creating a critical challenge - how to maintain ECF [K] and membrane potential in a narrow range during feast and famine. Adaptations to maintain ECF [K] include sensing the K intake, sensing ECF [K] vs. desired set-point and activating mediators that regulate K distribution between ECF and ICF, and regulate renal K excretion. In this focused review, we discuss the basis of these adaptions, including (1) potential mechanisms for rapid feedforward signaling to kidney and muscle after a meal (before a rise in ECF [K]), (2) how skeletal muscles sense and respond to changes in ECF [K], (3) effects of K on aldosterone biosynthesis, and (4) how the kidney responds to changes in ECF [K] to modify K excretion. The concepts of sexual dimorphisms in renal K handling adaptation are introduced, and the molecular mechanisms that can account for the benefits of a K-rich diet to maintain cardiovascular health are discussed. Although the big picture of K homeostasis is becoming more clear, we also highlight significant pieces of the puzzle that remain to be solved, including knowledge gaps in our understanding of initiating signals, sensors and their connection to homeostatic adjustments of ECF [K].
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Affiliation(s)
- Alicia A McDonough
- Department of Physiology and Neuroscience, University of Southern California Keck School of Medicine, Los Angeles, CA, USA.
| | - Robert A Fenton
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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30
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Long K, Su D, Li X, Li H, Zeng S, Zhang Y, Zhong Z, Lin Y, Li X, Lu L, Jin L, Ma J, Tang Q, Li M. Identification of enhancers responsible for the coordinated expression of myosin heavy chain isoforms in skeletal muscle. BMC Genomics 2022; 23:519. [PMID: 35842589 PMCID: PMC9288694 DOI: 10.1186/s12864-022-08737-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/04/2022] [Indexed: 11/19/2022] Open
Abstract
Background Skeletal muscles consist of fibers of differing contractility and metabolic properties, which are primarily determined by the content of myosin heavy chain (MYH) isoforms (MYH7, MYH2, MYH1, and MYH4). The regulation of Myh genes transcription depends on three-dimensional chromatin conformation interaction, but the mechanistic details remain to be determined. Results In this study, we characterized the interaction profiles of Myh genes using 4C-seq (circular chromosome conformation capture coupled to high-throughput sequencing). The interaction profile of Myh genes changed between fast quadriceps and slow soleus muscles. Combining chromatin immunoprecipitation-sequencing (ChIP-seq) and transposase accessible chromatin with high-throughput sequencing (ATAC-seq), we found that a 38 kb intergenic region interacting simultaneously with fast Myh genes promoters controlled the coordinated expression of fast Myh genes. We also identified four active enhancers of Myh7, and revealed that binding of MYOG and MYOD increased the activity of Myh7 enhancers. Conclusions This study provides new insight into the chromatin interactions that regulate Myh genes expression. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08737-9.
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Affiliation(s)
- Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Duo Su
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaokai Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hengkuan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Sha Zeng
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhining Zhong
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Lin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xuemin Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lu Lu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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31
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Walsh CJ, Batt J, Herridge MS, Mathur S, Bader GD, Hu P, Khatri P, Dos Santos CC. Comprehensive multi-cohort transcriptional meta-analysis of muscle diseases identifies a signature of disease severity. Sci Rep 2022; 12:11260. [PMID: 35789175 PMCID: PMC9253003 DOI: 10.1038/s41598-022-15003-1] [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: 11/12/2021] [Accepted: 05/03/2022] [Indexed: 11/09/2022] Open
Abstract
Muscle diseases share common pathological features suggesting common underlying mechanisms. We hypothesized there is a common set of genes dysregulated across muscle diseases compared to healthy muscle and that these genes correlate with severity of muscle disease. We performed meta-analysis of transcriptional profiles of muscle biopsies from human muscle diseases and healthy controls. Studies obtained from public microarray repositories fulfilling quality criteria were divided into six categories: (i) immobility, (ii) inflammatory myopathies, (iii) intensive care unit (ICU) acquired weakness (ICUAW), (iv) congenital muscle diseases, (v) chronic systemic diseases, (vi) motor neuron disease. Patient cohorts were separated in discovery and validation cohorts retaining roughly equal proportions of samples for the disease categories. To remove bias towards a specific muscle disease category we repeated the meta-analysis five times by removing data sets corresponding to one muscle disease class at a time in a "leave-one-disease-out" analysis. We used 636 muscle tissue samples from 30 independent cohorts to identify a 52 gene signature (36 up-regulated and 16 down-regulated genes). We validated the discriminatory power of this signature in 657 muscle biopsies from 12 additional patient cohorts encompassing five categories of muscle diseases with an area under the receiver operating characteristic curve of 0.91, 83% sensitivity, and 85.3% specificity. The expression score of the gene signature inversely correlated with quadriceps muscle mass (r = -0.50, p-value = 0.011) in ICUAW and shoulder abduction strength (r = -0.77, p-value = 0.014) in amyotrophic lateral sclerosis (ALS). The signature also positively correlated with histologic assessment of muscle atrophy in ALS (r = 0.88, p-value = 1.62 × 10-3) and fibrosis in muscular dystrophy (Jonckheere trend test p-value = 4.45 × 10-9). Our results identify a conserved transcriptional signature associated with clinical and histologic muscle disease severity. Several genes in this conserved signature have not been previously associated with muscle disease severity.
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Affiliation(s)
- C J Walsh
- Keenan Research Center for Biomedical Science, Saint Michael's Hospital, Toronto, ON, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - J Batt
- Keenan Research Center for Biomedical Science, Saint Michael's Hospital, Toronto, ON, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - M S Herridge
- Interdepartmental Division of Critical Care, University Health Network, University of Toronto, Toronto, ON, Canada
| | - S Mathur
- Department of Physical Therapy, University of Toronto, Toronto, ON, Canada
| | - G D Bader
- The Donnelly Center, University of Toronto, Toronto, ON, Canada
| | - P Hu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - P Khatri
- Stanford Institute for Immunity, Transplantation and Infection (ITI), Stanford University School of Medicine, Stanford, CA, USA.,Department of Medicine, Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, CA, USA
| | - C C Dos Santos
- Keenan Research Center for Biomedical Science, Saint Michael's Hospital, Toronto, ON, Canada. .,Interdepartmental Division of Critical Care, University of Toronto, Toronto, ON, Canada.
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32
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Smith LB, Anderson CV, Withangage MHH, Koch A, Roberts TJ, Liebl AL. Relationship between gene expression networks and muscle contractile physiology differences in Anolis lizards. J Comp Physiol B 2022; 192:489-499. [PMID: 35596083 DOI: 10.1007/s00360-022-01441-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 04/11/2022] [Accepted: 04/26/2022] [Indexed: 12/12/2022]
Abstract
Muscles facilitate most animal behavior, from eating to fleeing. However, to generate the variation in behavior necessary for survival, different muscles must perform differently; for instance, sprinting requires multiple rapid muscle contractions, whereas biting may require fewer contractions but greater force. Here, we use a transcriptomic approach to identify genes associated with variation in muscle contractile physiology among different muscles from the same individual. We measured differential gene expression between a leg and jaw muscle of Anolis lizards known to differ in muscle contractile physiology and performance. For each individual, one muscle was used to measure muscle contractile physiology, including contractile velocity (Vmax and V40), specific tension, power ratio, and twitch time, whereas the contralateral muscle was used to extract RNA for transcriptomic sequencing. Using the transcriptomic data, we found clear clustering of muscle type. Expression of genes clustered in gene ontology (GO) terms related to muscle contraction and extracellular matrix was, on average, negatively correlated with Vmax and slower twitch times but positively correlated to power ratio and V40. Conversely, genes related to the GO terms related to aerobic respiration were downregulated in muscles with higher power ratio and V40, and over-expressed as twitch time decreased. Determining the molecular mechanisms that underlie variation in muscle contractile physiology can begin to explain how organisms are able to optimize behavior under variable conditions. Future studies pursuing the effects of differential gene expression across muscle types in different environments might inform researchers about how differences develop across species, populations, and individuals varying in ecological history.
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Affiliation(s)
- Luke B Smith
- Department of Biology, University of South Dakota, Vermillion, SD, USA.,Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | | | - Miyuraj H Hikkaduwa Withangage
- Department of Biology, University of South Dakota, Vermillion, SD, USA.,College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - Andrew Koch
- Department of Biology, University of South Dakota, Vermillion, SD, USA
| | - Thomas J Roberts
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Andrea L Liebl
- Department of Biology, University of South Dakota, Vermillion, SD, USA.
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33
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Schuppe ER, Tobiansky D, Goller F, Fuxjager MJ. Specialized androgen synthesis in skeletal muscles that actuate elaborate social displays. J Exp Biol 2022; 225:275472. [PMID: 35587151 DOI: 10.1242/jeb.243730] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/12/2022] [Indexed: 11/20/2022]
Abstract
Androgens mediate the expression of many reproductive behaviors, including the elaborate displays used to navigate courtship and territorial interactions. In some vertebrates, males can produce androgen-dependent sexual behavior even when levels of testosterone (T) is low in the bloodstream. One idea is that select tissues make their own androgens from scratch to support behavioral performance. We first study this phenomenon in the skeletal muscles that actuate elaborate sociosexual displays in downy woodpeckers and two songbirds. We show that the woodpecker display muscle maintains elevated T when the testes are regressed in the non-breeding season. Both the display muscles of woodpeckers, as well as the display muscles in the avian vocal organ (syrinx or SYR) of songbirds, express all transporters and enzymes necessary to convert cholesterol into bioactive androgens locally. In a final analysis, we broaden our study by looking for these same transporters and enzymes in mammalian muscles that operate at different speeds. Using RNA-seq data, we find that the capacity for de novo synthesis is only present in "superfast" extraocular muscle. Together, our results suggest that skeletal muscle specialized to generate extraordinary twitch-times and/or extremely rapid contractile speeds may depend on androgenic hormones produced locally within the muscle itself. Our study therefore uncovers an important new dimension of androgenic regulation of behavior.
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Affiliation(s)
- Eric R Schuppe
- Department of Neurobiology and Behavior, Cornell University, 215 Tower Road, Ithaca, NY 14850, USA
| | - Daniel Tobiansky
- Department of Ecology, Evolution, and Organismal Biology, Brown University, 171 Meeting Street, Providence, RI 02912, USA
| | - Franz Goller
- Department of Biology, University of Utah, USA.,Institute for Zoophysiology, University of Münster, Germany
| | - Matthew J Fuxjager
- Department of Ecology, Evolution, and Organismal Biology, Brown University, 171 Meeting Street, Providence, RI 02912, USA
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34
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Depuydt CE, Goosens V, Janky R, D’Hondt A, De Bleecker JL, Noppe N, Derveaux S, Thal DR, Claeys KG. Unraveling the Molecular Basis of the Dystrophic Process in Limb-Girdle Muscular Dystrophy LGMD-R12 by Differential Gene Expression Profiles in Diseased and Healthy Muscles. Cells 2022; 11:cells11091508. [PMID: 35563815 PMCID: PMC9104122 DOI: 10.3390/cells11091508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/19/2022] [Accepted: 04/29/2022] [Indexed: 11/28/2022] Open
Abstract
Limb-girdle muscular dystrophy R12 (LGMD-R12) is caused by two mutations in anoctamin-5 (ANO5). Our aim was to identify genes and pathways that underlie LGMD-R12 and explain differences in the molecular predisposition and susceptibility between three thigh muscles that are severely (semimembranosus), moderately (vastus lateralis) or mildly (rectus femoris) affected in this disease. We performed transcriptomics on these three muscles in 16 male LGMD-R12 patients and 15 age-matched male controls. Our results showed that LGMD-R12 dystrophic muscle is associated with the expression of genes indicative of fibroblast and adipocyte replacement, such as fibroadipogenic progenitors and immune cell infiltration, while muscle protein synthesis and metabolism were downregulated. Muscle degeneration was associated with an increase in genes involved in muscle injury and inflammation, and muscle repair/regeneration. Baseline differences between muscles in healthy individuals indicated that muscles that are the most affected by LGMD-R12 have the lowest expression of transcription factor networks involved in muscle (re)generation and satellite stem cell activation. Instead, they show relative high levels of fetal/embryonic myosins, all together indicating that muscles differ in their baseline regenerative potential. To conclude, we profiled the gene expression landscape in LGMD-R12, identified baseline differences in expression levels between differently affected muscles and characterized disease-associated changes.
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Affiliation(s)
- Christophe E. Depuydt
- Laboratory for Muscle Diseases and Neuropathies, Department of Neurosciences, KU Leuven, and Leuven Brain Institute (LBI), Herestraat 49, 3000 Leuven, Belgium;
| | - Veerle Goosens
- Department of Radiology, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium; (V.G.); (N.N.)
| | - Rekin’s Janky
- VIB Nucleomics Core, Herestraat 49, 3000 Leuven, Belgium; (R.J.); (S.D.)
| | - Ann D’Hondt
- Department of Neurology, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium;
| | - Jan L. De Bleecker
- Department of Neurology, University Hospital Gent, Corneel Heymanslaan 10, 9000 Gent, Belgium;
| | - Nathalie Noppe
- Department of Radiology, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium; (V.G.); (N.N.)
| | - Stefaan Derveaux
- VIB Nucleomics Core, Herestraat 49, 3000 Leuven, Belgium; (R.J.); (S.D.)
| | - Dietmar R. Thal
- Department of Pathology, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium;
- Laboratory for Neuropathology, Department of Imaging and Pathology, KU Leuven, and Leuven Brain Institute (LBI), Herestraat 49, 3000 Leuven, Belgium
| | - Kristl G. Claeys
- Laboratory for Muscle Diseases and Neuropathies, Department of Neurosciences, KU Leuven, and Leuven Brain Institute (LBI), Herestraat 49, 3000 Leuven, Belgium;
- Department of Neurology, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium;
- Correspondence: ; Tel.: +32-16-344280; Fax: +32-16-344285
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35
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Casanova-Vallve N, Duglan D, Vaughan ME, Pariollaud M, Handzlik MK, Fan W, Yu RT, Liddle C, Downes M, Delezie J, Mello R, Chan AB, Westermark PO, Metallo CM, Evans RM, Lamia KA. Daily running enhances molecular and physiological circadian rhythms in skeletal muscle. Mol Metab 2022; 61:101504. [PMID: 35470095 PMCID: PMC9079800 DOI: 10.1016/j.molmet.2022.101504] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022] Open
Abstract
Objective Exercise is a critical component of a healthy lifestyle and a key strategy for the prevention and management of metabolic disease. Identifying molecular mechanisms underlying adaptation in response to chronic physical activity is of critical interest in metabolic physiology. Circadian rhythms broadly modulate metabolism, including muscle substrate utilization and exercise capacity. Here, we define the molecular and physiological changes induced across the daily cycle by voluntary low intensity daily exercise. Methods Wildtype C57BL6/J male and female mice were housed with or without access to a running wheel for six weeks. Maximum running speed was measured at four different zeitgeber times (ZTs, hours after lights on) using either electrical or manual stimulation to motivate continued running on a motorized treadmill. RNA isolated from plantaris muscles at six ZTs was sequenced to establish the impact of daily activity on genome-wide transcription. Patterns of gene expression were analyzed using Gene Set Enrichment Analysis (GSEA) and Detection of Differential Rhythmicity (DODR). Blood glucose, lactate, and ketones, and muscle and liver glycogen were measured before and after exercise. Results We demonstrate that the use of mild electrical shocks to motivate running negatively impacts maximum running speed in mice, and describe a manual method to motivate running in rodent exercise studies. Using this method, we show that time of day influences the increase in exercise capacity afforded by six weeks of voluntary wheel running: when maximum running speed is measured at the beginning of the nighttime active period in mice, there is no measurable benefit from a history of daily voluntary running, while maximum increase in performance occurs at the end of the night. We show that daily voluntary exercise dramatically remodels the murine muscle circadian transcriptome. Finally, we describe daily rhythms in carbohydrate metabolism associated with the time-dependent response to moderate daily exercise in mice. Conclusions Collectively, these data indicate that chronic nighttime physical activity dramatically remodels daily rhythms of murine muscle gene expression, which in turn support daily fluctuations in exercise performance. Daily voluntary running dramatically remodels the mouse muscle circadian transcriptome. Daily voluntary running maximally increases mouse running speed in the late active period. Muscle and liver glycogen content exhibit robust daily rhythms in laboratory mice. Use of mild electric shocks to motivate running in mice impairs maximum running speed.
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Affiliation(s)
| | - Drew Duglan
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Megan E Vaughan
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Marie Pariollaud
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Michal K Handzlik
- Department of Bioengineering, University of California, La Jolla, San Diego, CA 92093, USA; Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Weiwei Fan
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ruth T Yu
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Christopher Liddle
- Storr Liver Centre, Westmead Institute for Medical Research and University of Sydney School of Medicine, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Julien Delezie
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Rebecca Mello
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Alanna B Chan
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Pål O Westermark
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Christian M Metallo
- Department of Bioengineering, University of California, La Jolla, San Diego, CA 92093, USA; Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ronald M Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Katja A Lamia
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA.
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36
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Sundar S, Rimkus B, Meemaduma PS, deLap S, LaFave N, Racca AW, Hettige P, Moore J, Gage M, Shehaj A, Konow N. Bridging the muscle genome to phenome across multiple biological scales. J Exp Biol 2022; 225:jeb243630. [PMID: 35288729 PMCID: PMC9080751 DOI: 10.1242/jeb.243630] [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: 10/05/2021] [Accepted: 03/08/2022] [Indexed: 11/20/2022]
Abstract
Muscle is highly hierarchically organized, with functions shaped by genetically controlled expression of protein ensembles with different isoform profiles at the sarcomere scale. However, it remains unclear how isoform profiles shape whole-muscle performance. We compared two mouse hindlimb muscles, the slow, relatively parallel-fibered soleus and the faster, more pennate-fibered tibialis anterior (TA), across scales: from gene regulation, isoform expression and translation speed, to force-length-velocity-power for intact muscles. Expression of myosin heavy-chain (MHC) isoforms directly corresponded with contraction velocity. The fast-twitch TA with fast MHC isoforms had faster unloaded velocities (actin sliding velocity, Vactin; peak fiber velocity, Vmax) than the slow-twitch soleus. For the soleus, Vactin was biased towards Vactin for purely slow MHC I, despite this muscle's even fast and slow MHC isoform composition. Our multi-scale results clearly identified a consistent and significant dampening in fiber shortening velocities for both muscles, underscoring an indirect correlation between Vactin and fiber Vmax that may be influenced by differences in fiber architecture, along with internal loading due to both passive and active effects. These influences correlate with the increased peak force and power in the slightly more pennate TA, leading to a broader length range of near-optimal force production. Conversely, a greater force-velocity curvature in the near-parallel fibered soleus highlights the fine-tuning by molecular-scale influences including myosin heavy and light chain expression along with whole-muscle characteristics. Our results demonstrate that the individual gene, protein and whole-fiber characteristics do not directly reflect overall muscle performance but that intricate fine-tuning across scales shapes specialized muscle function.
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Affiliation(s)
- SaiLavanyaa Sundar
- Department of Biological Sciences, University of Massachusetts, Lowell, MA 01854, USA
- UMass Movement Center, University of Massachusetts, Lowell, MA 01854, USA
| | - Barbora Rimkus
- Department of Biological Sciences, University of Massachusetts, Lowell, MA 01854, USA
- UMass Movement Center, University of Massachusetts, Lowell, MA 01854, USA
| | - Prabath S. Meemaduma
- UMass Movement Center, University of Massachusetts, Lowell, MA 01854, USA
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | - Samuel deLap
- Department of Biological Sciences, University of Massachusetts, Lowell, MA 01854, USA
- UMass Movement Center, University of Massachusetts, Lowell, MA 01854, USA
| | - Nicholas LaFave
- Department of Biological Sciences, University of Massachusetts, Lowell, MA 01854, USA
- UMass Movement Center, University of Massachusetts, Lowell, MA 01854, USA
| | - Alice W. Racca
- Department of Biological Sciences, University of Massachusetts, Lowell, MA 01854, USA
- UMass Movement Center, University of Massachusetts, Lowell, MA 01854, USA
| | - Pabodha Hettige
- UMass Movement Center, University of Massachusetts, Lowell, MA 01854, USA
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | - Jeffrey Moore
- Department of Biological Sciences, University of Massachusetts, Lowell, MA 01854, USA
- UMass Movement Center, University of Massachusetts, Lowell, MA 01854, USA
| | - Matthew Gage
- UMass Movement Center, University of Massachusetts, Lowell, MA 01854, USA
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | - Andrea Shehaj
- Department of Biological Sciences, University of Massachusetts, Lowell, MA 01854, USA
- UMass Movement Center, University of Massachusetts, Lowell, MA 01854, USA
| | - Nicolai Konow
- Department of Biological Sciences, University of Massachusetts, Lowell, MA 01854, USA
- UMass Movement Center, University of Massachusetts, Lowell, MA 01854, USA
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37
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Mader T, Chaillou T, Alves ES, Jude B, Cheng AJ, Kenne E, Mijwel S, Kurzejamska E, Vincent CT, Rundqvist H, Lanner JT. Exercise reduces intramuscular stress and counteracts muscle weakness in mice with breast cancer. J Cachexia Sarcopenia Muscle 2022; 13:1151-1163. [PMID: 35170227 PMCID: PMC8978016 DOI: 10.1002/jcsm.12944] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Patients with breast cancer exhibit muscle weakness, which is associated with increased mortality risk and reduced quality of life. Muscle weakness is experienced even in the absence of loss of muscle mass in breast cancer patients, indicating intrinsic muscle dysfunction. Physical activity is correlated with reduced cancer mortality and disease recurrence. However, the molecular processes underlying breast cancer-induced muscle weakness and the beneficial effect of exercise are largely unknown. METHODS Eight-week-old breast cancer (MMTV-PyMT, PyMT) and control (WT) mice had access to active or inactive in-cage voluntary running wheels for 4 weeks. Mice were also subjected to a treadmill test. Muscle force was measured ex vivo. Tumour markers were determined with immunohistochemistry. Mitochondrial biogenesis and function were assessed with transcriptional analyses of PGC-1α, the electron transport chain (ETC) and antioxidants superoxide dismutase (Sod) and catalase (Cat), combined with activity measurements of SOD, citrate synthase (CS) and β-hydroxyacyl-CoA-dehydrogenase (βHAD). Serum and intramuscular stress levels were evaluated by enzymatic assays, immunoblotting, and transcriptional analyses of, for example, tumour necrosis factor-α (TNF-α) and p38 mitogen-activated protein kinase (MAPK) signalling. RESULTS PyMT mice endured shorter time and distance during the treadmill test (~30%, P < 0.05) and ex vivo force measurements revealed ~25% weaker slow-twitch soleus muscle (P < 0.001). This was independent of cancer-induced alteration of muscle size or fibre type. Inflammatory stressors in serum and muscle, including TNF-α and p38 MAPK, were higher in PyMT than in WT mice (P < 0.05). Cancer-induced decreases in ETC (P < 0.05, P < 0.01) and antioxidant gene expression were observed (P < 0.05). The exercise intervention counteracted the cancer-induced muscle weakness and was accompanied by a less aggressive, differentiated tumour phenotype, determined by increased CK8 and reduced CK14 expression (P < 0.05). In PyMT mice, the exercise intervention led to higher CS activity (P = 0.23), enhanced β-HAD and SOD activities (P < 0.05), and reduced levels of intramuscular stressors together with a normalization of the expression signature of TNFα-targets and ETC genes (P < 0.05, P < 0.01). At the same time, the exercise-induced PGC-1α expression, and CS and β-HAD activity was blunted in muscle from the PyMT mice as compared with WT mice, indicative that breast cancer interfere with transcriptional programming of mitochondria and that the molecular adaptation to exercise differs between healthy mice and those afflicted by disease. CONCLUSIONS Four-week voluntary wheel running counteracted muscle weakness in PyMT mice which was accompanied by reduced intrinsic stress and improved mitochondrial and antioxidant profiles and activities that aligned with muscles of healthy mice.
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Affiliation(s)
- Theresa Mader
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Thomas Chaillou
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Biomedicum, Stockholm, Sweden.,School of Health Sciences, Örebro University, Örebro, Sweden
| | - Estela Santos Alves
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Baptiste Jude
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Arthur J Cheng
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Biomedicum, Stockholm, Sweden.,Muscle Health Research Centre, School of Kinesiology and Health Science, Faculty of Health Toronto, York University, Toronto, Ontario, Canada
| | - Ellinor Kenne
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Sara Mijwel
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Biomedicum, Stockholm, Sweden.,Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Ewa Kurzejamska
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Clara Theresa Vincent
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.,Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Helene Rundqvist
- Department of Laboratory Medicine, Clinical Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Johanna T Lanner
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Biomedicum, Stockholm, Sweden
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RNA Sequencing of Whole Blood Defines the Signature of High Intensity Exercise at Altitude in Elite Speed Skaters. Genes (Basel) 2022; 13:genes13040574. [PMID: 35456380 PMCID: PMC9027771 DOI: 10.3390/genes13040574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/08/2022] [Accepted: 03/21/2022] [Indexed: 12/18/2022] Open
Abstract
Although high altitude training has been increasingly popular among endurance athletes, the molecular and cellular bases of this adaptation remain poorly understood. We aimed to define the underlying physiological changes and screen for potential biomarkers of adaptation using transcriptional profiling of whole blood. Seven elite female speed skaters were profiled on the 18th day of high-altitude adaptation. Whole blood RNA-seq before and after an intense 1 h skating bout was used to measure gene expression changes associated with exercise. In order to identify the genes specifically regulated at high altitudes, we have leveraged the data from eight previously published microarray datasets studying blood expression changes after exercise at sea level. Using cell type-specific signatures, we were able to deconvolute changes of cell type abundance from individual gene expression changes. Among these were PHOSPHO1, with a known role in erythropoiesis, and MARC1 with a role in endogenic NO metabolism. We find that platelet and erythrocyte counts uniquely respond to altitude exercise, while changes in neutrophils represent a more generic marker of intense exercise. Publicly available data from both single cell atlases and exercise-related blood profiling dramatically increases the value of whole blood RNA-seq for the dynamic evaluation of physiological changes in an athlete’s body.
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39
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Goto A, Kokabu S, Dusadeemeelap C, Kawaue H, Matsubara T, Tominaga K, Addison WN. Tongue Muscle for the Analysis of Head Muscle Regeneration Dynamics. J Dent Res 2022; 101:962-971. [PMID: 35193429 DOI: 10.1177/00220345221075966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Tongue muscle damage impairs speaking and eating, thereby degrading overall health and quality of life. Skeletal muscles of the body are diverse in embryonic origin, anatomic location, and gene expression profiles. Responses to disease, atrophy, aging, or drugs vary among different muscles. Currently, most muscle studies are focused on limb muscles and the tongue is neglected. The regenerative ability of tongue muscle remains unknown, and thus there is need for tongue muscle research models. Here, we present a comprehensive characterization of the spatiotemporal dynamics in a mouse model of tongue muscle regeneration and establish a method for the isolation of primary tongue-derived satellite cells. We compare and contrast our observations with the tibialis anterior (TA) limb muscle. Acute injury was induced by intramuscular injection of cardiotoxin, a cytolytic agent, and examined at multiple timepoints. Initially, necrotic myofibers with fragmented sarcoplasm became infiltrated with inflammatory cells. Concomitantly, satellite cells expanded rapidly. Seven days postinjury, regenerated myofibers with centralized nuclei appeared. Full regeneration, as well as an absence of fibrosis, was evident 21 d postinjury. Primary tongue-derived satellite cells were isolated by enzymatic separation of tongue epithelium from mesenchyme followed by magnetic-activated cell sorting. We observed that tongue displays an efficient regenerative response similar to TA but with slightly faster kinetics. In vitro, tongue-derived satellite cells differentiated robustly into mature myotubes with spontaneous contractile behavior and myogenic marker expression. Comparison of gene expression signatures between tongue and TA-derived satellite cells revealed differences in the expression of positional-identity genes, including the HOX family. In conclusion, we have established a model for tongue regeneration useful for investigations of orofacial muscle biology. Furthermore, we showed that tongue is a viable source of satellite cells with unique properties and inherited positional memory.
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Affiliation(s)
- A Goto
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Kitakyushu, Fukuoka, Japan.,Division of Oral and Maxillofacial Surgery, Kyushu Dental University, Kitakyushu, Fukuoka, Japan
| | - S Kokabu
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Kitakyushu, Fukuoka, Japan
| | - C Dusadeemeelap
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Kitakyushu, Fukuoka, Japan
| | - H Kawaue
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Kitakyushu, Fukuoka, Japan
| | - T Matsubara
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Kitakyushu, Fukuoka, Japan
| | - K Tominaga
- Division of Oral and Maxillofacial Surgery, Kyushu Dental University, Kitakyushu, Fukuoka, Japan
| | - W N Addison
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Kitakyushu, Fukuoka, Japan
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40
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Valentine WJ, Mostafa SA, Tokuoka SM, Hamano F, Inagaki NF, Nordin JZ, Motohashi N, Kita Y, Aoki Y, Shimizu T, Shindou H. Lipidomic Analyses Reveal Specific Alterations of Phosphatidylcholine in Dystrophic Mdx Muscle. Front Physiol 2022; 12:698166. [PMID: 35095541 PMCID: PMC8791236 DOI: 10.3389/fphys.2021.698166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
In Duchenne muscular dystrophy (DMD), lack of dystrophin increases the permeability of myofiber plasma membranes to ions and larger macromolecules, disrupting calcium signaling and leading to progressive muscle wasting. Although the biological origin and meaning are unclear, alterations of phosphatidylcholine (PC) are reported in affected skeletal muscles of patients with DMD that may include higher levels of fatty acid (FA) 18:1 chains and lower levels of FA 18:2 chains, possibly reflected in relatively high levels of PC 34:1 (with 16:0_18:1 chain sets) and low levels of PC 34:2 (with 16:0_18:2 chain sets). Similar PC alterations have been reported to occur in the mdx mouse model of DMD. However, altered ratios of PC 34:1 to PC 34:2 have been variably reported, and we also observed that PC 34:2 levels were nearly equally elevated as PC 34:1 in the affected mdx muscles. We hypothesized that experimental factors that often varied between studies; including muscle types sampled, mouse ages, and mouse diets; may strongly impact the PC alterations detected in dystrophic muscle of mdx mice, especially the PC 34:1 to PC 34:2 ratios. In order to test our hypothesis, we performed comprehensive lipidomic analyses of PC and phosphatidylethanolamine (PE) in several muscles (extensor digitorum longus, gastrocnemius, and soleus) and determined the mdx-specific alterations. The alterations in PC 34:1 and PC 34:2 were closely monitored from the neonate period to the adult, and also in mice raised on several diets that varied in their fats. PC 34:1 was naturally high in neonate’s muscle and decreased until age ∼3-weeks (disease onset age), and thereafter remained low in WT muscles but was higher in regenerated mdx muscles. Among the muscle types, soleus showed a distinctive phospholipid pattern with early and diminished mdx alterations. Diet was a major factor to impact PC 34:1/PC 34:2 ratios because mdx-specific alterations of PC 34:2 but not PC 34:1 were strictly dependent on diet. Our study identifies high PC 34:1 as a consistent biochemical feature of regenerated mdx-muscle and indicates nutritional approaches are also effective to modify the phospholipid compositions.
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Affiliation(s)
- William J. Valentine
- Department of Molecular Therapy, National Center for Neurology and Psychiatry (NCNP), National Institute of Neuroscience, Kodaira, Tokyo, Japan
- Department of Lipid Signaling, National Center for Global Health and Medicine (NCGM), Shinjuku-ku, Japan
- *Correspondence: William J. Valentine,
| | - Sherif A. Mostafa
- Department of Lipid Signaling, National Center for Global Health and Medicine (NCGM), Shinjuku-ku, Japan
- Weill Cornell Medicine—Qatar, Doha, Qatar
| | - Suzumi M. Tokuoka
- Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Fumie Hamano
- Department of Lipid Signaling, National Center for Global Health and Medicine (NCGM), Shinjuku-ku, Japan
- Life Sciences Core Facility, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Natsuko F. Inagaki
- Department of Lipid Signaling, National Center for Global Health and Medicine (NCGM), Shinjuku-ku, Japan
| | - Joel Z. Nordin
- Department of Molecular Therapy, National Center for Neurology and Psychiatry (NCNP), National Institute of Neuroscience, Kodaira, Tokyo, Japan
- Department of Laboratory Medicine, Centre for Biomolecular and Cellular Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Norio Motohashi
- Department of Molecular Therapy, National Center for Neurology and Psychiatry (NCNP), National Institute of Neuroscience, Kodaira, Tokyo, Japan
| | - Yoshihiro Kita
- Life Sciences Core Facility, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Center for Neurology and Psychiatry (NCNP), National Institute of Neuroscience, Kodaira, Tokyo, Japan
- Yoshitsugu Aoki,
| | - Takao Shimizu
- Department of Lipid Signaling, National Center for Global Health and Medicine (NCGM), Shinjuku-ku, Japan
| | - Hideo Shindou
- Department of Lipid Signaling, National Center for Global Health and Medicine (NCGM), Shinjuku-ku, Japan
- Department of Medical Lipid Science, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
- Hideo Shindou,
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Riley LA, Zhang X, Douglas CM, Mijares JM, Hammers DW, Wolff CA, Wood NB, Olafson HR, Du P, Labeit S, Previs MJ, Wang ET, Esser KA. The skeletal muscle circadian clock regulates titin splicing through RBM20. eLife 2022; 11:76478. [PMID: 36047761 PMCID: PMC9473687 DOI: 10.7554/elife.76478] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/31/2022] [Indexed: 02/01/2023] Open
Abstract
Circadian rhythms are maintained by a cell-autonomous, transcriptional-translational feedback loop known as the molecular clock. While previous research suggests a role of the molecular clock in regulating skeletal muscle structure and function, no mechanisms have connected the molecular clock to sarcomere filaments. Utilizing inducible, skeletal muscle specific, Bmal1 knockout (iMSBmal1-/-) mice, we showed that knocking out skeletal muscle clock function alters titin isoform expression using RNAseq, liquid chromatography-mass spectrometry, and sodium dodecyl sulfate-vertical agarose gel electrophoresis. This alteration in titin's spring length resulted in sarcomere length heterogeneity. We demonstrate the direct link between altered titin splicing and sarcomere length in vitro using U7 snRNPs that truncate the region of titin altered in iMSBmal1-/- muscle. We identified a mechanism whereby the skeletal muscle clock regulates titin isoform expression through transcriptional regulation of Rbm20, a potent splicing regulator of titin. Lastly, we used an environmental model of circadian rhythm disruption and identified significant downregulation of Rbm20 expression. Our findings demonstrate the importance of the skeletal muscle circadian clock in maintaining titin isoform through regulation of RBM20 expression. Because circadian rhythm disruption is a feature of many chronic diseases, our results highlight a novel pathway that could be targeted to maintain skeletal muscle structure and function in a range of pathologies.
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Affiliation(s)
- Lance A Riley
- Department of Physiology and Functional Genomics, University of FloridaGainesvilleUnited States,Myology Institute, University of FloridaGainesvilleUnited States
| | - Xiping Zhang
- Department of Physiology and Functional Genomics, University of FloridaGainesvilleUnited States,Myology Institute, University of FloridaGainesvilleUnited States
| | - Collin M Douglas
- Department of Physiology and Functional Genomics, University of FloridaGainesvilleUnited States,Myology Institute, University of FloridaGainesvilleUnited States
| | - Joseph M Mijares
- Department of Physiology and Functional Genomics, University of FloridaGainesvilleUnited States,Myology Institute, University of FloridaGainesvilleUnited States
| | - David W Hammers
- Myology Institute, University of FloridaGainesvilleUnited States,Department of Pharmacology and Therapeutics, University of FloridaGainesvilleUnited States
| | - Christopher A Wolff
- Department of Physiology and Functional Genomics, University of FloridaGainesvilleUnited States,Myology Institute, University of FloridaGainesvilleUnited States
| | - Neil B Wood
- Department of Molecular Physiology and Biophysics, University of VermontBurlingtonUnited States
| | - Hailey R Olafson
- Department of Molecular Genetics of Microbiology, Center for Neurogenetics, University of FloridaGainesvilleUnited States
| | - Ping Du
- Department of Physiology and Functional Genomics, University of FloridaGainesvilleUnited States
| | - Siegfried Labeit
- Medical Faculty Mannheim, University of HeidelbergMannheimGermany
| | - Michael J Previs
- Department of Molecular Physiology and Biophysics, University of VermontBurlingtonUnited States
| | - Eric T Wang
- Myology Institute, University of FloridaGainesvilleUnited States,Department of Molecular Genetics of Microbiology, Center for Neurogenetics, University of FloridaGainesvilleUnited States
| | - Karyn A Esser
- Department of Physiology and Functional Genomics, University of FloridaGainesvilleUnited States,Myology Institute, University of FloridaGainesvilleUnited States
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42
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Ehrlich KC, Deng HW, Ehrlich M. Epigenetics of Mitochondria-Associated Genes in Striated Muscle. EPIGENOMES 2021; 6:1. [PMID: 35076500 PMCID: PMC8788487 DOI: 10.3390/epigenomes6010001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/04/2021] [Accepted: 12/16/2021] [Indexed: 11/16/2022] Open
Abstract
Striated muscle has especially large energy demands. We identified 97 genes preferentially expressed in skeletal muscle and heart, but not in aorta, and found significant enrichment for mitochondrial associations among them. We compared the epigenomic and transcriptomic profiles of the 27 genes associated with striated muscle and mitochondria. Many showed strong correlations between their tissue-specific transcription levels, and their tissue-specific promoter, enhancer, or open chromatin as well as their DNA hypomethylation. Their striated muscle-specific enhancer chromatin was inside, upstream, or downstream of the gene, throughout much of the gene as a super-enhancer (CKMT2, SLC25A4, and ACO2), or even overlapping a neighboring gene (COX6A2, COX7A1, and COQ10A). Surprisingly, the 3' end of the 1.38 Mb PRKN (PARK2) gene (involved in mitophagy and linked to juvenile Parkinson's disease) displayed skeletal muscle/myoblast-specific enhancer chromatin, a myoblast-specific antisense RNA, as well as brain-specific enhancer chromatin. We also found novel tissue-specific RNAs in brain and embryonic stem cells within PPARGC1A (PGC-1α), which encodes a master transcriptional coregulator for mitochondrial formation and metabolism. The tissue specificity of this gene's four alternative promoters, including a muscle-associated promoter, correlated with nearby enhancer chromatin and open chromatin. Our in-depth epigenetic examination of these genes revealed previously undescribed tissue-specific enhancer chromatin, intragenic promoters, regions of DNA hypomethylation, and intragenic noncoding RNAs that give new insights into transcription control for this medically important set of genes.
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Affiliation(s)
- Kenneth C. Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA; (K.C.E.); (H.-W.D.)
| | - Hong-Wen Deng
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA; (K.C.E.); (H.-W.D.)
| | - Melanie Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA; (K.C.E.); (H.-W.D.)
- Tulane Cancer Center and Hayward Genetics Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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Girgis J, Yang D, Chakroun I, Liu Y, Blais A. Six1 promotes skeletal muscle thyroid hormone response through regulation of the MCT10 transporter. Skelet Muscle 2021; 11:26. [PMID: 34809717 PMCID: PMC8607597 DOI: 10.1186/s13395-021-00281-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/29/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The Six1 transcription factor is implicated in controlling the development of several tissue types, notably skeletal muscle. Six1 also contributes to muscle metabolism and its activity is associated with the fast-twitch, glycolytic phenotype. Six1 regulates the expression of certain genes of the fast muscle program by directly stimulating their transcription or indirectly acting through a long non-coding RNA. We hypothesized that additional mechanisms of action of Six1 might be at play. METHODS A combined analysis of gene expression profiling and genome-wide location analysis data was performed. Results were validated using in vivo RNA interference loss-of-function assays followed by measurement of gene expression by RT-PCR and transcriptional reporter assays. RESULTS The Slc16a10 gene, encoding the thyroid hormone transmembrane transporter MCT10, was identified as a gene with a transcriptional enhancer directly bound by Six1 and requiring Six1 activity for full expression in adult mouse tibialis anterior, a predominantly fast-twitch muscle. Of the various thyroid hormone transporters, MCT10 mRNA was found to be the most abundant in skeletal muscle, and to have a stronger expression in fast-twitch compared to slow-twitch muscle groups. Loss-of-function of MCT10 in the tibialis anterior recapitulated the effect of Six1 on the expression of fast-twitch muscle genes and led to lower activity of a thyroid hormone receptor-dependent reporter gene. CONCLUSIONS These results shed light on the molecular mechanisms controlling the tissue expression profile of MCT10 and identify modulation of the thyroid hormone signaling pathway as an additional mechanism by which Six1 influences skeletal muscle metabolism.
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Affiliation(s)
- John Girgis
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada.,Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Dabo Yang
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Imane Chakroun
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Yubing Liu
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Alexandre Blais
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada. .,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada. .,University of Ottawa Centre for Inflammation, Immunity and Infection (CI3), Ottawa, Ontario, Canada.
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44
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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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45
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Hunt LC, Graca FA, Pagala V, Wang YD, Li Y, Yuan ZF, Fan Y, Labelle M, Peng J, Demontis F. Integrated genomic and proteomic analyses identify stimulus-dependent molecular changes associated with distinct modes of skeletal muscle atrophy. Cell Rep 2021; 37:109971. [PMID: 34758314 PMCID: PMC8852763 DOI: 10.1016/j.celrep.2021.109971] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/27/2021] [Accepted: 10/19/2021] [Indexed: 12/25/2022] Open
Abstract
Skeletal muscle atrophy is a debilitating condition that occurs with aging and disease, but the underlying mechanisms are incompletely understood. Previous work determined that common transcriptional changes occur in muscle during atrophy induced by different stimuli. However, whether this holds true at the proteome level remains largely unexplored. Here, we find that, contrary to this earlier model, distinct atrophic stimuli (corticosteroids, cancer cachexia, and aging) induce largely different mRNA and protein changes during muscle atrophy in mice. Moreover, there is widespread transcriptome-proteome disconnect. Consequently, atrophy markers (atrogenes) identified in earlier microarray-based studies do not emerge from proteomics as generally induced by atrophy. Rather, we identify proteins that are distinctly modulated by different types of atrophy (herein defined as “atroproteins”) such as the myokine CCN1/Cyr61, which regulates myofiber type switching during sarcopenia. Altogether, these integrated analyses indicate that different catabolic stimuli induce muscle atrophy via largely distinct mechanisms. Skeletal muscle wasting is caused by many catabolic stimuli, which were thought to act via shared mechanisms. Hunt et al. now show that distinct catabolic stimuli induce muscle wasting via largely different molecular changes. The authors identify atrophy-associated proteins (“atroproteins”) that may represent diagnostic biomarkers and/or therapeutic targets.
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Affiliation(s)
- Liam C Hunt
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Solid Tumor Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Flavia A Graca
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Solid Tumor Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Vishwajeeth Pagala
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yong-Dong Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yuxin Li
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Zuo-Fei Yuan
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Myriam Labelle
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Solid Tumor Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Solid Tumor Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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46
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Gene Expression Profiling of Skeletal Muscles. Genes (Basel) 2021; 12:genes12111718. [PMID: 34828324 PMCID: PMC8621074 DOI: 10.3390/genes12111718] [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: 09/23/2021] [Revised: 10/21/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing provides an opportunity for an in-depth biocomputational analysis to identify gene expression patterns between soleus and tibialis anterior, two well-characterized skeletal muscles, and analyze their gene expression profiling. RNA read counts were analyzed for differential gene expression using the R package edgeR. Differentially expressed genes were filtered using a false discovery rate of less than 0.05 c, a fold-change value of more than twenty, and an association with overrepresented pathways based on the Reactome pathway over-representation analysis tool. Most of the differentially expressed genes associated with soleus are coded for components of lipid metabolism and unique contractile elements. Differentially expressed genes associated with tibialis anterior encoded mostly for glucose and glycogen metabolic pathway regulatory enzymes and calcium-sensitive contractile components. These gene expression distinctions partly explain the genetic basis for skeletal muscle specialization, and they may help to explain skeletal muscle susceptibility to disease and drugs and further refine tissue engineering approaches.
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47
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Rasmussen M, Jin JP. Troponin Variants as Markers of Skeletal Muscle Health and Diseases. Front Physiol 2021; 12:747214. [PMID: 34733179 PMCID: PMC8559874 DOI: 10.3389/fphys.2021.747214] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/01/2021] [Indexed: 12/21/2022] Open
Abstract
Ca2 +-regulated contractility is a key determinant of the quality of muscles. The sarcomeric myofilament proteins are essential players in the contraction of striated muscles. The troponin complex in the actin thin filaments plays a central role in the Ca2+-regulation of muscle contraction and relaxation. Among the three subunits of troponin, the Ca2+-binding subunit troponin C (TnC) is a member of the calmodulin super family whereas troponin I (TnI, the inhibitory subunit) and troponin T (TnT, the tropomyosin-binding and thin filament anchoring subunit) are striated muscle-specific regulatory proteins. Muscle type-specific isoforms of troponin subunits are expressed in fast and slow twitch fibers and are regulated during development and aging, and in adaptation to exercise or disuse. TnT also evolved with various alternative splice forms as an added capacity of muscle functional diversity. Mutations of troponin subunits cause myopathies. Owing to their physiological and pathological importance, troponin variants can be used as specific markers to define muscle quality. In this focused review, we will explore the use of troponin variants as markers for the fiber contents, developmental and differentiation states, contractile functions, and physiological or pathophysiological adaptations of skeletal muscle. As protein structure defines function, profile of troponin variants illustrates how changes at the myofilament level confer functional qualities at the fiber level. Moreover, understanding of the role of troponin modifications and mutants in determining muscle contractility in age-related decline of muscle function and in myopathies informs an approach to improve human health.
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Affiliation(s)
- Monica Rasmussen
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Jian-Ping Jin
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, United States
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, United States
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48
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Abstract
Trauma, burn injury, sepsis, and ischemia lead to acute and chronic loss of skeletal muscle mass and function. Healthy muscle is essential for eating, posture, respiration, reproduction, and mobility, as well as for appropriate function of the senses including taste, vision, and hearing. Beyond providing support and contraction, skeletal muscle also exerts essential roles in temperature regulation, metabolism, and overall health. As the primary reservoir for amino acids, skeletal muscle regulates whole-body protein and glucose metabolism by providing substrate for protein synthesis and supporting hepatic gluconeogenesis during illness and starvation. Overall, greater muscle mass is linked to greater insulin sensitivity and glucose disposal, strength, power, and longevity. In contrast, low muscle mass correlates with dysmetabolism, dysmobility, and poor survival. Muscle mass is highly plastic, appropriate to its role as reservoir, and subject to striking genetic control. Defining mechanisms of muscle growth regulation holds significant promise to find interventions that promote health and diminish morbidity and mortality after trauma, sepsis, inflammation, and other systemic insults. In this invited review, we summarize techniques and methods to assess and manipulate muscle size and muscle mass in experimental systems, including cell culture and rodent models. These approaches have utility for studies of myopenia, sarcopenia, cachexia, and acute muscle growth or atrophy in the setting of health or injury.
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49
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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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Myofiber stretch induces tensile and shear deformation of muscle stem cells in their native niche. Biophys J 2021; 120:2665-2678. [PMID: 34087215 PMCID: PMC8390894 DOI: 10.1016/j.bpj.2021.05.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 05/02/2021] [Accepted: 05/18/2021] [Indexed: 12/28/2022] Open
Abstract
Muscle stem cells (MuSCs) are requisite for skeletal muscle regeneration and homeostasis. Proper functioning of MuSCs, including activation, proliferation, and fate decision, is determined by an orchestrated series of events and communication between MuSCs and their niche. A multitude of biochemical stimuli are known to regulate MuSC fate and function. However, in addition to biochemical factors, it is conceivable that MuSCs are subjected to mechanical forces during muscle stretch-shortening cycles because of myofascial connections between MuSCs and myofibers. MuSCs respond to mechanical forces in vitro, but it remains to be proven whether physical forces are also exerted on MuSCs in their native niche and whether they contribute to the functioning and fate of MuSCs. MuSC deformation in their native niche resulting from mechanical loading of ex vivo myofiber bundles was visualized utilizing mT/mG double-fluorescent Cre-reporter mouse and multiphoton microscopy. MuSCs were subjected to 1 h pulsating fluid shear stress (PFSS) with a peak shear stress rate of 6.5 Pa/s. After PFSS treatment, nitric oxide, messenger RNA (mRNA) expression levels of genes involved in regulation of MuSC proliferation and differentiation, ERK 1/2, p38, and AKT activation were determined. Ex vivo stretching of extensor digitorum longus and soleus myofiber bundles caused compression as well as tensile and shear deformation of MuSCs in their niche. MuSCs responded to PFSS in vitro with increased nitric oxide production and an upward trend in iNOS mRNA levels. PFSS enhanced gene expression of c-Fos, Cdk4, and IL-6, whereas expression of Wnt1, MyoD, Myog, Wnt5a, COX2, Rspo1, Vangl2, Wnt10b, and MGF remained unchanged. ERK 1/2 and p38 MAPK signaling were also upregulated after PFSS treatment. We conclude that MuSCs in their native niche are subjected to force-induced deformations due to myofiber stretch-shortening. Moreover, MuSCs are mechanoresponsive, as evidenced by PFSS-mediated expression of factors by MuSCs known to promote proliferation.
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